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https://api.github.com/repos/materialsproject/pymatgen/issues/2614 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2614/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2614/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2614/events | https://github.com/materialsproject/pymatgen/pull/2614 | 1,333,713,880 | PR_kwDOACgets486S6q | 2,614 | Class to handle Thermal displacements matrices | {
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"\n[](https://coveralls.io/builds/51541115)\n\nCoverage increased (+0.05%) to 63.567% when pulling **fccd68f68f7f829601e61efec48745f2cc5d2e92 on JaGeo:thermal_displacements** into **5ec1c1e40607bc52112308ee02dbca769e883ade on materialsproject:master**.\n... | 2022-08-09T19:49:32 | 2022-08-09T21:34:20 | 2022-08-09T21:34:20Z | MEMBER | {
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I have added a class and a function to handle and convert thermal displacement matrices from phonopy and potentially other codes.
This is a partial re-implementation of this matlab code from my PhD https://github.com/JaGeo/MolecularToolbox/
Tests and documentation have been added. | {
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"\n[](https://coveralls.io/builds/51719492)\n\nCoverage increased (+0.03%) to 63.269% when pulling **84b15743d7743c290d2a9dff2ca3642c3422984c on janosh:fix-mprester-inc_structure-doc-str** into **dda4cd31af37e1488d3c4f280d96bcda4aeabc97 on materialsproje... | 2022-08-10T18:52:56 | 2022-08-17T17:38:01 | 2022-08-17T17:31:31Z | MEMBER | {
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} | The docs for [`MPRester.get_entries_in_chemsys()`](https://github.com/janosh/pymatgen/blob/cb7620d5488b41798791f3f8ed7229bed9b5071d/pymatgen/ext/matproj.py#L863) and `MPRester.get_entry_by_material_id()` seem to be incorrect:
https://github.com/janosh/pymatgen/blob/cb7620d5488b41798791f3f8ed7229bed9b5071d/pymatgen/e... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2616 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2616/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2616/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2616/events | https://github.com/materialsproject/pymatgen/pull/2616 | 1,335,296,272 | PR_kwDOACgets48_h8E | 2,616 | [WIP] Update IEEE conversion routine for tetragonal systems | {
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"Hi @montoyjh,\r\n\r\nCan you expand on this point:\r\n\r\n> Fix an issue with precision on prior test data\r\n\r\nI don't mind adding an additional test here if necessary, but not sure what else required.",
"Bumping this because it seems like a serious bug. If there's no additional context for the precision issu... | 2022-08-10T23:07:59 | 2024-08-03T19:01:57 | CONTRIBUTOR | {
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} | ## Summary
Tentative fix for rotating tensorial properties for tetragonal systems.
## TODO (if any)
* Need to add data for testing tetragonal system that previously failed
* Fix an issue with precision on prior test data | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2617 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2617/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2617/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2617/events | https://github.com/materialsproject/pymatgen/pull/2617 | 1,336,182,180 | PR_kwDOACgets49CemU | 2,617 | Small extension of Thermal displacement matrices | {
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"Messed something up with git. If the tests pass, everything should be fine from my side.",
"Not sure what is going on with the other tests at the moment. "
] | 2022-08-11T16:09:43 | 2022-08-11T17:27:45 | 2022-08-11T17:27:44Z | MEMBER | {
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} | ## Summary
I have now also added an implementation of a quality criterion for computed thermal displacement matrices as defined in https://doi.org/10.1039/C9CE00794F
Once can now also initialize the class from thermal displacement matrices as defined in the cif only.
Very tiny fixes to the documentation have bee... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2618 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2618/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2618/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2618/events | https://github.com/materialsproject/pymatgen/issues/2618 | 1,336,513,566 | I_kwDOACgets5PqZQe | 2,618 | Unexpected behavior in CrystalNN: very low coordination numbers when adsorbates are present | {
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} | I have the following structure of CO on a Rh surface. When using `CrystalNN()` on a surface Rh atom without an adsorbate, I get a coordination number of 9. When getting the coordination number of the surface Rh with CO bound to it, I get a coordination number of 1. One would expect the coordination number of the Rh wit... | {
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"\n[](https://coveralls.io/builds/51633221)\n\nCoverage decreased (-0.002%) to 63.232% when pulling **b9b934127f8f0e53fb6c92ce595850191630761b on arosen93:rosen-dbands** into **fd83fe16afe1cb864abf8e7ca1e9dbc2f0888da8 on materialsproject:master**.\n"
] | 2022-08-12T18:53:06 | 2022-08-12T20:00:58 | 2022-08-12T19:14:55Z | MEMBER | {
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} | The docstrings for various DOS properties had the args in the wrong order. I updated the docstrings to match the order in the function calls. | {
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"\n[](https://coveralls.io/builds/51715669)\n\nCoverage decreased (-0.02%) to 63.222% when pulling **2fd2db7a0d9a3ae3b8e1949524d0d36e0df4e368 on nheinsdorf:master** into **dda4cd31af37e1488d3c4f280d96bcda4aeabc97 on materialsproject:master**.\n",
"Grea... | 2022-08-16T23:28:41 | 2022-08-26T20:42:38 | 2022-08-21T16:14:53Z | CONTRIBUTOR | {
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} | ## SUMMARY
I added a method to the SpaceGroup class that returns both the orbit (like the 'get_orbit'-method does) as well as the symmetry operations that generate it. As opposed to 'get_orbit' the method makes sure that the first element of the orbit is the point that has been passed to the function. Therefore the ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2621 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2621/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2621/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2621/events | https://github.com/materialsproject/pymatgen/pull/2621 | 1,341,840,852 | PR_kwDOACgets49U-UB | 2,621 | Lobsterin generation extension | {
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"\n[](https://coveralls.io/builds/51828534)\n\nCoverage increased (+0.09%) to 63.351% when pulling **6e9529df415c3305551b434e6971a8d578dabfb4 on naik-aakash:lobsterin_generation_extension** into **e1be8691d5efb0ea037b7edc964fd59dc41340ef on materialsproj... | 2022-08-17T14:19:47 | 2024-01-10T12:23:03 | 2022-08-23T12:54:39Z | CONTRIBUTOR | {
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} | ## Summary
* Added new option `standard_with_comp_range` for generating lobsterin files using vasp
* Added simple unit_test corresponding this new changes
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https://api.github.com/repos/materialsproject/pymatgen/issues/2622 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2622/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2622/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2622/events | https://github.com/materialsproject/pymatgen/pull/2622 | 1,342,358,914 | PR_kwDOACgets49Ws-1 | 2,622 | Integrate `pymatgen-ext-matproj` addon package | {
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"Please do not merge until I personally review this PR. @mkhorton ",
"\n[](https://coveralls.io/builds/51755597)\n\nCoverage decreased (-0.06%) to 63.208% when pulling **9228209451e89f4eb76d33ad7fc6d6acce460319 on munrojm:master** into **beac8d5361d8f5... | 2022-08-17T22:44:47 | 2022-09-01T19:13:32 | 2022-09-01T19:13:32Z | MEMBER | {
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} | ## Summary
This PR removes the `MPRester` code contained in `pymatgen.ext.matproj` and replaces it with an updated client in the external `pymatgen-ext-matproj` addon package. This addon provides access to both the updated and legacy Materials Project API.
## Additional dependencies introduced (if any)
`pymat... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2623 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2623/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2623/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2623/events | https://github.com/materialsproject/pymatgen/pull/2623 | 1,343,269,862 | PR_kwDOACgets49ZsOe | 2,623 | Structure Graphs from Lobster Data - Update | {
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"Automatic tests have't been triggered.",
"I think the precommit leads to these errors in pylint. It reformats the files in such a way that the lines are too long. I guess I have to go into the pre-commit config and see how to fix this.\r\n\r\nWill also try to fix the other issue.",
"\n[![Coverage Status](https... | 2022-08-18T15:25:12 | 2022-08-21T16:13:22 | 2022-08-21T16:13:14Z | MEMBER | {
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} | ## Summary
I have extended the structure graphs that can be derived by Lobster.
To do so, I have extended the method `with_local_env_strategy` to have the additional parameter edge_properties.
I am now also setting the node properties in get_bonded_structure to arrive at a networkx graph object that includes... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2624 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2624/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2624/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2624/events | https://github.com/materialsproject/pymatgen/issues/2624 | 1,343,710,964 | I_kwDOACgets5QF2b0 | 2,624 | MPXANESSet: COREHOLE setting inconsistent with literature | {
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"Ah, I have just noticed that there is logic in `FEFFDictSet` that changes `COREHOLE` to `RPA` when a reciprocal space calculation is invoked. \r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/2a88940b8a4a1eb84e0077dce934765caada9395/pymatgen/io/feff/sets.py#L202\r\n\r\nIn my opinion, there is still value i... | 2022-08-18T22:22:51 | 2022-09-28T18:09:47 | CONTRIBUTOR | {
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} | Both studies (cited below) that describe the development of high-throughput XANES workflows state that the 'RPA' method was chosen for screening of the core-hole potential. However `MPXANESSet.yaml` uses the default 'FSR' setting.
The ML paper (Zhenget al. 2018) seems to indicate that RPA gave more accurate results,... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2625 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2625/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2625/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2625/events | https://github.com/materialsproject/pymatgen/pull/2625 | 1,343,737,058 | PR_kwDOACgets49bQc- | 2,625 | IO support for res files (AIRSS results) | {
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"Thanks for working on this @ScottNotFound, it'll be a nice addition.\r\n\r\nIt looks like the PR is basically complete, are you waiting on anything besides linting? I'm not sure if the capitalized `CELL` etc. dataclass attributes on `Res` are a PEP8 violation, but otherwise the PR looks great.\r\n\r\nBeing unfamil... | 2022-08-18T23:05:28 | 2023-05-03T18:29:28 | 2022-08-31T21:47:19Z | CONTRIBUTOR | {
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} | ## Summary
Include a summary of major changes in bullet points:
* Adds res file io to handle results from airss searches, #2560
* This isn't proper support for the shelx format (does anyone use that anymore?), but if all we care about is airss then that's fine.
## Additional dependencies introduced (if any)
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} | Line 615 handles normalizing the surface energies on the wulff shape between 0 and 1 to get the corresponding color via the following:
` norm_e = (plane.e_surf - min(e_surf_on_wulff)) / (max(e_surf_on_wulff) - min(e_surf_on_wulff))`
This will cause a division by zero error if there is ever a Wulffshape... | {
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"\n[](https://coveralls.io/builds/51819547)\n\nCoverage increased (+0.0005%) to 63.267% when pulling **11e380c8d7452e25769317e5f670f0006dbabdc3 on janosh:doc-str-JmolNN-min_bond_distance** into **f87c9f502225d7d60d5c856fabb0a9d786fbc305 on materialsproje... | 2022-08-21T14:29:22 | 2022-08-21T16:12:20 | 2022-08-21T16:12:17Z | MEMBER | {
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"\n[](https://coveralls.io/builds/52044099)\n\nCoverage decreased (-0.002%) to 63.343% when pulling **56383d868c8925920a1aa2f7398ccee354fbc071 on janosh:gh-2070-disordered-nearneighbors** into **5a1f04aa43619f07d48348cf7606a5ae871bcc12 on materialsprojec... | 2022-08-22T18:29:23 | 2022-08-30T21:47:35 | 2022-08-30T21:21:29Z | MEMBER | {
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} | Closes #2070.
This PR fixes the `AttributeError` currently raised when passing disordered structures to methods like `get_cn()` and `get_bonded_structure()` of `CrystalNN` and other `NearNeighbors` subclasses.
Several open questions:
1. I added a helper function `_handle_disorder(structure: Structure, on_disorde... | {
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"\n[](https://coveralls.io/builds/51852857)\n\nCoverage decreased (-0.004%) to 63.342% when pulling **eb0de1300b78e9da30d1274d4ab500d9f475fe7d on arosen93:rosen-depre** into **5a1f04aa43619f07d48348cf7606a5ae871bcc12 on materialsproject:master**.\n"
] | 2022-08-22T20:23:52 | 2022-08-23T05:21:58 | 2022-08-23T05:21:57Z | MEMBER | {
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} | I changed
```python
from scipy.ndimage.filters import gaussian_filter1d
```
to
```python
from scipy.ndimage import gaussian_filter1d
```
in `pymatgen.electronic_structure.dos` since the former is deprecated. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2632 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2632/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2632/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2632/events | https://github.com/materialsproject/pymatgen/issues/2632 | 1,347,566,860 | I_kwDOACgets5QUj0M | 2,632 | Cannot import pbc_diff due to circular import | {
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"Hmm... I don't think any of this code has been changed in recent months/years..... But it seems to be a typing issue. This should be then jettisoned since typing is optinal."
] | 2022-08-23T08:42:45 | 2022-08-23T09:47:18 | 2022-08-23T09:47:18Z | MEMBER | {
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} | Using the latest pymatgen:
```python
from pymatgen.util.coord import pbc_diff
```
Gives
```python
from pymatgen.util.coord import pbc_diff
---------------------------------------------------------------------------
ImportError Traceback (most recent call last)
<ipython-input-... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2633 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2633/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2633/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2633/events | https://github.com/materialsproject/pymatgen/pull/2633 | 1,347,581,965 | PR_kwDOACgets49n3wD | 2,633 | Fix circular import | {
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"\n[](https://coveralls.io/builds/51867690)\n\nCoverage decreased (-0.003%) to 63.343% when pulling **8b2bb603f2135a74faaa0f5998e94cba7c955488 on utf:fix-circular-import** into **0abcca91396c22532322e901e54b52d5cf44767a on materialsproject:master**.\n"
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} | Fixes #2632
Importing pbc_diff directly fails due to a circular import. This doesn't seem to impact the code or tests since other modules are imported first. E.g. running the following works fine:
```python
from pymatgen.core import Composition
from pymatgen.util.coord import pbc_diff
```
The issue arrises... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2634 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2634/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2634/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2634/events | https://github.com/materialsproject/pymatgen/issues/2634 | 1,350,266,041 | I_kwDOACgets5Qe2y5 | 2,634 | Crash in Bader analysis due to missing file | {
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"@janosh: I'm guessing this can be closed as stale. It was likely addressed anyway in #3192. I've personally run thousands of Bader calcs and never got this error, for what it's worth.\r\n\r\n@pjf295: Let us know if you still get this error with newer versions of pymatgen.",
"Thanks Andrew. Closing as assumed fix... | 2022-08-25T03:26:05 | 2023-09-03T19:42:07 | 2023-09-03T19:42:07Z | NONE | {
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} | **Describe the bug**
A clear and concise description of what the bug is.
Bader seems to run normally, but fails stating a file does not exist. The details are below.
**To Reproduce**
Steps to reproduce the behavior:
The files necessary to reproduce the bug are too large to post here (800 MB CHGCAR), but the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2635 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2635/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2635/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2635/events | https://github.com/materialsproject/pymatgen/pull/2635 | 1,350,696,836 | PR_kwDOACgets49yPQR | 2,635 | store bond keys of ICOHP in graph edge prop | {
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"\n[](https://coveralls.io/builds/51973826)\n\nCoverage increased (+0.002%) to 63.353% when pulling **42293d5897ba71257226fb9b74a49f31374828be on naik-aakash:Lobster_structure_graph_update** into **2a88940b8a4a1eb84e0077dce934765caada9395 on materialspro... | 2022-08-25T10:42:17 | 2022-08-26T10:45:35 | 2022-08-26T10:43:34Z | CONTRIBUTOR | {
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} | ## Summary
Minor addition to Lobster graph edge properties
* Store ICOHPlist bond key in graph edge properties. Helps in getting further information from 'Lobsterpy' package
| {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2636 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2636/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2636/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2636/events | https://github.com/materialsproject/pymatgen/pull/2636 | 1,351,447,940 | PR_kwDOACgets490yoW | 2,636 | [WIP] Fix InsertionElectrode.get_summary_dict() | {
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"Thanks for this PR! Noting we're having some offline discussion about this.",
"It was decided that this issue would be resolved through a change in emmet which is being addressed in a separate PR (https://github.com/materialsproject/emmet/pull/520) so that `.get_summary_dict()` method would not need to be change... | 2022-08-25T21:02:49 | 2022-08-30T22:12:23 | 2022-08-30T22:12:23Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2639 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2639/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2639/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2639/events | https://github.com/materialsproject/pymatgen/pull/2639 | 1,352,775,597 | PR_kwDOACgets495Nhv | 2,639 | Fix descriptions in external tools | {
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"Not exactly sure how the linting is now failing in an nmr module. In any case, I only changed the documentation.",
"\n[](https://coveralls.io/builds/51994022)\n\nCoverage increased (+0.002%) to 63.352% when pulling **cbcc1e5f110413ce083bcc3f17aa9a5d6d... | 2022-08-26T22:06:26 | 2022-08-30T05:13:25 | 2022-08-26T22:59:20Z | MEMBER | {
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} | ## Summary
Descriptions of the external tools got mixed up. Switched the LobsterPy and the QuAcc description. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2640 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2640/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2640/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2640/events | https://github.com/materialsproject/pymatgen/pull/2640 | 1,353,110,292 | PR_kwDOACgets496Qwl | 2,640 | Better docs for WSWQ | {
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"\n[](https://coveralls.io/builds/52009989)\n\nCoverage increased (+0.0001%) to 63.35% when pulling **df5d6392f40ec20d91b71afacdd038b7cb7ec98f on jmmshn:get_elphon** into **555ddeb5c62dbc1c44b463b7932cc5f31dc98b39 on materialsproject:master**.\n",
"Loo... | 2022-08-27T18:12:58 | 2022-08-29T20:54:30 | 2022-08-29T20:54:28Z | CONTRIBUTOR | {
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Also added a `data` field to make combining the real/imag parts easier. | {
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"The likely reason is that you have to change the tolerance. Given that I don't have matbench installed, I can't verify the error.",
"It seems the segmentation fault is caused by magmom and high symprec(~=1e-2) from spglib.\r\nI've opened the corresponding issue page linked above.\r\nFor now, dropping magmom entr... | 2022-08-30T13:46:31 | 2023-05-22T17:51:14 | 2023-05-22T17:51:14Z | NONE | {
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} | ```python
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from matbench.bench import MatbenchBenchmark
## ----------------------------------------------------------------------------
def get_matbench_task(name):
mb = MatbenchBenchmark(autoload=False)
task = mb.tasks_map[f'matbench_{name}']
... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2642 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2642/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2642/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2642/events | https://github.com/materialsproject/pymatgen/pull/2642 | 1,358,119,895 | PR_kwDOACgets4-LFSJ | 2,642 | Add `as_dict()` method to `AirssProvider` | {
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"Hmm, I don't know the situations where `as_dict` methods are currently used, but I assume the use case is typically for databases? I wonder if it might be worth having `ResProvider` inherit from `MSONable` like a lot of other classes do. Otherwise I think the TITL entry, REM entries, and structure are enough to re... | 2022-09-01T01:25:31 | 2022-09-08T01:46:14 | 2022-09-08T01:44:35Z | MEMBER | {
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} | @mkhorton This is a small follow-up to #2625. I think a convenience method to turn the most important attributes of an `AirssProvider` into a dict would be nice to have.
```py
from pymatgen.io.res import AirssProvider
res_file = "/good_castep/NaLiTa2O6-28290-4142-1.res"
AirssProvider.from_file(res_file).as_dict... | {
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"Thanks "
] | 2022-09-01T15:01:56 | 2022-09-01T15:06:19 | 2022-09-01T15:06:10Z | CONTRIBUTOR | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2644 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2644/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2644/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2644/events | https://github.com/materialsproject/pymatgen/pull/2644 | 1,360,579,321 | PR_kwDOACgets4-TUuW | 2,644 | Integrate `mp-api.client.MPRester` into `pymatgen.ext.matproj` | {
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"@mkhorton @shyuep I have realized that `msgpack` is required as an install to properly pull BS and DOS data. It only depends on cython (which is already required through scipy), and is therefore lightweight. Let me know your thoughts and if this is okay.",
"\n[![Coverage Status](https://coveralls.io/builds/52356... | 2022-09-02T20:18:31 | 2022-09-12T20:31:47 | 2022-09-12T20:31:46Z | MEMBER | {
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} | ## Summary
- `mp-api` made an explicit dependency
- `MPRester` now detects the API key type (new or legacy) and instantiates the appropriate version of `MPRester`
## Additional dependencies introduced (if any)
`msgpack` is the only additional dependency added to enable BS and DOS data retrieval with the new... | {
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"\n[](https://coveralls.io/builds/52970829)\n\nCoverage remained the same at 63.38% when pulling **128f64d3eca7abc0851dfbc92d788784cf55487b on pre-commit-ci-update-config** into **6345c201d1973afddb813342bd62e481daeee26a on master**.\n",
"Outdated."
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updates:
- [github.com/PyCQA/autoflake: v1.4 → v1.6.1](https://github.com/PyCQA/autoflake/compare/v1.4...v1.6.1)
- [github.com/asottile/pyupgrade: v2.37.3 → v2.38.2](https://github.com/asottile/pyupgrade/compare/v2.37.3...v2.38.2)
- [github.com/psf/black: 22.6.0 → 22.8.0](https://github.com/p... | {
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"Please add tests for the new functionality...",
"\n[](https://coveralls.io/builds/52258489)\n\nCoverage increased (+0.009%) to 63.513% when pulling **1911784599024f43c75ee89f871c92f52e4b3f8f on gpetretto:bugfix** into **fcc81a59c204c0d3046e1312889725a... | 2022-09-06T20:55:06 | 2022-09-07T14:27:32 | 2022-09-07T14:27:29Z | CONTRIBUTOR | {
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} | ## Summary
While parsing a large OUTCAR file coming from an MD simulation I realized that a lot of time was taken by the `read_table_pattern` to extract the number of plane waves for kpoints. The quantitiy appears early in the file, but for very long simulations the execution of the regex on the rest of the file can... | {
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"Pls upgrade to Python 3.9 and reinstall pymatgen. ",
"Updating Python worked perfectly! Thank you :)\r\nSorry for the inconvenience."
] | 2022-09-07T18:34:49 | 2022-11-17T22:59:56 | 2022-11-17T22:59:56Z | NONE | {
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I've used pymatgen almost 2 years ago and especially the dopant suggestion feature from pymatgen, but pymatgen has been updated some times and my code is not running anymore. I have used this code example (https://matgenb.materialsvirtuallab.org/2018/11/06/Dopant-suggestions-using-Pymatgen.html) and I would lik... | {
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"\n[](https://coveralls.io/builds/52297180)\n\nCoverage decreased (-0.003%) to 63.516% when pulling **21d60b9964a352e121e032fc35b2b40404d9e30d on VvVLzy:master** into **00df8be39cd18e898a3c98ff9e944b831f9c62dc on materialsproject:master**.\n",
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"\n[](https://coveralls.io/builds/52401783)\n\nCoverage increased (+0.0001%) to 63.517% when pulling **598c872a48325aaa97ef61e78cfefae6e72b4ebd on janosh:release-ci** into **d26d374dabe01686950162132f24c66baaf298fe on materialsproject:master**.\n",
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} | I just noticed the `release` job GitHub action runs on a matrix strategy. That seems very odd since you can't release a package version to PyPI more than once. I might be missing sth?
I also changed the trigger to
```diff
on:
release:
- types: [created]
+ types: [published]
```
based on [this SO h... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2650 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2650/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2650/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2650/events | https://github.com/materialsproject/pymatgen/pull/2650 | 1,371,459,259 | PR_kwDOACgets4-3Yx8 | 2,650 | Fix some bugs for tem.py | {
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"\n[](https://coveralls.io/builds/52428361)\n\nCoverage increased (+0.002%) to 63.353% when pulling **2cf0e57a501ee80de4efa2548c18269c8db4ea7d on chunweizhu:fix-1** into **de1614a1e68f9d5fc5be896f2f88fa95276ee086 on materialsproject:master**.\n",
"Than... | 2022-09-13T13:27:25 | 2022-09-13T16:29:41 | 2022-09-13T16:29:36Z | CONTRIBUTOR | {
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} | Signed-off-by: chunweizhu <c_w_zhu@163.com>
## Summary
Include a summary of major changes in bullet points:
* fix the bugs when runing `TEMCalculator`
## Additional dependencies introduced (if any)
* List all new dependencies needed and justify why. While adding dependencies that bring
significantly us... | {
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"\n[](https://coveralls.io/builds/52450778)\n\nCoverage decreased (-0.002%) to 63.348% when pulling **d8271c414e1c7cacb449f731938f091e0a3ec8f6 on janosh:fix-gh-languages** into **deea7d2fc470a04b0394a1f6eb309c8f98cd6580 on materialsproject:master**.\n"
] | 2022-09-14T03:50:27 | 2022-09-14T04:11:11 | 2022-09-14T03:52:33Z | MEMBER | {
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} | The paths in `.gitattributes` work the same as in `.gitignore`. So to exclude HTML, rST and test files from the GitHub language calculation, were currently missing a few wildcards to include more deeply nested files.
This change should turn the language composition bar into almost pure Python (once GH had time to re... | {
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"I would just change it to else rather than elif. "
] | 2022-09-15T00:23:55 | 2022-09-15T16:55:57 | 2022-09-15T16:55:57Z | MEMBER | {
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```py
from pymatgen.ext.matproj import MPRester
elemental_reference_energies = MPRester().query(
{"nelements": 1}, ["material_id", "pretty_formula", "energy_per_atom"]
)
```
raises
```py
ValueError: API key ****************** is in an unknown format. Please check your API key at https://materialsproje... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2653 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2653/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2653/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2653/events | https://github.com/materialsproject/pymatgen/pull/2653 | 1,374,779,612 | PR_kwDOACgets4_CgHw | 2,653 | Fix GitHub language statistics - take 2 | {
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"\n[](https://coveralls.io/builds/52509637)\n\nCoverage remained the same at 63.351% when pulling **ea3dbca703b4fb9c398328eb3291e0775c80cbcd on janosh:fix-gh-languages-2** into **8670716641bd643545874aca972d79afd654e711 on materialsproject:master**.\n",
... | 2022-09-15T16:15:15 | 2022-09-15T17:00:50 | 2022-09-15T16:40:36Z | MEMBER | {
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} | I missed a few large HTML and test files in #2651:
```txt
dev_scripts/NIST Atomic Ionization Energies Output.html
test_files/cohp/bandOverlaps.lobster.1
test_files/cohp/bandOverlaps.lobster.2
test_files/cohp/bandOverlaps.lobster.new.1
test_files/cohp/bandOverlaps.lobster.new.2
test_files/cohp/lobsterin.1
test... | {
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"\n[](https://coveralls.io/builds/52510673)\n\nCoverage increased (+0.002%) to 63.355% when pulling **9a88b79ba68c2fa28605a09d5f182027615700a7 on janosh:gh-2652** into **e37284de4777ecb41e4c2b7f672e425e7dca5c71 on materialsproject:master**.\n"
] | 2022-09-15T16:50:14 | 2022-09-15T17:16:29 | 2022-09-15T16:55:56Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2655 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2655/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2655/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2655/events | https://github.com/materialsproject/pymatgen/issues/2655 | 1,375,363,060 | I_kwDOACgets5R-l_0 | 2,655 | PatchedPhaseDiagram raises on keep_all_spaces=True | {
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```py
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram
from pymatgen.ext.matproj import MPRester
entries = MPRester().get_entries("Li O".split())
PatchedPhaseDiagram(entries, keep_all_spaces=True)
```
raises
```py
AttributeError: 'set' object has no attribute 'sort'
```
<... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2656 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2656/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2656/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2656/events | https://github.com/materialsproject/pymatgen/pull/2656 | 1,375,365,487 | PR_kwDOACgets4_Eciw | 2,656 | Fix AttributeError: 'set' object has no attribute 'sort' from PatchedPhaseDiagram(keep_all_spaces=True) | {
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"\n[](https://coveralls.io/builds/52549822)\n\nCoverage decreased (-0.002%) to 63.352% when pulling **34460ced6b7446f8122faf2d360c3569fb036817 on janosh:gh-2655** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n",
"Thanks... | 2022-09-16T03:47:38 | 2022-09-20T18:36:31 | 2022-09-20T18:30:07Z | MEMBER | {
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"This one is actually still broken. Will submit another PR for this."
] | 2022-09-16T03:54:01 | 2022-09-20T18:37:45 | 2022-09-20T18:34:01Z | MEMBER | {
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} | @CompRhys Similar example to #2655 but leaving the default `keep_all_spaces=False`:
```py
from pymatgen.analysis.phase_diagram import PatchedPhaseDiagram
from pymatgen.ext.matproj import MPRester
entries = MPRester().get_entries("Li O".split())
PatchedPhaseDiagram(entries, keep_all_spaces=False)
```
also... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2658 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2658/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2658/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2658/events | https://github.com/materialsproject/pymatgen/pull/2658 | 1,376,471,523 | PR_kwDOACgets4_IH9K | 2,658 | write charge if set | {
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"\n[](https://coveralls.io/builds/52547566)\n\nCoverage increased (+0.0004%) to 63.355% when pulling **4b9c1981cc9b3acc063237d11d2eb62b4cd3470c on jmmshn:patch-vasprun-chg** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n"... | 2022-09-16T21:05:13 | 2022-09-23T19:06:22 | 2022-09-23T16:31:55Z | CONTRIBUTOR | {
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} | ## Set the structure_charge while parsing Potcar
Currently while creating the `Vasprun` object, the `_structure._charge` is `None` if the charge was determined to be 0. If we ensure that the `_charge` parameter is always set, then we can use the check
```
_structure._charge is None
```
To figure out if the char... | {
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"\n[](https://coveralls.io/builds/52634277)\n\nCoverage decreased (-0.006%) to 63.349% when pulling **5345eccb88a36ffa696974e09f3b13da946158ba on janosh:fix-ThermalDisplacementMatrices-compute_directionality_quality_criterion** into **722ea4648bbcd9e7929... | 2022-09-17T03:24:35 | 2022-09-23T17:51:41 | 2022-09-23T16:31:23Z | MEMBER | {
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https://github.com/materialsproject/pymatgen/blob/722ea4648bbcd9e792991e51365fed5b78eba3f4/pymatgen/phonon/thermal_displacements.py#L264-L270 | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2660 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2660/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2660/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2660/events | https://github.com/materialsproject/pymatgen/pull/2660 | 1,378,227,399 | PR_kwDOACgets4_Nqqb | 2,660 | Patch the cube spherical mask | {
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"\n[](https://coveralls.io/builds/52585233)\n\nCoverage remained the same at 63.355% when pulling **9fb6457c58c67a0bd7839dee0acc5669f9ab52e9 on nwinner:cube-patch** into **722ea4648bbcd9e792991e51365fed5b78eba3f4 on materialsproject:master**.\n",
"@nwi... | 2022-09-19T16:36:19 | 2022-09-29T20:26:14 | 2022-09-27T02:13:21Z | CONTRIBUTOR | {
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"I support this proposal. Pls implement and submit a PR. Thanks."
] | 2022-09-20T17:18:30 | 2023-03-18T04:26:11 | 2023-03-18T04:26:11Z | CONTRIBUTOR | {
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} | https://github.com/materialsproject/pymatgen/blob/722ea4648bbcd9e792991e51365fed5b78eba3f4/pymatgen/io/vasp/outputs.py#L5509
Currently, there are two Waveder objects basically accomplish the same thing be just have two different constructor methods.
They also cannot be serialized since their `__init__` requires the... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2662 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2662/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2662/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2662/events | https://github.com/materialsproject/pymatgen/pull/2662 | 1,379,900,390 | PR_kwDOACgets4_TM6I | 2,662 | Fix PatchedPhaseDiagram raises ValueError on empty spaces set | {
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"\n[](https://coveralls.io/builds/52627172)\n\nCoverage decreased (-0.007%) to 63.348% when pulling **2d3b25f113079d91ee913dc1fcc6f2bb0d3f403f on janosh:gh-2657** into **a9a1d483957afde9465d70eefc1c25992983660f on materialsproject:master**.\n"
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https://api.github.com/repos/materialsproject/pymatgen/issues/2663 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2663/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2663/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2663/events | https://github.com/materialsproject/pymatgen/pull/2663 | 1,382,136,780 | PR_kwDOACgets4_adkk | 2,663 | Additional test for thermal displacement matrices | {
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"Will fix the test. Sorry.",
"\n[](https://coveralls.io/builds/52682539)\n\nCoverage increased (+0.004%) to 63.349% when pulling **384b647490fb12515d425302a16beca1795cc2c7 on JaGeo:fix_displacements** into **6c23d744efbd892ec48346297d61b4f3f86b1478 on ... | 2022-09-22T09:32:07 | 2022-09-23T16:31:24 | 2022-09-23T16:31:18Z | MEMBER | {
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} | ## Summary
I have added an additional test to make sure that the error fixed in https://github.com/materialsproject/pymatgen/pull/2659 does not show up again. I have started from @janosh 's branch.
JG | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2664 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2664/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2664/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2664/events | https://github.com/materialsproject/pymatgen/issues/2664 | 1,383,116,664 | I_kwDOACgets5ScK94 | 2,664 | BVS Analyzer | {
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} | I'm trying to use BVSAnalyzer module. My structure is periodic, and I'm doing:
```
Fh = Structure.from_file("Fh_Ehm_2007.cif")
Fh.add_oxidation_state_by_element({"Fe":3, "O":-2})
Fh_bvs = bond_valence.BVAnalyzer()
Fh_valences =Fh_bvs.get_valences(Fh)
Fh_valences
```
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"\n[](https://coveralls.io/builds/52701226)\n\nCoverage increased (+0.002%) to 63.347% when pulling **7b350d1ed26eee7da2e4f09bc35185c14ed8d197 on orionarcher:fix_input_set_equality** into **6c23d744efbd892ec48346297d61b4f3f86b1478 on materialsproject:mas... | 2022-09-23T00:32:04 | 2023-05-08T19:50:14 | 2023-05-08T19:50:13Z | CONTRIBUTOR | {
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} | ## Summary
The current equality operation for InputSet's will fail if `InputSet.inputs` has mutable values. This happens often because InputSet is designed to support `InputFile`s as `inputs`. I have changed the equality operation to use `as_dict` which will coerce all nested elements to immutable types, enabling ea... | {
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"\n[](https://coveralls.io/builds/52819268)\n\nCoverage increased (+0.02%) to 63.368% when pulling **0116ad5ae528948f75923c1b9872077fa9695381 on jmmshn:patch_waveder** into **d7e9b7a7986f06601136190398d2dc2ecb7ca85d on materialsproject:master**.\n",
"T... | 2022-09-24T00:44:38 | 2022-09-29T16:25:44 | 2022-09-28T14:06:43Z | CONTRIBUTOR | {
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} | # Merge Waverder and Wavederf
Originally discussed in #2661
- Merge the two classes into one object with two constructors
- Allow the object to be serializable
- Modified to test files with `LVEL=.TRUE.` in INCAR
- Added comment about running with `LVEL=.TRUE`
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"@shyuep what do you think about this solution?\r\n\r\n`VolumetricData` is now defined in common, but in the `vasp.outputs` module we import it as `BaseVolumetricData` and define a new child class called `VolumetricData`. Its not especially elegant, but this way legacy code will import `VolumetricData` from the `va... | 2022-09-27T02:12:08 | 2022-12-13T18:08:55 | 2022-12-13T18:08:55Z | CONTRIBUTOR | {
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} | ## Summary
Migrate VolumetricData to a new `io.common` module, which can be used by other file formats such as hdf5 and cubes.
Update the vasp output module to use the new class in common.
Only "inelegance" is that a new `VaspVolumetricData` method had to be defined in `io.vasp.outputs` because from_file and w... | {
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"\n[](https://coveralls.io/builds/53115513)\n\nCoverage increased (+0.08%) to 63.433% when pulling **ad7b8d09fec69a36da5cbc79d01d8c910950a2ba on JaGeo:fix_displacements** into **d7e9b7a7986f06601136190398d2dc2ecb7ca85d on materialsproject:master**.\n",
... | 2022-09-27T10:16:28 | 2022-10-08T15:35:29 | 2022-10-08T14:58:24Z | MEMBER | {
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} | ## Summary
I have extended the ThermalDisplacementMatrices class. It can now also read cif files in P1 format, produce structures including Ucif as site_property (handy for sorting structures and thermal displacement properties, for example), and print VESTA files in P1 space group including vectors indicating the d... | {
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} | With the latest version 2022.9.21, the following:
```
from pymatgen.util.serialization import SlotPickleMixin
```
leads to the error `ImportError: cannot import name 'SlotPickleMixin' from 'pymatgen.util.serialization'`. I obtained this while I was trying to use [USPEX](https://uspex-team.org/). Reverting to a pr... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2670 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2670/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2670/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2670/events | https://github.com/materialsproject/pymatgen/pull/2670 | 1,391,171,282 | PR_kwDOACgets4_31B7 | 2,670 | Optical analysis VASP | {
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"\n[](https://coveralls.io/builds/53192707)\n\nCoverage increased (+0.07%) to 63.451% when pulling **bf6996c6d38b40616ac30ab12e6ee29b727bbd2d on jmmshn:optics** into **6345c201d1973afddb813342bd62e481daeee26a on materialsproject:master**.\n",
"This is ... | 2022-09-29T16:40:44 | 2022-10-12T01:02:56 | 2022-10-11T23:16:31Z | CONTRIBUTOR | {
"total": 0,
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} | ## More Flexible reproduction of VASP's optical code
Added `DielectricFunctionCalculator` class which will allow you to:
- Have full control of the matrix elements before and after Fermi's golden rule and before and after Kramers-Kronig transformation.
- This allows you to obtain the band-decomposed and kpoint-dec... | {
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"\n[](https://coveralls.io/builds/52883088)\n\nCoverage decreased (-0.003%) to 63.378% when pulling **86b12b2c1eea95953ea0ae6fa640718457a4c1f9 on rkingsbury:noeq** into **02873b378ab7540b6858744fdf0c6b9b5d2b0c21 on materialsproject:master**.\n"
] | 2022-09-29T18:08:40 | 2024-10-10T01:54:48 | 2022-09-30T13:50:02Z | CONTRIBUTOR | {
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} | ## Summary
Remove the `__eq__` method from `InputSet`, per discussion in #2665 (and will replace that PR).
Flagging @utf in case this change will affect development of VASP `InputSet` in `atomate2`.
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"\n[](https://coveralls.io/builds/55610575)\n\nCoverage: 19.367% (-7.9%) from 27.266% when pulling **52a75003529245a8e82abd2b2f59d0acff44c304 on nwinner:cp2k-2.0** into **d0ab147a6bc7b9bb8bae91432fdd85cca00c13a3 on materialsproject:master**.\n",
"Thank... | 2022-09-29T20:39:04 | 2023-01-03T19:56:40 | 2023-01-03T19:39:03Z | CONTRIBUTOR | {
"total": 0,
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} | ## Summary
PR for major updates to CP2K functionality in pmg, plus a minor edit to `compatibility.py`. PR has been geared towards simplifying certain features, while making others more compatible with the new `atomate2` package, which will use this version.
`inputs.py`
- New Kpoints section objects
- New ba... | {
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"I just noticed that @arosen93 changed that line `2208 \"charge\": self.charge`.\r\nCould you comment on this?",
"Hi @fraricci --- thanks for the ping and apologies about any issues. It looks like the change was made in [this PR](https://github.com/materialsproject/pymatgen/pull/2388) based on [this issue](https:... | 2022-09-30T18:10:12 | 2023-05-20T17:39:54 | 2023-05-20T17:39:54Z | CONTRIBUTOR | {
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} | Here what happens when I try to get a dict of a structure after applying a MagOrderingTransformation.
```
enumerator.transformations['afm'].apply_transformation(st).as_dict()
---------------------------------------------------------------------------
TypeError Traceback (most rec... | {
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"\n[](https://coveralls.io/builds/56598875)\n\nCoverage: 78.186% (-0.7%) from 78.875% when pulling **1fa997b2862421216d1b50ddabd137cc19b39236 on espottesmith:charge_transfer** into **cf4ab40036ec48f0248a55ce37051c947b594364 on materialsproject:master**.\... | 2022-10-01T21:24:42 | 2023-02-03T21:09:18 | 2023-02-03T21:04:44Z | CONTRIBUTOR | {
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} | ## Summary
This PR adds to the Q-Chem IO module in pymatgen, allowing for the following types of calculations:
- Calculations where the input is not well defined by a single molecule (e.g. fragment calculations)
- Charge- or spin-constrained DFT calculations (CDFT)
- Direct coupling (DC) calculations, which rely ... | {
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"Without the vasprun. I can't tell what really is happening. But this suggests that you don't really have a PDOS calculated or parsed. ",
"Hello,\n\nAttached please find my vasprun and doscar files as well as INCAR and\nPOSCAR.\n\nThanks,\n\nOn Mon, Oct 3, 2022 at 11:44 AM Shyue Ping Ong ***@***.***>\nwrote:\n\n... | 2022-10-03T17:53:36 | 2022-11-17T23:01:45 | NONE | {
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} | **Describe the bug**
I am trying to plot dos calculations using my own DFT-calculated doscar and vasprun. Pymatgen comes back with an error saying: KeyError: PeriodicSite. A screengrab of the error traceback attached. Please let me know how to resolve this issue.
Thanks.
*Expected behavior**
DOS should be plot... | {
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} | Doesn't this code mean all subclasses of `NbSetWeight` (like `DistanceNbSetWeight`) are always equal? What's the point of that?
https://github.com/materialsproject/pymatgen/blob/6345c201d1973afddb813342bd62e481daeee26a/pymatgen/analysis/chemenv/coordination_environments/chemenv_strategies.py#L2285-L2286
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"\n[](https://coveralls.io/builds/53115949)\n\nCoverage increased (+0.03%) to 63.413% when pulling **5c8284843f66331828fc2bf6a2c94b3a2f58162b on janosh:mypy-isinstance-__eq__** into **6345c201d1973afddb813342bd62e481daeee26a on materialsproject:master**.... | 2022-10-04T20:18:51 | 2022-10-08T16:43:35 | 2022-10-08T16:40:57Z | MEMBER | {
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"\n[](https://coveralls.io/builds/53122802)\n\nCoverage decreased (-0.0004%) to 63.412% when pulling **8b4e41dd359ae86989422266aef1a4b122976d1e on Ameyanagi:master** into **9026d4acc0cbcd785fb1f9ce5561f20991c7bdc9 on materialsproject:master**.\n",
"Tha... | 2022-10-07T02:54:59 | 2022-10-10T22:20:13 | 2022-10-09T19:29:59Z | CONTRIBUTOR | {
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} | ## Summary
- This PR fixes the sortation of the FEFF IO module to create ATOMS input.
- Main change is to sort the distance by `float` instead of `string`. This will prevent the sorting issue with atom distance above 10 angstroms.
- For example, an atom with a distance of "10 angstroms" was listed before an atom... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2679 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2679/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2679/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2679/events | https://github.com/materialsproject/pymatgen/pull/2679 | 1,400,604,251 | PR_kwDOACgets5AXWcS | 2,679 | Added get_proj_plot() method in phonon.plotter.PhononBSPlotter class | {
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"\n[](https://coveralls.io/builds/53257442)\n\nCoverage increased (+0.1%) to 63.556% when pulling **1e4869797ba3c2cac2419479ecc963f7afe18f39 on cnncnnzh:phonon_plot_proj** into **76bea1b34816f8f436d79522d782fccc72a8c198 on materialsproject:master**.\n",
... | 2022-10-07T04:30:35 | 2022-10-13T19:27:36 | 2022-10-13T19:27:36Z | CONTRIBUTOR | {
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## Summary
A method that allows users to plot the atom-resolved phonon band structures. The contribution from each type (or group) of atoms is calculated based on the magnitude of the eigendisplacements. Support 2 (rb), 3 (rgb) and 4 (cmyk) unique groups of atoms.
So far I just used the existing NaCl example f... | {
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"@munrojm @mkhorton I will let you answer these. For inc_structure, all new MPRester entries by default includes structure. The only problem is just that the inc_structure kwarg was dropped. The mp-api code just needs to add it back in. As for legacy, it should be up until end of this year at least.\r\n\r\nNote tha... | 2022-10-09T14:34:49 | 2023-05-20T14:26:40 | 2023-05-20T14:26:40Z | NONE | {
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} | The old MPRester is disabled (I guess because the legacy MP is offline) so I have to use the new MPRester (mp_api.client.MPRester). However, it seems that it is not as convenient as the old one. There are two major issues I have so far:
1. There is no "inc_structure=True" option for get_entries_in_chemsys. I checke... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2681 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2681/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2681/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2681/events | https://github.com/materialsproject/pymatgen/pull/2681 | 1,402,331,153 | PR_kwDOACgets5Ac4n9 | 2,681 | Add `on_error` kwarg to `PhaseDiagram.get_decomp_and_e_above_hull()` | {
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"\n[](https://coveralls.io/builds/53158321)\n\nCoverage decreased (-0.006%) to 63.406% when pulling **50f3cdca41bc1b7db7f79d85d124471a58ab2865 on pd-on-no-decomp-error** into **9026d4acc0cbcd785fb1f9ce5561f20991c7bdc9 on master**.\n"
] | 2022-10-09T16:48:03 | 2022-10-11T22:20:45 | 2022-10-11T22:20:43Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2682 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2682/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2682/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2682/events | https://github.com/materialsproject/pymatgen/pull/2682 | 1,403,496,804 | PR_kwDOACgets5AguOE | 2,682 | Fix `TqdmExperimentalWarning`: Using `tqdm.autonotebook.tqdm` in notebook mode | {
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"\n[](https://coveralls.io/builds/53146363)\n\nCoverage increased (+0.002%) to 63.415% when pulling **959fbc47229e9d21ec503b297cefb63dd36754ba on fix-tqdm-exp-warning** into **fdd7c746e970bc1d4470b9933efba211bf6f04db on master**.\n"
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} | Occurs when importing `from pymatgen.ext.matproj import MPRester` in Jupyter.
Rest of warning: `pymatgen/analysis/phase_diagram.py:26`: Use `tqdm.tqdm` instead to force console mode (e.g. in jupyter console). | {
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"\n[](https://coveralls.io/builds/53190207)\n\nCoverage remained the same at 63.412% when pulling **b4ab6acc6aacbef4ee2d0b506d65177e2ee30c69 on ci-py-version** into **356084c51f66aa3f742d674105da853e8d1cbc9e on master**.\n",
"Remaining error\r\n\r\n```... | 2022-10-11T21:19:32 | 2022-10-12T04:14:02 | 2022-10-11T22:05:57Z | MEMBER | {
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} | The most important Python version to run CI is the lowest supported (currently 3.8). Running in higher versions means we won't catch some SyntaxErrors e.g. from modern type annotations like `lst: list[int] = [1, 2, 3]` (which [I think was the reason](https://github.com/materialsproject/pymatgen/runs/8157637404?check_su... | {
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"\n[](https://coveralls.io/builds/53196460)\n\nCoverage increased (+0.004%) to 63.455% when pulling **589bdfc2ed88c682f8c2d9055f2c72a230b54649 on more-ppd-tests** into **8ae54c760db5c5f5bf49b30adba29c86a705eefc on master**.\n"
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"The dev scripts are of course rarely used. But they are used from time to time. E.g., when I need to regenerate the periodic_table.json file when certain properties are added.",
"\n[](https://coveralls.io/builds/53217636)\n\nCoverage decreased (-0.005... | 2022-10-12T16:11:57 | 2022-10-12T17:26:41 | 2022-10-12T17:15:48Z | MEMBER | {
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"Why would we bother to lint cmd_line? These are not our files. Other people are responsible for them. ",
"@shyuep My bad, didn't really look at those files. Reverting.",
"\n[](https://coveralls.io/builds/53230757)\n\nCoverage remained the same at 63... | 2022-10-13T01:10:44 | 2022-10-13T04:28:57 | 2022-10-13T04:20:54Z | MEMBER | {
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"\n[](https://coveralls.io/builds/53231442)\n\nCoverage decreased (-0.002%) to 63.455% when pulling **12ceeb284a50fda7e174a9facca43d6ed03c1317 on ppd-magic-methods** into **bba5a44de6a16fba32a91845032831175ca9e3c3 on master**.\n"
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https://api.github.com/repos/materialsproject/pymatgen/issues/2688 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2688/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2688/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2688/events | https://github.com/materialsproject/pymatgen/pull/2688 | 1,408,419,451 | PR_kwDOACgets5AxNA7 | 2,688 | Split CDER to real and imag parts | {
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"\n[](https://coveralls.io/builds/53381720)\n\nCoverage increased (+0.03%) to 63.59% when pulling **0948f42784cc84efc74ffaea1e3ccbd5a74dc05a on jmmshn:patch-optics-cder** into **db28d097bd291ac20c3c730ccb1c3769f59f0a31 on materialsproject:master**.\n",
... | 2022-10-13T20:59:51 | 2022-10-18T19:21:13 | 2022-10-18T19:21:13Z | CONTRIBUTOR | {
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} | ## Split CDER into real and imag parts
Serialization of complex ndarray is not supported by MSONable.
So any large object with complex numbers that need to be serialized should have the real and imaginary part split into two different arrays. | {
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"`mpr.query` has been replaced with `mpr.summary.search`. You can use that new method and pass all of your wildcard formulas to the `formula` argument."
] | 2022-10-14T04:01:50 | 2023-05-20T14:24:33 | 2023-05-20T14:24:33Z | NONE | {
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} | I have installed `pymatgen` v. 2022.9.21 on my Linux system and I have the MP API key. However, when I tried to use the MPRester to get data from the Materials Project, it provides several 'AttributeError:'s. For instance for a simple script as below, only the `m.get_structure_by_material_id` works.
```python
from... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2690 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2690/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2690/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2690/events | https://github.com/materialsproject/pymatgen/issues/2690 | 1,409,266,203 | I_kwDOACgets5T_7Ib | 2,690 | MpRester.query() is replaced with MpRester.summary.search() | {
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"See https://matsci.org/t/how-do-you-access-the-cif-data-in-the-new-api/44850",
"@munrojm Thank you for reply. This will help me definitely. Do I able to access all the elements of periodic table in single query instead of accessing the single element ?\r\n",
"If you would like to query structures containing an... | 2022-10-14T12:19:06 | 2023-05-20T14:22:53 | 2023-05-20T14:22:53Z | NONE | {
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} | **Describe the bug**
Before I used the MpRester.query() to download and access the all elements in the Material project but it changed to MpRester.summary.search() so I could pass the mongoDB query to download and access all the elements with properties = ['cif]
Can someone suggest a command or query to download... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2691 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2691/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2691/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2691/events | https://github.com/materialsproject/pymatgen/pull/2691 | 1,409,930,820 | PR_kwDOACgets5A2Pkd | 2,691 | Test methods downstream from `PD.get_decomp_and_e_above_hull_on_error()` can also ignore errors | {
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"@shyuep I removed `pydocstyle` in 7699c98 from `lint` CI as it was raising a lot of errors with the new config from cf8e0af. I think before it wasn't doing anything. At least I don't remember ever getting an error from it.",
"\n[](https://coveralls.io... | 2022-10-14T22:29:05 | 2022-10-15T04:33:15 | 2022-10-15T04:31:26Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2692 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2692/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2692/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2692/events | https://github.com/materialsproject/pymatgen/pull/2692 | 1,411,470,354 | PR_kwDOACgets5A7KvB | 2,692 | Updating Lammps inputs and inputsets/generators to facilitate integration into atomate2 | {
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"\n[](https://coveralls.io/builds/53522456)\n\nCoverage increased (+0.1%) to 63.647% when pulling **8a771252f9a252c1ee5e9af1bc9820a0be936928 on gbrunin:htmd** into **a429629ed543ec1d8ceb4f02300cb5c95328e6d4 on materialsproject:master**.\n",
"Thanks @gb... | 2022-10-17T12:15:12 | 2023-03-10T17:42:30 | 2023-03-10T17:42:30Z | CONTRIBUTOR | {
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} | ## Summary
Based on previous work from @manaslkht and @rkingsbury, I create this PR to integrate the LammpsInputFile object in pymatgen. Basic InputSet and InputGenerator are added as well, based on templates. For more advanced automatic tools and usage, the user is suggested to use atomate2's addon atomate2-lammps ... | {
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"Can't repro. Worked for me with both with new and old API key.\r\n\r\n@munrojm What's worrying though, I get different numbers of entries depending on which key I use:\r\n\r\n```py\r\nfrom pymatgen.ext.matproj import MPRester\r\n\r\nfor key in (old_api_key, new_api_key):\r\n mpr = MPRester(key)\r\n \r\n #... | 2022-10-17T13:21:18 | 2022-11-05T15:26:38 | 2022-11-05T08:17:00Z | NONE | {
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} | **Describe the bug**
When I try to replicate the tutorial on how to generate Pourbaix diagrams I run into a code error: `AttributeError: 'NoneType' object has no attribute 'contributions'`.
**Code**
```
from pymatgen.ext.matproj import MPRester
from pymatgen.analysis.pourbaix_diagram import PourbaixDiagram, Po... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2694 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2694/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2694/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2694/events | https://github.com/materialsproject/pymatgen/pull/2694 | 1,415,410,436 | PR_kwDOACgets5BIbFg | 2,694 | VASP Optics Masking, and plotting | {
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"\n[](https://coveralls.io/builds/53498078)\n\nCoverage increased (+0.03%) to 63.617% when pulling **a485734b043945e6bfdc5635b26a9b06dd121aaa on jmmshn:patch-optics-cder** into **221603977924450e6282f85432c0d914e8a20b6c on materialsproject:master**.\n",
... | 2022-10-19T18:26:07 | 2022-10-21T18:11:08 | 2022-10-21T18:10:41Z | CONTRIBUTOR | {
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} | ## Vasp optics masking and plotting features
Summary:
- Allow masking of matrix elements without recreating the object
- Allow users to access a filtered version of the matrix element data for analysis
You can now pass a `mask` kwarg in the calculation and get the portion of the dielectric function contribute... | {
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"@shyuep Updating `spglib` to v2 fixes the error on `master` CI reported by @nwinner in #2672 and @jmmshn in #2694. Not sure why this is necessary (i.e. why the error started occurring) but I don't think there are any implications for older pythons from upgrading `spglib` and maybe was overdue anyway.\r\n\r\nHoweve... | 2022-10-20T15:58:31 | 2022-10-20T18:30:19 | 2022-10-20T18:28:41Z | MEMBER | {
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} | An attempt to fix [CI failing even on `master`](https://github.com/materialsproject/pymatgen/actions/runs/3284341401/jobs/5410182347#step:5:17) noted e.g. here: https://github.com/materialsproject/pymatgen/pull/2672#issuecomment-1284403537 by updating `spglib` to v2+. | {
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"@munrojm Not sure how busy you are. If you have time, could you take a look at [this MPResterLegacy error in pymatgen's CI](https://github.com/materialsproject/pymatgen/actions/runs/3292206613/jobs/5427297154#step:5:61):\r\n\r\n```py\r\npymatgen\\ext\\tests\\test_matproj.py:426: \r\n_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _... | 2022-10-20T19:01:14 | 2022-10-20T19:45:16 | 2022-10-20T19:41:56Z | MEMBER | {
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} | The `text-linux` and `lint` CI workflows currently run twice for every PR due to being triggered both by push and PR to _any_ branch:
```yml
name: Testing Linux
on: [push, pull_request]
```
![Screen Shot 2022-10-20 at 12 00 16](https://user-images.githubusercontent.com/30958850/197035102-46e3f011-b153-4eb1-9... | {
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"> Following is outdated, see next comment.\r\n\r\nThis isn't super useful atm since `EntryLike` can only be imported like this:\r\n\r\n```py\r\nif TYPE_CHECKING:\r\n from pymatgen.util.typing import EntryLike\r\n```\r\n\r\ndue to `if TYPE_CHECKING` guard. A bare import\r\n\r\n```py\r\nfrom pymatgen.util.typing ... | 2022-10-21T01:52:56 | 2022-10-21T05:02:39 | 2022-10-21T05:00:52Z | MEMBER | {
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} | ```py
if TYPE_CHECKING: # needed to avoid circular imports
from pymatgen.analysis.phase_diagram import PDEntry
from pymatgen.entries import Entry
from pymatgen.entries.computed_entries import ComputedEntry, ComputedStructureEntry
# Entry or any of its subclasses or dicts that can be unpacked int... | {
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"\n[](https://coveralls.io/builds/53501797)\n\nCoverage increased (+0.006%) to 63.621% when pulling **564671f0f44de20ca350c45e9c29b4705be86664 on env-vars-override-pmgrc** into **fe42ce1fa2f471e256debb240e57e08415b6dd79 on master**.\n",
"If we're going... | 2022-10-21T04:37:05 | 2022-10-27T14:27:46 | 2022-10-21T20:15:45Z | MEMBER | {
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} | @shyuep @mkhorton `_load_pmg_settings()` currently reads env vars first and then overrides them with `.pmgrc.yaml`. It's usually the other way around.
This gives users no way to override on a case by case basis. E.g.
```sh
PMG_MAPI_KEY=xxxxxxxxxxxxxxxx python -c 'from pymatgen.ext.matproj import MPRester; MPRest... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2699 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2699/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2699/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2699/events | https://github.com/materialsproject/pymatgen/issues/2699 | 1,417,737,915 | I_kwDOACgets5UgPa7 | 2,699 | Add PMG_LEGACY_API_KEY to `.pmgrc.yaml` | {
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"Tagging @munrojm here. The new MPRester adaptor should choose either the legacy or new API based on the length of the API key. Is this not working?",
"> The new MPRester adaptor should choose either the legacy or new API based on the length of the API key. Is this not working?\r\n\r\n@mkhorton It is working for ... | 2022-10-21T04:55:20 | 2024-12-06T02:12:38 | 2022-10-21T20:49:25Z | MEMBER | {
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} | Is the `PMG_MAPI_KEY` used in [GH action](https://github.com/materialsproject/pymatgen/settings/secrets/actions) one of length 32 for the new API?
I think that's the reason we're getting [this error in CI](https://github.com/materialsproject/pymatgen/actions/runs/3294713178/jobs/5432504709#step:5:97):
> pymatgen.... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2700 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2700/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2700/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2700/events | https://github.com/materialsproject/pymatgen/pull/2700 | 1,417,745,989 | PR_kwDOACgets5BQXkH | 2,700 | Fix _MPResterLegacy tests in pymatgen/ext/tests/test_matproj.py failing due to new API key | {
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"\n[](https://coveralls.io/builds/53502622)\n\nCoverage increased (+0.003%) to 63.623% when pulling **51c96240cf2432b33c31564e20ef37a4addad52c on fix-mprester-legacy-ci** into **aad30d4706ebbafe40ad9977c0b6042e4fd33174 on master**.\n"
] | 2022-10-21T05:04:09 | 2022-10-21T20:50:55 | 2022-10-21T20:49:24Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2701 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2701/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2701/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2701/events | https://github.com/materialsproject/pymatgen/issues/2701 | 1,418,823,995 | I_kwDOACgets5UkYk7 | 2,701 | Regular release schedule and TestPyPI or PyPI option | {
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"I am unclear what a regular release schedule means. We release when there are a significant number of changes that warrant a release. For many people, they could be using 2019 versions of pymatgen and not notice a difference with the 2022 version.",
"> just a PyPI option for the current master branch\r\n\r\nMayb... | 2022-10-21T20:26:00 | 2022-10-22T13:44:37 | 2022-10-22T13:44:36Z | CONTRIBUTOR | {
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} | @shyuep @mkhorton @janosh I think it would be super helpful to have:
1. A regular (bi-weekly) release schedule, because downloading the repo from github is still too "technologically advanced" for some people.
2. A version of the code on TestPyPI (or just a PyPI option for the current master branch) that is always po... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2702 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2702/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2702/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2702/events | https://github.com/materialsproject/pymatgen/pull/2702 | 1,418,908,066 | PR_kwDOACgets5BUQDp | 2,702 | Test `_load_pmg_settings()` | {
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"\n[](https://coveralls.io/builds/53505135)\n\nCoverage increased (+0.01%) to 63.633% when pulling **345534a41ef55f7125ad3a1fce43d4a9c46d203f on test-load-settings** into **3b160fce1a35202d6d498565858400c79e1db05f on master**.\n"
] | 2022-10-21T22:11:33 | 2022-10-21T23:02:42 | 2022-10-21T23:00:45Z | MEMBER | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2703 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2703/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2703/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2703/events | https://github.com/materialsproject/pymatgen/pull/2703 | 1,419,411,957 | PR_kwDOACgets5BV5-4 | 2,703 | Pandas fix | {
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"\n[](https://coveralls.io/builds/53511594)\n\nCoverage remained the same at 63.628% when pulling **3ceb90f1c888c193eca18febcff19d5748abe5e5 on pandas-fix** into **929af6100884f38cb70307c0e13f701641d107b0 on master**.\n"
] | 2022-10-22T17:15:40 | 2022-10-22T17:43:02 | 2022-10-22T17:41:41Z | MEMBER | {
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} | Closes https://github.com/materialsproject/pymatgen/issues/2510. Update the deprecated `df.append` method to `pd.concat` in `pymatgen/io/lammps/data.py`.
Continuation of #2536. | {
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"Looks like this takes the runtime for the main `text-linux` workflow from [~18 min](https://github.com/materialsproject/pymatgen/actions/runs/3301921055/jobs/5448046731) down to [~9 min](https://github.com/materialsproject/pymatgen/actions/runs/3309228600/jobs/5462200922). The number of parallel jobs went from 4 t... | 2022-10-24T00:31:24 | 2022-10-25T23:01:54 | 2022-10-25T03:08:44Z | MEMBER | {
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"Downgrading python, pymatgen, and mp-api to the following using conda worked. \r\n`python=3.9.13`\r\n`mp-api=0.29.1`\r\n`pymatgen=2022.9.21`\r\n\r\nI get the following error instead. (I know I need to set up that .yaml file 😅) \r\n\r\n```\r\n/my/dir/miniconda3/envs/venv/lib/python3.9/site-packages/pymatgen/core/_... | 2022-10-24T09:55:52 | 2023-08-07T00:22:21 | 2023-01-20T23:47:39Z | NONE | {
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} | **Describe the bug**
For some reason when I import `mp_api.client` I get the following error
**To Reproduce**
Steps to reproduce the behavior:
1. create new virtual environment and install mp-api the one that pip got was `mp_api-0.29.3-py3-none-any.whl (69 kB)`
2. run `python` the version I'm using is `Python ... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2706 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2706/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2706/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2706/events | https://github.com/materialsproject/pymatgen/pull/2706 | 1,421,582,017 | PR_kwDOACgets5BdE4_ | 2,706 | Fix parsing of "Atomic configuration" in POTCAR | {
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"\n[](https://coveralls.io/builds/53590171)\n\nCoverage increased (+17.3%) to 80.956% when pulling **ea3b7547940c9fd397e6e965821227e6930bcbeb on yuzie007:atomic_configuration** into **302ca2c157c8e6f295fd2722c1af45775adf9d6f on materialsproject:master**.... | 2022-10-24T22:59:49 | 2022-10-25T16:01:18 | 2022-10-25T15:58:28Z | CONTRIBUTOR | {
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} | First of all, thank you so much for the development of pymatgen!
## Summary
Due to the missing regex option of `(?s)` (https://docs.python.org/3/library/re.html#re.S, which makes the `.` special character match any character at all, including a newline), "Atomic configuration" in POTCAR (52 and 54) was actually n... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2707 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2707/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2707/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2707/events | https://github.com/materialsproject/pymatgen/pull/2707 | 1,421,817,067 | PR_kwDOACgets5Bd2yZ | 2,707 | Merge `requirements{,-dev,-optional}.txt` into `setup.py` | {
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"\n[](https://coveralls.io/builds/53601073)\n\nCoverage increased (+0.0001%) to 81.723% when pulling **1bdd1b7c6f5b12079c48cc06a6e6443bec070ed3 on reqs-into-setup-py** into **523cfce173f4045878f503009e3e49909cd52a6f on master**.\n"
] | 2022-10-25T04:15:34 | 2022-10-25T21:37:24 | 2022-10-25T21:23:35Z | MEMBER | {
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} | Then replace `pip install -r requirements{,-dev,-optional}.txt` with editable `extras_require` installs in CI workflows.
E.g.
```diff
- pip install -r requirements.txt
- pip install -r requirements-optional.txt -r requirements-dev.txt
- pip install -e .
+ pip install -e '.[dev,optional]'
``` | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2708 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2708/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2708/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2708/events | https://github.com/materialsproject/pymatgen/pull/2708 | 1,423,149,503 | PR_kwDOACgets5BiU8u | 2,708 | Run full test suite on Windows | {
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"Maybe we shouldn't run on `macos` actually since it's limited to 5 concurrent runners so would come with significant wait times ([docs on GH action usage limits](https://docs.github.com/en/actions/learn-github-actions/usage-limits-billing-and-administration#usage-limits)) and it's unlikely to surface errors that w... | 2022-10-25T21:39:11 | 2022-11-01T03:39:36 | 2022-11-01T03:38:32Z | MEMBER | {
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} | Now that we auto-split tests onto 10 parallel runners using `pytest-split` (#2704), we could run all tests on all platforms (`ubuntu`, `mac`, `windows`).
Before, the largest test suite ([don't even think it was the full one](https://github.com/materialsproject/pymatgen/commit/5cb1270310cd25a3ba1f3bbb4584f84466592c31... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2709 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2709/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2709/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2709/events | https://github.com/materialsproject/pymatgen/issues/2709 | 1,423,412,882 | I_kwDOACgets5U146S | 2,709 | Showing wrong coordinates | {
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} | When using Materials Project Crystal Toolkit to view file, the displayed coordinates are wrong, No oxygen atom found in the center of the unit cell.
```
data_fcc
_audit_creation_method generated by ABACUS
_cell_length_a 3.02611
_cell_length_b 3.02611
_cell_length_c 3.02611
_cell_angle_alpha 60
_cell_angl... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2710 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2710/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2710/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2710/events | https://github.com/materialsproject/pymatgen/issues/2710 | 1,424,502,492 | I_kwDOACgets5U6C7c | 2,710 | Python 3.11 support | {
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} | [Now that Python 3.11 is out](https://docs.python.org/3.11/whatsnew/3.11.html), we should make sure `pymatgen` supports it. Just tried it out on M1 Pro running macOS 10.13 and encountered no problems. We should leave this open until we've [run CI in 3.11](https://github.com/actions/python-versions/releases/tag/3.11.0-3... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2711 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2711/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2711/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2711/events | https://github.com/materialsproject/pymatgen/pull/2711 | 1,426,357,734 | PR_kwDOACgets5BtEnb | 2,711 | Add `check_egg_sources_txt_for_completeness()` to `tasks.py` | {
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"You need `@task` only if it is a command that is invoked. E.g., `invoke release` means run the function called `release`. Since your new method is only used internally for checking the generated files, you do not need to add `@task`",
"> You need `@task` only if it is a command that is invoked. E.g., `invoke rel... | 2022-10-27T22:56:53 | 2022-10-27T23:24:40 | 2022-10-27T23:06:15Z | MEMBER | {
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} | Following discussion initiated by @sgbaird and @mkhorton in https://github.com/materialsproject/pymatgen/pull/2708#issuecomment-1292477362.
@shyuep I'm not familiar with `invoke`. The function I added `check_egg_sources_txt_for_completeness()` is not `@task` decorated. it's simply called by the `release` task. Every... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2712 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2712/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2712/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2712/events | https://github.com/materialsproject/pymatgen/pull/2712 | 1,430,606,276 | PR_kwDOACgets5B7JKv | 2,712 | Better error handling in `_load_pmg_settings()` | {
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"\n[](https://coveralls.io/builds/53773382)\n\nCoverage decreased (-11.5%) to 70.198% when pulling **7f70860f059a80918647186ed7ca3d8e5f463d46 on gh-2698-followup** into **25768faa7aa0a34ee4357a92bc92ae41ef21bc1d on master**.\n"
] | 2022-10-31T23:03:49 | 2022-11-01T00:33:36 | 2022-10-31T23:41:23Z | MEMBER | {
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This PR was triggered by taking another look at `_load_pmg_settings()` due to the error reported in #2705. Don't think the error there has anything to do with #2698 though. | {
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"My vote is no. In an ideal world, I would prefer these to be kw only args. I almost always write Structure.to(filename=\"hello.cif\"). We are already friendlier than pandas, which requires to_csv, to_excel etc to be specified. Matt can cast the deciding vote. I am fine if it changes. ",
"\n[![Coverage Status](ht... | 2022-10-31T23:39:52 | 2022-11-01T03:16:45 | 2022-11-01T03:02:26Z | MEMBER | {
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} | @shyuep @mkhorton It's a breaking change but was wondering if we could swap the order of kwargs `fmt` and `filename` in `Structure.to()`.
https://github.com/materialsproject/pymatgen/blob/25768faa7aa0a34ee4357a92bc92ae41ef21bc1d/pymatgen/core/structure.py#L2421-L2427
The annoying thing about having `fmt` first is... | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2714 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2714/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2714/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2714/events | https://github.com/materialsproject/pymatgen/pull/2714 | 1,430,821,669 | PR_kwDOACgets5B72wE | 2,714 | Add `python-version` 3.11 to GH action matrix strategy | {
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"\n[](https://coveralls.io/builds/56199303)\n\nCoverage: 78.846%. Remained the same when pulling **046782479d7d0324450c1c4bfb1b144ba5f2173a on test-py311** into **dcbbe002cc46dba726b6a84bb0c7533ce9c2941b on master**.\n",
"From the py3.11 test logs here... | 2022-11-01T03:50:24 | 2023-02-22T23:50:52 | 2023-02-22T23:50:51Z | MEMBER | {
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We don't actually need to merge into `master` as that would double CI budget consumption but should be run at least once to check `pymatgen` is Python 3.11 compatible. | {
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https://api.github.com/repos/materialsproject/pymatgen/issues/2715 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2715/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2715/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2715/events | https://github.com/materialsproject/pymatgen/pull/2715 | 1,430,840,074 | PR_kwDOACgets5B76u2 | 2,715 | Fix pydocstyle D202 | {
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"\n[](https://coveralls.io/builds/53778991)\n\nCoverage remained the same at 0.0% when pulling **4e91df7b51cb5dd367cad89f6cb38603590a150d on pydocstyle-D202** into **c1f1e95d93a1fab758610aeb9a68d5711e1fce82 on master**.\n"
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https://api.github.com/repos/materialsproject/pymatgen/issues/2716 | https://api.github.com/repos/materialsproject/pymatgen | https://api.github.com/repos/materialsproject/pymatgen/issues/2716/labels{/name} | https://api.github.com/repos/materialsproject/pymatgen/issues/2716/comments | https://api.github.com/repos/materialsproject/pymatgen/issues/2716/events | https://github.com/materialsproject/pymatgen/issues/2716 | 1,430,945,087 | I_kwDOACgets5VSn0_ | 2,716 | AttributeError: 'ChargeInsertionAnalyzer' object has no attribute 'get_local_extrema' | {
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I am using pymatgen v. 2022.9.21 on my Linux. I am working on an interstitial point defect. When I tried to use the 'ChargeInsertionAnalyzer' object from the pymatgen.analysis.defects.utils, pymatgen imports the object without any problem. However, when I used the 'ChargeInsertionAnalyzer' object to obtain... | {
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"Also fixes the readme CI status badge:\r\n\r\n\r\n\r\nNoticed that coverage was at 0% last night and 36% this morning. Not sure if that will auto-fix. We might want to transiti... | 2022-11-01T16:11:51 | 2022-11-01T16:35:13 | 2022-11-01T16:17:44Z | MEMBER | {
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} | The changes in c2124293 broke `.github/workflows/release.yml` causing
> Error: No file in /Users/runner/work/pymatgen/pymatgen matched to [**/requirements.txt], make sure you have checked out the target repository | {
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