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I_kwDOACgets5Vfurl
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Issue with Trajectory.extend()
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[
"My intuition is that that there may have been a change in the format (numpy.darray of shape `(steps, 3, 3)` vs list of numpy.ndarrays of shape (3, 3)) of the lattice property that the to_trajectory() method of Vasprun or the Trajectory.extend() function(s) may not have followed, or the opposite. Does this make sense ?\r\n",
"(sorry for the self-commenting)\r\nand indeed I can concatenate trajectories by converting the lattice to a list as follows:\r\n\r\n```\r\nimport os\r\nfrom pymatgen import core\r\nfrom pymatgen.io.vasp import Vasprun\r\nimport numpy as np\r\n\r\nprint('pymatgen core version {}'.format(core.__version__))\r\n\r\nroot_dir = os.getcwd()\r\ndir_names = [os.path.join(root_dir, dir_name) for dir_name in\r\n [d for d in os.listdir(root_dir) if os.path.isdir(d)]]\r\n\r\ntrajectories = []\r\nfor dir_name in dir_names:\r\n file_name = os.path.join(dir_name, 'vasprun.xml')\r\n vr = Vasprun(file_name)\r\n traj = vr.get_trajectory()\r\n # Convert lattice numpy.ndarray of shape (nframes, 3, 3) to list of\r\n # numpy.ndarray of shape (3, 3)\r\n if (not traj.constant_lattice) and (isinstance(traj.lattice, np.ndarray)):\r\n traj.lattice = [traj.lattice[i, :, :] for i in range(traj.lattice.shape[0])]\r\n\r\n trajectories.append(traj)\r\n print('trajectories[{}] with length {} created from file {}.'.format(\r\n len(trajectories)-1, len(traj), file_name))\r\n\r\nextended_traj = trajectories[0]\r\nfor traj in trajectories[1:]:\r\n extended_traj.extend(traj)\r\n\r\nprint('extended_traj of length {}.'.format(len(extended_traj)))\r\n```\r\n\r\nWhich now gives (warnings removed):\r\n\r\n```\r\ntrajectories[0] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622432/vasprun.xml.\r\ntrajectories[1] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622360/vasprun.xml.\r\ntrajectories[2] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622216/vasprun.xml.\r\nextended_traj of length 300.\r\n```\r\nSo I guess the question is: how should the lattice be defined in a Trajectory ?\r\n- a numpy.darray of shape (nframes, 3, 3) as implemented (if I am correct) in particular in Trajectory.from_structures(), in which case the extend() function needs to be modified, or \r\n- a list of numpy.darrays of shape (3, 3), in which case the [Trajectory.from_structures()](https://github.com/materialsproject/pymatgen/blob/8bc18da00b77a8bcb4af9d689f747128434515ae/pymatgen/core/trajectory.py#L416) method must be changed.\r\n\r\nOne possibility would be to control this behavior with an option in Trajectory.from_structures() and/or in Vasprun().to_trajectory()...\r\nPlease let me know what you think.",
"In fact the 'solution' described above did not work (it gave me an extended_traj lattice of length 400) and should definitely be diregarded.\r\n\r\nI think I finally got the real solution. The problem was in the Trajectory._combine_lattice() method, which should be:\r\n\r\n```\r\n@staticmethod\r\n def _combine_lattice(attr_1, attr_2, len_1, len_2):\r\n \"\"\"\r\n Helper function to combine trajectory properties such as site_properties or lattice\r\n \"\"\"\r\n if np.shape(attr_1) == (3, 3) and np.shape(attr_2) == (3, 3):\r\n attribute = attr_1\r\n attribute_constant = True\r\n elif np.ndim(attr_1) == 3 and np.ndim(attr_2) == 3: # np.shape changed to np.ndim\r\n attribute = np.concatenate((attr_1, attr_2), axis=0)\r\n attribute_constant = False\r\n else: \r\n # Deal with case where any of attr_1 (self.lattice) and attr_1 (trajectory.lattice) is a list of numpy.ndarrays of shape (3, 3) attribute = [attr_1.copy()] * len_1 if isinstance(attr_1, list) else attr_1.copy()\r\n attribute.extend([attr_2.copy()] * len_2 if isinstance(attr_2, list) else attr_2.copy())\r\n attribute_constant = False\r\n return attribute, attribute_constant\r\n```\r\nWhat I did was to change `elif np.shape(attr_1) == 3 and np.shape(attr_2) == 3:` to `elif np.ndim(attr_1) == 3 and np.ndim(attr_2) == 3:`.\r\nIt seems to work correctly, but I suspect that further tests might be needed.\r\n\r\nHowever I think this is not yet perfect. In the case where attr_1 or attr_2 is a list whereas the other is a numpy.ndarray, then the function will again try to extend a numpy ndarray, which will give the same error as above. My suggestion to correct this problem would be to :\r\n- convert both attr_1 and attr_2 to numpy ndarrays of shapes (len_1, 3, 3) and (len_2, 3, 3)\r\n- use `np.concatenate((attr_1, attr_2), axis=0)` as in the case above\r\n- raise a warning to indicate that the lattice type of the concatated trajectory is different from one of the two initial arrays.\r\n\r\nAnother possibility would be keep the type of the first trajectory and convert the second to that type...\r\n\r\nHoping this helps (and looking very much forward to reading your solution to this problem(s).\r\nSylvian.\r\n\r\n "
] | 2022-11-03T09:53:02
| 2022-11-03T15:41:29
|
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Dear pymatgen developpers,
I am facing an issue with the extend() method of Trajectory instances created from Vasprun.to_trajectory().
Attached below is a tests containing three subsequent MD runs conducted on Si, and a script (test_traj_extend.py) designed to extract and concatenate trajectories with pymatgen.
[Si_MD_2022-11-03.tar.gz](https://github.com/materialsproject/pymatgen/files/9927188/Si_MD_2022-11-03.tar.gz)
test_traj_extend.py script:
```
import os
from pymatgen import core
from pymatgen.io.vasp import Vasprun
print('pymatgen core version {}'.format(core.__version__))
root_dir = os.getcwd()
dir_names = [os.path.join(root_dir, dir_name) for dir_name in
[d for d in os.listdir(root_dir) if os.path.isdir(d)]]
trajectories = []
for dir_name in dir_names:
file_name = os.path.join(dir_name, 'vasprun.xml')
vr = Vasprun(file_name)
trajectories.append(vr.get_trajectory())
print('trajectories[{}] with length {} created from file {}.'.format(
len(trajectories)-1, len(trajectories[-1]), file_name))
extended_traj = trajectories[0]
for traj in trajectories[1:]:
extended_traj.extend(traj)
print('extended_traj of length {}.'.format(extended_traj))
```
I obtain the following error:
```
(base) cadarp02@escs-215-02:/data/VASP/tests/Si_MD_2022-11-03$ python test_traj_extend.py
pymatgen core version 2022.01.09
/home/cadarp02/.local/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:383: UnconvergedVASPWarning: /data/VASP/tests/Si_MD_2022-11-03/622432/vasprun.xml is an unconverged VASP run.
Electronic convergence reached: True.
Ionic convergence reached: False.
warnings.warn(msg, UnconvergedVASPWarning)
trajectories[0] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622432/vasprun.xml.
/home/cadarp02/.local/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:383: UnconvergedVASPWarning: /data/VASP/tests/Si_MD_2022-11-03/622360/vasprun.xml is an unconverged VASP run.
Electronic convergence reached: True.
Ionic convergence reached: False.
warnings.warn(msg, UnconvergedVASPWarning)
trajectories[1] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622360/vasprun.xml.
/home/cadarp02/.local/lib/python3.8/site-packages/pymatgen/io/vasp/outputs.py:383: UnconvergedVASPWarning: /data/VASP/tests/Si_MD_2022-11-03/622216/vasprun.xml is an unconverged VASP run.
Electronic convergence reached: True.
Ionic convergence reached: False.
warnings.warn(msg, UnconvergedVASPWarning)
trajectories[2] with length 100 created from file /data/VASP/tests/Si_MD_2022-11-03/622216/vasprun.xml.
Traceback (most recent call last):
File "test_traj_extend.py", line 21, in <module>
extended_traj.extend(traj)
File "/home/cadarp02/.local/lib/python3.8/site-packages/pymatgen/core/trajectory.py", line 177, in extend
self.lattice, self.constant_lattice = self._combine_lattice(
File "/home/cadarp02/.local/lib/python3.8/site-packages/pymatgen/core/trajectory.py", line 392, in _combine_lattice
attribute.extend([attr_2.copy()] * len_2 if isinstance(attr_2, list) else attr_2.copy())
AttributeError: 'numpy.ndarray' object has no attribute 'extend'
```
Can you please help me figure out what I may have done wrong and/or solve the problem ?
Thank you very much.
Best wishes.
Sylvian.
|
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PR_kwDOACgets5CSm5L
| 2,719
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Add `copy()` methods to `ComputedEntry` and `ComputedStructureEntry`
|
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[
"\n[](https://coveralls.io/builds/53947930)\n\nCoverage remained the same at 0.0% when pulling **39e244e67f76a0009da867d8817916c3c28124d7 on copy-computed-entry** into **0cfcbf682fe83018330cbf32750e10d0fbdde8e5 on master**.\n"
] | 2022-11-07T02:24:51
| 2022-11-07T02:55:08
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2022-11-07T02:55:08Z
|
MEMBER
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`MaterialsProject2020Compatibility` and `MaterialsProjectCompatibility` apply energy adjustments _in place_. Comparing adjustments between both correction schemes needs a way to copy computed entries.
I didn't add an abstract `copy()` method to `Entry` so other subclasses like `PDEntry` `ExpEntry` `TransformedPDEntry` `GrandPotPDEntry` `CostEntry` remain instantiable.
@shyuep I removed most of the stuff in `pyproject.toml` as it looked outdated. Let me know if any of that needs to stay.
|
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PR_kwDOACgets5CVe-u
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Fix tensor mapping
|
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[
"\n[](https://coveralls.io/builds/53970022)\n\nCoverage remained the same at 0.0% when pulling **e7602d45ab8c72c8e777a1bc0b3879fc6b7f2197 on utf:fix-tensor-mapping** into **dd884cfb532cc5531da8d0b9ee5a799b3943d070 on materialsproject:master**.\n",
"@utf Apologies for the breaking change!\r\n\r\nThanks for the fix and the new tests. Will try to make a new release right now (first time for me). Here goes nothing...",
"@utf Took some trial and error to weed out issues from the CI workflow rewrite. The new release is live now https://pypi.org/project/pymatgen/2022.11.7. Hope that unblocks atomate1/2 and amset.",
"Thanks very much @janosh!"
] | 2022-11-07T15:20:25
| 2022-11-09T23:02:18
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2022-11-07T22:57:11Z
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MEMBER
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A recent change (1bdd1b7c6f5b12079c48cc06a6e6443bec070ed3) broke tensor mapping by making the default tensor and value lists immutable tuples. Tests didn't catch this because there was no tests for creating a tensor mapping starting from an empty mapping.
This PR fixes the bug and adds a new test. If possible, please could you release a new version with this bug fix as currently atomate, atomate2, amset, and other packages are broken.
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PR_kwDOACgets5CWWWH
| 2,721
|
VaspInputSet couldn't write cif structures
|
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[
"Pls add a test for this. ",
"\n[](https://coveralls.io/builds/53993905)\n\nCoverage remained the same at 0.0% when pulling **10afe194ff9fa6bb7b0ca08fa27bd549975ab2ea on JiQi535:master** into **ffbebceafc3482e1a63008974a6da64e522e78c9 on materialsproject:master**.\n",
"@shyuep There is already a test for this actually.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ffbebceafc3482e1a63008974a6da64e522e78c9/pymatgen/io/vasp/tests/test_sets.py#L471\r\n\r\nThe tests are just not running because of\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/ffbebceafc3482e1a63008974a6da64e522e78c9/pymatgen/io/vasp/tests/test_sets.py#L60-L61\r\n\r\nWe're not setting `PMG_VASP_PSP_DIR`. This is not due to https://github.com/materialsproject/pymatgen/pull/2708 btw, looks like they weren't running before either.\r\n\r\nWhen I run\r\n\r\n```py\r\nexport PMG_VASP_PSP_DIR=/path/to/vasp/pseudo-potentials\r\npytest pymatgen/io/vasp/tests/test_sets.py -k test_write_input\r\n```\r\n\r\nI can reproduce the error @JiQi535 reported:\r\n\r\n```py\r\n> if fmt == \"cif\" or fnmatch(filename.lower(), \"*.cif*\"):\r\nE AttributeError: 'PosixPath' object has no attribute 'lower'\r\n```\r\n"
] | 2022-11-07T18:32:14
| 2022-11-08T04:38:51
|
2022-11-08T04:38:03Z
|
CONTRIBUTOR
|
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## Summary
This pr deals with the failure of writing .cif format structures by VaspInputSet. I encountered an error of `'PosixPath' object has no attribute 'lower'` when using the `write_input` method with `include_cif=True`. After casting the PosixPath to str, this problem is solved.
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PR_kwDOACgets5CW1co
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[pre-commit.ci] pre-commit autoupdate
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[
"\n[](https://coveralls.io/builds/54036761)\n\nCoverage remained the same at 0.0% when pulling **14b80dc160eee2e08cb13d89be34d57511b71bd4 on pre-commit-ci-update-config** into **dd884cfb532cc5531da8d0b9ee5a799b3943d070 on master**.\n"
] | 2022-11-07T20:36:22
| 2022-11-09T00:30:38
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2022-11-09T00:09:31Z
|
CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/PyCQA/autoflake: v1.6.1 → v1.7.7](https://github.com/PyCQA/autoflake/compare/v1.6.1...v1.7.7)
- [github.com/asottile/pyupgrade: v2.38.2 → v3.2.0](https://github.com/asottile/pyupgrade/compare/v2.38.2...v3.2.0)
- [github.com/psf/black: 22.8.0 → 22.10.0](https://github.com/psf/black/compare/22.8.0...22.10.0)
- [github.com/pre-commit/mirrors-mypy: v0.981 → v0.982](https://github.com/pre-commit/mirrors-mypy/compare/v0.981...v0.982)
- [github.com/codespell-project/codespell: v2.2.1 → v2.2.2](https://github.com/codespell-project/codespell/compare/v2.2.1...v2.2.2)
<!--pre-commit.ci end-->
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I_kwDOACgets5VxtOY
| 2,723
|
SpacegroupAnalyzer.get_symmetrized_structure() raises TypeError
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[] | 2022-11-07T22:25:16
| 2022-11-07T23:54:37
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2022-11-07T23:54:37Z
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MEMBER
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Using pymatgen `master` @ dd884cfb532cc5531da8d0b9ee5a799b3943d070 and `spglib` v2.0.2:
```py
import spglib
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
print(f"{spglib.__version__=}")
struct = Structure.from_str('{"@module": "pymatgen.core.structure", "@class": "Structure", "charge": 0.0, "lattice": {"matrix": [[3.6062699446, 0.0, -0.8583713603], [-0.20223522530000002, 3.6005949268, -0.8583713603], [0.0, 0.0, 7.98790154]], "pbc": [true, true, true], "a": 3.7070182499562314, "b": 3.7070182499460818, "c": 7.98790154, "alpha": 103.38852319946483, "beta": 103.3885231994275, "gamma": 89.96878548961709, "volume": 103.72064305511611}, "sites": [{"species": [{"element": "Co", "occu": 1.0}], "abc": [0.626832, 0.626832, 0.253544], "xyz": [2.1337578911682575, 2.2569681191558972, 0.9491752350186207], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.373168, 0.373168, 0.746456], "xyz": [1.2702768281317425, 1.3436268076441025, 5.321983584381379], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.5, 0.0, 0.0], "xyz": [1.8031349723, 0.0, -0.42918568015], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.0, 0.5, 0.0], "xyz": [-0.10111761265000001, 1.8002974634, -0.42918568015], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.749935, 0.250065, 0.5], "xyz": [2.6538960992889566, 0.900382770370242, 3.1355794097], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.250065, 0.749935, 0.5], "xyz": [0.7501386200110435, 2.700212156429758, 3.1355794097], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.879784, 0.879784, 0.759311], "xyz": [2.9948152814846316, 3.167745807079811, 4.554938728538589], "label": "Co", "properties": {}}, {"species": [{"element": "Co", "occu": 1.0}], "abc": [0.12021599999999999, 0.12021599999999999, 0.240689], "xyz": [0.4092194378153688, 0.43284911972018875, 1.7162200908614103], "label": "Co", "properties": {}}]}', fmt="json")
spg_analyzer = SpacegroupAnalyzer(struct, symprec=0.1, angle_tolerance=5)
sym_struct = spg_analyzer.get_symmetrized_structure()
>>> TypeError: 'NoneType' object is not subscriptable
```
<details>
<summary>stack trace</summary>
```py
TypeError Traceback (most recent call last)
/Users/janosh/dev/matbench-discovery/tmp/spglib_None_symmtries.py in line 6
9 struct = Structure.from_file("2-12269.json")
12 spg_analyzer = SpacegroupAnalyzer(struct, symprec=0.1, angle_tolerance=5)
----> 13 sym_struct = spg_analyzer.get_symmetrized_structure()
File ~/dev/pmg/pymatgen/symmetry/analyzer.py:285, in SpacegroupAnalyzer.get_symmetrized_structure(self)
275 """Get a symmetrized structure. A symmetrized structure is one where the sites
276 have been grouped into symmetrically equivalent groups.
277
278 Returns:
279 :class:`pymatgen.symmetry.structure.SymmetrizedStructure` object.
280 """
281 ds = self.get_symmetry_dataset()
282 sg = SpacegroupOperations(
283 self.get_space_group_symbol(),
284 self.get_space_group_number(),
--> 285 self.get_symmetry_operations(),
286 )
287 return SymmetrizedStructure(self._structure, sg, ds["equivalent_atoms"], ds["wyckoffs"])
File ~/dev/pmg/pymatgen/symmetry/analyzer.py:240, in SpacegroupAnalyzer.get_symmetry_operations(self, cartesian)
233 def get_symmetry_operations(self, cartesian=False):
234 """Return symmetry operations as a list of SymmOp objects. By default returns
...
--> 225 for t in d["translations"]:
226 trans.append([float(Fraction.from_float(c).limit_denominator(1000)) for c in t])
227 trans = np.array(trans)
TypeError: 'NoneType' object is not subscriptable
```
</details>
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PR_kwDOACgets5CXZHV
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Raise ValueError in SpacegroupAnalyzer.get_symmetrized_structure() if spglib returns no symmetries
|
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[
"I think we need to be clear what spglib not returning symmetries mean. If it is a problem assigning any symmetry at all, then it should be an error. If it is a P1 structure, then it should return a single symmetry operation - the identity.",
"Also, let's try to keep linting fixes separate from code fixes unless they are in the same file. This PR has 24 files changed and it is not possible to see what is relevant easily.",
"> I think we need to be clear what spglib not returning symmetries mean. If it is a problem assigning any symmetry at all, then it should be an error. If it is a P1 structure, then it should return a single symmetry operation - the identity.\r\n\r\nIt's the former. I think the structure should have spacegroup 225 (cF4). That's what I get when I decrease `symprec=1e-1` to e.g. `1e-2`. What type of error? `ValueError`?\r\n\r\n> Also, let's try to keep linting fixes separate from code fixes unless they are in the same file. This PR has 24 files changed and it is not possible to see what is relevant easily.\r\n\r\nGood point. I'll try to accumulate them over time into separate PRs.\r\n\r\nAlthough you can see the relevant changes by clicking on the commits with non-formatting messages like fb2fc72f.",
"If it is the former, you can have a ValueError that says spglib cannot determine symmetry and you may need to change the symprec. Unfortunately symmetry determination is always precision specific. Nothing much we can do on that front.\r\n\r\nFor linting fixes, you can directly push to master branch and there is no need to create PRs for it."
] | 2022-11-07T22:37:52
| 2022-11-08T02:48:11
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2022-11-07T23:54:36Z
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MEMBER
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Closes #2723.
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I_kwDOACgets5Vx7R0
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SpacegroupAnalyzer returns duplicate symmetry operations
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[
"`SpacegroupAnalyzer.get_symmetry_operations` calls `spglib.get_symmetry` with cell `self._cell`. The current implementation seems to attach magmoms in `self._cell` even when magmoms are not specified in `Structure`:\r\nhttps://github.com/materialsproject/pymatgen/blob/ffbebceafc3482e1a63008974a6da64e522e78c9/pymatgen/symmetry/analyzer.py#L79-L80\r\n\r\nFrom spglib v2, the behavior of `spglib.get_symmetry` with zero magmoms is changed. Now `spglib.get_symmetry` returns the same spatial symmetry with time_reversal=True and time-reversal=False. So the size doubles.\r\n(c.f. https://github.com/spglib/spglib/issues/150#issuecomment-1180158502)\r\n\r\nI am not sure a reason to attach magmoms in this case. But removing the above line will solve this issue.\r\n",
"Thanks a lot @lan496 !\r\n\r\nAs for pymatgen, I think removing the line you suggest is the way forward.\r\n\r\nOtherwise, adding a `unique` keyword parameter to `get_symmetry_operations` and following your suggestion in the comment linked (https://github.com/spglib/spglib/issues/150#issuecomment-1180158502) is an option too."
] | 2022-11-07T23:25:35
| 2022-11-09T23:45:13
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2022-11-09T23:45:13Z
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CONTRIBUTOR
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**Describe the bug**
The `SpacegroupAnalyzer` class returns a list of symmetry operations, where each unique symop appears twice.
This seems to be related to the upgrade of spglib, since the issue occurs with spglib >= 2, but not with earlier versions.
**To Reproduce**
Steps to reproduce the behavior:
```python
from pymatgen.core import Structure, Lattice
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
lattice = Lattice([[3, 3, 0], [0, 3, 3], [3, 0, 3]])
species = 3 * ["A"] + ["D"]
coords = (
(0.25, 0.25, 0.25), (0.75, 0.75, 0.75), (0.5, 0.5, 0.5), (0, 0, 0)
)
structure = Structure(lattice, species, coords)
sga = SpacegroupAnalyzer(structure)
symops = sga.get_symmetry_operations()
# each symop appears twice!
for i in range(0, len(symops) - 1, 2):
assert symops[i] == symops[i + 1]
```
**Expected behavior**
The list of symmetry operations should not contain duplicates.
**Desktop (please complete the following information):**
- OS: Linux
- Version: 2022.11.1
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PR_kwDOACgets5CXq0c
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Release v2022.11.7
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[
"If you install sphinx, it shouldn't be giving errors. ",
"\n[](https://coveralls.io/builds/53991186)\n\nCoverage remained the same at 0.0% when pulling **af5fd94bed5af12a87c69601d09a5035a3fb6159 on release** into **ffbebceafc3482e1a63008974a6da64e522e78c9 on master**.\n",
"Sorry, in a rush earlier. I did install `sphinx`. Then got errors about missing `sphinx_rtd_theme`. Installed that. Then got errors about missing sphinx extensions. Installed those too. Then got errors about missing `GITHUB_RELEASES_TOKEN`, and so on.",
"@shyuep Does the large line deletion count mean sth went wrong? After my last comment, I reverted the auto-pushed commit af5fd94 and got `invoke release` to run error-free locally but got the same results. The 22k deleted lines look suspicious.",
"If the deleted lines are html files, then it is ok. ",
"Yes, no Python files changed except `setup.py` and `pymatgen/__init__.py`.",
"This did not get released to pypi only GitHub. E.g., https://pypi.org/project/pymatgen/ the latest version is still 2022.11.1",
"@utf Yeah, I saw the [release workflow failed](https://github.com/materialsproject/pymatgen/actions/runs/3416368703/jobs/5686441847) but got drawn away by another problem last night so didn't have time to debug this yet. Let me take a look now.",
"So the problem is I didn't notice `setup.py` imports `numpy` when I did #2707. Now that the CI scripts have single-line installs for (almost) all deps\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/d17a0f4e42203a460fecae78a5009928cc5e3330/.github/workflows/test.yml#L54\r\n\r\n`numpy` won't be installed until after `python setup.py` has run which already tries to import `numpy`. I think the correct way to fix this is to use `setuptools`'s [`fetch_build_eggs`](http://code.nabla.net/doc/setuptools/api/setuptools/dist/setuptools.dist.Distribution.html#setuptools.dist.Distribution.fetch_build_eggs) which \"resolves pre-setup requirements\"."
] | 2022-11-08T00:04:18
| 2022-11-08T15:40:41
|
2022-11-08T04:23:34Z
|
MEMBER
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As requested by @utf in #2720, here's a new release to unblock downstream repos like atomate, atomate2, amset.
@shyuep `invoke release` is giving me a bunch of sphinx errors. Can we release without updating docs since last doc update is just 6 days old?
|
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PR_kwDOACgets5CdKV3
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|
Do not introduce zero magmoms in SpacegroupAnalyzer
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[
"\n[](https://coveralls.io/builds/54033086)\n\nCoverage remained the same at 0.0% when pulling **803d750cab12206bedddd9b0103e44782612a241 on lbluque:master** into **d17a0f4e42203a460fecae78a5009928cc5e3330 on materialsproject:master**.\n",
"This is great! Thanks @lbluque. Just tried out your changes on another 5 structures for which `spglib` with 0 magmons gave me no symmetries. This fix works for all of them!\r\n\r\nI think it might still be useful to keep the test that raises `ValueError` on the `Co8` structure I added in #2724. Just so we keep the nicer error message in case a similar problem reappears in the future. We can just manually insert `magmoms = [0] * len(struct)` in the test `_cell` to still make it raise the `ValueError`."
] | 2022-11-08T19:39:33
| 2022-11-08T22:15:48
|
2022-11-08T22:14:36Z
|
CONTRIBUTOR
|
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## Summary
Do not introduce zero `magmoms` in `SpacegroupAnalyzer` following changes in spglib >= 2. See #2725
## TODO
- With this change, the exception tested in the unit test added in #2724 is not raised.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [X] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [X] Type annotations are **highly*- encouraged. Run [`mypy`](https://github.com/python/mypy) `path/to/file.py` to type check your code.
- [X] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply `pip install -U pre-commit && pre-commit install` in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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PR_kwDOACgets5CdLpk
| 2,728
|
Fix release CI workflow
|
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[
"@shyuep Maybe we use this hack in `setup.py` for now so we no longer rely on some other `pip` command installing `numpy` first before `pip install .`?\r\n\r\n```py\r\nimport subprocess\r\n\r\ntry:\r\n import numpy\r\nexcept ImportError:\r\n subprocess.run(['pip', 'install', 'numpy'])\r\n import numpy\r\n```",
"\n[](https://coveralls.io/builds/54032450)\n\nCoverage remained the same at 0.0% when pulling **32068db77a742c79983ce55ecc71a59275f6e378 on fix-release-wf** into **d17a0f4e42203a460fecae78a5009928cc5e3330 on master**.\n"
] | 2022-11-08T19:43:58
| 2022-11-08T22:01:47
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2022-11-08T22:00:48Z
|
MEMBER
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I'm a bit confused after https://github.com/materialsproject/pymatgen/pull/2726#issuecomment-1307409880. As I understand the docs, `pyproject.toml`'s [`[build-system].requires`](https://setuptools.pypa.io/en/latest/userguide/dependency_management.html#build-system-requirement) is supposed to already handle installing `numpy` and `cython` prior to running `setup.py` so there should be no need for [`fetch_build_eggs`](https://github.com/materialsproject/pymatgen/pull/2726#issuecomment-1307419037).
But the [failed release workflow](https://github.com/materialsproject/pymatgen/actions/runs/3416368703/jobs/5686441847) suggests that's not happening. I think the only reason this hasn't come up in CI before is that the `test.yml` workflow installs `m3gnet` first, then `pymatgen` and `m3gnet` comes with `numpy`. Before #2707, all CI workflows installed `requirements.txt` first before running `pip install .` so unless I'm mistaken, the `build-system.require` hasn't actually setup the build-time requirements for a while?
https://github.com/materialsproject/pymatgen/blob/d17a0f4e42203a460fecae78a5009928cc5e3330/.github/workflows/test.yml#L51-L55
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PR_kwDOACgets5Cd_1M
| 2,729
|
Fix failing piezo tests
|
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[
"\n[](https://coveralls.io/builds/54035904)\n\nCoverage remained the same at 0.0% when pulling **511364e28f2dfdca90b6731d650a16a353fa8236 on fix-failing-piezo-tests** into **6b520e307fea25d890261b3916ecfc6fe802ae94 on master**.\n"
] | 2022-11-08T23:10:05
| 2022-11-09T00:02:51
|
2022-11-09T00:01:46Z
|
MEMBER
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The change in #2727 has resulted in smaller arrays returned by `BornEffectiveCharge.get_BEC_operations` and `ForceConstantMatrix.get_FCM_operations`. I think this may be related to the duplication of symmetry ops mentioned in #2725.
This PR updates the test files to match the new output.
- `test_files/piezo_sensitivity/fcmops.npy`
- `test_files/piezo_sensitivity/becops.npy`
|
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I_kwDOACgets5V6iSO
| 2,730
|
Split energy corrections into structure/composition-dependent terms in `entry.energy_adjustments`
|
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[
"Hi @janosh , you have definitely found an interesting edge case here. We do not actually have any _structure_ dependent corrections. Rather, some corrections depend on _oxidation state_, and if there is no oxidation state information available, pymatgen tries to guess based on the composition (see [code block](https://github.com/materialsproject/pymatgen/blob/1e47fe7244e4bbc8daff3923abdf7e761c7ca415/pymatgen/entries/compatibility.py#L1025)).\r\n\r\nHowever, entries downloaded from the MP API have oxidation state information appended to the `.data` attribute that is determined using more sophisticated methods based on structure during the build process. The corrections will use that information if it's present. Is that where you got the `ComputedStructureEntry`?\r\n\r\nWhat's happening here is that for whatever reason, the `O` in `cse` is being classified as a superoxide, whereas it's classified as an oxide in `ce`. A different correction is applied depending on superoxide / oxide, and that leads to the difference, at least for the MP2020 corrections. I suspect something similar is happening with the legacy ones as well, but as you can see those are harder to parse due to some technical limitations.\r\n\r\nCan you inspect the `.data[\"oxidation_states\"]` attribute of each of your entries? I think that might shed further light. ",
"> Is that where you got the `ComputedStructureEntry`?\r\n\r\nThe CSE was published in [this paper](https://www.nature.com/articles/s41524-020-00481-6).\r\n\r\n> Can you inspect the .data[\"oxidation_states\"] attribute of each of your entries? I think that might shed further light.\r\n\r\nThe oxidation states are all empty:\r\n\r\n```py\r\ncse_mp2020.data={'oxidation_states': {}}\r\nce_mp2020.data={'oxidation_states': {}}\r\ncse_legacy.data={'oxidation_states': {}}\r\nce_legacy.data={'oxidation_states': {}}\r\n```",
"<details>\r\n<summary>Here are the full reprs</summary>\r\n\r\n```\r\ncse_mp2020=wbm-step-2-34803 ComputedStructureEntry - Mn1 O4 (MnO4)\r\nEnergy (Uncorrected) = -29.9509 eV (-5.9902 eV/atom)\r\nCorrection = -2.3120 eV (-0.4624 eV/atom)\r\nEnergy (Final) = -32.2629 eV (-6.4526 eV/atom)\r\nEnergy Adjustments:\r\n MP2020 anion correction (superoxide): -0.6440 eV (-0.1288 eV/atom)\r\n MP2020 GGA/GGA+U mixing correction (Mn): -1.6680 eV (-0.3336 eV/atom)\r\nParameters:\r\n potcar_symbols = ['PAW_PBE Mn_pv 07Sep2000', 'PAW_PBE O 08Apr2002']\r\n hubbards = {'O': 0.0, 'Mn': 3.9}\r\n potcar_spec = [{'titel': 'PAW_PBE Mn_pv 07Sep2000', 'hash': None}, {'titel': 'PAW_PBE O 08Apr2002', 'hash': None}]\r\n is_hubbard = True\r\n run_type = GGA+U\r\nData:\r\n oxidation_states = {}\r\n\r\nce_mp2020=wbm-step-2-34803 ComputedEntry - Mn1 O4 (MnO4)\r\nEnergy (Uncorrected) = -29.9509 eV (-5.9902 eV/atom)\r\nCorrection = -4.4160 eV (-0.8832 eV/atom)\r\nEnergy (Final) = -34.3669 eV (-6.8734 eV/atom)\r\nEnergy Adjustments:\r\n MP2020 anion correction (oxide): -2.7480 eV (-0.5496 eV/atom)\r\n MP2020 GGA/GGA+U mixing correction (Mn): -1.6680 eV (-0.3336 eV/atom)\r\nParameters:\r\n potcar_symbols = ['PAW_PBE Mn_pv 07Sep2000', 'PAW_PBE O 08Apr2002']\r\n hubbards = {'O': 0.0, 'Mn': 3.9}\r\n potcar_spec = [{'titel': 'PAW_PBE Mn_pv 07Sep2000', 'hash': None}, {'titel': 'PAW_PBE O 08Apr2002', 'hash': None}]\r\n is_hubbard = True\r\n run_type = GGA+U\r\nData:\r\n oxidation_states = {}\r\n\r\ncse_legacy=wbm-step-2-34803 ComputedStructureEntry - Mn1 O4 (MnO4)\r\nEnergy (Uncorrected) = -29.9509 eV (-5.9902 eV/atom)\r\nCorrection = -1.9728 eV (-0.3946 eV/atom)\r\nEnergy (Final) = -31.9237 eV (-6.3847 eV/atom)\r\nEnergy Adjustments:\r\n MP Anion Correction : -0.2920 eV (-0.0584 eV/atom)\r\n MP Advanced Correction : -1.6809 eV (-0.3362 eV/atom)\r\nParameters:\r\n potcar_symbols = ['PAW_PBE Mn_pv 07Sep2000', 'PAW_PBE O 08Apr2002']\r\n hubbards = {'O': 0.0, 'Mn': 3.9}\r\n potcar_spec = [{'titel': 'PAW_PBE Mn_pv 07Sep2000', 'hash': None}, {'titel': 'PAW_PBE O 08Apr2002', 'hash': None}]\r\n is_hubbard = True\r\n run_type = GGA+U\r\nData:\r\n oxidation_states = {}\r\n\r\nce_legacy=wbm-step-2-34803 ComputedEntry - Mn1 O4 (MnO4)\r\nEnergy (Uncorrected) = -29.9509 eV (-5.9902 eV/atom)\r\nCorrection = -4.4900 eV (-0.8980 eV/atom)\r\nEnergy (Final) = -34.4409 eV (-6.8882 eV/atom)\r\nEnergy Adjustments:\r\n MP Anion Correction : -2.8092 eV (-0.5618 eV/atom)\r\n MP Advanced Correction : -1.6809 eV (-0.3362 eV/atom)\r\nParameters:\r\n potcar_symbols = ['PAW_PBE Mn_pv 07Sep2000', 'PAW_PBE O 08Apr2002']\r\n hubbards = {'O': 0.0, 'Mn': 3.9}\r\n potcar_spec = [{'titel': 'PAW_PBE Mn_pv 07Sep2000', 'hash': None}, {'titel': 'PAW_PBE O 08Apr2002', 'hash': None}]\r\n is_hubbard = True\r\n run_type = GGA+U\r\nData:\r\n oxidation_states = {}\r\n```\r\n</details>\r\n",
"Thanks @janosh . So in this case the presence of the structure is triggering pymatgen to detect peroxides/superoxides (see [code block](https://github.com/materialsproject/pymatgen/blob/1e47fe7244e4bbc8daff3923abdf7e761c7ca415/pymatgen/entries/compatibility.py#L982) )\r\n\r\nIf you were to instantiate either the legacy or MP2020 corrections with `correct_peroxide=False`, then you should get the same answer whether or not a structure is present. As far as I'm aware, this check is the only place in the corrections where the structure is used.\r\n\r\nAs confusing as this all is, it is intended behavior. Basically, the corrections try to utilize as much information to make the best guess they can about the oxidation states of the respective ions.\r\n\r\n",
"@rkingsbury Thanks for taking the time to look into this! \r\n\r\n> Basically, the corrections try to utilize as much information to make the best guess they can about the oxidation states of the respective ions.\r\n\r\nThat's what I figured. And you're right, if I pass `correct_peroxide=False`, CE and CSE corrections become equal:\r\n\r\n```\r\ncse_mp2020.correction=-4.416\r\nce_mp2020.correction=-4.416\r\ncse_legacy.correction=-4.49\r\nce_legacy.correction=-4.49\r\n```\r\n\r\nSo it doesn't make sense to split this structure-dependent part into its own energy adjustment?\r\n",
"> So it doesn't make sense to split this structure-dependent part into its own energy adjustment?\r\n\r\nCorrect. Our correction scheme is really not \"structure based\" (with this one small exception) and the correction that is applied is still a composition-based anion correction. The structure just happens to be used in this one case to classify the anion as a superoxide/peroxide/oxide. So I think it could be misleading to separate out a \"structure-dependent\" energy adjustment. However if you think edits to any of the associated docstrings or documentation are in order to make this clearer, I'd be supportive of that.",
"> The structure just happens to be used in this one case to classify the anion as a superoxide/peroxide/oxide.\r\n\r\nIt's also used to classify sulfides vs polysulfides.\r\n\r\nI'll add a paragraph to the `MaterialsProject2020Compatibility` doc string to highlight this corner-case structure dependence."
] | 2022-11-09T05:30:39
| 2022-11-09T22:59:26
|
2022-11-09T22:59:26Z
|
MEMBER
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I noticed both the old and 2020 MP energy correction schemes are structure-dependent. Here's an example `ComputedStructureEntry` that when converted to ComputedEntry each copy corrected with both old and new correction scheme gives 4 different energies.
[cse.json.zip](https://github.com/materialsproject/pymatgen/files/9967586/cse.json.zip)
```py
import gzip
import json
from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
with gzip.open("cse.json.zip") as f:
cse = ComputedStructureEntry.from_dict(json.load(f))
cse_mp2020 = cse.copy()
cse_legacy = cse.copy()
ce_mp2020 = ComputedEntry.from_dict(cse.to_dict())
ce_legacy = ce_mp2020.copy()
MaterialsProject2020Compatibility().process_entry(cse_mp2020)
MaterialsProject2020Compatibility().process_entry(ce_mp2020)
MaterialsProjectCompatibility().process_entry(cse_legacy)
MaterialsProjectCompatibility().process_entry(ce_legacy)
print(f"{cse_mp2020.correction=:.4}")
print(f"{ce_mp2020.correction=:.4}")
print(f"{cse_legacy.correction=:.4}")
print(f"{ce_legacy.correction=:.4}")
print(f"{cse_mp2020.energy_adjustments=}\n")
print(f"{ce_mp2020.energy_adjustments=}\n")
print(f"{cse_legacy.energy_adjustments=}\n")
print(f"{ce_legacy.energy_adjustments=}\n")
```
This script prints
```
cse_mp2020.correction=-2.312
ce_mp2020.correction=-4.416
cse_legacy.correction=-1.973
ce_legacy.correction=-4.49
cse_mp2020.energy_adjustments=[CompositionEnergyAdjustment:
Name: MP2020 anion correction (superoxide)
Value: -0.644 eV
Uncertainty: 0.030 eV
Description: Composition-based energy adjustment (-0.161 eV/atom x 4.0 atoms)
Generated by: MaterialsProject2020Compatibility, CompositionEnergyAdjustment:
Name: MP2020 GGA/GGA+U mixing correction (Mn)
Value: -1.668 eV
Uncertainty: 0.005 eV
Description: Composition-based energy adjustment (-1.668 eV/atom x 1.0 atoms)
Generated by: MaterialsProject2020Compatibility]
ce_mp2020.energy_adjustments=[CompositionEnergyAdjustment:
Name: MP2020 anion correction (oxide)
Value: -2.748 eV
Uncertainty: 0.008 eV
Description: Composition-based energy adjustment (-0.687 eV/atom x 4.0 atoms)
Generated by: MaterialsProject2020Compatibility, CompositionEnergyAdjustment:
Name: MP2020 GGA/GGA+U mixing correction (Mn)
Value: -1.668 eV
Uncertainty: 0.005 eV
Description: Composition-based energy adjustment (-1.668 eV/atom x 1.0 atoms)
Generated by: MaterialsProject2020Compatibility]
cse_legacy.energy_adjustments=[ConstantEnergyAdjustment:
Name: MP Anion Correction
Value: -0.292 eV
Uncertainty: nan eV
Description: Constant energy adjustment (-0.292 eV)
Generated by: MaterialsProjectCompatibility, ConstantEnergyAdjustment:
Name: MP Advanced Correction
Value: -1.681 eV
Uncertainty: nan eV
Description: Constant energy adjustment (-1.681 eV)
Generated by: MaterialsProjectCompatibility]
ce_legacy.energy_adjustments=[ConstantEnergyAdjustment:
Name: MP Anion Correction
Value: -2.809 eV
Uncertainty: nan eV
Description: Constant energy adjustment (-2.809 eV)
Generated by: MaterialsProjectCompatibility, ConstantEnergyAdjustment:
Name: MP Advanced Correction
Value: -1.681 eV
Uncertainty: nan eV
Description: Constant energy adjustment (-1.681 eV)
Generated by: MaterialsProjectCompatibility]
```
Currently the list of energy adjustments only discerns anion corrections from MP advanced corrections.
@rkingsbury @computron Would it be possible to split this further to show structure-dependent corrections and simpler composition-only-corrections separately?
|
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PR_kwDOACgets5CkFDn
| 2,731
|
Document rare structure dependence of MaterialsProjectCompatibility corrections
|
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[
"Thanks @janosh ! There appear to be a bunch of linting changes in here in other parts of pymatgen. Not sure if that was intentional or not; no objections, just calling your attention to it.",
"\n[](https://coveralls.io/builds/54078707)\n\nCoverage remained the same at 0.0% when pulling **912897f42767214574b0015df376b8a47eaab4ad on docs-mp2020-compat-structure-dependence** into **a77c08880421a6fa787dd12072bf5c86bc68d00c on master**.\n"
] | 2022-11-09T22:20:17
| 2022-11-09T23:00:36
|
2022-11-09T22:59:24Z
|
MEMBER
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Closes #2730.
Relevant commit in this PR is d1f6f9277dab6cabf6340eab5d5cb653fe43abe6.
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I_kwDOACgets5WCq_A
| 2,732
|
Loose endpoints in NEB string_relax()
|
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[] | null |
[
"@fucaline Good catch! Thanks for reporting.",
"Do you have a minimal example that failed before and works with your fix so we can add a test for this?",
"I don't have a clean minimal example unfortunately. Only my project data, that I can provide but it's not a very clean and comprehensive example. ",
"I see. I'll merge as-is then."
] | 2022-11-10T09:23:30
| 2022-11-18T18:02:40
|
2022-11-18T18:02:40Z
|
NONE
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I found a bug in the method `string_relax()`, in `class NEBPathfinder`:
The endpoints are not kept fixed as expected due to numpy array operation the line 234: ` s0 = s` wich does not effectively save the state of `s`. https://github.com/materialsproject/pymatgen/blob/6b520e307fea25d890261b3916ecfc6fe802ae94/pymatgen/analysis/path_finder.py#L234
Later, line 258,
```
# Fix endpoints
s[0] = s0[0]
s[-1] = s0[-1]
```
does not recover the inital and final points.
**Solution**
I changed to `s0 = np.copy(s)` and it resolved the issue in my code.
|
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PR_kwDOACgets5Cp-0f
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Markdown readme
|
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[
"This change allows us to have a single source of truth for GH and PyPI pages since `setup.py` currently contains basically a diverged copy of the rST readme as markdown.",
"\n[](https://coveralls.io/builds/54117084)\n\nCoverage increased (+32.9%) to 32.908% when pulling **7eb3e16fecd6272fb7d735e09bdc62b4735b1f08 on markdown-readme** into **29b05524bcf5584722dc7f6bedbe99fe46d80f0a on master**.\n"
] | 2022-11-10T21:04:47
| 2022-11-12T15:40:18
|
2022-11-12T15:36:28Z
|
MEMBER
|
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Convert the readme from rST to markdown:
```sh
pandoc --from rst --to gfm README.rst --output README.md
```
Any objections @shyuep? markdown is more readable, much more widely used and understood than rST so should allow more people to contribute updates/corrections.
|
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PR_kwDOACgets5CyHR1
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|
Fix extremum_icohpvalue() for ICOBILIST.lobster files
|
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[
"\n[](https://coveralls.io/builds/54164378)\n\nCoverage remained the same at 0.0% when pulling **823c80d0fb6de92aa09d8d1445da00a349557bbd on naik-aakash:fix_icobi_extremum** into **607e48d882a2428d9ee8df019cdc7bd89b285ae4 on materialsproject:master**.\n",
"This PR is ready to be merged from my end. Can you please review and merge this @janosh. Also let me know if anything more needs to be done before it could be merged.",
"Thanks @naik-aakash!",
"> Thanks @naik-aakash!\r\n\r\nYou are welcome "
] | 2022-11-13T17:04:02
| 2022-11-21T11:39:55
|
2022-11-13T17:32:40Z
|
CONTRIBUTOR
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The value returned by the `extremum_icohpvalue()` method from `Icohplist.icohpcollection` instance was wrong for `ICOBILIST.lobster` file.
- Fixed the above stated issue
- Updated the tests to ensure these values are returned correctly
|
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PR_kwDOACgets5C-CTp
| 2,735
|
use `build` to build packages
|
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[
"Thanks.",
"Ah, good to know! I was wondering why `pyproject.toml` seemed to be ignored in #2728."
] | 2022-11-15T23:45:28
| 2022-11-16T20:00:03
|
2022-11-16T02:43:21Z
|
CONTRIBUTOR
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## Summary
Use [`build`](https://github.com/pypa/build) to release wheels.
I notice the current workflow to use `python setup.py sdist bdist_wheel` to build wheels, which will not follow `build-system` in `pyproject.toml`. I recommend the official PEP-517 build frontend, [`build`](https://github.com/pypa/build). The dependencies are not required to be manually installed any more.
build documentation: https://pypa-build.readthedocs.io/en/stable/index.html
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PR_kwDOACgets5DEGUB
| 2,736
|
Sunset module `pymatgen/util/serialization.py`
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[
"\n[](https://coveralls.io/builds/54298649)\n\nCoverage remained the same at 0.0% when pulling **81ce6414fec1d994e3eb93949a7bb7991a417f1e on sunset-util-serialization** into **f039377fe59e8cf71502e31d9f444951fe989d44 on master**.\n",
"Fine with me."
] | 2022-11-16T22:18:05
| 2022-11-16T22:53:24
|
2022-11-16T22:52:12Z
|
MEMBER
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Going by the module doc string
> Most features of this module have been moved to `monty`.
and the few call sites of this module, I think we can sunset `pymatgen/util/serialization.py`. Strictly speaking a breaking change but seems unlikely anyone would use this module externally. It's only used for pickling by `class PymatgenTest`. We could do a deprecation phase though if anyone wants.
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PR_kwDOACgets5DFyw1
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Fix lobsterout.get_doc() typo
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[
"\n[](https://coveralls.io/builds/54310290)\n\nCoverage remained the same at 0.0% when pulling **f2ab90511595ea35a7d258b5c9b2289173bd55cd on naik-aakash:fix_lobsterout_typo** into **dcf9e83dbd6ee80a99bd54b1a86da88898ba5cd3 on materialsproject:master**.\n",
"@janosh : This PR is ready to be merged! Please review and merge it if possible soon :)"
] | 2022-11-17T07:54:20
| 2022-11-21T11:39:49
|
2022-11-17T16:20:51Z
|
CONTRIBUTOR
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## Summary
There was typo in document generated. Thus fixed those
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{ADMIN,CONTRIBUTING,LICENSE}.{rst->md}
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[
"\n[](https://coveralls.io/builds/54343508)\n\nCoverage increased (+31.09%) to 31.089% when pulling **c12881becae1815de81f6ddaf545db965332c828 on admin-contrib-to-md** into **9e095faaf6e7f20add6d97b8130f0605944b6d45 on master**.\n",
"@shyuep Looks like `MANIFEST.in` pulls a lot of garbage into the source distribution incl. `.mypy_cache` files (which doesn't matter in CI where no cache exists but would send a lot of clutter to PyPI if someone ever published a local `pymatgen` release).\r\n\r\n```sh\r\nwc -l pymatgen.egg-info.old/SOURCES.txt\r\n8811\r\n```\r\n\r\nRemoving mypy cache leaves\r\n\r\n```sh\r\nsed -i '' '/.mypy_cache/d' pymatgen.egg-info.old/SOURCES.txt \r\nwc -l pymatgen.egg-info.old/SOURCES.txt \r\n1452\r\n```\r\n\r\nwhich still contains stuff that probably doesn't need to be published. Without `MANIFEST.in`:\r\n\r\n```sh\r\nwc -l pymatgen.egg-info/SOURCES.txt \r\n 432\r\n```\r\n\r\n<details>\r\n<summary>old 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it__.py\r\npymatgen/apps/borg/hive.py\r\npymatgen/apps/borg/queen.py\r\npymatgen/cli/__init__.py\r\npymatgen/cli/feff_plot_cross_section.py\r\npymatgen/cli/feff_plot_dos.py\r\npymatgen/cli/gaussian_analyzer.py\r\npymatgen/cli/get_environment.py\r\npymatgen/cli/pmg.py\r\npymatgen/cli/pmg_analyze.py\r\npymatgen/cli/pmg_config.py\r\npymatgen/cli/pmg_plot.py\r\npymatgen/cli/pmg_potcar.py\r\npymatgen/cli/pmg_query.py\r\npymatgen/cli/pmg_structure.py\r\npymatgen/command_line/OxideTersoffPotentials\r\npymatgen/command_line/__init__.py\r\npymatgen/command_line/bader_caller.py\r\npymatgen/command_line/bush.lib\r\npymatgen/command_line/chargemol_caller.py\r\npymatgen/command_line/critic2_caller.py\r\npymatgen/command_line/enumlib_caller.py\r\npymatgen/command_line/gulp_caller.py\r\npymatgen/command_line/lewis.lib\r\npymatgen/command_line/mcsqs_caller.py\r\npymatgen/command_line/vampire_caller.py\r\npymatgen/core/__init__.py\r\npymatgen/core/bond_lengths.json\r\npymatgen/core/bonds.py\r\npymatgen/core/composition.py\r\npymatgen/core/func_groups.json\r\npymatgen/core/interface.py\r\npymatgen/core/ion.py\r\npymatgen/core/lattice.py\r\npymatgen/core/libxc_docs.json\r\npymatgen/core/libxcfunc.py\r\npymatgen/core/molecular_orbitals.py\r\npymatgen/core/operations.py\r\npymatgen/core/periodic_table.json\r\npymatgen/core/periodic_table.py\r\npymatgen/core/py.typed\r\npymatgen/core/quad_data.json\r\npymatgen/core/reconstructions_archive.json\r\npymatgen/core/sites.py\r\npymatgen/core/spectrum.py\r\npymatgen/core/structure.py\r\npymatgen/core/surface.py\r\npymatgen/core/tensors.py\r\npymatgen/core/trajectory.py\r\npymatgen/core/units.py\r\npymatgen/core/xcfunc.py\r\npymatgen/electronic_structure/__init__.py\r\npymatgen/electronic_structure/bandstructure.py\r\npymatgen/electronic_structure/boltztrap.py\r\npymatgen/electronic_structure/boltztrap2.py\r\npymatgen/electronic_structure/cohp.py\r\npymatgen/electronic_structure/core.py\r\npymatgen/electronic_structure/dos.py\r\npymatgen/electronic_structure/plotter.py\r\npymatgen/entries/MITCompatibility.yaml\r\npymatgen/entries/MP2020Compatibility.yaml\r\npymatgen/entries/MPCompatibility.yaml\r\npymatgen/entries/__init__.py\r\npymatgen/entries/calc_compounds.json.gz\r\npymatgen/entries/compatibility.py\r\npymatgen/entries/computed_entries.py\r\npymatgen/entries/correction_calculator.py\r\npymatgen/entries/entry_tools.py\r\npymatgen/entries/exp_compounds.json.gz\r\npymatgen/entries/exp_entries.py\r\npymatgen/entries/mixing_scheme.py\r\npymatgen/entries/data/g_els.json\r\npymatgen/entries/data/nist_gas_gf.json\r\npymatgen/ext/cod.py\r\npymatgen/ext/matproj.py\r\npymatgen/ext/optimade.py\r\npymatgen/io/adf.py\r\npymatgen/io/ase.py\r\npymatgen/io/atat.py\r\npymatgen/io/babel.py\r\npymatgen/io/cif.py\r\npymatgen/io/core.py\r\npymatgen/io/cssr.py\r\npymatgen/io/cube.py\r\npymatgen/io/fiesta.py\r\npymatgen/io/gaussian.py\r\npymatgen/io/jarvis.py\r\npymatgen/io/lmto.py\r\npymatgen/io/nwchem.py\r\npymatgen/io/packmol.py\r\npymatgen/io/phonopy.py\r\npymatgen/io/prismatic.py\r\npymatgen/io/pwscf.py\r\npymatgen/io/res.py\r\npymatgen/io/shengbte.py\r\npymatgen/io/template.py\r\npymatgen/io/wannier90.py\r\npymatgen/io/xcrysden.py\r\npymatgen/io/xr.py\r\npymatgen/io/xyz.py\r\npymatgen/io/zeopp.py\r\npymatgen/io/abinit/__init__.py\r\npymatgen/io/abinit/abiobjects.py\r\npymatgen/io/abinit/abitimer.py\r\npymatgen/io/abinit/inputs.py\r\npymatgen/io/abinit/netcdf.py\r\npymatgen/io/abinit/pseudos.py\r\npymatgen/io/abinit/variable.py\r\npymatgen/io/cp2k/__init__.py\r\npymatgen/io/cp2k/inputs.py\r\npymatgen/io/cp2k/outputs.py\r\npymatgen/io/cp2k/sets.py\r\npymatgen/io/cp2k/settings.yaml\r\npymatgen/io/cp2k/utils.py\r\npymatgen/io/exciting/__init__.py\r\npymatgen/io/exciting/inputs.py\r\npymatgen/io/feff/MPELNESSet.yaml\r\npymatgen/io/feff/MPEXAFSSet.yaml\r\npymatgen/io/feff/MPEXELFSSet.yaml\r\npymatgen/io/feff/MPXANESSet.yaml\r\npymatgen/io/feff/__init__.py\r\npymatgen/io/feff/inputs.py\r\npymatgen/io/feff/outputs.py\r\npymatgen/io/feff/sets.py\r\npymatgen/io/lammps/CoeffsDataType.yaml\r\npymatgen/io/lammps/__init__.py\r\npymatgen/io/lammps/data.py\r\npymatgen/io/lammps/inputs.py\r\npymatgen/io/lammps/outputs.py\r\npymatgen/io/lammps/utils.py\r\npymatgen/io/lammps/templates/md.txt\r\npymatgen/io/lobster/__init__.py\r\npymatgen/io/lobster/inputs.py\r\npymatgen/io/lobster/lobsterenv.py\r\npymatgen/io/lobster/outputs.py\r\npymatgen/io/lobster/lobster_basis/BASIS_PBE_54_max.yaml\r\npymatgen/io/lobster/lobster_basis/BASIS_PBE_54_min.yaml\r\npymatgen/io/lobster/lobster_basis/BASIS_PBE_54_standard.yaml\r\npymatgen/io/qchem/__init__.py\r\npymatgen/io/qchem/inputs.py\r\npymatgen/io/qchem/outputs.py\r\npymatgen/io/qchem/sets.py\r\npymatgen/io/qchem/utils.py\r\npymatgen/io/vasp/MITRelaxSet.yaml\r\npymatgen/io/vasp/MPAbsorptionSet.yaml\r\npymatgen/io/vasp/MPHSERelaxSet.yaml\r\npymatgen/io/vasp/MPRelaxSet.yaml\r\npymatgen/io/vasp/MPSCANRelaxSet.yaml\r\npymatgen/io/vasp/MVLGWSet.yaml\r\npymatgen/io/vasp/MVLRelax52Set.yaml\r\npymatgen/io/vasp/VASPIncarBase.yaml\r\npymatgen/io/vasp/__init__.py\r\npymatgen/io/vasp/help.py\r\npymatgen/io/vasp/incar_parameters.json\r\npymatgen/io/vasp/inputs.py\r\npymatgen/io/vasp/optics.py\r\npymatgen/io/vasp/outputs.py\r\npymatgen/io/vasp/sets.py\r\npymatgen/io/vasp/vasp_potcar_file_hashes.json\r\npymatgen/io/vasp/vasp_potcar_pymatgen_hashes.json\r\npymatgen/io/vasp/vdW_parameters.yaml\r\npymatgen/io/xtb/__init__.py\r\npymatgen/io/xtb/inputs.py\r\npymatgen/io/xtb/outputs.py\r\npymatgen/optimization/__init__.py\r\npymatgen/optimization/linear_assignment.pyx\r\npymatgen/optimization/linear_assignment_numpy.py\r\npymatgen/optimization/neighbors.pyx\r\npymatgen/phonon/__init__.py\r\npymatgen/phonon/bandstructure.py\r\npymatgen/phonon/dos.py\r\npymatgen/phonon/gruneisen.py\r\npymatgen/phonon/ir_spectra.py\r\npymatgen/phonon/plotter.py\r\npymatgen/phonon/thermal_displacements.py\r\npymatgen/symmetry/__init__.py\r\npymatgen/symmetry/analyzer.py\r\npymatgen/symmetry/bandstructure.py\r\npymatgen/symmetry/groups.py\r\npymatgen/symmetry/kpath.py\r\npymatgen/symmetry/maggroups.py\r\npymatgen/symmetry/settings.py\r\npymatgen/symmetry/site_symmetries.py\r\npymatgen/symmetry/structure.py\r\npymatgen/symmetry/symm_data.json\r\npymatgen/symmetry/symm_data.yaml\r\npymatgen/symmetry/symm_data_magnetic.sqlite\r\npymatgen/symmetry/symm_ops.json\r\npymatgen/symmetry/symm_ops.yaml\r\npymatgen/transformations/__init__.py\r\npymatgen/transformations/advanced_transformations.py\r\npymatgen/transformations/site_transformations.py\r\npymatgen/transformations/standard_transformations.py\r\npymatgen/transformations/transformation_abc.py\r\npymatgen/util/__init__.py\r\npymatgen/util/convergence.py\r\npymatgen/util/coord.py\r\npymatgen/util/coord_cython.pyx\r\npymatgen/util/io_utils.py\r\npymatgen/util/num.py\r\npymatgen/util/plotly_chempot_layouts.json\r\npymatgen/util/plotly_interface_rxn_layouts.json\r\npymatgen/util/plotly_pd_layouts.json\r\npymatgen/util/plotting.py\r\npymatgen/util/provenance.py\r\npymatgen/util/string.py\r\npymatgen/util/testing.py\r\npymatgen/util/typing.py\r\npymatgen/util/structures/BaNiO3.json\r\npymatgen/util/structures/CsCl.json\r\npymatgen/util/structures/Graphite.json\r\npymatgen/util/structures/He_BCC.json\r\npymatgen/util/structures/K2O2.json\r\npymatgen/util/structures/La2CoO4F.json\r\npymatgen/util/structures/Li10GeP2S12.json\r\npymatgen/util/structures/Li2O.json\r\npymatgen/util/structures/Li2O2.json\r\npymatgen/util/structures/Li3V2(PO4)3.json\r\npymatgen/util/structures/LiFePO4.json\r\npymatgen/util/structures/NaFePO4.json\r\npymatgen/util/structures/Pb2TiZrO6.json\r\npymatgen/util/structures/Si.json\r\npymatgen/util/structures/SiO2.json\r\npymatgen/util/structures/Si_SiO2_Interface.json\r\npymatgen/util/structures/Sn.json\r\npymatgen/util/structures/SrTiO3.json\r\npymatgen/util/structures/TiO2.json\r\npymatgen/util/structures/TlBiSe2.json\r\npymatgen/util/structures/VO2.json\r\npymatgen/vis/ElementColorSchemes.yaml\r\npymatgen/vis/__init__.py\r\npymatgen/vis/plotters.py\r\npymatgen/vis/structure_chemview.py\r\npymatgen/vis/structure_vtk.py\r\n```\r\n</details>\r\n\r\n<details>\r\n<summary>new SOURCES.txt</summary>\r\n\r\n```txt\r\nLICENSE\r\nREADME.md\r\npyproject.toml\r\nsetup.cfg\r\nsetup.py\r\npymatgen.egg-info/PKG-INFO\r\npymatgen.egg-info/SOURCES.txt\r\npymatgen.egg-info/dependency_links.txt\r\npymatgen.egg-info/entry_points.txt\r\npymatgen.egg-info/requires.txt\r\npymatgen.egg-info/top_level.txt\r\npymatgen/alchemy/__init__.py\r\npymatgen/alchemy/filters.py\r\npymatgen/alchemy/materials.py\r\npymatgen/alchemy/transmuters.py\r\npymatgen/analysis/adsorption.py\r\npymatgen/analysis/aflow_prototypes.json\r\npymatgen/analysis/atomic_subshell_photoionization_cross_sections.csv\r\npymatgen/analysis/bond_dissociation.py\r\npymatgen/analysis/bond_valence.py\r\npymatgen/analysis/bonds_jmol_ob.yaml\r\npymatgen/analysis/bvparam_1991.yaml\r\npymatgen/analysis/chempot_diagram.py\r\npymatgen/analysis/cn_opt_params.yaml\r\npymatgen/analysis/cost.py\r\npymatgen/analysis/costdb_elements.csv\r\npymatgen/analysis/dimensionality.py\r\npymatgen/analysis/disorder.py\r\npymatgen/analysis/energy_models.py\r\npymatgen/analysis/eos.py\r\npymatgen/analysis/ewald.py\r\npymatgen/analysis/excitation.py\r\npymatgen/analysis/fragmenter.py\r\npymatgen/analysis/functional_groups.py\r\npymatgen/analysis/graphs.py\r\npymatgen/analysis/hhi.py\r\npymatgen/analysis/hhi_data.csv\r\npymatgen/analysis/icsd_bv.yaml\r\npymatgen/analysis/interface.py\r\npymatgen/analysis/interface_reactions.py\r\npymatgen/analysis/ionic_radii.json\r\npymatgen/analysis/local_env.py\r\npymatgen/analysis/molecule_matcher.py\r\npymatgen/analysis/molecule_structure_comparator.py\r\npymatgen/analysis/nmr.py\r\npymatgen/analysis/op_params.yaml\r\npymatgen/analysis/path_finder.py\r\npymatgen/analysis/phase_diagram.py\r\npymatgen/analysis/piezo.py\r\npymatgen/analysis/piezo_sensitivity.py\r\npymatgen/analysis/pourbaix_diagram.py\r\npymatgen/analysis/prototypes.py\r\npymatgen/analysis/quasiharmonic.py\r\npymatgen/analysis/reaction_calculator.py\r\npymatgen/analysis/structure_analyzer.py\r\npymatgen/analysis/structure_matcher.py\r\npymatgen/analysis/substrate_analyzer.py\r\npymatgen/analysis/surface_analysis.py\r\npymatgen/analysis/thermochemistry.py\r\npymatgen/analysis/transition_state.py\r\npymatgen/analysis/vesta_cutoffs.yaml\r\npymatgen/analysis/wulff.py\r\npymatgen/analysis/xps.py\r\npymatgen/analysis/chemenv/__init__.py\r\npymatgen/analysis/chemenv/connectivity/__init__.py\r\npymatgen/analysis/chemenv/connectivity/connected_components.py\r\npymatgen/analysis/chemenv/connectivity/connectivity_finder.py\r\npymatgen/analysis/chemenv/connectivity/environment_nodes.py\r\npymatgen/analysis/chemenv/connectivity/structure_connectivity.py\r\npymatgen/analysis/chemenv/coordination_environments/__init__.py\r\npymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometry_finder.py\r\npymatgen/analysis/chemenv/coordination_environments/structure_environments.py\r\npymatgen/analysis/chemenv/coordination_environments/voronoi.py\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/A#2.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/AC#12.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_1#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_2#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BO_3#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_1#10.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/BS_2#10.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#12.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/C#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/CO#11.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#20.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DD#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DDPN#8.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/DI#11.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/ET#7.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/FO#7.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#10.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/H#11.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HA#12.json\r\npymatgen/analysis/chemenv/coordination_environments/coordination_geometries_files/HB#8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es/Pb2TiZrO6.json\r\npymatgen/util/structures/Si.json\r\npymatgen/util/structures/SiO2.json\r\npymatgen/util/structures/Si_SiO2_Interface.json\r\npymatgen/util/structures/Sn.json\r\npymatgen/util/structures/SrTiO3.json\r\npymatgen/util/structures/TiO2.json\r\npymatgen/util/structures/TlBiSe2.json\r\npymatgen/util/structures/VO2.json\r\npymatgen/vis/ElementColorSchemes.yaml\r\npymatgen/vis/__init__.py\r\npymatgen/vis/plotters.py\r\npymatgen/vis/structure_chemview.py\r\npymatgen/vis/structure_vtk.py\r\n```\r\n</details>\r\n\r\nAny reason to include all of `docs_rst/` and `docs/*.html`?",
"You can exclude the mypy cache of course. The only reason why MANIFEST.in is there is to include things like the readme, license, etc. It hasn't been updated in a while, and so doesn't take into account things like the linting generated files, etc.",
"What about excluding doc files? Were they packaged intentionally?"
] | 2022-11-17T19:02:02
| 2022-11-18T00:25:25
|
2022-11-18T00:02:33Z
|
MEMBER
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Follow up to #2733.
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| 1,454,204,917
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PR_kwDOACgets5DKRUV
| 2,739
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rm `MANIFEST.in`
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"\n[](https://coveralls.io/builds/54343838)\n\nCoverage decreased (-36.3%) to 0.0% when pulling **8053a85d6dc4fc15251c11474e1f4c9f4f623335 on bye-manifest** into **58685c4218df91c7ccb228ce743584a5ea3067c0 on master**.\n"
] | 2022-11-18T00:10:08
| 2022-11-18T00:34:57
|
2022-11-18T00:33:42Z
|
MEMBER
|
{
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|
Following discussion in https://github.com/materialsproject/pymatgen/pull/2738#issuecomment-1319346557, this PR removes the `MANIFEST.in` file since it pulled a lot of unnecessary files like `.mypy_cache` and `docs/*`, `docs_rst/*`, `dev_scripts/` into the source distribution. It's job is taken over by `setup.py` with slight modifications.
<details>
<summary>Old `SOURCES.txt` (1452 lines after removing `.mypy_cache` lines</summary>
```txt
.gitattributes
.gitignore
.pre-commit-config.yaml
CHANGES.rst
CITATION.cff
CONTRIBUTING.rst
LICENSE.rst
MANIFEST.in
README.md
SECURITY.md
metadata.yml
pylintrc
pyproject.toml
setup.cfg
setup.py
tasks.py
.github/PULL_REQUEST_TEMPLATE.md
.github/dependabot.yml
.github/ISSUE_TEMPLATE/bug_report.md
.github/ISSUE_TEMPLATE/feature_request.md
.github/workflows/lint.yml
.github/workflows/test.yml
cmd_line/bader/Linux_64bit/bader
cmd_line/boltztrap/Darwin_64bit/BoltzTraP
cmd_line/boltztrap/Darwin_64bit/x_trans
cmd_line/boltztrap/Linux_64bit/x_trans
cmd_line/enum/README
cmd_line/enum/Linux_64bit/enum.x
cmd_line/enum/Linux_64bit/makestr.x
cmd_line/gulp/Libraries/belashchenko.lib
cmd_line/gulp/Libraries/bks.lib
cmd_line/gulp/Libraries/bresme_water.lib
cmd_line/gulp/Libraries/bush.lib
cmd_line/gulp/Libraries/carbonate.lib
cmd_line/gulp/Libraries/catlow.lib
cmd_line/gulp/Libraries/clayFF.lib
cmd_line/gulp/Libraries/clerirosato.lib
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pymatgen/phonon/__init__.py
pymatgen/phonon/bandstructure.py
pymatgen/phonon/dos.py
pymatgen/phonon/gruneisen.py
pymatgen/phonon/ir_spectra.py
pymatgen/phonon/plotter.py
pymatgen/phonon/thermal_displacements.py
pymatgen/symmetry/__init__.py
pymatgen/symmetry/analyzer.py
pymatgen/symmetry/bandstructure.py
pymatgen/symmetry/groups.py
pymatgen/symmetry/kpath.py
pymatgen/symmetry/maggroups.py
pymatgen/symmetry/settings.py
pymatgen/symmetry/site_symmetries.py
pymatgen/symmetry/structure.py
pymatgen/symmetry/symm_data.json
pymatgen/symmetry/symm_data.yaml
pymatgen/symmetry/symm_data_magnetic.sqlite
pymatgen/symmetry/symm_ops.json
pymatgen/symmetry/symm_ops.yaml
pymatgen/transformations/__init__.py
pymatgen/transformations/advanced_transformations.py
pymatgen/transformations/site_transformations.py
pymatgen/transformations/standard_transformations.py
pymatgen/transformations/transformation_abc.py
pymatgen/util/__init__.py
pymatgen/util/convergence.py
pymatgen/util/coord.py
pymatgen/util/coord_cython.pyx
pymatgen/util/io_utils.py
pymatgen/util/num.py
pymatgen/util/plotly_chempot_layouts.json
pymatgen/util/plotly_interface_rxn_layouts.json
pymatgen/util/plotly_pd_layouts.json
pymatgen/util/plotting.py
pymatgen/util/provenance.py
pymatgen/util/string.py
pymatgen/util/testing.py
pymatgen/util/typing.py
pymatgen/util/structures/BaNiO3.json
pymatgen/util/structures/CsCl.json
pymatgen/util/structures/Graphite.json
pymatgen/util/structures/He_BCC.json
pymatgen/util/structures/K2O2.json
pymatgen/util/structures/La2CoO4F.json
pymatgen/util/structures/Li10GeP2S12.json
pymatgen/util/structures/Li2O.json
pymatgen/util/structures/Li2O2.json
pymatgen/util/structures/Li3V2(PO4)3.json
pymatgen/util/structures/LiFePO4.json
pymatgen/util/structures/NaFePO4.json
pymatgen/util/structures/Pb2TiZrO6.json
pymatgen/util/structures/Si.json
pymatgen/util/structures/SiO2.json
pymatgen/util/structures/Si_SiO2_Interface.json
pymatgen/util/structures/Sn.json
pymatgen/util/structures/SrTiO3.json
pymatgen/util/structures/TiO2.json
pymatgen/util/structures/TlBiSe2.json
pymatgen/util/structures/VO2.json
pymatgen/vis/ElementColorSchemes.yaml
pymatgen/vis/__init__.py
pymatgen/vis/plotters.py
pymatgen/vis/structure_chemview.py
pymatgen/vis/structure_vtk.py
```
</details>
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| 1,454,219,574
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PR_kwDOACgets5DKUmj
| 2,740
|
Fix loose endpoints in `NEBPathfinder.string_relax()`
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"\n[](https://coveralls.io/builds/54370786)\n\nCoverage decreased (-36.3%) to 0.0% when pulling **f7df26aefcdc736e48c810541b93c0c787daf457 on fix-gh-2732** into **58685c4218df91c7ccb228ce743584a5ea3067c0 on master**.\n"
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| 2022-11-18T18:39:45
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2022-11-18T18:02:39Z
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MEMBER
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Closes #2732.
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PR_kwDOACgets5DOdvy
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Resurrect `requirements{,optional}.txt`
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2022-11-18T16:51:47Z
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MEMBER
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@shyuep Same contents they were deleted with in 8b5440b5.
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| 1,455,538,615
|
PR_kwDOACgets5DO0wd
| 2,742
|
Enable `dependabot` for `pip`
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2022-11-18T17:55:06Z
|
MEMBER
|
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Auto-updates `requirements{,-optional}.txt` monthly.
@shyuep Decided against using the `req.txt` files in `test.yml` workflow. We're installing purely from `setup.py` there.
https://github.com/materialsproject/pymatgen/blob/b950dc16388d2d07c1ae602195c3b9cbfe586af3/.github/workflows/test.yml#L56
By installing unpinned packages in CI, we catch breaking changes in dependencies sooner. Once something breaks CI, we can compare with `requirements.txt` for a "last working version" to see which update was the culprit.
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PR_kwDOACgets5DO4DO
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Bump galore from 0.6.1 to 0.7.0
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"\n[](https://coveralls.io/builds/54370347)\n\nCoverage remained the same at 0.0% when pulling **ad75bcb69dfa97c8274d709e596ed7fee81abf35 on dependabot/pip/galore-0.7.0** into **eb9baff90407a3be02d33ebbd8d2fb3c88f73ea5 on master**.\n"
] | 2022-11-18T17:55:38
| 2022-11-18T19:03:30
|
2022-11-18T19:03:28Z
|
CONTRIBUTOR
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Bumps [galore](https://github.com/SMTG-UCL/galore) from 0.6.1 to 0.7.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/SMTG-UCL/galore/releases">galore's releases</a>.</em></p>
<blockquote>
<h2>Bug fixes and depency updates</h2>
<p>This release doesn't add any features, but fixes some errors and updates the installation setup.</p>
<h2>Changelog</h2>
<ul>
<li>Updated setup.py to add a [vasp] extra; this handles Pymatgen installation which can be tricky on older Python versions.</li>
<li>Update the [vasp] extra to handle some compatibility breaks between dependencies and different Python versions.</li>
<li>Fix some incorrect values in Al k-alpha XPS cross-sections</li>
<li>Pymatgen CompleteDOS was not correctly accepted by galore.process_pdos()</li>
<li>Implement previously ineffective "offset" option in galore.plot.plot_pdos(), add a matching option to galore.plot.plot_tdos()</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/SMTG-UCL/galore/blob/master/CHANGELOG.rst">galore's changelog</a>.</em></p>
<blockquote>
<h2><code>[0.7.0] <https://github.com/smtg-ucl/galore/compare/0.6.2...0.7.0></code>__ - 2021-07-06</h2>
<ul>
<li>
<p>Continuous integration has been migrated from Travis to Github Actions</p>
</li>
<li>
<p>Minimum Python version has been increased to 3.5.</p>
<ul>
<li>Python 3.4 was not available through Github actions. It is not wise to
support a platform we cannot test.</li>
</ul>
</li>
<li>
<p>BUGFIX: missing import affecting process_pdos</p>
</li>
</ul>
<h2><code>[0.6.2] <https://github.com/smtg-ucl/galore/compare/0.6.1...0.6.2></code>__ - 2021-05-24</h2>
<ul>
<li>Updated setup.py to add a [vasp] extra; this handles Pymatgen
installation which can be tricky on older Python versions.</li>
<li>Update the [vasp] extra to handle some compatibility breaks between
dependencies and different Python versions.</li>
<li>Fix some incorrect values in Al k-alpha XPS cross-sections</li>
<li>BUGFIX: Pymatgen CompleteDOS was not correctly accepted by galore.process_pdos()</li>
<li>Implement previously ineffective "offset" option in
galore.plot.plot_pdos(), add a matching option to
galore.plot.plot_tdos()</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/SMTG-UCL/galore/commit/222f3f05787d36b754356ceb13dba854939c2d16"><code>222f3f0</code></a> Version number bump - 0.7.0 (<a href="https://github-redirect.dependabot.com/SMTG-UCL/galore/issues/39">#39</a>)</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/0e67a8a34ec721d699a3a93d82e15a86d81a1cae"><code>0e67a8a</code></a> BUGFIX: missing import statement in <strong>init</strong>.py (<a href="https://github-redirect.dependabot.com/SMTG-UCL/galore/issues/37">#37</a>)</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/45592086f2c1aa9e54f9ec6b3b3f401ec4333390"><code>4559208</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/SMTG-UCL/galore/issues/36">#36</a> from SMTG-UCL/gh-actions</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/e75ce04f4854025fe1ace53aba951809c4bb4a3e"><code>e75ce04</code></a> Add CI for Python 3.8</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/d4a5d7e8d9fb6e2b7aba7ea42e1f435a5592e566"><code>d4a5d7e</code></a> Changelog/setup/READY update; drop Python 3.4</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/ec944958d836672915922ce7efafcb3644bdb579"><code>ec94495</code></a> GH actions: coveralls tweaks</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/969dbb0e9b969fb2b28753275a451323362e4e53"><code>969dbb0</code></a> GH actions: add coverage checking</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/3bca7b15c9dbade192ca75c13d3683b40d8ff25f"><code>3bca7b1</code></a> GH actions: tweak GPAW build</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/ce6e5a41cfa873ca6f3b75912d68ad0f40dcb6f4"><code>ce6e5a4</code></a> GH actions: force GPAW import</li>
<li><a href="https://github.com/SMTG-UCL/galore/commit/efdbd0b11336409675c0eabac7bb52693a1c0029"><code>efdbd0b</code></a> GH actions: GPAW dependencies</li>
<li>Additional commits viewable in <a href="https://github.com/SMTG-UCL/galore/compare/0.6.1...0.7.0">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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PR_kwDOACgets5DO4FP
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Bump mypy from 0.982 to 0.991
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[
"\n[](https://coveralls.io/builds/54370367)\n\nCoverage remained the same at 0.0% when pulling **4cab2280d05e26987329a74d637f0897fd4236c9 on dependabot/pip/mypy-0.991** into **eb9baff90407a3be02d33ebbd8d2fb3c88f73ea5 on master**.\n"
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| 2022-11-18T20:48:11
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2022-11-18T20:48:10Z
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CONTRIBUTOR
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Bumps [mypy](https://github.com/python/mypy) from 0.982 to 0.991.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/python/mypy/commit/b7788fcc4d140bbeb56531ab054bcdd53e298d30"><code>b7788fc</code></a> Update version to remove "+dev" for releasing 0.991</li>
<li><a href="https://github.com/python/mypy/commit/6077d1966e8dc84be44b9e30f590a604561b72b3"><code>6077d19</code></a> manually CP typeshed <a href="https://github-redirect.dependabot.com/python/mypy/issues/9130">#9130</a></li>
<li><a href="https://github.com/python/mypy/commit/ab0ea1ec4499b8b589bd3a5da7fdd08d9e00990e"><code>ab0ea1e</code></a> Fix crash with function redefinition (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14064">#14064</a>)</li>
<li><a href="https://github.com/python/mypy/commit/592a9cee1368542ba252cf665ffac0f46ff783c0"><code>592a9ce</code></a> Fix another crash with report generation on namespace packages (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14063">#14063</a>)</li>
<li><a href="https://github.com/python/mypy/commit/1650ae00deb47ab315d5613492950dd75d51cc1a"><code>1650ae0</code></a> Update --no-warn-no-return docs for empty body changes (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14065">#14065</a>)</li>
<li><a href="https://github.com/python/mypy/commit/b9daa313a5326e0bb315422cafe0b1f62a33cec6"><code>b9daa31</code></a> Don't ignore errors in files passed on the command line (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14060">#14060</a>)</li>
<li><a href="https://github.com/python/mypy/commit/02fd8a54e72be4a8ed83049d86d1335b164283c2"><code>02fd8a5</code></a> Filter out wasm32 wheel in upload-pypi.py (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14035">#14035</a>)</li>
<li><a href="https://github.com/python/mypy/commit/131c8d707a3071e1d3e4dca81db47a567d25aa81"><code>131c8d7</code></a> Fix crash on inference with recursive alias to recursive instance (<a href="https://github-redirect.dependabot.com/python/mypy/issues/14038">#14038</a>)</li>
<li><a href="https://github.com/python/mypy/commit/136833884fcf44dd0a6c07743ee0691ff878aad9"><code>1368338</code></a> Change version to 0.991+dev in preparation for the point release</li>
<li><a href="https://github.com/python/mypy/commit/b71dc3da0d8c6a4e116eef98a7ff8591145338be"><code>b71dc3d</code></a> Remove +dev from version</li>
<li>Additional commits viewable in <a href="https://github.com/python/mypy/compare/v0.982...v0.991">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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PR_kwDOACgets5DO4HU
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Bump f90nml from 1.1.2 to 1.4.3
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2022-11-18T19:05:29Z
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[//]: # (dependabot-start)
⚠️ **Dependabot is rebasing this PR** ⚠️
Rebasing might not happen immediately, so don't worry if this takes some time.
Note: if you make any changes to this PR yourself, they will take precedence over the rebase.
---
[//]: # (dependabot-end)
Bumps [f90nml](https://github.com/marshallward/f90nml) from 1.1.2 to 1.4.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/marshallward/f90nml/releases">f90nml's releases</a>.</em></p>
<blockquote>
<h2>Version 1.4.1 release</h2>
<p>1.4.1:
- Bugfix: Several cogroup issues related to management of internal keys and
todict() output were fixed. Thanks to GitHub user <a href="https://github.com/poluhh"><code>@poluhh</code></a> and Rasmus H.
Fogh for reporting.
- Bugfix: Empty lists [] are now displayed as comma-delimited blanks.
Thanks to William Dawson for reporting.</p>
<h2>Version 1.4 release</h2>
<ul>
<li>
<p>Ordering of duplicate keys is now preserved, through the introduction of two
new classes. The <code>Cogroup</code> class extends the <code>list</code> previously associated
with the values of a duplicate key. The <code>NmlKey</code> class extends <code>str</code> and
externally holds the namelist key, but also contains an internal key to
distinguish between duplicates.</p>
</li>
<li>
<p>A repeated key is no longer initialized with a list, and must now be
explicitly declared as a cogroup with the <code>add_cogroup</code> function.</p>
</li>
<li>
<p>A performance issue related to the detection of values in a line has been
fixed. Thanks to Stephen LeDoux for reporting and Philip Cross for fixing
this issue.</p>
</li>
</ul>
<h2>v1.3.1</h2>
<p>No release notes provided.</p>
<h2>v1.3</h2>
<p>Version 1.3 release</p>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/marshallward/f90nml/blob/main/CHANGELOG">f90nml's changelog</a>.</em></p>
<blockquote>
<p>1.4.4:
- Bugfix: Cogroup namelist initialization from a cogroup was fixed.
Thanks to Rasmus Fogh for reporting.</p>
<p>1.4.2:
- Bugfix: Case-insensitive del now works as intended.
Thanks to GitHub user <a href="https://github.com/mandresm"><code>@mandresm</code></a> for reporting.</p>
<p>1.4.1:
- Bugfix: Several cogroup issues related to management of internal keys and
todict() output were fixed. Thanks to GitHub user <a href="https://github.com/poluhh"><code>@poluhh</code></a> and Rasmus H.
Fogh for reporting.
- Bugfix: Empty lists [] are now displayed as comma-delimited blanks.
Thanks to William Dawson for reporting.</p>
<p>1.4:
- Ordering of duplicate keys is now preserved, through the introduction of
two new classes. The Cogroup extends the list previously associated with
the values of a duplicate key. The NmlKey extends str and externally
holds the namelist key, but also contains an internal key to distinguish
between duplicates.
- A repeated key is no longer initialized with a list, and must now be
explicitly declared as a cogroup with the <code>add_cogroup</code> function.
- A performance issue related to the detection of values in a line has been
fixed. Thanks to Stephen LeDoux for reporting and Philip Cross for
fixing this issue.</p>
<p>1.3.1:
- String splitting is now an optional feature, enabled by the split_strings
property. Default string array output again resembles v1.2 output.
- Bugfix: For arrays of strings, a split string element will no longer
insert erroneous commas. Thanks to Jared Lewis for reporting.</p>
<p>1.3:
- Strings which exceed the column limit are now split across multiple
lines. Thanks to Xi Chen for reporting.
- We now raise ValueError if we reach and EOF before a namelist group has
been terminated. It is also raised for various StopIteration scenarios.
- Namelist output with repeated values can now use repeat tokens if
enabled. Thanks to Holger Wolff for contributing this feature.
- Bugfix: Preserve newlines in the reads() string parser. This fixes a bug
in the handling of tokens outside of namelist groups. Thanks to GitHub
user <a href="https://github.com/coreur"><code>@coreur</code></a> for reporting.
- Patching now supports the addition of new namelist groups. Thanks to
Cory Kramer for reporting and suggesting this issue.</p>
<p>1.2:
- Bugfix: Repeated null arrays as final elements now parse correctly.
- Bugfix: Preprossor comment token # now correctly disabled on default.
- Bugfix: Several indexing issues with array patching have been fixed.</p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/marshallward/f90nml/commit/bb93aec913d77d92b5a6199484ab8943bd1f8596"><code>bb93aec</code></a> Version 1.4.3</li>
<li><a href="https://github.com/marshallward/f90nml/commit/c126a5f47957bc01ea51c5f87e63035169fc5c79"><code>c126a5f</code></a> Test: set from cogroup</li>
<li><a href="https://github.com/marshallward/f90nml/commit/3d854879afe23f6f63c03a5424909b6f0a253975"><code>3d85487</code></a> Cogroup initialization support</li>
<li><a href="https://github.com/marshallward/f90nml/commit/b02f6c832b9aaf705ddd417d24874834a0b252a1"><code>b02f6c8</code></a> Version 1.4.2 update</li>
<li><a href="https://github.com/marshallward/f90nml/commit/0fdcedd12fe0d1aef22845ee7aa28224dc36258a"><code>0fdcedd</code></a> Case-insensitive del fix</li>
<li><a href="https://github.com/marshallward/f90nml/commit/3e24a974fcb2437eb8b50174ab141d604fcffc98"><code>3e24a97</code></a> Removal of Travis test configuration</li>
<li><a href="https://github.com/marshallward/f90nml/commit/7fbba7cedd02852be94832bb3de6151a385cebde"><code>7fbba7c</code></a> Version 1.4.1 update</li>
<li><a href="https://github.com/marshallward/f90nml/commit/1b6630b2999b8823407a1cf04c0ffd8a0426ff83"><code>1b6630b</code></a> Pypy: Pop internal key for cogroup reorder</li>
<li><a href="https://github.com/marshallward/f90nml/commit/d270d91445a0e54000292040487de81850a30053"><code>d270d91</code></a> Cogroup tests</li>
<li><a href="https://github.com/marshallward/f90nml/commit/5cf112edb0877d1202ded1c50c689bfa968c4238"><code>5cf112e</code></a> Namelist cogroup key init bugfix</li>
<li>Additional commits viewable in <a href="https://github.com/marshallward/f90nml/compare/v1.1.2...v1.4.3">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5DO4Iu
| 2,746
|
Bump seekpath from 1.9.4 to 2.0.1
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[
"\n[](https://coveralls.io/builds/54370295)\n\nCoverage remained the same at 0.0% when pulling **baeac4d068d8ffdeea094f04396e065e0cbaf638 on dependabot/pip/seekpath-2.0.1** into **eb9baff90407a3be02d33ebbd8d2fb3c88f73ea5 on master**.\n"
] | 2022-11-18T17:55:49
| 2022-11-18T19:04:39
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2022-11-18T19:04:35Z
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CONTRIBUTOR
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Bumps [seekpath](https://github.com/giovannipizzi/seekpath) from 1.9.4 to 2.0.1.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/giovannipizzi/seekpath/blob/develop/CHANGELOG.md">seekpath's changelog</a>.</em></p>
<blockquote>
<h1>v2.0.0</h1>
<ul>
<li>Dropped python 2 support</li>
<li>Moved out the web tool to <a href="https://github.com/materialscloud-org/tools-seekpath">tools-seekpath</a>, based on <a href="https://github.com/materialscloud-org/tools-barebone">tools-barebone</a>, whose codebases mostly take inspiration from the web tool implemented in seekpath v1.x</li>
</ul>
<h1>v1.x</h1>
<p>First versions of seekpath, supportinb both python 2 an python 3, and providing a web tool to interactively inspect the results of seekpath (hosted on the <a href="http://www.materialscloud.org/tools/seekpath/">Materials Cloud tools section</a>).</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/672e8c1229b39a923d27de5705125faae0bc3df1"><code>672e8c1</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/giovannipizzi/seekpath/issues/91">#91</a> from giovannipizzi/release_v2.0.1</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/4be92afa47671986cb195b015543912e3cdd21ea"><code>4be92af</code></a> Removed docs for legacy wrappers, now removed</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/8c06ad3fd04d2a8bcd91bf8e0d654240a98e3cc4"><code>8c06ad3</code></a> Upping version number</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/b4e17523f2fdc448782a820430f267647f0d832a"><code>b4e1752</code></a> Docs were lost in the v1 -> v2 migration...</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/886959b0f9561260b0de1ba520c7a6b65a91cd72"><code>886959b</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/giovannipizzi/seekpath/issues/89">#89</a> from giovannipizzi/release_2.0.0a2</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/5b777f8f7f14de76fe6ed70af9157cb7ddac4598"><code>5b777f8</code></a> Adding minimal changelog</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/d26f46338ea9f49642610fdce9f118339352d169"><code>d26f463</code></a> Preparing for 2.0.0 release: upping version</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/d10fa5ed57570fcff8308f11f88896361c1db00f"><code>d10fa5e</code></a> Adding also installation of BZ dependencies (scipy)</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/b34477404d94ccf30a91b96eabe62e41139623c0"><code>b344774</code></a> Disabling prospector for now</li>
<li><a href="https://github.com/giovannipizzi/seekpath/commit/824ae69ac7e8da45b0e6fa0b1ad0c7ac4f55db13"><code>824ae69</code></a> Fix to GitHub actions</li>
<li>Additional commits viewable in <a href="https://github.com/giovannipizzi/seekpath/compare/v1.9.4...v2.0.1">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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PR_kwDOACgets5DO4LD
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Bump jarvis-tools from 2020.7.14 to 2022.9.16
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[
"\n[](https://coveralls.io/builds/54372577)\n\nCoverage remained the same at 0.0% when pulling **9c9ba01c89dbfb8d938d8efc83a0eeb1f3a69f9b on dependabot/pip/jarvis-tools-2022.9.16** into **5768dbe8658e1102aa500abc0ec23e61ad97eeea on master**.\n"
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2022-11-18T19:05:10Z
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CONTRIBUTOR
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Bumps [jarvis-tools](https://github.com/usnistgov/jarvis) from 2020.7.14 to 2022.9.16.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/usnistgov/jarvis/releases">jarvis-tools's releases</a>.</em></p>
<blockquote>
<h2>v2022.09.16</h2>
<ul>
<li>Qiskit dependence upgraded.</li>
</ul>
<h2>v2022.08.27</h2>
<ul>
<li>Phase diagram added</li>
<li>PhononDOS module and Debye temperature calculations</li>
<li>Coverage increase</li>
</ul>
<h2>v2022.1.10</h2>
<ul>
<li>QE input fix</li>
<li>Atoms class xyz header fix</li>
</ul>
<h2>v2021.12.16</h2>
<ul>
<li>Quantum espresso inputs/outputs update</li>
<li>XANES POSCAR writer added</li>
<li>Python compatibility to 3.8 and 3.9 and got rid of fractions.gcd function</li>
<li>Fixed ase_to_atoms module</li>
<li>Docs requirements added</li>
</ul>
<h2>v2021.10.03</h2>
<ul>
<li>Fixed k-point automatic mesh bug</li>
<li>Upgraded QMOF database</li>
<li>Added Zeo++ surface area module</li>
</ul>
<h2>v2021.08.18</h2>
<ul>
<li>Updates dft_3d and edos_pdos database</li>
<li>Added substitution defects</li>
</ul>
<h2>v2021.08.05</h2>
<ul>
<li>hMOF, jqe_tb3, jff database added</li>
<li>LAMMPS parse_folder update</li>
<li>Elastic tensor list update</li>
</ul>
<h2>v2021.07.19</h2>
<ul>
<li>Added magpie.json</li>
</ul>
<h2>v2021.07.18</h2>
<ul>
<li>Surface builder update</li>
<li>Chemical only magpie descriptors added</li>
<li>pdb_core dataset added</li>
<li>zeopp tempfile bugfix.</li>
<li>removed test_figshare.py from pytest because of Error 137 in action</li>
<li>Do not use dft_3d for pytests because of memory issues</li>
</ul>
<h2>v2021.07.10</h2>
<ul>
<li>Added more tutorials and docs</li>
<li>Added pytraj module</li>
<li>Added HPOV and PDBBind database</li>
</ul>
<h2>v2021.07.05</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/usnistgov/jarvis/commit/cb2227b0b5107d95ea9e543a6fd7d14b70aeda85"><code>cb2227b</code></a> Qiskit upgraded (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/254">#254</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/10219eaae585bced4b08ed22c317b56442a66d09"><code>10219ea</code></a> Develop (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/250">#250</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/84552008f416b6396c45d76fbe5a624b54cabd8b"><code>8455200</code></a> Develop (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/249">#249</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/136444409c355b8e9748fc1fd568d6030f99e587"><code>1364444</code></a> Develop (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/239">#239</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/30a2c0d933ab56a0ef638b99149fc576a85bd255"><code>30a2c0d</code></a> Bump tensorflow from 2.7.0 to 2.8.0 in /docs (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/224">#224</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/dc70af1911daeac6269d683e007d32cff39883fb"><code>dc70af1</code></a> Bump numpy from 1.20.0 to 1.21.0 (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/238">#238</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/2c2241dbd47c7d3ec5f0f7a78e7231e7705b43f7"><code>2c2241d</code></a> Develop (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/236">#236</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/217eb3719f9ffce8f2bde9ae73f3961e42660217"><code>217eb37</code></a> Bump numpy from 1.20.0 to 1.21.0 (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/220">#220</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/904d6249ee5d72e9315c100ae5f7ce8565dc7f91"><code>904d624</code></a> Bump numpy from 1.20.0 to 1.21.0 in /docs (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/219">#219</a>)</li>
<li><a href="https://github.com/usnistgov/jarvis/commit/efa782b08872fae0f74c2eacf38cc74bc59f8e14"><code>efa782b</code></a> Bump pillow from 8.4.0 to 9.0.0 in /docs (<a href="https://github-redirect.dependabot.com/usnistgov/jarvis/issues/218">#218</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/usnistgov/jarvis/compare/v2020.7.14...v2022.09.16">compare view</a></li>
</ul>
</details>
<br />
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|
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I_kwDOACgets5W7qhk
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PeriodicNeighbor: AttributeError: species_string
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[
"`PeriodicNeighbor` is meant to be a container `Site`-like object for temporary analysis. This is why it forgoes all the conversions/checks that are in `PeriodicSite` (which can be slow and expensive when you are searching across many neighbors). Serialization to a dict was not planned as a use case.",
"Maybe it makes sense to overwrite the *from_dict()* method then and throw an exception. However, *PeriodicNeighbor* is returned by many Structure/IStructure methods and it would help the user if it was possible to directly serialize those outputs.",
"Implementing a serialization protocol isn't difficult. but I have to understand the situations in which such an application is actually used. Do you simply need the site or do you need the additional information like distances etc.? To just have the site, it is easy for me to implement a as_site method that will automatically convert a PeriodicNeighbor to PeriodicSite and that will be serializable (but lose the distance and index information). To implement a proper as_dict method requires more effort. All these are important considerations."
] | 2022-11-21T19:43:33
| 2022-11-22T16:02:18
|
2022-11-22T16:02:18Z
|
NONE
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It seems that deserialization of PeriodicNeighbor is not properly converting all types:
```python
from pymatgen.core import Site, PeriodicSite
from pymatgen.core.structure import PeriodicNeighbor
from pymatgen.core.lattice import Lattice
from pymatgen.core.periodic_table import get_el_sp
from pymatgen.core.composition import Composition
lattice = Lattice([[6.175883999999999, 6.175884, 6.175884000000001], [6.175884, -6.175884, -6.175884], [-6.175884, 6.175884, -6.175884]], [True, True, True])
site1 = PeriodicNeighbor(Composition({get_el_sp('Fe2+'): 1}), [0,0,0], lattice)
site2 = PeriodicNeighbor.from_dict(site1.as_dict())
# Printing site works:
print(site1)
# Converting to dict and back throws an error when printing:
print(site2)
# Initial _species type: <class 'pymatgen.core.composition.Composition'>
print(type(site1._species))
```
The reason is that the deserialized object *site2* has an invalid *_species* property which is not a Composition object. Any call to *species_string* or *is_ordered* will fail.
```bash
$ python -m pip freeze | grep 'pymatgen'
pymatgen==2022.11.7
```
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I_kwDOACgets5W8Xsq
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Repro template
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[] | 2022-11-21T22:18:04
| 2024-01-08T08:55:25
|
2024-01-08T08:55:24Z
|
MEMBER
|
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Many big projects offer repro templates that spin up an environment with everything needed make a minimal reproducible example simply by clicking a link.
Having something like this for `pymatgen` would make it much easier for users (esp. newcomers) to point out problems and reduce workload on maintainers if they get high-quality reproductions.
We could try out [GitHub's new Codespaces](https://docs.github.com/en/codespaces) for this.
Here's what that might look like:
We'd link this codespace in our issue template and invite people to launch it, copy-paste their code into it and then paste the link to the codespace into their issue. (This would also ensure the error occurs on `master` and isn't due to outdated versions.
All we'd need to do is create a `.devcontainer/devcontainer.json` file that tells GitHub how to spin up our codespace and create a file like `test_files/repro-template.ipynb` with some common imports and maybe a dummy structure or simple `MPRester` query to get people up and running.
```json5
// .devcontainer/devcontainer.json
{
"image": "mcr.microsoft.com/devcontainers/universal:2",
"hostRequirements": {
"cpus": 4
},
"waitFor": "onCreateCommand",
"updateContentCommand": "python -m pip install -r requirements.txt && python -m pip install -e .",
"customizations": {
"codespaces": {
"openFiles": ["test_files/repro_tempalte.ipynb"]
},
"vscode": {
"extensions": [
"ms-toolsai.jupyter",
"ms-python.python"
]
}
}
}
```
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I_kwDOACgets5XG2g9
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Moving the namespace pymatgen.io.lammps into external add-on package
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[
"I am not in favor of moving a package that is already in pymatgen to an external add on, especially a package that is actively used by a number of people. I developed the add-on option to deal with less commonly used modules, not to remove critical functionality. LAMMPS is used on a daily basis, no least by my group. \n\nonce it goes out of the main pymatgen repo, there is the danger that backward compatibility will be gone and many codes are going to break. \n\nI am not sure what is meant by \"easier control of developments\". I don't think we have been tardy on the processing of PRs. ",
"Hello @shyuep,\r\n\r\nThank you very much for your input. We perfectly understand your point. We started this issue specifically to know whether people were still using that part and from the recent development activity in that module (and somehow also from the development activity of lammps workflows in atomate v1), we mistakenly thought that it was not used so much anymore. So I'm glad to see that it still is!\r\n\r\nFrom this first comment from you, I think we should indeed continue in this direction keeping what exists in pymatgen and not remove this part to put it outside.\r\n\r\nAs for the easier control of developments, this was not at all a complaint on anything. What you and the pymatgen team are doing at managing and maintaining the package is great work, but I'm sure also very time-consuming on your side, so we thank you for that. The purpose of getting it out would have been to \"remove a thorn from your foot\" (this is a bare translation of a french expression, not sure if this makes any sense in English ;-).\r\n\r\nBest,",
"Thanks. I certainly appreciate all contributions. I totally understand the desire to do a separate add-on package. It is more of a judgment call whether something is often used. LAMMPS is certainly a core software used in my group at least (almost as much as VASP). Pls go ahead and submit your changes when ready and we will review. Just a note that it is my impression that my student @manaslkht has been working with the MP team on LAMMPS changes, particularly for atomate2 as well.",
"@shyuep Just to clarify the PR mentioned (#2692) is building on top of Ryan's and my contributions that aimed at developing a high-throughput architecture for LAMMPS in pymatgen. @gbrunin took over this work and is currently leading this effort in collaboration with the MP team. ",
"Ok. I would suggest everyone starts by submitting PRs. In general, PRs coming in bite sized doses are easier to handle. E.g, improvement to LAMMPS Input, LAMMPS Output etc, can come in separate PRs. The users can also adjust to the code in the mean time. One massive PR is hard to go through.",
"@gbrunin thanks for the nice work on the LAMMPS integration and for raising this discussion. I have no objections to either solution.\r\n"
] | 2022-11-23T09:53:13
| 2022-11-28T06:02:57
|
CONTRIBUTOR
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We are currently working on adding functionalities to the Lammps interface of pymatgen (see #2692, that will be closed soon). After discussion with @JaGeo, @davidwaroquiers, @ml-evs, and @gmrigna, we believe it would be better to have a separate add-on [pymatgen-io-lammps](https://github.com/Matgenix/pymatgen-io-lammps) in order to have an easier control of the developments and because it would make more sense to have it as a separate package for most pymatgen users. The last developments (apart from linting etc) in this namespace date back to more than 1 year.
There are different ways to fix the conflict between the namespace and the external package:
1. What is currently in `pymatgen.io.lammps` would be integrated into this add-on, and `pymatgen.io.lammps` would be deleted. This would have to be fine with the previous contributors to the code, who would be cited in the contributors of the new package (@rkingsbury @orionarcher @htz1992213 @chc273 @adengz @matk86, let us know here if you are not ok with this solution).
2. Alternatively, the current `pymatgen.io.lammps` could be renamed lammps_legacy for instance.
Please let us know if any of these solutions suits you or if we need to discuss.
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CVE-2022-42964 ReDOS vulnerability in GaussianInput
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[
"Looks like this stems from `^(\\w+)*` in https://github.com/materialsproject/pymatgen/blob/7a51c9b3e993ba5b6cc57bbdf5c293feb045611e/pymatgen/io/gaussian.py#L93\r\n\r\nwhich you can explode with `\"0\" * 100 + \"!\"`.\r\n\r\nI'm not a Gaussian user, but is this part of the regex necessary? Can the input be satisfied with `^(\\w)*`...?",
"@ScottNotFound I don't think it is possible to change `^(\\w+)*` to `^(\\w)*`.\r\n\r\nThis regex is for example looking for lines such as \r\n\r\n```\r\nC1\r\nC2 1 CC\r\nH3 1 CH1 2 asp2\r\nH4 1 CH1 2 asp2 3 180.\r\nH5 2 CH2 1 asp3 3 D1\r\nH6 2 CH2 1 asp3 5 D2\r\n```\r\n\r\nThe line starts by an element symbol which could be (optionally) followed by a number. \r\nIf only chemical elements were valid items here, the Regex could had been `[a-zA-Z]{1,2}`. But, as for the above example you ca write C1 or C.\r\n\r\nUsing the following regex line 93 for the class attribute `_zmat_patt` should be ok. The tests in `test_gaussian.py` are valid.\r\n\r\n```\r\n_zmat_patt = re.compile(r\"^(\\w+)([\\s,]+(\\w+)[\\s,]+(\\w+)){0,3}[\\-\\.\\s,\\w]*$\")\r\n```\r\n\r\nIt looks like it fixes the vulnerability:\r\n\r\n```\r\n1: Done in 0.0005118846893310547\r\n21: Done in 6.198883056640625e-05\r\n41: Done in 5.817413330078125e-05\r\n61: Done in 7.319450378417969e-05\r\n81: Done in 9.799003601074219e-05\r\n101: Done in 0.00012993812561035156\r\n121: Done in 0.0001690387725830078\r\n141: Done in 0.00022125244140625\r\n161: Done in 0.00026917457580566406\r\n181: Done in 0.00033211708068847656\r\n201: Done in 0.0004401206970214844\r\n221: Done in 0.0005009174346923828\r\n241: Done in 0.0005931854248046875\r\n261: Done in 0.0006520748138427734\r\n281: Done in 0.0007491111755371094\r\n301: Done in 0.0008258819580078125\r\n321: Done in 0.00090789794921875\r\n341: Done in 0.001276254653930664\r\n361: Done in 0.0011610984802246094\r\n381: Done in 0.0013689994812011719\r\n401: Done in 0.0014448165893554688\r\n421: Done in 0.001538991928100586\r\n441: Done in 0.0017888545989990234\r\n461: Done in 0.0019121170043945312\r\n481: Done in 0.0019729137420654297\r\n501: Done in 0.002460002899169922\r\n521: Done in 0.0028901100158691406\r\n541: Done in 0.002777099609375\r\n561: Done in 0.0030379295349121094\r\n581: Done in 0.0029418468475341797\r\n601: Done in 0.0033109188079833984\r\n621: Done in 0.003364086151123047\r\n641: Done in 0.0034112930297851562\r\n661: Done in 0.003716707229614258\r\n681: Done in 0.0038809776306152344\r\n701: Done in 0.004051923751831055\r\n721: Done in 0.004559993743896484\r\n741: Done in 0.004487037658691406\r\n761: Done in 0.0049211978912353516\r\n781: Done in 0.00495600700378418\r\n801: Done in 0.00517582893371582\r\n821: Done in 0.005485057830810547\r\n841: Done in 0.005793094635009766\r\n861: Done in 0.005961894989013672\r\n881: Done in 0.007217884063720703\r\n901: Done in 0.006846904754638672\r\n921: Done in 0.007014751434326172\r\n941: Done in 0.00799417495727539\r\n961: Done in 0.007646322250366211\r\n981: Done in 0.008347272872924805\r\n1001: Done in 0.008255958557128906\r\n```\r\n",
"@gVallverdu FYI, debian has been including your proposed fix since June 2023: https://salsa.debian.org/debichem-team/pymatgen/-/commit/dcba4226dfc59789070bd1f7aa40b953e7722651 "
] | 2022-11-28T11:15:24
| 2024-07-17T17:32:22
|
CONTRIBUTOR
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**Describe the bug**
A CVE-2022-42964 ReDOS vulnerability in GaussianInput has been reported in the GaussianInput.from_string method.
An exponential ReDoS (Regular Expression Denial of Service) can be triggered in the pymatgen PyPI package, when an attacker is able to supply arbitrary input to the GaussianInput.from_string method
The report was made at https://research.jfrog.com/vulnerabilities/pymatgen-redos-xray-257184/
and documented by Debian at https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1024017 (see also https://security-tracker.debian.org/tracker/CVE-2022-42964 )
**To Reproduce**
Steps to reproduce the behavior:
1. Use test code CVE-2022-42964.py
```
import time
from pymatgen.io.gaussian import GaussianInput
def str_and_from_string(i):
ans = """#P HF/6-31G(d) SCF=Tight SP
H4 C1
0 1
"""
vulnerable_input = ans + 'C'+'0' * i + '!'+'\n'
GaussianInput.from_string(vulnerable_input)
for i in range(1000):
start = time.time()
str_and_from_string(i)
print(f"{i}: Done in {time.time() - start}")
```
2. `python3 CVE-2022-42964.py`
3. Output shows exponentially growing execution time for what should be a trivial constant loop
**Expected behavior**
Creating strings of the kind in this example should require the same millisecond time in each iteration.
**Screenshots**
```
$ python3 CVE-2022-42964.py
0: Done in 0.0006997585296630859
1: Done in 4.506111145019531e-05
2: Done in 3.814697265625e-05
3: Done in 4.291534423828125e-05
4: Done in 5.6743621826171875e-05
5: Done in 6.365776062011719e-05
6: Done in 5.555152893066406e-05
7: Done in 7.033348083496094e-05
8: Done in 0.00010371208190917969
9: Done in 0.00017571449279785156
10: Done in 0.0003418922424316406
11: Done in 0.0006191730499267578
12: Done in 0.0012633800506591797
13: Done in 0.002537250518798828
14: Done in 0.005010366439819336
15: Done in 0.009590387344360352
16: Done in 0.01953911781311035
17: Done in 0.03992795944213867
18: Done in 0.07311630249023438
19: Done in 0.13045120239257812
20: Done in 0.2530491352081299
21: Done in 0.5362303256988525
22: Done in 1.0537843704223633
23: Done in 2.012873888015747
24: Done in 4.074865102767944
25: Done in 8.38607931137085
26: Done in 17.248133182525635
27: Done in 38.30663585662842
28: Done in 79.40008401870728
...
```
**Desktop:**
- OS: Debian Linux
- Linux Version 6.0.8-1 (debian unstable)
**Additional context**
Python 3.10.8
pymatgen 2022.11.7
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TypeError: 'NoneType' object is not subscriptable
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[
"Hi @pbenner , I probably won't have time to fix it soon. If you would like to submit a PR, I assume this is also welcome from the maintainers.",
"Thanks for reporting @pbenner!"
] | 2022-11-29T08:07:38
| 2023-05-20T15:25:00
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2023-05-20T15:25:00Z
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NONE
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https://github.com/materialsproject/pymatgen/blob/7a51c9b3e993ba5b6cc57bbdf5c293feb045611e/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py#L1630
The following code exits with a fairly cryptic error message:
```python
from pymatgen.analysis.bond_valence import BVAnalyzer
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import SimplestChemenvStrategy
from pymatgen.analysis.chemenv.coordination_environments.coordination_geometry_finder import LocalGeometryFinder
from pymatgen.analysis.chemenv.coordination_environments.structure_environments import LightStructureEnvironments
from pymatgen.analysis.chemenv.utils.defs_utils import AdditionalConditions
#oxides = mp_icsd_query("Q0tUKnAE52sy7hVO", experimental_data = True)
#structure = oxides[1270]['structure']
from pymatgen.ext.matproj import MPRester
mid = 'mp-554015'
with MPRester("Q0tUKnAE52sy7hVO") as m:
structure = m.get_structure_by_material_id(mid, conventional_unit_cell=True)
strategy = SimplestChemenvStrategy(distance_cutoff=1.4, angle_cutoff=0.3)
bv = BVAnalyzer()
oxid_states = bv.get_valences(structure)
lgf = LocalGeometryFinder()
lgf.setup_structure(structure = structure)
se = lgf.compute_structure_environments(only_cations = True, valences = oxid_states, additional_conditions = [AdditionalConditions.ONLY_ANION_CATION_BONDS])
# BUG:
lse = LightStructureEnvironments.from_structure_environments(strategy = strategy, structure_environments = se)
# Traceback (most recent call last):
# File ".../pymatgen/analysis/chemenv/coordination_environments/structure_environments.py", line 1630, in from_structure_environments
# ce_dict["permutation"] = ce_and_neighbors["ce_dict"]["permutation"]
# TypeError: 'NoneType' object is not subscriptable
```
The following checks should be included (with appropriate error handling):
```python
for isite, site in enumerate(structure):
site_ces_and_nbs_list = strategy.get_site_ce_fractions_and_neighbors(site, strategy_info=True)
# Fix 1: Check if site_ces_and_nbs_list is None
if site_ces_and_nbs_list is not None:
for ce_and_neighbors in site_ces_and_nbs_list:
# Fix 2: Check if ce_dict is None or ce_symbol is 'UNKNOWN:14'
if ce_and_neighbors['ce_dict'] is not None:
# Now we can safely access 'permuation'
print(ce_and_neighbors['ce_dict']['permutation'])
```
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Bump phonopy from 2.4.2 to 2.16.3
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[
"\n[](https://coveralls.io/builds/54744329)\n\nCoverage increased (+27.9%) to 27.913% when pulling **1c7b202b645270ed80b718d4dee918a7452f2273 on dependabot/pip/phonopy-2.16.3** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on master**.\n"
] | 2022-12-01T12:03:22
| 2022-12-02T16:48:08
|
2022-12-02T16:48:07Z
|
CONTRIBUTOR
|
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Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.4.2 to 2.16.3.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
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- `@dependabot merge` will merge this PR after your CI passes on it
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- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
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- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
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PR_kwDOACgets5EDayc
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Bump sympy from 1.10.1 to 1.11.1
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[
"\n[](https://coveralls.io/builds/54744294)\n\nCoverage remained the same at 0.0% when pulling **f413ef5095b7095f595ae4d1cf6f7ae4c730520d on dependabot/pip/sympy-1.11.1** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on master**.\n"
] | 2022-12-01T12:03:29
| 2022-12-02T16:47:53
|
2022-12-02T16:47:52Z
|
CONTRIBUTOR
|
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Bumps [sympy](https://github.com/sympy/sympy) from 1.10.1 to 1.11.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/sympy/sympy/releases">sympy's releases</a>.</em></p>
<blockquote>
<h2>SymPy 1.11.1</h2>
<p>See <a href="https://github.com/sympy/sympy/wiki/release-notes-for-1.11.1">https://github.com/sympy/sympy/wiki/release-notes-for-1.11.1</a> for the release notes.</p>
<!-- raw HTML omitted -->
<p><strong>Note</strong>: Do not download the <strong>Source code (zip)</strong> or the <strong>Source code (tar.gz)</strong>
files below.</p>
<h2>SymPy 1.11</h2>
<p>See <a href="https://github.com/sympy/sympy/wiki/release-notes-for-1.11">https://github.com/sympy/sympy/wiki/release-notes-for-1.11</a> for the release notes.</p>
<!-- raw HTML omitted -->
<p><strong>Note</strong>: Do not download the <strong>Source code (zip)</strong> or the <strong>Source code (tar.gz)</strong>
files below.</p>
<h2>SymPy 1.11rc1</h2>
<p>See <a href="https://github.com/sympy/sympy/wiki/release-notes-for-1.11">https://github.com/sympy/sympy/wiki/release-notes-for-1.11</a> for the release notes.</p>
<!-- raw HTML omitted -->
<p><strong>Note</strong>: Do not download the <strong>Source code (zip)</strong> or the <strong>Source code (tar.gz)</strong>
files below.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/sympy/sympy/commit/41d909580eccfba8aa576b934291d4ffe7fdc9cc"><code>41d9095</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/sympy/sympy/issues/23976">#23976</a> from oscarbenjamin/pr_lambdify_cse_111</li>
<li><a href="https://github.com/sympy/sympy/commit/b63902ec99f95555016e5a8326ea603ca32254b9"><code>b63902e</code></a> fix(ci): pin scipy version under pypy in CI</li>
<li><a href="https://github.com/sympy/sympy/commit/0ccf084a88366024ce6b5a1f488e7aa3e62d6fe7"><code>0ccf084</code></a> maint(release): bump version to 1.11.1</li>
<li><a href="https://github.com/sympy/sympy/commit/47eca9c0dd1deb8c1e044d0a21c6f31a359e10cb"><code>47eca9c</code></a> fix(lambdify): make cse=True work with non-lists</li>
<li><a href="https://github.com/sympy/sympy/commit/26f7bdbe3f860e7b4492e102edec2d6b429b5aaf"><code>26f7bdb</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/sympy/sympy/issues/23958">#23958</a> from oscarbenjamin/pr_aesara_111</li>
<li><a href="https://github.com/sympy/sympy/commit/15ade13694a2ea531666d1f2868defca04b80d84"><code>15ade13</code></a> fix(aesara): don't use deprecated functions</li>
<li><a href="https://github.com/sympy/sympy/commit/8ce582b49844d2da068149757aa8ddf4bc6d3dbe"><code>8ce582b</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/sympy/sympy/issues/23947">#23947</a> from oscarbenjamin/pr_bump_111</li>
<li><a href="https://github.com/sympy/sympy/commit/e9b6bb7ee566c5b387958c6b3c2e34ab31ca28a7"><code>e9b6bb7</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/sympy/sympy/issues/23946">#23946</a> from oscarbenjamin/pr_scipy_star_111</li>
<li><a href="https://github.com/sympy/sympy/commit/5ec3fa4dfb1a8684e716a6edb787f3352904beac"><code>5ec3fa4</code></a> maint(release): bump version to 1.11 final</li>
<li><a href="https://github.com/sympy/sympy/commit/6bd7abdf998c1f7c271b4783d0d7f7cd9d5e8530"><code>6bd7abd</code></a> fix(lambdify): don't import * from scipy</li>
<li>Additional commits viewable in <a href="https://github.com/sympy/sympy/compare/sympy-1.10.1...sympy-1.11.1">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
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- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
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PR_kwDOACgets5EDa18
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Bump plotly from 5.9.0 to 5.11.0
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[
"\n[](https://coveralls.io/builds/54795460)\n\nCoverage remained the same at 0.0% when pulling **017c8b345849749ed09ef848626aae0cfe1bb80c on dependabot/pip/plotly-5.11.0** into **2051a5659f6477be09786bbf7134385c4a492cf7 on master**.\n"
] | 2022-12-01T12:03:35
| 2022-12-02T17:18:13
|
2022-12-02T16:46:57Z
|
CONTRIBUTOR
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.9.0 to 5.11.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.11.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.14.0 to version 2.16.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2161----2022-10-21">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add clustering options to <code>scattermapbox</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/5827">#5827</a>],
with thanks to <a href="https://github.com/elben10"><code>@elben10</code></a> for the contribution!</li>
<li>Add bounds to mapbox suplots [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6339">6339</a>]</li>
<li>Add <code>angle</code>, <code>angleref</code> and <code>standoff</code> to <code>marker</code> and add <code>backoff</code> to <code>line</code>; also introduce new arrow symbols to facilitate drawing networks [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6297">#6297</a>]</li>
<li>Add <code>minreducedwidth</code> and <code>minreducedheight</code> to layout for increasing control over automargin [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6307">#6307</a>]</li>
<li>Add <code>entrywidth</code> and <code>entrywidthmode</code> to legend [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6202">#6202</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6324">#6324</a>]</li>
</ul>
</li>
</ul>
<h2>v5.10.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.12.1 to version 2.14.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2140----2022-08-10">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add support for <code>sankey</code> links with arrows</li>
<li>Add <code>selections</code>, <code>newselection</code> and <code>activeselection</code> layout attributes to have persistent and editable selections over cartesian subplots</li>
<li>Add <code>unselected.line.color</code> and <code>unselected.line.opacity</code> options to <code>parcoords</code> trace</li>
<li>Display Plotly's new logo in the modebar</li>
</ul>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.11.0] - 2022-10-27</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.14.0 to version 2.16.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2161----2022-10-21">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add clustering options to <code>scattermapbox</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/5827">#5827</a>],
with thanks to <a href="https://github.com/elben10"><code>@elben10</code></a> for the contribution!</li>
<li>Add bounds to mapbox suplots [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6339">6339</a>]</li>
<li>Add <code>angle</code>, <code>angleref</code> and <code>standoff</code> to <code>marker</code> and add <code>backoff</code> to <code>line</code>; also introduce new arrow symbols to facilitate drawing networks [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6297">#6297</a>]</li>
<li>Add <code>minreducedwidth</code> and <code>minreducedheight</code> to layout for increasing control over automargin [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6307">#6307</a>]</li>
<li>Add <code>entrywidth</code> and <code>entrywidthmode</code> to legend [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6202">#6202</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6324">#6324</a>]</li>
</ul>
</li>
</ul>
<h2>[5.10.0] - 2022-08-11</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.12.1 to version 2.14.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2140----2022-08-10">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add support for <code>sankey</code> links with arrows</li>
<li>Add <code>selections</code>, <code>newselection</code> and <code>activeselection</code> layout attributes to have persistent and editable selections over cartesian subplots</li>
<li>Add <code>unselected.line.color</code> and <code>unselected.line.opacity</code> options to <code>parcoords</code> trace</li>
<li>Display Plotly's new logo in the modebar</li>
</ul>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/e7eb42d2be75e4e61747fa81e9e96da1ad73fcd4"><code>e7eb42d</code></a> version changes for 5.11.0</li>
<li><a href="https://github.com/plotly/plotly.py/commit/9fe0de6ef33197baefc750d2e26557b6222def30"><code>9fe0de6</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3939">#3939</a> from plotly/fix-typo</li>
<li><a href="https://github.com/plotly/plotly.py/commit/595313f9f9978dd4ed182e9c4e786eab555a58d5"><code>595313f</code></a> fix typo</li>
<li><a href="https://github.com/plotly/plotly.py/commit/d12417014b3132c7026aa46c0b05f555f8627c33"><code>d124170</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3931">#3931</a> from plotly/docs-oct</li>
<li><a href="https://github.com/plotly/plotly.py/commit/79c49c157d6335c1c2dca79d4cc4c89ae1fa8f34"><code>79c49c1</code></a> standoff example</li>
<li><a href="https://github.com/plotly/plotly.py/commit/e909b325e96e16ce7d6356942fde7bcae7b8e4c7"><code>e909b32</code></a> Create dumbbell-plots.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/2d3714bf59a003ffcc6cc565a0ff65dabb196ccc"><code>2d3714b</code></a> Update marker-style.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/fded25c80fd5dda133121c52eae23d2d2985ab90"><code>fded25c</code></a> add marker updates</li>
<li><a href="https://github.com/plotly/plotly.py/commit/bd896eea9949a6dd9181ed49528e71c203570589"><code>bd896ee</code></a> Update setting-graph-size.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/94196a6050238cd6ee864a76a1911d9da3ad3d7f"><code>94196a6</code></a> Update legend.md</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.9.0...v5.11.0">compare view</a></li>
</ul>
</details>
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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Bump networkx from 2.7.1 to 2.8.8
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[
"\n[](https://coveralls.io/builds/54745229)\n\nCoverage remained the same at 0.0% when pulling **85292a75cfb7e2c941426373d339252be78883f9 on dependabot/pip/networkx-2.8.8** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on master**.\n"
] | 2022-12-01T12:03:43
| 2022-12-02T16:47:43
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2022-12-02T16:47:37Z
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Bumps [networkx](https://github.com/networkx/networkx) from 2.7.1 to 2.8.8.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/networkx/networkx/releases">networkx's releases</a>.</em></p>
<blockquote>
<h2>NetworkX 2.8.8</h2>
<p><strong>Full Changelog</strong>: <a href="https://github.com/networkx/networkx/compare/networkx-2.8.7...networkx-2.8.8">https://github.com/networkx/networkx/compare/networkx-2.8.7...networkx-2.8.8</a></p>
<h2>NetworkX 2.8.7</h2>
<p><strong>Full Changelog</strong>: <a href="https://github.com/networkx/networkx/compare/networkx-2.8.6...networkx-2.8.7">https://github.com/networkx/networkx/compare/networkx-2.8.6...networkx-2.8.7</a></p>
<h2>NetworkX 2.8.6</h2>
<p><strong>Full Changelog</strong>: <a href="https://github.com/networkx/networkx/compare/networkx-2.8.5...networkx-2.8.6">https://github.com/networkx/networkx/compare/networkx-2.8.5...networkx-2.8.6</a></p>
<h2>NetworkX 2.8.5</h2>
<p><strong>Full Changelog</strong>: <a href="https://github.com/networkx/networkx/compare/networkx-2.8.4...networkx-2.8.5">https://github.com/networkx/networkx/compare/networkx-2.8.4...networkx-2.8.5</a></p>
<h2>NetworkX 2.8.4</h2>
<h2>What's Changed</h2>
<ul>
<li>Clean up maximal_independent_set tests by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5567">networkx/networkx#5567</a></li>
<li>MAINT: Cleanup centrality module, remove unused variables by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5308">networkx/networkx#5308</a></li>
<li>importorskip scipy instead of numpy for total spanning tree by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5693">networkx/networkx#5693</a></li>
<li>Add initial_graph parameter to scale_free_graph and deprecate create_using by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5697">networkx/networkx#5697</a></li>
<li>Add docstring example for attr transfer to linegraph. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5698">networkx/networkx#5698</a></li>
<li>Update ISMAGS.analyze_symmetry docstring. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5696">networkx/networkx#5696</a></li>
<li>Add default value p=2 for minkowski distance metric. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5700">networkx/networkx#5700</a></li>
<li>Use inline math by <a href="https://github.com/szhorvat"><code>@szhorvat</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5701">networkx/networkx#5701</a></li>
<li>Update multigraph docstrings to reflect <code>remove_edges_from</code> behavior. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5699">networkx/networkx#5699</a></li>
<li>Update simple_cycles docstring w/ yields and examples by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5709">networkx/networkx#5709</a></li>
<li>Chromatic polynomial by <a href="https://github.com/lucasmccabe"><code>@lucasmccabe</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5675">networkx/networkx#5675</a></li>
<li>Catch ':' explicitly while working with pydot by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5710">networkx/networkx#5710</a></li>
<li>Revert "Add workaround for pytest failures on 3.11b2" by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5717">networkx/networkx#5717</a></li>
<li>Default to lightmode for documentation by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5715">networkx/networkx#5715</a></li>
<li>Dont compute all biconnected components in <code>is_biconnected()</code> by <a href="https://github.com/matusvalo"><code>@matusvalo</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5688">networkx/networkx#5688</a></li>
<li>Some more changes to make pytest-randomly happy by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5719">networkx/networkx#5719</a></li>
<li>Add durations flag to coverage run on CI. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5718">networkx/networkx#5718</a></li>
<li>Recover order of layers in multipartite_layout when layers are sortable by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5705">networkx/networkx#5705</a></li>
<li>Update doc requirements by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5711">networkx/networkx#5711</a></li>
<li>Touchups to MG and MDG edges docstrings. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5708">networkx/networkx#5708</a></li>
<li>Add PendingDeprecation for pydot by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5721">networkx/networkx#5721</a></li>
<li>Add example of topo_order kwarg to dag_longest_path by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5728">networkx/networkx#5728</a></li>
<li>CI: add pytest-randomly workflow. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/4553">networkx/networkx#4553</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/szhorvat"><code>@szhorvat</code></a> made their first contribution in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5701">networkx/networkx#5701</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a href="https://github.com/networkx/networkx/compare/networkx-2.8.3...networkx-2.8.4">https://github.com/networkx/networkx/compare/networkx-2.8.3...networkx-2.8.4</a></p>
<h2>NetworkX 2.8.3</h2>
<h2>What's Changed</h2>
<ul>
<li>added example to closeness.py by <a href="https://github.com/Lukong123"><code>@Lukong123</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5645">networkx/networkx#5645</a></li>
<li>Extract valid kwds from the function signature for draw_networkx_* by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5660">networkx/networkx#5660</a></li>
<li>Error out when pydot fails to correctly parse node names by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5667">networkx/networkx#5667</a></li>
<li>Remove redundant py2 numeric conversions - Take 2 by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5661">networkx/networkx#5661</a></li>
<li>Correcting a typo in the references by <a href="https://github.com/RATCOinc"><code>@RATCOinc</code></a> in <a href="https://github-redirect.dependabot.com/networkx/networkx/pull/5677">networkx/networkx#5677</a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/networkx/networkx/commit/9256ef670730b741105a9264197353004bd6719f"><code>9256ef6</code></a> Designate 2.8.8 release</li>
<li><a href="https://github.com/networkx/networkx/commit/5da3df4bd397dc1f567eea5c26c42936285d98b8"><code>5da3df4</code></a> Update pytest</li>
<li><a href="https://github.com/networkx/networkx/commit/8d69d625fdf97347a2eefe4cc4ec913c8756efb8"><code>8d69d62</code></a> Amount of nodes and edges have mistakes when reading adjlist file (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6132">#6132</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/f9b4874dabb589de68e2cae4c7950380fa2c8771"><code>f9b4874</code></a> Added an example in all_pairs_node_connectivity (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6126">#6126</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/11d7bf8be5d566bdcd1a93fa25101a5da29f6c9e"><code>11d7bf8</code></a> Improve test coverage for cycles.py (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6152">#6152</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/c817a800f748fe3653913b264fcd4fdab66c030a"><code>c817a80</code></a> Add example for fiedler_vector (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6155">#6155</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/a130cb6f4c1727b0caf71776f61e557546ff179f"><code>a130cb6</code></a> Increase covering coverage (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6099">#6099</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/f215fb0acc64d7ed86178479c4af972bba1f0280"><code>f215fb0</code></a> Renamed test functions in test_lowest_common_ancestors (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6110">#6110</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/040c356fcfa9c7de1e913d63f0ef9dcc10a5b218"><code>040c356</code></a> Increased test coverage algorithms/matching.py (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6095">#6095</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/2baa77640281f01a66e238235ed16f08b08597a7"><code>2baa776</code></a> Improve test coverage in algorithms shortest paths unweighted.py (<a href="https://github-redirect.dependabot.com/networkx/networkx/issues/6121">#6121</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/networkx/networkx/compare/networkx-2.7.1...networkx-2.8.8">compare view</a></li>
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PR_kwDOACgets5EDa-8
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Bump beautifulsoup4 from 4.10.0 to 4.11.1
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[
"\n[](https://coveralls.io/builds/54744807)\n\nCoverage remained the same at 0.0% when pulling **2f08c88058c5ff4d0a47c3279cb7833da03e5e59 on dependabot/pip/beautifulsoup4-4.11.1** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on master**.\n"
] | 2022-12-01T12:03:50
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2022-12-02T16:46:29Z
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CONTRIBUTOR
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Bumps [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) from 4.10.0 to 4.11.1.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
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Update to the hashing systems for PotcarSingle that fixes some small bugs and allows for verification with the sha256 hash written in new POTCARs
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[
"\n[](https://coveralls.io/builds/55189565)\n\nCoverage remained the same at 0.0% when pulling **0884c63cd368600da416fbed2eaa7da91730bac0 on MichaelWolloch:master** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on materialsproject:master**.\n",
"Please also note the corresponding thread on [matsci](https://matsci.org/t/potcar-warning-msg/34562/8)!",
"I should have checked the test set... Of course the `test_potcar_file_hash_warning` needs to be updated. However, I have no time today, and probably also until next week. Will work on it then, and until then I am thankful for other tips, and of course any discussion!\r\nMaybe @rkingsbury wants to comment here as well?\r\n",
"Thanks for all the work on this @MichaelWolloch, all look like great enhancements. I'll add my $0.02 below, although @mkhorton and other maintainers may have a different view on a few of the points.\r\n\r\n> I decided to raise an ValueError upon a failed hash comparison using the SHA256 internal hash. It can not mean anything else than that the POTCAR file is corrupted IMO, so execution should stop. A warning is not enough I think.\r\n\r\nI advise against this change based on previous experience. We initially raised a `ValueError` instead of a warning and that caused a lot of pushback and confusion from users, so we relaxed to a warning. That said, that initial implementation was buggier than it is now and there were cases where the error/warning was being raised when it should not have been. Basically, I would encourage either 1) doing extensive testing against many versions of POTCARs across different systems to make sure there are no spurious `ValueError` OR 2) keeping the warning instead.\r\n\r\n> Feature 3: A validation is added to check file integrity. This is done comparing the file to the SHA256 hash in it, or, if there is no hash, with the md5 hashes saved in vasp_potcar_file_hashes.json.\r\n\r\n>I think using the internal SHA256 hash to validate the file is a good idea, since it should be working also with new POTCARS that might come out, while the saved hashes list in vasp_potcar_file_hashes.json and vasp_potcar_pymatgen_hashes.json would need to be updated. (This might of course still be true for the metadata hashes if completely new potentials come out.)\r\n\r\nExcellent; this is a more future-proof approach and I'm glad to see VASP has started to include this information in their files.\r\n\r\n> The warnings returned at a failed hash comparisons were switched around. The changed metadata warning was issued after a failed full-file hash comparison, and vice versa.\r\n\r\nGood catch\r\n\r\n",
"Tanks for your input @rkingsbury \r\n\r\nI just pushed a small commit that should resolve the failed tests. I also added a test for the sha256 hash and a corresponding modified POTCAR with a hash that should result in a raised `ValueError`\r\n\r\n> Thanks for all the work on this @MichaelWolloch, all look like great enhancements. I'll add my $0.02 below, although @mkhorton and other maintainers may have a different view on a few of the points.\r\n\r\nWould be great if more people can get in on this discussion!\r\n \r\n> I advise against this change based on previous experience. We initially raised a `ValueError` instead of a warning and that caused a lot of pushback and confusion from users, so we relaxed to a warning. That said, that initial implementation was buggier than it is now and there were cases where the error/warning was being raised when it should not have been. Basically, I would encourage either 1) doing extensive testing against many versions of POTCARs across different systems to make sure there are no spurious `ValueError` OR 2) keeping the warning instead.\r\n\r\nI understand the concern, but I think due to only new POTCARS having these sha256 hashes, the problem is not really that complex. I just let a loop run over some potcar folders in Georg Kresse's home directory (which probably includes experimental and unreleased stuff), and of the 4737 POTCARs found, all 1562 that had a hash did complete the verification process. The other 3175 did not have a hash, and I did not check them against the pymatgen stored hashes for the moment, but I saw a lot of warnings, suggesting that they are not, or not correctly, hashed. So this is good news for the robustness of the sha256 hashes I think. I will run some more tests on all currently officially downloadable POTCARs next week.\r\nHowever, I am not totally opposed to change this into a warning as well. Lets see what the other maintainers want.\r\n\r\nOn a different note: I am not sure why some tests fail for (ubuntu-latest, 3.8, 1), but I am pretty sure that this is nothing I did.",
"> I understand the concern, but I think due to only new POTCARS having these sha256 hashes, the problem is not really that complex. I just let a loop run over some potcar folders in Georg Kresse's home directory (which probably includes experimental and unreleased stuff), and of the 4737 POTCARs found, all 1562 that had a hash did complete the verification process. The other 3175 did not have a hash, and I did not check them against the pymatgen stored hashes for the moment, but I saw a lot of warnings, suggesting that they are not, or not correctly, hashed. So this is good news for the robustness of the sha256 hashes I think. I will run some more tests on all currently officially downloadable POTCARs next week.\r\n> However, I am not totally opposed to change this into a warning as well. Lets see what the other maintainers want.\r\n\r\nSounds great. Thanks for your work on this.",
"Hi again,\r\n\r\nI now checked the sha256 and md5 hashes (both for whole files and for metadata) for all POTCARs that can be downloaded from the VASP portal. Those are the following sets:\r\n\r\n1. **91 set**: LDA, PBE, and PW91 PAW sets & LDA and PW91 USPP sets which are all outdated.\r\n2. **52 set**: LDA and PBE PAW sets with early GW variants. However, sha256 hashes have been added here!\r\n3. **5254 set**: LDA and PBE for both the .52 (originally released 2012) and the .54 (2015) sets that were left \"original\" and thus do not contain any hashes.\r\n4. **54 set**: LDA and PBE for the .54 set with GW potentials and hashes. This is the recommended set.\r\n\r\nLooping through all directories and loading POTCARS with the new PotcarSingle class leads to this output:\r\n~~~\r\n##############################\r\n14930 total potentials checked.\r\n6005 have a sha256 hash and the file matches.\r\n0 have a sha256 hash and the file does not match.\r\n0 completed both file and metadata md5 comparison with saved pymatgen data.\r\n0 completed only file md5 comparison with saved pymatgen data.\r\n8925 completed only metadata md5 comparison with saved pymatgen data.\r\n0 complete neither file or metadata md5 comparison with saved pymatgen data.\r\n##############################\r\n~~~\r\nOf course a lot of those potentials will be duplicated, since they have not changed between releases!\r\n\r\nSo if sha256 hashes are there, they work. No exceptions (I also tested this for some unreleased PBE POTCARs, and also there all hashes worked. I think this means that it is save to actually keep the `ValueError` and not revert to a warning.\r\n\r\nThe metadata hashes also work, This is the good news. However, none of the file hashes work, which is troublesome. I had expected the 5254 set at least to work. I think more investigation and maybe some re-hashing has to happen.\r\nI do not think that I made a mistake in my checks, I only check file hashes if no sha256 hash is found in the file, so actually I expected most to pass the test.\r\n\r\nDoes someone has a POTCAR to test that actually passes the file hash without warnings? I always thought the problem with my potentials were the sha256 hash lines, which I assumed to be also be part of the header before I looked into the code.",
"OK, I think I solved the problem with the file hashes! There was another bug that was pretty hard to catch.\r\nThe `get_potcar_file_hash(self)` method converts the whole file into a hash, this was done using `md5(str(self).encode(\"utf-8\")).hexdigest()`, which is a perfectly valid way to do it. However, in the beginning of the class there is the following line:\r\n`self.data = data # raw POTCAR as a string` The ONLY difference between `self.data` and `str(self)` seems to be an empty line at the end of the string that is present for str(self), but not in self.data (and also not in the actual POTCAR).\r\n\r\nSo I tried to change the line to `md5(self.data.encode(\"utf-8\")).hexdigest()` and rerun the loop over all POTCARs.\r\n\r\nAnd now everything works as expected:\r\n\r\n~~~\r\n##############################\r\n14930 total potentials checked.\r\n6005 have a sha256 hash and the file matches.\r\n0 have a sha256 hash and the file does not match.\r\n8925 completed both file and metadata md5 comparison with saved pymatgen data.\r\n0 completed only file md5 comparison with saved pymatgen data.\r\n0 completed only metadata md5 comparison with saved pymatgen data.\r\n0 completed neither file or metadata md5 comparison with saved pymatgen data.\r\n##############################\r\n~~~\r\n\r\nApparently the hashes were created either using `PotcarSingle.data` strings, or another way of reading in the POTCARs. However, the checks were done using the string representation of the class instance. And of course the extra line changes the hashes.\r\n\r\nI think now all the questions are resolved, and this should be ready to merge.\r\nOr is there the need for another unit test, that checks the sha256 and md5 hashes for a valid POTCAR?\r\nMaybe @rkingsbury and @mkhorton can comment on this? Of course @espenfl is also more than welcome to chime in, as are all other interested parties.",
"> OK, I think I solved the problem with the file hashes! There was another bug that was pretty hard to catch. The `get_potcar_file_hash(self)` method converts the whole file into a hash, this was done using `md5(str(self).encode(\"utf-8\")).hexdigest()`, which is a perfectly valid way to do it. However, in the beginning of the class there is the following line: `self.data = data # raw POTCAR as a string` The ONLY difference between `self.data` and `str(self)` seems to be an empty line at the end of the string that is present for str(self), but not in self.data (and also not in the actual POTCAR).\r\n> \r\n> So I tried to change the line to `md5(self.data.encode(\"utf-8\")).hexdigest()` and rerun the loop over all POTCARs.\r\n> \r\n> And now everything works as expected:\r\n> \r\n> ```\r\n> ##############################\r\n> 14930 total potentials checked.\r\n> 6005 have a sha256 hash and the file matches.\r\n> 0 have a sha256 hash and the file does not match.\r\n> 8925 completed both file and metadata md5 comparison with saved pymatgen data.\r\n> 0 completed only file md5 comparison with saved pymatgen data.\r\n> 0 completed only metadata md5 comparison with saved pymatgen data.\r\n> 0 completed neither file or metadata md5 comparison with saved pymatgen data.\r\n> ##############################\r\n> ```\r\n> \r\n> Apparently the hashes were created either using `PotcarSingle.data` strings, or another way of reading in the POTCARs. However, the checks were done using the string representation of the class instance. And of course the extra line changes the hashes.\r\n> \r\n\r\nThank you for all the thorough testing and bugfixing @MichaelWolloch! I remember that newline thing causing issues in the past and I thought that the way we had it (before your changes) was required to in order to get the tests to pass on the development system at the time, but either something has changed or I missed something back then.\r\n\r\n\r\n> I think now all the questions are resolved, and this should be ready to merge. Or is there the need for another unit test, that checks the sha256 and md5 hashes for a valid POTCAR? Maybe @rkingsbury and @mkhorton can comment on this? Of course @espenfl is also more than welcome to chime in, as are all other interested parties.\r\n\r\nYes I think it would be a good idea to include a unit test for a valid POTCAR. I realize now that we only test for invalid ones. I think you should be able to use one of the POTCARs already distributed in pymatgen's test files for this\r\n\r\n> So if sha256 hashes are there, they work. No exceptions (I also tested this for some unreleased PBE POTCARs, and also there all hashes worked. I think this means that it is save to actually keep the ValueError and not revert to a warning.\r\n\r\nI'm on board with raising a `ValueError` given your extensive testing. However, I am still a bit worried that we might run into system- or OS-specific differences in hashing and I would hate for the `ValueError` to prevent users from doing their work if they really want to ignore it. So I suggest we provide a keyword argument to `Potcar` (passed through to `PotcarSingle`) that makes it possible to disable the hash checking by converting the `ValueError` to a warning.\r\n\r\nThoughts @mkhorton ?\r\n\r\n",
"Thank you @MichaelWolloch for your efforts on this PR -- this has been a pain point for a while!\r\n\r\n> I just let a loop run over some potcar folders in Georg Kresse's home directory (which probably includes experimental and unreleased stuff), and of the 4737 POTCARs found, all 1562 that had a hash did complete the verification process.\r\n\r\nPerhaps not unreleased stuff, but since these are hashes only, is the current pymatgen dataset missing anything important that could be added? Does it need to be updated? It seems like, based on your most recent comment, the pymatgen dataset may actually be \"complete\"(?)\r\n\r\n> However, I am still a bit worried that we might run into system- or OS-specific differences in hashing and I would hate for the ValueError to prevent users from doing their work if they really want to ignore it. \r\n\r\nI'm not so worried about this specifically. There should be nothing OS-specific that would change the hash if it's written correctly. My only major concern is an incomplete pymatgen dataset.",
"> Perhaps not unreleased stuff, but since these are hashes only, is the current pymatgen dataset missing anything important that could be added? Does it need to be updated? It seems like, based on your most recent comment, the pymatgen dataset may actually be \"complete\"(?)\r\n\r\nThis is a very good point. I initially assumed that the added sha256 hashes screwed up the cashed md5 hashes, since I always got the familiar warnings, but of course now that I have discovered the other bugs, this is actually quite unlikely. In my previous test runs I did not check the md5 hashes for the POTCARs that have a sha256 hashes, but I did now, and all is fine, the hash library is complete:\r\n~~~\r\n##############################\r\n14930 total potentials checked.\r\n0 have a sha256 hash and file matches, but no md5 check worked.\r\n6005 have a sha256 hash and file matches, and both md5 checks worked.\r\n0 have a sha256 hash and file matches, but only metadata md5 check worked.\r\n0 have a sha256 hash and file matches, but only file md5 check worked.\r\n0 have a sha256 hash and the file does not match.\r\n8925 have no sha256 hash and completed both file and metadata md5 comparison with saved pymatgen data.\r\n0 completed only file md5 comparison with saved pymatgen data.\r\n0 completed only metadata md5 comparison with saved pymatgen data.\r\n0 completed neither file or metadata md5 comparison with saved pymatgen data.\r\n##############################\r\n~~~\r\n\r\nNow of course the whole sha256 thing is a little less pressing. But I would still keep this functionality for file integrity checks, since it makes adoption of new potentials quicker. E.g. I ran a loop over an unreleased set, and of course the updated potentials (115 of 1655) fail both the file and the metadata checks. I am happy to talk to my VASP company colleagues, to ensure that once these potentials are launched, I can update the pymatgen hash files ASAP, but of course this does not mean that all users upgrade their version although they might upgrade their potentials. So I feel that my changes regarding file validation of POTCARs is still a superior solution. Of course warnings regarding the metadata will still be printed, but no warnings about possible file corruption will be shown if the sha256 hash matches the file.\r\n\r\n> > However, I am still a bit worried that we might run into system- or OS-specific differences in hashing and I would hate for the ValueError to prevent users from doing their work if they really want to ignore it.\r\n> \r\n> I'm not so worried about this specifically. There should be nothing OS-specific that would change the hash if it's written correctly. My only major concern is an incomplete pymatgen dataset.\r\n\r\nI also do not think that platform specifics should play a role. We force uft8 encoding specifically (you have to specify encoding in the python 3 version of hashlib), and I found nothing on the net of hashlib showing any platform dependency if string encoding is handled correctly.",
"> I am happy to talk to my VASP company colleagues, to ensure that once these potentials are launched, I can update the pymatgen hash files ASAP\r\n\r\nThis would certainly be appreciated!\r\n\r\nIn terms of this PR, I would like to merge it. Are there any remaining changes you would like to make before a merge?",
"> > I am happy to talk to my VASP company colleagues, to ensure that once these potentials are launched, I can update the pymatgen hash files ASAP\r\n> \r\n> This would certainly be appreciated!\r\n\r\nI will keep on it!\r\n> \r\n> In terms of this PR, I would like to merge it. Are there any remaining changes you would like to make before a merge?\r\n\r\nI just removed the parsing of the copyright lines since it in fact only parsed the last of the three lines, and is not needed. Other than that, I think that I am happy with the changes.",
"Merging. Thanks again @MichaelWolloch! Noting a test failure unrelated to this PR.",
"Thanks a lot for fixing this and thanks to @MichaelWolloch for contribs. Greatly appreciated.",
"@mkhorton Any eta for release containing this fix? Thanks.",
"Hi @mkhorton , I just found a BIG bug!\r\nUnfortunately I tested this only for single POTCARs not multi element ones! (Also nothing in the unit tests) and there is a problem with the sha256 hashes when reading POTCARs from a file. Again a newline at the end of the file was missing, so a similar problem as for the md5 hashes. As @rkingsbury mentioned there was some confusion about this previously.\r\n\r\nI will make a new pull request immediatly!\r\n",
"Noted; will continue discussion in new PR."
] | 2022-12-01T12:05:37
| 2022-12-19T18:59:16
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2022-12-15T18:50:56Z
|
CONTRIBUTOR
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This pull request has been updated quite a bit from the initial small bugfix. It now allows to use the SHA256 hash that is found in the latest POTCAR sets to be used to verify the POTCAR.
## Summary
- Fix 1: Booleans in `self.PSCTR.values()` are now detected correctly and converted to strings as intended.
- Fix 2: Warnings regarding failed hash comparison are now longer switched.
- Feature 1: SHA256 line and CPRYR lines are now parsed into `self.PSCTR`, but not added to the metadata hash string to retain compatibility
- Feature 2: Instead trying to identify the POTCAR twice (once using metadata only, then again using the whole file hash), only the metadata is used to identify the POTCAR and return the corresponding functional list and symbol.
- Feature 3: A validation is added to check file integrity. This is done comparing the file to the SHA256 hash in it, or, if there is no hash, with the md5 hashes saved in ` vasp_potcar_file_hashes.json`.
Previously the check for boolean actually tried to add the string `"<class 'bool'>"` to the hash which is obviously wrong. However, this never happened, because `bool` is a subclass of `int` in python for historical reason. Thus the booleans were actually converted correctly to strings when converting the other integers in the `if isinstance(v, int):` check.
By putting the check for booleans first, we can correctly convert them and theoretically do something different with them in the future.
An alternative fix for this would be to just remove lines 2134 and 2135 altogether, but I think my version is clearer and better.
The warnings returned at a failed hash comparisons were switched around. The changed metadata warning was issued after a failed full-file hash comparison, and vice versa.
I think using the internal SHA256 hash to validate the file is a good idea, since it should be working also with new POTCARS that might come out, while the saved hashes list in ` vasp_potcar_file_hashes.json` and ` vasp_potcar_pymatgen_hashes.json` would need to be updated. (This might of course still be true for the metadata hashes if completely new potentials come out.)
I decided to raise an ValueError upon a failed hash comparison using the SHA256 internal hash. It can not mean anything else than that the POTCAR file is corrupted IMO, so execution should stop. A warning is not enough I think.
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PR_kwDOACgets5EJ0F9
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Added missing keyword from LOBSTER 4.1 to lobsterin generation class
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[
"\n[](https://coveralls.io/builds/54793251)\n\nCoverage remained the same at 0.0% when pulling **f8190ef1821eca798d3d12d35c8388fb562790b7 on naik-aakash:lobster_lsodos** into **7a51c9b3e993ba5b6cc57bbdf5c293feb045611e on materialsproject:master**.\n",
"Hi @janosh, This PR is ready to be merged. ",
"Thank you!"
] | 2022-12-02T15:49:15
| 2024-01-10T12:23:18
|
2022-12-02T16:46:13Z
|
CONTRIBUTOR
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Added new parameter tag for writing orthonormalized DOSCAR
## LSODOS keyword was missing in lobsterin generation class
- Added this keyword
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Cyclic dependencies between pymatgen and mp-api
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[
"@munrojm i will let you handle this. ",
"@munrojm Since I haven't heard about nor encountered any recent problems with circular imports, I assume this is fixed?",
"@jan-janssen Feel free to chime in if there's anything new to report."
] | 2022-12-05T14:40:20
| 2023-05-19T22:45:01
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2023-05-19T22:45:01Z
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CONTRIBUTOR
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Pymatgen requires mp-api and mp-api requires pymatgen:
- https://github.com/materialsproject/api/blob/main/setup.py
- https://github.com/materialsproject/pymatgen/blob/master/setup.py
This currently prevents the conda-forge robot to upgrade both packages to python 3.11 compatibility:
```
(4) Error: not solvable ([bot CI job](https://github.com/regro/autotick-bot/actions/runs/3583067254)): main: ['linux_64_python3.11.____cpython: Encountered problems while solving:\n - package mp-api-0.27.3-pyhd8ed1ab_1 requires pymatgen >=2022.3.7, but none of the providers can be installed\n', 'osx_64_python3.11.____cpython: Encountered problems while solving:\n - package mp-api-0.27.3-pyhd8ed1ab_1 requires pymatgen >=2022.3.7, but none of the providers can be installed\n', 'osx_arm64_python3.11.____cpython: Encountered problems while solving:\n - package mp-api-0.27.3-pyhd8ed1ab_1 requires pymatgen >=2022.3.7, but none of the providers can be installed\n', 'win_64_python3.11.____cpython: Encountered problems while solving:\n - package mp-api-0.27.3-pyhd8ed1ab_1 requires pymatgen >=2022.3.7, but none of the providers can be installed\n']
Immediate Children: aiida-crystal17, atomman, m3gnet, xraylarch
```
https://conda-forge.org/status/
|
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[pre-commit.ci] pre-commit autoupdate
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[
"\n[](https://coveralls.io/builds/54863624)\n\nCoverage remained the same at 0.0% when pulling **c271251a885dbaabaf5c426b1889fe2b87595684 on pre-commit-ci-update-config** into **d2f74b7c9c88e611d1188328610033a6f5029bb6 on master**.\n"
] | 2022-12-05T21:33:58
| 2022-12-05T22:28:32
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2022-12-05T22:06:36Z
|
CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
- [github.com/PyCQA/autoflake: v1.7.7 → v2.0.0](https://github.com/PyCQA/autoflake/compare/v1.7.7...v2.0.0)
- [github.com/asottile/pyupgrade: v3.2.0 → v3.3.0](https://github.com/asottile/pyupgrade/compare/v3.2.0...v3.3.0)
- [github.com/pre-commit/pre-commit-hooks: v4.3.0 → v4.4.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.3.0...v4.4.0)
- [github.com/PyCQA/flake8: 5.0.4 → 6.0.0](https://github.com/PyCQA/flake8/compare/5.0.4...6.0.0)
- [github.com/pre-commit/mirrors-mypy: v0.982 → v0.991](https://github.com/pre-commit/mirrors-mypy/compare/v0.982...v0.991)
<!--pre-commit.ci end-->
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PR_kwDOACgets5EZjw-
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Fix CI
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[
"\n[](https://coveralls.io/builds/54864226)\n\nCoverage remained the same at 0.0% when pulling **1520bb032dacbdf8bfa0d600e86f60705f8591e1 on fix-ci** into **caeeb3e36df814f1ba831cfbd7bd784c160e0a14 on master**.\n",
"Merging for now as it's unclear how to fix the remaining error."
] | 2022-12-05T22:30:33
| 2022-12-05T23:02:55
|
2022-12-05T23:02:54Z
|
MEMBER
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Only a partial fix for
```py
TypeError: Object of type ndarray is not JSON serializable
in with open("tmp_dir/lse.json", "w") as f:
> json.dump(lse.as_dict(), f)
pymatgen/analysis/chemenv/coordination_environments/tests/test_read_write.py:81:
```
so far. Another error seems to have popped up in https://github.com/materialsproject/pymatgen/commit/0eb1e3d72fd894b7ba39a5129fbd8b18aedf4b46#commitcomment-92101165
|
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| 1,478,931,312
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I_kwDOACgets5YJrNw
| 2,768
|
Interactive convex hull plot not refreshing when dragged/rotated
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[
"Hi @deecadance, are you still having this issue? If so, what browser are you using? I wrote most of the Plotly phase diagram code and have never seen an issue like this before.",
"Hi! I just tried, and yes I am still having it. I am using Safari (15.4) on a M1 Macbook pro (OS 12.3.1)\r\n\r\nI hadn't thought of the obvious \"try a different browser\" check. I just tried and I do **not** have this problem on google chrome. This kind of fixes the problem for me.",
"Hi @deecadance That is great to hear (also a little problematic for other Safari users). I will look into it more...",
"@deecadance is this still a common problem for you?",
"Hi! I just tried, the problem is gone! Thanks :)",
"Fixed in https://github.com/materialsproject/pymatgen/pull/3032."
] | 2022-12-06T12:01:16
| 2023-06-05T18:38:03
|
2023-06-05T18:37:20Z
|
NONE
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I'm encountering an issue while using `pymatgen` to visualize convex hulls in a Jupyter notebook, particularly when using Plotly as a backend (`matplotlib` works fine). After an initial successful render of the convex hull, using any interactive tool (zoom, rotation, etc.) doesn't clear the previous image, and it fails to re-render unstable points and convex hull lines (`show_unstable`).
This issue occurred spontaneously, potentially after a software update, and persists even after updating to the latest versions. The problem is not data-specific and occurs with any dataset.
Here's a screenshot for reference:
To replicate the issue, I use the following code to plot data from a pandas dataframe:
```python
hull=pg.CompoundPhaseDiagram(entry_list,terminal_list,normalize_terminal_compositions=True)
hull.transform_entries(entry_list,terminal_list)
plot_hull=pg.PDPlotter(hull,show_unstable=False,markersize=20.5,linewidth=1.5, markerfacecolor=(200/255,80/255,30/255),markeredgecolor=(200/255,80/255,30/255), alpha = 1.0, color = 'gray')
handle=plot_hull.get_plot(label_stable=True, label_unstable=False, energy_colormap=None)
```
System Info:
- OS: Mac OSX Monterey 12.3.1 (13-inches MacBook pro, M1 2020)
- pymatgen version: 7.11.2022
- plotly version: 5.11.0
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PR_kwDOACgets5EhJgJ
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Cython linting
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"\n[](https://coveralls.io/builds/54899940)\n\nCoverage decreased (-27.2%) to 0.0% when pulling **a080203f0c0a9fb3a7221c91f1ea76e12413fa27 on cython-lint** into **e612cc55363a8e3c34b7f3e6f942447bceeb56a9 on master**.\n"
] | 2022-12-06T17:46:42
| 2022-12-06T18:11:34
|
2022-12-06T17:59:15Z
|
MEMBER
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2892c3d672 add pre-commit hook cython-lint
411f14611a fix cython unused imports and variables
a080203f0c double-quote-cython-strings
|
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I_kwDOACgets5YdkhT
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|
Critic2Caller generates incorrect input in script
|
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[
"I realized I made a type above. The command currently generated takes the form:\r\n`load int.CHGCAR id chg_int zpsp C 4.0 N 5.0` where C and N are the total charges of the PAW pseudopotentials used in this example. This statement is flagged as an error by critic2. Perhaps what the authors intended was\r\n`load int.CHGCAR id chg_int core zpsp C 4.0 N 5.0`\r\nor simply moving the zpsp statement to the next line also works:\r\n```\r\nload int.CHGCAR id chg_int \r\nzpsp C 4.0 N 5.0\r\n```",
"I have now fixed the code in critic2caller.py so that structuregraphs can be generated. There were two problems.\r\n1. The zpsp command in the original code generated an error in critic two. Moving the zpsp command to a new input line solved the problem.\r\n2. The code uses linear algebra routines to determine the eigenvalues and eigenvectors of the field_hessian. The linear algebra routines require a 2D matrix as input. The original code in critic2caller stored the field_hessian in a one dimensional list. Using numpy's reshape function to format the field_hessian as a 3x3 matrix fixes the error. A diff of the content is show below.\r\n\r\n```\r\n197c197\r\n< input_script[-2] += zpsp_str\r\n---\r\n> input_script += [zpsp_str]\r\n272a273\r\n> \r\n390c391\r\n< self.field_hessian = field_hessian\r\n---\r\n> self.field_hessian = np.array(field_hessian).reshape([3,3])\r\n464a466\r\n> \r\n499a502\r\n> \r\n657c660\r\n< field_hessian=p[\"hessian\"],\r\n---\r\n> field_hessian=np.array(p[\"hessian\"]).reshape([3,3]),\r\n681a685\r\n> \r\n840c844\r\n< unique_critical_points[unique_idx].field_hessian = hessian\r\n---\r\n> unique_critical_points[unique_idx].field_hessian = np.array(hessian).reshape([3,3])\r\n\r\n```",
"Sorry for the _very_ late reply. We'd be happy to take PR that fixes this, especially if it includes additional tests."
] | 2022-12-08T09:27:45
| 2023-05-27T19:41:55
|
NONE
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**Describe the bug**
The Critic2Caller.from_path method should read in the charge densities from a Vasp calculation (AECCAR0 and AECCAR2) to generate the a total electron density field. The script the runs the external critic2 program generates a syntax error and critic2 fails resulting in a failure. In particular, the comand zpsp (that defines the core contribution for an atom by setting the pseudopotential charge) must be executed on a line by itself. The script incorrectly places the load command and the zpsp command on the same line
For my example. The script generates:
`load int.CHGCAR id chg_int zpsp C 4.0 N 5.0`
leading to the syntax error (and failure of critic2)
ERROR : load int.CHGCAR id chg_int zpsp C 4.0 N 5.0
ERROR (load): wrong syntax in ZPSP
The command should read
`load int.CHGCAR id chg_int
zpsp C 4.0 N 5.0`
**To Reproduce**
The files are too large to post, but the above comments should allow the issue to be reproduced.
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
The critic2 information should be returned to the caller for further processing.
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: OS independent
- Version (e.g. latest pip version as of 08-Dec-2022
**Additional context**
The source code from critic2caller (below) adds the zpsp_str to the end of the load CHGCAR command . I believe the last line input_script should read
input_script += [zpsp_str]
Original code for reference
# Load data to use for analysis
if chgcar:
input_script += ["load int.CHGCAR id chg_int", "integrable chg_int"]
if zpsp:
zpsp_str = " zpsp " + " ".join([f"{symbol} {zval}" for symbol, zval in zpsp.items()])
input_script[-2] += zpsp_str
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PR_kwDOACgets5E8wrm
| 2,771
|
Add `setup.py` `project_urls`
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[
"\n[](https://coveralls.io/builds/55030995)\n\nCoverage remained the same at 0.0% when pulling **955dc7be13ee2002d84aedaa6152a1a0b4fdb16f on setup-py-project-urls** into **a6019e1d5332db2e8fa208858cc2c95ce093b12c on master**.\n"
] | 2022-12-09T22:17:51
| 2022-12-09T22:36:13
|
2022-12-09T22:18:34Z
|
MEMBER
|
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Will look like this in the [PyPI side bar](https://pypi.org/project/pymatgen):
<img src="https://user-images.githubusercontent.com/30958850/206804607-2ae993dd-153b-4a6a-8ceb-054de5e28a7f.png" height="300" alt="PyPI" />
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PR_kwDOACgets5FTu0h
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|
Added methods to compute and compare DOS fingerprints
|
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[
"\n[](https://coveralls.io/builds/55439494)\n\nCoverage: 46.362% (-0.5%) from 46.884% when pulling **8309b1b21dc91b2a969c5da7f4b105c1bb139e23 on naik-aakash:dos_fingerprinting** into **b56698019098247ff54f50997a67c562b4375fc3 on materialsproject:master**.\n",
"> You could replace one \"finger print\" with fingerprint in the documentation but otherwise it looks fine from my side.\r\n\r\nThanks for the review @JaGeo 😄 ",
"Hi @janosh , This PR is ready to be merge. ",
"Hi @janosh , all suggestions have been incorporated now. And tests seems to pass as well. 😄 ",
"Hi @janosh , thank you for the really useful tips and suggestions. 😃 ",
"Hi @janosh , I do not know why so many tests are failing. I looked at Failed tests and they do not have anything to do with this PR. I hope it could still be merged.",
"@naik-aakash Sorry for the delay here. Back from traveling now. PR looks good! Made a few last changes. Failures like you said are unrelated. Ready to merge.",
"> @naik-aakash Sorry for the delay here. Back from traveling now. PR looks good! Made a few last changes. Failures like you said are unrelated. Ready to merge.\r\n\r\n@janosh No worries! Thank you. Happy Holidays "
] | 2022-12-13T11:18:33
| 2024-01-10T12:23:21
|
2022-12-24T01:01:11Z
|
CONTRIBUTOR
|
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## Compute and compare fingerprints of project and total density of states.
This functionality could be really useful to compare the DOS of materials from different softwares (eg:- LOBSTER and VASP ) or versions (Eg:- VASP v5 and VASP v6)
- Added method to compute fingerprints
- Added method to compare two DOS fingerprints (tanimoto index and dot product)
- Added test cases for the corresponding methods
|
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Colorbar label for PDPlotter
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[
"\n[](https://coveralls.io/builds/55115288)\n\nCoverage remained the same at 0.0% when pulling **c0b08ec29fbc9b45c00c0dca0ad80130e4020b29 on ab5424:cbar** into **b9dea8f3a88fb92e5d39a772e33d44e632b62514 on materialsproject:master**.\n",
"Thanks Alexander!"
] | 2022-12-13T14:05:30
| 2022-12-22T15:13:28
|
2022-12-21T18:38:39Z
|
CONTRIBUTOR
|
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## Summary
- Fix cbar label position
- Update label (colours were only valid for the default colormap)
before and after:
 
## Checklist
- [x] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
|
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PR_kwDOACgets5FZ780
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Fix typo in Poscar get_string
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"\n[](https://coveralls.io/builds/55141666)\n\nCoverage remained the same at 0.0% when pulling **93fe3372732ce757bdcbe8e12e832d4d0ccacffa on dgaines2:fix-poscar** into **0760f06d74577c4625119b723b5d219823615e11 on materialsproject:master**.\n"
] | 2022-12-14T06:25:57
| 2022-12-14T20:53:46
|
2022-12-14T20:52:59Z
|
CONTRIBUTOR
|
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## Summary
Fix typo in documentation of default significant digits for Poscar get_string method
|
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PR_kwDOACgets5FkJ4o
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Fix lobster out doc
|
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[
"Hello @janosh , this PR is ready to be merged. Please review and let us know if anything needs to be changed.",
"\n[](https://coveralls.io/builds/55204262)\n\nCoverage decreased (-12.7%) to 25.73% when pulling **829f271330db41032d1ab6602445da6feabd104e on naik-aakash:fix_lobster_out_doc** into **a9aa9f4c8602d5bc8df7f8a4b23b4e4eb38eebf2 on materialsproject:master**.\n",
"Looks good, thanks @naik-aakash!"
] | 2022-12-15T17:03:06
| 2024-01-10T12:23:19
|
2022-12-16T14:34:44Z
|
CONTRIBUTOR
|
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## Updated naming conventions of lobsterout task_doc and attributes to follow snake case
- Updated corresponding test cases
|
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PR_kwDOACgets5FyxVx
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BUG FIX for merged pull request #2762
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"\n[](https://coveralls.io/builds/55285203)\n\nCoverage decreased (-25.4%) to 19.412% when pulling **f4d4abc0b11988204950eb0b83bd56aab15ca794 on MichaelWolloch:master** into **3b5b90e4f13a4418f3b93a4a97c55b8640e7cf84 on materialsproject:master**.\n",
"I have no idea why so many test fail, but I think that these must be unrelated? `pytest pymatgen/io/vasp/tests/` completes for me without errors.\r\n~~~\r\nSKIPPED [1] pymatgen/io/vasp/tests/test_outputs.py:1692: h5py required for HDF5 support.\r\n241 passed, 1 skipped in 144.37s (0:02:24)\r\n~~~",
"Thanks @MichaelWolloch, no worries, these things happen! We haven't released yet so still time to address :)",
"Frustrating the tests are failing, this will require some investigation; I think a `mypy` update has caught previously-un-caught issues too.\r\n\r\nI agree the failures are unrelated to this PR; I will go ahead and merge since this is critical.",
"Thanks @mkhorton for addressing this quickly and good luck with figuring out what is happening with all those failed tests.",
"@MichaelWolloch Just to confirm, the test file path here had a typo? If yes, I fixed it in e3bcad7 and there's nothing more to do.\r\n\r\n```diff\r\n- PymatgenTest.TEST_FILES_DIR / \"POT_GGA_PAW_PBE_54\" / \"POTCAR.Fe_O.gz\"\r\n+ PymatgenTest.TEST_FILES_DIR / \"POT_GGA_PAW_PBE_54\" / \"POTCAR.O.gz\"\r\n```",
"Hi @janosh,\r\n\r\nthanks for spotting the problem, although your fix was not quite right. I actually forgot to add the correct file (`POTCAR.Fe_O.gz`) to my commit. The corresponding unit test should check a POTCAR combined of two PotcarSingles (Fe and O) where one has a sha256 hash in the header, and one does not (See Feature 1 in the decription of this PR). This was not originally checked, and thus I did not realize that without this test in the initial PR about the hashes [here](https://github.com/materialsproject/pymatgen/pull/2762#issuecomment-1357796844).\r\n\r\nLocally the tests passed for me, because I had the file in the correct folder, but I forgot to add it to the commit. Then I think other tests failed before that for unrelated reasons, so I did not spot the missing file error then.\r\n\r\nI was on holiday until today, so I did not notice your comment 3 days ago until now. I think I have to make a new PR to upload the new file and change back the file loading line?\r\n\r\nCheers, Michael\r\n",
"Yes, if you could make a PR to add the file, that would be great!",
"Pull request is done: #2796\r\n\r\nCurrently waiting for the tests to complete.\r\n"
] | 2022-12-19T15:24:57
| 2023-01-09T15:06:33
|
2022-12-19T19:48:49Z
|
CONTRIBUTOR
|
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## There was a bug in PR #2762 when using sha256 hashes for multi-element POTCARs which completely breaks their use!
- Fix 1: Changed regex when reading a POTCAR from a file so that the newline symbol (`\n`) is included in the last line.
- Fix 2: Added CPYR parsing again to avoid some warnings
- Feature 1: Added a unit test that reads a two-element POTCAR, where one has a sha256 hash and the other has not. validates both hashes.
Sorry for not completely testing this with actual workflows!
|
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I_kwDOACgets5ZmpQ3
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Wrong equation in analysis/diffraction/tem.py get_interplanar_angle
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[
"@mkhorton Pls assign to Jason or Frank.",
"Tagging @welltemperedpaprika and @thefrankwan as original authors of this module.",
"@EurusWei, since you have suggested a fix, you are also welcome to submit a brief PR with your suggested change."
] | 2022-12-19T17:19:24
| 2022-12-20T23:13:14
|
NONE
|
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**Describe the bug**
In the function get_interplnar_angle of module analysis/diffraction/tem.py, there are some typos that are circled in the attached screenshot and should be corrected as below.
**To Reproduce**
1. r1_norm = np.sqrt(
p1[0] ** 2 * a_star**2
+ p1[1] ** 2 * b_star**2
+ p1[2] ** 2 * c_star**2
+ 2 * p1[0] * p1[1] * a_star * b_star * cos_gamma_star
+ 2 * p1[0] * p1[2] * a_star * c_star * cos_beta_star
+ 2 * p1[1] * p1[2] * b_star * c_star * cos_alpha_star
)
2. r2_norm = np.sqrt(
p2[0] ** 2 * a_star**2
+ p2[1] ** 2 * b_star**2
+ p2[2] ** 2 * c_star**2
+ 2 * p2[0] * p2[1] * a_star * b_star * cos_gamma_star
+ 2 * p2[0] * p2[2] * a_star * c_star * cos_beta_star
+ 2 * p2[1] * p2[2] * b_star * c_star * cos_alpha_star
)
3. r1_dot_r2 = (
p1[0] * p2[0] * a_star**2
+ p1[1] * p2[1] * b_star**2
+ p1[2] * p2[2] * c_star**2
+ (p1[0] * p2[1] + p2[0] * p1[1]) * a_star * b_star * cos_gamma_star
+ (p1[0] * p2[2] + p2[0] * p1[2]) * a_star * c_star * cos_beta_star
+ (p1[1] * p2[2] + p2[1] * p1[2]) * b_star * c_star * cos_alpha_star
)
**Screenshots**
Attached below.
**Desktop (please complete the following information):**
- OS: (e.g. Mac)
- Version (e.g. 2020.07)
<img width="535" alt="Screen Shot 2022-12-19 at 11 11 09 AM" src="https://user-images.githubusercontent.com/34314178/208483103-a09c3904-78cb-4080-8585-ae704b67ae55.png">
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I_kwDOACgets5ZmpWz
| 2,778
|
Symmetry data space group encoding
|
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[] | 2022-12-19T17:19:44
| 2022-12-19T17:19:44
|
NONE
|
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In the symmetry data _space_group_encoding_ object returns the point groups which are not listed in the _point_group_encoding_.
For example, **I-4c2 (120)** group has the corresponding point group symbol **-4m2** which is not in _point_group_encoding_,
There is just its acronym **-42m**.
By simple analysis to get the proper translation:
```
-31m : -3m,
-3m1 : -3m
-4m2 : -42m
-62m :-6m2
312 : 32
31m : 3m
321 : 32
3m1 : 3m
```
can symm_data files be modified accordingly?
|
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| 1,503,895,083
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I_kwDOACgets5Zo54r
| 2,779
|
Critic2Caller code bug fix (repost with a clearer title)
|
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[] | null |
[
"Thanks @pjf295, would you be willing to submit a small PR with the fix? To verify, which version of `critic2` is this, so that we can indicate in the docstring? (This code did use to work with an earlier version.)",
"Hi Matthew,\n\n The patch is for the latest version of Critic2 downloaded December 8, 2022. Unfortunately, it seems that the author doesn’t make changes to the version number (now 1.1) very frequently.\nI must admit, I have not submitted a pull request before so I will have to look up the procedure. Are there any details I should know about the submission process (branch etc.?)\n\nBest wishes,\n Paul Fons\n\n\n\nPaul Fons\n***@***.***\n\nKeio University, Faculty of Science and Technology, Department of Electronics and Electrical Engineering\n\n〒223-8522 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan\nKeio University Faculty of Science and Technology Yagami Campus.\n\n〒223-8522 横浜市港北区日吉3-14-1 慶應義塾大学理工学部電気情報工学科 23-315 \n\n\n\n> On Dec 21, 2022, at 8:11, Matthew Horton ***@***.***> wrote:\n> \n> \n> Thanks @pjf295 <https://github.com/pjf295>, would you be willing to submit a small PR with the fix? To verify, which version of critic2 is this, so that we can indicate in the docstring? (This code did use to work with an earlier version.)\n> \n> —\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/2779#issuecomment-1360436264>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQT5S3HDRXKL33ZU3R3BFNLWOI4J5ANCNFSM6AAAAAATD75CMQ>.\n> You are receiving this because you were mentioned.\n> \n\n",
"For a small change like this, it's actually possible to do via the GitHub website -- for a first PR, this is a good procedure :) \r\n\r\nTo do this, you would navigate to https://github.com/materialsproject/pymatgen/blob/master/pymatgen/command_line/critic2_caller.py and click the edit button: https://github.com/materialsproject/pymatgen/edit/master/pymatgen/command_line/critic2_caller.py \r\n\r\nFrom there, you can propose your change and the reasoning.\r\n\r\nTypically, this would need to be accompanied with a test, but I can review your PR myself and make additional changes as appropriate.",
"Hi Matthew,\n\n Got it. I will submit a PR later today.\n\nBest wishes,\n Paul\n\n\nPaul Fons\n***@***.***\n\nKeio University, Faculty of Science and Technology, Department of Electronics and Electrical Engineering\n\n〒223-8522 3-14-1 Hiyoshi, Kohoku-ku, Yokohama, Kanagawa 223-8522, Japan\nKeio University Faculty of Science and Technology Yagami Campus.\n\n〒223-8522 横浜市港北区日吉3-14-1 慶應義塾大学理工学部電気情報工学科 23-315 \n\n\n\n> On Dec 21, 2022, at 8:39, Matthew Horton ***@***.***> wrote:\n> \n> \n> For a small change like this, it's actually possible to do via the GitHub website -- for a first PR, this is a good procedure :)\n> \n> To do this, you would navigate to https://github.com/materialsproject/pymatgen/blob/master/pymatgen/command_line/critic2_caller.py <https://github.com/materialsproject/pymatgen/blob/master/pymatgen/command_line/critic2_caller.py> and click the edit button: https://github.com/materialsproject/pymatgen/edit/master/pymatgen/command_line/critic2_caller.py <https://github.com/materialsproject/pymatgen/edit/master/pymatgen/command_line/critic2_caller.py>\n> From there, you can propose your change and the reasoning.\n> \n> Typically, this would need to be accompanied with a test, but I can review your PR myself and make additional changes as appropriate.\n> \n> —\n> Reply to this email directly, view it on GitHub <https://github.com/materialsproject/pymatgen/issues/2779#issuecomment-1360477859>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AQT5S3BUXEY7LBVDSURSN2LWOI7RNANCNFSM6AAAAAATD75CMQ>.\n> You are receiving this because you were mentioned.\n> \n\n"
] | 2022-12-20T02:32:12
| 2022-12-20T23:40:25
|
NONE
|
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**Describe the bug**
Critic2Caller crashes due to incorrect array shape. A second bug generates incorrect input to critic2 resulting in a critic2 syntax error that aborts the run.
The corrected code is attached.
**To Reproduce**
Any attempt to use Critic2Caller fails. This includes Critic2Caller.from_path() and Critic2Caller_from_chgcar()
1. Attempting to use Critic2Caller.from_path() or Critic2Caller_from_chgcar() both fail with an error due to improper array shape being given to numpy's linalg and trace methods (lines 418 and 407). These routines expect a 2D matrix and the field_hessian list is one dimensional.
There is also a syntax error generated in the input code for critic2 regarding the zpsp statement. This should be on a line by itself in the input, not appended to the load command.
3.
The chgcar files used are too big to post here, but any set of chgcars will fail due to the above reasons.
**Expected behavior**
A Critic2Analysis object should be returned
**Screenshots**
If applicable, add screenshots to help explain your problem.
**Desktop (please complete the following information):**
- OS: version independent (but this was on Centos 7)
- Version "2022.11.7"
**Additional context**
Add any other context about the problem here.
I have now fixed the code in critic2caller.py so that structuregraphs can be generated. There were two problems.
The zpsp command in the original code generated an error in critic two. Moving the zpsp command to a new input line solved the problem.
The code uses linear algebra routines to determine the eigenvalues and eigenvectors of the field_hessian. The linear algebra routines require a 2D matrix as input. The original code in critic2caller stored the field_hessian in a one dimensional list. Using numpy's reshape function to format the field_hessian as a 3x3 matrix fixes the error. A diff of the content is show below.
```
197c197
< input_script[-2] += zpsp_str
---
> input_script += [zpsp_str]
272a273
>
390c391
< self.field_hessian = field_hessian
---
> self.field_hessian = np.array(field_hessian).reshape([3,3])
464a466
>
499a502
>
657c660
< field_hessian=p["hessian"],
---
> field_hessian=np.array(p["hessian"]).reshape([3,3]),
681a685
>
840c844
< unique_critical_points[unique_idx].field_hessian = hessian
---
> unique_critical_points[unique_idx].field_hessian = np.array(hessian).reshape([3,3])
```
[critic2_caller.py.zip](https://github.com/materialsproject/pymatgen/files/10264242/critic2_caller.py.zip)
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https://github.com/materialsproject/pymatgen/pull/2780
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PR_kwDOACgets5F7t3h
| 2,780
|
Fix typo in equation that computes interplanar angels
|
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[
"Thanks @EurusWei, much appreciated for catching this!\r\n\r\nCan you suggest a good test for this function, e.g. a known input and output?",
"\n[](https://coveralls.io/builds/55374209)\n\nCoverage decreased (-0.3%) to 46.594% when pulling **4c0cd6526cdf6d48f661dcd7c2a1b31f76919d11 on EurusWei:fix-equation** into **b56698019098247ff54f50997a67c562b4375fc3 on materialsproject:master**.\n",
"> Thanks @EurusWei, much appreciated for catching this!\r\n> \r\n> Can you suggest a good test for this function, e.g. a known input and output?\r\n\r\nHi Horton,\r\n\r\nHas this catch been confirmed to be true? I am comparing the diffraction patterns (DPs) generated before and after the fix to those on the MaterialsProject website. I found the code before the fix generated DPs matched the MaterialsProject, instead of after the fix. Based on symmetry I am sure the equation should be fixed, but I don't know why the above phenomenon happens (not what I expected). Do you know how the MaterialsProject website generates their DPs?\r\n\r\n",
"Yes, I do -- the MP website uses the `TEMCalculator` exactly from *pymatgen*. At time of writing, this is [pymatgen 2022.11.7](https://materialsproject.org/healthcheck).\r\n\r\nWe, at Materials Project, are likely switching to use functionality from py4DSTEM in future, and this is being worked on by @sezelt (and is looking really nice!) but right now, all functionality is unmodified from *pymatgen*.",
"> \r\nI see, that makes sense. Since I don't have much background in this field, I cannot tell which DP is more accurate, before or after the fix. What about this: I will give you some examples that I find having discrepancies in DPs before and after the fix, together with my calculation results, and your group can help identify if this fix makes sense. After that you can either add some tests or directly merge the fix."
] | 2022-12-21T07:36:06
| 2024-08-03T19:01:57
|
NONE
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## Summary
In the function get_interplnar_angle of module analysis/diffraction/tem.py, there are some typos about the angels and index.
## Todo (if any)
N/A
## Checklist
Work-in-progress pull requests are encouraged, but please put \[WIP\] in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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PR_kwDOACgets5GOGmh
| 2,782
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Fix `coord_list_mapping_pbc()`
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"\n[](https://coveralls.io/builds/55466420)\n\nCoverage: 0.0% (-46.6%) from 46.576% when pulling **6ad8648c478da7acec36e30c5c20b20c1a0c15df on fix-coord_list_mapping_pbc** into **d947703cbacd78c8f9bdab7c97b2bb131758c795 on master**.\n"
] | 2022-12-26T22:44:11
| 2022-12-26T23:01:41
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2022-12-26T23:01:40Z
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MEMBER
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`coord_list_mapping_pbc()` in `pymatgen/util/coord_cython.pyx` raises
```py
AttributeError: module 'numpy' has no attribute 'int'
```
https://github.com/materialsproject/pymatgen/blob/d947703cbacd78c8f9bdab7c97b2bb131758c795/pymatgen/util/coord_cython.pyx#L254
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PR_kwDOACgets5GcQOW
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Bump spglib from 2.0.1 to 2.0.2
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"\n[](https://coveralls.io/builds/55553841)\n\nCoverage: 19.401% (+19.4%) from 0.0% when pulling **9f884c24a8e964990a9625d67f51406c9c0971d5 on dependabot/pip/spglib-2.0.2** into **2b3bc2ee2cb9a0b377301be22897230f00b43bc3 on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-01-01T12:02:38
| 2023-01-05T21:55:22
|
2023-01-05T21:55:12Z
|
CONTRIBUTOR
|
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Bumps [spglib](https://github.com/spglib/spglib) from 2.0.1 to 2.0.2.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/spglib/spglib/commit/42cf4f6bea3419f720308713deb5ddb81350bcd9"><code>42cf4f6</code></a> Merge branch 'rc'</li>
<li><a href="https://github.com/spglib/spglib/commit/d42642194e8eb734a9b19c220184d972e478eeda"><code>d426421</code></a> Merge branch 'develop' into rc</li>
<li><a href="https://github.com/spglib/spglib/commit/2c516fe73f6aec5fb54be50e6595830a35305a2c"><code>2c516fe</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/spglib/spglib/issues/198">#198</a> from lan496/release-2.0.2</li>
<li><a href="https://github.com/spglib/spglib/commit/ba3b7475eb784b18652cca41e5352d69d609177e"><code>ba3b747</code></a> Prepare v2.0.2</li>
<li><a href="https://github.com/spglib/spglib/commit/36d570bc3fbeda20903bfbbb7db05e40d284a319"><code>36d570b</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/spglib/spglib/issues/196">#196</a> from lan496/fix-segfault-magdataset</li>
<li><a href="https://github.com/spglib/spglib/commit/4e8bf3872b4c2c113d687bf43ec93e25bccd629c"><code>4e8bf38</code></a> Fix possible segmentation fault in <code>get_magnetic_dataset</code></li>
<li><a href="https://github.com/spglib/spglib/commit/9218fa14771d967a20f00764b335bc2a265790a1"><code>9218fa1</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/spglib/spglib/issues/195">#195</a> from lan496/issue-194-mag-symprec</li>
<li><a href="https://github.com/spglib/spglib/commit/4dd11a6a61d316737d67af305230eb211e1351da"><code>4dd11a6</code></a> Skip to determine time-reversal part for non-overlapped operations</li>
<li><a href="https://github.com/spglib/spglib/commit/1cdac20004462087ab0299472bdd5fa62779391f"><code>1cdac20</code></a> Format</li>
<li><a href="https://github.com/spglib/spglib/commit/feb1605414b29a99783fb06866f32d6f9a92f084"><code>feb1605</code></a> Fix typo in flags</li>
<li>Additional commits viewable in <a href="https://github.com/spglib/spglib/compare/v2.0.1...v2.0.2">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5GcQQl
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Bump matplotlib from 3.5.2 to 3.6.2
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[
"\n[](https://coveralls.io/builds/55553869)\n\nCoverage: 19.401% (+19.4%) from 0.0% when pulling **bc0e9c9d6f12bb778a0e6ed828960b72656f4bc9 on dependabot/pip/matplotlib-3.6.2** into **2b3bc2ee2cb9a0b377301be22897230f00b43bc3 on master**.\n",
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] | 2023-01-01T12:02:46
| 2023-01-05T21:55:22
|
2023-01-05T21:55:12Z
|
CONTRIBUTOR
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Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.5.2 to 3.6.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<h2>REL: v3.6.2</h2>
<p>This is the second bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Avoid mutating dictionaries passed to <code>subplots</code></li>
<li>Fix <code>bbox_inches='tight'</code> on a figure with constrained layout enabled</li>
<li>Fix auto-scaling of <code>ax.hist</code> density with <code>histtype='step'</code></li>
<li>Fix compatibility with PySide6 6.4</li>
<li>Fix evaluating colormaps on non-NumPy arrays</li>
<li>Fix key reporting in pick events</li>
<li>Fix thread check on PyPy 3.8</li>
<li>Handle input to <code>ax.bar</code> that is all NaN</li>
<li>Make rubber band more visible on Tk and Wx backends</li>
<li>Restore (and warn on) seaborn styles in <code>style.library</code></li>
<li>Restore <code>get_renderer</code> function in deprecated <code>tight_layout</code></li>
<li>nb/webagg: Fix resize handle on WebKit browsers (e.g., Safari)</li>
</ul>
<h2>REL: v3.6.1</h2>
<p>This is the first bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>A warning is no longer raised when constrained layout explicitly
disabled and tight layout is applied</li>
<li>Add missing <code>get_cmap</code> method to <code>ColormapRegistry</code></li>
<li>Adding a colorbar on a <code>ScalarMappable</code> that is not attached to an
<code>Axes</code> is now deprecated instead of raising a hard error</li>
<li>Fix <code>barplot</code> being empty when first element is NaN</li>
<li>Fix <code>FigureManager.resize</code> on GTK4</li>
<li>Fix <code>fill_between</code> compatibility with NumPy 1.24 development version</li>
<li>Fix <code>hexbin</code> with empty arrays and log scaling</li>
<li>Fix <code>resize_event</code> deprecation warnings when creating figure on macOS</li>
<li>Fix build in mingw</li>
<li>Fix compatibility with PyCharm's interagg backend</li>
<li>Fix crash on empty <code>Text</code> in PostScript backend</li>
<li>Fix generic font families in SVG exports</li>
<li>Fix horizontal colorbars with hatches</li>
<li>Fix misplaced mathtext using <code>eqnarray</code></li>
<li><code>stackplot</code> no longer changes the Axes cycler</li>
</ul>
<h2>REL: v3.6.0</h2>
<p>Highlights of this release include:</p>
<ul>
<li>Figure and Axes creation / management
<ul>
<li><code>subplots</code>, <code>subplot_mosaic</code> accept <em>height_ratios</em> and <em>width_ratios</em> arguments</li>
<li>Constrained layout is no longer considered experimental</li>
<li>New <code>layout_engine</code> module</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/matplotlib/matplotlib/commit/dc0328fb9c1c8817b07a5121a106a06be3571433"><code>dc0328f</code></a> REL: v3.6.2</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/d05801e966144190574faaa23f02cd0f44fc5a7a"><code>d05801e</code></a> Merge branch 'v3.6.1-doc' into v3.6.x</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/7a9b9b629a212414b65c7b0188cd49df09d1adf5"><code>7a9b9b6</code></a> DOC: Update GitHub stats for 3.6.2</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/4334ef8fabb2ce3ceafa90729183e5a9ec8c8dd3"><code>4334ef8</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24341">#24341</a> from meeseeksmachine/auto-backport-of-pr-24301-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/83345978de0a17d1594f20ec55503abfcc084998"><code>8334597</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24301">#24301</a>: Restore get_renderer function in deprecated tight_layout</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/8e3f12054bbc50cb6142f3bcb107f96e016fe48b"><code>8e3f120</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24337">#24337</a> from meeseeksmachine/auto-backport-of-pr-24238-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/a55a2d603b8787bed39abf97cf8c2ffd4a155eb2"><code>a55a2d6</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24336">#24336</a> from meeseeksmachine/auto-backport-of-pr-24335-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/290eec713bb72af5f2528ea23d21615d2321fda8"><code>290eec7</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24238">#24238</a>: Update example and docstring to encourage the use of func...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/f40803484ec762d44931d46988fee4767315878a"><code>f408034</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24335">#24335</a>: Fix missing word in ImageMagickWriter docstring.</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/831f145e0ddf884202658073a1f11dc209e5d201"><code>831f145</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24330">#24330</a> from meeseeksmachine/auto-backport-of-pr-24282-on-v...</li>
<li>Additional commits viewable in <a href="https://github.com/matplotlib/matplotlib/compare/v3.5.2...v3.6.2">compare view</a></li>
</ul>
</details>
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5GcQRg
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Bump phonopy from 2.16.3 to 2.17.1
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"\n[](https://coveralls.io/builds/55553907)\n\nCoverage: 19.401% (+19.4%) from 0.0% when pulling **53349c35c092b7763a63df5d45423fd211cbac42 on dependabot/pip/phonopy-2.17.1** into **2b3bc2ee2cb9a0b377301be22897230f00b43bc3 on master**.\n",
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] | 2023-01-01T12:02:49
| 2023-01-05T21:55:23
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2023-01-05T21:55:13Z
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CONTRIBUTOR
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Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.16.3 to 2.17.1.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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PR_kwDOACgets5GcQSv
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Bump boltztrap2 from 22.3.2 to 22.12.1
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] | 2023-01-01T12:02:53
| 2023-01-05T21:55:24
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2023-01-05T21:55:13Z
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CONTRIBUTOR
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[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
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---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5GcQWA
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Bump h5py from 3.6.0 to 3.7.0
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"\n[](https://coveralls.io/builds/55553937)\n\nCoverage: 19.401% (+19.4%) from 0.0% when pulling **19da48218e505d93009b9915ab592e2dc086c711 on dependabot/pip/h5py-3.7.0** into **2b3bc2ee2cb9a0b377301be22897230f00b43bc3 on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-01-01T12:03:05
| 2023-01-05T21:55:24
|
2023-01-05T21:55:14Z
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CONTRIBUTOR
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Bumps [h5py](https://github.com/h5py/h5py) from 3.6.0 to 3.7.0.
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/h5py/h5py/commit/fcaca1d1b81d25c0d83b11d5bdf497469b5980e9"><code>fcaca1d</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/h5py/h5py/issues/2103">#2103</a> from takluyver/rever-3.7</li>
<li><a href="https://github.com/h5py/h5py/commit/c075cfc66f0333c024e53cb28f5c153bd61b8285"><code>c075cfc</code></a> Manually adjust release notes for 3.7</li>
<li><a href="https://github.com/h5py/h5py/commit/94d50257fc203856084a8a48b009cecb9cd12416"><code>94d5025</code></a> Rename & link release notes</li>
<li><a href="https://github.com/h5py/h5py/commit/67b139af9e21da7873d319eedd31a47b84265aee"><code>67b139a</code></a> Updated CHANGELOG for 3.7.0</li>
<li><a href="https://github.com/h5py/h5py/commit/c5b50ee7ede294e4624358b26862da19e745fe92"><code>c5b50ee</code></a> bumped version to 3.7.0</li>
<li><a href="https://github.com/h5py/h5py/commit/4c1c27c59d7362e7af33f57bd528a123d9fb20e9"><code>4c1c27c</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/h5py/h5py/issues/2101">#2101</a> from julesghub/py310-compat-2100</li>
<li><a href="https://github.com/h5py/h5py/commit/449256cb1db482806a68dd573bea3c5241662cea"><code>449256c</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/h5py/h5py/issues/2099">#2099</a> from matham/update</li>
<li><a href="https://github.com/h5py/h5py/commit/214eb0ab6b0ce66a636893ebacc1b91e5378250d"><code>214eb0a</code></a> Add release note for updating bundled HDF5</li>
<li><a href="https://github.com/h5py/h5py/commit/0ad1605ce811b4514f53b529cda13b3e7db55b7b"><code>0ad1605</code></a> Update Azure job name for HDF5 1.12.2</li>
<li><a href="https://github.com/h5py/h5py/commit/568efd20815a3d407d6a3f8117b82459b4557fa5"><code>568efd2</code></a> Setting mpi4py (3.1.0) for py310</li>
<li>Additional commits viewable in <a href="https://github.com/h5py/h5py/compare/3.6.0...3.7.0">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
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I_kwDOACgets5aYVX5
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Many failing tests
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"Hey @JaGeo, some tests started failing when we went from `numpy` 1.23.0 to 1.24.0 in CI. @mkhorton and me fixed some of those. I think there's just 1 of those remaining that requires updating 2 test files.\r\n\r\nFor other test failures I'm not sure how they arose. There's one in `ReadWriteChemenvTest.test_read_write_structure_environments()` which i discussed with @shyuep here\r\nhttps://github.com/materialsproject/pymatgen/commit/0eb1e3d72fd894b7ba39a5129fbd8b18aedf4b46#commitcomment-92101479. Tried to fix it a while back but gave up.\r\n\r\nAnother in `pymatgen/analysis/tests/test_piezo_sensitivity.py`. I hope that's all of them but not sure.\r\n\r\nAnyway, plan is to fix them asap but haven't had time recently. PRs welcome of course.\r\n",
"@janosh Thanks for looking into it.",
"I fixed 7 failing tests. There's just 1 left (I think) that's not straightforward to debug (the one in `ReadWriteChemenvTest.test_read_write_structure_environments` I mentioned). Maybe someone else has better luck than me with that one.",
"Came here to post about this. Thanks for looking at it @janosh!",
"I think it is related to PeriodicNeigbors and as_dict and from_dict for this one. Species is still a dict after from_dict. I am trying to work on it but I am somehow stuck. \r\nThis then leads to an error when the light structure environments are compared here (https://github.com/materialsproject/pymatgen/blob/e3bcad781fb83978fd7394ffc16d880e9ba9ab8d/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py#L2080)\r\n\r\nChanges are potentially required here\r\nhttps://github.com/materialsproject/pymatgen/blob/e3bcad781fb83978fd7394ffc16d880e9ba9ab8d/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py#L2096 \r\nand here:\r\nhttps://github.com/materialsproject/pymatgen/blob/e3bcad781fb83978fd7394ffc16d880e9ba9ab8d/pymatgen/analysis/chemenv/coordination_environments/structure_environments.py#L2125\r\n",
"Thank you very much for looking into this @janosh and thank you for the work.",
"I think one problem might be the following:\r\n```Python\r\nfrom pymatgen.core.composition import Composition\r\ncomp=Composition({'O2-': 1.0})\r\nprint(comp == comp.as_dict())\r\n```\r\n\r\nThis leads to False. I do not think that it should lead to False, right? If you replace O2- with O, it is also false. Furthermore, O2- is actually not allowed as an entry as it is not an Element but the init works and it only raises an exception when you try to get a string.\r\n\r\n But there seems to be more than this. Not sure how to go on from here. I would like to try to avoid making drastic changes in these important core classes.",
"A composition is not a dict. So it makes sense that they are not equal. ",
"Well, other can be a dict: https://github.com/materialsproject/pymatgen/blob/6b520e307fea25d890261b3916ecfc6fe802ae94/pymatgen/core/composition.py#L163\r\n\r\nI personally think there are some holes in the current implementation of Composition. There should be a check that the string can actually be converted into an Element and` __eq__` should either not work for dicts in general or cover all cases. Potentially speed of code is an issue then.",
"I don't see this as a hole at all. Composition subclasses dict. So comparison with another dict is fine. But it stands to reason that the keys must be valid composition keys (Element or Species). You can of course try to convert the dict keys using get_el_sp, but that will slow down equality comparisons considerably. It is the same that {\"1\": 2} is not going to be equals to {1: 2}. One has a string key and the other has a int key.\r\n\r\nWe should not be changing the core classes to fix a problem with chemenv. If there is anything to be fixed, it has to be chemenv that needs to be changed.",
"Agreed. \r\n\r\nI think the error is related to PeriodicNeighbors and the from_dict and as_dict there... but I did not see an easy way to fix it...",
"One potential expensive way of fixing it is to convert the PeriodicNeighbors to a standard PeriodicSite object. Or the from_dict will have to reconsitute the actual Species in ChemEnv.",
"I have implemented the conversion to PeriodicSite and could start a pull request. I just don't know how expensive it would be. I would need to do a large test... \r\nWith the other option, I was a bit lost as I also saw problems with the coordinates as well and I am not sure where they are coming from. Maybe some Cartesian, fractional coordinates mess up or a problem with to_unit_cell or similar."
] | 2023-01-02T12:08:11
| 2023-01-06T17:09:31
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2023-01-06T17:09:31Z
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MEMBER
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**Describe the bug**
Hi all,
there are currently many, many failing tests connected to evaluations of structures. Once the new year vacations are over, it would be great to resolve it so that contributing gets easier again.
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[pre-commit.ci] pre-commit autoupdate
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"\n[](https://coveralls.io/builds/55582654)\n\nCoverage: 0.0%. Remained the same when pulling **0f5993d9938d18e89ea4b78f717b860c27713f1e on pre-commit-ci-update-config** into **2b3bc2ee2cb9a0b377301be22897230f00b43bc3 on master**.\n"
] | 2023-01-02T22:21:43
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2023-01-03T03:04:47Z
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CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
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- [github.com/PyCQA/isort: 5.10.1 → 5.11.4](https://github.com/PyCQA/isort/compare/5.10.1...5.11.4)
- [github.com/psf/black: 22.10.0 → 22.12.0](https://github.com/psf/black/compare/22.10.0...22.12.0)
- [github.com/MarcoGorelli/cython-lint: v0.9.1 → v0.10.1](https://github.com/MarcoGorelli/cython-lint/compare/v0.9.1...v0.10.1)
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[
"Generally the stacked plots are not meant to be used in this manner. Stacking two different DOS makes very little sense. Stacked plots are used to visualize the breakdown of the total DOS into spd decomposed or orbital or atomic decomposed PDOS. In these cases, the energy ranges are always the same."
] | 2023-01-04T08:27:34
| 2023-01-05T17:04:31
|
2023-01-05T17:04:31Z
|
CONTRIBUTOR
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**Describe the bug**
In the method "get_plot" of the DosPlotter class in electronic_structure/plotter.py it is assumed for stacked plots that start energy and energy interval of the DOSes to be plotted are the same. Densities of the same index, not necessarily of the same energy are summed if "stack" is True. This leads to wrong DOS values in the plot if e.g. the DOSes have different start energies.
I will fix this bug by only allowing for stacked plots if start energies and energy intervals of the DOSes are the same and will PR it along with other modifications of the DosPlotter class. In the future a further refinement of the "density stacking" to also allow for different start energies would be nice.
**To Reproduce**
e.g. with Lobster's projected DOS. Files from Screenshot example can be sent upon request.
```
import os
from pymatgen.io.lobster import Doscar
from pymatgen.electronic_structure.plotter import DosPlotter
directory = "path-to-dos1"
directory2 = "path-to-dos2"
doscar = Doscar(
doscar=os.path.join(directory, "DOSCAR.lobster.gz"), structure_file=os.path.join(directory, "POSCAR.gz")
)
doscar2 = Doscar(
doscar=os.path.join(directory2, "DOSCAR.lobster.gz"), structure_file=os.path.join(directory, "POSCAR.gz")
)
plotter = DosPlotter(stack=True)
plotter.add_dos("dos1", doscar.tdos)
plotter.add_dos("dos2", doscar2.tdos)
plotter.show()
```
**Screenshots**
The screenshots show a part of the DOS of Fe, bcc, spin-polarized and non-spin-polarized. The peak of the non-spin-polarized DOS at -53 eV is larger in the stacked plot although the DOS of the spin-polarized case is 0 at that value. This is due to different start energies (-59.4 eV for spin-pol., -58.4 eV for non-spin-pol.) - the peaks of the spin-polarized case at -54 eV and of the non-spin-polarized case at -53 eV are summed up in the stacked plot.
**Desktop (please complete the following information):**
- OS: independent
- Version: 2022.11.7
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PR_kwDOACgets5Gxzgl
| 2,791
|
Fixed charge function for Structure obj (also fix for #2673)
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[
"\n[](https://coveralls.io/builds/55719654)\n\nCoverage: 78.063% (+7.9%) from 70.155% when pulling **9128d73dd3a7ec32e2a942c66032d7aa183c0990 on fraricci:fix_struct_charge_oxi_state** into **811dd75a7f1848212dddfc9cfa12402e78e57c0f on materialsproject:master**.\n",
"@fraricci Thanks for this fix! Could it be that you have \"Allow edits from maintainers\" unchecked? Maybe that's why pre-commit.ci wasn't able to auto-fix the lint error.",
"yes, that's right. Sorry about that."
] | 2023-01-06T03:11:14
| 2023-01-17T18:08:55
|
2023-01-17T15:21:53Z
|
CONTRIBUTOR
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AFAIK, a site.species in Structure can be either an Element or a Species obj.
The Element obj does not have an "oxi_state" attribute and the current function handle
this case setting the oxi_state value to zero.
But it fails when a site.species is a Species obj with an oxi_state set to None.
This is the case when a spin is added to a structure (via e.g. add_spin_by_site()) or
when using the MagOrderingTransformation .
The edit to the function proposed here handles this case and should solve the issue #2673
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One attempt to fix ChemEnv error in tests
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[
"Linting still fails but tests are running through. \r\nPlease let me know what you think and if you have any better/faster ideas (@shyuep , @janosh). Both species and coordinates are influenced when using from_dict and as_dict from PeriodicNeighbors.",
"\n[](https://coveralls.io/builds/55714194)\n\nCoverage: 78.018% (+7.9%) from 70.155% when pulling **f31ab03451448d5feb60a861b7ef128078560747 on JaGeo:bug_fix** into **811dd75a7f1848212dddfc9cfa12402e78e57c0f on materialsproject:master**.\n",
"Thanks. This is fine. I'd rather it be working and slower. Someone else can go figure out a faster method if it bothers them. Most people would not care. ",
"This doesn't look like much a slowdown anyway.",
"Thanks @JaGeo. Good to have green CI again. Like you said, makes contributing much easier. I'll close #2788 now.",
"Just adding this here: https://github.com/materialsproject/pymatgen/blob/c1a7f5d7635f85e7bc490658d52b70867ed24614/pymatgen/core/structure.py#L158 \r\nThis name is a bit unfortunate. If as_dict as inherited from PeriodicSites is then used, \"coords\" (typically fractional coordinates but now cartesian ones due to the overloading) is used and this might lead to the other problems with from_dict and as_dict for PeriodicNeighbors (besides the dict issue for the species). ",
"In any case, I am happy that the issue is fixed now. Thanks @shyuep @janosh "
] | 2023-01-06T16:17:02
| 2023-01-06T17:13:44
|
2023-01-06T16:42:43Z
|
MEMBER
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## Summary
As discussed in https://github.com/materialsproject/pymatgen/issues/2788, one way of fixing the ChemEnv error in the tests would be converting the PeriodicNeighbor object in a PeriodicSite object. I have implemented this. It might however affect the execution speed.
If someone else, manages to fix the as_dict from PeriodicNeighbor in a cheaper way, I would prefer this, of course.
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PR_kwDOACgets5G1ymu
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|
Prefer generator over list comprehension where equivalent
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"\n[](https://coveralls.io/builds/55720316)\n\nCoverage: 78.737% (-0.001%) from 78.738% when pulling **f1f156206d84fd8744f62519f40b0968d9737e45 on list-to-gen** into **c1a7f5d7635f85e7bc490658d52b70867ed24614 on master**.\n"
] | 2023-01-06T18:21:32
| 2023-01-06T20:54:25
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2023-01-06T20:54:24Z
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MEMBER
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`"\.join\(\[(.+)\]\)` -> `".join($1)`
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I_kwDOACgets5axtLG
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`invoke update-changelog` broken
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[
"You can delete the dependabot related change log. We don't need to put those in the changelog at all. ",
"I wouldn't want them in there either but there are a dozen of them so don't feel like hand-curating the log. I'll tweak `update_changelog()` then."
] | 2023-01-06T18:31:48
| 2023-01-09T21:48:34
|
2023-01-09T21:48:34Z
|
MEMBER
|
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@shyuep I was asked to make a new release. No objections from you?
Problem is `invoke update-changelog` recently started adding a bunch of rST incompatible markdown and HTML into `CHANGES.rst`. Example:
```rst
* PR #2757 from @materialsproject dependabot/pip/phonopy-2.16.3
Bumps [phonopy](https://phonopy.github.io/phonopy/) from 2.4.2 to 2.16.3.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself)
- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
</details>
```
Looks like this stems from re-activating `dependabot` in #2742 as per your request. What's your preference for fixing? We could either convert `CHANGES.rst` to markdown or modify `update_changelog()`.
https://github.com/materialsproject/pymatgen/blob/c1a7f5d7635f85e7bc490658d52b70867ed24614/tasks.py#L250-L291
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PR_kwDOACgets5G985b
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added DOSCAR.LSO.lobster file attribute to Lobsterout, updated tests
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"Hi @janosh ,This PR is ready to be merged. Thanks !!",
"\n[](https://coveralls.io/builds/55797711)\n\nCoverage: 78.127% (-0.6%) from 78.738% when pulling **4144af6668f0f28b9cdff939895ec4d5d744b44e on naik-aakash:lobsterout_doc_update** into **0d2062a01bf0ccb36cb736c9a5d139787c55e4c1 on materialsproject:master**.\n",
"Thanks!"
] | 2023-01-09T11:48:12
| 2024-01-10T12:23:23
|
2023-01-10T14:11:11Z
|
CONTRIBUTOR
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## Lobsterout.get_doc() method updated
- Added has_doscar_lso: bool attribute to Lobsterout (checks if DOSCAR.LSO.lobster file is written during lobster run)
- Updated corresponding tests
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PR_kwDOACgets5G_HbM
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Added a missing multi element POTCAR file
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[
"@MichaelWolloch Thanks for the fix! 👍 ",
"Thank you @janosh for finding the missing file!",
"\n[](https://coveralls.io/builds/55766276)\n\nCoverage: 78.019% (-0.7%) from 78.738% when pulling **fd99292abc2cda5340db03a7f954d764671608e6 on MichaelWolloch:master** into **0d2062a01bf0ccb36cb736c9a5d139787c55e4c1 on materialsproject:master**.\n"
] | 2023-01-09T15:05:24
| 2023-01-09T15:29:57
|
2023-01-09T15:21:25Z
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CONTRIBUTOR
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and reverted the file loading change in commit e3bcad781fb83978fd7394ffc16d880e9ba9ab8d
## Summary
- Fix 1: Fixed a unit test that failed due to a missing file by actually committing the new file. The unit test was already fixed by @janosh in e3bcad781fb83978fd7394ffc16d880e9ba9ab8d, by taking another POTCAR, but this kind of defeated the purpose of the test which was to check multi-element POTCARs.
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PR_kwDOACgets5G_Y4_
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`isort` auto insert `__future__` annotations import
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Release v2023.1.9
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| 2023-01-09T21:50:46
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2023-01-09T21:48:33Z
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Excludes `dependabot` PRs in task `update_changelog()`. Closes #2794.
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PR_kwDOACgets5HCyT5
| 2,799
|
Added 4-color electronic band plot in BSDOSPlotter
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[
"\n[](https://coveralls.io/builds/56318143)\n\nCoverage: 78.154% (-0.7%) from 78.897% when pulling **7dbe175a6c830a49a59758e498358139f8900673 on cnncnnzh:ele_band_color** into **cd37811b94554656088ffbe6a3ca1235708a5019 on materialsproject:master**.\n",
"`test_files/SrBa2Sn2O7.json` is just 1 line now which is great but still 13.7 MB. pymatgen is really slow to clone since it's already 830 MB.\r\n\r\n\r\n\r\nWe're planning to bring this down if at all possible but definitely don't want to add to it. Could you check how much of that JSON data is actually necessary for the test? Maybe some keys with large data can be removed?",
"Sorry to drag this out so much...",
"I totally understand. The removal of unnecessary keys doesn't make any big effect. I rerun the calculation with a shorter k path and a smaller number of k points. Now the .json file is ~4 MB. The plot is not pretty but I think it's enough for the purpose of testing. Does that work? Or do you need an even smaller file? ",
"Thanks! 4 MB is still pretty big but acceptable imo. Only remaining suggestion would be to generate the plotting data on the fly with `np.random.rand()` since like you say, we don't care what the plot looks like. But I leave that to you if you want to look into that or call it finished here.",
"I will try that. Should I just randomize the 'projections' in the data? ",
"Yes, that would be great",
"Hi Janosh, when I randomize the projection from every atom, the lines turn completely black, which makes sense to me. So for each k and each band, I randomly pick up two atoms and assign random contributions to them. Does that sound good to you?\r\n[pband.pdf](https://github.com/materialsproject/pymatgen/files/10442852/pband.pdf)\r\n",
"> Does that sound good to you?\r\n\r\nPerfect!",
"Hi Janosh, I saw that this request is still open. Is there any further change that I need to make? ",
"Sorry, I should have been more clear. I thought you were still going to remove the large [JSON file](https://github.com/materialsproject/pymatgen/blob/cbaadb808b81fd4a31dee0733b2277d5630a8fbd/test_files/SrBa2Sn2O7_random.json) and replace it with some calls to `np.random.rand` directly in the test code. (so as to keep repo size and clone time down).",
"Sorry, I misunderstood your meaning. I generated the random data and save them in .json. I'll generate them in the test.py file."
] | 2023-01-10T07:03:43
| 2023-01-26T14:34:54
|
2023-01-26T14:31:58Z
|
CONTRIBUTOR
|
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## Summary
Added a feature that supports cmyk band structure plot for 4-element structures, and added the corresponding _cmyk_triangle method for legend.
|
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PR_kwDOACgets5HMjHS
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|
use `cibuildwheel` to build linux wheels
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[
"\n[](https://coveralls.io/builds/55943589)\n\nCoverage: 78.085% (-0.7%) from 78.8% when pulling **1d01c44a6ec182fb21fc42e54e78f1941e480393 on njzjz:cibuildwheel** into **44f24db50d3b59ad9bf448c523564c114f472f19 on materialsproject:master**.\n",
"Thanks, but there seem to be errors with regard to wheel building. The tests need to pass before we merge.",
"@shyuep I notice that in the `cmd_line` directory, some binary files link to external dependencies outside the repository. I don't know if they should be packaged into wheels. I tried to fix these libraries on Linux but skipped those on macos.\r\n\r\nThe lint failure is not related to this PR, but is caused by [a new ruff version](https://github.com/charliermarsh/ruff/releases/tag/v0.0.252)."
] | 2023-01-11T22:05:50
| 2023-02-25T18:56:00
|
2023-02-25T18:56:00Z
|
CONTRIBUTOR
|
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## Summary
Include a summary of major changes in bullet points:
- refactor the wheel build workflow using [cibuildwheel](https://github.com/pypa/cibuildwheel)
- build manylinux2014 wheels
## Checklist
Work-in-progress pull requests are encouraged, but please put \[WIP\] in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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I_kwDOACgets5bSKpt
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`ComputedEntry.__eq__` method not suitable for new MP entry_id format
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[
"Closing with merged fix PR #2802 "
] | 2023-01-12T23:34:58
| 2023-01-25T17:29:39
|
2023-01-25T17:29:39Z
|
MEMBER
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Materials Project recently introduced new R2SCAN data, and with it, a new `entry_id` naming scheme where entry IDs include the functional type (e.g., _mp-9-R2SCAN_ ).
Because of this, there is now an issue that will likely be more frequently encountered: `ComputedEntry` objects with the same `entry_id` may evaluate as being equal, even when they have different `energy_adjustments` (i.e., for different mixing schemes).
For example, this currently makes it problematic to create `EntrySet` objects containing entries downloaded from MP, because entries are incorrectly being flagged as duplicates. Here's an example of code that illustrates this directly. This applies with `mp-api==0.30.5` and `pymatgen==2023.1.9`. (Future mp-api releases will not return multiple types of entries, though):
```python
from mp_api.client import MPRester
with MPRester() as mpr:
ents = mpr.get_entries_in_chemsys("Y-Mn-O")
r2_scan_ymno3 = []
for e in ents:
if "mp-19385-R2SCAN" in e.entry_id:
r2_scan_ymno3.append(e)
e1, e2 = r2_scan_ymno3 # two entries with the same entry_id
print("Entry objects equal?", e1 == e2)
print("Energies equal?", e1.energy == e2.energy)
```
This prints:
```
Entry objects equal? True
Energies equal? False
```
I suggest we make the `ComputedEntry.__eq__` method a little more encompassing to account for situations like this. I will make a PR shortly with a proposed fix @munrojm @mkhorton
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PR_kwDOACgets5HSaGP
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Fix for `ComputedEntry.__eq__` to allow more robust checking with new MP entries
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[
"I am a bit concerned as to why this is needed. Technically entry_ids should be unique. Why would there be an instance where there are many same entry_ids with different energies?",
"@shyuep Please see the example in Issue #2801 for why this may be a more common problem now. In short, the new R2SCAN data added to MP can be downloaded with or without the new mixing scheme adjustment; in both cases, the entries have the same `entry_id` and are said to be equal, even when they have different final energies.",
"I don't think this is a wise way of dealing with mixing adjustments. The way the entry adjustments are done is that the adjustments are stored differently from the raw energies from the calculations themselves. That logical framework should be maintained. I am unclear what kind of situation would require a user to download both types of entries.",
"I agree that, in principle, entries should represent calculation results independent of whatever corrections are applied. However, in practice, it is often the final (corrected) energy & composition that are most important in analysis... so it becomes problematic when two entry objects are considered equal and behave differently (e.g., in phase diagram construction). \r\n\r\nWhile this particular situation was an undesired result of `MPRester` returning both entry types (which was fixed yesterday in the last `mp-api` release), I still think the situation could arise again for people querying new MP entry data. Perhaps this Issue/PR could be left open and reevaluated if it becomes a problem again for someone else?",
"Yes, the `entry_id` maps to a specific calculation (e.g., combination of total energy, functional/methods, etc.), but a specific calculation may be adjusted or corrected in multiple ways, leading to different final energies with the same entry_id.",
"There is a difference between whether something can happen and whether something should happen. I get that you can apply different corrections to the same entry. But for all practical purposes, you use one definitive value of the energy for a material. Someone needs to educate me on a situation where differently corrected entries are useful in a scientific application. ",
"Isn't this mostly a question of which behavior is least likely to mislead users? Telling them two entries are equal even if they have different energy adjustments seems like it would surprise people. Like the `5 == '5'` debacle in JS. Imagine as a user testing\r\n\r\n```py\r\nentry_1 == entry_2\r\n>>> True\r\n```\r\n\r\nbut then seeing\r\n\r\n```py\r\nentry_1.energy_adjustments\r\n>>> [a, b, c]\r\n\r\nentry_2.energy_adjustments\r\n>>> [x, y, z]\r\n```",
"It is a balance between efficiency and use case. If someone can explain to me an actual useful situation where you want multiple entries with different corrections, I am more than happy to sacrifice efficiency to make it happen. I would also point out that corrections can be applied and changed at any time. That is actually the only way to ensure that a set of entries have a consistent set of corrections. ",
"I would also point out that mismanaging entries can have severe consequences for the accuracy of an analysis. Let's say the user intends to use entries that only has one correction scheme (say the normal MP PBE/PBE+U correction scheme). But there are multiple entries with different correction schemes present and one of the correction schemes result in a lower energy than the MP correction scheme. What will happen if you do any phase diagram or thermodynamic analysis based on ground states is that the lower energy entry will prevail. \r\n\r\nIn short, the MP API needs to return one and only one entry per entry id, with a well-defined default correction scheme. Return multiple entries per entry id is a recipe for disaster, regardless of whether we check for energy equality. If an advanced computational person wants to explore different correction schemes and their effects, they can do so with post-processing using the correction schemes implemented in pymatgen.",
"I just want to add to this thread and explain what the API is doing and how the data is structured. Entry data is returned via the thermo endpoint, which has a `thermo_id` as its key. This is a combination of the MPID and a `ThermoType` which indicates the mixing scheme. The entries returned are consistent with the `ThermoType` that is requested. By default, this is set to GGA/GGA+U. \r\n\r\nNow that we have R2SCAN data, we build and offer thermo data using three schemes. Mixed GGA/GGA+U, mixed GGA/GGA+U/R2SCAN, and sole R2SCAN. Since each `ComputedStructureEntry` is associated with a calculation, the `entry_id` now contains the MPID and the run type (e.g. R2SCAN). Because of the multiple schemes, we now have the same `ComputedStructureEntry` associated with an R2SCAN calculation being used both in the GGA/GGA+U/R2SCAN thermo data where it has a correction applied, and in the sole R2SCAN thermo data where it does not. ",
"@shyuep During this morning's MP update meeting, @mkhorton and me both voted in favor of merging this PR. Would you like to hold off and discuss this some more?",
"Agreed; the logic here is \"what is expected behavior?\"\r\n\r\nSpecifically, the example of `entry1 == entry2 == True` even if `entry1.energy != entry2.energy` or `entry1.energy_adjustments != entry2.energy_adjustments`.\r\n\r\nRegardless of what Materials Project is doing with its entry_ids, this behavior seems unexpected and incorrect.",
"One more quick comment regarding the concern about efficiency. The new scheme is this:\r\n```python\r\nif self.entry_id != other.entry_id:\r\n return False\r\n```\r\nThis means that the code will still perform just as fast as before for collections of entry objects where all entry IDs are unique. The next steps in equality checking only occur for entries that share the same `entry_id`. ",
"@mkhorton @janosh I agree only partly. By default, all objects do not implement equals and you only check for equality based on the id. The question here is - what should we encourage the user to do? Mess around with multiple entries with the same entry_id but different corrections, or just have one entry with a single entry_id. I doubt you will say let the user go ahead and play around with entries as they see fit.",
"@shyuep Isn't what users do with the code beside the point? All we care about is that the equality operation between entries doesn't return misleading results no matter what users decide to do.",
"@janosh By that argument, this code should never exist in Python:\r\n\r\n```\r\nIn [3]: class A:\r\n ...: def __init__(self, a):\r\n ...: self.a = a\r\n ...: \r\n\r\nIn [4]: A(1) == A(1)\r\nOut[4]: False\r\n```\r\n\r\nIt does. And it is the *default* unless you implement something else.",
"Anyway, since both @janosh and @mkhorton already voted, just go ahead and merge it for now. I will revert only if there are complaints about speed, despite my misgivings about allowing users to have two entries with different corrections.",
"Thanks @mattmcdermott and @shyuep for green lighting!",
"Thanks for merge.\r\n\r\nRegarding the \"this code should never exist in Python [...] it is the *default*\" argument, I would offer a counter-example:\r\n\r\n```\r\nIn [1]: from dataclasses import dataclass\r\n\r\nIn [2]: @dataclass\r\n ...: class A:\r\n ...: a: int\r\n ...:\r\n\r\nIn [3]: A(1) == A(2)\r\nOut[3]: False\r\n```\r\n\r\nSemantically, I think the purpose of something like an `Entry` is fairly well-aligned with what dataclasses have been designed for, and there the default behavior is to return `False`. The default behavior of a minimal subclass of object is different, because there, speed is the absolute concern since everything is an object, and any default behavior will therefore have a penalty associated with it.\r\n\r\nThat's all I have to offer here; not relevant now we're merging, but perhaps in case a similar instance occurs in future.",
"@mkhorton Actually a ComputedEntry is deliberately **not** a dataclass... anyways...",
"Perhaps it should be; its purpose is to store data. I always thought these did not use dataclasses simply because they predate dataclasses in the standard library. I mention this not to create an argument, but sincerely think they're very useful and appropriate -- I know @jmmshn has opinions on this too.",
"2cents: I guess we part of the reason we didn't use dataclasses because they have difficult with handling inheritance even after things were \"[fixed](https://medium.com/@aniscampos/python-dataclass-inheritance-finally-686eaf60fbb5)\" in python 3.10\r\nBut they do save a tremendous amount of dev time when it comes to building the APIs so I think they should be used wherever some objects gets very close to the what we serve the users.",
"It is true that entries predate dataclasses. But that is not the only reason why entries do not use dataclasses. Don't get me wrong, I think dataclasses are great for a lot of purposes. But in the case of entries, I see the use of dataclasses as hindering rather than improving readability. Inheritance was one big factor. People may not realize this now, but the idea of having a GrandPotEntry being an inherited version of Entry and using essentially the same phase diagram code otherwise was something that had major implications for the rest of the design of the code.\r\n\r\nAlso, I still prefer my entries defined by structure/composition uniqueness rather than internal property uniqueness.",
"This PR addresses a related issue reported here https://github.com/CompRhys/pymatgen/issues/1: unequal hash for equal entries. Before, pymatgen broke the only requirement placed on a hash function, which is that objects which [compare equal have the same hash value](https://docs.python.org/3/reference/datamodel.html#object.__hash__). Thanks for pointing that out @CompRhys!\r\n\r\n```py\r\n>>> from pymatgen.entries.computed_entries import ComputedEntry\r\n>>> from pymatgen.analysis.phase_diagram import PDEntry\r\n>>> pdentry = PDEntry(\"NaCl\", -1.3)\r\n>>> centry = ComputedEntry(\"NaCl\", -1.3)\r\n>>> hash(pdentry) == hash(centry)\r\nFalse\r\n>>> pdentry == centry\r\n# before this PR\r\nTrue\r\n# after\r\nFalse\r\n```\r\n\r\nEdit: My mistake. Looks like this was fixed earlier (not sure when) but `pdentry != centry` already before this PR."
] | 2023-01-12T23:46:28
| 2023-01-26T15:08:28
|
2023-01-24T22:38:36Z
|
MEMBER
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This PR addresses #2801.
In summary, I made the check between `entry_id` values only capable of returning `False`, so that if two entries have the same `entry_id` they will only evaluate as equal if they also have the same energy and composition. I also added a test to check this.
This does slow down certain operations like `EntrySet` creation, but only when there are many entries with duplicate entry_id values. If all entries have unique entry_ids (as was common before the new MP entry naming scheme), then this should not affect performance.
Please let me know if you can think of any other problems this might cause -- in my experience, bugs with entry equality checking are particularly insidious... @mkhorton @munrojm
## Checklist
- [x] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass..
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PR_kwDOACgets5HVqT_
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Add some weight-fraction-based functions
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[
"\n[](https://coveralls.io/builds/55931430)\n\nCoverage: 78.086% (-0.8%) from 78.844% when pulling **59756e21d83f95c0722db523aa26de8123cdf6e9 on amkrajewski:add_weightbasedfunctions** into **ff0f26a5be5f96123a617a578a99d4d0043d2b95 on materialsproject:master**.\n",
"Thanks for the useful contribution!"
] | 2023-01-13T15:14:13
| 2023-01-13T20:05:47
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2023-01-13T20:05:40Z
|
CONTRIBUTOR
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## Summary
When working with metallic alloys, weight-fraction-based notations such as Ti64 / Ti-6V-4Al or NiTiNOL60 / Ni-40Ti are commonly employed in both industrial specifications and scientific literature. Regardless of the numerous downsides of this situation, including errors in scientific experiments or NLP-parsing when they are mistaken for atomic fractions or chemical formulas, being able to create a Composition object from them (under correct interpretation) would be a useful pymatgen feature.
- Composition class method to initialize it from a dictionary of weight fractions
- Composition property giving a dictionary of weight fractions
- concise tests for the two above were added
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pymatgen/io/vasp/inputs.py md5 call gets an error when FIPS is enabled
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[
"Adding `usedforsecurity=False` to the `hashlib.md5` calls in `pymatgen/io/vasp/inputs.py` fixes the issue for us. I suspect the same argument should also be added to the calls in `pymatgen/io/abinit/pseudos.py` as well, but I didn't see any other relevant calls."
] | 2023-01-13T19:52:06
| 2023-06-23T02:35:36
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2023-06-23T02:35:36Z
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CONTRIBUTOR
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**Describe the bug**
`pymatgen/io/vasp/inputs.py` calls `hashlib.md5` for hashing in a way that generates an error on RedHat systems that have FIPS enabled.
**To Reproduce**
On a RedHat machine that has FIPS enabled, do any pymatgen operation that reads a potcar, e.g. `Potcar.from_file("POTCAR"))`
The resulting output is
```py
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/outputs.py", line 401, in __init__
self.update_potcar_spec(parse_potcar_file)
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/outputs.py", line 1148, in update_potcar_spec
potcar = self.get_potcars(path)
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/outputs.py", line 1118, in get_potcars
potcar = get_potcar_in_path(os.path.split(self.filename)[0])
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/outputs.py", line 1103, in get_potcar_in_path
pc = Potcar.from_file(os.path.join(p, fn))
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/inputs.py", line 2240, in from_file
single = PotcarSingle(p)
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/inputs.py", line 1811, in __init__
self.hash = self.get_potcar_hash()
File "/home/Software/python/system/extra/lib64/python3.9/site-packages/pymatgen/io/vasp/inputs.py", line 2151, in get_potcar_hash
return md5(hash_str.lower().encode("utf-8")).hexdigest()
ValueError: [digital envelope routines: EVP_DigestInit_ex] disabled for FIPS
```
**Expected behavior**
successful parsing of the POTCAR file
**Environment (please supply relevant versions and platform info):**
Rocky Linux 8 with FIPS enabled
**Additional context**
This discussion https://github.com/s3tools/s3cmd/issues/1005 strongly indicates adding the `usedforsecurity=False` to the `md5()` call will avoid the error, which is caused because md5 is not a secure hash for security purposes. I'm currently checking this locally and will post a followup when I see if it works.
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PR_kwDOACgets5HflG9
| 2,805
|
Fix `Molecule.insert()`
|
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"\n[](https://coveralls.io/builds/55995702)\n\nCoverage: 62.746% (-16.06%) from 78.803% when pulling **9ccee9ff3adf38869989667b724ea934ec65e29e on fix-molecule-insert** into **00609e54b17ecf0706000ea1ad2af58cd6601571 on master**.\n"
] | 2023-01-16T20:18:05
| 2023-01-17T15:17:27
|
2023-01-17T15:17:26Z
|
MEMBER
|
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b3bbaf04f5 replace set methods `(union|intersection|difference)` with arithmetic operators
5f8a9fc3d2 standardize type names in doc strings: `string`->`str`, `integer`->`int`, etc.
6f99428d65 fix `Molecule.insert()` doesn't return what the doc str says
|
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Q-Chem 6 + Misc Updates
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[
"\n[](https://coveralls.io/builds/56330871)\n\nCoverage: 78.165% (-0.7%) from 78.873% when pulling **83254b4b8ce029071abf87034286d4e63ad05924 on samblau:qchem** into **8f5a6f58657b361e07f08f51d3a674d70b6faf0c on materialsproject:master**.\n",
"Alright y'all, this is a big one. @espottesmith, @rkingsbury, @mkhorton, any chance some or all of you are interested in reviewing? Thank you!",
"Need to fix test_sets.py given the change from assertEqual -> assert that has been implemented in the midst of this large PR",
"Thanks @samblau, this looks great!",
"Thanks @samblau ! Sorry I didn't get a chance to review before now but all looks good to me.",
"@mkhorton Thanks for merging! Could you or @shyuep please release a new version of pymatgen when convenient? Thank you!",
"@samblau 2023.1.30 was released today."
] | 2023-01-17T21:56:47
| 2023-01-30T16:57:15
|
2023-01-26T21:30:12Z
|
CONTRIBUTOR
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## Summary
- Major changes to Q-Chem IO (inputs.py and outputs.py) to accommodate differences and new features in version 6+
- Additional parsing capabilities for HOMO/LUMO, dipoles, NBO info (hyperbonds and 3C bonds) in outputs.py
- Utility for processing a parsed binary Hessian scratch file
- Overdue updates to default values in sets.py and new defaults associated with differences and new features in Q-Chem 6+
|
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PR_kwDOACgets5HoyWv
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|
Unignore flake8 B028 and fix occurrences
|
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"\n[](https://coveralls.io/builds/56071003)\n\nCoverage: 78.806%. Remained the same when pulling **790dea5a1b9d9a2c5aa19bb2fbf22d2ace3e6d96 on flake8-B028** into **e1c075ce74301ee63cc827b6fec0753fdd65a5dd on master**.\n"
] | 2023-01-18T15:38:24
| 2023-01-18T18:56:19
|
2023-01-18T18:53:09Z
|
MEMBER
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https://github.com/PyCQA/flake8-bugbear/releases/tag/23.1.14
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Normalized DOS
|
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[
"\n[](https://coveralls.io/builds/56115232)\n\nCoverage: 78.631% (-0.2%) from 78.806% when pulling **71144a2b069444565738c34e252528a972887985 on jmmshn:patch_dos** into **582cb8319f0215a528bb0b0ab8bf43695aec5390 on materialsproject:master**.\n",
"@mkhorton, @munrojm, @janosh once this is updates and released can we update the x-axis of the Density of States display on the website to have the proper units?",
"> can we update the x-axis of the Density of States display on the website to have the proper units?\r\n\r\nSure thing. Let me know if there's something you need me to do.",
"Love your commit messages btw. 😄 ",
"> > can we update the x-axis of the Density of States display on the website to have the proper units?\r\n> \r\n> Sure thing. Let me know if there's something you need me to do.\r\n\r\nI think I just need a release once this get merged. Then maybe update the data that gets pull by the API depending on @munrojm's opinion.",
"@janosh some tests failed due to a GitHub actions error. I just made some minor changes to plotting module and tests are passing now.",
"Had a chat with Jason, will move forward and update the API once this is merged."
] | 2023-01-18T20:51:57
| 2023-01-19T20:38:37
|
2023-01-19T20:12:47Z
|
CONTRIBUTOR
|
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## Normalize Density of States
Currently the Density of states data is extensive (at lease when you use `Vasprun.complete_dos`).
This proposed change allow you to use call `Vasprun.complete_dos_normalized` to get the density of states in units of states $/ \text{eV} / \mathbb A^3$
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KeyError of elemental references in pre-computed phase diagram
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[] | null |
[
"\n[](https://coveralls.io/builds/56164632)\n\nCoverage: 78.129% (-0.7%) from 78.807% when pulling **cd146e322c65a4ee3db483561706e149e058dcb8 on peikai:master** into **d9b8697181e28f0400ecf313d8b69a1cacafcfc7 on materialsproject:master**.\n",
"@peikai, I appreciate you making this PR. I just patched the API client to temporarily resolve this issue yesterday as we were having plotting issues on the front-end with the pre-computed data. I also found an additional change that needs to be made to for some ternary compounds. Namely, `qhull_data` needs to be a numpy array, and not a list. Although, it looks like you don't have that issue. In any case, to fix your local problems before this is merged, you can update `mp-api` as well.\r\n\r\n@janosh, this relates to the emmet issue I tagged you in regarding `PhaseDiagram` de-serialization problems with monty.",
"@peikai Thanks for this PR. Do we really need `pymatgen/analysis/tests/pre_computed_phase_diagram_Li-Fe-O.json`? Maybe you can re-use an existing test file in the `test_files/` dir? The repo size is already approaching 1GB which we really need to get down.",
"@munrojm Thanks for the information. The updated mp-api works. And this PR would fix the issue in pymatgen.\r\n"
] | 2023-01-20T02:30:17
| 2023-01-23T16:40:11
|
2023-01-21T20:26:19Z
|
CONTRIBUTOR
|
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##
When I try to plot a pre-computed phase diagrams that are retrieved via get_phase_diagram_from_chemsys() method,
> phaseDiagram = mpr.get_phase_diagram_from_chemsys('Li-Fe-O')
> plotter = PDPlotter(phaseDiagram)
a KeyError raises as shown below, which arises from the inconsistence on object stored in el_refs dictionary, i.e., the keys stored in phaseDiagram.el_refs are **str** object (_dict_keys(['O', 'Fe', 'Li'])_), instead of the **Element** object (_dict_keys([Element O, Element Fe, Element Li])_).
The pre-computed phase diagrams in database might not be updated conveniently. So, I add some codes in pymatgen.analysis.phase_diagram.PhaseDiagram class, to update keys in elemental reference dictionary to Element object, in case it loads a pre-computed phase diagram. A corresponding test unit is also added to check the keys in el_refs dictionary,
KeyError message:
>Traceback (most recent call last):
File "D:\Seafile\peikai\My Libraries\Repos\Volume-Planning-for-Anodes\phase_diagram_mixscheme.py", line 37, in <module>
plotter = PDPlotter(phase_diagram, show_unstable=0, backend='matplotlib')
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 2111, in __init__
self._min_energy = min(self._pd.get_form_energy_per_atom(e) for e in self._pd.stable_entries)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 2111, in <genexpr>
self._min_energy = min(self._pd.get_form_energy_per_atom(e) for e in self._pd.stable_entries)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 577, in get_form_energy_per_atom
return self.get_form_energy(entry) / entry.composition.num_atoms
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 564, in get_form_energy
return entry.energy - sum(comp[el] * self.el_refs[el].energy_per_atom for el in comp.elements)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 564, in <genexpr>
return entry.energy - sum(comp[el] * self.el_refs[el].energy_per_atom for el in comp.elements)
~~~~~~~~~~~~^^^^
KeyError: Element Li
|
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PR_kwDOACgets5IL664
| 2,810
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Unittest2pytest
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[
"\n[](https://coveralls.io/builds/56150535)\n\nCoverage: 78.841% (+0.03%) from 78.809% when pulling **fca8ad8b2c60a3b5a26b2fe4192e69db60510f55 on unittest2pytest** into **1d7eb7d893316d7bbfa1c3c7a56e5bc7ce485906 on master**.\n"
] | 2023-01-20T05:32:15
| 2023-01-20T18:45:37
|
2023-01-20T18:39:03Z
|
MEMBER
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```sh
unittest2pytest --write --nobackups pymatgen/analysis
```
(using unmerged unittest2pytest#66)
followed by
```sh
isort --add-import 'from pytest import approx' $(git status -s | cut -c4-)
```
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I_kwDOACgets5cbeGg
| 2,812
|
Importing very large CIF files in pymatgen
|
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[] | 2023-01-20T11:31:53
| 2023-01-20T15:03:48
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2023-01-20T15:03:48Z
|
NONE
|
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**Is your feature request related to a problem? Please describe.**
I am attempting to use Pymatgen for the analysis of a supercell containing ~10,000 atoms. I am getting the following warning message:
```
UserWarning: Issues encountered while parsing CIF: Some fractional co-ordinates rounded to ideal values to avoid issues with finite precision.
warnings.warn("Issues encountered while parsing CIF: %s" % "\n".join(self.warnings))
```
I understand the rationale for including this feature, but in my specific circumstance this will harm my analysis.
**Describe the solution you'd like**
The `from_file()` method should have an optional argument to force pymatgen to accept the atomic positions given in the CIF.
**Describe alternatives you've considered**
N/A
**Additional context**
N/A
|
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PR_kwDOACgets5IO1P_
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|
allowed frac_tolerance to be passed as an argument to structure.from_file()
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[] | null |
[
"This is already supported. There is no need for a specific frac_tolerance in from_file."
] | 2023-01-20T17:17:06
| 2023-01-20T17:23:58
|
2023-01-20T17:18:15Z
|
NONE
|
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## Summary
Include a summary of major changes in bullet points:
- added frac_tolerance as an argument to from_file, to be passed to the CifParser init
- fixed a very minor typo
## Checklist
Work-in-progress pull requests are encouraged, but please put \[WIP\] in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [ ] Doc strings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html). Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are *highly* encouraged. Run [`mypy path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most errors prior to submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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PR_kwDOACgets5IPcok
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|
Convenience function to get the normalized DOS
|
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[
"\n[](https://coveralls.io/builds/56153681)\n\nCoverage: 78.13% (-0.7%) from 78.843% when pulling **f54ad812f2c4b1b58a5c1e56dc66448dc9c83419 on jmmshn:patch_dos** into **97ca2dab27c6929efd937da34422d733e2e1824d on materialsproject:master**.\n"
] | 2023-01-20T20:06:03
| 2023-01-20T20:29:37
|
2023-01-20T20:29:37Z
|
CONTRIBUTOR
|
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## Added Convenience to obtain the normalized CompleteDos object
Added tests to make sure calling it multiple time still only gives one result.
|
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PR_kwDOACgets5IViwt
| 2,815
|
Raise ValueError when building phase diagram without entries.
|
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[
"\n[](https://coveralls.io/builds/56197231)\n\nCoverage: 78.133% (-0.7%) from 78.846% when pulling **cc690eb8410f642e92dd847fa1fd3978e39f7848 on peikai:master** into **dcbbe002cc46dba726b6a84bb0c7533ce9c2941b on materialsproject:master**.\n"
] | 2023-01-23T15:18:09
| 2023-01-28T04:09:30
|
2023-01-28T04:09:30Z
|
CONTRIBUTOR
|
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I committed some codes to raise a specific ValueError exception and hint a specific reason message for the attempt to build a phase diagram with no entries. A corresponding unittest was also added.
Scenario:
In the cases that there are not enough entries to form a complete phase diagram, the processing operation of the mixing scheme would fail and might return an empty list, i.e., entryList = []. That would cause an error in PhaseDiagram class when computing data, as shown below. To raise a specific exception is necessary.
Run:
> entryList = MaterialsProjectDFTMixingScheme().process_entries(entryList, clean=True)
> phase_diagram = PhaseDiagram(entryList)
Errors:
>Generating mixing state data from provided entries.
D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\entries\mixing_scheme.py:508: UserWarning: GGA(+U) entries do not form a complete PhaseDiagram.
warnings.warn(f"{self.run_type_1} entries do not form a complete PhaseDiagram.")
Entries contain R2SCAN calculations for 0 of 0 GGA(+U) hull entries.
GGA(+U) energies will be adjusted to the R2SCAN scale
D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\entries\mixing_scheme.py:215: UserWarning: WARNING! GGA(+U) entries do not form a complete PhaseDiagram. No energy adjustments will be applied.
warnings.warn(str(exc))
Processing complete. Mixed entries contain 0 GGA(+U) and 0 R2SCAN entries.
>Traceback (most recent call last):
phase_diagram = PhaseDiagram(entryList)
^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 366, in __init__
computed_data = self._compute()
^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 445, in _compute
form_e = -np.dot(data, vec)
^^^^^^^^^^^^^^^^^
File "<__array_function__ internals>", line 180, in dot
ValueError: shapes (0,) and (1,) not aligned: 0 (dim 0) != 1 (dim 0)
|
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PR_kwDOACgets5IYod5
| 2,816
|
Bug in get_plotly method in the WulffShape
|
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[
"\n[](https://coveralls.io/builds/56218953)\n\nCoverage: 78.128% (-0.7%) from 78.846% when pulling **27b6a69418671f50464f481f9c2f2c006fc38f3f on CifLord:wulff_bug** into **dcbbe002cc46dba726b6a84bb0c7533ce9c2941b on materialsproject:master**.\n",
"@CifLord Thanks! Could you add or modify an existing test that would have triggered the error and now passes thanks to the `if max(e_surf_on_wulff) == min(e_surf_on_wulff):` case?"
] | 2023-01-24T02:35:24
| 2023-03-16T02:34:44
|
2023-03-16T02:34:44Z
|
CONTRIBUTOR
|
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## Summary
Minor bug fix to the plotly interface for the WulffShape class.
- Plotly WulffShape was trying to normalize the value of each surface energy by zero whenever only one facet existed on the Wulff Shape. The normalized surface energy of only one facet on the shape will be changed to 1 by default to avoid division by zero.
|
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I_kwDOACgets5c4tD4
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|
to_cube function has a bug
|
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[
"Thanks for reporting! 👍 "
] | 2023-01-26T15:54:49
| 2023-03-24T04:49:17
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2023-03-24T04:49:17Z
|
NONE
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**Describe the bug**
The [`to_cube` function](https://github.com/materialsproject/pymatgen/blob/e513400b77dc3810b45a6529437971e7762a250e/pymatgen/io/common.py#L334-L378) of VolumetricData has a bug: it stores in lines 4-6 the real-space vectors instead of the size of a voxel.
**To Reproduce**
1. Get any cube file
2. run the following code, that should return the same file (apart from cosmetics):
```python
from pymatgen.io.common import VolumetricData
cubefile = VolumetricData.from_cube(IN_FNAME)
cubefile.to_cube(OUT_FNAME)
```
3. check the content of the two files. You will see that lines 4-6 are wrong.
E.g. in my case, original file (lines 4-6):
```
72 0.170589 0.000000 0.000000
80 0.000000 0.163473 0.000000
108 -0.114105 0.000000 0.125017
```
Output file:
```
72 12.282408 0.000000 0.000000
80 0.000000 13.077840 0.000000
108 -12.323340 0.000000 13.501836
```
**Expected behavior**
The correct values are written in the cube file.
It should be as simple as changing the following lines:
https://github.com/materialsproject/pymatgen/blob/e513400b77dc3810b45a6529437971e7762a250e/pymatgen/io/common.py#L349-L365
to something like (untested, but should work)
```
file.write(
f"\t {self.dim[0]} "
f"{self.structure.lattice.matrix[0][0] / self.dim[0] * ang_to_bohr :.6f} "
f"{self.structure.lattice.matrix[0][1] / self.dim[0] * ang_to_bohr :.6f} "
f"{self.structure.lattice.matrix[0][2] / self.dim[0] * ang_to_bohr :.6f} \n"
)
```
and analogously for the following two lines.
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PR_kwDOACgets5Inv_9
| 2,818
|
Minor fix to `get_element_profile`
|
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[
"\n[](https://coveralls.io/builds/56388449)\n\nCoverage: 78.163% (-0.7%) from 78.873% when pulling **35ffd5e57c7fa5b00a9b069131bc2412e2b1fbab on jmmshn:patch_profil** into **8f5a6f58657b361e07f08f51d3a674d70b6faf0c on materialsproject:master**.\n",
"Thanks @jmmshn! 👍 "
] | 2023-01-26T20:07:33
| 2023-01-30T00:29:14
|
2023-01-30T00:27:04Z
|
CONTRIBUTOR
|
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# Minor fixes to the return types of `get_element_profile` and electrode
`get_element_profile` fix:
The entries returned is given as `dict_keys` but that's rarely what people want.
- Return a list of entries instead.
- Also return the critical composition, which is usually useful information.
electrode fixes:
- Linting on some docs
- require framework formula for the `from_steps` constructor.
|
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PR_kwDOACgets5IugqL
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Raise ValueError when trying to create PhaseDiagram without entries
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[
"\n[](https://coveralls.io/builds/56388374)\n\nCoverage: 78.165% (-0.7%) from 78.875% when pulling **a047696e706d7044f0a6b8361d87e518b8452361 on peikai:EmptyEntryList** into **ef98f0b3b6c4315bbd4a24d1ab1cc3fb4c5012ec on materialsproject:master**.\n",
"Thanks @peikai! 👍 ",
"Great!"
] | 2023-01-28T05:27:57
| 2023-01-30T12:08:12
|
2023-01-30T00:18:55Z
|
CONTRIBUTOR
|
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I committed some codes to raise a specific ValueError exception and hint a specific reason message for the attempt to build a phase diagram with no entries. A corresponding unittest was also added.
Scenario:
In the cases that there are not enough entries to form a complete phase diagram, the processing operation of the mixing scheme would fail and might return an empty list, i.e., entryList = []. That would cause an error in PhaseDiagram class when computing data, as shown below. To raise a specific exception is necessary.
Run:
> entryList = MaterialsProjectDFTMixingScheme().process_entries(entryList, clean=True)
> phase_diagram = PhaseDiagram(entryList)
Errors:
>Generating mixing state data from provided entries.
D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\entries\mixing_scheme.py:508: UserWarning: GGA(+U) entries do not form a complete PhaseDiagram.
warnings.warn(f"{self.run_type_1} entries do not form a complete PhaseDiagram.")
Entries contain R2SCAN calculations for 0 of 0 GGA(+U) hull entries.
GGA(+U) energies will be adjusted to the R2SCAN scale
D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\entries\mixing_scheme.py:215: UserWarning: WARNING! GGA(+U) entries do not form a complete PhaseDiagram. No energy adjustments will be applied.
warnings.warn(str(exc))
Processing complete. Mixed entries contain 0 GGA(+U) and 0 R2SCAN entries.
>Traceback (most recent call last):
phase_diagram = PhaseDiagram(entryList)
^^^^^^^^^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 366, in __init__
computed_data = self._compute()
^^^^^^^^^^^^^^^
File "D:\Anaconda\envs\pymatgen2023\Lib\site-packages\pymatgen\analysis\phase_diagram.py", line 445, in _compute
form_e = -np.dot(data, vec)
^^^^^^^^^^^^^^^^^
File "<__array_function__ internals>", line 180, in dot
ValueError: shapes (0,) and (1,) not aligned: 0 (dim 0) != 1 (dim 0)
|
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PR_kwDOACgets5JAJJi
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|
Bump numpy from 1.23.2 to 1.24.1
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[
"\n[](https://coveralls.io/builds/56500831)\n\nCoverage: 78.703% (-0.7%) from 79.414% when pulling **4a70121830ef8d3c6043ab0addc5bdd47227bc61 on dependabot/pip/numpy-1.24.1** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-02-01T12:06:47
| 2023-02-03T17:48:07
|
2023-02-03T17:47:50Z
|
CONTRIBUTOR
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Bumps [numpy](https://github.com/numpy/numpy) from 1.23.2 to 1.24.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.24.1</h2>
<h1>NumPy 1.24.1 Release Notes</h1>
<p>NumPy 1.24.1 is a maintenance release that fixes bugs and regressions
discovered after the 1.24.0 release. The Python versions supported by
this release are 3.8-3.11.</p>
<h2>Contributors</h2>
<p>A total of 12 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.</p>
<ul>
<li>Andrew Nelson</li>
<li>Ben Greiner +</li>
<li>Charles Harris</li>
<li>Clément Robert</li>
<li>Matteo Raso</li>
<li>Matti Picus</li>
<li>Melissa Weber Mendonça</li>
<li>Miles Cranmer</li>
<li>Ralf Gommers</li>
<li>Rohit Goswami</li>
<li>Sayed Adel</li>
<li>Sebastian Berg</li>
</ul>
<h2>Pull requests merged</h2>
<p>A total of 18 pull requests were merged for this release.</p>
<ul>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22820">#22820</a>: BLD: add workaround in setup.py for newer setuptools</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22830">#22830</a>: BLD: CIRRUS_TAG redux</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22831">#22831</a>: DOC: fix a couple typos in 1.23 notes</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22832">#22832</a>: BUG: Fix refcounting errors found using pytest-leaks</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22834">#22834</a>: BUG, SIMD: Fix invalid value encountered in several ufuncs</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22837">#22837</a>: TST: ignore more np.distutils.log imports</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22839">#22839</a>: BUG: Do not use getdata() in np.ma.masked_invalid</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22847">#22847</a>: BUG: Ensure correct behavior for rows ending in delimiter in...</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22848">#22848</a>: BUG, SIMD: Fix the bitmask of the boolean comparison</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22857">#22857</a>: BLD: Help raspian arm + clang 13 about __builtin_mul_overflow</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22858">#22858</a>: API: Ensure a full mask is returned for masked_invalid</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22866">#22866</a>: BUG: Polynomials now copy properly (<a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22669">#22669</a>)</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22867">#22867</a>: BUG, SIMD: Fix memory overlap in ufunc comparison loops</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22868">#22868</a>: BUG: Fortify string casts against floating point warnings</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22875">#22875</a>: TST: Ignore nan-warnings in randomized out tests</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22883">#22883</a>: MAINT: restore npymath implementations needed for freebsd</li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22884">#22884</a>: BUG: Fix integer overflow in in1d for mixed integer dtypes <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22877">#22877</a></li>
<li><a href="https://github-redirect.dependabot.com/numpy/numpy/pull/22887">#22887</a>: BUG: Use whole file for encoding checks with <code>charset_normalizer</code>.</li>
</ul>
<h2>Checksums</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/numpy/numpy/commit/a28f4f2a472dc826d043abf4442ba258bbd6ade5"><code>a28f4f2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22888">#22888</a> from charris/prepare-1.24.1-release</li>
<li><a href="https://github.com/numpy/numpy/commit/f8fea39ad76e7a24895af6a59ddd5fbdee466eb3"><code>f8fea39</code></a> REL: Prepare for the NumPY 1.24.1 release.</li>
<li><a href="https://github.com/numpy/numpy/commit/6f491e08e8fa84d939f91f1404ea4cc8ccbf9bc1"><code>6f491e0</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22887">#22887</a> from charris/backport-22872</li>
<li><a href="https://github.com/numpy/numpy/commit/48f5fe454fedeea0128857909f2d2fe4aec3d5df"><code>48f5fe4</code></a> BUG: Use whole file for encoding checks with <code>charset_normalizer</code> [f2py] (<a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22">#22</a>...</li>
<li><a href="https://github.com/numpy/numpy/commit/0f3484ac2e4e2113ad33a29372538e48ac78e184"><code>0f3484a</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22883">#22883</a> from charris/backport-22882</li>
<li><a href="https://github.com/numpy/numpy/commit/002c60d1a667357ffdfe35290b1595cc18d5ee4f"><code>002c60d</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22884">#22884</a> from charris/backport-22878</li>
<li><a href="https://github.com/numpy/numpy/commit/38ef9ce08e1cd4e562fbb4578911a1df55e05687"><code>38ef9ce</code></a> BUG: Fix integer overflow in in1d for mixed integer dtypes <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22877">#22877</a> (<a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22878">#22878</a>)</li>
<li><a href="https://github.com/numpy/numpy/commit/bb00c689afb052b0556f06bf8e55f79c99901cde"><code>bb00c68</code></a> MAINT: restore npymath implementations needed for freebsd</li>
<li><a href="https://github.com/numpy/numpy/commit/64e09c34237a837975cf42e074d3bb55dc955146"><code>64e09c3</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/numpy/numpy/issues/22875">#22875</a> from charris/backport-22869</li>
<li><a href="https://github.com/numpy/numpy/commit/dc7bac6b42b7c695e6d0ef7fdbc534e3f98a90b9"><code>dc7bac6</code></a> TST: Ignore nan-warnings in randomized out tests</li>
<li>Additional commits viewable in <a href="https://github.com/numpy/numpy/compare/v1.23.2...v1.24.1">compare view</a></li>
</ul>
</details>
<br />
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You can trigger Dependabot actions by commenting on this PR:
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Bump plotly from 5.11.0 to 5.13.0
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[
"\n[](https://coveralls.io/builds/56500771)\n\nCoverage: 78.166% (-1.2%) from 79.414% when pulling **cd5ee81dbcb71b99d10f0684223c43c1f4c9d8a6 on dependabot/pip/plotly-5.13.0** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-02-01T12:06:55
| 2023-02-03T17:48:07
|
2023-02-03T17:47:51Z
|
CONTRIBUTOR
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.13.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.13.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>v5.12.0</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
<li><code>marker.angle</code> attribute now accepts iterables where appropriate [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4013">#4013</a>]</li>
<li><code>selector=0</code> now correctly returns the first trace in <code>.select_traces()</code> and related methods [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3817">#3817</a>]</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.13.0] - 2023-01-23</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>[5.12.0] - 2023-01-12</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://github-redirect.dependabot.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
<li><code>marker.angle</code> attribute now accepts iterables where appropriate [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4013">#4013</a>]</li>
<li><code>selector=0</code> now correctly returns the first trace in <code>.select_traces()</code> and related methods [<a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3817">#3817</a>]</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/502f22005dcfbe7f12aae097a1e3dd9cddd4ae9d"><code>502f220</code></a> version changes for v5.13.0</li>
<li><a href="https://github.com/plotly/plotly.py/commit/97ad010f665c39b6ecba4c8bb2ccbc46ee65f2b0"><code>97ad010</code></a> Merge branch 'doc-prod'</li>
<li><a href="https://github.com/plotly/plotly.py/commit/f13d299249be2fed59f97995b4ddc79868aaaacb"><code>f13d299</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4036">#4036</a> from plotly/fix_cell_number</li>
<li><a href="https://github.com/plotly/plotly.py/commit/b3366376cc9012edb7d86486c63a3a5e129f5635"><code>b336637</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3804">#3804</a> from lyenliang/patch-1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/473318fd755dd2ea7b28e0503f38fd6b656abfcf"><code>473318f</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3944">#3944</a> from quinten-goens/patch-1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/bb77a280953a9ee8c24c6ea8b5c00f23fa3cc570"><code>bb77a28</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3921">#3921</a> from A1fus/patch-1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/3837f119fcf8f2c1c43d6a3e1937500ca706ba01"><code>3837f11</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/4016">#4016</a> from Engrr-Muneeb/patch-2</li>
<li><a href="https://github.com/plotly/plotly.py/commit/09928f1f28d752174c63e547541f962bd745eae8"><code>09928f1</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3972">#3972</a> from nelson123-lab/patch-1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/e7400ef3a1f2f198863198c3d37a74d57944b720"><code>e7400ef</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3973">#3973</a> from Kerybas/patch-1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/db6746ee4d25819ed983a0ff4ef1194c62640174"><code>db6746e</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/plotly/plotly.py/issues/3962">#3962</a> from plotly/dumbbell-updates-2</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.13.0">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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- `@dependabot reopen` will reopen this PR if it is closed
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- `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself)
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PR_kwDOACgets5JAJRk
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Bump cython from 0.29.32 to 0.29.33
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"\n[](https://coveralls.io/builds/56500819)\n\nCoverage: 78.21% (-1.2%) from 79.414% when pulling **52f5fb57f138d105a7c71bc4013ec02dd0bedad2 on dependabot/pip/cython-0.29.33** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-02-01T12:07:06
| 2023-02-03T17:48:07
|
2023-02-03T17:47:52Z
|
CONTRIBUTOR
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Bumps [cython](https://github.com/cython/cython) from 0.29.32 to 0.29.33.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/cython/cython/blob/master/CHANGES.rst">cython's changelog</a>.</em></p>
<blockquote>
<h1>0.29.33 (2023-01-06)</h1>
<h2>Features added</h2>
<ul>
<li>The <code>cythonize</code> and <code>cython</code> commands have a new option <code>-M</code> / <code>--depfile</code>
to generate <code>.dep</code> dependency files for the compilation unit. This can be used
by external build tools to track these dependencies.
The <code>cythonize</code> option was already available in Cython :ref:<code>0.29.27</code>.
Patches by Evgeni Burovski and Eli Schwartz. (Github issue :issue:<code>1214</code>)</li>
</ul>
<h2>Bugs fixed</h2>
<ul>
<li>
<p><code>const</code> fused types could not be used with memory views.
Patch by Thomas Vincent. (Github issue :issue:<code>1772</code>)</p>
</li>
<li>
<p><code>wstr</code> usage was removed in Python 3.12 and later (PEP-623).
(Github issue :issue:<code>5145</code>)</p>
</li>
<li>
<p>A type check assertion for Cython functions failed in debug Python builds.
(Github issue :issue:<code>5031</code>)</p>
</li>
<li>
<p>Fixed various compiler warnings.
Patches by Lisandro Dalcin et al. (Github issues :issue:<code>4948</code>, :issue:<code>5086</code>)</p>
</li>
<li>
<p>Fixed error when calculating complex powers of negative numbers.
(Github issue :issue:<code>5014</code>)</p>
</li>
<li>
<p>Corrected a small mis-formatting of exception messages on Python 2.
(Github issue :issue:<code>5018</code>)</p>
</li>
<li>
<p>The <code>PyUnicode_AsUTF8AndSize()</code> C-API function was missing from the CPython declarations.
(Github issue :issue:<code>5163</code>)</p>
</li>
<li>
<p>A performance problem in the compiler was resolved when nesting conditional expressions.
(Github issue :issue:<code>5197</code>)</p>
</li>
<li>
<p>Test suite problems with recent NumPy and CPython versions were resolved.
(Github issues :issue:<code>5183</code>, :issue:<code>5190</code>)</p>
</li>
</ul>
<h2>Other changes</h2>
<ul>
<li>The undocumented, untested and apparently useless syntax
<code>from somemodule cimport class/struct/union somename</code> was deprecated
in anticipation of its removal in Cython 3. The type
modifier is not needed here and a plain <code>cimport</code> of the name will do.
(Github issue :issue:<code>4905</code>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/cython/cython/commit/d675bf287ba2b60c362a1fac80f8338565756675"><code>d675bf2</code></a> Prepare release of 0.29.33.</li>
<li><a href="https://github.com/cython/cython/commit/c21b39d498d9b078abf3704dd71d957ee9b6a8f7"><code>c21b39d</code></a> Update changelog.</li>
<li><a href="https://github.com/cython/cython/commit/cf19b86385cf9aee013ffc70443b8f40952708df"><code>cf19b86</code></a> Avoid exponential recursion when coercing nested conditional expressions.</li>
<li><a href="https://github.com/cython/cython/commit/2cff1bfc9151f770196b33c5ae0a27a1445110f4"><code>2cff1bf</code></a> Update tox.ini a little and include it in sdist.</li>
<li><a href="https://github.com/cython/cython/commit/78bb64051f57944dcec839899b3cecd311113050"><code>78bb640</code></a> Update changelog.</li>
<li><a href="https://github.com/cython/cython/commit/08e44780f027ce2d8306557d73a5c07b4dea66a6"><code>08e4478</code></a> Add support of const fused type memory views (<a href="https://github-redirect.dependabot.com/cython/cython/issues/3118">GH-3118</a>) (<a href="https://github-redirect.dependabot.com/cython/cython/issues/5076">GH-5076</a>)</li>
<li><a href="https://github.com/cython/cython/commit/60fe73184a855b5a0bcd3a1cf6c2b3993e2bafee"><code>60fe731</code></a> [0.29.x] Avoid using asyncio.get_event_loop (<a href="https://github-redirect.dependabot.com/cython/cython/issues/5188">GH-5188</a>)</li>
<li><a href="https://github.com/cython/cython/commit/c99616ac78fba3eae59647d2ead79d20cedb7603"><code>c99616a</code></a> numpy.int -> numpy.int_ (<a href="https://github-redirect.dependabot.com/cython/cython/issues/5190">#5190</a>)</li>
<li><a href="https://github.com/cython/cython/commit/3b1597ce99b9534bccc644c3bdf4fa2b54267e92"><code>3b1597c</code></a> Add PyUnicode_AsUTF8AndSize to cpython imports [0.29.x] (<a href="https://github-redirect.dependabot.com/cython/cython/issues/5164">#5164</a>)</li>
<li><a href="https://github.com/cython/cython/commit/011c19875b68ea79c583b6d6c238694777cddd0c"><code>011c198</code></a> Add 'cpow' as a forward compatibility to 0.29.x (<a href="https://github-redirect.dependabot.com/cython/cython/issues/5060">GH-5060</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/cython/cython/compare/0.29.32...0.29.33">compare view</a></li>
</ul>
</details>
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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Bump matplotlib from 3.5.2 to 3.6.3
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[
"\n[](https://coveralls.io/builds/56501163)\n\nCoverage: 78.166% (-1.2%) from 79.414% when pulling **2740e02eb72864269ac5ff2c5786cc8061434ead on dependabot/pip/matplotlib-3.6.3** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n",
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] | 2023-02-01T12:07:16
| 2023-02-03T17:48:07
|
2023-02-03T17:47:53Z
|
CONTRIBUTOR
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Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.5.2 to 3.6.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<h2>REL: v3.6.3</h2>
<p>This is the third bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Fix Artist removal from <code>axes_grid1</code> Axes classes</li>
<li>Fix <code>inset_locator</code> in subfigures</li>
<li>Fix <code>scatter</code> on masked arrays with units</li>
<li>Fix colorbar ticks with log norm contours</li>
<li>Fix deprecation warnings in GTK4 backend</li>
<li>Fix using relative paths in <code>HTMLWriter</code></li>
<li>Improve failure message from rcParams string validation for tuple inputs</li>
<li>Improve performance of QtAgg backends</li>
<li>No longer modify <code>pil_kwargs</code> argument to <code>imsave</code> and <code>savefig</code></li>
</ul>
<h2>REL: v3.6.2</h2>
<p>This is the second bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Avoid mutating dictionaries passed to <code>subplots</code></li>
<li>Fix <code>bbox_inches='tight'</code> on a figure with constrained layout enabled</li>
<li>Fix auto-scaling of <code>ax.hist</code> density with <code>histtype='step'</code></li>
<li>Fix compatibility with PySide6 6.4</li>
<li>Fix evaluating colormaps on non-NumPy arrays</li>
<li>Fix key reporting in pick events</li>
<li>Fix thread check on PyPy 3.8</li>
<li>Handle input to <code>ax.bar</code> that is all NaN</li>
<li>Make rubber band more visible on Tk and Wx backends</li>
<li>Restore (and warn on) seaborn styles in <code>style.library</code></li>
<li>Restore <code>get_renderer</code> function in deprecated <code>tight_layout</code></li>
<li>nb/webagg: Fix resize handle on WebKit browsers (e.g., Safari)</li>
</ul>
<h2>REL: v3.6.1</h2>
<p>This is the first bugfix release of the 3.6.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>A warning is no longer raised when constrained layout explicitly
disabled and tight layout is applied</li>
<li>Add missing <code>get_cmap</code> method to <code>ColormapRegistry</code></li>
<li>Adding a colorbar on a <code>ScalarMappable</code> that is not attached to an
<code>Axes</code> is now deprecated instead of raising a hard error</li>
<li>Fix <code>barplot</code> being empty when first element is NaN</li>
<li>Fix <code>FigureManager.resize</code> on GTK4</li>
<li>Fix <code>fill_between</code> compatibility with NumPy 1.24 development version</li>
<li>Fix <code>hexbin</code> with empty arrays and log scaling</li>
<li>Fix <code>resize_event</code> deprecation warnings when creating figure on macOS</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/matplotlib/matplotlib/commit/c23ccdde6f0f8c071b09a88770e24452f2859e99"><code>c23ccdd</code></a> REL: v3.6.3</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/abcbf3d11524fa53b08243bc0aa85dd942439454"><code>abcbf3d</code></a> DOC: Update switcher versions</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/e45012855f26113068e22a535b68dbf32dddd0be"><code>e450128</code></a> DOC: Update GitHub stats for 3.6.3</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/86abc59886afc17be22764d57dafc75c7fae5b0a"><code>86abc59</code></a> Merge branch 'v3.6.2-doc' into v3.6.x</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/4f30cf4d6b68c6f0f22ffe2efd5395befb81857f"><code>4f30cf4</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24939">#24939</a> from meeseeksmachine/auto-backport-of-pr-23390-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/c8e25ef50eb8397dd5783e84f1216dc4be61fd63"><code>c8e25ef</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24936">#24936</a> from meeseeksmachine/auto-backport-of-pr-24927-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/88a15373ec4fead581dea278dda5907ac5c0bca1"><code>88a1537</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/23390">#23390</a>: FIX: colorbar contour with log norm should default to log...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/5348ee28733acd0a26b6649f384e1d27b88f0e15"><code>5348ee2</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24927">#24927</a>: DOC: Remove space after directive name, before double-colon</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/65044a2fe7dc7fc8ce5989c20ba7536afe817274"><code>65044a2</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24932">#24932</a> from dstansby/auto-backport-of-pr-24783-on-v3.6.x</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/5e2bf2cea0ecc3673c82808c871c292497249658"><code>5e2bf2c</code></a> Backport PR <a href="https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/24783">#24783</a>: inset locator fix with tests added</li>
<li>Additional commits viewable in <a href="https://github.com/matplotlib/matplotlib/compare/v3.5.2...v3.6.3">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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You can trigger Dependabot actions by commenting on this PR:
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Bump scipy from 1.9.0 to 1.10.0
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[
"\n[](https://coveralls.io/builds/56501371)\n\nCoverage: 78.166% (-1.2%) from 79.414% when pulling **48a18d43ca7ecc62739976f4b0c0a8988de7f18b on dependabot/pip/scipy-1.10.0** into **0a6633446c7ab505e85acf4e0760eccd721bd94d on master**.\n",
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-02-01T12:07:29
| 2023-02-03T17:48:07
|
2023-02-03T17:47:54Z
|
CONTRIBUTOR
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Bumps [scipy](https://github.com/scipy/scipy) from 1.9.0 to 1.10.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/scipy/scipy/releases">scipy's releases</a>.</em></p>
<blockquote>
<h1>SciPy 1.10.0 Release Notes</h1>
<p>SciPy <code>1.10.0</code> is the culmination of <code>6</code> months of hard work. It contains
many new features, numerous bug-fixes, improved test coverage and better
documentation. There have been a number of deprecations and API changes
in this release, which are documented below. All users are encouraged to
upgrade to this release, as there are a large number of bug-fixes and
optimizations. Before upgrading, we recommend that users check that
their own code does not use deprecated SciPy functionality (to do so,
run your code with <code>python -Wd</code> and check for <code>DeprecationWarning</code> s).
Our development attention will now shift to bug-fix releases on the
1.10.x branch, and on adding new features on the main branch.</p>
<p>This release requires Python <code>3.8+</code> and NumPy <code>1.19.5</code> or greater.</p>
<p>For running on PyPy, PyPy3 <code>6.0+</code> is required.</p>
<h1>Highlights of this release</h1>
<ul>
<li>A new dedicated datasets submodule (<code>scipy.datasets</code>) has been added, and is
now preferred over usage of <code>scipy.misc</code> for dataset retrieval.</li>
<li>A new <code>scipy.interpolate.make_smoothing_spline</code> function was added. This
function constructs a smoothing cubic spline from noisy data, using the
generalized cross-validation (GCV) criterion to find the tradeoff between
smoothness and proximity to data points.</li>
<li><code>scipy.stats</code> has three new distributions, two new hypothesis tests, three
new sample statistics, a class for greater control over calculations
involving covariance matrices, and many other enhancements.</li>
</ul>
<h1>New features</h1>
<h1><code>scipy.datasets</code> introduction</h1>
<ul>
<li>A new dedicated <code>datasets</code> submodule has been added. The submodules
is meant for datasets that are relevant to other SciPy submodules ands
content (tutorials, examples, tests), as well as contain a curated
set of datasets that are of wider interest. As of this release, all
the datasets from <code>scipy.misc</code> have been added to <code>scipy.datasets</code>
(and deprecated in <code>scipy.misc</code>).</li>
<li>The submodule is based on <a href="https://www.fatiando.org/pooch/latest/">Pooch</a>
(a new optional dependency for SciPy), a Python package to simplify fetching
data files. This move will, in a subsequent release, facilitate SciPy
to trim down the sdist/wheel sizes, by decoupling the data files and
moving them out of the SciPy repository, hosting them externally and</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/scipy/scipy/commit/dde50595862a4f9cede24b5d1c86935c30f1f88a"><code>dde5059</code></a> REL: 1.10.0 final [wheel build]</li>
<li><a href="https://github.com/scipy/scipy/commit/7856f281b016c585b82d03723c4494bcdbdcd4a5"><code>7856f28</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/scipy/scipy/issues/17696">#17696</a> from tylerjereddy/treddy_110_final_prep</li>
<li><a href="https://github.com/scipy/scipy/commit/205b6243c6d075d05695e7ac6d007e0f03bfbf42"><code>205b624</code></a> DOC: add missing author</li>
<li><a href="https://github.com/scipy/scipy/commit/1ab9f1b10145f0a974d5531700e72d1fb4229b76"><code>1ab9f1b</code></a> DOC: update 1.10.0 relnotes</li>
<li><a href="https://github.com/scipy/scipy/commit/ac2f45fbe1e39a8f52c1ea2e68764009f02973c0"><code>ac2f45f</code></a> MAINT: integrate._qmc_quad: mark as private with preceding underscore</li>
<li><a href="https://github.com/scipy/scipy/commit/3e0ae1a21f51ebee3a77733c42700d87a0c35d7d"><code>3e0ae1a</code></a> REV: integrate.qmc_quad: delay release to SciPy 1.11.0</li>
<li><a href="https://github.com/scipy/scipy/commit/34cdf05c86548de1c4ca1b2798cdc23885af807b"><code>34cdf05</code></a> MAINT: FFT pybind11 fixups</li>
<li><a href="https://github.com/scipy/scipy/commit/843500aabde17aaf1eec65c589d50bd12ee35039"><code>843500a</code></a> Merge pull request <a href="https://github-redirect.dependabot.com/scipy/scipy/issues/17689">#17689</a> from mdhaber/gh17686</li>
<li><a href="https://github.com/scipy/scipy/commit/089924b61012a106ffa4f58939b0180124051a0b"><code>089924b</code></a> REL: integrate.qmc_quad: remove from release notes</li>
<li><a href="https://github.com/scipy/scipy/commit/3e47110f10e3267d228e9da84174f3cee325e7c3"><code>3e47110</code></a> REL: 1.10.0rc3 unreleased</li>
<li>Additional commits viewable in <a href="https://github.com/scipy/scipy/compare/v1.9.0...v1.10.0">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
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