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commit 3376f27a9c5a4cac1590169f2212361ab6c94388
Merge: 4b66ebc90 7b27d26b9
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Wed Mar 2 16:41:24 2022 -0800

    Merge pull request #2450 from munrojm/master

    Add monty `cached_class` to other compatibility schemes

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commit 2ad326e61ef19f62dd9f680e4e910ab023b8c1d9
Author: Jason <jmunro@lbl.gov>
Date:   Wed Mar 2 15:34:37 2022 -0800

    Add cached class to other compat. schemes

commit 4b66ebc908cf8cb0322152d64f7491ccb2a84213
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Wed Mar 2 10:36:49 2022 -0800

    Update reqs

commit 7d79eca034cbb58ec971eb1545ea06fe568f765a
Merge: 3d40b31b0 b7542b69c
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Mar 2 06:43:00 2022 -0800

    Merge pull request #2449 from janosh/actions-checkout-v3

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commit b7542b69cef567c539e1742d3ad44eea958b2bf5
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Mar 2 11:01:04 2022 +0000

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commit 3d40b31b076aa10d49dbba59a712348c40ee98d3
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Mon Feb 28 10:26:59 2022 -0800

    Add additional logic to guard against .pmgrc.yml parsing issue

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commit 412820112d459b77d84340412e9836ea84ebd5d8
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Fri Feb 25 18:41:28 2022 -0800

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commit 657a01cd7d163484495674f762d7be068776ae06
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Fri Feb 25 17:37:30 2022 -0800

    Set camera center to origin

    Thanks @mattmcdermott

commit a9678c3107902885e22eb0a4f4736b157cce7be5
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Fri Feb 25 17:07:29 2022 -0800

    Update changelog for v2022.2.25

commit c70ca529586d848134c2e0e4d9362a0e37d1fdde
Merge: 03e8b9981 961f2cd29
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Fri Feb 25 10:56:11 2022 -0800

    Merge pull request #2447 from mattmcdermott/cpd_fix

    Fix bug in `ChemicalPotentialDiagram` initialization (interior point), improve default plots

commit 961f2cd298e3b3575d7998f794ca6c72515e1b7e
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 23:03:53 2022 -0800

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commit eb10af1b52fd23d2d374316fbd8f55a2abbd1dfe
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 22:43:47 2022 -0800

    fix broken test caused by numerical precision

commit 957038771134a1aff12b57cefb94cd655f9b8880
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 15:52:08 2022 -0800

    fix broken test due to sorting of array

commit 8dd710abbdda4ebd71a9c4039628d36cdbb28b40
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 15:29:53 2022 -0800

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commit 6cfc8009d7121f02f4ff9fcd8c064f07716e1fdf
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 14:53:53 2022 -0800

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commit 27ec945602ad3dc42fac27bdd4cd2c1bf14ecd7d
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 12:25:24 2022 -0800

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Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Thu Feb 24 11:44:28 2022 -0800

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commit cc9491c1d87ed4dd669571be27d9f6fbd37affb9
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Wed Feb 23 17:36:35 2022 -0800

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commit e85efac61ba2e5f696c1752fad435faa0494f5d3
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Wed Feb 23 17:17:07 2022 -0800

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commit 0de7d8f66018743dcf2f0686b6f3a7ffa7840498
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Wed Feb 23 13:54:43 2022 -0800

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commit d6d01675f460d5d4bd3864ec54ac2f858fbf465b
Author: Matthew McDermott <mcdermott@berkeley.edu>
Date:   Wed Feb 23 13:34:27 2022 -0800

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commit 03e8b9981535acace1fc84406c8c027626ebbad4
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Thu Feb 24 10:09:47 2022 -0800

    Fix casting issues due to numpy.

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Date:   Thu Feb 24 09:23:44 2022 -0800

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Date:   Thu Feb 24 09:05:49 2022 -0800

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Date:   Thu Feb 24 09:04:43 2022 -0800

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commit 1217240a8df11769879ae5b69e1363884b3de5f2
Author: JaGeo <janine.george@bam.de>
Date:   Thu Feb 24 18:03:38 2022 +0100

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Author: JaGeo <janine.george@bam.de>
Date:   Thu Feb 24 17:58:23 2022 +0100

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Date:   Thu Feb 24 17:19:38 2022 +0100

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Merge: 4547c2516 8427738c3
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Feb 24 06:47:48 2022 -0800

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    Fix Structure.from_file() for .yml ext

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Date:   Wed Feb 23 09:57:27 2022 -0800

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Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Tue Feb 22 15:31:42 2022 -0800

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Date:   Mon Feb 21 16:18:17 2022 -0800

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commit a78eb0ce018fd5a10c7bbac7c050c8361e551f41
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Mon Feb 21 20:29:43 2022 +0000

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commit dfa4cdebdb1bc903dbd3958cffc1d194937ce877
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Mon Feb 21 19:23:51 2022 +0000

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Date:   Mon Feb 21 19:02:12 2022 +0000

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Date:   Mon Feb 21 19:01:31 2022 +0000

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commit a3f8f941ab48daaee588de4929573da75ca4c9ce
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Date:   Sun Feb 20 19:08:02 2022 -0800

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commit 8427738c341d2230647c83e7b3924920f1a1faeb
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Date:   Fri Feb 18 21:54:28 2022 +0000

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commit 293628a3ed6f403a83d7b1cd9044c29bf1c339ae
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Fri Feb 18 21:50:08 2022 +0000

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commit 7ed4ddf15a844f6e79f10e9e295df899a0e16f27
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Date:   Fri Feb 18 21:47:56 2022 +0000

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Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Tue Feb 15 15:43:16 2022 -0800

    Merge pull request #2434 from JaGeo/master

    Small changes to Lobster classes

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Date:   Tue Feb 15 15:43:11 2022 -0800

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Date:   Tue Feb 15 09:18:16 2022 -0800

    Merge pull request #2430 from janosh/unpin-dev-reqs

    Remove deprecated structure_2_lmpdata()

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Date:   Tue Feb 15 09:18:05 2022 -0800

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Date:   Tue Feb 15 09:17:31 2022 -0800

    Merge pull request #2432 from janosh/fix-type-annos

    Fix and add some type annotations

commit 0cf5e2ec818e9951f8277864f1b42b7572cdebe7
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Date:   Tue Feb 15 09:17:09 2022 -0800

    Merge pull request #2433 from janosh/fix-struct-apply_operation

    Fix Structure.apply_operation() return val

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commit dcca8df0887cc907fc66dc181b182725e6bf2740
Author: JaGeo <janine.george@bam.de>
Date:   Tue Feb 15 17:38:49 2022 +0100

    Use of Loewdin charges possible

commit 88dbf90d70c9d7524723ea5a45c7f3f3301da8e7
Author: JaGeo <janine.george@bam.de>
Date:   Tue Feb 15 17:31:16 2022 +0100

    Small changes lobsterin

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commit 4b37fb4d289d20e9cf7b59566298fc08bfc1ec77
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Feb 15 10:46:24 2022 +0000

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commit d046df07a51ee8a8dd6e8e749aac170bccee531a
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Feb 15 10:36:36 2022 +0000

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commit dcd34566be1cff272a4e87e11aef56f5aef926db
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Date:   Mon Feb 14 20:52:05 2022 +0000

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Date:   Mon Feb 14 20:29:30 2022 +0000

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Date:   Mon Feb 14 06:41:55 2022 -0800

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Date:   Thu Feb 10 07:59:47 2022 -0800

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Date:   Thu Feb 10 07:08:39 2022 -0800

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Date:   Thu Feb 10 07:07:44 2022 -0800

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Date:   Thu Feb 10 07:07:36 2022 -0800

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Date:   Wed Feb 9 22:28:57 2022 -0800

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Date:   Wed Feb 9 08:46:47 2022 -0800

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Date:   Mon Feb 7 11:54:59 2022 -0800

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    Add --backup flag to pmg config

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Date:   Mon Feb 7 19:47:01 2022 +0000

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Date:   Mon Feb 7 15:27:05 2022 +0000

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commit 88666339b5891f5d2cec6833e7cbbe04c136df90
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Mon Feb 7 15:26:32 2022 +0000

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Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Feb 7 07:03:13 2022 -0800

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Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Feb 7 07:01:59 2022 -0800

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commit a60cd95a4ddf60e0e32d241616ab4f7f6925048e
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Feb 7 06:57:39 2022 -0800

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Date:   Mon Feb 7 06:52:56 2022 -0800

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Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Feb 7 06:45:43 2022 -0800

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Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Feb 7 06:44:53 2022 -0800

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Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Sun Feb 6 19:41:05 2022 -0800

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commit a66ab854bac8eb71272d35de2c489197b3e7dd1c
Author: Andrew <asrosen93@gmail.com>
Date:   Sun Feb 6 18:17:00 2022 -0800

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Date:   Sun Feb 6 21:19:23 2022 +0000

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Date:   Sun Feb 6 21:18:49 2022 +0000

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Date:   Thu Feb 3 23:20:47 2022 -0800

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Date:   Wed Feb 2 01:06:48 2022 -0800

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Date:   Wed Feb 2 01:03:49 2022 -0800

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    Fix Zeo++ installation instructions

commit eeb2a9111d6d68ff9b2ec42f2afe59d1181e8af8
Merge: ef5b33c0e c6d38b11d
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Mon Jan 31 08:39:31 2022 -0800

    Merge pull request #2357 from arosen93/rosen-ddec

    Create a ChargemolAnalysis command line caller (for DDEC6, CM5 analysis)

commit ef5b33c0e4e44ab125bf09aa73ea6ee061583eeb
Merge: fcfe61146 e578fca0d
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Mon Jan 31 08:38:43 2022 -0800

    Merge pull request #2399 from arosen93/rosen-asemags

    ASEAtomsAdaptor: magmom/charge site properties in Structure/Molecule become initial (rather than final) magmoms/charges in Atoms object

commit fcfe611463710f7dfa77a53e13a83080bfba9195
Merge: 4753ce59e ce3615803
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Mon Jan 31 08:37:44 2022 -0800

    Merge pull request #2397 from janosh/drop-deprecated

    Delete overdue deprecations

commit 4753ce59e67f3d07e7a126b7cfbaf3c11259e1e9
Merge: 07794afb6 76088c3f1
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Mon Jan 31 08:36:11 2022 -0800

    Merge pull request #2401 from janosh/gha-auto-pip-cache

    Use setup-python automatic pip caching in CI

commit e578fca0d451231cf18cf92c9a17e0353b8b18ce
Author: Andrew <asrosen93@gmail.com>
Date:   Mon Jan 31 00:05:13 2022 -0800

    Fix spelling on some code comments

commit b2b23d228234b138ffa1e2445a9e4828f9b4c509
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Sun Jan 30 15:21:17 2022 -0800

    Fix codecomment linting in ASEAtomsAdaptor

commit 4be3160113b59dd5580475485c9d9e0dc202e34d
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Sun Jan 30 15:15:56 2022 -0800

    Update code comments for ASEAtomsAdaptor

commit 76088c3f1e8512f50f792b753a0ed65c237ac625
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Sun Jan 30 13:14:43 2022 +0000

    setup.py long_desc fix broken links

commit ebc4cd53b2f26669494c5d0f6259b90f7fc56b49
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Sun Jan 30 13:06:20 2022 +0000

    use correct cache-dependency-paths

commit eb1599f1ac2142052e53bb7d10f83eb1465aa36b
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Sun Jan 30 10:16:57 2022 +0000

    missed one

commit e060233439d9738fb5b9e51a8f0c79c2fc336b92
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Sun Jan 30 10:09:12 2022 +0000

    setup-python use auto pip caching

commit f7175b8baf09a7fb8ba423055804e1aea7d6e225
Merge: 51c3cb109 07794afb6
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Sun Jan 30 02:04:25 2022 -0800

    Merge branch 'materialsproject:master' into rosen-zeo

commit 51c3cb109ab4974be18897864b6ceaa4c63aa730
Author: Andrew <asrosen93@gmail.com>
Date:   Sun Jan 30 00:59:02 2022 -0800

    Update zeo++ installation steps

commit ce3615803666b28726e56f1a1fd11c3676b06c60
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Sat Jan 29 18:05:20 2022 +0000

    delete overdue deprecations

commit c5e4e24ceebc3491f0d554836e67d6c68ad6306c
Merge: ea11ee670 07794afb6
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Fri Jan 28 23:10:33 2022 -0800

    Merge branch 'materialsproject:master' into rosen-asemags

commit ea11ee67096d0bb5ca02a1d6d144ac11fcb8a972
Author: Andrew <asrosen93@gmail.com>
Date:   Fri Jan 28 22:43:14 2022 -0800

    Update ASEAtomsAdaptor tests

commit 209db4b70cbb8b1e65bdd9efd9097c2bf949d9f7
Author: Andrew <asrosen93@gmail.com>
Date:   Fri Jan 28 22:17:16 2022 -0800

    Make magmom convention consistent with ASEAtomsAdaptor

commit 07794afb624f7613b3dbcebdf0034cab4c9ee7ea
Merge: 645a79bce 08ff11c43
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 27 12:17:27 2022 -0800

    Merge pull request #2394 from JaGeo/master

    Fix issue with gzipped DOSCAR files in Lobster module

commit 645a79bce73535a0da5fe30b5bfee02ee18b0988
Merge: 72849371a 9c3b416d6
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 27 12:17:06 2022 -0800

    Merge pull request #2395 from samblau/qchem

    Q-Chem Updates

commit 9c3b416d6dd77b94189a8cb4e3a3510375877a34
Author: samblau <samblau1@gmail.com>
Date:   Thu Jan 27 11:40:35 2022 -0800

    Run black

commit dde992dd0a68e3912e4dee076a003a3895678634
Merge: b4f43512f 72849371a
Author: samblau <samblau1@gmail.com>
Date:   Thu Jan 27 11:19:49 2022 -0800

    Merge branch 'master' into qchem

commit 08ff11c436018a2ffd8c8a81fdfd5d0865d83edc
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date:   Thu Jan 27 19:43:22 2022 +0100

    apply black

commit 32719b7aae340533b6541bcc3563d0d10f650202
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date:   Thu Jan 27 19:22:27 2022 +0100

    fix linting

commit 745c4f8c55f231610249bd81c05c0fcf2b2276a8
Merge: c4df24fd6 72849371a
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date:   Thu Jan 27 19:10:56 2022 +0100

    Merge branch 'master' of https://github.com/materialsproject/pymatgen

commit c4df24fd66a2f51c1c14c90ab54b15208db65eb0
Author: jgeorge <jgeorge@sv2218.zit.bam.de>
Date:   Thu Jan 27 18:44:59 2022 +0100

    Fix problem zipped DOSCAR problem in Lobster module

commit 72849371a03ffda519e1f590776001b9076c9cd8
Merge: 85ea9dcc6 4f87d606b
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 27 08:05:58 2022 -0800

    Merge pull request #2391 from janosh/compat.process_entry

    Compat.process_entry

commit 85ea9dcc6fbb77cfe5d2fed1bdc365fd0856e8ee
Merge: f7525fce0 0498587d4
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 27 08:05:20 2022 -0800

    Merge pull request #2392 from janosh/drop-ordered-dict

    Drop OrderedDict

commit f7525fce039293a091374c890ea1ca1bf40aafa8
Merge: a13843919 7fd109a71
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 27 08:04:48 2022 -0800

    Merge pull request #2393 from vorwerkc/qe_kpoints_output

    Write k-point grids to QE input file

commit 7fd109a7143350b5dba492dfb4aa755b5a602d8a
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date:   Thu Jan 27 08:56:36 2022 -0600

    Remove debugging comment.

commit 8661eeda3952da112f158320955a6b0bb1b2753a
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date:   Thu Jan 27 08:52:55 2022 -0600

    Prevent workflows for forks again.

commit 0498587d46934de9d6ff20e99da624e5d9e82e57
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 27 14:32:46 2022 +0000

    fix symbol_to_oxinum in pymatgen/io/cif.py

commit 278da04bf01316ce718ee70105fda21b0475de64
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 27 11:35:53 2022 +0000

    fix mypy error in pymatgen/io/lobster/inputs.py

commit 0af8a0c66bd54a3dc83a3f33792d48ca0bf22632
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 27 11:22:37 2022 +0000

    update doc strings mentioning OrderedDict

commit 4348e1de1162ceb9f923505d38a53e22c811fa6c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 27 11:18:40 2022 +0000

    remove unused sort_dict in pymatgen/util/num.py

commit 7d6110f1c8d5a553010827bae9f6187bc1ed5598
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 27 11:17:47 2022 +0000

    replace OrderedDict with dict which are insertion-ordered anyway in p37+

commit 67df7d627cd3ee9f3fe54cd0f4ae69dbb47c421f
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date:   Wed Jan 26 18:18:18 2022 -0600

    Re-activate linting and tests

commit b59380d49b808286462e65668b0a3d6cb7a65673
Author: Christian Vorwerk <vorwerk@uchicago.edu>
Date:   Wed Jan 26 18:10:00 2022 -0600

    Fix formatting of kpoints output and add corresponding test.

commit 4f87d606bc831e3294ffa2fd0c0c0a93f80e3d35
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 20:49:23 2022 +0000

    ignore type error, add mypy commit hook to catch these errors locally before PR

commit 803c97e4241aeaf00abb1b947820737fa36656d7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 20:30:49 2022 +0000

    use try/except in Compatibility.process_entry() to avoid double work

commit a13843919e6fe57fad7e1056b2af260462bb76cb
Merge: 17ce53597 46e2b3f32
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Wed Jan 26 12:08:28 2022 -0800

    Merge branch 'master' of github.com:materialsproject/pymatgen

commit 17ce5359759130a6e420024aa6a0ce3fa48e2f0d
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Wed Jan 26 10:41:09 2022 -0800

    Fix tests.

commit 46e2b3f32a550be6432716a24ae27a630f6a25b8
Merge: d6dbe43bc 04d7a9918
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:28:34 2022 -0800

    Merge pull request #2380 from janosh/flynt-aggressive

    flynt --aggressive

commit d6dbe43bcd4aadf6c5505eaef454984c730e33ec
Merge: be0a675cb c4bd7150d
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:28:13 2022 -0800

    Merge pull request #2385 from janosh/autoflake

    Autoflake

commit be0a675cb38ba35251fcd8207271886a040c48c4
Merge: 420c77530 b706b6560
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:27:49 2022 -0800

    Merge pull request #2388 from arosen93/rosen-charge

    Store the actual charge and spin_mult in structure.as_dict()

commit c4bd7150de5203a7e3a4c53adda47745ab1f7b6d
Merge: c3592de6d 420c77530
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:27:27 2022 -0800

    Merge branch 'master' into autoflake

commit 420c77530975ed6a36ab9f69b1313ba1befe377c
Merge: 4eca6adca dfd56f670
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:26:48 2022 -0800

    Merge pull request #2387 from janosh/readme-badges

    Fix readme badges

commit 4eca6adca23cc6f68140aea3b735b6be17ac9a73
Merge: 6c31f7e38 ff60e222a
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Wed Jan 26 10:26:10 2022 -0800

    Merge pull request #2389 from janosh/pdentry-repr

    override PDEntry.__repr__ to include name attr if not fallback value

commit ff60e222aa9df1d2a8dc6e6f740495306bbfc815
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 18:14:04 2022 +0000

    override PDEntry.__repr__ to include name attr if not fallback value

commit b706b6560ea94f1444bb48d0cdb960b255ec850d
Author: Andrew <asrosen93@gmail.com>
Date:   Wed Jan 26 10:00:08 2022 -0800

    Fix as_dict() test assertions

commit 36d62f7d0e1598feaf833746a8b536504e1a7813
Author: Andrew <asrosen93@gmail.com>
Date:   Wed Jan 26 09:51:28 2022 -0800

    Add tests for default charge/spin mult

commit b872a046fa641a4633672e1fd39a542b033e14c8
Author: Andrew <asrosen93@gmail.com>
Date:   Wed Jan 26 08:38:20 2022 -0800

    Store the actual charge and spin_mult in as_dict()

commit dfd56f6706c44ef35716280786fe796b6fcbd025
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 14:40:26 2022 +0000

    uniform shield.io readme badges brought onto 1 line, fix GH CI badge, add PyPI download badge

commit c3592de6d003fd0439af90d3ddf19bd5c0b81b4c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 10:41:26 2022 +0000

    fix self.assertEqual(str(self.cellin), ans)
    in FiestaInputTest.test_str_and_from_string()

commit 2c542054e1fb21b7a04379e0bbf5a7c3024f9f20
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 10:24:52 2022 +0000

    remove annoying pylint commit hook, keeps complaining about missing types for standard lib modules like math

    pymatgen/analysis/phase_diagram.py:2929:48: I1101: Module 'math' has no 'sqrt' member, but source is unavailable. Consider adding this module to extension-pkg-allow-list if you want to perform analysis based on run-time introspection of living objects. (c-extension-no-member)

commit f7171f4d753a035c432924d7d5ba5eaad0e74d60
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 10:23:55 2022 +0000

    typos

commit 644df535de16868762f6d5a117bc095f249ba3ae
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 09:07:42 2022 +0000

    fix UnboundLocalError: local variable 'coord' referenced before assignment in pymatgen/util/tests/test_coord.py

commit a3dda95ac600033ee466fd0714429dd777e1a233
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:58:14 2022 +0000

    revert openbabel try-except imports

commit 5c1458b36ed82b9b8b62c7cd0c9ed96ad13583c7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:42:23 2022 +0000

    convert os + warnings + numpy to own imports in test modules instead of from starred imports

commit 797d99e34ecf42390875d5463c9cb71844ad642c
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:34:17 2022 +0000

    reduce namespace pollution in pymatgen/util/tests/test_coord.py

commit f76bcd336b294afebf3d367cb522ba9a6aec234a
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:24:41 2022 +0000

    autoflake -ri --remove-all-unused-imports --ignore-init-module-imports pymatgen

commit 41b1009224ca0b96f9046a9883aaa43dba41c8a9
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:17:50 2022 +0000

    autoflake expand star imports

commit 6f7c428da87193946cd0b04f5052923b8dda0f14
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:14:34 2022 +0000

    autoflake remove unused imports + useless pass statements

commit 04d7a99182cfea007e048b1e5700208bb4e721c3
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Wed Jan 26 08:07:42 2022 +0000

    fix KpointsTest.test_init() failing due to change in Kpoints.__str__()

commit b4f43512fc7e9b88a8fcfab41dca2085e4b7374d
Author: samblau <samblau1@gmail.com>
Date:   Tue Jan 25 16:26:30 2022 -0800

    Turn non-NBO output tests back on

commit 20537e4819cc1a25329ff38efe18fa96045a5e98
Merge: b22aba284 6c31f7e38
Author: samblau <samblau1@gmail.com>
Date:   Tue Jan 25 16:21:26 2022 -0800

    Merge branch 'master' into qchem

commit a3b9c2b45705bbff4c025503fd55fb8aef3ca496
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Jan 25 20:09:44 2022 +0000

    fix self.assertEqual(gau.to_string(cart_coords=False), gau_str) due to charge_str = f"{self.charge}" in gau.to_string()

commit deb84ec8060926e217a8546d08d4e73ab6323fce
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Jan 25 19:32:04 2022 +0000

    more auto-conversions from flynt ./pymatgen --aggressive (checked these all more carefully)

commit 6c31f7e38268986bd23110c2fbd4f14a09042a2a
Merge: 5a05f662d 8b697ed4f
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Tue Jan 25 11:01:30 2022 -0800

    Merge pull request #2379 from janosh/flynt

    Flynt

commit 8b697ed4fa702bb2b7ddefb4d9fb9a60fa6a3657
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Jan 25 15:28:30 2022 +0000

     fix ValueError: Format specifier missing precision

commit d068c1e39b4168a93de04745ff8af1a5fe4117c0
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Jan 25 15:02:16 2022 +0000

    commit hook auto fixes in files changed by prev commit

commit 265a2a2b828e8f1cd3063df5571d72c200346769
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Tue Jan 25 15:00:32 2022 +0000

    flynt ./pymatgen (automatic f-string conversion)

commit 5a05f662d35ab3c0d93f252f1c73e813e87c75f6
Merge: bc5af845c 5f09cfbe8
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Tue Jan 25 06:56:09 2022 -0800

    Merge branch 'master' of github.com:materialsproject/pymatgen

commit bc5af845cca5953f7d7623a64341c5bb862839ed
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Tue Jan 25 06:54:31 2022 -0800

    Fix.

commit 5f09cfbe8b575090faaf5901ccab37e50fccf677
Merge: 1a46190f4 671fd7f6a
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Tue Jan 25 06:49:36 2022 -0800

    Merge pull request #2356 from arosen93/rosen-bader

    Minor cleanup of bader_caller.py + new get_partial_charge() convenience function

commit 1a46190f48020669bf34266c81eebf87b89373e1
Merge: cf0f4a327 776dabac8
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Tue Jan 25 06:47:47 2022 -0800

    Merge pull request #2362 from janosh/qa

    QA

commit cf0f4a327329ff31a0af2a5f5a29cbb7ca3ce874
Merge: d8810634d 31f9f33cd
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Tue Jan 25 06:47:27 2022 -0800

    Merge pull request #2371 from arosen93/rosen-ase-props

    Pass oxidation states between Pymatgen structure/molecule and ASE Atoms

commit d8810634ddebac6171b8833aadc87ca0e0dac461
Merge: 41e171b5a c5b8d495e
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Mon Jan 24 17:28:34 2022 -0800

    Merge pull request #2369 from arosen93/rosen-energy

    Return the correct Vasprun().final_energy for VASP 6+ and change the default Outcar().final_energy to be energy(sigma->0)

commit c5b8d495e400e49a66aad90ddbb2ca31c91ee8f9
Author: Andrew <asrosen93@gmail.com>
Date:   Mon Jan 24 16:30:40 2022 -0800

    Do 1e-7 check in final_energy

commit ee423599fe370547250cc281d7c7935afc67cbf9
Author: Andrew <asrosen93@gmail.com>
Date:   Mon Jan 24 16:25:23 2022 -0800

    Update vasprun.final_energy check to be version-independent

commit 41e171b5aeae63bf73c130f7ef451fd77aa46e0f
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Jan 24 06:25:14 2022 -0800

    Update docs

commit d3b37eb5fb04a919a81c45bed780ce4c4d60477a
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Jan 24 06:23:34 2022 -0800

    Minor update.

commit 8808f7198a49b8358267fc36a1ba7a09cc8484ac
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Jan 24 06:22:28 2022 -0800

    Update changelog.

commit 5b8f704904fff3097ff45c1d182582b553bde686
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Mon Jan 24 06:20:01 2022 -0800

    fix deprecated default flow style in YAML.
    Fixes #2373.

commit 31f9f33cd3ea19aec9196163b285f8fbe512aace
Author: Andrew <asrosen93@gmail.com>
Date:   Sun Jan 23 21:08:34 2022 -0800

    Pass oxi states between ASE and pymatgen

    Now oxidation states are passed between ASE and Pymatgen structure objects. Several new tests have been added.

commit afe802b10f7907b22141e2154f323900a412e351
Merge: 3cf1b4206 4813709cb
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Sat Jan 22 22:42:36 2022 -0800

    Merge branch 'materialsproject:master' into rosen-energy

commit 3cf1b42067209f8743f7512cc13976948b9cc32d
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 21:39:36 2022 -0800

    Fix Outcar test

commit 844f185b41b9c9af9e1e6bd26515f7a74eb0ce32
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 21:39:16 2022 -0800

    Update Outcar() docs

commit a9eff3f577fa7b2251f57173b4c054fc4a110e7a
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 21:22:13 2022 -0800

    Fix vasprun energy parsing for vdW

commit e10abaaef87379349f0d064f1222c84a32a88681
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 20:14:20 2022 -0800

    Add tests to address energy parsing issue with Vasprun

commit 18ee0cc8f8fec8d4a1664ec782e2368ed6028d78
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 19:16:06 2022 -0800

    Fix dielect OUTCAR test

commit 4813709cbccd35543e192cef6b7cf78153624cd6
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Sat Jan 22 18:22:37 2022 -0800

    Fix memory error

commit fe4af2dd3523b1b686c23176fb549a98403f25e1
Author: Andrew <asrosen93@gmail.com>
Date:   Sat Jan 22 18:09:47 2022 -0800

    Return the correct e_0_energy with Vasprun and Outcar .final_energy

commit 7ac21b710e68e723d8fb556410787965740cac04
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Sat Jan 22 17:01:37 2022 -0800

    Comment out bad test.

commit c07cd2bebfec5f68a3fd29d5c01c4a5f0d1501a7
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Sat Jan 22 16:39:59 2022 -0800

    Fix wannier.

commit 362e26fd69a121f5855ffc413de361b0c8cd1a9e
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Sat Jan 22 16:04:30 2022 -0800

    Fix numpy int deprecations. Fixes #2366.

commit ae3f1b77d75b397735ee7cf16fcd77d8f487d85e
Merge: 729a26f2f 6753761b1
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Fri Jan 21 12:14:48 2022 -0800

    Merge branch 'master' of github.com:materialsproject/pymatgen

commit 729a26f2f0d9b6ca083dcaffb86402b5e0be96ee
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Fri Jan 21 12:14:35 2022 -0800

    Fix release workflow.

commit 776dabac89585ad7b9a5274f53515aa09ecf39e3
Merge: 05fcc2797 6753761b1
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Fri Jan 21 06:17:56 2022 +0000

    Merge branch 'master' into qa

commit 593a18872ba19735f9d8296998a0f45aa179b2c9
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 20:18:03 2022 -0800

    Fix max_row kwarg in periodic table heatmap plotter

commit c6d38b11dadf4ed5ada3f98cb7bf58a34960eb62
Merge: 43d9fc768 6753761b1
Author: Andrew S. Rosen <asrosen93@gmail.com>
Date:   Thu Jan 20 19:51:40 2022 -0800

    Merge branch 'materialsproject:master' into rosen-ddec

commit b06efb1205af52e2eed8547ef68a672ef1ca3b05
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 19:36:14 2022 -0800

    Fix from_row_and_group test

commit 55bf07a9c24e363f7f8d8fb396575d49879cf3fd
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 19:16:59 2022 -0800

    Fix from_row_and_group test

commit a5082776043f530c5f67303b53a0e9614306ae6a
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 19:09:25 2022 -0800

    Fix row and group test

commit 235e1b5d39c7c33454393fe7383ad17c2d4ce422
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 18:58:08 2022 -0800

    Add new for test from_row_and_group

commit 5353523c642b473e306927fd195052a58f9998c9
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 18:51:47 2022 -0800

    Add test cases for new group/row convention

commit 5c29d1d4b917865055eb83894eab6b4f5854ae6f
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 18:00:49 2022 -0800

    Fix ptable plotter

commit 0d8038a487bab90f26a0ef2577bf74823f53c35f
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 17:38:07 2022 -0800

    Fiz el.z typo in ptable plotter

commit 19247c6060830b561f3c2e70ecb7030b7895e7ad
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 17:35:02 2022 -0800

    Fix ptable plotter for new lanthanoid/actinoid group #

commit 43d9fc768396929310db3dde0745a2b613145f30
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 17:15:12 2022 -0800

    Use fstring in ChargemolAnalysis

commit 3979c7410573f4e6e7bbe0176784691292ba5417
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 16:51:23 2022 -0800

    Add code comment for ChargemolAnalysis.summary

commit 46415dab1cbf8c830434e21bf79e85da06a377ce
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 16:47:35 2022 -0800

    Add test for get_charge() in ChargemolAnalysis

commit 4ce2389ea83d1cbc831970fd49ba37ad8317acdb
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 16:40:33 2022 -0800

    Add tests for Chargemol

commit 6753761b1f332b70507b8e019114ac65c45b5c75
Merge: 9cc63cac1 5792dcb1a
Author: Matthew Horton <mkhorton@users.noreply.github.com>
Date:   Thu Jan 20 14:08:06 2022 -0800

    Merge pull request #2358 from arosen93/rosen-mags

    Don't perform dict type-check on the MAGMOM flag in io.vasp.sets (fixes downstream Atomate issue)

commit 5792dcb1a66814c4390ad64b73dd2f899fa32cdd
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 13:10:07 2022 -0800

    Fix MPStaticSet test

commit 9cc63cac182dcf219c2a1791d7e36d3fe3c2c3b5
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Thu Jan 20 12:46:24 2022 -0800

    Update docs

commit 6ba78931fef96af12779a1221727ba0353a1ceb6
Author: Shyue Ping Ong <shyuep@gmail.com>
Date:   Thu Jan 20 12:45:13 2022 -0800

    Update changelog.

commit 91c7fb0642f8fc37a76bab491da2e3631aee1f83
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 12:36:39 2022 -0800

    Remove typecheck from magmom test

    Remove the typecheck for MAGMOM being a dict

commit d5370df167e92aa4293a1bd15cc49c327be46cbd
Merge: fd553a8e8 e181a7fb8
Author: Shyue Ping Ong <shyuep@users.noreply.github.com>
Date:   Thu Jan 20 12:19:57 2022 -0800

    Merge pull request #2365 from janosh/fix_get_potcar_symbols

    Fix Lobsterin()._get_potcar_symbols()

commit 200bb9c882adac3786b1c126d9b7e74d17b5957f
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 12:14:44 2022 -0800

    Lint fix

commit 2cfdc3cdc0fde394b86a670ca0714a3c49e88e9c
Merge: 42bcf08f9 7c550b987
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 11:46:50 2022 -0800

    Merge remote-tracking branch 'origin/rosen-mags' into rosen-mags

commit 42bcf08f92bd7267824edd7d1dcfe79d23ca3769
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 11:46:45 2022 -0800

    Remove TypeError when MAGMOM is not a dict

commit e181a7fb800d7dff1a1074bc0be25f10e8558034
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 19:18:06 2022 +0000

    ensure POTCAR data has utf-8 encoding

commit 6c57902c8fa7834c30c40e6ccb4ac6066edf6dfb
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 11:02:21 2022 -0800

    mypy fix

commit 05fcc2797fce6f5b01c0c3c4c993575f49f984c7
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 15:15:49 2022 +0000

    update hash for vdW_parameters.yaml in SetChangeCheckTest

commit 8b4fb15b32e1694438e39b636efdb46e009f1442
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 11:12:42 2022 +0000

    add autoflake cmmit hook

commit d7b4fba0cb04a5b80829613674f936b1418f9b54
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 11:06:39 2022 +0000

    add pyupgrade commit hook

commit 862bf7b4c36da03cd4fda3beb5b0394e66ff7f34
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 11:03:53 2022 +0000

    pyupgrade --py38-plus **/*.py

commit 586bea41032781c8ccac1a6fdfc6ad3d96baa555
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 10:53:06 2022 +0000

    apply end-of-file-fixer + trailing-whitespace

commit 9f13e8c2ea91baf692329b41487e7cf771437df5
Author: Janosh Riebesell <janosh.riebesell@gmail.com>
Date:   Thu Jan 20 10:52:08 2022 +0000

    update pre-commit config, exclude (docs|test_files), use standalone flake8 hook

commit c8893438b69642122950547b7ff17a844c258c33
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 02:17:35 2022 -0800

    mypy fix

commit ac26d556340a7fcdfe58ee53f02b432407418565
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 02:02:38 2022 -0800

    Introduce test suite for ChargemolAnalysis

commit 671fd7f6a15261715c594694e4e3aad5e4b47d6f
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 01:18:04 2022 -0800

    Add two more bader tests

commit b1dc48d41bec78cc8dd79b0a3dbfe717aadf2d42
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 01:14:41 2022 -0800

    Finalize chargemol_caller.py

    Creates chargemol_caller.py for DDEC/CM5 analysis

commit 646d13853acb5ae247954e82f5a77829d568f842
Author: Andrew <asrosen93@gmail.com>
Date:   Thu Jan 20 01:12:48 2022 -0800

    finalize bader_caller cleanup

    Minor code clarifications for bader_caller. Also adds new get_partial_chage() convenience function

commit d33eb3138dfc0017b4de0ac40b9c79fecfbe6865
Merge: 32bda0f32 7b2757a80
Author: Andrew <asrosen93@gmail.com>
Date:   Wed Jan 19 15:40:11 2022 -0800

    Merge remote-tracking branch 'origin/rosen-ddec' into rosen-ddec

commit 32bda0f3207d7878bfcc5e6c38290a0ac5b87ce2
Author: Andrew <asrosen93@gmail.com>
Date:   Wed Jan 19 15:40:…
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2 changes: 1 addition & 1 deletion .github/ISSUE_TEMPLATE/bug_report.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ Steps to reproduce the behavior:
3. Scroll down to '....'
4. See error

Provide any example files that are needed to reproduce the error,
Provide any example files that are needed to reproduce the error,
especially if the bug pertains to parsing of a file.

**Expected behavior**
Expand Down
14 changes: 7 additions & 7 deletions .github/PULL_REQUEST_TEMPLATE.md
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,15 +10,15 @@ Include a summary of major changes in bullet points:
## Additional dependencies introduced (if any)

* List all new dependencies needed and justify why. While adding dependencies that bring
significantly useful functionality is perfectly fine, adding ones that
significantly useful functionality is perfectly fine, adding ones that
add trivial functionality, e.g., to use one single easily implementable
function, is frowned upon. Provide a justification why that dependency is needed.
function, is frowned upon. Provide a justification why that dependency is needed.
Especially frowned upon are circular dependencies, e.g., depending on derivative
modules of pymatgen such as custodian or Fireworks.

## TODO (if any)

If this is a work-in-progress, write something about what else needs
If this is a work-in-progress, write something about what else needs
to be done

* Feature 1 supports A, but not B.
Expand All @@ -33,15 +33,15 @@ Before a pull request can be merged, the following items must be checked:
- [ ] Code is in the [standard Python style](https://www.python.org/dev/peps/pep-0008/). The easiest way to handle this
is to run the following in the **correct sequence** on your local machine. Start with running
[black](https://black.readthedocs.io/en/stable/index.html) on your new code. This will automatically reformat
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
your code to PEP8 conventions and removes most issues. Then run
[pycodestyle](https://pycodestyle.readthedocs.io/en/latest/), followed by
[flake8](http://flake8.pycqa.org/en/latest/).
- [ ] 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.
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.

Note that the CI system will run all the above checks. But it will be much more efficient if you already fix most
errors prior to submitting the PR. It is highly recommended that you use the pre-commit hook provided in the pymatgen
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.
68 changes: 36 additions & 32 deletions .github/workflows/lint.yml
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Expand Up @@ -4,41 +4,45 @@ on: [push, pull_request]

jobs:
build:
# prevent this action from running on forks
if: github.repository == 'materialsproject/pymatgen'
runs-on: ubuntu-latest
strategy:
max-parallel: 1
matrix:
python-version: [3.9]
steps:
- uses: actions/checkout@v2
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt --quiet
- name: mypy
run: |
mypy --version
rm -rf .mypy_cache
mypy pymatgen
- name: pydocstyle
run: |
pydocstyle --count pymatgen
- name: pylint
run: |
pylint pymatgen
- name: black
run: |
black --version
black --check --diff --color pymatgen
- name: flake8
run: |
flake8 --version
flake8 --count --show-source --statistics pymatgen
# exit-zero treats all errors as warnings.
flake8 --count --exit-zero --max-complexity=20 --statistics pymatgen
- uses: actions/checkout@v3
with:
fetch-depth: 0
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
cache: pip
cache-dependency-path: requirements-dev.txt
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt --quiet
- name: mypy
run: |
mypy --version
rm -rf .mypy_cache
mypy pymatgen
- name: pydocstyle
run: |
pydocstyle --count pymatgen
- name: pylint
run: |
pylint pymatgen
- name: black
run: |
black --version
black --check --diff --color pymatgen
- name: flake8
run: |
flake8 --version
flake8 --count --show-source --statistics pymatgen
# exit-zero treats all errors as warnings.
flake8 --count --exit-zero --max-complexity=20 --statistics pymatgen
38 changes: 16 additions & 22 deletions .github/workflows/release.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -2,11 +2,13 @@ name: Release

on:
release:
types: [ created ]
types: [created]
workflow_dispatch:

jobs:
test:
# prevent this action from running on forks
if: github.repository == 'materialsproject/pymatgen'

strategy:
max-parallel: 20
Expand All @@ -31,18 +33,12 @@ jobs:
GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries

steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
- uses: actions/checkout@v3
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.8
- uses: actions/cache@v2
if: startsWith(runner.os, 'macOS')
with:
path: ~/Library/Caches/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
python-version: 3.9
cache: pip
- name: Install dependencies
run: |
pip install --upgrade pip wheel
Expand All @@ -58,23 +54,20 @@ jobs:
strategy:
max-parallel: 2
matrix:
os: [ macos-latest, windows-latest ]
python-version: [ 3.7, 3.8 ]
os: [macos-latest, windows-latest]
python-version: ['3.8', '3.9', '3.10']
runs-on: ${{ matrix.os }}

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- uses: actions/cache@v2
if: startsWith(runner.os, 'macOS')
with:
path: ~/Library/Caches/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
cache: pip
cache-dependency-path: |
requirements.txt
setup.py
- name: Install dependencies
run: |
pip install --upgrade pip wheel
Expand All @@ -87,5 +80,6 @@ jobs:
run: |
pip install setuptools wheel twine
python setup.py sdist bdist_wheel
twine upload dist/*.whl
twine upload --skip-existing dist/*.whl
twine upload --skip-existing dist/*.tar.gz
continue-on-error: true
34 changes: 13 additions & 21 deletions .github/workflows/test.yml → .github/workflows/test-linux.yml
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,14 @@
# This workflow runs only on Ubuntu and aims to be more complete than the Mac and Windows workflows.
# In particular, Openbabel and many of the external command line dependencies are included for testing.defaults:
# The ext package is also only tested in this workflow. Coverage is also computed based on this platform.
name: Testing
name: Testing Linux

on: [ push, pull_request ]
on: [push, pull_request]

jobs:

test:
# prevent this action from running on forks
if: github.repository == 'materialsproject/pymatgen'
strategy:
max-parallel: 20
matrix:
Expand All @@ -17,7 +18,7 @@ jobs:
pkg_id: 1
- pkg: pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
pkg_id: 2
- pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line
- pkg: pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext
pkg_id: 3
- pkg: pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line
pkg_id: 4
Expand All @@ -31,17 +32,10 @@ jobs:
GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- uses: conda-incubator/setup-miniconda@v2
with:
python-version: 3.8
- name: Cache pip
uses: actions/cache@v2
with:
path: ~/.cache/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
python-version: 3.9
- name: Install OpenBabel and Libs
shell: bash -l {0}
run: |
Expand Down Expand Up @@ -72,15 +66,13 @@ jobs:
needs: test
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.8
uses: actions/setup-python@v1
- uses: actions/checkout@v3
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install deps
run: |
python -m pip install --upgrade pip
pip install -r requirements-dev.txt
python-version: 3.9
- name: Install Coverage
run: pip install coverage
- name: Download coverage-1
uses: actions/download-artifact@v1
with:
Expand Down
35 changes: 14 additions & 21 deletions .github/workflows/test-macwin.yml → .github/workflows/test-mac.yml
View file
Original file line number Diff line number Diff line change
@@ -1,20 +1,22 @@
name: Testing Mac Windows
name: Testing Mac

on: [ pull_request ]
on: [pull_request]

jobs:
test:
# prevent this action from running on forks
if: github.repository == 'materialsproject/pymatgen'

strategy:
max-parallel: 20
matrix:
os: [ macos-latest, windows-latest ]
python-version: [ 3.8 ]
os: [macos-latest]
python-version: ['3.10']
# This distribution of tests is designed to ensure an approximately even time to finish for parallel jobs.
pkg:
- pymatgen/analysis/defects pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism
- pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
- pymatgen/electronic_structure pymatgen/symmetry pymatgen/ext pymatgen/command_line
- pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext
- pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line

runs-on: ${{ matrix.os }}
Expand All @@ -26,30 +28,21 @@ jobs:
GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries

steps:
- uses: actions/checkout@v2
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
- uses: actions/cache@v2
if: startsWith(runner.os, 'macOS')
with:
path: ~/Library/Caches/pip
key: ${{ runner.os }}-pip-${{ hashFiles('requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
- uses: actions/cache@v2
if: startsWith(runner.os, 'Windows')
with:
path: ~\AppData\Local\pip\Cache
key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
restore-keys: |
${{ runner.os }}-pip-
cache: pip
cache-dependency-path: |
requirements.txt
requirements-dev.txt
setup.py
- name: Install dependencies
run: |
pip install --upgrade pip wheel
pip install -r requirements.txt
pip install -r requirements-optional.txt -r requirements-dev.txt
pip install -r requirements-dev.txt
pip install -e .
- name: pytest ${{ matrix.pkg }}
run: |
Expand Down
49 changes: 49 additions & 0 deletions .github/workflows/test-win.yml
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,49 @@
name: Testing Windows

on: [pull_request]

jobs:
test:
# prevent this action from running on forks
if: github.repository == 'materialsproject/pymatgen'

strategy:
max-parallel: 20
matrix:
os: [windows-latest]
python-version: ['3.9']
# This distribution of tests is designed to ensure an approximately even time to finish for parallel jobs.
pkg:
- pymatgen/analysis/defects pymatgen/analysis/chemenv pymatgen/analysis/elasticity pymatgen/analysis/magnetism
- pymatgen/analysis --ignore=pymatgen/analysis/defects --ignore=pymatgen/analysis/chemenv --ignore=pymatgen/analysis/elasticity --ignore=pymatgen/analysis/magnetism
- pymatgen/electronic_structure pymatgen/symmetry pymatgen/command_line pymatgen/ext
- pymatgen --ignore=pymatgen/analysis --ignore=pymatgen/electronic_structure --ignore=pymatgen/symmetry --ignore=pymatgen/ext --ignore=pymatgen/command_line

runs-on: ${{ matrix.os }}

env:
PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
MPLBACKEND: "Agg"
PMG_TEST_FILES_DIR: ${{ github.workspace }}/test_files
GULP_LIB: ${{ github.workspace }}/cmd_line/gulp/Libraries

steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python-version }}
cache: pip
cache-dependency-path: |
requirements.txt
requirements-dev.txt
setup.py
- name: Install dependencies
run: |
pip install --upgrade pip wheel
pip install -r requirements.txt
pip install -r requirements-dev.txt
pip install -e .
- name: pytest ${{ matrix.pkg }}
run: |
pytest ${{ matrix.pkg }}
1 change: 1 addition & 0 deletions .gitignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -10,6 +10,7 @@ dependencies/spglib*/build
*.swp
*.swo
*.pyd
*.c
pymatgen/pymatgen.cfg
dist
_build
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