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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
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<h2>REL: v3.7.1</h2>
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<h3>Updated</h3>
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updates:
- [github.com/MarcoGorelli/cython-lint: v0.14.0 → v0.15.0](https://github.com/MarcoGorelli/cython-lint/compare/v0.14.0...v0.15.0)
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Replace calls to df.append() with pd.concat() and df.iteritems() with df.items(). | {
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"Could you zip the log file and load it as `test_files/molecules/EC.log.gz` using e.g. `monty`?",
"I have zipped `test_files/molecules/EC.log` to `test_files/molecules/EC.log.gz` and set the `zopen mode in GaussianOutput` to `\"rt\"` to load `.gz` file."
] | 2023-04-10T08:43:51 | 2023-04-27T14:49:13 | 2023-04-27T14:49:12Z | CONTRIBUTOR | {
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} | When route lines in gaussian output file like:
```plaintext
----------------------------------------------------------------------
# B3LYP/6-311++G(2d,p) EmpiricalDispersion=GD3BJ SCRF=(SMD,READ) freq
opt=(loose,maxcyc=400)
----------------------------------------------------------------------
```
If we... | {
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"AIRSS IO support was initially added by @ScottNotFound in https://github.com/materialsproject/pymatgen/pull/2625. Maybe he can briefly chime in if this an easy fix or would take some work.",
"This is easy to add to the parser, just need to add an extra field and relevant parsing. I can do a fix tomorrow. Is ther... | 2023-04-12T13:10:09 | 2023-04-19T00:30:42 | 2023-04-19T00:30:42Z | NONE | {
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} | When using the AIRSS code with spin-polarized DFT calculations, the resulting ShelX `.res` files contain spin values. However, `ResParser` is unable to read these `.res` files with spin values.
Error message:
```py
pymatgen.io.res.ParseError: Failed to parse ion entry Li 1 -0.0000000000000 0.2500000000000 0... | {
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"Thanks! 👍 ",
"Thanks for merging!"
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} | ## Summary
This fixes the issue that the Gaussian input file fails to read multiple lines.
- When the route input has multiple lines as below, GaussianInput.from_string() fails around the parsing of the route. This was due to inappropriate line counting when the route is separated in multiple lines.
- few lines o... | {
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"Wow, that was fast! Thanks a lot, @ScottNotFound! 🎉 "
] | 2023-04-18T15:33:25 | 2023-04-19T00:30:41 | 2023-04-19T00:30:41Z | CONTRIBUTOR | {
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- Fix #2938
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"Thanks @mueslo. For future reference, could you add a failing example as JSON or CIF to the PR description using `<details>`?\r\n\r\n```md\r\n<details><summary>example</summary>\r\n<p>\r\n\r\nhi there!\r\n\r\n</p>\r\n</details> \r\n```",
"@janosh I added some details and a minimal working example. Could you plea... | 2023-04-18T17:52:01 | 2023-05-07T01:26:13 | 2023-05-07T01:26:13Z | CONTRIBUTOR | {
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- Fix duplicate point group operations returned in `SpacegroupAnalyzer.get_point_group_operations`
Retains original ordering, i.e. identity operation E always stays first.
Background: `get_point_group_operations` ultimately uses `spglib.get_symmetry`. However, this only returns unique tuples of (rot... | {
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"@rkingsbury Could you take a look? Not familiar with the `PourbaixDiagram` myself.\r\n\r\n@johanzhuohan Please post code snippets in the future. They are much more usable than screenshots.",
"Sure! I was not quite sure how to insert the code, but I will do that next time!",
"Hi @johanzhuohan , thanks for repor... | 2023-04-18T21:59:12 | 2023-06-09T05:48:13 | 2023-06-09T05:48:13Z | NONE | {
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} | **Describe the bug**
[Related matsci post](https://matsci.org/t/47247)
The Pourbaix diagram sometimes includes the multientry with a different composition than the one initially used to generate the pourbaix diagram. This only occurs for some initial compositions. What could be the reason for this?
Also, in the ... | {
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"Thanks for the detailed explanation! Sounds to me like this change makes sense. Not a surface guy myself so an important question before we change this behavior is if you could imagine this breaking any existing code? I.e. are there use cases where returning an equivalent but different set of indices might affect ... | 2023-04-19T13:29:42 | 2023-04-20T14:28:15 | 2023-04-20T14:28:15Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
I recently noticed that when generating symmetrically distinct Miller indices using the `get_symmetrically_miller_indices()` of `pymatgen.core.surface`, some of the Miller indices that appear when `max_index=2` weren't there for `max_index=3`. My expec... | {
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"Thanks @espottesmith! Could you briefly explain the major differences between `Trajectory` and `MoleculeOptimizeTrajectory`? I understand latter is meant to handle `Molecule`s but I'm curious what is preventing an object agnostic `Trajectory` class that handles both `Structure`s and Mols?\r\n\r\nAlso, are you anti... | 2023-04-19T14:48:14 | 2023-04-25T17:46:54 | 2023-04-25T17:46:54Z | CONTRIBUTOR | {
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We are nearing the inclusion of a large dataset of molecules and molecular properties to the Materials Project. This PR adds some features to pymatgen which will be useful for the molecules data pipeline in emmet, namely graph hashes and a Trajectory class that works for Molecules.
The graph hashing co... | {
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"Duplicate of #2900. As a temporary workaround, try the `get_plotly()` method instead.",
"I see - using get_plotly worked! Thank you!"
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I've been struggling with the WulffShape.show() function. I am using the exact code from the tutorial scripts from https://matgenb.materialsvirtuallab.org/2017/04/03/Slab-generation-and-Wulff-shape.html. While the script outputs information about the Wulff Construction such as the weighted surface energy and... | {
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} | The attached mCIF file downloaded straight from the Bilbao Crystallographic Server displays fine in Vesta and can be read by `CifParser` but fails in `Structure.from_file`
```py
from pymatgen.io.cif import CifParser
CifParser("./1.6_NiO.mcif") # works
Structure.from_file("./1.6_NiO.mcif") # fails
```
Er... | {
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"Nicely done and great comments! 👍 "
] | 2023-04-20T09:16:21 | 2023-04-20T14:28:55 | 2023-04-20T13:34:18Z | CONTRIBUTOR | {
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Fix: `conv_hkl_list` is now sorted with respect to the maximum of the absolute values of the individual Miller indices it contains, before it is iterated over, ensuring that the unique Miller indices returned contain the lowest indices possible. | {
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Since matplotlib does not allow us to set auto_add_to_figure=True in Axes3D anymore passed ver. 3.6.0, I had to add the ax object to the Figure in order for it to properly display. Should now be backward/forward compatible for all versions of matplotlib. | {
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"Pls provide a unit test to confirm the new functionality. Thanks. ",
"Hi @shyuep, @janosh, I have added a unit test in `test_files/vasp`. Not sure if I put the file in the right place though. Let me know if this follows the guildlines. Thanks!",
"@chiang-yuan Thanks! The test should go into [`pymatgen/io/vasp/... | 2023-04-24T01:40:33 | 2023-04-30T20:23:20 | 2023-04-30T20:23:19Z | CONTRIBUTOR | {
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```python
poscar = Poscar(
structure,
selective_dynamics=boolean_array
)
```
and the code would produce an error:
```
ValueError: The truth value of an array with more than one element is ambiguo... | {
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"@rkingsbury @shyuep I've been in that same situation and would also welcome such a change. Any reservations/things to be aware of from your side?",
"I have no reservations on enabling this. But there are two approaches to this. One is to create a ComputedEntry.from_settings factory method. This will make it expl... | 2023-04-24T23:23:57 | 2023-07-12T23:03:17 | 2023-07-12T23:03:17Z | NONE | {
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} | **Issue**: [MP2020Compatibility](https://github.com/materialsproject/pymatgen/blob/83a87bb5039414aeb68f25162b5c1403478028d8/pymatgen/entries/compatibility.py#L821-L1097) (and all other compatibility modules) currently requires a ComputedEntry object containing VASP settings and POTCAR information to operate. This makes... | {
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if ("UKS" or "UNRESTRICTED_KOHN_SHAM" or "LSD" or "SPIN_POLARIZED") in self.data["dft"].values():
return True
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`"UKS" or "UNRESTRICTED_KOHN_SHAM" or "LSD" or "SPIN_POLARIZED"` short-circuits to `"UKS"` and so won't return `True` even if `"UNRESTRICTED_KOHN_SHAM"` or `"LSD"` or `"SPIN_POLARIZE... | {
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} | 678627b72 remove unused type ignore
484d133be ruff auto doc str format
0ba2f868d drop B031 from ruff ignore
579ac1e3e rename single-letter and non-snake-case vars
2dee11169 self.assertArrayEqual -> assert | {
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"@yuuukuma You deleted the file `test_files/vasprun.xml.dfpt.ionic` which is causing a test to fail. Please restore it. Also, could you add/modify a test that for the new `cell_filter_kwargs`?"
] | 2023-04-29T01:26:01 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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} | ## Summary
Add cell_filter_kwargs to relax method that is passed to ExpCellFilter
This extension allows us to e.g. relax lattice constant along particular directions, e.g.,
```
structure.relax(cell_filter_kwargs={"mask": (1,1,0,0,0,1)}))
```
Then, the lattice is optimized only in xy-plane.
Because the change... | {
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"This seems more like a support question than an issue with `pymatgen`. Such questions are better asked on https://matsci.org/c/pymatgen or in GH discussion. I'll convert this to a discussion."
] | 2023-04-30T08:26:12 | 2023-05-01T00:40:57 | 2023-05-01T00:40:57Z | NONE | {
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} | My code works well
```python
import matplotlib.pyplot as plt
from pymatgen.electronic_structure.plotter import BSPlotter
from pymatgen.io.vasp import Vasprun
# Extract the band structure data from the vasprun.xml file
vasprun = Vasprun("Bulk_fcc_Si_bandstructure/vasprun.xml")
band_structure = vasprun.get_band... | {
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<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
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<h2>v2.12.3</h2>
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<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/astanin/python-tabulate/blob/master/CHANGELOG">tabulate's changelog</a>.</em></p>
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<li>0.9.0: Drop support for Python 2.7, 3.5, 3.6.
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<h2>v1.24.3</h2>
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"It's currently linked from the [intro page](https://pymatgen.org/introduction.html?highlight=addons) where I agree it has limited visibility. Happy to feature it more prominently if you have any ideas?",
"Ah, thanks. \r\n\r\nMaybe, we could link it here directly below or above \"Writing add-ons\": \r\n![image](h... | 2023-05-02T07:04:16 | 2023-05-02T15:07:19 | 2023-05-02T15:07:19Z | MEMBER | {
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@janosh , I am wondering where the addons page is actually linked in the current version of the documentation? I only found it via external search.
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"I don't really have any concerns. I think whether Yb_2 or Yb_3 depends on what you are calculating. VASP \"recommends\" Yb_2 as the PSP. See https://www.vasp.at/wiki/index.php/Available_PAW_potentials. This was probably the reason why we used that in the first place. For HT efforts, we have to select one. I am fin... | 2023-05-02T18:16:29 | 2023-05-05T00:18:57 | 2023-05-02T18:49:16Z | MEMBER | {
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} | [The docs](https://docs.materialsproject.org/methodology/mof-methodology/calculation-parameters/psuedopotentials) are incorrect on what pseudo-potential the `EntrySet`s use for `Yb`. Docs say `Yb_3`, actual is `Yb_2`. Just to list a few:
https://github.com/materialsproject/pymatgen/blob/a7ee5adf02e0ac8c0b9e150d10f63... | {
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"Should one mark this as a breaking change? It's a rather drastic change. ",
"Yes, this change will be highlighted in the next release notes. I'll also change the PR title to make this clearer.",
"I would suggest you document the change to Yb_3 in the input sets yaml themselves. E.g., `# May 2 2023: Changed to ... | 2023-05-02T18:24:12 | 2023-05-02T18:59:48 | 2023-05-02T18:49:15Z | MEMBER | {
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"I agree. I did not write this though. I think the switch to KSPACING is relatively recent."
] | 2023-05-04T00:57:49 | 2023-05-06T14:40:43 | 2023-05-06T14:40:43Z | MEMBER | {
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} | @shyuep I think there's a subtle operator precedence bug here:
https://github.com/materialsproject/pymatgen/blob/ed66c977d8c2c1168a9945d64f5d043d9263fc43/pymatgen/io/vasp/sets.py#L633-L638
`and` has higher precedence than `or` but unless I'm mistaken we actually want to evaluate the `or` first. The thing that thr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2971 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2971/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2971/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2971/events | https://github.com/materialsproject/pymatgen/issues/2971 | 1,695,045,496 | I_kwDOACgets5lCFd4 | 2,971 | `pytest.raises() as exc_info` has no `.exception` | {
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} | We're misusing `pytest.raises()` in at least 4 places in 2 files. 2 Examples below where it should be
```diff
- str(context.exception)
+ str(context.value)
```
https://github.com/materialsproject/pymatgen/blob/ed66c977d8c2c1168a9945d64f5d043d9263fc43/pymatgen/io/vasp/tests/test_sets.py#L505-L516
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"@jmmshn asked for a new release which I think we're ready for once this is merged."
] | 2023-05-04T01:11:33 | 2023-05-06T14:40:43 | 2023-05-06T14:40:42Z | MEMBER | {
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} | Follow up to #2969.
Instead of changing from `Yb_2` to `Yb_3` everywhere, we issue a warning in pre-`PBE_54` input sets that `Yb_2` will give very bad results for most systems since Yb is usually Yb3+.
Reason: The better fix `Yb_3` only became available in the `PBE_54` set of PSPs so using it in pre-`PBE_54` inpu... | {
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} | ## Summary
Both copy and deepcopy are currently broken for the `InputSet` object. This PR implements dunder methods to fix both. There very well may be a more elegant solution but I couldn't find it!
- Feature 1: `__copy__` and `__deepcopy__` dunder methods
## Checklist
- [x] Doc strings have been added in ... | {
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"I think you'll have to provide more information to get useful answers. I'm converting this to a discussion since this doesn't sound like a code issue."
] | 2023-05-06T11:37:06 | 2023-05-06T17:26:10 | 2023-05-06T17:26:10Z | NONE | {
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When I calculate a Si test by using a atomate workflow, the INCAR include MAGMOM label, and the second step calculation stop. How should I deal with this problem. | {
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525fc2667 fix `PLR5501`: collapsible-else-if | {
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"Yup it was removed because the server was far too fragile. Would be happy to have it back as an optional dependency."
] | 2023-05-08T13:20:13 | 2023-05-08T17:01:31 | MEMBER | {
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As shown here
https://gitlab.com/muellergroup/k-pointGridGenerator there is a way to generate these kpoi... | {
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2ad001e13 add ruff ISC (flake8-implicit-str-concat) | {
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16f6da354 drop custom `ArrayLike` fallback type, make `numpy.typing.ArrayLike` required | {
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"Great. Thanks! I have a small request. Can you provide a simple benchmark of the difference in speed (if any) between old and new version? This is a rather core part of the code. I would want to make sure that the efficiency is not compromised.",
"I've never written a test for `cython` code. @stichri Is there a ... | 2023-05-09T17:33:02 | 2023-05-10T14:20:48 | 2023-05-10T12:07:43Z | CONTRIBUTOR | {
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} | ## Summary
The `pbc_shortest_vectors` function leaks all memory allocated to store the fractional coordinates of surrounding periodic sites. As a result, memory consumption keeps creeping up when (heavily) calling the function, see [this memory profile](https://github.com/materialsproject/pymatgen/files/11433457/v20... | {
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"Totally forgot to tag @JaGeo :D ",
"Thanks for writing it down! I will work on a fix as soon as I get to it. I never use the average COHP/ICOHP. 😅 \r\n\r\n(@janosh , I am assigning myself)",
"Can be closed then, @janosh or @QuantumChemist ",
"@JaGeo Thanks. Btw, if you include \"closes #issue-number\" or \... | 2023-05-11T15:58:25 | 2023-05-12T14:40:25 | 2023-05-12T14:10:17Z | CONTRIBUTOR | {
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} | When trying to access the cohp and the icohp feature of CompleteCohp for a COHPCAR.lobster file, one gets the same output. In the following minimal code, the sum is 0 (and also the individual entries for each energy point is 0).
## Minimal code to reproduce the issue
cohp_test = CompleteCohp.from_file(filename="p... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2986 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2986/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2986/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2986/events | https://github.com/materialsproject/pymatgen/pull/2986 | 1,707,275,820 | PR_kwDOACgets5QXonC | 2,986 | Fix average error | {
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"Thanks!! @JaGeo 😃 "
] | 2023-05-12T09:22:35 | 2023-05-12T14:20:11 | 2023-05-12T13:40:45Z | MEMBER | {
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Closes https://github.com/materialsproject/pymatgen/issues/2985. There was a simple typo. As I usually never use the average cohp, it never even occurred to me to test it. I adapted all tests and included a test to now also test the average cohp.
I also gzipped some `COHPCARs` to start reducing test fi... | {
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8fded9b45 fix all `ruff`-detected doc string errors in `pymatgen/core` | {
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"Not an expert on this but maybe @jmmshn can comment.",
"That sounds like it would work. TBH I made this with defects in mind so the K-point problem was not super bad for me.\r\nI never actually used pymatgen's generated kpoints in calculations so it might work.\r\n\r\nAlthough one problem to be aware of is tha... | 2023-05-14T09:59:23 | 2023-07-11T21:25:16 | CONTRIBUTOR | {
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Firstly, thanks to the developers for the recent addition of the `pymatgen.io.vasp.optics` module, this is very very useful! 🙌
For large k-point meshes or large numbers of electronic bands, these functions can become slow on a desktop computer (e.g. taking ~7 minutes for a 8x8x8 kpoint mesh for a CdTe primitiv... | {
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"Thanks for the fix! 👍 This sounds sensible. We should definitely have tests for these functions."
] | 2023-05-14T10:39:43 | 2023-05-14T15:15:39 | 2023-05-14T15:15:39Z | CONTRIBUTOR | {
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Firstly, thanks to the developers for the recent addition of the `pymatgen.io.vasp.optics` module, it's been very very useful! 🙌
This is just a small fix for a suspected typo in handling `ismear` in the `delta_func()` and `step_func()` functions. `ISMEAR` is zero for Gaussian smearing, and indeed in the docstr... | {
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} | 1273014de ignore some `ruff` doc string errors and fix all remaining
a6dd53e72 `ruff` enable doc rules in pre-commit
c349a806c fix `mypy` error
dea2aa043 2nd try fix `mypy`
d3e4d2b57 prefix unused func args with underscore
f7b4a5006 `ruff` enable `flynt` rules | {
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"Welp, sorry @janosh. I thought this would be a trivial add. But I'm not sure how to make the `mypy` overlord happy with this...",
"`mypy` can be a pain. The problem you ran into is that untyped functions are not type-checked. As soon as you add types to a function, it can surface errors that were already lurking... | 2023-05-16T04:38:12 | 2023-05-16T14:22:18 | 2023-05-16T14:16:46Z | MEMBER | {
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"Ci failure is due to flaky test:\r\n\r\n```py\r\n @unittest.skipIf(\r\n not SETTINGS.get(\"PMG_MAPI_KEY\") or website_down,\r\n \"PMG_MAPI_KEY environment variable not set or MP is down.\",\r\n )\r\n def test_get_snls_mp(self):\r\n with OptimadeRester(\"mp\") as optimade:\r\n ... | 2023-05-16T14:52:41 | 2023-05-23T15:46:00 | 2023-05-16T15:40:24Z | MEMBER | {
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} | 4 main motivations for this change:
1. reduces chance of circular imports
2. can help contributors run tests without installing extra deps like `pymatgen.analysis.defects` if they were previously in a test's import stack but only used for type hints
3. helps with readability by clearly separating type-only imports... | {
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"@JaGeo We're trying to move away from type hint comments:\r\n\r\n```diff\r\n- list_orb_icohp = [] # type: List[dict]\r\n+ list_orb_icohp: list[dict] = []\r\n```",
"Thanks! Will change this!",
"Locally, mypy is finally passing... ",
"Seems like most of the tests are passing now. macos tests haven't started ye... | 2023-05-16T21:23:26 | 2023-05-17T08:23:17 | 2023-05-17T04:59:33Z | MEMBER | {
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@janosh, I have added support for orbital-resolved icohplists and included tests.
(@naik-aakash , FYI. I think it should be very useful for some of our currenct projects) | {
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"I'm in favor of this! If someone is going to try this, I would also suggest doing some light reorganization of the test files so that it's clearer which ones go with which parts of the code. \r\n\r\nFor example, move a lot of the test files in the root directory that are associated with VASP IO into a `vasp/` subd... | 2023-05-17T16:40:04 | 2024-03-18T09:41:32 | MEMBER | {
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502158daa re-export `DummySpecie` + `SiteCollection` from `pymatgen.core` | {
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from pymatgen.core import Species
Species("O2-")
>>> ValueError: 'O2-' is not a valid Element
``` | {
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```py
Species("O-").oxi_state
>>> -1
Species("Fe2+").oxi_state
>>> 2
``` | {
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"Why was `ElementBase` created to start with, presumably for good reason? I vaguely remember this, can try and find the PR. ",
"Here's the PR: https://github.com/materialsproject/pymatgen/pull/2005 by @jmmshn.\r\n\r\nIt also lists subclasses as the reason for creating `ElementBase`.",
"I see the mention for API... | 2023-05-18T00:51:03 | 2023-05-18T15:39:30 | 2023-05-18T15:39:30Z | MEMBER | {
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"Minimal example\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nFeO = Structure(\r\n lattice=Lattice.cubic(5),\r\n species=(\"Fe\", \"O\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\n\r\nstructure.to(\"FeO.json.gz\")\r\nstructure.to(\"FeO.json.bz2\")\r\n```",
"@ml-evs Could you... | 2023-05-20T15:20:42 | 2023-05-20T17:16:26 | 2023-05-20T16:01:43Z | MEMBER | {
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} | ffae4ea4e support writing structures to compressed JSON files
ba9918395 check structure equality writing and reading from .json.gz .json.bz2 .json.xz .json.lzma
Related: #2994 helps with reducing test file sizes | {
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"For the new Rester, reading the API key from `.pmgrc.yaml` or env variable required passing no args, i.e.\r\n\r\n```diff\r\n- MPRester(None)\r\n+ MPRester()\r\n```\r\n\r\nThanks for making the upper case work as well @ml-evs!"
] | 2023-05-21T14:56:19 | 2023-05-22T10:50:47 | 2023-05-21T22:42:26Z | CONTRIBUTOR | {
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Both the new and legacy versions of `MPRester` accepted `api_key=None` to be passed as an argument, triggering a fallback to the settings version of the key. The new behavior of the dynamic `MPRester` is to attempt to use the `None` value directly, i.e., without checking for an externally configured value... | {
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f9edf06a1 skip StructureTest.test_relax() if tensorflow missing
0948d7062 MoleculeGraph.find_rings() only sort cycle once
ba2d98c69 drop -x (exit on error) from pytest addopts
b48009e2a rerun pytest --store-durations --durations-path test_files/.pytest-split-d... | {
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"@mkhorton, @guymoore13 have you guys seen this error before, and know a potential solution?",
"First thing I would check is your `spglib` version. What version are you running? This recently saw a 2.0 release and had a few bugs which were fixed with the latest version. ",
"I'm using spglib 2.0.2",
"For addit... | 2023-05-23T00:27:18 | 2023-06-13T22:53:23 | NONE | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3007 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3007/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3007/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3007/events | https://github.com/materialsproject/pymatgen/pull/3007 | 1,721,199,435 | PR_kwDOACgets5RGZI8 | 3,007 | Bump requests from 2.28.1 to 2.31.0 | {
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"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... | 2023-05-23T05:15:49 | 2023-05-23T17:43:23 | 2023-05-23T17:43:12Z | CONTRIBUTOR | {
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<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/psf/requests/releases">requests's releases</a>.</em></p>
<blockquote>
<h2>v2.31.0</h2>
<h2>2.31.0 (2023-05-22)</h2>
<p><strong>Security</strong></p>
<ul>
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"Hey @SelfMade2001, the purpose of selective dynamics is to enable only certain degrees of freedom during relaxations. If you enable selective dynamics, but allow all degrees of freedom to relax, as in your first example, then selective dynamics is not used. That's why pymatgen ignores it\r\n\r\nIf that's unclear, ... | 2023-05-23T15:16:00 | 2024-02-13T08:20:08 | 2024-02-13T08:20:08Z | NONE | {
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Here is some test file called P... | {
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} | 742f4616e simplify: `structure.sites` -> `structure`
9eb253cd5 `ruff` unignore `SIM115`, fix `pymatgen/io/qchem/tests/test_inputs.py`
04e4fd6ee `ruff` unignore `RET501` and fix unnecessary `return None`
46ed47125 `ruff` unignore and fix `PLW3301`
6e74192ac `ruff` unignore `PLW0603` and fix use of `globals`
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"Thanks for reporting! Minimal code to trigger the error:\r\n\r\n```py\r\nimport numpy as np\r\n\r\nfrom pymatgen.core import Lattice, Structure\r\nfrom pymatgen.io.ase import AseAtomsAdaptor\r\n\r\nstructure = Structure(\r\n lattice=Lattice.cubic(5),\r\n species=(\"Fe\", \"O\"),\r\n coords=((0, 0, 0), (0.... | 2023-05-24T00:45:42 | 2023-05-24T17:32:22 | 2023-05-24T17:32:22Z | CONTRIBUTOR | {
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} | **Describe the bug**
`AseAtomsAdaptor.get_atoms(structure, **kwargs)` checks numpy boolean array against python nested list. This is a bug similar to my previous PR (#2951).
https://github.com/materialsproject/pymatgen/blob/233070151070c0d839ebb23d93afc6f17540e760/pymatgen/io/ase.py#L107-L111
The `ValueError:... | {
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} | Closes #3011.
71e888dd9 refactor LammpsData.get_string()
a1d3509b6 refactor ase import, AseAtomsAdaptor.get_atoms() check is_struct
a21543c71 fix ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() when structure.selective_dynamics has type np.array
bf56232b... | {
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"[One thing left to do](https://github.com/materialsproject/pymatgen/pull/3014/files#diff-e9cfd9b89de7ff172f8b6e26e92bb559f6f61ae34d0ee3c08c8b06954e1f69c1R65):\r\n\r\n```\r\n# TODO (janosh): replace assert_array_almost_equal decimal kwarg with assert_allclose() atol and rtol kwargs\r\n```\r\n\r\n"
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} | Drop unused `PymatgenTest` methods, rename existing ones from camel to snake case and replace `assert_almost_equal` with `assert_allclose` as recommended by numpy docs.
8ad0792d4 breaking: drop internally unused PymatgenTest.get_mp_structure()
868179215 breaking: drop internally unused PymatgenTest.assertDictsAl... | {
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"@lbluque NICE! Very useful for all structure manipulations! Merging as teh lint errors are unrelated to PR.",
"@stichri Since you did a great job on https://github.com/materialsproject/pymatgen/pull/2983 checking for memory leaks, would be hugely appreciated if you have the time to take these changes for a spin ... | 2023-05-25T19:15:25 | 2023-05-26T19:29:33 | 2023-05-25T20:17:38Z | CONTRIBUTOR | {
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} | ## Summary
Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.
For example here are the runtimes for searching for all neighbors within a 5A cutoff in a 32 atom FCC (on my laptop with Intel i7 (2.8 GHz) CPU):
- version 2023.5.10: `955 µs ± 35.4 µs per loop (mean ± std. dev. of 7 runs, ... | {
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"Yes, this is definitely true. I fixed it within the LobsterSet by replacing the standard value. \r\n\r\nSee https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/vasp/sets.py#L2789",
"I'm open to changing to `W_sv`. It would need adequate highlighting in the chang... | 2023-05-26T05:35:46 | 2023-06-01T00:41:02 | 2023-06-01T00:41:02Z | CONTRIBUTOR | {
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} | **Describe the bug**
When creating an input set using the PBE_54 POTCAR setting, the code looks for the non-existent W_pv POTCAR. [This has been replaced by W_sv in the 5.4 version.](https://www.vasp.at/wiki/index.php/Available_PAW_potentials#Recommended_potentials_for_DFT_calculations)
**To Reproduce**
1. Establi... | {
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d86e0b0f8 MaterialsProjectCompatibility issue silencable deprecation warning
e7a644539 SymmetrizedStructure type hints | {
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from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pymatgen.core import Lattice, Structure
structure = Structure(
lattice=Lattice.cubic(3),
species=("Fe", "Fe"),
coords=((0, 0, 0), (0.5, 0.5, 0.5)),
)
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7d3eba415 drop .values where not needed, else replace with .to_numpy(), noqa false positives
`pandas.DataFrame().values` is deprecated and slated for removal in a future `pandas` version. | {
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"Closing with reasoning in https://github.com/materialsproject/pymatgen/issues/2107#issuecomment-1569239404."
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"Pinging @JaGeo and @arosen93 for review.",
"Actually, the PR title is inaccurate. There are input sets that don't have any restrictions on `user_potcar_settings` which I didn't touch. So far, I only changed the input sets that ensure `user_potcar_functional in (\"PBE_52\", \"PBE_54\")`. So would make sense to mo... | 2023-05-30T21:12:53 | 2023-06-01T03:16:37 | 2023-06-01T00:41:01Z | MEMBER | {
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Breaking: `DictSet` drop deprecated kwarg `potcar_functional: str = None`, use `user_potcar_functional: str = None` instead (in ac51e26) | {
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"Makes sense to me @arosen93 . I didn't know much about the robustness of bandgap detection when I wrote this."
] | 2023-05-31T05:16:00 | 2023-06-02T15:04:31 | 2023-06-02T15:04:31Z | MEMBER | {
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This checks if `bandgap` is strictly equal to zero, but there are likely going to be edge cases where `bandgap` is some very small value (say, 1e-6 eV) that should also be flagged as metallic... | {
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"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... | 2023-06-01T12:57:29 | 2023-06-01T14:06:54 | 2023-06-01T14:06:43Z | CONTRIBUTOR | {
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<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/jiffyclub/palettable/blob/master/CHANGELOG.rst">palettable's changelog</a>.</em></p>
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<h2>Version 3.3.2</h2>
<ul>
<li>Set <code>python_requi... | {
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<details>
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<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
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https://api.github.com/repos/materialsproject/pymatgen/issues/3026 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3026/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3026/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3026/events | https://github.com/materialsproject/pymatgen/pull/3026 | 1,736,273,878 | PR_kwDOACgets5R5kQg | 3,026 | Bump monty from 2022.9.9 to 2023.5.8 | {
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} | Remove superfluous structure argument docstring from `SQSTransformation` init
Ensure:
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] All tests and linting pass.
Tip: Install `pre-commit` hooks to a... | {
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"Thanks!"
] | 2023-06-01T18:04:49 | 2023-06-02T01:23:49 | 2023-06-01T19:01:40Z | CONTRIBUTOR | {
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} | This is a quick fix to allow direct initialisation of the `DictSet` class, which was possible before but broke in https://github.com/materialsproject/pymatgen/pull/2972 due to the `Yb_2` check querying `self.CONFIG`, which is only defined if `DictSet` was being initialised from a subclass and not directly.
This fix... | {
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"@janosh I think this is good to go. \r\n\r\nThe tests for `PDPlotter` have always been somewhat minimal (just checking if the functions can run); let me know if you think more is needed here.",
"@mattmcdermott Nice work! This looks like a huge improvement! Thanks for all the screenshots to showcase. You probably... | 2023-06-02T00:14:51 | 2023-06-05T17:47:35 | 2023-06-03T00:55:12Z | MEMBER | {
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} | ## Summary
The `PDPlotter` class has been overdue for updates for quite some time. This PR adds missing functionality that has been living in the MP Phase Diagram app. I have also addressed some issues / requested features.
- Feature: unary (1 component) plots. Code adapted from @mkhorton.
- Feature: 2D ternary ... | {
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"Can you post the `Structure.to(\"gh-3033.json\")`? This works for me on current `master`\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nstructure = Structure(\r\n lattice=Lattice.cubic(3),\r\n species=(\"Fe\", \"Fe\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\nstructure.species... | 2023-06-02T00:40:07 | 2023-06-06T00:42:37 | 2023-06-06T00:42:37Z | CONTRIBUTOR | {
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```
print(struct.species)
```
yields the error
```
File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/structure.py:248 in <listcomp>
return [site.specie for site in self]
File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/sites.py:75 in __getattr__
... | {
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"Similar to #3033, it works for me:\r\n\r\n```py\r\nfrom mp_api.client import MPRester\r\n\r\nwith MPRester() as mpr:\r\n struct = mpr.get_structure_by_material_id(\"mp-1153\", conventional_unit_cell=True)\r\n\r\nprint(struct.species)\r\n>>> [Element Li, Element Li, Element Li, Element Li, Element Li, Element Li... | 2023-06-02T00:53:58 | 2023-06-02T01:58:30 | 2023-06-02T01:58:29Z | CONTRIBUTOR | {
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```
from mp_api.client import MPRester
api_key = "*****"
with MPRester(api_key) as mpr:
struct = mpr.get_structure_by_material_id('mp-1153',
conventional_unit_cell=True)
print(struct.species)
```
yields the error
```
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"Agreed."
] | 2023-06-02T01:23:19 | 2023-06-03T03:11:04 | 2023-06-03T01:11:44Z | MEMBER | {
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"Thanks for adding those unit tests! Greatly appreciated!! "
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"The odd thing is, I just ran this test locally and it passes.\r\n\r\n```sh\r\npytest pymatgen/ext/tests/test_matproj.py -k test_pourbaix_mpr_pipeline\r\n```",
"Hi @janosh , I'm not sure what's happening here, but in general yes, changes to the database or API pipeline could potentially trigger test failures here... | 2023-06-03T17:30:02 | 2023-09-05T21:47:52 | 2023-09-05T21:47:52Z | MEMBER | {
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} | @rkingsbury `test_pourbaix_mpr_pipeline` has [started failing recently](https://github.com/materialsproject/pymatgen/actions/runs/5161568900/jobs/9298662810#step:7:31). Based on the call to Rester and the larger than expected number of `stable_entries`, is this because of new data in MP? If so, could we refactor this t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3040 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3040/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3040/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3040/events | https://github.com/materialsproject/pymatgen/issues/3040 | 1,740,053,621 | I_kwDOACgets5ntxx1 | 3,040 | `LMAXMIX` should be set based on the presence of s, p, d, f electrons not based on Z | {
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} | Currently, `LMAXMIX` is set as follows:
https://github.com/materialsproject/pymatgen/blob/67ba063073b468cb33b93f2dc3841fd6ae3941d5/pymatgen/io/vasp/sets.py#L529-L543
However, this is based on Z value and not based on the presence or lack of s, p, d, or f electrons (see [VASP manual](https://www.vasp.at/wiki/index... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/3041 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/3041/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/3041/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/3041/events | https://github.com/materialsproject/pymatgen/pull/3041 | 1,740,450,007 | PR_kwDOACgets5SH9Jb | 3,041 | Fix LMAXMIX default in VASP INCAR now set based on element blocks in structure | {
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"I don't have a unit test for this one yet. We can copy it from the Atomate2 PR once I add it there. I have a unit test in my [Quacc code](https://github.com/Quantum-Accelerators/quacc/blob/3e2e6c2281c214ada86fcba44d43750017844a2a/tests/calculators/vasp/test_vasp.py#L63-L75), but it's not quite the same.",
"@aros... | 2023-06-04T15:59:32 | 2023-07-27T18:26:57 | 2023-06-04T18:12:33Z | MEMBER | {
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} | Closes #3040.
@arosen93 Do you have a good test case for this by any chance? | {
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