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Bump pylint from 2.3.1 to 2.4.0
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2019-09-24T21:54:44Z
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Bumps [pylint](https://github.com/PyCQA/pylint) from 2.3.1 to 2.4.0.
<details>
<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
>
> * New check: ``import-outside-toplevel``
>
> This check warns when modules are imported from places other than a
> module toplevel, e.g. inside a function or a class.
>
> * Handle inference ambiguity for ``invalid-format-index``
>
> Close [#2752](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2752)
>
> * Removed Python 2 specific checks such as ``relative-import``,
> ``invalid-encoded-data``, ``missing-super-argument``.
>
> * Support forward references for ``function-redefined`` check.
>
> Close [#2540](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2540)
>
> * Handle redefinitions in case of type checking imports.
>
> Close [#2834](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2834)
>
> * Added a new check, ``consider-using-sys-exit``
>
> This check is emitted when we detect that a quit() or exit() is invoked
> instead of sys.exit(), which is the preferred way of exiting in program.
>
> Close [#2925](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2925)
>
> * ``useless-suppression`` check now ignores ``cyclic-import`` suppressions,
> which could lead to false postiives due to incomplete context at the time
> of the check.
>
> Close [#3064](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3064)
>
> * Added new checks, ``no-else-break`` and ``no-else-continue``
>
> These checks highlight unnecessary ``else`` and ``elif`` blocks after
> ``break`` and ``continue`` statements.
>
> Close [#2327](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2327)
>
> * Don't emit ``protected-access`` when a single underscore prefixed attribute
> is used inside a special method
>
> Close [#1802](https://github-redirect.dependabot.com/PyCQA/pylint/issues/1802)
>
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`fce8bff`](https://github.com/PyCQA/pylint/commit/fce8bff8acc8dfa625529bde5c28691d94fad51e) Try again to do a release
- [`6775a00`](https://github.com/PyCQA/pylint/commit/6775a008486b6031ea36ff1ba4cf720a3edeb1d3) use a token for travis releases
- [`15209f6`](https://github.com/PyCQA/pylint/commit/15209f6642c8f9b2e1e100cdc8272d18f9363df6) Prepare release
- [`d9ed7d1`](https://github.com/PyCQA/pylint/commit/d9ed7d1db99d3b5ea84de4937997fae0dc22545f) Simplify and improve the logic of consider-iterating-dictionary
- [`d23a16e`](https://github.com/PyCQA/pylint/commit/d23a16e3cb454e6343bc3772c82dca172f3eb6a8) Add regression test for old-division and floats. Close [#3039](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3039)
- [`3e1f61d`](https://github.com/PyCQA/pylint/commit/3e1f61d0df4ded6479c5b109d495b8a1cd2cde31) Squash multiple checks for special classes into a single function
- [`ab79ac0`](https://github.com/PyCQA/pylint/commit/ab79ac0b53658fff9474d601baac5d6b831e5e5e) Disable too-few-public-methods for data classes. Close [#3025](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3025)
- [`7924325`](https://github.com/PyCQA/pylint/commit/79243257dc7e136dbfd6850e9285a01c909687bf) Document the new arguments for the private methods in docparams
- [`4b0395e`](https://github.com/PyCQA/pylint/commit/4b0395e32062ad2d50f617d778c1b755c7f066bd) Disable too-many-public-methods for humonguous class
- [`ce2af67`](https://github.com/PyCQA/pylint/commit/ce2af67d0e96e26c1999e1a53e36cf1460d9d647) Exempt kwonly arguments when they are annotated from missing-type-doc. Close ...
- Additional commits viewable in [compare view](https://github.com/PyCQA/pylint/compare/pylint-2.3.1...pylint-2.4.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pylint&package-manager=pip&previous-version=2.3.1&new-version=2.4.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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|
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MDU6SXNzdWU0OTc4NjQ0MDg=
| 1,602
|
Adding New Version to Conda
|
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[] | null |
[
"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 the conda-forge version is now the official one."
] | 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 the Anaconda version more frequently. I'm not sure if it would make sense to sync it with the PyPi build, but that would be wonderful.
**Describe alternatives you've considered**
Waiting until the version is updated. What's the release schedule? At least that way I can know when to expect installation problems with matminer users.
|
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MDExOlB1bGxSZXF1ZXN0MzIwOTQzNjgx
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path_finder midpoint
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[] | 2019-09-24T20:13:31
| 2019-10-02T18:42:38
|
2019-10-02T18:42:37Z
|
CONTRIBUTOR
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## Summary
Added an optional input of a midpoint image to the NEBPathfinder module
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MDU6SXNzdWU0OTgyMTk3NzI=
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Pymatgen error
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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 \nshowing the following error.\n\nTraceback (most recent call last):\n File \"setup2.py\", line 4, in <module>\n from pymatgen.ext.matproj import MPRester\nImportError: No module named pymatgen.ext.matproj\n\nI don't understand why it's happening.\n\nyour support will be helpful,\nRamya\n\n\nQuoting Shyue Ping Ong <notifications@github.com>:\n\n> You will have to give more details than that. It is impossible for \n> us to know what happened based on that one liner description. There \n> is a template for reporting Issues.\n>\n> --\n> You are receiving this because you authored the thread.\n> Reply to this email directly or view it on GitHub:\n> https://github.com/materialsproject/pymatgen/issues/1604#issuecomment-535001853\n\n\n",
"It is unclear what script this is. And as far as I know, it should work. I can only conclude that someone uninstalled your pymatgen. Pls reinstall and try again.",
"I completely installed pymatgen but when I run python program it always shows \"module 'pymatgen' has no attribute 'Structure'\" error. Since I can see structure.py in anaconda3/lib/python3.8/site-packages/pymatgen/core/structure.py",
"Pymatgen's structure object is now in pymatgen.core. Do `from pymatgen.core import Structure`."
] | 2019-09-25T11:20:03
| 2022-01-21T16:18:28
|
2019-11-11T14:53:03Z
|
NONE
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Suddenly, pymatgen stopped working with this error. May, I know the reason behind this error
*ImportError: No module named pymatgen.ext.matproj
|
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| 498,443,660
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MDExOlB1bGxSZXF1ZXN0MzIxMzc0MDEw
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|
Bump tabulate from 0.8.3 to 0.8.5
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[] | 2019-09-25T18:12:27
| 2019-09-25T18:33:36
|
2019-09-25T18:33:26Z
|
CONTRIBUTOR
|
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Bumps [tabulate](https://github.com/astanin/python-tabulate) from 0.8.3 to 0.8.5.
<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.
</details>
<details>
<summary>Commits</summary>
- See full diff in [compare view](https://github.com/astanin/python-tabulate/commits/v0.8.5)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tabulate&package-manager=pip&previous-version=0.8.3&new-version=0.8.5)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
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| 498,443,812
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MDExOlB1bGxSZXF1ZXN0MzIxMzc0MTI0
| 1,606
|
Bump phonopy from 1.11.12.121 to 2.3.2.post11
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2019-09-25T18:12:49
| 2019-09-25T18:53:30
|
2019-09-25T18:53:14Z
|
CONTRIBUTOR
|
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Bumps [phonopy](http://atztogo.github.io/phonopy/) from 1.11.12.121 to 2.3.2.post11.
[](https://dependabot.com/compatibility-score.html?dependency-name=phonopy&package-manager=pip&previous-version=1.11.12.121&new-version=2.3.2.post11)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
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MDExOlB1bGxSZXF1ZXN0MzIxMzc0MjQ5
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|
Bump pylint from 2.4.0 to 2.4.1
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[] | 2019-09-25T18:13:13
| 2019-09-25T18:33:57
|
2019-09-25T18:33:41Z
|
CONTRIBUTOR
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Bumps [pylint](https://github.com/PyCQA/pylint) from 2.4.0 to 2.4.1.
<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
>
>
> * Exempt type checking definitions defined in both clauses of a type checking guard
>
> Close [#3127](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3127)
>
>
> * Exempt type checking definitions inside the type check guard
>
> In a7f236528bb3758886b97285a56f3f9ce5b13a99 we added basic support
> for emitting `used-before-assignment` if a variable was only defined
> inside a type checking guard (using `TYPE_CHECKING` variable from `typing`)
> Unfortunately that missed the case of using those type checking imports
> inside the guard itself, which triggered spurious used-before-assignment errors.
>
> Close [#3119](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3119)
>
> * Require astroid >= 2.3 to avoid any compatibility issues.
</details>
<details>
<summary>Commits</summary>
- [`5d2fbaf`](https://github.com/PyCQA/pylint/commit/5d2fbaf76f234ff572e6be84ac1252af2eeea8bb) Prepare 2.4.1
- [`3159b17`](https://github.com/PyCQA/pylint/commit/3159b1744caee14068b4d875bb5adaa5ffbebd44) Exempt type checking definitions defined in both clauses of a type checking g...
- [`2fa5d43`](https://github.com/PyCQA/pylint/commit/2fa5d435df32ff363596de6e0285c13264e4ba30) Exempt type checking definitions inside the type check guard
- [`2600815`](https://github.com/PyCQA/pylint/commit/26008155931784eb933a5cd3a09f109cf105fd1b) Require astroid >= 2.3
- See full diff in [compare view](https://github.com/PyCQA/pylint/compare/pylint-2.4.0...pylint-2.4.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pylint&package-manager=pip&previous-version=2.4.0&new-version=2.4.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzIxODQyODA0
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Bump mypy from 0.720 to 0.730
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[] | 2019-09-26T18:08:22
| 2019-09-26T18:15:13
|
2019-09-26T18:15:00Z
|
CONTRIBUTOR
|
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Bumps [mypy](https://github.com/python/mypy) from 0.720 to 0.730.
<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) Document error codes ([#7451](https://github-redirect.dependabot.com/python/mypy/issues/7451))
- [`99475b2`](https://github.com/python/mypy/commit/99475b21705816a48a5f2cc0380907d21a93442f) Don't serialize redefined symbol nodes ([#7499](https://github-redirect.dependabot.com/python/mypy/issues/7499))
- [`8c17dd8`](https://github.com/python/mypy/commit/8c17dd863121138b20d92184786ed3777d4c574c) Don't compile mypyc/lib-rt/setup.py ([#7497](https://github-redirect.dependabot.com/python/mypy/issues/7497))
- [`41db9a0`](https://github.com/python/mypy/commit/41db9a0c570a3e190f3749cf0b681a31823dc0f7) Pass is_classmethod to bind_self() also for superype ([#7491](https://github-redirect.dependabot.com/python/mypy/issues/7491))
- [`2bdbacf`](https://github.com/python/mypy/commit/2bdbacf32a2b5201200dc2ed8ef5c7175b8de739) Attempt to fix travis on Python 3.8 beta ([#7492](https://github-redirect.dependabot.com/python/mypy/issues/7492))
- [`09c243d`](https://github.com/python/mypy/commit/09c243dcc12935b989367f31d1d25d7fd0ec634c) Point error to incompatible argument instead of call expression ([#7470](https://github-redirect.dependabot.com/python/mypy/issues/7470))
- [`88e2b67`](https://github.com/python/mypy/commit/88e2b67c4c2e8590dbee4aec272b3727b9566f0b) Support pickling of extension classes ([#7481](https://github-redirect.dependabot.com/python/mypy/issues/7481))
- [`9f1b8e9`](https://github.com/python/mypy/commit/9f1b8e930b812385fc866b3145785f7bb59361ef) Fix missing quotes in sample python snippet ([#7487](https://github-redirect.dependabot.com/python/mypy/issues/7487))
- [`37e5be1`](https://github.com/python/mypy/commit/37e5be10c845be3c036721c9462ef9cd90469236) Add http:// in front of the docs url for strict-optional ([#7485](https://github-redirect.dependabot.com/python/mypy/issues/7485))
- Additional commits viewable in [compare view](https://github.com/python/mypy/compare/v0.720...v0.730)
</details>
<br />
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MDU6SXNzdWU1MDAyNDczODU=
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Custom options in Bader Charge Analysis
|
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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 ways.",
"We can leave this issue open, we should add these features to the Bader caller. My point was that you would be welcome to add these features and submit the patch (PR) yourself if it's an urgent concern."
] | 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 function or class might hope to this feature.
|
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Speed up finding neighbor points with cython
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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 have `.pyx` files inside `pymatgen.optimization` -- you could put the new neighbors `.pyx` file inside that folder. You could then add `try: ... except ImportError: ...` inside `pymatgen.core.structure` and if it fails to import, then fall back to the old pure python version?\r\n\r\nI'm also open to other ideas.\r\n\r\nThis would work if the Python and Cython functions are functionally equivalent.",
"@mkhorton Thanks for the suggestion.. The code also used c++ and it seems that c++ is even more troublesome for distribution. I will go back and revise it. Thanks again. ",
"Wait first... \r\n personally, I don't think we should avoid C-extensions. With the conda-forge distributions, c extensions are fine. In any case, we already have them for coord_pbc and spglib.",
"I would say a good 50% of first-time-user queries we have are from broken C extensions.\r\n\r\nI think pymatgen should be *fast*, so I'm on-board with including C extensions, but if we already have a pure Python implementation why not fall back to that gracefully if the C extensions don't compile?",
"The spglib extensions aren't an issue because a lot of pymatgen can be used without them, the coord_pbc extensions are the ones that cause users problems (e.g. if they're just installing pymatgen to do some basic manipulations, or use the rester, etc.)",
"Do they cause issues in conda installs? If not, we should just point them there....",
"FYI, numpy is basically in all of pymatgen, and it is largely c....",
"Yeah, I don't know -- maybe numpy has more wheels available (e.g. see https://pypi.org/project/numpy/1.17.2/#files) or it's just pre-installed on more systems. In either case, we definitely do get queries about import errors with coord_cython.",
"Maybe something like this will help our wheel coverage https://github.com/joerick/cibuildwheel -- I'll investigate further. I still think having a graceful Python fallbacks makes sense if we already have a working, consistent pure Python version though.",
"I know we get queries. I am saying we should just point them to a conda install and tell them to go debug themselves if they do not want to use conda. Check out https://anaconda.org/conda-forge/pymatgen/files . As far as we are concerned, we have complete coverage of Win-OSX-Linux here. Since the uploading to conda-forge channel, we have gotten ~5k downloads in a matter of 1 month (it took us three years to get to 20k in the matsci channel). \r\n\r\nMy problem with maintaining a separate python version is the biggest no-no of coding - duplication. If I write the same routine in two different ways in two places, I have to remember to change two places when I make any changes to the API. ",
"Yes, that's true, and arguably something we've encountered already.\n\nThe flip side of this discussion is that by adding a second program\nlanguage (C) we're reducing the pool of people that can read and understand\nthe algorithm, including making improvements to it. It'll in practice\nbecome static/dead code. At least having the Python version gives us a\n\"reference\" implementation that's more readable, and easier to compare the\noutput of the optimized version to and see when they disagree.\n\nAs an example of both points we have a bug in the linear assignment code\nwith a fix proposed (see\nhttps://github.com/materialsproject/pymatgen/issues/1212) that is still\nopen because I'm not sure that anyone has a good understanding of that code\n(e.g. if there's a bug in\nhttps://github.com/materialsproject/pymatgen/blob/67e4fbc78890f93a8db0b38166eca3015c6cc4ca/pymatgen/optimization/linear_assignment.pyx#L80\nI'm not sure I'd ever find it).\n\nOn Mon, Sep 30, 2019 at 12:58 PM Shyue Ping Ong <notifications@github.com>\nwrote:\n\n> I know we get queries. I am saying we should just point them to a conda\n> install and tell them to go debug themselves if they do not want to use\n> conda. Check out https://anaconda.org/conda-forge/pymatgen/files . As far\n> as we are concerned, we have complete coverage of Win-OSX-Linux here. Since\n> the uploading to conda-forge channel, we have gotten ~5k downloads in a\n> matter of 1 month (it took us three years to get to 20k in the matsci\n> channel).\n>\n> My problem with maintaining a separate python version is the biggest no-no\n> of coding - duplication. If I write the same routine in two different ways\n> in two places, I have to remember to change two places when I make any\n> changes to the API.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1610?email_source=notifications&email_token=AAWWWRFMIV7MQGJKGBFKMCDQMJK6VA5CNFSM4I37IJT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD764W4I#issuecomment-536726385>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRFWRI5B37JFTRZVAL3QMJK6VANCNFSM4I37IJTQ>\n> .\n>\n",
"> so I'm on-board with including C extensions, but if we already have a pure Python implementation why not fall back to that gracefully if the C extensions don\r\n\r\nIf the C extension does not compile then user would not be able to install in the first place right? It seems that the `linear_assignment` fallback to python was deleted. ",
"> If the C extension does not compile then user would not be able to install in the first place right? \r\n\r\nI don't know, but I don't think so; I've seen installations where pymatgen is apparently installed but the Cython code doesn't work. So you can attempt to import pymatgen but you get an ImportError when the specific Cython submodule tries to get imported, e.g. `ImportError: cannot import name coord_cython`.",
"Just to add something to this discussion: I see you're keen on keeping the readability of python code with the speed of c. Have you put any thought into using [numba](https://numba.pydata.org/)? I've had success with applying numba to speed up my code. It allows you to get speed ups in performance critical sections while maintaining the readability of python. You literally only need to add a decorator to the function that you want to speed up. This also removes the problem of having to compile c code when distributing pymatgen.",
"I think numba’s a great suggestion, I know it plays nicely with numpy too.\n\nMight be worth comparing the speed to Cython; if it’s similar it will be a\nlot easier for us to optimize other parts of pymatgen too.\n\nOn Tue, Oct 1, 2019 at 11:24, Mark Turiansky <notifications@github.com>\nwrote:\n\n> Just to add something to this discussion: I see you're keen on keeping the\n> readability of python code with the speed of c. Have you put any thought\n> into using numba <https://numba.pydata.org/>? I've had success with\n> applying numba to speed up my code. It allows you to get speed ups in\n> performance critical sections while maintaining the readability of python.\n> You literally only need to add a decorator to the function that you want to\n> speed up. This also removes the problem of having to compile c code when\n> distributing pymatgen.\n>\n> —\n> You are receiving this because you were mentioned.\n>\n>\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1610?email_source=notifications&email_token=AAWWWRH7Q4REPZSNVNXL7TLQMOIWZA5CNFSM4I37IJT2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEACICCY#issuecomment-537166091>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe-auth/AAWWWREPTEKUW5DCIJ5TBILQMOIWZANCNFSM4I37IJTQ>\n> .\n>\n",
"Yes, numba plays nicely with numpy, and can even be faster than the numpy implementation in certain cases. My experience has been that numba is comparable to cython (sometimes faster because they use aggressive optimizations), e.g., [here's a comparison](https://jakevdp.github.io/blog/2013/06/15/numba-vs-cython-take-2/).",
"> Just to add something to this discussion: I see you're keen on keeping the readability of python code with the speed of c. Have you put any thought into using [numba](https://numba.pydata.org/)? I've had success with applying numba to speed up my code. It allows you to get speed ups in performance critical sections while maintaining the readability of python. You literally only need to add a decorator to the function that you want to speed up. This also removes the problem of having to compile c code when distributing pymatgen.\r\n\r\nGood suggestion! @mturiansky I played with numba long time ago and my experience was that you have to enable `nopython` mode to speed it up, and in that case some python object does not work. I prefer cython for this since it is statically typed and there will be fewer unexpected behaviors except for some memory handling. If you can try use numba to optimize some `pymatgen` code and show the results, that should be extremely helpful.\r\n",
"> I really like this code and these optimizations, but can we discuss how we expose this to the user?\r\n> \r\n> Some users have trouble compiling C extensions, so it would be nice to have a pure Python fallback for those users.\r\n> \r\n> I see that currently you have an `@deprecated` `get_all_neighbors_py`. We already have `.pyx` files inside `pymatgen.optimization` -- you could put the new neighbors `.pyx` file inside that folder. You could then add `try: ... except ImportError: ...` inside `pymatgen.core.structure` and if it fails to import, then fall back to the old pure python version?\r\n> \r\n> I'm also open to other ideas.\r\n> \r\n> This would work if the Python and Cython functions are functionally equivalent.\r\n\r\nThe `try: ... except ImportError` fall back to python is implemented in the latest commit. Thanks for the great suggestion. \r\n",
"My understanding of numba's \"nopython\" mode is just that you have to be strict with your types going in (which is fine) and that you have to avoid allocating new Python objects inside your loop (which you're not doing here, since you mentioned you're avoiding creating new Site objects).\r\n\r\nThis blog post makes a very compelling case for numba, https://jakevdp.github.io/blog/2013/06/15/numba-vs-cython-take-2/\r\n\r\nI too would be very interested in seeing a proof-of-concept -- for now this current solution looks good (@chc273, make sure you catch the `except ImportError` immediately after the `from ... import ...` line and put the remainder of that code in an `else` clause).\r\n\r\n",
"A choice quote:\r\n\r\n> Since then, Numba has had a few more releases, and both the interface and the performance has improved. On top of being much easier to use (i.e. automatic type inference by `autojit`) it's now about 50% faster, and is even a few percent faster than the Cython option.\r\n\r\n> And though I've seen similar things for months, I'm still incredibly impressed by the results enabled by Numba: a single function decorator results in a 1300x speedup of simple Python code. I'm becoming more and more convinced that Numba is the future of fast scientific computing in Python",
"> Good suggestion! @mturiansky I played with numba long time ago and my experience was that you have to enable `nopython` mode to speed it up, and in that case some python object does not work. I prefer cython for this since it is statically typed and there will be fewer unexpected behaviors except for some memory handling. If you can try use numba to optimize some `pymatgen` code and show the results, that should be extremely helpful.\r\n\r\n@chc273 You're right, nopython mode is necessary to get the speedup. The best way to approach the problem is essentially how you would with cython. You wrote a separate function `find_neighbors_in_sphere` which takes and returns numpy arrays and handles no other python objects. This is something numba handles quite well. You would essentially do the same with numba, write a separate python function that only handles numpy arrays and slap the numba `njit` decorator on it.\r\n\r\nI don't really have time at the moment to play around with optimizing some pymatgen, but I have a smallish example on my forked repository that speeds up wavecar processing (not much though because it's IO limited). You can see it [here](https://github.com/mturiansky/pymatgen/blob/hacks/pymatgen/io/vasp/outputs.py#L4058-L4090). All I did was move the \"_generate_G_points\" function outside the class and slap the `njit` on it. This function only takes numpy arrays as input and output so it's a prime candidate for numba optimization. I even made numba optional with [this try,except statement](https://github.com/mturiansky/pymatgen/blob/hacks/pymatgen/io/vasp/outputs.py#L45-L49).",
"@mturiansky was moving it outside the class necessary?",
"@mkhorton I believe so because if you have the `self` python object, then numba will complain. Maybe there's a way to do it with static methods or something but moving it outside was an easy solution.\r\n\r\nThey're working on support for classes, but it's in [beta](https://numba.pydata.org/numba-doc/dev/user/jitclass.html).",
"I am merging this now. If someone else want to take up the mantle of numba-ing it, ifine.",
"@chc273 I have sped up the get_all_neighbors function in Structure further by avoiding PeriodicSite construction. The main reason why PeriodicSite init is so slow is because of all the checks implemented. These checks are unnecessary when we are just creating a neighbor. \r\n\r\nNow the get_all_neighbors return a PeriodicNeighbor, which is much faster. Profiling suggests it shaves ~1s off a 10x10x10 Li2O cell with r = 5. Pls test it out. It is in the nnspeedup branch for now to make sure I haven't broken anything.",
"ok @shyuep ",
"> @chc273 I have sped up the get_all_neighbors function in Structure further by avoiding PeriodicSite construction. The main reason why PeriodicSite init is so slow is because of all the checks implemented. These checks are unnecessary when we are just creating a neighbor.\r\n> \r\n> Now the get_all_neighbors return a PeriodicNeighbor, which is much faster. Profiling suggests it shaves ~1s off a 10x10x10 Li2O cell with r = 5. Pls test it out. It is in the nnspeedup branch for now to make sure I haven't broken anything.\r\n\r\n@shyuep It does seem to increase the speed by 30% amount a few cases I tested with atom number > 1000. The speed is still throttled by the loop step, particularly, the comparison of site (line 1243) and the construction of neighbor object. \r\n\r\n\r\n",
"I sped it up further a litte by using a trick with checking the if statements. This is probably as fast as it is going to get. The PeriodicNeighor constructor is barebones and requires very few ops. So it is at the limit of what we can do.",
"> I sped it up further a litte by using a trick with checking the if statements. This is probably as fast as it is going to get. The PeriodicNeighor constructor is barebones and requires very few ops. So it is at the limit of what we can do.\r\n\r\nI agree, there does not seem to be other things to optimize in python. The issue seems to be also in the use of `dict` and `list` append, and for those we cannot optimize much in python. \r\n\r\nThe users can always use `Lattice.get_points_in_sphere` or just the cython func to gain much more speed if they know what they are doing. Thanks for the efforts. ",
"Fantastic speed-up :-)"
] | 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 sphere centers directly will be of value.
Here I am isolating a `find_neighbors_in_spheres` function that takes a two sets of cartesian coordinates `all_coords` and `center_coords`, as well as a `lattice` matrix and a cutoff radius `r`. The function will return all neighbors within `r` for `center_coords` that are in a lattice constructed by `lattice` matrix and `all_coords` point coordinates. This is written in `cython` syntax, and compiled to cpp.
The return data structure for the `find_neighbors_in_spheres` are four `np.ndarray`s:
`index1`, `index2`, `offsets`, `d`, where `index1` is a 1d array (size n) of `center_coords` indices, `index2` is a 1d array (size n) of `all_coords` indices, `offsets` is a 2d array (size nx3) that stores the image offset vectors for each `all_coords[index2]`, and `d` is a 1d array (size n) measuring the distance between center points and the neighbor points.
The new `find_points_in_spheres` should be extremely fast for specific purposes if accessed directly. However, it does not accelerate `Structure.get_all_neighbors` by much due to the slow speed of constructing sites and append to lists etc. Test results show that `find_points_in_spheres` takes less than 1% of the total time in `Structure.get_all_neighbors` when the system is large (> 1000 atoms), and is even less when the system size is even larger.
I also changed the definition of image offset vectors. In previous implementations, all site coordinates were first wrapped inside the periodic boundary and the image offset vectors are defined w.r.t. the wrapped sites. It is fine if the initial sites are all within the unit cell, but is problematic when we have initial coordinates of the structure that are outside the unit cell.
For example, if we have a structure `s=Structure(Lattice.cube(1), ['H', 'H'], [[1.1, 0, 0], [0.05, 0, 0]])`, previous implementation will find unexpected `image` offsets for neighbors of the second atom. Comparing `s.get_all_neighbors(0.06)[1]` and `s.get_all_neighbors_old(0.06, include_image=True)[1]`, the `old` version will give a neighbor `H(0.1, 0, 0)` with `image=(0, 0, 0)`. Apparently, this neighbor is a `(-1, 0, 0)` shifted `H[1.1, 0, 0]`.
Include a summary of major changes in bullet points:
* `find_points_in_spheres` cython implementation
* Changed the image offset vectors definition
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Bump pytest from 5.1.3 to 5.2.0
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[] | 2019-09-30T23:03:07
| 2019-09-30T23:14:24
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2019-09-30T23:14:16Z
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.1.3 to 5.2.0.
<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](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/1682): Passing
> arguments to pytest.fixture() as positional arguments is
> deprecated - pass them as a keyword argument instead.
>
> Features
> --------
>
> - [\#1682](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/1682): The
> `scope` parameter of `@pytest.fixture` can now be a callable that
> receives the fixture name and the `config` object as keyword-only
> parameters. See [the
> docs](https://docs.pytest.org/en/fixture.html#dynamic-scope) for
> more information.
> - [\#5764](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5764): New
> behavior of the `--pastebin` option: failures to connect to the
> pastebin server are reported, without failing the pytest run
>
> Bug Fixes
> ---------
>
> - [\#5806](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5806): Fix
> "lexer" being used when uploading to bpaste.net from `--pastebin`
> to "text".
> - [\#5884](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5884): Fix
> `--setup-only` and `--setup-show` for custom pytest items.
>
> Trivial/Internal Changes
> ------------------------
>
> - [\#5056](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5056): The
> HelpFormatter uses `py.io.get_terminal_width` for better
> width detection.
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.2.0 (2019-09-28)
> =========================
>
> Deprecations
> ------------
>
> - [\#1682](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/1682): Passing arguments to pytest.fixture() as positional arguments is deprecated - pass them as a keyword argument instead.
>
> Features
> --------
>
> - [\#1682](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/1682): The `scope` parameter of `@pytest.fixture` can now be a callable that receives the fixture name and the `config` object as keyword-only parameters. See [the docs](https://docs.pytest.org/en/fixture.html#dynamic-scope) for more information.
> - [\#5764](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5764): New behavior of the `--pastebin` option: failures to connect to the pastebin server are reported, without failing the pytest run
>
> Bug Fixes
> ---------
>
> - [\#5806](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5806): Fix "lexer" being used when uploading to bpaste.net from `--pastebin` to "text".
> - [\#5884](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5884): Fix `--setup-only` and `--setup-show` for custom pytest items.
>
> Trivial/Internal Changes
> ------------------------
>
> - [\#5056](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5056): The HelpFormatter uses `py.io.get_terminal_width` for better width detection.
</details>
<details>
<summary>Commits</summary>
- [`068ef90`](https://github.com/pytest-dev/pytest/commit/068ef90b92a9e9205af31cb3d82e7d2a433ff969) Preparing release version 5.2.0
- [`065773a`](https://github.com/pytest-dev/pytest/commit/065773aa97a02731e5eec05e29204b50850d9248) Use 'python3' instead of 'python3.6' on tox
- [`b622768`](https://github.com/pytest-dev/pytest/commit/b62276826c708ec4138c622b396fec711d5a836c) Merge pull request [#5886](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5886) from nicoddemus/setup-plan-custom-items-5884
- [`7bdfba3`](https://github.com/pytest-dev/pytest/commit/7bdfba3578455b58589e5834fea3feaf932018bd) Fix --setup-only and --setup-show for custom pytest items
- [`6bfd30d`](https://github.com/pytest-dev/pytest/commit/6bfd30d169c3192befb4cfd9b267caad7efb56cd) Merge pull request [#5878](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5878) from blueyed/codecov-retry-6
- [`7731e45`](https://github.com/pytest-dev/pytest/commit/7731e456151337a2830736115396d023c8188884) ci: codecov: use 6 retries with curl
- [`8806b1f`](https://github.com/pytest-dev/pytest/commit/8806b1f531683daebd819a297d059ee199879efb) Merge pull request [#5875](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5875) from asottile/patch-1
- [`19c9e53`](https://github.com/pytest-dev/pytest/commit/19c9e536044b969bf7c5377e7b0a5dff55a6accf) Make sure to quote `sys.executable` as we're running a shell
- [`c28b631`](https://github.com/pytest-dev/pytest/commit/c28b63135f53028bb0bcfb129f1dce757b4dfc0e) Merge master into features ([#5874](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5874))
- [`7c64d5d`](https://github.com/pytest-dev/pytest/commit/7c64d5d88243259e0bbd3a472e5ca7510d5cd9dc) Do not call python directly but use sys.executable. Fixes [#5872](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5872) ([#5873](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5873))
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.1.3...5.2.0)
</details>
<br />
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Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzIzMDEwMjk1
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|
Bump pylint from 2.4.1 to 2.4.2
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[] | 2019-09-30T23:03:28
| 2019-09-30T23:14:17
|
2019-09-30T23:14:03Z
|
CONTRIBUTOR
|
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Bumps [pylint](https://github.com/PyCQA/pylint) from 2.4.1 to 2.4.2.
<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`` can skip submodules. Close [#3135](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3135)
>
> * ``self-assigning-variable`` skips class level assignments.
>
> Close [#2930](https://github-redirect.dependabot.com/PyCQA/pylint/issues/2930)
>
> * ``consider-using-sys-exit`` is exempted when `exit()` is imported from `sys`
>
> Close [#3145](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3145)
>
> * Exempt annotated assignments without variable from ``class-variable-slots-conflict``
>
> Close [#3141](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3141)
>
> * Fix ``utils.is_error`` to account for functions returning early.
>
> This fixes a false negative with ``unused-variable`` which was no longer triggered
> when a function raised an exception as the last instruction, but the body of the function
> still had unused variables.
>
> Close [#3028](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3028)
</details>
<details>
<summary>Commits</summary>
- [`f7850aa`](https://github.com/PyCQA/pylint/commit/f7850aa8d9403d86e7f6d16a8974736180b043f2) Prepare 2.4.2
- [`6198797`](https://github.com/PyCQA/pylint/commit/6198797aac41f938dd752620efe04b3e8503e2d1) Pin mypy and typed-ast to fix the CI
- [`aa587ec`](https://github.com/PyCQA/pylint/commit/aa587eca1ec8a98c42fce6fac6f207bfb9f3a06e) Add the missing rc file for class_variable_slots_conflict
- [`552fa8a`](https://github.com/PyCQA/pylint/commit/552fa8a26c5f5f6c7661697bc4c9c835c3b7daa3) Fix ``utils.is_error`` to account for functions returning early.
- [`4ec293c`](https://github.com/PyCQA/pylint/commit/4ec293ce4700bfaca89d01c45e707f40c2913d49) Exempt annotated assignments without variable from ``class-variable-slots-con...
- [`1d3b07a`](https://github.com/PyCQA/pylint/commit/1d3b07a7280a1aad5eed1e937b8161113d1f049e) ``consider-using-sys-exit`` is exempted when `exit()` is imported from `sys`
- [`ae3d421`](https://github.com/PyCQA/pylint/commit/ae3d4211175e27c6e45d4f67e764425655d7e18e) Pin astroid to the latest minor release
- [`2777743`](https://github.com/PyCQA/pylint/commit/277774397023211bf89ca58a2c92a6c7b8fb39fb) Rename attributes to prepare for the astroid dataclass transform
- [`fde732e`](https://github.com/PyCQA/pylint/commit/fde732e0e9a4f224c5ae48ad942c6d955aa0a8e6) Bump master to 2.4.2
- [`d8fae01`](https://github.com/PyCQA/pylint/commit/d8fae0124b60abb40d833e78fb32fe355143889b) ``self-assigning-variable`` skips class level assignments.
- Additional commits viewable in [compare view](https://github.com/PyCQA/pylint/compare/pylint-2.4.1...pylint-2.4.2)
</details>
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[](https://dependabot.com/compatibility-score.html?dependency-name=pylint&package-manager=pip&previous-version=2.4.1&new-version=2.4.2)
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MDExOlB1bGxSZXF1ZXN0MzIzMjY3NjQw
| 1,613
|
Include additional check to avoid problems for summed cohps
|
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[] | null |
[
"Thanks."
] | 2019-10-01T13:18:42
| 2019-10-01T15:20:01
|
2019-10-01T15:19:56Z
|
MEMBER
|
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Hello!
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,
JG
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MDU6SXNzdWU1MDA5MTUxMzI=
| 1,614
|
Structure.to method silently ignores user specified file format
|
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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. First, I think keeping a list of supported outputs from Structure.to would be helpful. Secondly, I agree that raising an exception makes more sense than falling back to a default (if you want json/yaml you can ask for it). Thirdly, we should at least make sure to include all formats we support natively (e.g. the lammps format) and let the users know about the ASE/OpenBabel adaptors.\r\n\r\nThere are some other improvements to be made also; that method has a lot of duplicate code for writing to file, it'd be better to get the string representation first and write to file as a final step. Also the `from_file` and `from_str` methods are inconsistent and `from_file` should use `from_str` directly.",
"I pushed a change that fixes item 1. But for item 2, I believe that PDB is actually supported if you have Openbabel installed.",
"Thanks @mkhorton and @shyuep for the quick responses.\r\n\r\nI have installed Open Babel (or Pybel, anyway), but the file formats supported by the pymatgen.Structure.to method seem to be\r\n- .cif\r\n- .mcif (is this supposed to be the macromolecular cif format mmcif? it seems to write .cif syntax)\r\n- .poscar\r\n- .cssr\r\n- .json\r\n- .xsf\r\n- mcsqs\r\n- prismatic\r\n- yaml\r\n\r\nwhich doesn't seem to cover all the methods in pymatgen.io, or include .pdb.\r\n\r\nThis is getting off-topic from the title of this thread though, so I suppose we should probably wrap this up.\r\n\r\n-Peter",
"Ok. Yeah, I usually don't think of PDB files as a Structure type. Feel free to add the function at a time of your convenience."
] | 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 complaint).
**To Reproduce**
Steps to reproduce the behavior:
1. create a Structure instance
2. run Structure.to(fmt="nonsense", filename="more.nonsense")
**Expected behavior**
Structure.to method admits it is unable to fulfill your request for nonsense (raise if structure format not supported).
**Desktop (please complete the following information):**
- Version 2019.9.16
|
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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 separated A and B systems in order to see the change of charge density, we need to use something like functions above. But these AB, A, and B are totally different systems (or structure) that conflict with `self.structure != other.structure` conditions.
It would be better to compare the dimension of grid, axis grid or other information.
But if they have different dimensions, I expect that numpy array automatically causes an error.
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MDU6SXNzdWU1MDE0ODYwNTI=
| 1,616
|
XCrySDen parser fails to handle element symbols instead of atomic numbers
|
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[] | 2019-10-02T13:22:50
| 2019-10-02T18:42:12
|
2019-10-02T18:42:12Z
|
CONTRIBUTOR
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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 file will result in an error:
```
CRYSTAL
PRIMVEC
11.45191956 0.00000000 0.00000000
5.72596044 9.91765288 0.00000000
-14.31490370 -8.26471287 23.37613199
PRIMCOORD
1 1
Ag -0.71644986 -0.41364333 1.19898200 0.00181803 0.00084718 0.00804832
```
**Expected behavior**
I expect the structure to parse correctly (for instance, one which outputs, when printed):
```
Full Formula (Ag1)
Reduced Formula: Ag
abc : 11.451920 11.451920 28.629801
angles: 120.000008 120.000008 59.999996
Sites (1)
# SP a b c
--- ---- -------- -------- --------
0 Ag 0.001035 0.001035 0.051291
```
**Additional context**
In order to solve the problem, one can simply modify the XCrySDen parser file to attempt to convert elemental symbols into atomic numbers.
Current:
```
tokens = lines[j].split()
species.append(int(tokens[0]))
```
Fixed:
```
tokens = lines[j].split()
if tokens[0].isalpha():
Z = Element(tokens[0]).Z
else:
Z = int(tokens[0])
species.append(Z)
```
With an import statement `from pymatgen.core.periodic_table import Element`
at the top of the file.
I can provide the above fix in a pull request shortly.
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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 two different conventions yields the same result.",
"Thanks."
] | 2019-10-02T15:23:01
| 2019-10-02T18:42:17
|
2019-10-02T18:42:12Z
|
CONTRIBUTOR
|
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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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MDExOlB1bGxSZXF1ZXN0MzIzODI4NTAy
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NN speedup
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[] | 2019-10-02T16:04:19
| 2019-10-02T18:43:25
|
2019-10-02T18:35:17Z
|
MEMBER
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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 having checks (which are unnecessary since the NN sites are constructed in a controlled environment).
* One backwards incompatible thing introduced is that we have to rename Neighbor.distance to Neighbor.nn_distance. distance is actually a method name in Site/PeriodicSite. All uses within Pymatgen have been fixed.
* @mkhorton and @chc273 Pls review.
## Additional dependencies introduced (if any)
* None
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
|
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| 502,748,168
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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.",
"@chc273 Just pushed a fix.",
"Thanks ! I'll let them know to update their Xcode also"
] | 2019-10-04T17:09:36
| 2019-10-04T17:30:58
|
2019-10-04T17:30:47Z
|
MEMBER
|
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User report:
```
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=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps
cwd: /Users/.../uw/pymatgen/
Complete output (18 lines):
running develop
running egg_info
writing pymatgen.egg-info/PKG-INFO
writing dependency_links to pymatgen.egg-info/dependency_links.txt
writing entry points to pymatgen.egg-info/entry_points.txt
writing requirements to pymatgen.egg-info/requires.txt
writing top-level names to pymatgen.egg-info/top_level.txt
reading manifest file 'pymatgen.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
writing manifest file 'pymatgen.egg-info/SOURCES.txt'
running build_ext
building 'pymatgen.optimization.neighbors' extension
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/Users/.../miniconda3/envs/pmg/include -arch x86_64 -I/Users/.../miniconda3/envs/pmg/include -arch x86_64 -I/Users/.../miniconda3/envs/pmg/include/python3.6m -I/Users/.../miniconda3/envs/pmg/lib/python3.6/site-packages/numpy/core/include -c pymatgen/optimization/neighbors.cpp -o build/temp.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.o -Wno-cpp -Wno-unused-function -O2 -march=native -std=c++11 -stdlib=libc++
g++ -bundle -undefined dynamic_lookup -L/Users/.../miniconda3/envs/pmg/lib -arch x86_64 -L/Users/.../miniconda3/envs/pmg/lib -arch x86_64 -arch x86_64 build/temp.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.o -o build/lib.macosx-10.7-x86_64-3.6/pymatgen/optimization/neighbors.cpython-36m-darwin.so
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum deployment target of OS X 10.9 [-Wdeprecated]
ld: library not found for -lstdc++
clang: error: linker command failed with exit code 1 (use -v to see invocation)
error: command 'g++' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /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=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' develop --no-deps Check the logs for full command output.
```
@chc273 This shouldn't be too hard to fix, you have to link to `libc++` on macOS instead since `libstdc++` is not supported anymore. There are a few other Python codes that have had similar issues (including BoltzTraP I think?)
|
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fix c++ link args
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[] | 2019-10-04T17:28:56
| 2019-10-04T17:29:56
|
2019-10-04T17:29:56Z
|
CONTRIBUTOR
|
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## Summary
Fix macos compilation error by adding `-stdlib=libc++` link flag
|
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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 find out about errors, no one can fix them.",
"This seems related to https://github.com/materialsproject/pymatgen/commit/c0736012333d1ddda8ba3dde3e0745840482c6aa and https://github.com/materialsproject/pymatgen/commit/fb327af84439cad8c71d6325fec464f8eb522e27 and the re-definition of the `Neighbor` tuple, and in part may be due to the re-definition of image offset vectors in https://github.com/materialsproject/pymatgen/pull/1610 ?\r\n\r\nI'm surprised this didn't cause a test failure, a lot of code upstream relies on that `Neighbor` functionality.",
"A lot of tests were changed in that recent re-factoring, so I'm hesitant to assign blame on this.",
"@mkhorton The only recent test changed was just renaming of variables...",
"Some numbers changed in the FEFF tests, in the local_env tests and elsewhere -- they do look like fairly simple changes due to orderings or floating point arithmetic though, so perhaps it is a case of insufficient test coverage.\r\n\r\n@JSX can you re-run with the latest pymatgen? I'm confused how you're getting a return type of `PeriodicSite` and not `PeriodicNeighbor`.",
"If I run the example code given, I get\r\n\r\n```\r\n[[{'image': (-1, 0, 0),\r\n 'site': PeriodicSite: Li (-0.9809, 0.1200, 4.3019) [-0.0982, 0.0180, 0.8279],\r\n 'site_index': 3,\r\n 'weight': 0.9975959536111771},\r\n {'image': (0, 0, 1),\r\n 'site': PeriodicSite: Li (1.0560, 3.8112, 6.0457) [0.0960, 0.5180, 1.1609],\r\n 'site_index': 7,\r\n 'weight': 0.9307434704883277},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (4.2205, 0.1177, 3.4839) [0.4018, 0.0180, 0.6609],\r\n 'site_index': 1,\r\n 'weight': 1.0}],\r\n [{'image': (0, -1, 0),\r\n 'site': PeriodicSite: Li (3.6528, -2.0276, 1.0346) [0.3494, -0.2732, 0.1905],\r\n 'site_index': 6,\r\n 'weight': 0.9266800713864679},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (1.5799, 1.6645, 3.6072) [0.1484, 0.2268, 0.6905],\r\n 'site_index': 0,\r\n 'weight': 1.0},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.7954, 1.6576, 4.2207) [0.6484, 0.2268, 0.7983],\r\n 'site_index': 2,\r\n 'weight': 0.9913899497983444}],\r\n [{'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (4.2205, 0.1177, 3.4839) [0.4018, 0.0180, 0.6609],\r\n 'site_index': 1,\r\n 'weight': 0.9934050363859691},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.2229, 3.8201, 1.7585) [0.5960, 0.5180, 0.3279],\r\n 'site_index': 5,\r\n 'weight': 0.9225875754353673},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (9.4391, 0.1098, 4.4057) [0.9018, 0.0180, 0.8279],\r\n 'site_index': 3,\r\n 'weight': 1.0}],\r\n [{'image': (0, -1, 1),\r\n 'site': PeriodicSite: Li (8.9196, -2.0513, 6.8570) [0.8494, -0.2732, 1.2983],\r\n 'site_index': 4,\r\n 'weight': 0.9275148223048283},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.7954, 1.6576, 4.2207) [0.6484, 0.2268, 0.7983],\r\n 'site_index': 2,\r\n 'weight': 1.0},\r\n {'image': (1, 0, 0),\r\n 'site': PeriodicSite: Li (11.9999, 1.6544, 3.7110) [1.1484, 0.2268, 0.6905],\r\n 'site_index': 0,\r\n 'weight': 0.9996236544431264}],\r\n [{'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.2229, 3.8201, 1.7585) [0.5960, 0.5180, 0.3279],\r\n 'site_index': 5,\r\n 'weight': 1.0},\r\n {'image': (1, 0, 0),\r\n 'site': PeriodicSite: Li (11.4247, 3.8178, 0.9405) [1.0960, 0.5180, 0.1609],\r\n 'site_index': 7,\r\n 'weight': 0.9956714113657653},\r\n {'image': (0, 1, -1),\r\n 'site': PeriodicSite: Li (9.3796, 7.5235, -0.8252) [0.9018, 1.0180, -0.1721],\r\n 'site_index': 3,\r\n 'weight': 0.9241801961783966}],\r\n [{'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (3.6446, 5.3694, 1.0126) [0.3494, 0.7268, 0.1905],\r\n 'site_index': 6,\r\n 'weight': 0.9867380992160973},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.7954, 1.6576, 4.2207) [0.6484, 0.2268, 0.7983],\r\n 'site_index': 2,\r\n 'weight': 0.9192706638788241},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (8.8601, 5.3625, 1.6261) [0.8494, 0.7268, 0.2983],\r\n 'site_index': 4,\r\n 'weight': 1.0}],\r\n [{'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (1.0047, 3.8280, 0.8367) [0.0960, 0.5180, 0.1609],\r\n 'site_index': 7,\r\n 'weight': 1.0},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (6.2229, 3.8201, 1.7585) [0.5960, 0.5180, 0.3279],\r\n 'site_index': 5,\r\n 'weight': 0.9880414066867201},\r\n {'image': (0, 1, 0),\r\n 'site': PeriodicSite: Li (4.2124, 7.5147, 3.4620) [0.4018, 1.0180, 0.6609],\r\n 'site_index': 1,\r\n 'weight': 0.9264472924665904}],\r\n [{'image': (-1, 0, 0),\r\n 'site': PeriodicSite: Li (-1.5599, 5.3727, 1.5223) [-0.1506, 0.7268, 0.2983],\r\n 'site_index': 4,\r\n 'weight': 0.9969865181704477},\r\n {'image': (0, 0, -1),\r\n 'site': PeriodicSite: Li (1.5286, 1.6813, -1.6018) [0.1484, 0.2268, -0.3095],\r\n 'site_index': 0,\r\n 'weight': 0.9305096708562495},\r\n {'image': (0, 0, 0),\r\n 'site': PeriodicSite: Li (3.6446, 5.3694, 1.0126) [0.3494, 0.7268, 0.1905],\r\n 'site_index': 6,\r\n 'weight': 1.0}]]\r\n```\r\n\r\nWhich does not seem unreasonable?",
"the example code gives me:\r\n\r\n```\r\n---------------------------------------------------------------------------\r\nException Traceback (most recent call last)\r\n<ipython-input-1-392fe7858277> in <module>\r\n 57 \r\n 58 strat = MinimumDistanceNN(cutoff=4.0)\r\n---> 59 strat.get_all_nn_info(ss)\r\n\r\n~/repos/js_mp/pymatgen/pymatgen/analysis/local_env.py in get_all_nn_info(self, structure)\r\n 363 \"\"\"\r\n 364 \r\n--> 365 return [self.get_nn_info(structure, n) for n in range(len(structure))]\r\n 366 \r\n 367 def get_nn_shell_info(self, structure, site_idx, shell):\r\n\r\n~/repos/js_mp/pymatgen/pymatgen/analysis/local_env.py in <listcomp>(.0)\r\n 363 \"\"\"\r\n 364 \r\n--> 365 return [self.get_nn_info(structure, n) for n in range(len(structure))]\r\n 366 \r\n 367 def get_nn_shell_info(self, structure, site_idx, shell):\r\n\r\n~/repos/js_mp/pymatgen/pymatgen/analysis/local_env.py in get_nn_info(self, structure, n)\r\n 1166 w = min_dist / dist\r\n 1167 siw.append({'site': nn,\r\n-> 1168 'image': self._get_image(structure, nn),\r\n 1169 'weight': w,\r\n 1170 'site_index': self._get_original_site(structure,\r\n\r\n~/repos/js_mp/pymatgen/pymatgen/analysis/local_env.py in _get_image(structure, site)\r\n 502 \"\"\"\r\n 503 original_site = structure[\r\n--> 504 NearNeighbors._get_original_site(structure, site)]\r\n 505 image = np.around(\r\n 506 np.subtract(site.frac_coords, original_site.frac_coords))\r\n\r\n~/repos/js_mp/pymatgen/pymatgen/analysis/local_env.py in _get_original_site(structure, site)\r\n 515 if site.is_periodic_image(s):\r\n 516 return i\r\n--> 517 raise Exception('Site not found!')\r\n 518 \r\n 519 def get_bonded_structure(self, structure, decorate=False, weights=True):\r\n\r\nException: Site not found!\r\n```\r\n\r\n",
"Yup, I get the same, I can't replicate the bug. @jsx could this be related to the compilation issue fixed this morning, maybe your installation is broken if you installed it manually before the fix?",
"I think it's unrelated to this bug but we do have some commented-out tests in master:\r\n https://github.com/materialsproject/pymatgen/blob/c15b090e128b6d4f1bb15f4ed6e71bb06042ff1d/pymatgen/core/tests/test_structure.py#L408\r\n\r\nThey should probably be uncommented or removed.",
"OK, I only updated the code earlier but did not rerun the compile. Recompiling did fix the problem.\r\n",
"Yes I I commented those because they are just a cross check between the old and new get neighbors code that is quite slow. ",
"Great, glad to hear it!",
"Thanks!!",
"@shyuep maybe we could add a `skipIf` instead, if they're useful for development purposes rather than deleting them? I think there are probably a few tests we could use that for",
"Sure."
] | 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]],
'a': 10.42,
'b': 7.397,
'c': 5.21,
'alpha': 90.35,
'beta': 88.86,
'gamma': 90.12,
'volume': 401.4},
'sites': [{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.1484, 0.2268, 0.6905],
'xyz': [1.58, 1.665, 3.607],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.4018, 0.01796, 0.6609],
'xyz': [4.22, 0.1177, 3.484],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.6484, 0.2268, 0.7983],
'xyz': [6.795, 1.658, 4.221],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.9018, 0.01796, 0.8279],
'xyz': [9.438, 0.1098, 4.406],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.8494, 0.7268, 0.2983],
'xyz': [8.859, 5.363, 1.626],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.596, 0.518, 0.3279],
'xyz': [6.223, 3.82, 1.759],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.3494, 0.7268, 0.1905],
'xyz': [3.644, 5.37, 1.013],
'label': 'Li',
'properties': {}},
{'species': [{'element': 'Li', 'occu': 1}],
'abc': [0.09603, 0.518, 0.1609],
'xyz': [1.005, 3.828, 0.837],
'label': 'Li',
'properties': {}}]})
strat = MinimumDistanceNN(cutoff=4.0)
strat.get_all_nn_info(ss)
```
This code hits an `Exception: Site not found!`.
This is resulting from the fract that
```
site = ss.sites[0]
ss.get_neighbors(site, 4.0)
```
is given weird results (as in the images are not periodic images and way too far away):
```
# neighbors
[PeriodicSite: Li (44.1557, 0.7690, 18.5834) [4.2205, 0.1177, 3.4839],
PeriodicSite: Li (11.2826, 28.0793, 31.5183) [1.0560, 3.8112, 6.0457],
PeriodicSite: Li (10.4804, 28.2912, 4.3789) [1.0047, 3.8280, 0.8367],
PeriodicSite: Li (-10.0012, 0.8252, 22.3044) [-0.9809, 0.1200, 4.3019]]
```
Using the v2019.10.2 code the result is:
```
[Neighbor(site=PeriodicSite: Li (4.2205, 0.1177, 3.4839) [0.4018, 0.0180, 0.6609], distance=3.062818554812417, index=1, image=(0.0, 0.0, 0.0)),
Neighbor(site=PeriodicSite: Li (1.0560, 3.8112, 6.0457) [0.0960, 0.5180, 1.1609], distance=3.290722580310412, index=7, image=(0.0, 0.0, 1.0)),
Neighbor(site=PeriodicSite: Li (1.0047, 3.8280, 0.8367) [0.0960, 0.5180, 0.1609], distance=3.5618844127309797, index=7, image=(0.0, 0.0, 0.0)),
Neighbor(site=PeriodicSite: Li (-0.9809, 0.1200, 4.3019) [-0.0982, 0.0180, 0.8279], distance=3.070199456729333, index=3, image=(-1.0, 0.0, 0.0))]
```
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MDExOlB1bGxSZXF1ZXN0MzI0ODE0NDc3
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Bump pytest-cov from 2.7.1 to 2.8.0
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[] | 2019-10-04T19:15:31
| 2019-10-04T19:18:30
|
2019-10-04T19:18:16Z
|
CONTRIBUTOR
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Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.7.1 to 2.8.0.
<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 when using [cleanup\_on\_signal](https://pytest-cov.readthedocs.io/en/latest/subprocess-support.html#if-you-got-custom-signal-handling) or [cleanup\_on\_sigterm](https://pytest-cov.readthedocs.io/en/latest/subprocess-support.html#if-you-got-custom-signal-handling). See: [\#294](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/issues/294). The 2.7.x releases of pytest-cov should be considered broken regarding aforementioned cleanup API.
> - Added compatibility with future xdist release that deprecates some internals (match pytest-xdist master/worker terminology). Contributed by Thomas Grainger in [\#321](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/321)
> - Fixed breakage that occurs when multiple reporting options are used. Contributed by Thomas Grainger in [\#338](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/338).
> - Changed internals to use a stub instead of `os.devnull`. Contributed by Thomas Grainger in [\#332](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/332).
> - Added support for Coverage 5.0. Contributed by Ned Batchelder in [\#319](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/319).
> - Added support for float values in `--cov-fail-under`. Contributed by Martín Gaitán in [\#311](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/311).
> - Various documentation fixes. Contributed by Juanjo Bazán, Andrew Murray and Albert Tugushev in [\#298](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/298), [\#299](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/299) and [\#307](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/307).
> - Various testing improvements. Contributed by Ned Batchelder, Daniel Hahler, Ionel Cristian Mărieș and Hugo van Kemenade in [\#313](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/313), [\#314](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/314), [\#315](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/315), [\#316](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/316), [\#325](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/325), [\#326](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/326), [\#334](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/334) and [\#335](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/335).
> - Added the `--cov-context` CLI options that enables coverage contexts. Only works with coverage 5.0+. Contributed by Ned Batchelder in [\#345](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/pull/345).
</details>
<details>
<summary>Commits</summary>
- [`5df26bd`](https://github.com/pytest-dev/pytest-cov/commit/5df26bd6a1ad2756d5bbd658be24d83f052e4420) Bump version: 2.7.1 → 2.8.0
- [`9f227c2`](https://github.com/pytest-dev/pytest-cov/commit/9f227c292d53cab9fd17822e9896fa4934740272) Add xdist 0.30 and update bootstrap.py to work better (on windows too).
- [`5cc697f`](https://github.com/pytest-dev/pytest-cov/commit/5cc697fc2d2c5aa4aca93dbf0e1e2bf2e3df6bf0) Add a note about the cleanup fix.
- [`7c01530`](https://github.com/pytest-dev/pytest-cov/commit/7c01530fd079467275ec2fe27d7512aee34ea248) Update changelog and authors.
- [`994fb00`](https://github.com/pytest-dev/pytest-cov/commit/994fb00badbc523278342d9c6903aa4dff96ebd1) Update for coverage 5.0a8
- [`5f70ec4`](https://github.com/pytest-dev/pytest-cov/commit/5f70ec4e9da7e21123e6732bf8b7b79725fb49fb) Sort imports and add isort as a check.
- [`a4d952d`](https://github.com/pytest-dev/pytest-cov/commit/a4d952dbdf4c895c6232abdcaf72a8b4e521aa54) The --cov-context option for setting context per test
- [`419a010`](https://github.com/pytest-dev/pytest-cov/commit/419a010782cb7d00c3dde7d296f1595696393e8f) No need to skip for coverage < 4, we don't support coverage < 4
- [`f4a4a29`](https://github.com/pytest-dev/pytest-cov/commit/f4a4a29a703640ee433245ddac2bc6bd02242abc) Pytest 5.2 is out
- [`d3bac1b`](https://github.com/pytest-dev/pytest-cov/commit/d3bac1b0aefd326efa7a3f85e9a47259e61598a8) Properly deal with configurable HTML output dirs
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest-cov/compare/v2.7.1...v2.8.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest-cov&package-manager=pip&previous-version=2.7.1&new-version=2.8.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzI0ODYwMTAw
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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 molecules and surfaces in a periodic lattice. Some other softwares, for example, lammps do have nonperiodic boundaries by setting 'boundary' keyword. For me I want to have structure and molecule somewhat unified in our attempts to build unified models. I do like ASE's approach of using \"Atoms\", but its not handy when dealing with complex crystal-based computations. Those computations are also not compatible with molecules. Are we interested in pursuing the unification which may sacrifice certain functionality or make those difficult to use?"
] | 2019-10-04T21:42:54
| 2019-10-06T18:13:45
|
2019-10-06T17:15:03Z
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CONTRIBUTOR
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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 non-periodic dimension. Previous one was not robust and needs to supply a large enough lattice to make it correct. This is fixed in this PR.
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MDExOlB1bGxSZXF1ZXN0MzI1MzAxNDg5
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Fix reading lobsterout
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[] | 2019-10-07T13:27:16
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2019-10-07T16:19:28Z
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MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MzI1NTMzNDk1
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Bump pytest-cov from 2.8.0 to 2.8.1
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[] | 2019-10-07T23:15:24
| 2019-10-07T23:51:43
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2019-10-07T23:51:24Z
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CONTRIBUTOR
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Bumps [pytest-cov](https://github.com/pytest-dev/pytest-cov) from 2.8.0 to 2.8.1.
<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.dependabot.com/pytest-dev/pytest-cov/issues/348) -regression when only certain reports (html or xml) are used then `--cov-fail-under` always fails.
</details>
<details>
<summary>Commits</summary>
- [`33894b5`](https://github.com/pytest-dev/pytest-cov/commit/33894b550e6445525461ae5dacd3cbbcf381ea41) Bump version: 2.8.0 → 2.8.1
- [`3aa43a0`](https://github.com/pytest-dev/pytest-cov/commit/3aa43a035631d005e5f64e62ff8d6876cc01ab19) Be more strict - return None so problems like [#348](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/issues/348) will trip up the later Non...
- [`a078b55`](https://github.com/pytest-dev/pytest-cov/commit/a078b5531896c7a5c12024dd9b1882607317ae99) Update changelog.
- [`5ef4767`](https://github.com/pytest-dev/pytest-cov/commit/5ef47676af88bd79764e234d0ace463dcaac4437) Fix regression described in [#348](https://github-redirect.dependabot.com/pytest-dev/pytest-cov/issues/348) - not all reports returning the total.
- See full diff in [compare view](https://github.com/pytest-dev/pytest-cov/compare/v2.8.0...v2.8.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest-cov&package-manager=pip&previous-version=2.8.0&new-version=2.8.1)
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Bump pytest from 5.2.0 to 5.2.1
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[] | 2019-10-07T23:15:46
| 2019-10-07T23:50:33
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2019-10-07T23:50:21Z
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.2.0 to 5.2.1.
<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://github-redirect.dependabot.com/pytest-dev/pytest/issues/5902): Fix
> warnings about deprecated `cmp` attribute in `attrs>=19.2`.
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.2.1 (2019-10-06)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5902](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5902): Fix warnings about deprecated `cmp` attribute in `attrs>=19.2`.
</details>
<details>
<summary>Commits</summary>
- [`12cc729`](https://github.com/pytest-dev/pytest/commit/12cc729f6b50abbd3708dfc64e76ff454852b805) Preparing release version 5.2.1
- [`1c5efff`](https://github.com/pytest-dev/pytest/commit/1c5efffd904e0068a3e7b4090d94bbe589be66bf) Add changelog entry for [#5902](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5902)
- [`8c9ea5e`](https://github.com/pytest-dev/pytest/commit/8c9ea5e055e7ef7a7d33db65c781adee16b55bc0) Fix warnings with attrs 19.2 and fix object assertions ([#5902](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5902))
- [`c58b0fb`](https://github.com/pytest-dev/pytest/commit/c58b0fb4acefefc81a12ab92ad3f37384218ee78) Use ATTRS_EQ_FIELD for attrs 19.2 compat
- [`4011af6`](https://github.com/pytest-dev/pytest/commit/4011af68cd84a69f0b222503eb5f2dc71bdd7e83) Merge pull request [#5910](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5910) from pytest-dev/asottile-patch-1
- [`9637b3e`](https://github.com/pytest-dev/pytest/commit/9637b3e376d6e94c10af5c7132f97fd3cb308125) Fix dynamic scoping changelog link
- [`33c3ec6`](https://github.com/pytest-dev/pytest/commit/33c3ec66b77b8e5b3abbe0a81aafceafec1932ee) Merge pull request [#5898](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5898) from kevinjfoley/doc-typo-fix
- [`a79acf2`](https://github.com/pytest-dev/pytest/commit/a79acf279a80bbbac0a05d8fadf62649753c668a) Fix warnings with attrs 19.2 and fix object assertions
- [`9a4c0b9`](https://github.com/pytest-dev/pytest/commit/9a4c0b991b07dff83896999717545b2b44b38901) Update doc: pytest section in setup.cfg ([#5894](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5894))
- [`b490f5f`](https://github.com/pytest-dev/pytest/commit/b490f5f97915ebe63666e1a51816f81c43d16267) Fix doc typo
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.2.0...5.2.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.2.0&new-version=5.2.1)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzI2MDM4MjM1
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Eigenval object
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[
"Great. Thanks!"
] | 2019-10-09T02:31:25
| 2019-10-09T04:00:03
|
2019-10-09T03:58:16Z
|
CONTRIBUTOR
|
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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 future.
## Checklist
Work-in-progress pull requests are encouraged, but please put [WIP]
in the pull request title.
Before a pull request can be merged, the following items must be checked:
- [x] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/).
Run [pycodestyle](https://pycodestyle.readthedocs.io/en/latest/) and [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
|
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MDExOlB1bGxSZXF1ZXN0MzI2MTc5Mzg4
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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
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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 it is supplied by the user.
Best,
JG
## Checklist
Before a pull request can be merged, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
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- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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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 works
with open(f't.json', 'w') as f:
json.dump(sym, f, cls=MontyEncoder)
with open(f't.json') as f:
sym = json.load(f, cls=MontyDecoder)
```
Still throws
> TypeError: __init__() got an unexpected keyword argument 'charge'
|
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| 506,818,546
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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 `ValenceIonicRadiusEvaluator` calculates ionic radii for the whole structure simultaneously.
I've therefore enabled caching of the `ValenceIonicRadiusEvaluator` class using the `lru_cache` functionality in `functools`. In my testing, for some structures this result in a 10x speedup.
|
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| 506,863,601
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MDExOlB1bGxSZXF1ZXN0MzI3OTY0Mjc0
| 1,631
|
Workflow refactoring
|
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[] | null |
[
"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 details on how to adjust your build configuration on: https://docs.travis-ci.com/user/common-build-problems/#build-times-out-because-no-output-was-received\r\nThe build has been terminated\r\n```\r\n\r\nCould you restart the travis bot? Thanks.",
"I will just wait for CircleCI to pass the etsts and will merge after that."
] | 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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MDU6SXNzdWU1MDc2NDg2OTk=
| 1,632
|
Documentation for conda installation
|
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[] | 2019-10-16T06:42:15
| 2019-10-16T13:16:05
|
2019-10-16T13:16:05Z
|
CONTRIBUTOR
|
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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](https://pymatgen.org/installation.html#step-3-install-pymatgen)) :
conda install --channel matsci pymatgen
**Expected behavior**
Installation of pymatgen
**Solution**
It is of course working if you use the right channel (conda-forge). => change the documentation on the webpage. I haven't checked if the documentation of other related packages also refers to the matsci channel (For monty I think it does not).
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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 and end point positions. In some cases, the so called bad arrangement that you show might actually be the desired arrangement, e.g., if I have multiple types of the same species and I need to apply some tricks, e.g., setting different U values for Fe2+ and Fe3+ in Fe3O4. \r\n\r\nThe rule is always - the user knows what he is doing. So he should have done the sorting using Structure.get_sorted_structure if that is what he wants.",
"If there is a max line length from VASP, we should check for that when writing the POSCAR: if we know it will cause a bug because the full line isn't read by VASP then we should raise an error.",
"Ok, I see the uses cases. I'll try and add some documentation so that this is clear. "
] | 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 that can even be truncated when read in. This also leads to huge POTCARs due to the non-sequential repeat.
**Expected Behavior**
The issue is due to conflicting prescriptions of order. `Poscar` is written assuming preordered structures. But the current structures are not enforcing order. My intuition is that Poscar should reorder the structure by default to make reasonable input files. This can cause problems for anyone expecting the site indicies to stay the same. This might be mitigated by making this a flag in `Poscar`? The other option is to enforce ordering atoms in `Slab` and any other complex structures. I don't see any problems with this, but this site ordering issue is AFAIK unique to VASP.
**Example code**
```
from pymatgen.util.testing import PymatgenTest
from pymatgen.core.surface import SlabGenerator
from pymatgen.io.vasp.inputs import Poscar
sio2 = PymatgenTest.get_structure("SiO2")
slabgen = SlabGenerator(sio2,miller_index=(1,1,0),min_slab_size=5,min_vacuum_size=3,in_unit_planes=True)
poscar = Poscar(slabgen.get_slab(0))
print(poscar)
```
Output:
```
Si15 O30
1.0
5.518918 0.000000 0.000000
-0.000000 4.354187 7.541673
0.000000 0.000000 40.222254
Si O Si O Si O Si O Si O
3 6 3 6 3 6 3 6 3 6
direct
0.000010 0.522709 0.119322 Si
0.333344 0.477288 0.065339 Si
0.666677 0.000003 0.065338 Si
0.129333 0.584963 0.071972 O
0.462667 0.160740 0.011695 O
0.796000 0.254296 0.041333 O
0.870690 0.839261 0.071972 O
0.537356 0.745704 0.011695 O
0.204023 0.415036 0.041334 O
0.000010 0.522709 0.244322 Si
0.333344 0.477288 0.190339 Si
0.666677 0.000003 0.190338 Si
0.129333 0.584963 0.196972 O
0.462667 0.160740 0.136695 O
0.796000 0.254296 0.166333 O
0.870690 0.839261 0.196972 O
0.537356 0.745704 0.136695 O
0.204023 0.415036 0.166334 O
0.000010 0.522709 0.369322 Si
0.333344 0.477288 0.315339 Si
0.666677 0.000003 0.315338 Si
0.129333 0.584963 0.321972 O
0.462667 0.160740 0.261695 O
0.796000 0.254296 0.291333 O
0.870690 0.839261 0.321972 O
0.537356 0.745704 0.261695 O
0.204023 0.415036 0.291334 O
0.000010 0.522709 0.494322 Si
0.333344 0.477288 0.440339 Si
0.666677 0.000003 0.440338 Si
0.129333 0.584963 0.446972 O
0.462667 0.160740 0.386695 O
0.796000 0.254296 0.416333 O
0.870690 0.839261 0.446972 O
0.537356 0.745704 0.386695 O
0.204023 0.415036 0.416334 O
0.000010 0.522709 0.619322 Si
0.333344 0.477288 0.565339 Si
0.666677 0.000003 0.565338 Si
0.129333 0.584963 0.571972 O
0.462667 0.160740 0.511695 O
0.796000 0.254296 0.541333 O
0.870690 0.839261 0.571972 O
0.537356 0.745704 0.511695 O
0.204023 0.415036 0.541334 O
```
|
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| 508,235,867
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MDExOlB1bGxSZXF1ZXN0MzI5MDY3MTY0
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Bump mypy from 0.730 to 0.740
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[] | null |
[] | 2019-10-17T05:02:35
| 2019-10-17T05:26:37
|
2019-10-17T05:26:24Z
|
CONTRIBUTOR
|
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Bumps [mypy](https://github.com/python/mypy) from 0.730 to 0.740.
<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) Fix __init_subclass__ type check ([#7723](https://github-redirect.dependabot.com/python/mypy/issues/7723))
- [`9751449`](https://github.com/python/mypy/commit/975144969199d388a3c34e74a0a23825e33b7e74) Remove new_semantic_analyzer from config parameters ([#7529](https://github-redirect.dependabot.com/python/mypy/issues/7529))
- [`6a5cc35`](https://github.com/python/mypy/commit/6a5cc35039fec6fae9cc88b6840d2d3775c4a8cf) Sync typeshed ([#7682](https://github-redirect.dependabot.com/python/mypy/issues/7682))
- [`2288371`](https://github.com/python/mypy/commit/228837190169769b2bb15d183305ae712434dc11) Always show the cause of error in dmypy suggest ([#7680](https://github-redirect.dependabot.com/python/mypy/issues/7680))
- [`263ba7f`](https://github.com/python/mypy/commit/263ba7fe4f0d6d5993180c923a547c01a85ea7bb) Support FIXME names for unknown types in dmypy suggest ([#7679](https://github-redirect.dependabot.com/python/mypy/issues/7679))
- [`40f4d66`](https://github.com/python/mypy/commit/40f4d6628d52113e191386d7256d9988382666d8) Improve color and terminal width overrides ([#7674](https://github-redirect.dependabot.com/python/mypy/issues/7674))
- [`33e3558`](https://github.com/python/mypy/commit/33e35589ce37136e334bddd057c37d250cb917d9) Fix operator error messages for __div__ and __cmp__ on python 2 ([#7671](https://github-redirect.dependabot.com/python/mypy/issues/7671))
- [`c95ecc1`](https://github.com/python/mypy/commit/c95ecc1952b4f804662e37b36c0779b32226f88b) Only return a declared type from __new__ if it is a subtype of the class ([#7656](https://github-redirect.dependabot.com/python/mypy/issues/7656))
- [`6f8480c`](https://github.com/python/mypy/commit/6f8480c9d1dcbcacc8bc248665cfbb42c9920270) Update examples of mutable and non-mutable mapping in cheat sheet ([#7620](https://github-redirect.dependabot.com/python/mypy/issues/7620))
- Additional commits viewable in [compare view](https://github.com/python/mypy/compare/v0.730...v0.740)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=mypy&package-manager=pip&previous-version=0.730&new-version=0.740)
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| 508,235,957
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MDExOlB1bGxSZXF1ZXN0MzI5MDY3MjM1
| 1,635
|
Bump networkx from 2.3 to 2.4
|
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[] | null |
[] | 2019-10-17T05:02:54
| 2019-10-17T05:26:56
|
2019-10-17T05:26:38Z
|
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 3.8. This is the last release to support Python 3.5.
>
> Release notes
> -------------
>
> See release/release\_2.4.
</details>
<details>
<summary>Commits</summary>
- [`fd0ecd2`](https://github.com/networkx/networkx/commit/fd0ecd22723cb30a365511d324841a85caad589c) Designate 2.4 release
- [`5fce67a`](https://github.com/networkx/networkx/commit/5fce67a8d7bf47643bc0dc57769741822c194e0e) Update release notes
- [`5027409`](https://github.com/networkx/networkx/commit/50274092b762ebc4f350f7f08970b098f4ae2d65) Bump release version
- [`61f1374`](https://github.com/networkx/networkx/commit/61f1374200adbf9b436649a3b02698d04cebfadc) Designate 2.4rc2 release
- [`d1f0bb8`](https://github.com/networkx/networkx/commit/d1f0bb8dbf49e1b21e7f0e4a7ddd021a7f780ab5) Merge pull request [#3655](https://github-redirect.dependabot.com/networkx/networkx/issues/3655) from jarrodmillman/prep-rc2
- [`de010f4`](https://github.com/networkx/networkx/commit/de010f4930525dfe2b82dd468a601cdf77b0c466) Fix heading level
- [`9da9995`](https://github.com/networkx/networkx/commit/9da999589d20dbf879716c82ac5627eb04a461fc) Update travis
- [`d324a40`](https://github.com/networkx/networkx/commit/d324a405a2b4d583b147ef654be7633b337adac3) Release wheels
- [`56f178f`](https://github.com/networkx/networkx/commit/56f178f82a50e35efaa0abebb120d94f4b49e0cc) Finalize release notes
- [`068dfef`](https://github.com/networkx/networkx/commit/068dfefbfabcc3df673a49f5b3e0659c40af101d) Merge pull request [#3652](https://github-redirect.dependabot.com/networkx/networkx/issues/3652) from jarrodmillman/speedup-appveyor
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MDExOlB1bGxSZXF1ZXN0MzI5MzY1MTI5
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|
Bump numpy from 1.17.2 to 1.17.3
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| 2019-10-17T16:58:56
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2019-10-17T16:58:41Z
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Bumps [numpy](https://github.com/numpy/numpy) from 1.17.2 to 1.17.3.
<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 against NumPy 1.17.2 along with a
> some documentation improvements. The Python versions supported in this release
> are 3.5-3.8.
>
> Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and
> OpenBLAS >= 3.7 to avoid errors on the Skylake architecture.
>
>
> Highlights
> ==========
>
> - Wheels for Python 3.8
> - Boolean ``matmul`` fixed to use booleans instead of integers.
>
>
> Compatibility notes
> ===================
>
> - The seldom used ``PyArray_DescrCheck`` macro has been changed/fixed.
>
>
> Contributors
> ============
>
> A total of 7 people contributed to this release. People with a "+" by their
> names contributed a patch for the first time.
>
> * Allan Haldane
> * Charles Harris
> * Kevin Sheppard
> * Matti Picus
> * Ralf Gommers
> * Sebastian Berg
> * Warren Weckesser
>
>
> Pull requests merged
> ====================
>
> A total of 12 pull requests were merged for this release.
>
> * [#14456](https://github-redirect.dependabot.com/numpy/numpy/issues/14456): MAINT: clean up pocketfft modules inside numpy.fft namespace.
> * [#14463](https://github-redirect.dependabot.com/numpy/numpy/issues/14463): BUG: random.hypergeometic assumes npy_long is npy_int64, hung...
> * [#14502](https://github-redirect.dependabot.com/numpy/numpy/issues/14502): BUG: random: Revert [gh-14458](https://github-redirect.dependabot.com/numpy/numpy/issues/14458) and refix [gh-14557](https://github-redirect.dependabot.com/numpy/numpy/issues/14557).
> * [#14504](https://github-redirect.dependabot.com/numpy/numpy/issues/14504): BUG: add a specialized loop for boolean matmul.
> * [#14506](https://github-redirect.dependabot.com/numpy/numpy/issues/14506): MAINT: Update pytest version for Python 3.8
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`ff3df08`](https://github.com/numpy/numpy/commit/ff3df08438d570b0ccdda3f8a008278d8a4ad394) REL: NumPy 1.14.5 release.
- [`89208b4`](https://github.com/numpy/numpy/commit/89208b4db4de332b7e361860018c2882fe567678) Merge pull request [#14704](https://github-redirect.dependabot.com/numpy/numpy/issues/14704) from charris/prepare-1.17.3-release
- [`f6725ad`](https://github.com/numpy/numpy/commit/f6725ad6500cd1802f0044a82ad8eb72dd48f381) REL: Prepare for 1.17.3 release.
- [`acb10b0`](https://github.com/numpy/numpy/commit/acb10b090d327d6cc5b818f2dc32089e5e3d636c) Merge pull request [#14687](https://github-redirect.dependabot.com/numpy/numpy/issues/14687) from charris/backport-14605
- [`7758dd1`](https://github.com/numpy/numpy/commit/7758dd1b166303f50452ab1e74e27cf250d23171) BUG: properly define PyArray_DescrCheck
- [`51826db`](https://github.com/numpy/numpy/commit/51826db9928b549e02a98bfa90e317b9a9bd940b) Merge pull request [#14578](https://github-redirect.dependabot.com/numpy/numpy/issues/14578) from charris/backport-14531
- [`dc441ee`](https://github.com/numpy/numpy/commit/dc441ee71f71c6662b9682ffc65751e839cc0c3a) BUG: random: Create a legacy implementation of random.binomial.
- [`df93b2b`](https://github.com/numpy/numpy/commit/df93b2bd8855471829b09e641175c11c31e05b9b) Merge pull request [#14563](https://github-redirect.dependabot.com/numpy/numpy/issues/14563) from rgommers/bport-fftlicense
- [`5504e6d`](https://github.com/numpy/numpy/commit/5504e6d5d2ae5df55a3a91542989e5cba804305c) DOC: remove note about Pocketfft license file (non-existing here).
- [`2053327`](https://github.com/numpy/numpy/commit/205332701cffadf116c992c780682aedb72a0055) Merge pull request [#14519](https://github-redirect.dependabot.com/numpy/numpy/issues/14519) from charris/backport-14498
- Additional commits viewable in [compare view](https://github.com/numpy/numpy/compare/v1.17.2...v1.17.3)
</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzI5MzY1Mjc2
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|
Bump networkx from 2.3 to 2.4
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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]\r\n\r\nOk this was deprecated in 2.1 https://networkx.github.io/documentation/stable/release/release_2.1.html?highlight=connected_component_subgraphs"
] | 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 3.8. This is the last release to support Python 3.5.
>
> Release notes
> -------------
>
> See release/release\_2.4.
</details>
<details>
<summary>Commits</summary>
- [`fd0ecd2`](https://github.com/networkx/networkx/commit/fd0ecd22723cb30a365511d324841a85caad589c) Designate 2.4 release
- [`5fce67a`](https://github.com/networkx/networkx/commit/5fce67a8d7bf47643bc0dc57769741822c194e0e) Update release notes
- [`5027409`](https://github.com/networkx/networkx/commit/50274092b762ebc4f350f7f08970b098f4ae2d65) Bump release version
- [`61f1374`](https://github.com/networkx/networkx/commit/61f1374200adbf9b436649a3b02698d04cebfadc) Designate 2.4rc2 release
- [`d1f0bb8`](https://github.com/networkx/networkx/commit/d1f0bb8dbf49e1b21e7f0e4a7ddd021a7f780ab5) Merge pull request [#3655](https://github-redirect.dependabot.com/networkx/networkx/issues/3655) from jarrodmillman/prep-rc2
- [`de010f4`](https://github.com/networkx/networkx/commit/de010f4930525dfe2b82dd468a601cdf77b0c466) Fix heading level
- [`9da9995`](https://github.com/networkx/networkx/commit/9da999589d20dbf879716c82ac5627eb04a461fc) Update travis
- [`d324a40`](https://github.com/networkx/networkx/commit/d324a405a2b4d583b147ef654be7633b337adac3) Release wheels
- [`56f178f`](https://github.com/networkx/networkx/commit/56f178f82a50e35efaa0abebb120d94f4b49e0cc) Finalize release notes
- [`068dfef`](https://github.com/networkx/networkx/commit/068dfefbfabcc3df673a49f5b3e0659c40af101d) Merge pull request [#3652](https://github-redirect.dependabot.com/networkx/networkx/issues/3652) from jarrodmillman/speedup-appveyor
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MDU6SXNzdWU1MDg3NzQ4NDk=
| 1,638
|
Changing the VoronoiNN default tolerance value
|
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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 Voronoi though and assume a tolerance of 0 that may need to be updated to keep tol=0 in those cases, e.g. see:\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/b7588712eb6f37ef2ff5cfa47667e2df33e8c11d/pymatgen/analysis/local_env.py#L3335",
"The Voronoi tessellation has also been unstable in some cases too. I'm not sure we need so many NN strategies really, but maybe they're useful somewhere. I think Voronoi may be used in some other places too (defects, chemenv?) though I'm not sure if they use the NN class directly.",
"Yep, I'm aware of `VoronoiNN_modified`. Although, it has been deprecated for some time now, so perhaps it should just be removed entirely.\r\n\r\nThat's a good point about other classes that rely on VoronoiNN though, those would have to be updated.",
"Yeah let's just remove the modified one, it doesn't have a deprecated date set and it's not used elsewhere so may as well remove it now.",
"Closed with https://github.com/materialsproject/pymatgen/commit/e79d2806b2f9696fcc31069d2ccf400b3c371901"
] | 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 than `tol` fraction of the largest face are not included in the tessellation.
In our benchmark, we've been using VoronoiNN with a default `tol` value of 0.5. This gives very close to optimal results as shown by the plot below.
The default value of `tol` in pymatgen is 0, which as you can see is highly unoptimized. Is there any reason for this? If not, would you be against changing the default to 0.4/0.5?
*Plot shows benchmark score (lower is better) computed using VoronoiNN with different tolerances.*
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MDExOlB1bGxSZXF1ZXN0MzI5NzM3NjUw
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Bump pylint from 2.4.2 to 2.4.3
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[] | 2019-10-18T13:26:10
| 2019-10-18T14:57:19
|
2019-10-18T14:57:03Z
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CONTRIBUTOR
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Bumps [pylint](https://github.com/PyCQA/pylint) from 2.4.2 to 2.4.3.
<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 PyLinter object to sub processes to allow using custom
> PyLinter classes.
>
> PyLinter object (and all its members except reporter) needs to support
> pickling so the PyLinter object can be passed to worker processes.
>
> * Refactor file checking
>
> Remove code duplication from file checking.
>
> * Fix an issue with ``unnecessary-comprehension`` in comprehensions with additional repacking of elements.
>
> Close [#3148](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3148)
>
> * ``import-outside-toplevel`` is emitted for ``ImportFrom`` nodes as well.
>
> Close [#3175](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3175)
>
> * Do not emit ``no-method-argument`` for functions using positional only args.
>
> Close [#3161](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3161)
>
> * ``consider-using-sys-exit`` is no longer emitted when `exit` is imported in the local scope.
>
> Close [#3147](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3147)
>
> * `invalid-overridden-method` takes `abc.abstractproperty` in account
>
> Close [#3150](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3150)
>
> * Fixed ``missing-yield-type-doc`` getting incorrectly raised when
> a generator does not document a yield type but has a type annotation.
>
> Closes [#3185](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3185)
>
> * ``typing.overload`` functions are exempted from ``too-many-function-args``
>
> Close [#3170](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3170)
</details>
<details>
<summary>Commits</summary>
- [`7807af3`](https://github.com/PyCQA/pylint/commit/7807af3a9d956f885e1ab94e01c915ca7db3b03f) Prepare 2.4.3
- [`57513cc`](https://github.com/PyCQA/pylint/commit/57513ccefafc61b711d19f08c6de91acc5d4ec8f) Disable too-many-locals for complex function
- [`ccb1d05`](https://github.com/PyCQA/pylint/commit/ccb1d05636f18231809aead61f73ad9d2ae46458) ``typing.overload`` functions are exempted from ``too-many-function-args``
- [`89a18ef`](https://github.com/PyCQA/pylint/commit/89a18eff3f10b2ca9bd3a16ced978580586ad89e) Fixed ``missing-yield-type-doc`` ignoring type annotation ([#3195](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3195))
- [`30c1504`](https://github.com/PyCQA/pylint/commit/30c1504b3c3eba44cf9fa2614dedc812810c7dc8) Disable too-few-public-methods
- [`237d110`](https://github.com/PyCQA/pylint/commit/237d1107767b06119d849a46a85ac170e1f2f39d) `invalid-overridden-method` takes `abc.abstractproperty` in account
- [`273412f`](https://github.com/PyCQA/pylint/commit/273412fba6b83acd524c265228638abde6411a4c) Squash is_property_deleter and use is_property_setter_or_deleter instead
- [`32aad00`](https://github.com/PyCQA/pylint/commit/32aad0073a7cb255039c18f56ffcba1c37551c0b) ``consider-using-sys-exit`` is no longer emitted when `exit` is imported in t...
- [`a494977`](https://github.com/PyCQA/pylint/commit/a494977e4f4a9f201f3a1b4bb6591e219ac308b7) Do not emit ``no-method-argument`` for functions using positional only args.
- [`d3eda2e`](https://github.com/PyCQA/pylint/commit/d3eda2e8a7952fd456815fe0cab98bb9f14efcfc) ``import-outside-toplevel`` is emitted for ``ImportFrom`` nodes as well.
- Additional commits viewable in [compare view](https://github.com/PyCQA/pylint/compare/pylint-2.4.2...pylint-2.4.3)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pylint&package-manager=pip&previous-version=2.4.2&new-version=2.4.3)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
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MDExOlB1bGxSZXF1ZXN0MzI5NzQ1NzU5
| 1,640
|
Modification in lobsterin class
|
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[] | null |
[
"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 title.
Before a pull request can be merged, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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| 509,155,118
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MDExOlB1bGxSZXF1ZXN0MzI5ODAwMTg3
| 1,641
|
Added ability to make Gaussian input file without a geometry
|
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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 items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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Bump pandas from 0.25.1 to 0.25.2
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[] | 2019-10-21T13:30:45
| 2019-10-21T14:22:30
|
2019-10-21T14:22:20Z
|
CONTRIBUTOR
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 0.25.1 to 0.25.2.
<details>
<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
> and bug fixes. We recommend that all users upgrade to this version.
>
> See the full [whatsnew](https://pandas.pydata.org/pandas-docs/version/0.25/whatsnew/v0.25.2.html) for a list of all the changes.
>
> The release can be installed with conda from the defaults and conda-forge channels:
>
> ```
> conda install pandas
> ```
>
> Or via PyPI:
>
> ```
> python3 -m pip install --upgrade pandas
> ```
>
> Please report any issues with the release on the [pandas issue tracker](https://github.com/pandas-dev/pandas/issues).
</details>
<details>
<summary>Commits</summary>
- [`0efc71b`](https://github.com/pandas-dev/pandas/commit/0efc71b53f019c6c5a8da7a38e08646ca75c17d9) RLS: 0.25.2
- [`0a7e632`](https://github.com/pandas-dev/pandas/commit/0a7e6328812474ae6b33f2b48862ad088c19a83b) Backport PR [#29057](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29057): CI: xfail on numpy 1.18 ([#29059](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29059))
- [`148ddac`](https://github.com/pandas-dev/pandas/commit/148ddacb230c71b930dcee551155d2796fe2ede6) Backport PR [#29013](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29013): TST: restore xfail for test_apply ([#29028](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29028))
- [`b83ce8e`](https://github.com/pandas-dev/pandas/commit/b83ce8ec09cc54a0304ed87a95b5e1aaa732b964) Backport PR [#29010](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29010): Setuptools CI fixup ([#29015](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29015))
- [`480ac20`](https://github.com/pandas-dev/pandas/commit/480ac20a7965ef64a730384203a65b358e6573f9) Backport PR [#29000](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29000): DOC: 0.25.2 whatsnew cleanup ([#29005](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29005))
- [`15fe865`](https://github.com/pandas-dev/pandas/commit/15fe8654581d4975ff52526b527a4ad586001369) Backport PR [#28730](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28730): CI: 3.8 build ([#29002](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29002))
- [`aebba0d`](https://github.com/pandas-dev/pandas/commit/aebba0d1c2af43da056e24bad6a43f6c999a0a91) Backport PR [#28982](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28982) on branch 0.25.x (Document 3.8 compatibility) ([#28999](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28999))
- [`505b1a7`](https://github.com/pandas-dev/pandas/commit/505b1a70da9584257b20f849a20ffa286ad2255e) BUG: use EA.astype in ExtensionBlock.to_native_types ([#28841](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28841)) ([#28985](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28985))
- [`c4865df`](https://github.com/pandas-dev/pandas/commit/c4865dfb94a0fdfecbdb4d593d7bf53a7980f7d2) Backport PR [#28680](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28680): BUG: Fix RangeIndex.get_indexer for decreasing RangeIndex...
- [`c6bde55`](https://github.com/pandas-dev/pandas/commit/c6bde551f6a9610348b7abdf96573c7409ae6db4) Fix a typo in "computation.rst" in document. ([#28400](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28400)) ([#28737](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/28737))
- Additional commits viewable in [compare view](https://github.com/pandas-dev/pandas/compare/v0.25.1...v0.25.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pandas&package-manager=pip&previous-version=0.25.1&new-version=0.25.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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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 encourage the adsorption analysis using the minimal cell (i. e. with `AdsorptionSiteFinder.generate_adsorption_structures` and it's `repeat` kwarg because it'll be more computationally efficient, but I think we can refactor to ensure that it'll work otherwise.",
"Just a quick update, I've tried refactoring to use spglib to determine symmetrically equivalent sites of adsorption structures, rather than doing so manually, and the issue persists.",
"Some high-throughput related work may be affected"
] | 2019-10-23T08:16:31
| 2023-08-13T16:32:55
|
2023-08-13T16:32:55Z
|
NONE
|
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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")
struct = SpacegroupAnalyzer(struct).get_conventional_standard_structure()
slabs = generate_all_slabs(struct, max_index=1, min_slab_size=8.0, min_vacuum_size=15.0)
for n, slabs in enumerate([slab for slab in slabs if slab.miller_index == (1, 1, 1)]):
slabs_bak = slabs.copy()
slabs.make_supercell([[3, 0, 0],
[0, 3, 0],
[0, 0, 1]])
fig = plt.figure()
ax = fig.add_subplot(111)
plot_slab(slabs, ax, adsorption_sites=True)
asf = AdsorbateSiteFinder(slabs)
n_site = asf.find_adsorption_sites()
print(slabs.miller_index)
print(n_site)
print(len(n_site['all']))
plt.savefig(str(n) + '-Au-111.png', img_format='png')
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.
**Expected behavior**
generally, there are 4 different sites in Au(111)
**Screenshots**
**Desktop (please complete the following information):**
- OS: Windows
- Version 2019.10.16
**annex:**
[Au_POSCAR.zip](https://github.com/materialsproject/pymatgen/files/3760995/Au_POSCAR.zip)
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| 511,324,274
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MDExOlB1bGxSZXF1ZXN0MzMxNTQyOTI3
| 1,644
|
Bump netcdf4 from 1.5.2 to 1.5.3
|
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[] | 2019-10-23T13:29:21
| 2019-10-23T14:24:34
|
2019-10-23T14:24:24Z
|
CONTRIBUTOR
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Bumps [netcdf4](https://github.com/Unidata/netcdf4-python) from 1.5.2 to 1.5.3.
<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 masked that are not filled when auto_fill is off
> (issue [#972](https://github-redirect.dependabot.com/Unidata/netcdf4-python/issues/972)).
> * python 3.8 binary wheels.
</details>
<details>
<summary>Commits</summary>
- See full diff in [compare view](https://github.com/Unidata/netcdf4-python/commits)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=netcdf4&package-manager=pip&previous-version=1.5.2&new-version=1.5.3)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
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- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
- `@dependabot ignore this major version` will close this PR and stop Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself)
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MDExOlB1bGxSZXF1ZXN0MzMxNzU5NzYw
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|
small bug fixes
|
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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 types of imports might be used by other people down the stream.",
"@shyuep \r\nIt looks like `VaspInput` was part of the module import when everything was imported via wildcard, but when you updated it for mypy support it wasn't explicitly added in. Since `custodian` depends on this import, we can assume other packages do as well, so it's probably best to bring it to the module level.\r\n"
] | 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}}'
```
resulted in:
```
Loading configurations for atomate for submitting Jimmy's jobs
Are you sure? This will modify 12 entries. (Y/N)y
Traceback (most recent call last):
File "/Users/lik/miniconda3/envs/pmg/bin/lpad", line 11, in <module>
load_entry_point('FireWorks', 'console_scripts', 'lpad')()
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/scripts/lpad_run.py", line 1176, in lpad
args.func(args)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/scripts/lpad_run.py", line 427, in defuse_fws
lp.defuse_fw(f)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 808, in defuse_fw
self.rerun_fw(fw_id, rerun_duplicates)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 1491, in rerun_fw
updated_ids = wf.rerun_fw(fw_id)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/firework.py", line 873, in rerun_fw
m_fw._rerun()
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 1840, in _rerun
self.full_fw._rerun()
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 1940, in full_fw
self._get_launch_data(launch_field)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 1955, in _get_launch_data
fw = self.partial_fw # assure stage 1
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/core/launchpad.py", line 1933, in partial_fw
self._fw = Firework.from_dict(data)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 155, in _decorator
new_args[0] = {k: _recursive_load(v) for k, v in args[0].items()}
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 155, in <dictcomp>
new_args[0] = {k: _recursive_load(v) for k, v in args[0].items()}
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 118, in _recursive_load
return {k: _recursive_load(v) for k, v in obj.items()}
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 118, in <dictcomp>
return {k: _recursive_load(v) for k, v in obj.items()}
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 121, in _recursive_load
return [_recursive_load(v) for v in obj]
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 121, in <listcomp>
return [_recursive_load(v) for v in obj]
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 113, in _recursive_load
return load_object(obj)
File "/Users/lik/miniconda3/envs/pmg/lib/python3.7/site-packages/FireWorks-1.9.4-py3.7.egg/fireworks/utilities/fw_serializers.py", line 329, in load_object
mod = __import__(modname, globals(), locals(), [classname], 0)
File "/Users/lik/repos/js_mp/atomate/atomate/vasp/firetasks/__init__.py", line 5, in <module>
from .run_calc import *
File "/Users/lik/repos/js_mp/atomate/atomate/vasp/firetasks/run_calc.py", line 23, in <module>
from custodian.vasp.handlers import VaspErrorHandler, AliasingErrorHandler, \
File "/Users/lik/repos/js_mp/custodian/custodian/vasp/handlers.py", line 23, in <module>
from pymatgen.io.vasp import Poscar, VaspInput, Incar, Kpoints, Vasprun, \
ImportError: cannot import name 'VaspInput' from 'pymatgen.io.vasp' (/Users/lik/repos/js_mp/pymatgen/pymatgen/io/vasp/__init__.py)
```
|
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MDExOlB1bGxSZXF1ZXN0MzMyNTIzMjg4
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|
Bump pytest from 5.2.1 to 5.2.2
|
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[] | 2019-10-25T13:50:46
| 2019-10-25T14:59:51
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2019-10-25T14:59:37Z
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CONTRIBUTOR
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.2.1 to 5.2.2.
<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://github-redirect.dependabot.com/pytest-dev/pytest/issues/5206): Fix
> `--nf` to not forget about known nodeids with partial
> test selection.
> - [\#5906](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5906): Fix
> crash with `KeyboardInterrupt` during `--setup-show`.
> - [\#5946](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5946): Fixed
> issue when parametrizing fixtures with numpy arrays (and possibly
> other sequence-like types).
> - [\#6044](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6044): Properly
> ignore `FileNotFoundError` exceptions when trying to remove old
> temporary directories, for instance when multiple processes try to
> remove the same directory (common with `pytest-xdist` for example).
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.2.2 (2019-10-24)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5206](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5206): Fix `--nf` to not forget about known nodeids with partial test selection.
> - [\#5906](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5906): Fix crash with `KeyboardInterrupt` during `--setup-show`.
> - [\#5946](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5946): Fixed issue when parametrizing fixtures with numpy arrays (and possibly other sequence-like types).
> - [\#6044](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6044): Properly ignore `FileNotFoundError` exceptions when trying to remove old temporary directories, for instance when multiple processes try to remove the same directory (common with `pytest-xdist` for example).
</details>
<details>
<summary>Commits</summary>
- [`b27ba97`](https://github.com/pytest-dev/pytest/commit/b27ba977219260528f4e47c9614c129d680dee90) Preparing release version 5.2.2
- [`2b56c7e`](https://github.com/pytest-dev/pytest/commit/2b56c7e1cefe58e4a94073a30ad0d698f366c7d4) Update Tidelift docs with latest campaign ([#6053](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6053))
- [`2bee7d7`](https://github.com/pytest-dev/pytest/commit/2bee7d7c3ed4bc80169f2ad1ff6af7ca2db3da7d) Update Tidelift docs with latest campaign
- [`713b9e5`](https://github.com/pytest-dev/pytest/commit/713b9e54c31a8ec66c59ebe44c3e86a9b60fa7c7) Review rm_rf handling of FileNotFoundErrors ([#6044](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6044))
- [`ba4b8c8`](https://github.com/pytest-dev/pytest/commit/ba4b8c869c70f6c46b780a1e1478ec75da61417a) Review rm_rf handling of FileNotFoundErrors
- [`82e9013`](https://github.com/pytest-dev/pytest/commit/82e9013e73ca6da796ff85627875936887ba213e) Merge pull request [#6004](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6004) from blueyed/fix-nf
- [`14142b9`](https://github.com/pytest-dev/pytest/commit/14142b911377d5354acf07ca1c9a7f11e9298b84) tests: remove unnecessary test, clarify ([#6013](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6013))
- [`0123b29`](https://github.com/pytest-dev/pytest/commit/0123b29ed754afd77b737845e5a205cc2404afbe) tests: remove unnecessary test, clarify
- [`16efa1b`](https://github.com/pytest-dev/pytest/commit/16efa1bfef19ee41f3a74f464139b4129ff804dc) Merge pull request [#6009](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6009) from yoavcaspi/fix_keyboardInterrupt_on_setup_show
- [`5624e36`](https://github.com/pytest-dev/pytest/commit/5624e366c1c812e200231e70c6ba2f15dc04a323) add more indications to the result of the tests
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.2.1...5.2.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.2.1&new-version=5.2.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDU6SXNzdWU1MTM4MTg0ODk=
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Compilation error from pip
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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.",
"@mkhorton I doubt it is an issue with linear assignment. By all means, try switching to scipy and see if it works. But if the compiler flags are the issue, there are other modules that require compilation as well.",
"What I said with the compilation flags is wrong.\r\nFrom first glance I assumed, that you have `-maybe-uninitialized` as warning and treat warnings as errors.\r\nI retried on Ubuntu with the same steps and it seems indeed related to SuSe Linux.\r\nHere is the full output of my attempts\r\n[Open_Suse_installation.txt](https://github.com/materialsproject/pymatgen/files/3788647/Open_Suse_installation.txt).\r\n\r\nI think the problematic line is the linking step here:\r\n```\r\n /home/weser/test_conda/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges\r\n /home/weser/test_conda/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges\r\n /home/weser/test_conda/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges\r\n /home/weser/test_conda/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges\r\n /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: file not recognized: file format not recognized\r\n```\r\n\r\nSince It seems to be an issue in the C standard library linking in OpenSuse I will keep that issue open, but try to cure it myself.",
"I found the reason and it has indeed nothing to do with `pymatgen`. I am sorry for the hassle.\r\n\r\nThe problem was that I used `pip` from anaconda and conda ships their own linker. Which we can also see from the path. `/home/weser/test_conda/compiler_compat/ld`.\r\nThe relevant compiler flag was `gcc [...] -B /home/weser/test_conda/compiler_compat [...]` \r\nIf one uses the system's `pip` without anaconda, then everything works fine."
] | 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/anaconda3/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/limanni/anaconda3/include/python3.7m -I/home/limanni/anaconda3/lib/python3.7/site-packages/numpy/core/include -c pymatgen/optimization/linear_assignment.c -o build/temp.linux-x86_64-3.7/pymatgen/optimization/linear_assignment.o
In file included from /home/limanni/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1832:0,
from /home/limanni/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /home/limanni/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from pymatgen/optimization/linear_assignment.c:569:
/home/limanni/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
#warning "Using deprecated NumPy API, disable it with " \
^~~~~~~
pymatgen/optimization/linear_assignment.c: In function '__pyx_pf_8pymatgen_12optimization_17linear_assignment_16LinearAssignment___init__.isra.43':
pymatgen/optimization/linear_assignment.c:4673:42: warning: '__pyx_v_last' may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_45 = (__pyx_v_last + 1);
~~~~~~~~~~~~~~^~~~
pymatgen/optimization/linear_assignment.c:3115:7: note: '__pyx_v_last' was declared here
int __pyx_v_last;
^~~~~~~~~~~~
pymatgen/optimization/linear_assignment.c:3959:20: warning: '__pyx_v_j2' may be used uninitialized in this function [-Wmaybe-uninitialized]
__pyx_t_37 = __pyx_v_j1;
~~~~~~~~~~~^~~~~~~~~~~~
pymatgen/optimization/linear_assignment.c:3129:7: note: '__pyx_v_j2' was declared here
int __pyx_v_j2;
^~~~~~~~~~
pymatgen/optimization/linear_assignment.c:4694:96: warning: '__pyx_v_m' may be used uninitialized in this function [-Wmaybe-uninitialized]
(__pyx_v_v[__pyx_v_j1]) = (((__pyx_v_v[__pyx_v_j1]) + (__pyx_v_d[__pyx_v_j1])) - __pyx_v_m);
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
pymatgen/optimization/linear_assignment.c:3125:26: note: '__pyx_v_m' was declared here
__pyx_t_5numpy_float_t __pyx_v_m;
^~~~~~~~~
gcc -pthread -shared -B /home/limanni/anaconda3/compiler_compat -L/home/limanni/anaconda3/lib -Wl,-rpath=/home/limanni/anaconda3/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.7/pymatgen/optimization/linear_assignment.o -o build/lib.linux-x86_64-3.7/pymatgen/optimization/linear_assignment.cpython-37m-x86_64-linux-gnu.so
/home/limanni/anaconda3/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges
/home/limanni/anaconda3/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges
/home/limanni/anaconda3/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges
/home/limanni/anaconda3/compiler_compat/ld: /usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: unable to initialize decompress status for section .debug_aranges
/usr/lib64/gcc/x86_64-suse-linux/7/../../../../lib64/crti.o: file not recognized: file format not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
----------------------------------------
ERROR: Command errored out with exit status 1: /home/limanni/anaconda3/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-j94_8mxw/pymatgen/setup.py'"'"'; __file__='"'"'/tmp/pip-install-j94_8mxw/pymatgen/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' install --record /tmp/pip-record-soi2u6bs/install-record.txt --single-version-externally-managed --compile Check the logs for full command output.
```
The used compiler is:
`gcc (SUSE Linux) 7.4.1 20190905 [gcc-7-branch revision 275407]`
**Expected behavior**
IMHO it would be a good idea to not have such harsh compilation flags when shipping.
**Desktop (please complete the following information):**
- NAME="openSUSE Leap"
- VERSION="15.1"
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MDExOlB1bGxSZXF1ZXN0MzMzNjU1NjM0
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|
Bump flake8 from 3.7.8 to 3.7.9
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[] | 2019-10-29T14:34:07
| 2019-10-29T14:36:36
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2019-10-29T14:36:14Z
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CONTRIBUTOR
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Bumps [flake8](https://gitlab.com/pycqa/flake8) from 3.7.8 to 3.7.9.
<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 branch 'backport_pr_340' into '3.7-maintenance'
- [`04d3f9d`](https://gitlab.com/pycqa/flake8/commit/04d3f9dcafcc8fe3eabf66ba13b999c2e5b38f60) Fix travis-ci
- [`ee740f4`](https://gitlab.com/pycqa/flake8/commit/ee740f4a92b2856e7c62f12c37abd6f8b9b987ff) Merge branch 'backport_pr_366' into '3.7-maintenance'
- [`04f49a7`](https://gitlab.com/pycqa/flake8/commit/04f49a7a777c3ceb14b8e8d5b52b12366f84f9a7) Only use multiprocessing when the method is fork
- See full diff in [compare view](https://gitlab.com/pycqa/flake8/compare/3.7.8...3.7.9)
</details>
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MDExOlB1bGxSZXF1ZXN0MzM0NTEzNjEw
| 1,649
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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
|
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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.
Before a pull request can be merged, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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| 515,083,904
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MDExOlB1bGxSZXF1ZXN0MzM0NjAwNTUz
| 1,650
|
fix previous destructive usage of input LammpsData
|
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[] | null |
[
"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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MDExOlB1bGxSZXF1ZXN0MzM1MTM5ODkz
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MPRester: get NOMAD download info for MP raw files
|
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[] | 2019-10-31T20:37:18
| 2019-11-01T17:47:46
|
2019-11-01T03:24:03Z
|
MEMBER
|
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## Summary
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 `task_types` for each material id. In addition, the zip archive downloaded from NOMAD will contain a `manifest.json` which maps each sub-directory (e.g. vasprun.xml) to its according `task_id/external_id`. See screenshot for example usage. @markus1978
## 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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
|
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MDExOlB1bGxSZXF1ZXN0MzM1NDQ3NzQ2
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Bump tqdm from 4.36.1 to 4.37.0
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[] | 2019-11-01T14:26:14
| 2019-11-01T14:37:50
|
2019-11-01T14:27:07Z
|
CONTRIBUTOR
|
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|
Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.36.1 to 4.37.0.
<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))
> - better unicode widechar support ([#803](https://github-redirect.dependabot.com/tqdm/tqdm/issues/803) -> [#410](https://github-redirect.dependabot.com/tqdm/tqdm/issues/410), [#805](https://github-redirect.dependabot.com/tqdm/tqdm/issues/805))
> - fix example/tqdm_wget unknown total ([#826](https://github-redirect.dependabot.com/tqdm/tqdm/issues/826))
> - add `stacklevel=2` to warnings ([#821](https://github-redirect.dependabot.com/tqdm/tqdm/issues/821))
> - misc framework updates
> + snapcraft version fix
> + update issue/pr templates ([#830](https://github-redirect.dependabot.com/tqdm/tqdm/issues/830))
> + update unit tests
> - misc documentation updates
> + update parallel (multiprocessing, ThreadPoolExecutor) example ([#407](https://github-redirect.dependabot.com/tqdm/tqdm/issues/407))
> + add slides, video images
> + add CII Best Practices badge
> + add repology badge
> + update badge icons
</details>
<details>
<summary>Commits</summary>
- [`cd7f61b`](https://github.com/tqdm/tqdm/commit/cd7f61b4562fb2f4aad560edf094a2ddad1ae3b7) bump version, merge branch 'devel'
- [`b17b594`](https://github.com/tqdm/tqdm/commit/b17b5940d8b03786bb57f2fba12cd2508a3c5a94) update parallel example
- [`b3589f6`](https://github.com/tqdm/tqdm/commit/b3589f6736e037eb160e0329814006447eaf347c) silly syntax error fix
- [`59f457a`](https://github.com/tqdm/tqdm/commit/59f457a8ceb64f6aaf02113c035516c2caa181d4) potential future pandas fix
- [`84102ab`](https://github.com/tqdm/tqdm/commit/84102ab0ced2d01b6b3bb1d6224eee8c08019578) update issue/pr templates
- [`5f0eb91`](https://github.com/tqdm/tqdm/commit/5f0eb91ac1ebff8f73195f2d2026a837f225dc14) Revert "remove broken funding link"
- [`9baa46e`](https://github.com/tqdm/tqdm/commit/9baa46e84fc910e4cf7d070de6a00b4c3342506e) fix example/tqdm_wget unknown total
- [`6e50fa2`](https://github.com/tqdm/tqdm/commit/6e50fa2719117525f7172569792e0d734d7198d8) add stacklevel=2 to more warnings
- [`45f0785`](https://github.com/tqdm/tqdm/commit/45f07854ce8644249e96105d8a4ffaf0d9e78063) Merge branch 'mnt_warning_level' into devel
- [`fa2e30f`](https://github.com/tqdm/tqdm/commit/fa2e30fb7f83f8b82eccbc01980eed5d0ceaff53) MNT: set stack level on warnings
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.36.1...v4.37.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.36.1&new-version=4.37.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzM2MzAzMjEz
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|
Bump pandas from 0.25.2 to 0.25.3
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[] | 2019-11-04T14:22:47
| 2019-11-04T14:29:13
|
2019-11-04T14:29:03Z
|
CONTRIBUTOR
|
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 0.25.2 to 0.25.3.
<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 fixes. We recommend that all users upgrade to this version.
>
> See the full [whatsnew](https://pandas.pydata.org/pandas-docs/version/0.25/whatsnew/v0.25.3.html) for a list of all the changes.
>
> The release can be installed with conda from the defaults and conda-forge channels:
>
> ```
> conda install pandas
> ```
>
> Or via PyPI:
>
> ```
> python3 -m pip install --upgrade pandas
> ```
>
> Please report any issues with the release on the [pandas issue tracker](https://github.com/pandas-dev/pandas/issues).
</details>
<details>
<summary>Commits</summary>
- [`62a87bf`](https://github.com/pandas-dev/pandas/commit/62a87bf4a2af02a8d3bc271ad26e5994292b8e6a) RLS: 0.25.3
- [`60185e1`](https://github.com/pandas-dev/pandas/commit/60185e1754bc0626c79704ba37eb46832c0f2bfd) Backports for 0.25.3 ([#29313](https://github-redirect.dependabot.com/pandas-dev/pandas/issues/29313))
- See full diff in [compare view](https://github.com/pandas-dev/pandas/compare/v0.25.2...v0.25.3)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pandas&package-manager=pip&previous-version=0.25.2&new-version=0.25.3)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzM3MjAwMTQ2
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[WIP] Remove use of custom LinearAssignment from StructureMatcher
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[] | null |
[
"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, hence the need to profile before merging.\r\n\r\nAlso making a note of this project: https://github.com/src-d/lapjv",
"Noting this as a case where algorithms disagree (this is not caught by tests, the differences seem unimportant):\r\n\r\n```\r\nsm_atoms = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,\r\n primitive_cell=False, scale=True,\r\n attempt_supercell=True,\r\n allow_subset=True,\r\n supercell_size='num_atoms',\r\n comparator=OrderDisorderElementComparator())\r\nsm_sites = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,\r\n primitive_cell=False, scale=True,\r\n attempt_supercell=True,\r\n allow_subset=True,\r\n supercell_size='num_sites',\r\n comparator=OrderDisorderElementComparator())\r\nlp = Lattice.orthorhombic(10, 20, 30)\r\npcoords = [[0, 0, 0],\r\n [0.5, 0.5, 0.5]]\r\nls = Lattice.orthorhombic(20, 20, 30)\r\nscoords = [[0, 0, 0],\r\n [0.75, 0.5, 0.5]]\r\nprim = Structure(lp, [{'Na': 0.5}, {'Cl': 0.5}], pcoords)\r\nsupercell = Structure(ls, ['Na', 'Cl'], scoords)\r\nsupercell.make_supercell([[-1, 1, 0], [0, 1, 1], [1, 0, 0]])\r\n```\r\n\r\n`sm_atoms.get_s2_like_s1(supercell, prim)` current gives:\r\n```\r\nStructure Summary\r\nLattice\r\n abc : 28.284271247461902 36.05551275463989 20.0\r\n angles : 90.0 135.0 66.90653073020157\r\n volume : 12000.0\r\n A : -20.0 -20.0 -2.4492935982947065e-15\r\n B : 1.2246467991473533e-15 -20.0 -30.0\r\n C : 20.0 0.0 1.2246467991473533e-15\r\nPeriodicSite: Na:0.500 (0.0000, 0.0000, -0.0000) [-0.0000, 0.0000, 0.0000]\r\nPeriodicSite: Cl:0.500 (-5.0000, -30.0000, -15.0000) [1.0000, 0.5000, 0.7500]\r\nPeriodicSite: Na:0.500 (-10.0000, -20.0000, -0.0000) [1.0000, 0.0000, 0.5000]\r\nPeriodicSite: Cl:0.500 (-15.0000, -30.0000, -15.0000) [1.0000, 0.5000, 0.2500]\r\n```\r\n\r\n`sm_atoms.get_s2_like_s1(supercell, prim)` via SciPy gives:\r\n```\r\nStructure Summary\r\nLattice\r\n abc : 28.284271247461902 36.05551275463989 20.0\r\n angles : 90.0 135.0 66.90653073020157\r\n volume : 12000.0\r\n A : -20.0 -20.0 -2.4492935982947065e-15\r\n B : 1.2246467991473533e-15 -20.0 -30.0\r\n C : 20.0 0.0 1.2246467991473533e-15\r\nPeriodicSite: Na:0.500 (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]\r\nPeriodicSite: Cl:0.500 (-5.0000, -30.0000, -15.0000) [1.0000, 0.5000, 0.7500]\r\nPeriodicSite: Na:0.500 (10.0000, -20.0000, -30.0000) [0.0000, 1.0000, 0.5000]\r\nPeriodicSite: Cl:0.500 (5.0000, -10.0000, -15.0000) [0.0000, 0.5000, 0.2500]\r\n```\r\n\r\nTimings for each are 4.05 ms ± 109 µs per loop (mean ± std. dev. of 7 runs, 100 loops each) and 3.8 ms ± 54.6 µs per loop (mean ± std. dev. of 7 runs, 100 loops each) respectively.\r\n\r\nThe full test suite is 5s 736ms for current code and 6s 617 ms using SciPy, so there doesn't seem to be much between them for timings -- presumably there was a good reason to implement the Cythonized code since it seems like a large effort, but it doesn't seem to show in the current test suite.",
"Closing for now (\"if it's not broken...\"), may revisit later.",
"Added a benchmark link from @shyamd https://github.com/berhane/LAP-solvers"
] | 2019-11-06T06:50:57
| 2021-02-13T17:27:55
|
2019-11-06T08:13:34Z
|
MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MzM4NTk1MTM2
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TemCalculator
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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 is_perm(hkl1 : Union[List,Tuple],hkl2 : Union[List,Tuple]) -> bool:\r\n \"\"\"\r\n Determines if two HKL indicies are permutations of each other.\r\n This does not consider crystallographic symmetry, just index symmetry\r\n \"\"\"\r\n if len(hkl1) != len(hkl2):\r\n return False\r\n\r\n counts = defaultdict(int)\r\n for i in hkl1:\r\n counts[abs(i)] += 1\r\n\r\n for j in hkl2:\r\n counts[abs(j)] -= 1\r\n\r\n return sum(counts.values()) == 0\r\n```\r\n\r\nAlso, can you make some tests for `get_unique_families` so that we catch errors?",
"> 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\n> There may also be issues where your code isn't correct. For instance: `is_perm([1,1,1],[1,-1,1])`\r\n> \r\n> Maybe something like this?\r\n> \r\n> ```\r\n> from collections import defaultdict\r\n> \r\n> def is_perm(hkl1 : Union[List,Tuple],hkl2 : Union[List,Tuple]) -> bool:\r\n> \"\"\"\r\n> Determines if two HKL indicies are permutations of each other.\r\n> This does not consider crystallographic symmetry, just index symmetry\r\n> \"\"\"\r\n> if len(hkl1) != len(hkl2):\r\n> return False\r\n> \r\n> counts = defaultdict(int)\r\n> for i in hkl1:\r\n> counts[abs(i)] += 1\r\n> \r\n> for j in hkl2:\r\n> counts[abs(j)] -= 1\r\n> \r\n> return sum(counts.values()) == 0\r\n> ```\r\n> \r\n> Also, can you make some tests for `get_unique_families` so that we catch errors?\r\n\r\nis_perm and get_unique_families are part of the core code, I will make the change but it will cause conflict when I merge. Is that ok? I will take a look at the deleted codes and put them back if necessary.",
"That's fine. You're improving code that is already there and that can include \"core\" code. When you update now there shouldn't be a conflict anymore. Just make sure its a new commit and not reverting an old commit. ",
"Thanks @welltemperedpaprika, I'll take another look",
"Added a few more comments -- this looks very close to being ready to merge, thanks for your patience waiting for the review.",
"> Added a few more comments -- this looks very close to being ready to merge, thanks for your patience waiting for the review.\r\n\r\nThanks! I have addressed the changes and updated the code. ",
"Thanks, just had a chance to take another look at this, have got it working now. I have a few style tweaks to ask before we merge.\r\n\r\n<img width=\"595\" alt=\"image\" src=\"https://user-images.githubusercontent.com/2976580/76127403-6916a600-5fb6-11ea-857a-84fd071633b8.png\">\r\n\r\nCould you remove the \"trace 1\" legend (it doesn't tell us anything) so that the colorbar is better aligned, maybe slightly increase the zoom to be more like the above (contrast on the higher order dots is so low you can't see them, and default zoom makes points overlap, see below). Finally, could you add a plot title (the \"2D Diffraction Pattern, Beam Direction: 001\") instead of the current label and just leave it as a default font. Also, for beam directions that are negative can you make sure to use the overbar (utils to convert to unicode in pymatgen.util.string might be helpful here).\r\n\r\nFinally, what are your thoughts on making the colorbar optional? I think intensity is fairly clear + it doesn't tell us much from a quantitative perspective. If the colorbar was non-grey I think this would be a different matter.\r\n\r\n<img width=\"595\" alt=\"image\" src=\"https://user-images.githubusercontent.com/2976580/76127466-92cfcd00-5fb6-11ea-8442-a70d5a9756ec.png\">\r\n",
"This also now has some minor merge conflicts, should be easy to resolve though",
"> This also now has some minor merge conflicts, should be easy to resolve though\r\n\r\nThanks! I will address the suggestions and make changes accordingly in the next few days. ",
"Should be good to go now.",
"> Thanks, just had a chance to take another look at this, have got it working now. I have a few style tweaks to ask before we merge.\r\n> \r\n> <img alt=\"image\" width=\"595\" src=\"https://user-images.githubusercontent.com/2976580/76127403-6916a600-5fb6-11ea-857a-84fd071633b8.png\">\r\n> \r\n> Could you remove the \"trace 1\" legend (it doesn't tell us anything) so that the colorbar is better aligned, maybe slightly increase the zoom to be more like the above (contrast on the higher order dots is so low you can't see them, and default zoom makes points overlap, see below). Finally, could you add a plot title (the \"2D Diffraction Pattern, Beam Direction: 001\") instead of the current label and just leave it as a default font. Also, for beam directions that are negative can you make sure to use the overbar (utils to convert to unicode in pymatgen.util.string might be helpful here).\r\n> \r\n> Finally, what are your thoughts on making the colorbar optional? I think intensity is fairly clear + it doesn't tell us much from a quantitative perspective. If the colorbar was non-grey I think this would be a different matter.\r\n> \r\n> <img alt=\"image\" width=\"595\" src=\"https://user-images.githubusercontent.com/2976580/76127466-92cfcd00-5fb6-11ea-8442-a70d5a9756ec.png\">\r\n\r\nThanks, I've addressed the changes. I agree that the colorbar isn't necessary, so I took it out. I also zoomed in a little bit on the x and y axis. It helps on some structures.",
"Ok, I'm still having some issues with the title formatting and some other small issues, but no show stoppers. I'm happy to take a look at it myself and/or we can iterate on it in an additional PR.\r\n\r\nI'm going to merge this in now. Thanks again @welltemperedpaprika, @thefrankwan and @shyamd for all your work on this PR!",
"@mkhorton This shouldn't be merged. The TEM calculator uses IPython.display for some reason. It is failing on Appveyor. IPYthon is not a dependency of pymatgen. Pls revoke.",
"It looks like all the tests are passing. Where is the Appyveyor test?",
"appveyor.yml. In any case, no Ipython.",
"Ok, will either fix or revert the PR before next release. This shouldn't use IPython.display.",
"I am surprised the tests pass. Ipython is definitely not anywhere in the req list. Maybe one of the other dependencies installed it? It is certainly not on appveyor. ",
"There are other issues with this. \r\n\r\n- `from __future__` imports should never be used anymore.\r\n- what is with all the #type: ignore. We didn't set up type checking just so people can ignore them. Unless there is a good justification for ignoring types for something, the default should not be to pepper the entire code with type ignores.\r\n\r\n",
"* Agreed about `__future__`\r\n* Given that our type hint policy is currently that type hints are optional, and this is a non-core module, I thought this was fine, and at least was a starting point for someone to fully add type hints at a later date.",
"@mkhorton Type hints are optional if they are writing a NEW module and using type hints on the new module. Here, the type hints are being introduced willy nilly on imports that are properly type-hinted (e.g., Structure). The whole point is for non-core classes to rely on the type hints to ensure correct behavior.\r\n\r\nI have taken it on myself to remove all the extraneous code and to remove the #type:ignores. In fact, they did nothing at all. The unittest class name was XRDCalculatorTest, instead of TEMCalculatorTest.",
"Ok, thanks for removing them and fixing the name.",
"Sorry about the issues ... Thanks for the help!",
"@mkhorton Sorry for the troubles. I recently noticed that if the beam direction is set to 100, or -100, the pattern fails to generate, due to a division by zero error in one of the calculations. I have rewritten the calculation process to avoid that. It is now working. Furthermore, I added a new method to get the interplanar angle between planes, since the previous implementation in the code did not consider crystal systems. Sorry! And Thank you!",
"No problem, this functionality has not been formally released yet. Please make sure the previous issue receives a new test when you fix it. Thanks!",
"You'll have to create a new pull request too"
] | 2019-11-08T09:49:49
| 2020-03-28T04:12:12
|
2020-03-15T19:24:30Z
|
CONTRIBUTOR
|
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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 generate_points to be using numpy arrays rather than nested for loops.
- Vectorized methods to reduce for loops when looping over dictionaries, if possible.
- Changed original implementation of prettytable to pandas dataframe.
- Removed TEM Dot object to a more lightweight named tuple.
- Will be used to generate dataset analyzing material differences in TEM space.
- Updated structural factors. Matches international table of crystallography.
Request submitted by Jason Liang, student working with Shyam.
|
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MDExOlB1bGxSZXF1ZXN0MzM5MDA3Mzc1
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|
Extend grosspop class
|
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[] | 2019-11-09T12:44:35
| 2019-11-11T14:07:46
|
2019-11-11T14:07:46Z
|
MEMBER
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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, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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MDU6SXNzdWU1MjA3NDE0MjE=
| 1,657
|
ImportError: cannot import name 'normpdf' from 'matplotlib.mlab'
|
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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 pymatgen.io.gaussian)\r\n"
] | 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 error.
Or, downgrading 'matplotlib' version
I refered,
https://stackoverflow.com/questions/12877794/whats-the-correct-usage-of-matplotlib-mlab-normpdf
|
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MDExOlB1bGxSZXF1ZXN0MzM5NDMxMTIy
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|
Bump numpy from 1.17.3 to 1.17.4
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[] | 2019-11-11T13:18:36
| 2019-11-11T14:07:39
|
2019-11-11T14:07:30Z
|
CONTRIBUTOR
|
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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 against NumPy 1.17.3 along with
> some build improvements. The Python versions supported in this release
> are 3.5-3.8.
>
> Downstream developers should use Cython >= 0.29.13 for Python 3.8 support and
> OpenBLAS >= 3.7 to avoid errors on the Skylake architecture.
>
>
> Highlights
> ==========
>
> * Fixed `np.random.random_integers` biased generation of 8 and 16 bit integers.
> * Fixed `np.einsum` regression on Power9 and z/Linux.
> * Fixed histogram problem with signed integer arrays.
>
>
> Contributors
> ============
>
> A total of 5 people contributed to this release. People with a "+" by their
> names contributed a patch for the first time.
>
> * Charles Harris
> * Chris Burr +
> * Matti Picus
> * Qiming Sun +
> * Warren Weckesser
>
>
> Pull requests merged
> ====================
>
> A total of 8 pull requests were merged for this release.
>
> * [#14758](https://github-redirect.dependabot.com/numpy/numpy/issues/14758): BLD: declare support for python 3.8
> * [#14781](https://github-redirect.dependabot.com/numpy/numpy/issues/14781): BUG: random: biased samples from integers() with 8 or 16 bit...
> * [#14851](https://github-redirect.dependabot.com/numpy/numpy/issues/14851): BUG: Fix _ctypes class circular reference. ([#13808](https://github-redirect.dependabot.com/numpy/numpy/issues/13808))
> * [#14852](https://github-redirect.dependabot.com/numpy/numpy/issues/14852): BLD: add 'apt update' to shippable
> * [#14855](https://github-redirect.dependabot.com/numpy/numpy/issues/14855): BUG: Fix `np.einsum` errors on Power9 Linux and z/Linux
> * [#14857](https://github-redirect.dependabot.com/numpy/numpy/issues/14857): BUG: lib: Fix histogram problem with signed integer arrays.
> * [#14858](https://github-redirect.dependabot.com/numpy/numpy/issues/14858): BLD: Prevent -flto from optimising long double representation...
> * [#14866](https://github-redirect.dependabot.com/numpy/numpy/issues/14866): MAINT: move buffer.h -> npy_buffer.h to avoid conflicts
>
>
> Checksums
> =========
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`346f5b6`](https://github.com/numpy/numpy/commit/346f5b61e5a0da82f46760a66101589e7b776426) REL: NumPy 1.17.4 release.
- [`6793723`](https://github.com/numpy/numpy/commit/679372397e2427f87cbbbc96e955e687118c58a8) Merge pull request [#14872](https://github-redirect.dependabot.com/numpy/numpy/issues/14872) from charris/prepare-1.17.4-release
- [`f03fff8`](https://github.com/numpy/numpy/commit/f03fff89ffed5ba569655c0b70235cd68bde33e3) REL: Prepare for 1.17.4 release.
- [`20b5b08`](https://github.com/numpy/numpy/commit/20b5b08f173047acac9fa84235f28b9bc17390fe) Merge pull request [#14866](https://github-redirect.dependabot.com/numpy/numpy/issues/14866) from charris/backport-14830
- [`955f9cc`](https://github.com/numpy/numpy/commit/955f9cca9c09b2e6f84915765735e83e014a27d4) MAINT: move buffer.h -> npy_buffer.h to avoid conflicts
- [`4b94219`](https://github.com/numpy/numpy/commit/4b94219045b1fcc78b39dcfdc88d8f2df8a1a098) Merge pull request [#14858](https://github-redirect.dependabot.com/numpy/numpy/issues/14858) from charris/backport-14827
- [`abf284b`](https://github.com/numpy/numpy/commit/abf284be056ab9c01aeed6485081131e53b872ea) Merge pull request [#14857](https://github-redirect.dependabot.com/numpy/numpy/issues/14857) from charris/backport-14381
- [`41b0d44`](https://github.com/numpy/numpy/commit/41b0d443edacdcf2ab5be418b08e1a305b657077) BLD: Review feedback for clang -flto fix
- [`285a612`](https://github.com/numpy/numpy/commit/285a612abecd464ddd4520032fff3667d725d248) BLD: Prevent -flto from optimising long double representation check away
- [`159507a`](https://github.com/numpy/numpy/commit/159507a9d2120df2fbb14dbf1b11e5c20ad9b67a) BUG: lib: Fix histogram problem with signed integer arrays.
- Additional commits viewable in [compare view](https://github.com/numpy/numpy/compare/v1.17.3...v1.17.4)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=numpy&package-manager=pip&previous-version=1.17.3&new-version=1.17.4)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
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| 520,958,383
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MDExOlB1bGxSZXF1ZXN0MzM5NDMxMzk1
| 1,659
|
Bump tqdm from 4.37.0 to 4.38.0
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[] | 2019-11-11T13:19:04
| 2019-11-11T14:07:28
|
2019-11-11T14:07:17Z
|
CONTRIBUTOR
|
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.37.0 to 4.38.0.
<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.com/tqdm/tqdm/issues/838) -> [#839](https://github-redirect.dependabot.com/tqdm/tqdm/issues/839))
> + use `self.refresh()` in more places
> + add and update performance tests
> + support args for `TqdmDefaultWriteLock.acquire()`
> - fix colorama on win ([#678](https://github-redirect.dependabot.com/tqdm/tqdm/issues/678), [#764](https://github-redirect.dependabot.com/tqdm/tqdm/issues/764))
> - framework updates
> + CI cleanup
> * move to stages (check/test/deploy)
> * auto deploy notes
> * deploy only on parent repo
> * separate docker deploy
> + update documentation sync/generation
> - update examples
> - update documentation
> - add and update tests
> - misc tidy and linting
</details>
<details>
<summary>Commits</summary>
- [`69179d8`](https://github.com/tqdm/tqdm/commit/69179d8bf877aa8df49324cd59ae44dcc1422fce) Merge branch 'devel'
- [`0743062`](https://github.com/tqdm/tqdm/commit/0743062a8c88982e051731835825952ebb46b245) use new cleanup
- [`f44a3f6`](https://github.com/tqdm/tqdm/commit/f44a3f681ab298ed80c89b75398059e71e47eaa0) remove unneeded sudo
- [`265d46a`](https://github.com/tqdm/tqdm/commit/265d46a434aa00e71ea71cea8550525ffd9360de) deploy notes and only parent repo
- [`b8e8c6e`](https://github.com/tqdm/tqdm/commit/b8e8c6e3719b373a6f98e50ad340019df13edb57) Merge branch 'locking' into devel
- [`b1fdd0c`](https://github.com/tqdm/tqdm/commit/b1fdd0c4787c2e7189ca3a277c16ef0034cf084b) update example
- [`1599ada`](https://github.com/tqdm/tqdm/commit/1599ada42dedce16ff2f1988ddffd1641cd9f5fd) update docs
- [`464165c`](https://github.com/tqdm/tqdm/commit/464165c3cb7b6f1e1917e62bbaa5d349cdc436ee) fix py3.4 tests
- [`166e1bc`](https://github.com/tqdm/tqdm/commit/166e1bc5dcae974ff39b99e3d51d2b67a18dde71) liting and minor tidy
- [`213f302`](https://github.com/tqdm/tqdm/commit/213f30288c3b30e6841f06838a5d669e3f19dd4a) fix silly lock bug, tighten perf tests
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.37.0...v4.38.0)
</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzM5NDMxNTEy
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|
Bump scipy from 1.3.1 to 1.3.2
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[] | 2019-11-11T13:19:18
| 2019-11-11T14:07:15
|
2019-11-11T14:07:04Z
|
CONTRIBUTOR
|
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Bumps [scipy](https://github.com/scipy/scipy) from 1.3.1 to 1.3.2.
<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
> =====
>
> * CJ Carey
> * Dany Vohl
> * Martin Gauch +
> * Ralf Gommers
> * Matt Haberland
> * Eric Larson
> * Nikolay Mayorov
> * Sam McCormack +
> * Andrew Nelson
> * Tyler Reddy
> * Pauli Virtanen
> * Huize Wang +
> * Warren Weckesser
> * Joseph Weston +
>
> A total of 14 people contributed to this release.
> People with a "+" by their names contributed a patch for the first time.
> This list of names is automatically generated, and may not be fully complete.
</details>
<details>
<summary>Commits</summary>
- [`78904d6`](https://github.com/scipy/scipy/commit/78904d646f6fea3736aa7698394aebd2872e2638) REL: SciPy 1.3.2 release commit
- [`f472fce`](https://github.com/scipy/scipy/commit/f472fcee99d23acdd6ad526d8330d3a2013d12c7) Merge pull request [#11032](https://github-redirect.dependabot.com/scipy/scipy/issues/11032) from tylerjereddy/relnotes_132_update_again
- [`11be02b`](https://github.com/scipy/scipy/commit/11be02b69fe972af00a2c76d44c211b4987271a2) DOC, MAINT: 1.3.2 relnotes update
- [`520b27e`](https://github.com/scipy/scipy/commit/520b27e5ec09518bcb6881efca7ca15c4d75bd20) DOC: Typo in _peak_finding.py ([#11025](https://github-redirect.dependabot.com/scipy/scipy/issues/11025))
- [`7f8a742`](https://github.com/scipy/scipy/commit/7f8a7420abfa132042e8a24c77f078b2a0d1e4cc) Merge pull request [#10996](https://github-redirect.dependabot.com/scipy/scipy/issues/10996) from tylerjereddy/relnotes_132
- [`66a1d8b`](https://github.com/scipy/scipy/commit/66a1d8b845f56f595adebf9387ca96d1a808e949) DOC: update 1.3.2 release notes
- [`dd88b7f`](https://github.com/scipy/scipy/commit/dd88b7f1560200b80ed201dabbebb540f98a83ca) Merge pull request [#10970](https://github-redirect.dependabot.com/scipy/scipy/issues/10970) from tylerjereddy/backports_132
- [`458fae1`](https://github.com/scipy/scipy/commit/458fae19c268a7312ec917689d2e96f0d9e4c986) DOC: Fix typo in sp.stats.wilcoxon docsting
- [`732e22e`](https://github.com/scipy/scipy/commit/732e22ed13400593fec50bc0f6aaacaa181dad5b) MAINT: use 3.8 stable in CI
- [`d213dc1`](https://github.com/scipy/scipy/commit/d213dc1645eea2d6abf9366c496a46b0107d2c62) BUG: Fix signal.unique_roots ([#10961](https://github-redirect.dependabot.com/scipy/scipy/issues/10961))
- Additional commits viewable in [compare view](https://github.com/scipy/scipy/compare/v1.3.1...v1.3.2)
</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzM5OTIwMjMx
| 1,661
|
Fix broken plotting of fatbands from lobster and extension of Doscar class for lobster
|
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[] | null |
[
"Thanks."
] | 2019-11-12T13:52:51
| 2019-11-12T15:38:08
|
2019-11-12T15:38:03Z
|
MEMBER
|
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## 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 additional test that might help to avoid such changes of tests in the future.
I have also extended the Doscar class to also read in the integrated total density of states from Lobster. Tests have been added as well.
Best,
JG
## Checklist
Before a pull request can be merged, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
Note that the CI system will run all the above checks. But it will be much more
efficient if you already fix most errors prior to submitting the PR. It is
highly recommended that you use the pre-commit hook provided in the pymatgen
repository. Simply `cp pre-commit .git/hooks` and a check will be run prior to
allowing commits.
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MDU6SXNzdWU1MjE5NDU0NjQ=
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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 just fine and you can subsequently just call python and type `from pymatgen import Structure`. These instructions are pretty clear in the pymatgen.org documentation page itself.\r\n\r\nIf this does not work, you need to provide context - what is your OS (and version)? What conda version are you using? ",
"Dear Shyue Ping Ong,\n\n\nThank you so much! Please forgive my ignorance. I simply followed the instruction on the website and only input “conda install -c conda-forge pymatgen”. Thus, it took me forever to install it. In another word, is it possible for beginner to update the instruction on the website. I sincerely appreciate your effort and time.\n\nFollowing your instruction, I successfully installed pymatgen using conda.\n\n\nAppreciatively,\nLeon\n\nSent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows 10\n\n________________________________\nFrom: Shyue Ping Ong <notifications@github.com>\nSent: Tuesday, November 12, 2019 11:11:07 PM\nTo: materialsproject/pymatgen <pymatgen@noreply.github.com>\nCc: Leon <wly_ustc@hotmail.com>; Author <author@noreply.github.com>\nSubject: Re: [materialsproject/pymatgen] installation improvement (#1662)\n\n\nIt 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\n\nconda create -n pmg_env python\nconda activate pmg_env\nconda install -c conda-forge pymatgen\n\n\nshould work just fine and you can subsequently just call python and type from pymatgen import Structure. These instructions are pretty clear in the pymatgen.org documentation page itself.\n\nIf this does not work, you need to provide context - what is your OS (and version)? What conda version are you using?\n\n—\nYou are receiving this because you authored the thread.\nReply to this email directly, view it on GitHub<https://github.com/materialsproject/pymatgen/issues/1662?email_source=notifications&email_token=AET6HTIGZFG4UCDJ2LGD5KLQTN45XA5CNFSM4JMQDQZ2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOED42AWA#issuecomment-553230424>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AET6HTOVEDUMFDU52VZXXXDQTN45XANCNFSM4JMQDQZQ>.\n"
] | 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 to install pymatgen using "conda" because cond always find all kinds of conflicts and looks for incompatible package although I installed a new conda. I had to use pip to install it. However, I could not quickly figure out the environment settings for conda and/or python. So, I am able to "import pymargen", however I could not import structure, etc. sub-modules.
I tried to modified numy*.json for pymatgen. I failed.
**Describe the solution you'd like**
Is that possible to provide a setting program (like bash scripts) which can be used to merge settings/environment for pymatgen into conda's enviroment. So, we can run python scripts like, "from pymatgen import Structure, ...."
**Describe alternatives you've considered**
Provide us a instruction to show how to configure the environment for pymatgen in conda environment.
**Additional context**
Add any other context or screenshots about the feature request here.
|
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MDExOlB1bGxSZXF1ZXN0MzQwNDY1MDE0
| 1,663
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Bump phonopy from 1.11.12.121 to 2.4.0.post5
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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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Bumps [phonopy](http://atztogo.github.io/phonopy/) from 1.11.12.121 to 2.4.0.post5.
[](https://dependabot.com/compatibility-score.html?dependency-name=phonopy&package-manager=pip&previous-version=1.11.12.121&new-version=2.4.0.post5)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
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MDU6SXNzdWU1MjIzOTgwNjY=
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BandStructureSymmLine.apply_scissor missing appropriate tests
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[] | 2019-11-13T18:32:09
| 2023-06-20T17:56:39
|
2023-06-20T17:56:39Z
|
MEMBER
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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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MDU6SXNzdWU1MjI1MTU1OTA=
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non symmetric structure matching
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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.",
"Addressed in https://github.com/materialsproject/pymatgen/pull/1763/commits"
] | 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 Structure
sm = StructureMatcher(comparator=ElementComparator(), #ignored_species=['Li'],
ltol=0.6,
stol=0.6,
angle_tol=6,)
ll = [{'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': None, 'lattice': {'matrix': [[3.552429, -7.7e-05, -1.2e-05], [-1.776307, 4.493682, -1.516445], [-2.4e-05, 0.015372, 6.79461]], 'a': 3.552429000854767, 'b': 5.064390379245857, 'c': 6.794627388684385, 'alpha': 107.3029149646663, 'beta': 90.00039873290154, 'gamma': 110.53397277501261, 'volume': 108.5475442552993}, 'sites': [{'species': [{'element': 'Zn', 'occu': 1}], 'abc': [0.0, 0.0, 0.0], 'xyz': [0.0, 0.0, 0.0], 'label': 'Zn', 'properties': {}}, {'species': [{'element': 'V', 'occu': 1}], 'abc': [0.202219, 0.404425, 0.664665], 'xyz': [-3.027048399991218e-05, 1.8275590023669999, 3.902848759896999], 'label': 'V', 'properties': {}}, {'species': [{'element': 'V', 'occu': 1}], 'abc': [0.797781, 0.595575, 0.335335], 'xyz': [1.776128270484, 2.681417997633, 1.3753042401029998], 'label': 'V', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.045267, 0.090522, 0.735745], 'xyz': [-4.716591000020851e-06, 0.418083468585, 4.861828156955999], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.954733, 0.909478, 0.264255], 'xyz': [1.7761027165910002, 4.090893531415, 0.4163248430440001], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.348735, 0.697498, 0.886166], 'xyz': [-0.00013552055499983987, 3.1479294987929993, 4.96343082583], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.651265, 0.302502, 0.113834], 'xyz': [1.776233520555, 1.3610475012069998, 0.31472217417], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.301682, 0.603347, 0.429131], 'xyz': [-3.591309499998087e-05, 2.7178229258719995, 2.000831622311], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.698318, 0.396653, 0.570869], 'xyz': [1.776133913095, 1.7911540741279997, 3.2773213776889993], 'label': 'O', 'properties': {}}]},
{'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': None, 'lattice': {'matrix': [[3.649555, -0.000166, -0.000313], [-1.824697, 4.621356, -1.922552], [0.001005, -0.534278, 6.968492]], 'a': 3.649555017197302, 'b': 5.327537575019908, 'c': 6.988943750336885, 'alpha': 115.22517955539189, 'beta': 89.9964612523979, 'gamma': 110.02995567671185, 'volume': 113.77868577785667}, 'sites': [{'species': [{'element': 'V', 'occu': 1}], 'abc': [0.19506, 0.391251, 0.613949], 'xyz': [-0.0014153089020000095, 1.480058332574, 3.526037248576], 'label': 'V', 'properties': {}}, {'species': [{'element': 'V', 'occu': 1}], 'abc': [0.840701, 0.682389, 0.378393], 'xyz': [1.8234116618870002, 2.9512558878640003, 1.3246371172149998], 'label': 'V', 'properties': {}}, {'species': [{'element': 'Zn', 'occu': 1}], 'abc': [0.914539, 0.830279, 0.008518], 'xyz': [1.822661340272, 3.8323120448459997, -1.537183187859], 'label': 'Zn', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.069406, 0.139892, 0.722232], 'xyz': [-0.0012336552340000031, 0.2606065436599999, 4.763896545682], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.001661, 0.004527, 0.323955], 'xyz': [-0.0018729176889999996, -0.152161426604, 2.2487739130630002], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.379414, 0.759986, 0.891724], 'xyz': [-0.0011557308520002887, 3.0356743630199996, 4.752740199353999], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.707794, 0.416383, 0.124187], 'xyz': [1.823485128654, 1.8577861995579996, 0.06465660706600007], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.343825, 0.688655, 0.454374], 'xyz': [-0.0013218187900000896, 2.939700809258, 1.8422189192229999], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.73784, 0.47673, 0.570957], 'xyz': [1.8234736721750002, 1.8979668003939993, 3.061940127964], 'label': 'O', 'properties': {}}]},
{'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': None, 'lattice': {'matrix': [[3.645155, -0.000213, -0.000419], [-1.822446, 4.63216, -1.934007], [0.000783, -0.543676, 6.984346]], 'a': 3.6451550303046094, 'b': 5.340280775817409, 'c': 7.005474520243508, 'alpha': 115.3671422051412, 'beta': 89.99990235685013, 'gamma': 109.95445919212213, 'volume': 114.09436416758835}, 'sites': [{'species': [{'element': 'V', 'occu': 1}], 'abc': [0.194888, 0.390915, 0.613841], 'xyz': [-0.001543872946999961, 1.47700869574, 3.5311639285089997], 'label': 'V', 'properties': {}}, {'species': [{'element': 'V', 'occu': 1}], 'abc': [0.840649, 0.682382, 0.378449], 'xyz': [1.8209878847899998, 2.954969908359, 1.3231349627489999], 'label': 'V', 'properties': {}}, {'species': [{'element': 'Zn', 'occu': 1}], 'abc': [0.914717, 0.830418, 0.009165], 'xyz': [1.820900459902, 3.8414514176189996, -1.542405960259], 'label': 'Zn', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.070181, 0.14147, 0.722328], 'xyz': [-0.0014352297410000652, 0.26258432891899997, 4.771355301359], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.001276, 0.003805, 0.324117], 'xyz': [-0.0020294056390000002, -0.15858953708, 2.256385841203], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.379509, 0.760009, 0.89145], 'xyz': [-0.0010082277690003111, 3.035742483823, 4.756173501366], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.707728, 0.416342, 0.124543], 'xyz': [1.8211149624770002, 1.8607009725879997, 0.06434652345200009], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.344306, 0.689673, 0.455214], 'xyz': [-0.0014866301660001666, 2.947113419838, 1.8453954061190003], 'label': 'O', 'properties': {}}, {'species': [{'element': 'O', 'occu': 1}], 'abc': [0.737577, 0.47627, 0.569921], 'xyz': [1.821052381158, 1.8961493697029999, 3.0591068980130003], 'label': 'O', 'properties': {}}]}]
l_structs = [Structure.from_dict(vv) for vv in ll]
print((sm.fit(l_structs[0], l_structs[2])))
print(sm.fit(l_structs[2], l_structs[0]))
print(len(sm.group_structures(l_structs)))
aa = l_structs.pop(0)
l_structs = l_structs + [aa]
print(len(sm.group_structures(l_structs)))
```
This results in
```
True
False
1
2
```
|
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| 522,864,321
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MDExOlB1bGxSZXF1ZXN0MzQwOTc5MDE4
| 1,666
|
Bump pylint from 2.4.3 to 2.4.4
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[] | 2019-11-14T13:36:52
| 2019-11-15T08:06:34
|
2019-11-15T08:06:25Z
|
CONTRIBUTOR
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Bumps [pylint](https://github.com/PyCQA/pylint) from 2.4.3 to 2.4.4.
<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 found in type annotations from ``unused-import``
>
> The previous code was assuming that only ``typing`` names need to be
> exempted, but we need to do that for the rest of the type comment
> names as well.
>
> Close [#3112](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3112)
>
> * Relax type import detection for names that do not come from the ``typing`` module
>
> Close [#3191](https://github-redirect.dependabot.com/PyCQA/pylint/issues/3191)
</details>
<details>
<summary>Commits</summary>
- [`d0a597b`](https://github.com/PyCQA/pylint/commit/d0a597b34a0e39a7dd64cdf685f3147f147f52a4) Prepare 2.4.4
- [`7946f13`](https://github.com/PyCQA/pylint/commit/7946f13c27a422d8c55c553c670d4062b47f7bc0) Relax type import detection for names that do not come from the ``typing`` mo...
- [`c51afc0`](https://github.com/PyCQA/pylint/commit/c51afc0fa6f757587701e251f07e96cc9c6b70d8) Mark this branch as 2.4.4
- [`2ac25f6`](https://github.com/PyCQA/pylint/commit/2ac25f63bc9e34cefd18c55751a36e30c16d7d14) Exempt all the names found in type annotations from ``unused-import``
- See full diff in [compare view](https://github.com/PyCQA/pylint/compare/pylint-2.4.3...pylint-2.4.4)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pylint&package-manager=pip&previous-version=2.4.3&new-version=2.4.4)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzQxMTczMTYy
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Sign flip
|
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[] | null |
[
"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 Bader, the raw output is the total amount of charge for the atom. It would be weird for both to have a sign flip?\n\nAlso here fields 0-3 in Zn, and 4-7 is Te. I think it would make more sense for Te to be the negative transfer since its more electronegative than Zn?\n\nMartin\n\n\n> On Nov 14, 2019, at 1:04 PM, Matthew Horton <notifications@github.com> wrote:\n> \n> Test will likely need to be updated also. What system did you verify this against?\n\n",
"Actually - upon further investigation - I'm not entirely sure this is the right conclusion."
] | 2019-11-14T20:58:54
| 2019-11-15T00:45:36
|
2019-11-15T00:45:36Z
|
CONTRIBUTOR
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Correcting sign in BaderAnalysis' get_charge_transfer method
|
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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/3850578/OUTCAR.txt)\r\n\r\n"
] | 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 0.1360: real time 0.1339
atom = 2 type = 2 l = 3
onsite density matrix
spin component 1
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
spin component 2
0.0000 0.0000 0.0000 0.0000 19.2672 **1.6427-28.9219**
0.0000 0.0000 0.0000 0.0000 19.0213 -1.8641-31.3417
0.0000 0.0000 0.0000 0.0000 18.2881 -5.4857-33.4018
0.0000 0.0000 0.0000 0.0000 17.0809 -9.1595-35.0760
0.0000 0.0000 0.0000 0.0000 15.4217-12.8227-36.3455
0.0000 0.0000 0.0000 0.0000 13.3405-16.4136-37.1994
0.0000 0.0000 0.0000 0.0000 10.8748-19.8728-37.6345
**Expected behavior**
Could you divide these two numbers?
**Desktop (please complete the following information):**
- Version '2019.11.11'
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MDExOlB1bGxSZXF1ZXN0MzQxMzI4NDI5
| 1,669
|
update significant figures of get_gb_data test
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| 2019-11-15T08:06:04
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2019-11-15T08:06:04Z
|
CONTRIBUTOR
|
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## Summary
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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| 523,388,241
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MDExOlB1bGxSZXF1ZXN0MzQxNDAwNzIw
| 1,670
|
Fix regular expression in read_onsite_density_matrices in Outcar
|
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[] | null |
[
"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/test_outputs.py#L974",
"I have added the test."
] | 2019-11-15T10:30:33
| 2019-11-18T16:45:05
|
2019-11-18T16:40:26Z
|
CONTRIBUTOR
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To parse the connected numbers, modify the regular expression.
See Issue #1668
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MDExOlB1bGxSZXF1ZXN0MzQxNDY5Nzcy
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|
Bump pytest from 5.2.2 to 5.2.3
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| 2019-11-15T19:46:47
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2019-11-15T19:46:34Z
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CONTRIBUTOR
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.2.2 to 5.2.3.
<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://github-redirect.dependabot.com/pytest-dev/pytest/issues/5830): The
> first test in a package (`__init__.py`) marked with
> `@pytest.mark.skip` is now correctly skipped.
> - [\#6099](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6099): Fix
> `--trace` when used with parametrized functions.
> - [\#6183](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6183): Using
> `request` as a parameter name in `@pytest.mark.parametrize` now
> produces a more user-friendly error.
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.2.3 (2019-11-14)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#5830](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5830): The first test in a package (`__init__.py`) marked with `@pytest.mark.skip` is now correctly skipped.
> - [\#6099](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6099): Fix `--trace` when used with parametrized functions.
> - [\#6183](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6183): Using `request` as a parameter name in `@pytest.mark.parametrize` now produces a more user-friendly error.
</details>
<details>
<summary>Commits</summary>
- [`dd9a27c`](https://github.com/pytest-dev/pytest/commit/dd9a27cf543c39f91039ecd7aa6aa595b3e79330) Adjust CHANGELOG
- [`5e8c47f`](https://github.com/pytest-dev/pytest/commit/5e8c47faad91ccf49897a290efd62bcac1971ff7) Preparing release version 5.2.3
- [`92d6a05`](https://github.com/pytest-dev/pytest/commit/92d6a0500b9f528a9adcd6bbcda46ebf9b6baf03) Show a better message when 'request' is used in parametrize ([#6184](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6184))
- [`6f2c0fd`](https://github.com/pytest-dev/pytest/commit/6f2c0fd2e8e8154c8129900c9a1c650068811404) Show a better message when 'request' is used in parametrize
- [`55a58bc`](https://github.com/pytest-dev/pytest/commit/55a58bcd3d15887610e1303f4076401bd16ba742) Merge pull request [#6173](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6173) from brettcannon/patch-1
- [`0b40749`](https://github.com/pytest-dev/pytest/commit/0b40749c9826d67ff44044608778d6ccd763e95a) Delineate syntactically that the 'match' argument to 'raises' is keyword-only
- [`adccb63`](https://github.com/pytest-dev/pytest/commit/adccb63de01965ff873038fa2b1bacfa7dbaf049) setup.cfg: fix check-manifest ignore [ci skip] ([#6156](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6156))
- [`41604ee`](https://github.com/pytest-dev/pytest/commit/41604eeb3e70c35103b5260b20419a817a0fe6ac) setup.cfg: fix check-manifest ignore [ci skip]
- [`85288b5`](https://github.com/pytest-dev/pytest/commit/85288b53218d4e0037dce9c34bd37f86fa9e212d) fix bug with nonskipped first test in package ([#5831](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5831))
- [`5f9db8a`](https://github.com/pytest-dev/pytest/commit/5f9db8a01721e10162769b96b82794dd069bbaeb) Merge pull request [#6138](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6138) from blueyed/ci-py38
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.2.2...5.2.3)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.2.2&new-version=5.2.3)
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You can trigger Dependabot actions by commenting on this PR:
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MDExOlB1bGxSZXF1ZXN0MzQxNTgxNDE5
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Gb mprest
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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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MDExOlB1bGxSZXF1ZXN0MzQyMTUwMTU1
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Bump phonopy from 1.11.12.121 to 2.4.1.post5
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"Superseded by #1724."
] | 2019-11-18T13:17:21
| 2019-12-23T13:29:56
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2019-12-23T13:29:54Z
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CONTRIBUTOR
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Bumps [phonopy](http://atztogo.github.io/phonopy/) from 1.11.12.121 to 2.4.1.post5.
[](https://dependabot.com/compatibility-score.html?dependency-name=phonopy&package-manager=pip&previous-version=1.11.12.121&new-version=2.4.1.post5)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
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MDExOlB1bGxSZXF1ZXN0MzQyMTUwMzQ3
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Bump pytest from 5.2.3 to 5.2.4
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| 2019-11-18T16:40:20
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2019-11-18T16:40:09Z
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CONTRIBUTOR
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.2.3 to 5.2.4.
<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://github-redirect.dependabot.com/pytest-dev/pytest/issues/6194): Fix
> incorrect discovery of non-test `__init__.py` files.
> - [\#6197](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6197): Revert
> "The first test in a package (`__init__.py`) marked with
> `@pytest.mark.skip` is now correctly skipped.".
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.2.4 (2019-11-15)
> =========================
>
> Bug Fixes
> ---------
>
> - [\#6194](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6194): Fix incorrect discovery of non-test `__init__.py` files.
> - [\#6197](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6197): Revert "The first test in a package (`__init__.py`) marked with `@pytest.mark.skip` is now correctly skipped.".
</details>
<details>
<summary>Commits</summary>
- [`c9a96cd`](https://github.com/pytest-dev/pytest/commit/c9a96cdee8ee7c1a9ead49b355fab9aef73196fe) Preparing release version 5.2.4
- [`19a15a9`](https://github.com/pytest-dev/pytest/commit/19a15a94eeb403631f847fab5fe5073bc56e8bcc) Merge pull request [#6197](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6197) from asottile/fix_init_py_discovery
- [`4e0f992`](https://github.com/pytest-dev/pytest/commit/4e0f99260d438d750b55a0881110658b8bba5a4a) Add regression tests for __init__.py breakage
- [`176c777`](https://github.com/pytest-dev/pytest/commit/176c7771fb4f3bd703bb6c9650cc32e31d548a2b) Revert "fix bug with nonskipped first test in package ([#5831](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5831))"
- [`e856638`](https://github.com/pytest-dev/pytest/commit/e856638ba086fcf5bebf1bebea32d5cf78de87b4) Preparing release version 5.2.3 ([#6190](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6190))
- [`d4e4ab5`](https://github.com/pytest-dev/pytest/commit/d4e4ab5b3d8bd8fd51430536808bfa3a0805689d) Update text in PR template ([#6188](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6188))
- [`e2a0987`](https://github.com/pytest-dev/pytest/commit/e2a0987156c7b95b27f454d3b8710fd36aa13758) Update advice about _called_from_test. ([#6168](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6168))
- [`bd68c2a`](https://github.com/pytest-dev/pytest/commit/bd68c2a3dca6e6aadd1f9a0e4810f53256d4f6a8) Update advice about _called_from_test.
- [`48ec7d2`](https://github.com/pytest-dev/pytest/commit/48ec7d28c6485da6dc220cd9a5acdbcfc6615ff1) Make whole checklist a comment to avoid incomplete TODOs in PRs
- [`350c27c`](https://github.com/pytest-dev/pytest/commit/350c27c8b441ea73a3c5bf45500659da364f090c) Update text in PR template
- See full diff in [compare view](https://github.com/pytest-dev/pytest/compare/5.2.3...5.2.4)
</details>
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MDExOlB1bGxSZXF1ZXN0MzQyMTUwNTIw
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Bump tabulate from 0.8.5 to 0.8.6
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| 2019-11-18T16:40:05
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2019-11-18T16:39:55Z
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CONTRIBUTOR
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Bumps [tabulate](https://github.com/astanin/python-tabulate) from 0.8.5 to 0.8.6.
<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.
</details>
<details>
<summary>Commits</summary>
- [`719087f`](https://github.com/astanin/python-tabulate/commit/719087f31acf9fecc393868a3b2799bbd3f07677) update benchmark table for v0.8.6
- [`f64df00`](https://github.com/astanin/python-tabulate/commit/f64df00772274ac03a11e29271aafbc7dc543953) update CHANGELOG for v0.8.6
- [`13a5681`](https://github.com/astanin/python-tabulate/commit/13a5681d6815e098ed2245a9655a22942659a4b3) enable numpy and pandas tests on appveyor
- [`3e2bccc`](https://github.com/astanin/python-tabulate/commit/3e2bccc20366b278eeb728a27c1d8dfe26d2e757) fix [#16](https://github-redirect.dependabot.com/astanin/python-tabulate/issues/16): remove misleading example showing support of the multiline headers i...
- [`19da809`](https://github.com/astanin/python-tabulate/commit/19da809040c2f55b657c514909573247ef1cb86f) README: update CI badge link (add appveyor)
- [`baeba94`](https://github.com/astanin/python-tabulate/commit/baeba9412c7696efd6117e3a5da318313b77ee32) add appveyor config
- [`1f2a99d`](https://github.com/astanin/python-tabulate/commit/1f2a99dbeec10ddef81b9ed919b8072bc72ef140) [minor] fix README.md lint warnings
- [`64b9e4b`](https://github.com/astanin/python-tabulate/commit/64b9e4bbdca16386bd269cc62ae3d8c4086cf2b9) README: update CI badge link
- [`1cec3ea`](https://github.com/astanin/python-tabulate/commit/1cec3ea50f3250165fb43eeb1f3b1b5237530968) README: update contributors list
- [`612f685`](https://github.com/astanin/python-tabulate/commit/612f68592f411569a9f52d79db0aac8b2ed0215c) retire support for Python versions < 3.5 as they reached end of life
- Additional commits viewable in [compare view](https://github.com/astanin/python-tabulate/compare/v0.8.5...v0.8.6)
</details>
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MDExOlB1bGxSZXF1ZXN0MzQyMzM3MTc5
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Add optional argument fig_close to add_fig_kwargs
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[] | 2019-11-18T20:03:11
| 2019-11-18T21:39:40
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2019-11-18T21:39:40Z
|
CONTRIBUTOR
|
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## Summary
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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [x] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All existing tests pass.
|
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MDExOlB1bGxSZXF1ZXN0MzQzMzYwODk5
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Bump pytest from 5.2.4 to 5.3.0
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2019-11-20T13:49:51Z
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.2.4 to 5.3.0.
<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](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6179): The
> default value of `junit_family` option will change to `xunit2` in
> pytest 6.0, given that this is the version supported by default in
> modern tools that manipulate this type of file.
>
> In order to smooth the transition, pytest will issue a warning in
> case the `--junitxml` option is given in the command line but
> `junit_family` is not explicitly configured in `pytest.ini`.
>
> For more information, [see the
> docs](https://docs.pytest.org/en/latest/deprecations.html#junit-family-default-value-change-to-xunit2).
>
> Features
> --------
>
> - [\#4488](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/4488): The
> pytest team has created the
> [pytest-reportlog](https://github.com/pytest-dev/pytest-reportlog)
> plugin, which provides a new `--report-log=FILE` option that writes
> *report logs* into a file as the test session executes.
>
> Each line of the report log contains a self contained JSON object
> corresponding to a testing event, such as a collection or a test
> result report. The file is guaranteed to be flushed after writing
> each line, so systems can read and process events in real-time.
>
> The plugin is meant to replace the `--resultlog` option, which is
> deprecated and meant to be removed in a future release. If you use
> `--resultlog`, please try out `pytest-reportlog` and
> provide feedback.
>
> - [\#4730](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/4730): When
> `sys.pycache_prefix` (Python 3.8+) is set, it will be used by pytest
> to cache test files changed by the assertion rewriting mechanism.
>
> This makes it easier to benefit of cached `.pyc` files even on file
> systems without permissions.
>
> - [\#5515](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5515): Allow
> selective auto-indentation of multiline log messages.
>
> Adds command line option `--log-auto-indent`, config option
> `log_auto_indent` and support for per-entry configuration of
></tr></table> ... (truncated)
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/master/CHANGELOG.rst).*
> pytest 5.3.0 (2019-11-19)
> =========================
>
> Deprecations
> ------------
>
> - [\#6179](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6179): The default value of `junit_family` option will change to `xunit2` in pytest 6.0, given that this is the version supported by default in modern tools that manipulate this type of file.
>
> In order to smooth the transition, pytest will issue a warning in case the `--junitxml` option is given in the command line but `junit_family` is not explicitly configured in `pytest.ini`.
>
> For more information, [see the docs](https://docs.pytest.org/en/latest/deprecations.html#junit-family-default-value-change-to-xunit2).
>
> Features
> --------
>
> - [\#4488](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/4488): The pytest team has created the [pytest-reportlog](https://github.com/pytest-dev/pytest-reportlog) plugin, which provides a new `--report-log=FILE` option that writes *report logs* into a file as the test session executes.
>
> Each line of the report log contains a self contained JSON object corresponding to a testing event, such as a collection or a test result report. The file is guaranteed to be flushed after writing each line, so systems can read and process events in real-time.
>
> The plugin is meant to replace the `--resultlog` option, which is deprecated and meant to be removed in a future release. If you use `--resultlog`, please try out `pytest-reportlog` and provide feedback.
>
> - [\#4730](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/4730): When `sys.pycache_prefix` (Python 3.8+) is set, it will be used by pytest to cache test files changed by the assertion rewriting mechanism.
>
> This makes it easier to benefit of cached `.pyc` files even on file systems without permissions.
>
> - [\#5515](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5515): Allow selective auto-indentation of multiline log messages.
>
> Adds command line option `--log-auto-indent`, config option `log_auto_indent` and support for per-entry configuration of indentation behavior on calls to `logging.log()`.
>
> Alters the default for auto-indention from `on` to `off`. This restores the older behavior that existed prior to v4.6.0. This reversion to earlier behavior was done because it is better to activate new features that may lead to broken tests explicitly rather than implicitly.
>
> - [\#5914](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5914): `pytester` learned two new functions, [no\_fnmatch\_line](https://docs.pytest.org/en/latest/reference.html#_pytest.pytester.LineMatcher.no_fnmatch_line) and [no\_re\_match\_line](https://docs.pytest.org/en/latest/reference.html#_pytest.pytester.LineMatcher.no_re_match_line).
>
> The functions are used to ensure the captured text *does not* match the given pattern.
>
> The previous idiom was to use `re.match`:
>
> ``` {.sourceCode .python}
> assert re.match(pat, result.stdout.str()) is None
> ```
>
> Or the `in` operator:
>
> ``` {.sourceCode .python}
> assert text in result.stdout.str()
> ```
>
> But the new functions produce best output on failure.
>
> - [\#6057](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6057): Added tolerances to complex values when printing `pytest.approx`.
></tr></table> ... (truncated)
</details>
<details>
<summary>Commits</summary>
- [`be59827`](https://github.com/pytest-dev/pytest/commit/be59827216612fd416818702be7e2b8448f4089d) Small fixes in the CHANGELOG for 5.3.0
- [`4b16b93`](https://github.com/pytest-dev/pytest/commit/4b16b93cf57bb58d6dd55fb4b4ffa2a0a2a344db) Preparing release version 5.3.0
- [`21622d0`](https://github.com/pytest-dev/pytest/commit/21622d0df43609b84644134a4741343d147df1eb) Merge remote-tracking branch 'upstream/master' into release-5.3.0
- [`d1e2d12`](https://github.com/pytest-dev/pytest/commit/d1e2d12b3feae7366b57b878f88a8b772817820e) python: remove unused pytest_make_parametrize_id hookimpl ([#6228](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6228))
- [`f36ea24`](https://github.com/pytest-dev/pytest/commit/f36ea240fe3579f945bf5d6cc41b5e45a572249d) Remove check for os.symlink, always there in py3+ ([#6227](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6227))
- [`4804d4b`](https://github.com/pytest-dev/pytest/commit/4804d4bc9824f7a6fb0153a25e896627dec37b3b) python: remove unused pytest_make_parametrize_id hookimpl
- [`b820b7e`](https://github.com/pytest-dev/pytest/commit/b820b7e384a0e86ed0954bd79b89f4ff928e2837) Merge pull request [#6224](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6224) from blueyed/visit_Assert-minor-cleanup
- [`8d3e8b1`](https://github.com/pytest-dev/pytest/commit/8d3e8b1c54ae5499e25101f5162cbe17f1cf7330) Revert "ci: use tox -vv" ([#6226](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6226))
- [`63a23d8`](https://github.com/pytest-dev/pytest/commit/63a23d876cad98d42f03cf6c6f397513e96ffcdb) Remove check for os.symlink, always there in py3+
- [`eeeb196`](https://github.com/pytest-dev/pytest/commit/eeeb19626b26072ff49735e221dc558363716b78) Merge pull request [#6202](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6202) from linw1995/fix_getmodpath
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.2.4...5.3.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.2.4&new-version=5.3.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)
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You can trigger Dependabot actions by commenting on this PR:
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MDExOlB1bGxSZXF1ZXN0MzQzNTk2MzQy
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Respect KSPACING setting in the INCAR
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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 warning generated. We now preserve this behavior so that if a user has specified KSPACING but also provided `user_kpoints_settings`, a warning is generated and KSPACING is ignored.",
"I can't for the life of me figure out a good way to resolve the mypy TypeHinting error at 1143 in `sets.py`. It's caused by the fact that the internal variable `kpoints` may take on either `Kpoints` or `None` types, depending on the situation. I tried instantiating it as a TypeVar or adding a check, e.g.\r\n```\r\nif super().kpoints is not None:\r\n kpoints = super().kpoints\r\nelse:\r\n return None\r\n```\r\n\r\nwithout any luck. Both the superclass (DictSet) and the local kpoints method are hinted with `Union[Kpoints,None]`\r\n\r\nAll other tests pass.",
"Also a note for code review - there are a couple of input sets that implement their own `kpoints` property methods, and I have not touched these. The sets are MPHSEBSSet, MPNonSCFSet, MVLGWSet, MVLSlabSet, MVLGBSet, MITMDSet, and MPMDSet. Most of them inherit from DictSet.kpoints, but not all. As such, some may still behave unexpectedly when KSPACING is supplied.\r\n\r\nI don't feel I know enough about the intended use of these input sets to modify the kpoints methods. Thoughts?",
"This looks good. As far as I can tell, this is an additive feature, you're not changing defaults and not responsible for the default settings or behavior of other sets (which are overriding kpoints for good reason). As long as existing tests pass without modification that's fine. The mypy failures will have to be fixed however, we can investigate those further."
] | 2019-11-20T19:25:46
| 2019-12-03T22:31:02
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2019-11-22T13:30:12Z
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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.
Currently, if a user adds KSPACING to user_incar_settings when initializing a VaspInputSet, the setting will be ignored and a KPOINTS file generated anyway. This PR ensures that the KSPACING setting passed to VASP as expected.
See also Custodian [#139](https://github.com/materialsproject/custodian/pull/139)
See also a [similar issue](https://gitlab.com/ase/ase/merge_requests/226/commits) recently fixed in ASE.
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Bump matplotlib from 3.1.1 to 3.1.2
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[] | 2019-11-22T13:26:28
| 2019-11-22T13:29:44
|
2019-11-22T13:29:36Z
|
CONTRIBUTOR
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Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.1.1 to 3.1.2.
<details>
<summary>Commits</summary>
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- [`b6b9366`](https://github.com/matplotlib/matplotlib/commit/b6b936691fb0016189565829676cd0d9cbe48cd1) Backport PR [#15528](https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/15528): Declutter home page
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- [`1c7d8da`](https://github.com/matplotlib/matplotlib/commit/1c7d8daf2856ca5aa9960032bcf5d3641c6cd61d) Backport PR [#15516](https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/15516): Add logo like font
- [`30493fe`](https://github.com/matplotlib/matplotlib/commit/30493fee7a30a9b9a7ec5f36be46754d193f70dd) Merge pull request [#15508](https://github-redirect.dependabot.com/matplotlib/matplotlib/issues/15508) from meeseeksmachine/auto-backport-of-pr-15489-on-v...
- Additional commits viewable in [compare view](https://github.com/matplotlib/matplotlib/compare/v3.1.1...v3.1.2)
</details>
<br />
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MDExOlB1bGxSZXF1ZXN0MzQ0NjU3MDE1
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|
Fixing bugs with run_type
|
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[] | null |
[
"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\" string), meaning that it's possible we'll identify a PBE calculation as LDA with the current logic. This is very much not our fault, but we might need to handle it ..."
] | 2019-11-22T19:03:09
| 2020-05-12T15:47:27
|
2019-11-22T19:47:44Z
|
NONE
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## Summary
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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MDExOlB1bGxSZXF1ZXN0MzQ0Njg0NDQy
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fix nomad test
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[
"Thanks @tschaume "
] | 2019-11-22T20:22:12
| 2019-11-23T02:16:16
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2019-11-23T02:16:16Z
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MEMBER
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GGA NSCF Line tasks were de-blessed for the tested materials
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MDU6SXNzdWU1Mjc2NjU4ODE=
| 1,682
|
involve solid state hydroxide in pourbaix diagram
|
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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_entries(["Fe"])`
`pbx = PourbaixDiagram(entries)`
`plotter = PourbaixPlotter(pbx)`
`plotter.get_pourbaix_plot().show()`
**Expected behavior**
from wikipedia
**Screenshots**
code output:
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| 528,086,069
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MDExOlB1bGxSZXF1ZXN0MzQ1MjE1NTIx
| 1,683
|
Bump tqdm from 4.38.0 to 4.39.0
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[] | 2019-11-25T13:26:25
| 2019-11-25T14:05:44
|
2019-11-25T14:05:41Z
|
CONTRIBUTOR
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.38.0 to 4.39.0.
<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) <- [#697](https://github-redirect.dependabot.com/tqdm/tqdm/issues/697))
> - avoid unnecessary `dedent` ([#837](https://github-redirect.dependabot.com/tqdm/tqdm/issues/837))
> - remove unneeded bar logic
> - misc code tidy
> - update documentation
> + document default argument overriding ([#370](https://github-redirect.dependabot.com/tqdm/tqdm/issues/370))
> + add missing `isatty()` ([#713](https://github-redirect.dependabot.com/tqdm/tqdm/issues/713))
> + update badges
> + add code of conduct
> - update framework
> + clean CI stages
> + update CI default `py3.6` => `py3.7`
> + automate snap releases ([#686](https://github-redirect.dependabot.com/tqdm/tqdm/issues/686) <- [#685](https://github-redirect.dependabot.com/tqdm/tqdm/issues/685))
</details>
<details>
<summary>Commits</summary>
- [`aaec694`](https://github.com/tqdm/tqdm/commit/aaec694aff03e10df3a0c6b2b561480b4d56cef8) bump version, merge branch 'devel'
- [`dfdf351`](https://github.com/tqdm/tqdm/commit/dfdf3513104f6b6e355574947bafab9d4d46744e) fix style
- [`80ade93`](https://github.com/tqdm/tqdm/commit/80ade932fafa716be5e9e10e552c8c27b442ed06) Add check for pandas builtin for progress apply
- [`83f2752`](https://github.com/tqdm/tqdm/commit/83f2752eaebfb54c1c301a6b453417888fa204ff) Replace dedent calls by dedented strings.
- [`58f9f1c`](https://github.com/tqdm/tqdm/commit/58f9f1c1342f35301258f5ff4f8ccb223693235c) Add missing isatty() method to DummyTqdmFile
- [`7d38b8a`](https://github.com/tqdm/tqdm/commit/7d38b8a0a8892f7598a44dfd163ef3f80fd8bf82) Merge branch 'snap' into devel
- [`8244327`](https://github.com/tqdm/tqdm/commit/8244327f078674a1bc8a4a918eedabd37b721918) ready for merge
- [`4e655ce`](https://github.com/tqdm/tqdm/commit/4e655ce2c0dfba8b75155947c29637345174637a) fix channels
- [`4c63100`](https://github.com/tqdm/tqdm/commit/4c63100f9f42bf7801a75b5d0194be5d51b3e737) fix and tidy snap
- [`d2265fe`](https://github.com/tqdm/tqdm/commit/d2265fe8292468db546aefad9eb3b23ac36eb253) TODO: revert before merge: travis snap build branch
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.38.0...v4.39.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.38.0&new-version=4.39.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (dependabot-automerge-end)
---
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| 528,086,461
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MDExOlB1bGxSZXF1ZXN0MzQ1MjE1ODQ3
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Bump scipy from 1.3.2 to 1.3.3
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[] | 2019-11-25T13:27:00
| 2019-11-25T14:09:17
|
2019-11-25T14:09:15Z
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CONTRIBUTOR
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Bumps [scipy](https://github.com/scipy/scipy) from 1.3.2 to 1.3.3.
<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
> compared to `1.3.2`. In particular, a test suite issue
> involving multiprocessing was fixed for Windows and
> Python `3.8` on macOS.
>
> Wheels were also updated to place `msvcp140.dll` at the
> appropriate location, which was previously causing issues.
>
> Authors
> =======
>
> Ilhan Polat
> Tyler Reddy
> Ralf Gommers
</details>
<details>
<summary>Commits</summary>
- [`802f4ea`](https://github.com/scipy/scipy/commit/802f4eac0eadd6c1372b0cf6c04d97ea26c00c57) REL: SciPy 1.3.3 release commit
- [`a96e6ae`](https://github.com/scipy/scipy/commit/a96e6ae9fb270b76984b60581d838ce2e5956c68) Merge pull request [#11102](https://github-redirect.dependabot.com/scipy/scipy/issues/11102) from tylerjereddy/backports_133_Nov20
- [`d7bf861`](https://github.com/scipy/scipy/commit/d7bf86159384aa5c8d3a4a90f3cd989814224e29) DOC, MAINT: update 1.3.3 release notes
- [`0f73186`](https://github.com/scipy/scipy/commit/0f73186bac7cbcfb20b10a0bf687ef273652c0f5) MAINT: TST: Skipped parallel tests for TestBrute
- [`bc051fb`](https://github.com/scipy/scipy/commit/bc051fba54aadaf6e5164eaaf0582fee991e7cd8) MAINT:TST: Skipped tests that use spawn start method
- [`f1946f2`](https://github.com/scipy/scipy/commit/f1946f2c1576b6a33d106e95bee7cf6f5eed6958) Merge pull request [#11040](https://github-redirect.dependabot.com/scipy/scipy/issues/11040) from tylerjereddy/prep_133
- [`332ea7a`](https://github.com/scipy/scipy/commit/332ea7ae9a8b9cf9876f4371f0b8a902c98ccf6b) MAINT: prepare for SciPy 1.3.3
- See full diff in [compare view](https://github.com/scipy/scipy/compare/v1.3.2...v1.3.3)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=scipy&package-manager=pip&previous-version=1.3.2&new-version=1.3.3)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
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[//]: # (dependabot-automerge-end)
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Wulffshape to plotly conversion
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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 Matthew Horton <notifications@github.com>\nwrote:\n\n> When you say it needs to be optimized for speed, how slow/fast is it\n> currently?\n>\n> —\n> You are receiving this because you modified the open/close state.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1685?email_source=notifications&email_token=AB5J5VXSYXJ523L45CBHHS3QVYGLPA5CNFSM4JSBIVN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFINYQI#issuecomment-558947393>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AB5J5VTVEGD6XAPN6LCLFM3QVYGLPANCNFSM4JSBIVNQ>\n> .\n>\n\n\n-- \n\nRichard Tran\nPhone: (415) 425-7660\nEmail: rit001@eng.ucsd.edu\n<https://acs-webmail.ucsd.edu/squirrelmail/src/compose.php?send_to=rit001%40ucsd.edu>\n",
"Ah, interesting. So what's the cause for the difference in speed? I'd like to understand how the process differs for the matplotlib vs plotly figure. I think 1s is ok, but it would be nice to get it on parity with the matplotlib version unless it's prohibitive.",
"@mkhorton I think it is just a fundamental backend issue. I doubt the actual mechanics of generation is different. Plot.ly may simply not be as well-optimized given it is web-based.\r\n",
"From my understanding, 3DMesh constructs its facets using a triangle mesh\nwhich requires both the vertices of the polyhedron (x, y, and z) in\naddition to a combination of the indices of the coordinates of the vertices\nto produce the triangular mesh (i, j, k). The simplest way for me to do\nthis and ensure the polyhedron is fully enclosed is by just using\nitertools.combinations to enumerate all possible combinations of i, j and\nk, however this can lead to redundancy. One solution I thought of may be to\ninstead find the center connecting all vertices in a facet and draw\ntriangles adjacent to each other that converge at this center point, thus\nsignificantly reducing the amount of triangles 3DMesh has to plot. I think\nthis should be able to reduce the plot generation time significantly, but\nit can be implemented without effecting any dependencies on the WulffShape\nso I figured I would add it in later.\n\nOn Wed, Nov 27, 2019 at 11:29 AM Matthew Horton <notifications@github.com>\nwrote:\n\n> Ah, interesting. So what's the cause for the difference in speed? I'd like\n> to understand how the process differs for the matplotlib vs plotly figure.\n> I think 1s is ok, but it would be nice to get it on parity with the\n> matplotlib version unless it's prohibitive.\n>\n> —\n> You are receiving this because you modified the open/close state.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1685?email_source=notifications&email_token=AB5J5VQYON65L7USNDFF6BDQV3DCFA5CNFSM4JSBIVN2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEFKQ6LY#issuecomment-559222575>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AB5J5VQRREX2ACW7FS3CDBDQV3DCFANCNFSM4JSBIVNQ>\n> .\n>\n\n\n-- \n\nRichard Tran\nPhone: (415) 425-7660\nEmail: rit001@eng.ucsd.edu\n<https://acs-webmail.ucsd.edu/squirrelmail/src/compose.php?send_to=rit001%40ucsd.edu>\n",
"@shyuep there's the generation time (time to create the plotly JSON itself, i.e. largely pre-processing to make the mesh vertices) and the rendering time (time to paint the screen), what I'm asking about is specifically the former. The former step should be roughly equivalent in both cases.\r\n\r\n@richardtran415 unless I mis-understood, isn't this just essentially a convex hull generation? Have you tried the SciPy convex hull? This will give you the triangular mesh directly from the co-ordinates.",
"(Or even SciPy Delaunay, since in this case you know you don't have any interior points.)",
"Regarding the requirements.txt, I just checked Plotly itself, and the package only has two requirements of its own (`six` and `retrying`), given that it’s so lightweight I have no objection to including it as a core requirement. Also, the plotly GraphObjects themselves are just convenience interfaces to their underlying JSON representation, so are also very lightweight to construct.",
"Actually I just realized the issue isn't so much enumerating through all possible combinations of a facet's indices, its moreso that if there are a lot of facets on a Wulff shape, another Mesh3d object is generated every time. However, I think this is neccesary as I would want to have every facet to contain the appropriate hoverinfo. For shapes with few systems, this may not be a big deal but for something on the extreme end of the spectrum like Hf (mp-103), it may take ~1 sec as I mentioned before. I've added six==1.11.0, retrying==1.3.3 and plotly==4.1.1 to the requirements.txt, hopefully this will give pymatgen the plotly compatibility it needs.",
"Thanks @richardtran415. Regarding the requirements, just Including plotly on its own should be sufficient (six and retrying should be pulled in automatically, I only mentioned them to note that plotly itself didn’t have many heavy dependencies).\r\n\r\nRegarding the mesh issue, I’ll try it out myself before merging but that makes sense.",
"So does each face have a distinct `go.Mesh` and a distinct hover label? Or is there one mesh for several symmetrically equivalent faces?",
"The former, each facet has a distinct go.Mesh and hover label. Do you think it may be more conputationally efficient to just sort the symmetrically equivalent facets and then plot one family of planes with one go.Mesh object instead?",
"Yes, perhaps. It's more that I'm just not sure how meaningful it is to label by specific plane rather than plane family given that they are equivalent and the orientation of the Wulff shape itself is essentially arbitrary. Your call though, I think it's ok either way.",
"Right, it is arbitrary how the Wulff shape is oriented, which is why the indices in all equivalent planes are the same value. Though I am interested in seeing how much of a difference creating one Mesh object for one family of planes will have. Let me test this out, I'll get back with some results later today.",
"Thanks for this @richardtran415, I'll merge this in as-is. I'm going to tidy up the plotly interface to try and create a more standard interface to plotly charts across pymatgen, but I can do this in another PR."
] | 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 Mesh3d object of course requires plotly (>=v4.0.0). As such, plotly==4.0.0 is added to requirements-optional.txt.
TODO:
- OK for some reason plotly does not have a showlegend option for surface plots or 3dmeshes. The Miller indices and surface energies of each facet with be given as hoverinfo instead until a later version of plotly supports legend generation for 3dMesh.
- Needs to be optimized for speed, right now itertools.combinations seems to be creating more triangles than needed to generate a facet. Will optimize in a future release.
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MDU6SXNzdWU1MjkxMzY2MjY=
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|
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 s py pz px dxy dyz dz2 dxz dx2 tot <--- header line\r\n 1 0.028 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.029 <--- toks line\r\n 2 0.028 0.000 0.000 0.001 0.000 0.000 0.000 0.000 0.000 0.029\r\n```\r\n\r\nPymatgen code pops the `ion` and `tot` in `header`.\r\n```\r\nelif headers is None and ionexpr.match(l):\r\n headers = l.split()\r\n headers.pop(0)\r\n headers.pop(-1)\r\n```\r\nBut it only pops the ion number in `toks` line.\r\n```\r\nelif expr.match(l):\r\n toks = l.split()\r\n index = int(toks.pop(0)) - 1 # Add toks.pop(-1) after this line\r\n num_data = np.array([float(t) for t in toks[:len(headers)]])\r\n```\r\nAfter adding `toks.pop(-1)`, I successfully create a `Procar` instance. ",
"Thanks. Can one of you make the changes in code to handle the PROCARs for different versions of vasp? This should be a simple if-else thing. Then add a example PROCAR and unittests and submit a PR and I will merge. Thanks."
] | 2019-11-27T06:05:21
| 2023-08-13T16:32:56
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2023-08-13T16:32:56Z
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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")
~/.local/lib/python3.6/site-packages/pymatgen/io/vasp/outputs.py in __init__(self, filename)
3319 for orb in range(len(headers)):
3320 phase_factors[spin][current_kpoint, current_band,
-> 3321 index, orb] = complex(num_data[2 * orb], num_data[2 * orb + 1])
3322 else:
3323 # old format of PROCAR (vasp 5.4.1 and before)
IndexError: index 17 is out of bounds for axis 0 with size 17
**Screenshots**
**Desktop (please complete the following information):**
- OS:Mac,
- Version [2018.9.30]
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MDU6SXNzdWU1MjkyNzM3NzY=
| 1,687
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CIFs with symmetrical molecules generated from CSD.
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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 can directly use the pymatgen.io.cif.CifParser class which has more fine-grained control."
] | 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:\ANACONDA3\envs\python3-env\lib\site-packages\pymatgen\io\cif.py:1001: UserWar
ning: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If
they are within the tolerance, they will be rescaled.
warnings.warn(msg)
C:\ANACONDA3\envs\python3-env\lib\site-packages\pymatgen\io\cif.py:1105: UserWar
ning: Species occupancies sum to more than 1!
warnings.warn(str(exc))
C:\ANACONDA3\envs\python3-env\lib\site-packages\pymatgen\io\cif.py:1107: UserWar
ning: Issues encountered while parsing CIF:
warnings.warn("Issues encountered while parsing CIF:")
C:\ANACONDA3\envs\python3-env\lib\site-packages\pymatgen\io\cif.py:1109: UserWar
ning: Some occupancies ([2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]) sum to > 1! If
they are within the tolerance, they will be rescaled.
warnings.warn(error)
C:\ANACONDA3\envs\python3-env\lib\site-packages\pymatgen\io\cif.py:1109: UserWar
ning: Species occupancies sum to more than 1!
**Desktop (please complete the following information):**
- OS: Windows
- Version 7
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MDExOlB1bGxSZXF1ZXN0MzQ3MDI0MDU0
| 1,688
|
Fix bug in ChemEnv
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[] | 2019-11-29T12:17:15
| 2019-12-02T03:36:47
|
2019-12-02T03:36:47Z
|
MEMBER
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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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MDExOlB1bGxSZXF1ZXN0MzQ3Mzc1ODgw
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More informative error message if ase is not installed
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[] | 2019-12-01T21:58:09
| 2019-12-02T00:49:07
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2019-12-02T00:49:07Z
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MDExOlB1bGxSZXF1ZXN0MzQ3NjI0ODg5
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Bump tqdm from 4.39.0 to 4.40.0
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] | 2019-12-02T13:29:06
| 2019-12-02T14:10:08
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2019-12-02T14:10:00Z
|
CONTRIBUTOR
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Bumps [tqdm](https://github.com/tqdm/tqdm) from 4.39.0 to 4.40.0.
<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/issues/802))
> + `notebook`: use `FloatProgress` <= `IntProgress` ([#471](https://github-redirect.dependabot.com/tqdm/tqdm/issues/471), [#456](https://github-redirect.dependabot.com/tqdm/tqdm/issues/456))
> + allow imprecision (`n <= total + epsilon`) ([#849](https://github-redirect.dependabot.com/tqdm/tqdm/issues/849))
> - fix unicode bar format arguments ([#803](https://github-redirect.dependabot.com/tqdm/tqdm/issues/803) -> [#851](https://github-redirect.dependabot.com/tqdm/tqdm/issues/851))
> - add `contrib` submodule ([#815](https://github-redirect.dependabot.com/tqdm/tqdm/issues/815))
> - add `wrapattr`, `utils.CallbackIOWrapper`, `contrib.DummyTqdmFile` ([#84](https://github-redirect.dependabot.com/tqdm/tqdm/issues/84) -> [#844](https://github-redirect.dependabot.com/tqdm/tqdm/issues/844))
> - update tests
> - update documentation
> - tidy automatic `snap` deployments
> - minor doc update ([#854](https://github-redirect.dependabot.com/tqdm/tqdm/issues/854))
</details>
<details>
<summary>Commits</summary>
- [`80464b2`](https://github.com/tqdm/tqdm/commit/80464b22931eeaf8757ea77157fc2e7b9c28d926) bump version, merge branch 'devel'
- [`5e4094e`](https://github.com/tqdm/tqdm/commit/5e4094e3831eb6b105834245d7f087f1abe4eede) silly deletion
- [`6a72c88`](https://github.com/tqdm/tqdm/commit/6a72c889cdd88d2e975e8a9a9a192b28286c66c8) Merge branch 'wrapattr' into devel
- [`866180c`](https://github.com/tqdm/tqdm/commit/866180c91f08bd60550ab74d3e9478acabeb4bba) self-contained `wrapattr` example
- [`ef653d8`](https://github.com/tqdm/tqdm/commit/ef653d814d9d8698bf4aba2429700969f8e59ff3) expand example of `wrapattr`
- [`1b40056`](https://github.com/tqdm/tqdm/commit/1b400564329b303962d077fe60229704dcb5db1d) document `wrapattr`, `utils.CallbackIOWrapper`
- [`1277ca0`](https://github.com/tqdm/tqdm/commit/1277ca06199556e46deefe20294f4f2ccc2e4270) create contrib submodule
- [`3cd6fb0`](https://github.com/tqdm/tqdm/commit/3cd6fb0e477395e3ee75bfb77c41f245dcedfc26) update docs
- [`4c48242`](https://github.com/tqdm/tqdm/commit/4c482425931b30ea5ee90617ab0ea793b6b7cc6c) refactor common into utils.ObjectWrapper
- [`644e8d0`](https://github.com/tqdm/tqdm/commit/644e8d0e90b43d1ab48ba57f11879814ca9989e1) sync docs
- Additional commits viewable in [compare view](https://github.com/tqdm/tqdm/compare/v4.39.0...v4.40.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=tqdm&package-manager=pip&previous-version=4.39.0&new-version=4.40.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (dependabot-automerge-end)
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<summary>Dependabot commands and options</summary>
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You can trigger Dependabot actions by commenting on this PR:
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Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
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MDExOlB1bGxSZXF1ZXN0MzQ3NjI1MDk2
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Bump mypy from 0.740 to 0.750
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"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [ci/circleci: pmglint](https://circleci.com/gh/materialsproject/pymatgen/9368?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-02T13:29:29
| 2019-12-02T14:10:19
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2019-12-02T14:10:11Z
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Bumps [mypy](https://github.com/python/mypy) from 0.740 to 0.750.
<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/more_types: Fix typso in advanced self-types ([#8006](https://github-redirect.dependabot.com/python/mypy/issues/8006))
- [`20b60b5`](https://github.com/python/mypy/commit/20b60b5678891a91fce9dc73f70e5c8bdbe25edb) Invoke get_dynamic_class_hook on method calls ([#7990](https://github-redirect.dependabot.com/python/mypy/issues/7990))
- [`fffb4b4`](https://github.com/python/mypy/commit/fffb4b40b744ccf90663d633db9576a1a93d067a) Implements module attribute suggestions ([#7971](https://github-redirect.dependabot.com/python/mypy/issues/7971))
- [`d9dea5f`](https://github.com/python/mypy/commit/d9dea5f3ad30bb449e4167b3e8476684ded0482e) Don't shorten long generic types in messages ([#7997](https://github-redirect.dependabot.com/python/mypy/issues/7997))
- [`23a719f`](https://github.com/python/mypy/commit/23a719fe57a269e776c15557c3e6f0a3af96ab3a) [mypyc] Fix some deserialization related issues ([#7989](https://github-redirect.dependabot.com/python/mypy/issues/7989))
- [`6cc6c66`](https://github.com/python/mypy/commit/6cc6c66b266515c4a18fd83cda89ebabfa254aae) Re-sync typeshed ([#7999](https://github-redirect.dependabot.com/python/mypy/issues/7999))
- [`a2e010d`](https://github.com/python/mypy/commit/a2e010dedd5a32cf0159918fe534724018847254) Preserve can_be_true and can_be_false when copying types ([#7991](https://github-redirect.dependabot.com/python/mypy/issues/7991))
- [`989626a`](https://github.com/python/mypy/commit/989626a86610017410fc07c8678b28200eedba80) Prevent dmypy from restarting if the configuration contains globs. ([#7960](https://github-redirect.dependabot.com/python/mypy/issues/7960))
- [`4c77d16`](https://github.com/python/mypy/commit/4c77d16b3a7befcc62a75e2a921c92e9b2328e62) [mypyc] Don't make classes non-extension because of children ([#7988](https://github-redirect.dependabot.com/python/mypy/issues/7988))
- Additional commits viewable in [compare view](https://github.com/python/mypy/compare/v0.740...v0.750)
</details>
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MDExOlB1bGxSZXF1ZXN0MzQ3NjI1MzQ5
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|
Bump pytest from 5.3.0 to 5.3.1
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"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [ci/circleci: pmglint](https://circleci.com/gh/materialsproject/pymatgen/9369?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-02T13:30:00
| 2019-12-02T14:11:11
|
2019-12-02T14:10:57Z
|
CONTRIBUTOR
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Bumps [pytest](https://github.com/pytest-dev/pytest) from 5.3.0 to 5.3.1.
<details>
<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
> ------------
>
> - [\#6231](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6231): Improve check for misspelling of `pytest.mark.parametrize`.
> - [\#6257](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6257): Handle exit.Exception raised in notify\_exception (via pytest\_internalerror), e.g. when quitting pdb from post mortem.
>
> Bug Fixes
> ---------
>
> - [\#5914](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5914): pytester: fix `no_fnmatch_line` when used after positive matching.
> - [\#6082](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6082): Fix line detection for doctest samples inside `property` docstrings, as a workaround to [bpo-17446](https://bugs.python.org/issue17446).
> - [\#6254](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6254): Fix compatibility with pytest-parallel (regression in pytest 5.3.0).
> - [\#6255](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6255): Clear the `sys.last_traceback`, `sys.last_type` and `sys.last_value` attributes by deleting them instead of setting them to `None`. This better matches the behaviour of the Python standard library.
>
</details>
<details>
<summary>Changelog</summary>
*Sourced from [pytest's changelog](https://github.com/pytest-dev/pytest/blob/5.3.1/CHANGELOG.rst).*
> pytest 5.3.1 (2019-11-25)
> =========================
>
> No significant changes.
>
> pytest 5.3.1 (2019-11-25)
> =========================
>
> Improvements
> ------------
>
> - [\#6231](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6231): Improve check for misspelling of `pytest.mark.parametrize`.
> - [\#6257](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6257): Handle exit.Exception raised in notify\_exception (via pytest\_internalerror), e.g. when quitting pdb from post mortem.
>
> Bug Fixes
> ---------
>
> - [\#5914](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/5914): pytester: fix `no_fnmatch_line` when used after positive matching.
> - [\#6082](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6082): Fix line detection for doctest samples inside `property` docstrings, as a workaround to [bpo-17446](https://bugs.python.org/issue17446).
> - [\#6254](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6254): Fix compatibility with pytest-parallel (regression in pytest 5.3.0).
> - [\#6255](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6255): Clear the `sys.last_traceback`, `sys.last_type` and `sys.last_value` attributes by deleting them instead of setting them to `None`. This better matches the behaviour of the Python standard library.
</details>
<details>
<summary>Commits</summary>
- [`05008f6`](https://github.com/pytest-dev/pytest/commit/05008f6b557ad35b71efd9e9ebca96c07402d793) Preparing release version 5.3.1
- [`9d90093`](https://github.com/pytest-dev/pytest/commit/9d900930dbf52fc79ac9414c1f6d9ec485f55e18) Merge pull request [#6242](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6242) from nicoddemus/testdir-changelog
- [`a8230d7`](https://github.com/pytest-dev/pytest/commit/a8230d77f45984e80c4b528cd6f1909128816ed5) Merge pull request [#6270](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6270) from blueyed/docs-log_cli
- [`b7d908f`](https://github.com/pytest-dev/pytest/commit/b7d908f4a5a8d27ab7cb84b2eb430830c641f7df) Merge pull request [#6269](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6269) from blueyed/docs
- [`b9dd0e6`](https://github.com/pytest-dev/pytest/commit/b9dd0e621004f8849f6487316b6ff85f9691d251) docs: add missing `log_cli` confval
- [`57f3dc1`](https://github.com/pytest-dev/pytest/commit/57f3dc19b9a26748f9238a0f9af8022c1cfcc106) tox: docs: --keep-going and posargs
- [`ed67312`](https://github.com/pytest-dev/pytest/commit/ed67312bca2b8b51c6b309df1201be0f89bbb6ae) Merge pull request [#6268](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6268) from felixonmars/patch-2
- [`b7bc52f`](https://github.com/pytest-dev/pytest/commit/b7bc52f770dd3352cfaf54ed5ec82df382013e2d) Correct a typo in _pytest/config/__init__.py
- [`d1eb89d`](https://github.com/pytest-dev/pytest/commit/d1eb89d6940d3081876f663622017d8952e77a80) Merge pull request [#6086](https://github-redirect.dependabot.com/pytest-dev/pytest/issues/6086) from kondratyev-nv/master
- [`5e09797`](https://github.com/pytest-dev/pytest/commit/5e097970df24a47a5944f29a6dca1eb1219b5b8e) Fix line detection for properties in doctest tests
- Additional commits viewable in [compare view](https://github.com/pytest-dev/pytest/compare/5.3.0...5.3.1)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pytest&package-manager=pip&previous-version=5.3.0&new-version=5.3.1)
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MDU6SXNzdWU1MzE2NTA4Mjg=
| 1,693
|
pymatgen.analysis.gb.grain.py generates strange structures with normal=True
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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 automatically. Of course, we can add a line code at the final step to make sure all the direct coordinates are within (0, 1). This part is straight forward.",
"Thank you for your reply. I created the above pull request according to your suggestion."
] | 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 Structure
from pymatgen.analysis.gb.grain import GrainBoundary, GrainBoundaryGenerator
Cu_conv = Structure.from_file("Cu_mp-30_conventional_standard.cif")
GB_Cu_conv = GrainBoundaryGenerator(Cu_conv)
Cu_GB4 = GB_Cu_conv.gb_from_parameters(
rotation_axis= [0,1,0],
rotation_angle=36.8698976458,
expand_times= 4,
vacuum_thickness= 1.0,
ab_shift= [0.0,0.0],
rm_ratio= 0.0,
plane=[0,0,1],
normal=True
)
Cu_GB4.to("cif",filename="Cu_GB4.cif")
```
"Cu_mp-30_conventional_standard.cif" is
<https://github.com/materialsproject/pymatgen/blob/master/test_files/grain_boundary/Cu_mp-30_conventional_standard.cif>.
**Screenshots**
**Desktop (please complete the following information):**
- OS: Ubuntu 16.04
- Version 2019.11.11
**Additional context**
The lines 635--639 of pymatgen.analysis.gb.grain.py may cause this anomaly.
```python
for site in top_grain:
all_coords.append(site.coords + half_lattice.matrix[2] * (1 + c_adjust) +
!!! unit_ab_adjust * np.linalg.norm(half_lattice.matrix[2] * (1 + c_adjust)) +
translation_v + ab_shift[0] * whole_matrix_with_vac[0] +
ab_shift[1] * whole_matrix_with_vac[1])
```
These lines append `all_coords[400:]` of top_grain with large minus values in the above parameter settings.
I'm not sure about the algorithm to generate these coordinates, so let me know the reference of this part.
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| 531,966,615
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MDU6SXNzdWU1MzE5NjY2MTU=
| 1,694
|
"pymatgen.io.lammps.data" Can't write file
|
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[] | null |
[
"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/CoeffsDataType.yaml'"
**To Reproduce**
Steps to reproduce the behavior:
The cif file I was using:
*************
data_H2CO
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 2.57520631
_cell_length_b 4.92688007
_cell_length_c 10.72047831
_cell_angle_alpha 90.00000000
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural H2CO
_chemical_formula_sum 'H8 C4 O4'
_cell_volume 136.01856262
_cell_formula_units_Z 4
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
H H0 1 0.613030 0.756578 0.148355 1.0
H H1 1 0.973662 0.576934 0.231306 1.0
H H2 1 0.386970 0.256578 0.351645 1.0
H H3 1 0.026338 0.076934 0.268694 1.0
H H4 1 0.113030 0.743422 0.851645 1.0
H H5 1 0.473662 0.923066 0.768694 1.0
H H6 1 0.886970 0.243422 0.648355 1.0
H H7 1 0.526338 0.423066 0.731306 1.0
C C8 1 0.194567 0.250018 0.000094 1.0
C C9 1 0.805433 0.750018 0.499906 1.0
C C10 1 0.694567 0.249982 0.999906 1.0
C C11 1 0.305433 0.749982 0.500094 1.0
O O12 1 0.972683 0.749006 0.182615 1.0
O O13 1 0.027317 0.249006 0.317385 1.0
O O14 1 0.472683 0.750994 0.817385 1.0
O O15 1 0.527317 0.250994 0.682615 1.0
*************
The code:
************
import pymatgen.core.structure as structure
import pymatgen.io.lammps.data as ld
in_stru = structure.Structure.from_file('mp.cif')
ldata = ld.LammpsData.from_structure(in_stru,atom_style = 'full')
print(ldata.structure)
ldata.write_file('new',distance=6, velocity=8, charge=4)
************
**Expected behavior*
I want to see the lammps file
**Screenshots**
**Desktop (please complete the following information):**
- OS: [Linux]
- Version [2019.11.11]
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| 532,337,763
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MDExOlB1bGxSZXF1ZXN0MzQ4NjA4MDY4
| 1,695
|
Add pymatgen.Molecule support to AseAtomsAdaptor
|
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[] | null |
[
"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 ``Molecule``s instead of ``Structure``s)
* Slightly extended tests
## 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 [flake8](http://flake8.pycqa.org/en/latest/) on your local machine.
- [x] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/) to type check your code.
- [x] There weren't any before in the module this is about, so it should be fine if my stuff doesn't have any either. Probably better for a separate PR.
- [x] Tests have been added for any new functionality or bug fixes.
- [ ] All existing tests pass.
- Only one way to find out for sure...
|
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| 532,426,072
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MDExOlB1bGxSZXF1ZXN0MzQ4Njc2MTQy
| 1,696
|
Force GrainBoundaryGenerator.gb_from_parameters to return fractional coords within unit cell
|
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[] | null |
[
"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.com/materialsproject/pymatgen/issues/1693))
* `pymatgen.analysis.gb.grain.gb_from_parameters()` now returns a structure with fractional coordinates in [0, 1).
* A Test for fractional coordinates has been added to `test_gb_from_parameters()` to check the fractional coords within [0, 1).
## Checklist
Before a pull request can be merged, the following items must be checked:
- [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 [flake8](http://flake8.pycqa.org/en/latest/)
on your local machine.
- [ ] Docstrings have been added in the [Google docstring format](https://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html).
Run [pydocstyle](http://www.pydocstyle.org/en/2.1.1/index.html) on your code.
- I have not modified Docstrings in this PR.
- [ ] Type annotations are **highly** encouraged. Run [mypy](http://mypy-lang.org/)
to type check your code.
- I have not added any functions.
- [x] Tests have been added for any new functionality or bug fixes.
- [ ] All existing tests pass.
- [x] A test `pymatgen.analysis.gb.tests.test_grain` passes.
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MDU6SXNzdWU1MzMxMDU4MDQ=
| 1,697
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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 is intended for bug reports or feature requests only. If you want help, please post in our [User Forum](https://discuss.matsci.org/c/pymatgen)."
] | 2019-12-05T03:46:57
| 2019-12-05T03:52:59
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2019-12-05T03:52:59Z
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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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MDExOlB1bGxSZXF1ZXN0MzUwMjY1NTMw
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Check POTCAR hashes when creating Vasp Input Sets
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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 the user is still informed that the \"symbol\" attribute exists and what it is.",
"A code comment to explain how the .json files were generated where they're loaded would also be useful, since it may be non-obvious what they are and what the distinction is between a \"file hash\" and a \"pymatgen hash\".",
"> 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 the user is still informed that the \"symbol\" attribute exists and what it is.\r\n\r\nThanks! See changes; I believe I implemented what you were asking in my latest batch of commits.\r\n\r\nAs for formatting, I took the somewhat extreme step of just formatting the entirety of these three files with black. I've become a fan of it recently, but unfortunately it doesn't allow you to only format a selection of text. The formatting changes are contained in a single commit, so let me know if it's a problem and I can revert.\r\n\r\n> A code comment to explain how the .json files were generated where they're loaded would also be useful, since it may be non-obvious what they are and what the distinction is between a \"file hash\" and a \"pymatgen hash\".\r\n\r\nSee edits to the docstring of `validate_potcar_hash`\r\n\r\n",
"Looks like `analysis/gb/grain.py` is triggering a linting failure. I'm not sure why that's happening as I haven't touched that file.",
"I should have fixed that, you might just need to merge changes from master\nback into your branch. There were a few trivial missing docstrings in the\ngrain boundary module.\n\nOn Sat, Dec 7, 2019 at 20:55, Ryan Kingsbury <notifications@github.com>\nwrote:\n\n> Looks like analysis/gb/grain.py is triggering a linting failure. I'm not\n> sure why that's happening as I haven't touched that file.\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/pull/1698?email_source=notifications&email_token=AAWWWRCPVUMRBJKBWXP354DQXR44LA5CNFSM4JXGBXV2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEGGV5WA#issuecomment-562912984>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AAWWWRAR4XYXPK2XHMLQ2QTQXR44LANCNFSM4JXGBXVQ>\n> .\n>\n",
"What is the proper way to fix `No library stub file for module 'pytest'`?",
"I'm also unsure how to interpret this error \r\n\r\n```\r\n$ export MODIFIED_FILES=`git diff --diff-filter=ACMRTUXB --name-only HEAD v2019.10.16 | grep -E 'pymatgen.*\\.(py)$' | sed '/test_/d' | tr '\\n' ' '`\r\n\r\nfatal: ambiguous argument 'v2019.10.16': unknown revision or path not in the working tree.\r\n```",
"I believe it's related to the previous issue, are you working on an outdated branch? Merge in changes from master?",
"> I believe it's related to the previous issue, are you working on an outdated branch? Merge in changes from master?\r\n\r\nI did that prior to the last few commits, but just did a pull/rebase again and found more changes. Fingers crossed...",
"Same error, `No library stub file for module 'pytest'`",
"Moved definition of the `potcar_functional` into the .yaml file that defines each `InputSet` and renamed `potcar_functional` argument to `user_potcar_functional`. See [discussion](https://github.com/materialsproject/pymatgen/pull/1708#issuecomment-564779903)\r\n",
"I was able to silence the `No library stub file for module 'pytest'` error from mypy by adding `# type: ignore` to the import statement. I'm not sure whether this is an acceptable long-term fix or not. See https://mypy.readthedocs.io/en/latest/running_mypy.html#missing-imports",
"The hashes .json files are still empty in this PR",
"> The hashes .json files are still empty in this PR\r\n\r\nAre you sure @mkhorton ? I see the hash data if I click on Files Changed.",
"<img width=\"854\" alt=\"image\" src=\"https://user-images.githubusercontent.com/2976580/70835655-90444980-1db2-11ea-93b3-43944153e42e.png\">\r\n\r\nShowing as empty to me ...",
"> <img alt=\"image\" width=\"854\" src=\"https://user-images.githubusercontent.com/2976580/70835655-90444980-1db2-11ea-93b3-43944153e42e.png\">\r\n> \r\n> Showing as empty to me ...\r\n\r\n@mkhorton I still see the hashes when I open this PR in a private window (without logging in). I'm not sure what's going on. Can you try clearing cache, etc.?\r\n\r\n\r\n",
"Thanks @rkingsbury !"
] | 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 POTCARs by symbol (really filename) and functional, which uniquely identify the hashes they should have. There may be cases in which a user wants to instantiate a `Poscar` object directly from an arbitrary file on disk, in which case it wouldn't make sense to check its hash against anything.
md5 hashes were computed for the pseudopotentials distributed with VASP 5.4.4. We hashed both the entire POTCAR file and also the data itself (via the pymatgen `get_potcar_hash()` method. Both sets of hashes are provided as `.json` files.
No new PSPs were added to the test_files. I copied an existing PSP for Fe that already existed in the test_files directory and made some small modifications to test the validation. However, I need some help to get these tests to work properly.
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MDExOlB1bGxSZXF1ZXN0MzUwNzE0Nzg0
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Bump pydocstyle from 4.0.1 to 5.0.0
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"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [ci/circleci: pmglint](https://circleci.com/gh/materialsproject/pymatgen/9395?utm_campaign=vcs-integration-link&utm_medium=referral&utm_source=github-build-link)\n- [build (3.7)](https://developer.github.com/actions/)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-09T13:27:36
| 2019-12-09T14:23:45
|
2019-12-09T14:23:32Z
|
CONTRIBUTOR
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Bumps [pydocstyle](https://github.com/PyCQA/pydocstyle) from 4.0.1 to 5.0.0.
<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
>
> - Support for Python 3.4 has been dropped ([#402](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/402)).
>
> New Features
>
> - Extend support for detecting missing arguments in Google style docstrings to method calls ([#384](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/384)).
> - Extend support for detecting missing argument description in Numpy style docstrings ([#407](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/407)).
> - Added support for Python 3.8 ([#423](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/423)).
> - Allow skipping errors on module level docstring via \#noqa ([#427](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/427)).
> - Whitespace is ignored with set options split across multiple lines ([#221](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/221)).
>
> Bug Fixes
>
> - Remove D413 from the google convention ([#430](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/430)).
> - Remove D413 from the pep257 convention ([#404](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/404)).
> - Replace semicolon with colon in D416 messages. ([#409](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/409))
> - D301 (Use r""" if any backslashes in a docstring) does not trigger on backslashes for line continuation or unicode literals `\u...` and `\N...` anymore. These are considered intended elements of the docstring and thus should not be escaped by using a raw docstring ([#365](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/365)).
> - Fix decorator parsing ([#411](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/411)).
> - Google-style sections no longer cause false errors when used with Numpy-style sections ([#388](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/388), [#424](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/424)).
> - D202: Allow a blank line after function docstring when followed by declaration of an inner function or class ([#395](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/395), [#426](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/426)).
> - Fix D401 and D404 checks not working for docstrings containing only one word and ending with non-alpha character ([#421](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/421))
</details>
<details>
<summary>Commits</summary>
- [`49766c8`](https://github.com/PyCQA/pydocstyle/commit/49766c82a0e0db0dfaa28d7132d2a51221ff98ae) Add 3.8 to supported version.
- [`7cf8da2`](https://github.com/PyCQA/pydocstyle/commit/7cf8da27ed64f8908e05c8b4810f524def864c3f) Bump version: 4.0.1 → 5.0.0
- [`e5c4237`](https://github.com/PyCQA/pydocstyle/commit/e5c42372f3ad2359bc18093f553a9cf566cfeb31) Update release date to today.
- [`7d16344`](https://github.com/PyCQA/pydocstyle/commit/7d1634448fd74b0c08d2dde0980ccd2b6781b724) [DOCONLY] Document that pep257 mode disables D413 ([#433](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/433))
- [`a1a4d0b`](https://github.com/PyCQA/pydocstyle/commit/a1a4d0b61eaf7bddd4c555d3e805a7911b863431) fix(checker): allow whitespace before inner functions and class ([#426](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/426))
- [`4aa5d96`](https://github.com/PyCQA/pydocstyle/commit/4aa5d965cf5f5f19ceacc55c4e1c2e9f81ad0dcc) Test cases for canonical examples of conventions ([#429](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/429))
- [`dbbf578`](https://github.com/PyCQA/pydocstyle/commit/dbbf578e031866d5cbd8614b7faad9af5edf435b) Remove D413 from the google convention ([#430](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/430))
- [`96092cd`](https://github.com/PyCQA/pydocstyle/commit/96092cde6613d8b56b5bbb7f7a1ddea9dd4a39d3) Strip whitespace in _fix_set_options ([#431](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/431))
- [`d3ea9a0`](https://github.com/PyCQA/pydocstyle/commit/d3ea9a06fdcfb96358992a688bbdd7533d6c11c7) Fix D401 and D404 checks not working for docstrings containing only one word ...
- [`667d9be`](https://github.com/PyCQA/pydocstyle/commit/667d9be515fc5848c7fdd0733e31db66276df104) Allow skip on module level messages ([#427](https://github-redirect.dependabot.com/PyCQA/pydocstyle/issues/427))
- Additional commits viewable in [compare view](https://github.com/PyCQA/pydocstyle/compare/4.0.1...5.0.0)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=pydocstyle&package-manager=pip&previous-version=4.0.1&new-version=5.0.0)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
If all status checks pass Dependabot will automatically merge this pull request.
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- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
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MDExOlB1bGxSZXF1ZXN0MzUwNzE0OTk4
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Bump coveralls from 1.8.2 to 1.9.2
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[
"One of your CI runs failed on this pull request, so Dependabot won't merge it.\n\n- [build (3.7)](https://developer.github.com/actions/)\n\nDependabot will still automatically merge this pull request if you amend it and your tests pass."
] | 2019-12-09T13:28:00
| 2019-12-09T14:23:27
|
2019-12-09T14:23:19Z
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CONTRIBUTOR
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Bumps [coveralls](https://github.com/coveralls-clients/coveralls-python) from 1.8.2 to 1.9.2.
<details>
<summary>Release notes</summary>
*Sourced from [coveralls's releases](https://github.com/coveralls-clients/coveralls-python/releases).*
> ## 1.9.2
> <a name="1.9.2"></a>
> ## 1.9.2 (2019-12-03)
>
> #### Bug Fixes
>
> * **github-actions:** fixup incorrect API usage ([#209](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/209))
>
> ## 1.9.1
> <a name="1.9.1"></a>
> ## 1.9.1 (2019-12-03)
>
> #### Compatibility
>
> * this release marks Python 3.8 as officially supported. Earlier versions probably
> supported Python 3.8 too, but now we're *sure*.
>
> ## 1.9.0
> <a name="1.9.0"></a>
> ## 1.9.0 (2019-12-03)
>
> #### Features
>
> * **support:** support Github Actions CI ([#207](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/207))
>
> #### Bug Fixes
>
> * **compatibility:** fixup `coverage.__version__` comparisons ([#208](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/208))
</details>
<details>
<summary>Changelog</summary>
*Sourced from [coveralls's changelog](https://github.com/coveralls-clients/coveralls-python/blob/master/CHANGELOG.md).*
> ## 1.9.2 (2019-12-03)
>
> #### Bug Fixes
>
> * **github:** fixup incorrect API usage ([#209](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/209)) ([https://github.com/coveralls-clients/coveralls-python/blob/master/c338cab4](https://github.com/coveralls-clients/coveralls-python/blob/master/c338cab4))
>
> <a name="1.9.1"></a>
> ## 1.9.1 (2019-12-03)
>
> #### Compatibility
>
> * this release marks Python 3.8 as officially supported. Earlier versions probably
> supported Python 3.8 too, but now we're *sure*.
>
> <a name="1.9.0"></a>
> ## 1.9.0 (2019-12-03)
>
> #### Features
>
> * **support:** support Github Actions CI ([#207](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/207)) ([https://github.com/coveralls-clients/coveralls-python/blob/master/817119c3](https://github.com/coveralls-clients/coveralls-python/blob/master/817119c3))
>
> #### Bug Fixes
>
> * **compatibility:** fixup coverage.__version__ comparisons ([#208](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/208)) ([https://github.com/coveralls-clients/coveralls-python/blob/master/03a57a9a](https://github.com/coveralls-clients/coveralls-python/blob/master/03a57a9a))
>
> <a name="1.8.2"></a>
</details>
<details>
<summary>Commits</summary>
- [`c23508d`](https://github.com/coveralls-clients/coveralls-python/commit/c23508dd017677c2f69c1b2bc1561671d7767d84) chore(release): bump version
- [`c338cab`](https://github.com/coveralls-clients/coveralls-python/commit/c338cab478f67cded2e22d0052064e3135e48bc9) fix(github): rename service to github-actions ([#209](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/209))
- [`7c6c9ed`](https://github.com/coveralls-clients/coveralls-python/commit/7c6c9ed1668cacb23595a527ef4839fa5be35b5c) test(ci): run github-actions also on pull requests ([#210](https://github-redirect.dependabot.com/coveralls-clients/coveralls-python/issues/210))
- [`1b78d92`](https://github.com/coveralls-clients/coveralls-python/commit/1b78d92b367d5aa31a4784950b56e5936f056230) docs: clean up badges
- [`eb22a61`](https://github.com/coveralls-clients/coveralls-python/commit/eb22a6164fa2f6513014ace40008f02b862dddd3) chore: mark py3.8 as compatible
- [`0e23356`](https://github.com/coveralls-clients/coveralls-python/commit/0e23356b3b5ca8e19b12a18fe72755c5317c5c1a) chore(ci): fixup bad interpreter link
- [`f62bd45`](https://github.com/coveralls-clients/coveralls-python/commit/f62bd4570afb4578f8d67ea2b0d225987ae456d6) fix(ci): fixup pypy3-7+ version compat
- [`bbc8115`](https://github.com/coveralls-clients/coveralls-python/commit/bbc8115c9026e917b77758e31a24f67afd59b029) tests: fix bad expectation for CircleCI
- [`6f5852e`](https://github.com/coveralls-clients/coveralls-python/commit/6f5852e7d0c6b59bd573ab1fd93f2f6beb6d50fb) tests: fix broken test when repo token set in env
- [`cc56f60`](https://github.com/coveralls-clients/coveralls-python/commit/cc56f6044491c58e0a17647697626f2df04d2584) docs(circleci): token is now required
- Additional commits viewable in [compare view](https://github.com/coveralls-clients/coveralls-python/compare/1.8.2...1.9.2)
</details>
<br />
[](https://dependabot.com/compatibility-score.html?dependency-name=coveralls&package-manager=pip&previous-version=1.8.2&new-version=1.9.2)
Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. You can also trigger a rebase manually by commenting `@dependabot rebase`.
[//]: # (dependabot-automerge-start)
If all status checks pass Dependabot will automatically merge this pull request.
[//]: # (dependabot-automerge-end)
---
<details>
<summary>Dependabot commands and options</summary>
<br />
You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating it. You can achieve the same result by closing it manually
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- `@dependabot badge me` will comment on this PR with code to add a "Dependabot enabled" badge to your readme
Additionally, you can set the following in your Dependabot [dashboard](https://app.dependabot.com):
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- Automerge options (never/patch/minor, and dev/runtime dependencies)
- Out-of-range updates (receive only lockfile updates, if desired)
- Security updates (receive only security updates, if desired)
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