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https://api.github.com/repos/materialsproject/pymatgen/issues/1601 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1601/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1601/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1601/events | https://github.com/materialsproject/pymatgen/pull/1601 | 497,848,103 | MDExOlB1bGxSZXF1ZXN0MzIwOTAwNTc2 | 1,601 | Bump pylint from 2.3.1 to 2.4.0 | {
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<summary>Changelog</summary>
*Sourced from [pylint's changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog).*
> What's New in Pylint 2.4.0?
> ===========================
>
> Release date: 2019-09-24
>
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"If you are using the Matsci channel, try changing to conda-forge. We are deprecating the matsci channel. That should be the latest version. ",
"Yes, I was using the \"matsci\" channel. Good to know about it being deprecated, I'll advise people to avoid it",
"Thanks. I have also updated all docs to note that t... | 2019-09-24T18:52:35 | 2019-09-24T20:30:37 | 2019-09-24T18:58:20Z | CONTRIBUTOR | {
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} | **Is your feature request related to a problem? Please describe.**
Yes, the current version of matminer requires a version of pymatgen that is newer than the one on Anaconda. Without the Anaconda version, installing matminer becomes pretty tricky for Windows users.
**Describe the solution you'd like**
Updating th... | {
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Added an optional input of a midpoint image to the NEBPathfinder module
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"You will have to give more details than that. It is impossible for us to know what happened based on that one liner description. There is a template for reporting Issues.",
"I am trying to use this script to generate the input files for the \ndefect physics. Till yesterday, it was working fine but suddenly it's... | 2019-09-25T11:20:03 | 2022-01-21T16:18:28 | 2019-11-11T14:53:03Z | NONE | {
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*ImportError: No module named pymatgen.ext.matproj
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<details>
<summary>Changelog</summary>
*Sourced from [tabulate's changelog](https://github.com/astanin/python-tabulate/blob/master/CHANGELOG).*
> - 0.8.5: Fix broken Windows package. Minor documentation updates.
> - 0.8.4: Bug fixes.
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<details>
<summary>Changelog</summary>
*Sourced from [pylint's changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog).*
> What's New in Pylint 2.4.1?
> ===========================
>
> Release date: 2019-09-25
>
>
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<details>
<summary>Commits</summary>
- [`7ad7f8b`](https://github.com/python/mypy/commit/7ad7f8bbe61e5e67aa7fd6f2efe280931dd2f620) Bump version to 0.730
- [`90776b8`](https://github.com/python/mypy/commit/90776b8b49dee8b5c84a7e90c1b563f2fd88f4f1) Docume... | {
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"Hi @Nokimann, I just noticed this myself recently. I opened a PR to add \"vacuum mode\" but didn't look at the other options. You'd be welcome to pick this up and add them if you'd like: https://github.com/materialsproject/pymatgen/pull/1597 ",
"@mkhorton Nice notification. So, we have to modify it in our own wa... | 2019-09-30T12:34:28 | 2023-08-13T16:32:55 | 2023-08-13T16:32:54Z | NONE | {
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} | I'm not sure Pymatgen deals with other custom options, e.g., -b neargrid | ongrid | weight.
When I check, only parse_atomic_densities=True is available, or I missed.
So can we parse the custom options by the variables, or manually changing the source code?
The double star (** keywords) at the end of any functio... | {
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"I really like this code and these optimizations, but can we discuss how we expose this to the user?\r\n\r\nSome users have trouble compiling C extensions, so it would be nice to have a pure Python fallback for those users.\r\n\r\nI see that currently you have an `@deprecated` `get_all_neighbors_py`. We already hav... | 2019-09-30T19:03:30 | 2019-10-02T16:18:22 | 2019-10-02T13:02:39Z | CONTRIBUTOR | {
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} | ## Summary
Previously, for finding neighbors from in a structure with given centering points, I need to use `Structure.get_all_neighbors` which has a python loop of constructing `PeriodicSite`. In cases where the sites are not used, this is very slow. Therefore, a general function that find points in different spher... | {
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.2.0
> pytest 5.2.0 (2019-09-28)
> =========================
>
> Deprecations
> ------------
>
> - [\#1682](... | {
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<details>
<summary>Changelog</summary>
*Sourced from [pylint's changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog).*
> What's New in Pylint 2.4.2?
> ===========================
>
> Release date: 2019-09-30
>
>
> * ``ignored-modules`... | {
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"Thanks."
] | 2019-10-01T13:18:42 | 2019-10-01T15:20:01 | 2019-10-01T15:19:56Z | MEMBER | {
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I included an additional test to make sure that two lists that should have the same length actually have the same lengths. These lists are parameters for "get_summed_icohp_by_label_and_orbital_list". I have also included a test to make sure an error will be raised if they have different lengths.
Best,
J... | {
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"Hi @PetMetz, thanks for opening this.\r\n\r\n1. is not a bug (though may not be the best decision either); this is a default output.\r\n\r\n2. yes, this is true; many formats are missing in the .to method, including formats supported via the ASE and OpenBabel adaptors.\r\n\r\nI think a few things might help here. ... | 2019-10-01T13:57:29 | 2019-10-02T18:44:24 | 2019-10-02T18:44:24Z | NONE | {
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} | **Describe the bug**
(1) pymatgen.Structure.to method silently writes YAML output if the requested structure file type is not in the decision tree.
(2) Writing Protein Data Bank (.pdb) structure format evidently supported in pymatgen.io.lammps.utils, but not in Structure.to method (this is probably a separate compl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1615 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1615/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1615/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1615/events | https://github.com/materialsproject/pymatgen/issues/1615 | 501,421,287 | MDU6SXNzdWU1MDE0MjEyODc= | 1,615 | Trouble with linear_add of VolumetricData object | {
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"Thanks for reporting this. I have pushed a fix that raises a warning instead of an error for different structures, but will throw an error if you try to sum spin and non-spin data, or that the dims of the data itself are different (numpy does that)."
] | 2019-10-02T11:04:24 | 2019-10-02T12:52:29 | 2019-10-02T12:51:30Z | NONE | {
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} | When I tried to use `__add__` or `__sub__` functions of `VolumetricData` object, it raised an error by
```
ValueError("Adding or subtraction operations can only be "
"performed for volumetric data with the exact "
"same structure.")
```
In some cases of subtraction from AB system to separate... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1616 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1616/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1616/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1616/events | https://github.com/materialsproject/pymatgen/issues/1616 | 501,486,052 | MDU6SXNzdWU1MDE0ODYwNTI= | 1,616 | XCrySDen parser fails to handle element symbols instead of atomic numbers | {
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} | **Describe the bug**
The XCrySDen file format supports the use of atomic symbols (such as "H") to specify elements. However, the parser assumes that the elements are always integers, resulting in a failure to cast a symbol as an integer.
**To Reproduce**
An attempt to parse the following (dummy) XCrySDen output fi... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1617 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1617/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1617/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1617/events | https://github.com/materialsproject/pymatgen/pull/1617 | 501,560,062 | MDExOlB1bGxSZXF1ZXN0MzIzODA5MDIy | 1,617 | Fixed bug in XCrySDen parser failing to parse element symbols | {
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"Thanks! Can you implement a simple unittest pls? ",
"Yes, I don't know why I didn't do that in the first place. Thanks for your patience :) I hope the new test suffices. I followed the lead of other files like test_pwscf.py of including a string to parse within the file, and demonstrate that parsing strings with... | 2019-10-02T15:23:01 | 2019-10-02T18:42:17 | 2019-10-02T18:42:12Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Closes #1616
## Additional dependencies introduced (if any)
The XCrySDen parser now imports from the `pymatgen.core.Element` module.
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} | ## Summary
Include a summary of major changes in bullet points:
* Introduced PeriodicNeighbor and Neighbor helper classes. These are essentially sites with attributes like distance, index and image (for PeriodicNeighbor) and skips all the usual checks for Sites.
* Greatly speeds up get_all_neighbors by not havin... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1619 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1619/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1619/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1619/events | https://github.com/materialsproject/pymatgen/issues/1619 | 502,748,168 | MDU6SXNzdWU1MDI3NDgxNjg= | 1,619 | Problem with compiling pymatgen on macOS due to C++ extensions | {
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"Just tell user to use `conda install -c conda-forge pymatgen`. ",
"Also, the current dev version of pymatgen actually does link libc++. It seems this user's Xcode is out of date.",
"To clarify, `python setup.py develop` is broken on macOS for development purposes. This is not just an end user issue.",
"@chc2... | 2019-10-04T17:09:36 | 2019-10-04T17:30:58 | 2019-10-04T17:30:47Z | MEMBER | {
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```
Running setup.py develop for pymatgen
ERROR: Command errored out with exit status 1:
command: /Users/.../miniconda3/envs/pmg/bin/python -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/Users/.../uw/pymatgen/setup.py'"'"'; __file__='"'"'/Users/.../uw/pymatgen/setup.py'"'"';f=ge... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1620 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1620/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1620/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1620/events | https://github.com/materialsproject/pymatgen/pull/1620 | 502,756,101 | MDExOlB1bGxSZXF1ZXN0MzI0Nzc4MzE0 | 1,620 | fix c++ link args | {
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Fix macos compilation error by adding `-stdlib=libc++` link flag
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https://api.github.com/repos/materialsproject/pymatgen/issues/1621 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1621/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1621/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1621/events | https://github.com/materialsproject/pymatgen/issues/1621 | 502,764,082 | MDU6SXNzdWU1MDI3NjQwODI= | 1,621 | local_env bug (regression from v2019.10.2) | {
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"I would leave this to @mkhorton to assign the right person to debug. From a glance, it seems a confusion between frac coords and coords. As far as my simple testing goes, it does not seem to be a bug within get_neighbor itself.\r\n\r\nBottom-line - if author does not provide good enough unittests for people to fin... | 2019-10-04T17:48:13 | 2019-10-04T20:33:12 | 2019-10-04T18:38:16Z | CONTRIBUTOR | {
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from pymatgen import Structure
from pymatgen.analysis.local_env import MinimumDistanceNN
ss = Structure.from_dict({'@module': 'pymatgen.core.structure',
'@class': 'Structure',
'charge': None,
'lattice': {'matrix': [[10.42, -0.01019, 0.1038],
[-0.008154, 7.397, -0.02193],
[0.05132, -0.01677, 5.209]]... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1622 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1622/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1622/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1622/events | https://github.com/materialsproject/pymatgen/pull/1622 | 502,801,181 | MDExOlB1bGxSZXF1ZXN0MzI0ODE0NDc3 | 1,622 | Bump pytest-cov from 2.7.1 to 2.8.0 | {
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<details>
<summary>Changelog</summary>
*Sourced from [pytest-cov's changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst).*
> 2.8.0 (2019-10-04)
> ==================
>
> - Fixed `RecursionError` that can occur... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1623 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1623/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1623/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1623/events | https://github.com/materialsproject/pymatgen/pull/1623 | 502,856,678 | MDExOlB1bGxSZXF1ZXN0MzI0ODYwMTAw | 1,623 | robust pbc considerations for get neighbors | {
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"@chc273 do you have any thoughts on wider support in pymatgen for mixed periodic boundary conditions? e.g. like ASE",
"> @chc273 do you have any thoughts on wider support in pymatgen for mixed periodic boundary conditions? e.g. like ASE\r\n\r\nI think it's more of a choice to make. VASP works fine by putting mol... | 2019-10-04T21:42:54 | 2019-10-06T18:13:45 | 2019-10-06T17:15:03Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Small changes to revise details of how to treat mixed periodic boundary and non-periodic boundary in the general `find_points_in_spheres` function.
If the structure has periodic and non-periodic boundary mixed case (2d material, 1d material etc) the find points in spheres function will not augment the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1624 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1624/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1624/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1624/events | https://github.com/materialsproject/pymatgen/pull/1624 | 503,452,209 | MDExOlB1bGxSZXF1ZXN0MzI1MzAxNDg5 | 1,624 | Fix reading lobsterout | {
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} | ## Summary
Hello!
I have made a small bug fix in the Lobsterout class. Now, gzipped files are also read correctly.
Best,
JG | {
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<details>
<summary>Changelog</summary>
*Sourced from [pytest-cov's changelog](https://github.com/pytest-dev/pytest-cov/blob/master/CHANGELOG.rst).*
> 2.8.1 (2019-10-05)
> ==================
>
> - Fixed [\#348](https://github-redirect... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1626 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1626/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1626/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1626/events | https://github.com/materialsproject/pymatgen/pull/1626 | 503,739,286 | MDExOlB1bGxSZXF1ZXN0MzI1NTMzNTky | 1,626 | Bump pytest from 5.2.0 to 5.2.1 | {
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.2.1
> pytest 5.2.1 (2019-10-06)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5902](https:... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1627 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1627/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1627/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1627/events | https://github.com/materialsproject/pymatgen/pull/1627 | 504,374,007 | MDExOlB1bGxSZXF1ZXN0MzI2MDM4MjM1 | 1,627 | Eigenval object | {
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"Great. Thanks!"
] | 2019-10-09T02:31:25 | 2019-10-09T04:00:03 | 2019-10-09T03:58:16Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Adds Eigenval object, which parses the EIGENVAL output file from a VASP run.
## Additional dependencies introduced (if any)
N/A
## TODO (if any)
To increase potential utility, it would help to add a function that creates a BandStructure object, but I don't have any plans to do this in the near... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1628 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1628/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1628/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1628/events | https://github.com/materialsproject/pymatgen/pull/1628 | 504,557,294 | MDExOlB1bGxSZXF1ZXN0MzI2MTc5Mzg4 | 1,628 | Changes to Lobster module and lobsterset | {
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"I will work on fixing the tests - sorry.",
"There are docstrings missing for a lot of classes in vasp sets. I didn't realize I would need to add the docstrings for all old classes as well. What would you suggest about this? ",
"No, this is fine as is. Thanks."
] | 2019-10-09T10:25:07 | 2019-10-09T14:19:00 | 2019-10-09T14:18:59Z | MEMBER | {
"total": 0,
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} | ## Summary
Hello!
-I have fixed to bugs in Lobsterin and Charge of the lobster module. gzipped files can now be read. A test is included.
-I have added type annotations in the Lobster module
-I made the lobsterset more flexible by adding a user_supplied_basis dict that is used instead of the standard basis when... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1629 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1629/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1629/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1629/events | https://github.com/materialsproject/pymatgen/issues/1629 | 504,840,027 | MDU6SXNzdWU1MDQ4NDAwMjc= | 1,629 | Symmetrized structure json serialization | {
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"Thanks. This should be fixed.\r\n"
] | 2019-10-09T19:13:20 | 2019-11-11T14:52:36 | 2019-11-11T14:52:31Z | NONE | {
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} | **Describe the bug**
symmetrized structure cannot be dumped and loaded
Thanks for fixing https://github.com/materialsproject/pymatgen/commit/2131e3e95477995947b43864ef9fda2294b2a6dc
This is a follow-up question.
**To Reproduce**
```
sym = SpacegroupAnalyzer(s).get_symmetrized_structure()
sym.copy() # now wor... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1630 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1630/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1630/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1630/events | https://github.com/materialsproject/pymatgen/pull/1630 | 506,818,546 | MDExOlB1bGxSZXF1ZXN0MzI3OTI5Mzk0 | 1,630 | Use caching in MinimumVIRENN class | {
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"Failing test is for `CrystalAIResterTest.test_query` nothing to do with this PR."
] | 2019-10-14T18:52:25 | 2019-10-14T19:40:28 | 2019-10-14T19:40:27Z | MEMBER | {
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} | ## Summary
The `MinimumVIRENN` near neighbors class relies on the `ValenceIonicRadiusEvaluator` which is extremely slow.
If using `MinimumVIRENN` to get the coordination of all sites in a structure, the `ValenceIonicRadiusEvaluator` class will be initialized once per site. This is very inefficient as `ValenceIoni... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1631 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1631/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1631/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1631/events | https://github.com/materialsproject/pymatgen/pull/1631 | 506,863,601 | MDExOlB1bGxSZXF1ZXN0MzI3OTY0Mjc0 | 1,631 | Workflow refactoring | {
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"Pls fix the docs. Thanks.",
"I think I've fixed the problems with the docstrings reported by pydocstyle but in the last build travis CI failed with \r\n\r\n```\r\nNo output has been received in the last 10m0s, this potentially indicates a stalled build or something wrong with the build itself.\r\nCheck the deta... | 2019-10-14T20:41:05 | 2019-10-16T20:45:27 | 2019-10-16T20:45:27Z | CONTRIBUTOR | {
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} | ## Summary
* Separate out the workflow portions of the abinit code from the analysis part
* Prepare integration with new emmet builder.
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https://api.github.com/repos/materialsproject/pymatgen/issues/1632 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1632/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1632/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1632/events | https://github.com/materialsproject/pymatgen/issues/1632 | 507,648,699 | MDU6SXNzdWU1MDc2NDg2OTk= | 1,632 | Documentation for conda installation | {
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} | Not really a bug per se but the documentation on how to install pymatgen with conda refers to the matsci channel while it is not working anymore (rest of the stack is the same, e.g. monty).
**To Reproduce**
Try to install pymatgen using the matsci channel as indicated on the web page ([pymatgen-conda-installation](... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1633 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1633/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1633/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1633/events | https://github.com/materialsproject/pymatgen/issues/1633 | 508,104,053 | MDU6SXNzdWU1MDgxMDQwNTM= | 1,633 | Poscar doesn't sort structure causing bad POSCARs | {
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"You are certainly welcome to add an option `sort_structure` to the Poscar class. But the default behavior has to be that the Poscar class simply generates the input *in the order that the user supplies it*. There are a lot of use cases where this is important. E.g., when doing NEB, I need a 1-1 mapping of start an... | 2019-10-16T21:16:25 | 2019-10-18T00:07:05 | 2019-10-18T00:07:05Z | NONE | {
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} | **Describe the bug**
The `Poscar` class doesn't appear to sort structure and there is no expectation in the standard structure class to sort the sites by elements. The result is more complex classes such as Slab can be generated with atoms grouped together by the original structure. This leads to unwieldy Poscar's tha... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1634 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1634/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1634/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1634/events | https://github.com/materialsproject/pymatgen/pull/1634 | 508,235,867 | MDExOlB1bGxSZXF1ZXN0MzI5MDY3MTY0 | 1,634 | Bump mypy from 0.730 to 0.740 | {
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<details>
<summary>Commits</summary>
- [`0662772`](https://github.com/python/mypy/commit/0662772b5a6b9029da0cf4aec857b9b1e34057a9) Bump version number to 0.740
- [`97d25cf`](https://github.com/python/mypy/commit/97d25cfb31132e9f9ce84056ecd51084ba7a7d97)... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1635 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1635/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1635/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1635/events | https://github.com/materialsproject/pymatgen/pull/1635 | 508,235,957 | MDExOlB1bGxSZXF1ZXN0MzI5MDY3MjM1 | 1,635 | Bump networkx from 2.3 to 2.4 | {
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<details>
<summary>Changelog</summary>
*Sourced from [networkx's changelog](https://github.com/networkx/networkx/blob/master/doc/news.rst).*
> NetworkX 2.4
> ============
>
> Release date: 16 October 2019
>
> Supports Python 3.5, 3.6, 3.7, and ... | {
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<details>
<summary>Release notes</summary>
*Sourced from [numpy's releases](https://github.com/numpy/numpy/releases).*
> ## v1.17.3
> NumPy 1.17.3 Release Notes
> ==========================
>
> This release contains fixes for bugs reported again... | {
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"Let's leave this open, looks like some methods need to be updated.",
"> [#2819] Deprecate connected_component_subgraphs, biconnected_component_subgraphs, attracting_component_subgraphs, strongly_connected_component_subgraphs, weakly_connected_component_subgraphs. Instead use: [G.subgraph(c) for c in *_components... | 2019-10-17T16:58:20 | 2019-11-06T06:31:16 | 2019-11-06T06:31:05Z | CONTRIBUTOR | {
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} | Bumps [networkx](https://github.com/networkx/networkx) from 2.3 to 2.4.
<details>
<summary>Changelog</summary>
*Sourced from [networkx's changelog](https://github.com/networkx/networkx/blob/master/doc/news.rst).*
> NetworkX 2.4
> ============
>
> Release date: 16 October 2019
>
> Supports Python 3.5, 3.6, 3.7, and ... | {
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"Have you seen this?\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/b7588712eb6f37ef2ff5cfa47667e2df33e8c11d/pymatgen/analysis/local_env.py#L1001 \r\n\r\nI'm on-board with changing the default, I'm not sure why it wasn't done previously. I'm sure you're already aware there are other NNs that rely on Voron... | 2019-10-17T23:41:11 | 2020-07-11T02:39:25 | 2020-07-11T02:39:25Z | MEMBER | {
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} | I'm working on a package to benchmark the performance of the NearNeighbor classes in pymatgen by comparing predicted coordination numbers against human determined coordination numbers (taken from the literature).
The performance of VoronoiNN can be tuned through a parameter, `tol`. Voronoi faces that are smaller tha... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1639 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1639/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1639/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1639/events | https://github.com/materialsproject/pymatgen/pull/1639 | 509,079,602 | MDExOlB1bGxSZXF1ZXN0MzI5NzM3NjUw | 1,639 | Bump pylint from 2.4.2 to 2.4.3 | {
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<details>
<summary>Changelog</summary>
*Sourced from [pylint's changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog).*
> What's New in Pylint 2.4.3?
> ===========================
>
> Release date: 2019-10-18
>
> Pass the actual PyLin... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1640 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1640/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1640/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1640/events | https://github.com/materialsproject/pymatgen/pull/1640 | 509,089,645 | MDExOlB1bGxSZXF1ZXN0MzI5NzQ1NzU5 | 1,640 | Modification in lobsterin class | {
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"Thanks."
] | 2019-10-18T13:42:55 | 2019-10-18T16:01:25 | 2019-10-18T16:01:20Z | MEMBER | {
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} | ## Summary
Modification in lobsterin class to make the choice of the basis even more flexible. This is needed for future developments.
I also included tests to do so.
* Feature 1 supports A, but not B.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request ti... | {
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"Thanks."
] | 2019-10-18T15:33:07 | 2019-10-18T16:20:21 | 2019-10-18T16:20:21Z | CONTRIBUTOR | {
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} | ## Summary
This change makes it possible to write Gaussian input files without needing a geometry,
which is useful in writing input files for restarting runs.
## Additional dependencies introduced (if any)
None
## TODO (if any)
None
## Checklist
Before a pull request can be merged, the following... | {
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<summary>Release notes</summary>
*Sourced from [pandas's releases](https://github.com/pandas-dev/pandas/releases).*
> ## v0.25.2
> This is a minor bug-fix release in the 0.25.x series and includes some regression fixes
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https://api.github.com/repos/materialsproject/pymatgen/issues/1643 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1643/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1643/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1643/events | https://github.com/materialsproject/pymatgen/issues/1643 | 511,155,710 | MDU6SXNzdWU1MTExNTU3MTA= | 1,643 | an adsorbatesitefinder bug | {
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"Thanks for the detailed bug report. Will check on this today.",
"Tagging @oxana-a and @mhsiron since this bug might affect their work.",
"So this only seems to happen when finding adsorption sites on a supercell, I suspect it's not testing all of the translational equivalencies.",
"In general, we should enc... | 2019-10-23T08:16:31 | 2023-08-13T16:32:55 | 2023-08-13T16:32:55Z | NONE | {
"total": 0,
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} | **Describe the bug**
i use generate_all_slabs to cleave surface Au with max_index=1, then i found when min_vacuum_size=15, got 5 sites, min_vacuum_size=10, got 4 sites. other parameters fix.
**To Reproduce**
Steps to reproduce the behavior:
code as shown:
struct = Structure.from_file(r"./bulk_library/Au_POSCAR")... | {
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<details>
<summary>Changelog</summary>
*Sourced from [netcdf4's changelog](https://github.com/Unidata/netcdf4-python/blob/master/Changelog).*
> version 1.5.3 (tag v1.5.3rel)
> ==============================
> * make sure arrays are mask... | {
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"Why not just change the atomate code to import properly from pymatgen.io.vasp.inputs and pymatgen.io.vasp.outputs?",
"I think the problem here is an import in custodian \r\nhttps://github.com/materialsproject/custodian/blob/2fdb6f672de5586b06dbc3f18b96268f7e1a4998/custodian/vasp/handlers.py#L23\r\nand these type... | 2019-10-23T21:48:52 | 2019-10-30T17:34:58 | 2019-10-30T17:34:58Z | CONTRIBUTOR | {
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} | # Small Bug Fixes
- Brought back import of `VaspInput` into `pymatgen.io.vasp` module which packages such as `custodian` depend on
- Fixed `from_hdf5` to instantiate the `cls` rather than just `VolumetricData`
# Old Text from Original PR
Running
```
(pmg) ❯ lpad defuse_fws -q '{"fw_id" : {"$gt" : 320140}}'
``... | {
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.2.2
> pytest 5.2.2 (2019-10-24)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5206](https:... | {
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"Looking at the error message, it does not seem to be a compiler flag issue. What is the compiler flag that is giving you an issue? \r\n\r\nWe do not have SuSe Linux on hand to try to debug this.",
"SciPy now has its own linear assignment code, perhaps we should switch to that instead of implementing our own.",
... | 2019-10-29T10:19:18 | 2019-11-05T09:35:09 | 2019-11-05T09:34:38Z | CONTRIBUTOR | {
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} | **Describe the bug**
Compilation bug when doing `pip install pymatgen`
**To Reproduce**
Steps to reproduce the behavior:
1. Download and install the currently recent [Anaconda](https://repo.anaconda.com/archive/Anaconda3-2019.10-Linux-x86_64.sh).
2. Type `pip install pymatgen`
```
gcc -pthread -B /home/limanni... | {
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<details>
<summary>Commits</summary>
- [`ee2920d`](https://gitlab.com/pycqa/flake8/commit/ee2920d775df18481d638c2da084d229d56f95b9) Release 3.7.9
- [`182cdf6`](https://gitlab.com/pycqa/flake8/commit/182cdf6c23a711af32b2dbd040dd89808f5b1d18) Merge bra... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1649 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1649/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1649/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1649/events | https://github.com/materialsproject/pymatgen/pull/1649 | 514,978,520 | MDExOlB1bGxSZXF1ZXN0MzM0NTEzNjEw | 1,649 | Extension of Lobsterin class | {
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"Thanks!"
] | 2019-10-30T20:58:40 | 2019-10-31T02:02:18 | 2019-10-31T02:02:16Z | MEMBER | {
"total": 0,
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} | ## Summary
Implemented generation of KPOINT files for fatband calculations with Lobster with ISYM=0.
I have included tests where I compare the generated outputs to IBZKPT files generated by VASP.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
... | {
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"Hi @htz1992213, this looks good but missing a few docstrings: https://travis-ci.org/materialsproject/pymatgen/builds/605287251#L1275",
"I would also suggest adding tests to make sure that the destructive usage problem will not happen again.",
"Thanks."
] | 2019-10-31T01:12:51 | 2019-11-06T22:51:58 | 2019-11-06T22:51:52Z | CONTRIBUTOR | {
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} | * Fix: Fixed the previous behavior that the CombinedData initializes by destructively using the input LammpsData objects, which causes errors when reusing those LammpsData.
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This PR adds a new convenience function `get_download_info` to MPRester which - for a list of material ids, task types, and file patterns - returns 1) a list of URLs pointing to zip downloads from the [NOMAD](https://nomad-coe.eu/) repository, and 2) a metadata dictionary with info about `task_ids` and `t... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1652 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1652/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1652/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1652/events | https://github.com/materialsproject/pymatgen/pull/1652 | 516,145,544 | MDExOlB1bGxSZXF1ZXN0MzM1NDQ3NzQ2 | 1,652 | Bump tqdm from 4.36.1 to 4.37.0 | {
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<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.37.0 stable
> - potential future pandas fix ([#824](https://github-redirect.dependabot.com/tqdm/tqdm/issues/824))
> - bett... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1653 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1653/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1653/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1653/events | https://github.com/materialsproject/pymatgen/pull/1653 | 517,184,809 | MDExOlB1bGxSZXF1ZXN0MzM2MzAzMjEz | 1,653 | Bump pandas from 0.25.2 to 0.25.3 | {
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<details>
<summary>Release notes</summary>
*Sourced from [pandas's releases](https://github.com/pandas-dev/pandas/releases).*
> ## v0.25.3
> This is a minor bug-fix release in the 0.25.x series and includes some regression fixes
> and bug fi... | {
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"As far as I can tell, the SciPy algorithm will scale more poorly than the current solution (SciPy uses Kuhn–Munkres rather than pymatgen's Jonker-Volgenant). However the SciPy solution is a lot simpler so less likely to contain bugs and might be faster in practice, especially for typical pymatgen problem sizes, he... | 2019-11-06T06:50:57 | 2021-02-13T17:27:55 | 2019-11-06T08:13:34Z | MEMBER | {
"total": 0,
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} | ## Summary
Remove use of custom LinearAssignment code to reduce our maintenance overhead, now uses SciPy version.
Before merging I want to profile to ensure there's no significant speed regression, and more manual checks to ensure correctness. | {
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"I think during your merge of the master branch, some of your code got deleted. Take a look at the diff for that commit.\r\n\r\nThere may also be issues where your code isn't correct. For instance: `is_perm([1,1,1],[1,-1,1])`\r\n\r\nMaybe something like this?\r\n```\r\nfrom collections import defaultdict\r\n\r\ndef... | 2019-11-08T09:49:49 | 2020-03-28T04:12:12 | 2020-03-15T19:24:30Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
Include a summary of major changes in bullet points:
- Edits made to Frank Wan's previous TEM calculator, a project under Shyam's direction:
- Changed method get_interplanar_spacing to call lattice.d_hkl rather than separately calculating for different crystal systems.
- Vectorized method... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1656 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1656/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1656/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1656/events | https://github.com/materialsproject/pymatgen/pull/1656 | 520,414,294 | MDExOlB1bGxSZXF1ZXN0MzM5MDA3Mzc1 | 1,656 | Extend grosspop class | {
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} | ## Summary
Hello!
Extension of the grosspop class. A structure file with grosspops as site properties can be generated. Tests have been included.
Best,
JG
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, t... | {
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"I found the official notification.\r\n\r\nCheck 'matplotlib.mlab removals' in\r\nhttps://matplotlib.org/3.1.0/api/api_changes.html\r\n\r\nAnd definitely, replacing just two parts:\r\n\r\n`from matplotlib.mlab import normpdf` -> `from scipy.stats import norm`\r\n`normpdf` -> `norm.pdf`\r\n(All is in the source of p... | 2019-11-11T05:02:12 | 2019-11-11T14:09:42 | 2019-11-11T14:09:42Z | NONE | {
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} | 'normpdf' is deprecated? So it might result in ImportError.
Just when typed `from matplotlib.mlab import normpdf`
it shows ImportError
I was trying to use function 'save_spectre_plot' in 'pymatgen.io.gaussian.GaussianOutput'
I expect replacing 'normpdf' in 'matplotlib' with 'norm' in 'scipy' might solve this er... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1658 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1658/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1658/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1658/events | https://github.com/materialsproject/pymatgen/pull/1658 | 520,958,064 | MDExOlB1bGxSZXF1ZXN0MzM5NDMxMTIy | 1,658 | Bump numpy from 1.17.3 to 1.17.4 | {
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} | Bumps [numpy](https://github.com/numpy/numpy) from 1.17.3 to 1.17.4.
<details>
<summary>Release notes</summary>
*Sourced from [numpy's releases](https://github.com/numpy/numpy/releases).*
> ## v1.17.4
> NumPy 1.17.4 Release Notes
> ==========================
>
> This release contains fixes for bugs reported again... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1659 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1659/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1659/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1659/events | https://github.com/materialsproject/pymatgen/pull/1659 | 520,958,383 | MDExOlB1bGxSZXF1ZXN0MzM5NDMxMzk1 | 1,659 | Bump tqdm from 4.37.0 to 4.38.0 | {
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<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.38.0 stable
> - support `lock_args` for e.g. non-blocking intermediate writes ([#838](https://github-redirect.dependabot.co... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1660 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1660/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1660/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1660/events | https://github.com/materialsproject/pymatgen/pull/1660 | 520,958,514 | MDExOlB1bGxSZXF1ZXN0MzM5NDMxNTEy | 1,660 | Bump scipy from 1.3.1 to 1.3.2 | {
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<details>
<summary>Release notes</summary>
*Sourced from [scipy's releases](https://github.com/scipy/scipy/releases).*
> ## SciPy 1.3.2
> SciPy `1.3.2` is a bug-fix and maintenance release that adds support for Python `3.8`.
>
> Authors
> =====
>... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1661 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1661/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1661/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1661/events | https://github.com/materialsproject/pymatgen/pull/1661 | 521,564,419 | MDExOlB1bGxSZXF1ZXN0MzM5OTIwMjMx | 1,661 | Fix broken plotting of fatbands from lobster and extension of Doscar class for lobster | {
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"Thanks."
] | 2019-11-12T13:52:51 | 2019-11-12T15:38:08 | 2019-11-12T15:38:03Z | MEMBER | {
"total": 0,
"completed": 0,
"percent_completed": 0
} | ## Summary
Hello,
There was a problem in LobsterBandStructureSymmLine due to the use of "Species". I have fixed this and reverted some changes in the tests that were done to account for this problem. Without the current pull request, plotting fatbands from Lobster isn't possible anymore. I have also included an ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1662 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1662/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1662/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1662/events | https://github.com/materialsproject/pymatgen/issues/1662 | 521,945,464 | MDU6SXNzdWU1MjE5NDU0NjQ= | 1,662 | installation improvement | {
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"It is rare that I have heard anyone complain about ease of installation with conda. As far as I know, after installing miniconda on your system, a series of commands such as\r\n\r\n```\r\nconda create -n pmg_env python\r\nconda activate pmg_env\r\nconda install -c conda-forge pymatgen\r\n```\r\n\r\nshould work jus... | 2019-11-13T04:02:56 | 2020-07-11T02:37:33 | 2020-07-11T02:37:33Z | NONE | {
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} | **Is your feature request related to a problem? Please describe.**
First, I have to admit that I just start using Python although it is popular. I noticed that my colleagues had similar experience although they have used python for a long while. The configuration is still a headache work.
It looks to take forever t... | {
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"Superseded by #1673."
] | 2019-11-13T13:33:04 | 2019-11-18T13:17:27 | 2019-11-18T13:17:25Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1664 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1664/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1664/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1664/events | https://github.com/materialsproject/pymatgen/issues/1664 | 522,398,066 | MDU6SXNzdWU1MjIzOTgwNjY= | 1,664 | BandStructureSymmLine.apply_scissor missing appropriate tests | {
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} | Applying a scissor correction to a metal is somewhat ill-defined, nevertheless there is logic in `apply_scissor` to do just that -- however, due to an indentation error, this logic has never returned a value.
Making a note here for whoever refactors BandStructure next that appropriate tests need to be added. | {
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"I agree that in principle, the relationship should be invertible. But we generally do not work with such high tolerances in matching structures.\r\n\r\nIn this case, the failure point is the angle tolerance. One of the angle differences is very large. If you set angle_tol to 10, you actually get consistent results... | 2019-11-13T22:42:56 | 2020-07-08T20:32:09 | 2020-07-08T20:32:08Z | CONTRIBUTOR | {
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} | **Describe the bug**
structure_A == structure_B does not mean structure_B == structure_A
This also results in the `group_structure` function returning different results depending on the order.
```python3
from pymatgen.analysis.structure_matcher import StructureMatcher, ElementComparator
from pymatgen import Stru... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1666 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1666/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1666/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1666/events | https://github.com/materialsproject/pymatgen/pull/1666 | 522,864,321 | MDExOlB1bGxSZXF1ZXN0MzQwOTc5MDE4 | 1,666 | Bump pylint from 2.4.3 to 2.4.4 | {
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<details>
<summary>Changelog</summary>
*Sourced from [pylint's changelog](https://github.com/PyCQA/pylint/blob/master/ChangeLog).*
> What's New in Pylint 2.4.4?
> ===========================
> Release date: 2019-11-13
>
> * Exempt all the names fou... | {
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"Thanks @mhsiron !",
"Test will likely need to be updated also. What system did you verify this against?",
"For ZnTe\n\nBut currently running on 50 other materials, so maybe I’ll wait!\n\nThis is the charge transfer data for Bader vs. DDEC:\n\n\nFor DDEC - the raw output is simply the charge transfer, while for... | 2019-11-14T20:58:54 | 2019-11-15T00:45:36 | 2019-11-15T00:45:36Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1668 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1668/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1668/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1668/events | https://github.com/materialsproject/pymatgen/issues/1668 | 523,289,731 | MDU6SXNzdWU1MjMyODk3MzE= | 1,668 | Fail to parse OUTCAR file when two numbers are connected in spin components | {
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"Pls provide a sample OUTCAR with this problem. I would think you can probably debug this by modifying one of the regex and submitting a PR.",
"Thanks for the prompt reply.\r\nPlease find the attached. I will also send the pull request soon.\r\n[OUTCAR.txt](https://github.com/materialsproject/pymatgen/files/38505... | 2019-11-15T06:52:59 | 2019-11-18T21:39:58 | 2019-11-18T21:39:58Z | CONTRIBUTOR | {
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} | **Describe the bug**
In the OUTCAR file, when there is a part such that, the Outcar parse fails, because the two float numbers are connected.
--------------------------------------- Iteration 1( 1) ---------------------------------------
POTLOK: cpu time 0.0040: real time 0.0065
SETDIJ: cpu time... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1669 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1669/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1669/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1669/events | https://github.com/materialsproject/pymatgen/pull/1669 | 523,295,328 | MDExOlB1bGxSZXF1ZXN0MzQxMzI4NDI5 | 1,669 | update significant figures of get_gb_data test | {
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Include a summary of major changes in bullet points:
* update significant figures of MPRester get_gb_data test when querying the work of separation | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1670 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1670/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1670/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1670/events | https://github.com/materialsproject/pymatgen/pull/1670 | 523,388,241 | MDExOlB1bGxSZXF1ZXN0MzQxNDAwNzIw | 1,670 | Fix regular expression in read_onsite_density_matrices in Outcar | {
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"Thanks @yuuukuma !",
"I saw you posted an example Outcar to the issue thread, would it be possible to add this to `test_files` and add a test too?\r\n\r\nHere would be an appropriate place to add it: https://github.com/materialsproject/pymatgen/blob/ff1a1239811dcd175259d4e77cd9d3daec8d6b05/pymatgen/io/vasp/tests... | 2019-11-15T10:30:33 | 2019-11-18T16:45:05 | 2019-11-18T16:40:26Z | CONTRIBUTOR | {
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See Issue #1668 | {
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.2.3
> pytest 5.2.3 (2019-11-14)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5830](https:... | {
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"Thanks!"
] | 2019-11-15T18:12:27 | 2019-11-15T19:46:01 | 2019-11-15T19:45:57Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* reformat code
* try pre-commit to test pydocstyle
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"Superseded by #1724."
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.2.4
> pytest 5.2.4 (2019-11-15)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#6194](https:... | {
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<details>
<summary>Changelog</summary>
*Sourced from [tabulate's changelog](https://github.com/astanin/python-tabulate/blob/master/CHANGELOG).*
> - 0.8.6: Bug fixes. Stop supporting Python 3.3, 3.4.
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Add optional argument `fig_close` to `add_fig_kwargs` to remove figure f
rom the pylab state machine. Default: False
## Checklist
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [fl... | {
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<details>
<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.3.0
> pytest 5.3.0 (2019-11-19)
> =========================
>
> Deprecations
> ------------
>
> - [\#6179](... | {
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"@mkhorton and I realized that we need to somehow handle the case when a user specifies KSPACING but there is ALSO a KPOINTS file or settings present (in `user_kpoints_settings`).\r\n\r\nIn VASP, if KSPACING is set and a KPOINTS file exists, the KPOINTS file overrides KSPACING and there is apprently no error or war... | 2019-11-20T19:25:46 | 2019-12-03T22:31:02 | 2019-11-22T13:30:12Z | CONTRIBUTOR | {
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} | ## Summary
VASP now [recommends](https://www.vasp.at/wiki/index.php/KSPACING) setting KSPACING in the INCAR file rather than supplying KPOINTS manually. This PR updates the teterror handler to accommodate calculations that use KSPACING instead of an explicit KPOINTS file.
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<summary>Commits</summary>
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"Thanks @shyamd ",
"Can we discuss this more? This line:\r\n\r\n```\r\n elif self.potcar_symbols[0].split()[0] == 'PAW':\r\n```\r\n\r\nis a little problematic because VASP has distributed (and continues to distribute) POTCARs that are actually PBE but have the \"PAW\" string (instead of the \"PAW_PBE\" str... | 2019-11-22T19:03:09 | 2020-05-12T15:47:27 | 2019-11-22T19:47:44Z | NONE | {
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GGA `run_type`s were not being properly detected. This fixes that bug.
* Properly detect GGA `run_type`s
* add tests for various `run_type`
* Moved BPARAM for rVV10 enforcement to MVL set | {
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"Thanks @tschaume "
] | 2019-11-22T20:22:12 | 2019-11-23T02:16:16 | 2019-11-23T02:16:16Z | MEMBER | {
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"Hi yuxin-chang,\r\n\r\nAs far as I can tell, this isn't a bug in pymatgen's pourbaix solving/plotting routine, it's an issue with the MP data and corrections for Fe(OH)2."
] | 2019-11-24T08:28:16 | 2023-08-13T16:32:55 | 2023-08-13T16:32:55Z | NONE | {
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} | **Describe the bug**
I tried to draw Fe-H2O pourbaix diagram, using pymatgen.analysis.pourbaix_diagram module. Comparing with the experimental pb diagram (they should match mostly), there should be Fe(OH)2 in the diagram, but the given diagram does not have Fe(OH)2.
**To Reproduce**
`entries = mpr.get_pourbaix_entr... | {
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<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.39.0 stable
> - add `pandas` builtin operations check ([#843](https://github-redirect.dependabot.com/tqdm/tqdm/issues/843) ... | {
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<details>
<summary>Release notes</summary>
*Sourced from [scipy's releases](https://github.com/scipy/scipy/releases).*
> SciPy 1.3.3 Release Notes
> ==========================
>
> SciPy `1.3.3` is a bug-fix release with no new features
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"When you say it needs to be optimized for speed, how slow/fast is it currently?",
"It takes ~1 seconds to generate a plotly Figure object from the\nwulffshape.get_plotly() method. It takes ~0.3 seconds to get a matplotlib\npyplot object from the wulffshape.get_plot() method.\n\nOn Tue, Nov 26, 2019 at 10:18 PM M... | 2019-11-27T04:40:59 | 2020-03-15T21:31:42 | 2020-03-15T21:31:42Z | CONTRIBUTOR | {
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} | This pull request introduces the get_plotly() method in the WulffShape class. This will be the base for website interfaces involving modelling Wulffshapes and Wulff shape morphology for things like Materials Project, CrystalToolkit, Cystalium.
### **Optional requirements:**
Plotly conversion of a WulffShape as a M... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1686 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1686/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1686/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1686/events | https://github.com/materialsproject/pymatgen/issues/1686 | 529,136,626 | MDU6SXNzdWU1MjkxMzY2MjY= | 1,686 | Procar can not read in PROCAR with SOC effect? | {
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"I have met the same bug today. I think this bug comes from the judgment statement used to judge the VASP version. In VASP 5.4.1 and before, the `toks` line and `header` line have the same length. \r\n\r\nPROCAR (VASP 5.4.1) looks like this\r\n```\r\nband 1 # energy -6.07967625 # occ. 1.00000000\r\n \r\nion ... | 2019-11-27T06:05:21 | 2023-08-13T16:32:56 | 2023-08-13T16:32:56Z | NONE | {
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} | **Describe the bug**
Procar(filename="PROCAR")
---------------------------------------------------------------------------
IndexError Traceback (most recent call last)
<ipython-input-220-d410e4cba7b4> in <module>
----> 1 Procar(filename="/Users/zhangruiqi/Work//band/PROCAR")
~/.lo... | {
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"This is not a bug but rather because the code detects that some of the atoms are effectively in the same place. Having more than one atom in a physical location makes no sense. But we are aware that some CIF files violate this.\r\n\r\nYou can resolve this by setting merge_tol to some large positive value or you ca... | 2019-11-27T11:01:39 | 2022-08-22T09:42:20 | 2019-11-27T15:05:15Z | NONE | {
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} | I am using pymatgen to generate VASP input files such as POSCAR from cif files generated from the CSD python API. This mostly works well, but if a molecule is symmetrical atoms can sometimes be labeled as such C1 C1A etc. which pymatgen does not deal with so well.
s = Structure.from_file("MCHTEP11.cif")
C:\ANACON... | {
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} | ## Summary
Hello,
I am fixing a bug that was introduced in this pull request:
https://github.com/materialsproject/pymatgen/commit/80aa5047cc0925cc1178d85aa691ebb7c51eebde#r36189539
I have not written a test yet but we are working on it. For now, I would like to fix the functionality.
Best,
JG | {
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<details>
<summary>Release notes</summary>
*Sourced from [tqdm's releases](https://github.com/tqdm/tqdm/releases).*
> ## tqdm v4.40.0 stable
> - officially support `float` for `n` and `total` ([#802](https://github-redirect.dependabot.com/tqdm/tqdm/iss... | {
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<details>
<summary>Commits</summary>
- [`d8aa685`](https://github.com/python/mypy/commit/d8aa68576dda9940aedd0f861f7789d7e679c292) Bump version to 0.750
- [`2af0ac0`](https://github.com/python/mypy/commit/2af0ac021335ec4a3e84a0ba739b4aea7e659c43) docs/m... | {
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<summary>Release notes</summary>
*Sourced from [pytest's releases](https://github.com/pytest-dev/pytest/releases).*
> ## 5.3.1
> pytest 5.3.1 (2019-11-25)
> =========================
>
> Improvements
> ------------
>
> - [\#... | {
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"The structure generated itself should be correct. Using the periodic boundary condition, you can move the top grain to match with the bottom grain. In other words, the large minus values in direct coordinates can be added up to (0,1) using the periodic boundary condition. The vesta software can do this automatical... | 2019-12-03T01:34:07 | 2019-12-08T09:22:06 | 2019-12-08T09:22:06Z | CONTRIBUTOR | {
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} | **Describe the bug**
`pymatgen.analysis.gb.grain.gb_from_parameters()` generates a $\Sigma 5 <001>$ tilt boundary of fcc whose top_grain has a large minus deviation in the b-axis when `normal=True`.
**To Reproduce**
Run followings and open the generated file `Cu_GB4.cif`.
```python
from pymatgen import Struc... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1694 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1694/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1694/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1694/events | https://github.com/materialsproject/pymatgen/issues/1694 | 531,966,615 | MDU6SXNzdWU1MzE5NjY2MTU= | 1,694 | "pymatgen.io.lammps.data" Can't write file | {
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"Pls install the 2019.12.3 version. I just fixed this."
] | 2019-12-03T12:58:06 | 2019-12-03T17:05:16 | 2019-12-03T16:49:27Z | NONE | {
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} | **Describe the bug**
I want to convert a ".cif" file to lammps coordination data but found
"pymatgen.io.lammps.data" Can't write lammps data file with the following error:
"FileNotFoundError: [Errno 2] No such file or directory: '/home/myuser/.conda/envs/pmg/lib/python3.6/site-packages/pymatgen/io/lammps/CoeffsDataT... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1695 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1695/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1695/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1695/events | https://github.com/materialsproject/pymatgen/pull/1695 | 532,337,763 | MDExOlB1bGxSZXF1ZXN0MzQ4NjA4MDY4 | 1,695 | Add pymatgen.Molecule support to AseAtomsAdaptor | {
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"Many thanks.\r\n",
"Thanks for merging! :+1: "
] | 2019-12-03T23:30:30 | 2019-12-04T00:02:37 | 2019-12-04T00:01:58Z | CONTRIBUTOR | {
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} | ## Summary
* Added ``pymatgen.Molecule`` support to ``AseAtomsAdaptor``:
* ``AseAtomsAdaptor.get_atoms()``now also accepts ``Molecule``s (previously, it would only accept ``Structure``s)
* New (static) method ``AseAtomsAdaptor.get_molecule()`` (analogous to the existing ``get_structure()``method, but returns `... | {
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"Thanks for the PR! Test failures are related to missing docstrings in grain.py, but these are not related to your changes so I will merge"
] | 2019-12-04T03:28:26 | 2019-12-08T09:25:47 | 2019-12-07T00:35:18Z | CONTRIBUTOR | {
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} | ## Summary
Current implementation sometimes returns a structure with fractional coordinates whose absolute value are greater than one. It is not wrong but inconvenient when it is used in external calculation modules (and also it seems many users think it as unexpected behavior).
(related to [#1693](https://github.c... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/1697 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/1697/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/1697/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/1697/events | https://github.com/materialsproject/pymatgen/issues/1697 | 533,105,804 | MDU6SXNzdWU1MzMxMDU4MDQ= | 1,697 | scripts directory of pymatgen | {
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"Hi @JabinHao, the scripts are defined via the `entry_points` of `setup.py`, see https://github.com/materialsproject/pymatgen/blob/c9b3385ad6ff06f0f1b26c4a6509b977b63be6e6/setup.py#L182 \r\n\r\nMost of them are defined in `pymatgen.cli.pmg`.\r\n\r\nNote that this is not an appropriate use of the Issues page, this i... | 2019-12-05T03:46:57 | 2019-12-05T03:52:59 | 2019-12-05T03:52:59Z | NONE | {
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} | **Describe the bug**
I cannot find the scripts directory of pymatgen’s github repo. It seems that in the new version you have built them in the "pmg", but i want to see the code of these scripts such as gen_potcar.py、vasp_example.py .etc. where can i find them
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"Thanks @rkingsbury! This looks basically good, there may be a pycodestyle error in there. Only comment is that I'd recommend leaving the `symbol` property in the class, but have it return `self._symbol`. Then, in your `__init__` set `self._symbol` instead of `self.symbol`, this way there's still a docstring and th... | 2019-12-07T02:10:00 | 2019-12-16T23:14:32 | 2019-12-16T22:55:04Z | CONTRIBUTOR | {
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} | When a VaspInput set is instantiated, check that the POTCAR hashes match the specified functional and POTCAR symbol (i.e., check that you are really using the POTCARs you intend). @mkhorton was consulted on this.
The check was implemented in `sets.py` rather than `input.py` because the `InputSets` specify their POTC... | {
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<details>
<summary>Changelog</summary>
*Sourced from [pydocstyle's changelog](https://github.com/PyCQA/pydocstyle/blob/master/docs/release_notes.rst).*
> 5.0.0 - December 9th, 2019
> ==========================
>
> Major Updates
>
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