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Bump matplotlib from 3.5.2 to 3.7.1
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] | 2023-04-01T12:59:29
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2023-04-04T16:31:21Z
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Bumps [matplotlib](https://github.com/matplotlib/matplotlib) from 3.5.2 to 3.7.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/matplotlib/matplotlib/releases">matplotlib's releases</a>.</em></p>
<blockquote>
<h2>REL: v3.7.1</h2>
<p>This is the first bugfix release of the 3.7.x series.</p>
<p>This release contains several bug-fixes and adjustments:</p>
<ul>
<li>Ensure Qhull license is included in binary wheels</li>
<li>Fix application of rcParams on Axes labels</li>
<li>Fix compatibility with Pandas datetime unit converter</li>
<li>Fix compatibility with latest GTK4</li>
<li>Fix import of styles with relative path</li>
<li>Fix Lasso unresponsiveness when clicking and immediately releasing</li>
<li>Fix pickling of draggable legends</li>
<li>Fix RangeSlider.set_val when new value is outside existing value</li>
<li>Fix size of Tk spacers when changing display DPI</li>
<li>Fix wrapped text in constrained layout</li>
<li>Improve compatibility with third-party backends</li>
<li>Improve error if animation save path does not exist</li>
</ul>
<h2>REL: v3.7.0</h2>
<p>Highlights of this release include:</p>
<ul>
<li>Plotting and Annotation improvements
<ul>
<li><code>hatch</code> parameter for pie</li>
<li>Polar plot errors drawn in polar coordinates</li>
<li>Additional format string options in <code>~matplotlib.axes.Axes.bar_label</code></li>
<li><code>ellipse</code> boxstyle option for annotations</li>
<li>The <em>extent</em> of <code>imshow</code> can now be expressed with units</li>
<li>Reversed order of legend entries</li>
<li><code>pcolormesh</code> accepts RGB(A) colors</li>
<li>View current appearance settings for ticks, tick labels, and gridlines</li>
<li>Style files can be imported from third-party packages</li>
</ul>
</li>
<li>Improvements to 3D Plotting
<ul>
<li>3D plot pan and zoom buttons</li>
<li><em>adjustable</em> keyword argument for setting equal aspect ratios in 3D</li>
<li><code>Poly3DCollection</code> supports shading</li>
<li>rcParam for 3D pane color</li>
</ul>
</li>
<li>Figure and Axes Layout
<ul>
<li><code>colorbar</code> now has a <em>location</em> keyword argument</li>
<li>Figure legends can be placed outside figures using constrained_layout</li>
<li>Per-subplot keyword arguments in <code>subplot_mosaic</code></li>
<li><code>subplot_mosaic</code> no longer provisional</li>
</ul>
</li>
<li>Widget Improvements
<ul>
<li>Custom styling of button widgets</li>
<li>Blitting in Button widgets</li>
</ul>
</li>
<li>Other Improvements
<ul>
<li>Source links can be shown or hidden for each Sphinx plot directive</li>
<li>Figure hooks</li>
</ul>
</li>
<li>New & Improved Narrative Documentation
<ul>
<li>Brand new :doc:<code>Animations </tutorials/introductory/animation_tutorial></code> tutorial.</li>
<li>New grouped and stacked <code>bar chart <../../gallery/index.html#lines_bars_and_markers></code>_ examples.</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/matplotlib/matplotlib/commit/b3bd929cf07ea35479fded8f739126ccc39edd6d"><code>b3bd929</code></a> REL: 3.7.1</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/7411f656d29faadf610842d9b5dd7d6936903ccb"><code>7411f65</code></a> DOC: Update release notes for 3.7.1</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/250cca95accc664be8a3fa051c7f4694b4fddf1b"><code>250cca9</code></a> Merge branch 'v3.7.0-doc' into v3.7.x</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/66232bce51dc2dd8020bec2f2730fdc807d275f6"><code>66232bc</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25377">#25377</a> from meeseeksmachine/auto-backport-of-pr-25372-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/5908554819d2614b1e73ff05d93ba89885eb87f8"><code>5908554</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25376">#25376</a> from meeseeksmachine/auto-backport-of-pr-25371-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/6e77a71ed8788c69e6efd38c3338afbf53780b4f"><code>6e77a71</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25375">#25375</a> from meeseeksmachine/auto-backport-of-pr-25364-on-v...</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/11c6af260751e205a90065a624025c635db6dc7f"><code>11c6af2</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25372">#25372</a>: Clean up Curve ArrowStyle docs</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/cdc7bde6856fe16b64d430ea95a6a7ffed9e9946"><code>cdc7bde</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25371">#25371</a>: Tk: Fix size of spacers when changing display DPI</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/feff33d0b5fc8c966e6af158733f18690d33ad88"><code>feff33d</code></a> Backport PR <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25364">#25364</a>: BLD: Pre-download Qhull license to put in wheels</li>
<li><a href="https://github.com/matplotlib/matplotlib/commit/4fcd0a0f3eca4c28ab5d4a756e96befa47e371b3"><code>4fcd0a0</code></a> Merge pull request <a href="https://redirect.github.com/matplotlib/matplotlib/issues/25370">#25370</a> from QuLogic/backport-25369</li>
<li>Additional commits viewable in <a href="https://github.com/matplotlib/matplotlib/compare/v3.5.2...v3.7.1">compare view</a></li>
</ul>
</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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[//]: # (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
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Bump plotly from 5.11.0 to 5.14.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-04-01T12:59:37
| 2023-04-04T16:31:32
|
2023-04-04T16:31:22Z
|
CONTRIBUTOR
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.14.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.14.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<ul>
<li>Added option to allow passing a column name as a <code>str</code> in <code>hover_data</code> and <code>custom_data</code> in <code>plotly.express</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4083">4083</a>]</li>
</ul>
<h2>v5.13.1</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://redirect.github.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://redirect.github.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>v5.13.0</h2>
<p>See the full release announcement with graphical examples on the forum: <a href="https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205">https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205</a></p>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://redirect.github.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://redirect.github.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://redirect.github.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://redirect.github.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://redirect.github.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>v5.12.0</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://redirect.github.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://redirect.github.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
<li><code>marker.angle</code> attribute now accepts iterables where appropriate [<a href="https://redirect.github.com/plotly/plotly.py/issues/4013">#4013</a>]</li>
<li><code>selector=0</code> now correctly returns the first trace in <code>.select_traces()</code> and related methods [<a href="https://redirect.github.com/plotly/plotly.py/issues/3817">#3817</a>]</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.14.0] - 2023-03-29</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<ul>
<li>Added option to allow passing a column name as a <code>str</code> in <code>hover_data</code> and <code>custom_data</code> in <code>plotly.express</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4083">4083</a>]</li>
</ul>
<h2>[5.13.1] - 2023-02-24</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://redirect.github.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://redirect.github.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>[5.13.0] - 2023-01-23</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://redirect.github.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://redirect.github.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://redirect.github.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://redirect.github.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://redirect.github.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>[5.12.0] - 2023-01-12</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://redirect.github.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed the usage of some deprecated NumPy types which were removed in NumPy 1.24 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3997">#3997</a>]</li>
<li>Fixed bug for trendlines with datetime axes [<a href="https://redirect.github.com/plotly/plotly.py/issues/3683">#3683</a>]</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/31e97dc6a62131bb9b33cc3cbcb77f40dcf4cb15"><code>31e97dc</code></a> fix date</li>
<li><a href="https://github.com/plotly/plotly.py/commit/ab8687da27d7aa68757a2cb645e38eaf73e53b71"><code>ab8687d</code></a> update changelog</li>
<li><a href="https://github.com/plotly/plotly.py/commit/ac674ef4a0370d27f32f75100c9118b929a51239"><code>ac674ef</code></a> Update README.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/8a75262e4f1c1d75e5803c47aab9763f46bbaea9"><code>8a75262</code></a> version changes for v5.14.0</li>
<li><a href="https://github.com/plotly/plotly.py/commit/5351836b2198a5662cd01a35ca3eb1a7f0f35f2b"><code>5351836</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4114">#4114</a> from not522/utf-8</li>
<li><a href="https://github.com/plotly/plotly.py/commit/f4609fcf955aa23eb1216f07823ea3a817ac9c4d"><code>f4609fc</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4104">#4104</a> from plotly/march-docs</li>
<li><a href="https://github.com/plotly/plotly.py/commit/846d1f7e44a1e9f852fffd0c550558f1313fd939"><code>846d1f7</code></a> Update CHANGELOG.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/690afe071e66e2ed8a369798f4ae727e0e211e7d"><code>690afe0</code></a> Update aggregations.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/7be3b7d6ac8dd52dabbede12e1208d730cd53906"><code>7be3b7d</code></a> Merge branch 'master' into march-docs</li>
<li><a href="https://github.com/plotly/plotly.py/commit/1860acc2f9d3179558bfcbe6997e4f4d6efe8adc"><code>1860acc</code></a> Specify utf-8 in script tag</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.14.0">compare view</a></li>
</ul>
</details>
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PR_kwDOACgets5NigJH
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pre-commit autoupdate
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[] | 2023-04-04T01:03:41
| 2023-04-04T01:37:26
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2023-04-04T01:37:23Z
|
CONTRIBUTOR
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<!--pre-commit.ci start-->
updates:
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PR_kwDOACgets5Niklz
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Fix breaking changes from pandas v2
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[] | 2023-04-04T01:31:51
| 2023-04-04T01:50:46
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2023-04-04T01:50:45Z
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MEMBER
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Closes #2914.
Replace calls to df.append() with pd.concat() and df.iteritems() with df.items().
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PR_kwDOACgets5N6tNj
| 2,937
|
fix GaussianOutput bug with multiple route lines
|
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[
"Could you zip the log file and load it as `test_files/molecules/EC.log.gz` using e.g. `monty`?",
"I have zipped `test_files/molecules/EC.log` to `test_files/molecules/EC.log.gz` and set the `zopen mode in GaussianOutput` to `\"rt\"` to load `.gz` file."
] | 2023-04-10T08:43:51
| 2023-04-27T14:49:13
|
2023-04-27T14:49:12Z
|
CONTRIBUTOR
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When route lines in gaussian output file like:
```plaintext
----------------------------------------------------------------------
# B3LYP/6-311++G(2d,p) EmpiricalDispersion=GD3BJ SCRF=(SMD,READ) freq
opt=(loose,maxcyc=400)
----------------------------------------------------------------------
```
If we use `GaussianOutput` to parse route lines, `route_parameters` would be looked like as follows, in which, `freq` and `opt` are concatenate.
```python
{'EmpiricalDispersion': 'GD3BJ',
'SCRF': '(SMD,READ)',
'freqopt': {'loose': None, 'maxcyc': '400'}}
```
Now, I fix the method to parse route lines, to give the right `route_parameters`:
```python
{'EmpiricalDispersion': 'GD3BJ',
'SCRF': '(SMD,READ)',
'freq': None,
'opt': {'loose': None, 'maxcyc': '400'}}
```
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I_kwDOACgets5jNuKm
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|
ResParser cannot read the res file with spin values
|
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[
"AIRSS IO support was initially added by @ScottNotFound in https://github.com/materialsproject/pymatgen/pull/2625. Maybe he can briefly chime in if this an easy fix or would take some work.",
"This is easy to add to the parser, just need to add an extra field and relevant parsing. I can do a fix tomorrow. Is there a standard way to represent spin in the `Site` class? I see mention of a `\"magmom\"` key in the properties, but I didn't know if this was standardized.",
"That would be great, thanks!\r\n\r\nUp and down spins are represented by the [`Spin`](https://github.com/materialsproject/pymatgen/blob/81bf5c8c5d4447a2f205a0c4c173c6026eca951e/pymatgen/electronic_structure/core.py#L14-L30) class which internally just stores 1 or -1."
] | 2023-04-12T13:10:09
| 2023-04-19T00:30:42
|
2023-04-19T00:30:42Z
|
NONE
|
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When using the AIRSS code with spin-polarized DFT calculations, the resulting ShelX `.res` files contain spin values. However, `ResParser` is unable to read these `.res` files with spin values.
Error message:
```py
pymatgen.io.res.ParseError: Failed to parse ion entry Li 1 -0.0000000000000 0.2500000000000 0.1118080000000 1.0 -0.01, expected 6 fields.
```
<details><summary>Example input file</summary>
```txt
TITL LiMn2O4-Imma-conv -0.0043 287.448784 -3.11129793E+004 0 0 28 (Imma) n - 1
REM
REM Run started: Mon, 03 Apr 2023 04:04:50 +0100 in
REM CASTEP 21.11| from code version 7d4405a8a+ HEAD Sat Nov 27 13:38:33 2021 +0000
REM Functional PBE for solids (2008) Relativity Koelling-Harmon Dispersion off
REM Cut-off 900.0000 eV Grid scale 2.0000 Gmax 46.1085 1/A FBSC none
REM MP grid 4 4 3 Offset 0.000 0.000 0.000 No. kpts 8 Spacing 0.05
REM Total runtime: 960.94 s
REM Overall efficiency: 81 %
REM
REM
REM ## AIRSS Version 0.9.3 July 2022 commit v0.9.3-15-g857f5392bdb2fb114d
REM
REM
REM COMMAND_LINE
REM
REM
REM O C19
REM O 2|1.1|17|20|23|20:21(qc=8)
REM Mn C19
REM Mn 3|1.8|1.8|0.6|12|14|16|30U:40:31:32(qc=7)
REM Li C19
REM Li 1|1.0|14|16|18|10U:20(qc=7)
REM Mn d: 3.90
REM
CELL 1.54180 5.71878 5.76216 8.72311 90.00000 90.00000 90.00000
LATT -1
SFAC Li O Mn
Li 1 -0.0000000000000 0.2500000000000 0.1118080000000 1.0 -0.01
Li 1 0.5000000000000 0.7500000000000 0.6118080000000 1.0 -0.01
Li 1 -0.0000000000000 0.7500000000000 -0.1118080000000 1.0 -0.01
Li 1 0.5000000000000 1.2500000000000 0.3881920000000 1.0 -0.01
O 2 -0.0000000000000 0.0291620000000 0.7529840000000 1.0 -0.04
O 2 0.5000000000000 0.5291620000000 1.2529840000000 1.0 -0.04
O 2 -0.0000000000000 0.4708380000000 0.7529840000000 1.0 -0.04
O 2 0.5000000000000 0.9708380000000 1.2529840000000 1.0 -0.04
O 2 -0.0000000000000 0.5291620000000 -0.7529840000000 1.0 -0.04
O 2 0.5000000000000 1.0291620000000 -0.2529840000000 1.0 -0.04
O 2 -0.0000000000000 -0.0291620000000 -0.7529840000000 1.0 -0.04
O 2 0.5000000000000 0.4708380000000 -0.2529840000000 1.0 -0.04
O 2 0.2261230000000 0.2500000000000 0.5282620000000 1.0 -0.17
O 2 0.7261230000000 0.7500000000000 1.0282620000000 1.0 -0.17
O 2 -0.2261230000000 0.2500000000000 0.5282620000000 1.0 -0.17
O 2 0.2738770000000 0.7500000000000 1.0282620000000 1.0 -0.17
O 2 -0.2261230000000 0.7500000000000 -0.5282620000000 1.0 -0.17
O 2 0.2738770000000 1.2500000000000 -0.0282620000000 1.0 -0.17
O 2 0.2261230000000 -0.2500000000000 -0.5282620000000 1.0 -0.17
O 2 0.7261230000000 0.2500000000000 -0.0282620000000 1.0 -0.17
Mn 3 -0.0000000000000 0.0000000000000 0.5000000000000 1.0 4.12
Mn 3 0.5000000000000 0.5000000000000 1.0000000000000 1.0 4.12
Mn 3 -0.0000000000000 0.5000000000000 0.5000000000000 1.0 4.12
Mn 3 0.5000000000000 1.0000000000000 1.0000000000000 1.0 4.12
Mn 3 0.2500000000000 0.2500000000000 0.7500000000000 1.0 3.31
Mn 3 -0.2500000000000 0.2500000000000 0.7500000000000 1.0 3.31
Mn 3 -0.2500000000000 0.7500000000000 -0.7500000000000 1.0 3.31
Mn 3 0.2500000000000 -0.2500000000000 -0.7500000000000 1.0 3.31
END
```
</details>
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PR_kwDOACgets5OKK0s
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fix on reading multiple route in Gaussian input file
|
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[
"Thanks! 👍 ",
"Thanks for merging!"
] | 2023-04-12T18:18:44
| 2023-04-17T19:37:06
|
2023-04-17T17:38:46Z
|
CONTRIBUTOR
|
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## Summary
This fixes the issue that the Gaussian input file fails to read multiple lines.
- When the route input has multiple lines as below, GaussianInput.from_string() fails around the parsing of the route. This was due to inappropriate line counting when the route is separated in multiple lines.
- few lines of code were added to parse the route and route_index.
- test files for routes with multiple lines.
Example of Gaussian input (header only) with multiple lines of the route that failed.
```
%nprocshared=28
%mem=60GB
%chk=test.chk
# opt freq wb97xd/gen nosymm scf=(qc,maxcycle=1024) geom=connectivity
pseudo=read
```
## Todo (if any)
## Checklist
Before a pull request can be merged, the following items must be checked:
- [x] Doc strings 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 path/to/file.py`](https://github.com/python/mypy) to type check your code. Should I also rewrite the other part of the codes?
- [x] 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. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Afterwards linters will run before every commit and abort if any issues pop up.
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PR_kwDOACgets5OhZIB
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Fix CI errors
|
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[] | 2023-04-17T21:45:18
| 2023-04-18T02:59:42
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2023-04-18T02:59:41Z
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MEMBER
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Not sure when these errors first started showing. Fixed in
- 2e48d23
- 2ca5798
|
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PR_kwDOACgets5Ol9kL
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Add ResParser support for reading files with spin values
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[
"Wow, that was fast! Thanks a lot, @ScottNotFound! 🎉 "
] | 2023-04-18T15:33:25
| 2023-04-19T00:30:41
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2023-04-19T00:30:41Z
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CONTRIBUTOR
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## Summary
- Fix #2938
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only return unique point group operations
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[
"Thanks @mueslo. For future reference, could you add a failing example as JSON or CIF to the PR description using `<details>`?\r\n\r\n```md\r\n<details><summary>example</summary>\r\n<p>\r\n\r\nhi there!\r\n\r\n</p>\r\n</details> \r\n```",
"@janosh I added some details and a minimal working example. Could you please trigger the tests?\r\n\r\nI also note that by default `SpacegroupAnalyzer._get_symmetry` also returns non-unique operations due the default `is_magnetic` being `True` in `spglib.get_symmetry`. However, passing `is_magnetic=False` is not a good option since the parameter is deprecated, so might give errors in the future when it is removed. For the time being I could also make `SpacegroupAnalyzer._get_symmetry` give only unique (rotations, translations) as part of this PR, if you think it might be a good idea.",
"@mueslo Very sorry for the long delay! I somehow wasn't pinged about this (or missed it). Thanks for the additional details. Tests running now.\r\n\r\n\r\n\r\n\r\n> For the time being I could also make SpacegroupAnalyzer._get_symmetry give only unique (rotations, translations) as part of this PR, if you think it might be a good idea.\r\n\r\nI'll defer to @shyuep on this decision who will be better informed to gauge the downstream implications. Incidentally, he just bumped `spglib` to v2.0.2 in 3d33aca.",
"@mueslo If this is ready to go, best remove \"WIP\" from PR title as that makes it more likely to receive attention.",
"@mueslo The linter will be fixed if you pull in `master`.",
"> > For the time being I could also make SpacegroupAnalyzer._get_symmetry give only unique (rotations, translations) as part of this PR, if you think it might be a good idea.\r\n> \r\n> I'll defer to @shyuep on this decision who will be better informed to gauge the downstream implications. Incidentally, he just bumped `spglib` to v2.0.2 in [3d33aca](https://github.com/materialsproject/pymatgen/commit/3d33aca90e7a4411c1ab9c4d6ea9d6fc9be1178c).\r\n\r\nI'll merge this for now. Feel free to open a new PR for `SpacegroupAnalyzer._get_symmetry`. "
] | 2023-04-18T17:52:01
| 2023-05-07T01:26:13
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2023-05-07T01:26:13Z
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CONTRIBUTOR
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## Summary
- Fix duplicate point group operations returned in `SpacegroupAnalyzer.get_point_group_operations`
Retains original ordering, i.e. identity operation E always stays first.
Background: `get_point_group_operations` ultimately uses `spglib.get_symmetry`. However, this only returns unique tuples of (rotation, translation, time_reversal), as of `spglib v2.0.2`. So if you have *n* translations and *m* time reversals you will get your rotation symmop *n*\**m* times.
This is very annoying when e.g. filling the Brillouin zone with potentially tens of thousands of k-points from the irreducible wedge, and then getting hundreds of thousands of unnecessary duplicate k-points thanks to non-unique symmetry operations
Since `SpacegroupAnalyzer._get_symmetry` only uses and returns (rotation, translation), it should actually also be made unique, however since `is_magnetic=True` in `spglib` is supposedly being deprecated, this should solve itself.
<details><summary>Example</summary>
<p>
Input:
```py
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
struc = Structure.from_spacegroup(223, np.eye(3), ['Ni'], [[0., 0., 0.]])
pgops = SpacegroupAnalyzer(struc).get_point_group_operations(cartesian=True)
```
</p>
</details>
<details><summary>Output before fix</summary>
```py
len(pgops) == 192
pgops ==
[Rot:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[-1. 0. 0.]
[ 0. -1. 0.]
[ 0. 0. -1.]]
tau
[0. 0. 0.],
Rot:
[[-1. 0. 0.]
[ 0. -1. 0.]
[ 0. 0. -1.]]
tau
[0. 0. 0.],
...]
```
</details>
<details><summary>Output after fix</summary>
```py
len(pgops) == 48
pgops ==
[Rot:
[[1. 0. 0.]
[0. 1. 0.]
[0. 0. 1.]]
tau
[0. 0. 0.],
Rot:
[[-1. 0. 0.]
[ 0. -1. 0.]
[ 0. 0. -1.]]
tau
[0. 0. 0.],
...]
```
</details>
<details><summary>Speed</summary>
I found rot.tobytes() seems to be the fastest hashable option for the set.
Overall, also thanks to the removed 3x3 matrix inversion and lookup instead, and the skipped SymmOp __init__s, the new function is >10% faster for both low and high counts of symmetry operations.
>>> %timeit sa.get_point_group_operations(cartesian=True)
>>> %timeit sa.get_point_group_operations_new(cartesian=True)
<<< 8.29 ms ± 48.9 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
<<< 6.76 ms ± 23.4 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)
Time taken drops further to ~5ms if not going via `self._get_symmetry()` which has unnecessary translation vector logic, but directly calling `spglib.get_symmetry()`, at the cost of duplicate code. So I did not include it in this PR.
</details>
## 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:
- [ ] Tests have been added for any new functionality or bug fixes.
- [ ] All linting and tests pass.
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I_kwDOACgets5jxXKm
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Pourbaix digram entry with a wrong composition
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[
"@rkingsbury Could you take a look? Not familiar with the `PourbaixDiagram` myself.\r\n\r\n@johanzhuohan Please post code snippets in the future. They are much more usable than screenshots.",
"Sure! I was not quite sure how to insert the code, but I will do that next time!",
"Hi @johanzhuohan , thanks for reporting this. To be honest I'm not entirely sure, but I agree with you that it does seem odd to get a MultiEntry whose composition is so different from the specified `comp_dict`.\r\n\r\nIf there is a bug, I think it probably resides in [this section of code](https://github.com/materialsproject/pymatgen/blob/713740f5b8bf27990d9d0c92ca154fae4164ec59/pymatgen/analysis/pourbaix_diagram.py#L709). Maybe you can scrutinize that and see if you can find anything? \r\n\r\nThis code contains the following comment\r\n```\r\n# Get balanced reaction coeffs, ensuring all < 0 or conc thresh\r\n # Note that we get reduced compositions for solids and non-reduced\r\n # compositions for ions because ions aren't normalized due to\r\n # their charge state.\r\n```\r\n\r\nBut I don't see where/how this actually happens, i.e., it seems like all entries (ion or solid) simply use their `.composition` attribute. So maybe there is some issue there?\r\n\r\n@montoyjh do you have any insight into this?",
"So I've finally found a moment to look into this - see [this branch on my fork](https://github.com/montoyjh/pymatgen/blob/30483eda08e9ba4dc9981572b48def42d45165c3/pymatgen/analysis/pourbaix_diagram.py#L745). I think I understand what's going wrong.\r\n\r\nIn the pourbaix diagram module, we're using the reaction coefficient solving capability of the `Reaction` class as a check to ensure that multi-entries were valid - essentially if all of the coefficients of a given set of entries were positive nonzero - it meant that there was a valid combination of coefficients (a negative coefficient meant that one of the \"reactants\" in the entry_list was actually a \"product\" and therefore the multi-entry combination wasn't valid). We occasionally come across a situation where a multi-entry candidate has two entries at the same non-charge-containing composition, e.g. Fe(s) and Fe[2+], so in the reaction context when we use `Reaction.get_coeff(composition)`, we end up getting the wrong coefficient for one of them, and that wrong coefficient might be positive instead of negative. I'm not 100% what the best solution is in this case. I could for example replace `react_coeffs = [-rxn.get_coeff(comp) for comp in entry_comps]` with `react_coeffs = [-coeff for coeff in rxn._coeff[:len(entry_list)]]` in order to ensure I'm getting the \"correct\" coefficients, but it feels a little non-idiomatic, just want to check in to see if anyone more familiar with the reaction class has advice.",
"Thanks for investigating @montoyjh . Pinging @mattmcdermott as I think he's quite familiar with the `Reaction` class.",
"I am not an avid user of pymatgen's Pourbaix diagrams, but my first take is that this might be a misuse of the functionality of the `Reaction` class (at least from a programming point of view). If we wanted to be very proper, we should probably make a new reaction class that takes in `Species` objects instead of `Composition` objects.\r\n\r\nThat being said, there has always been a sort of a gray area with using the `Reaction` class when you have duplicated compositions anyway, such as this one:\r\n```python\r\nrxn = Reaction([Composition(\"Fe2O3\"), Composition(\"Fe\"), Composition(\"O\")], [Composition(\"Fe\"), Composition(\"O\")])\r\nprint(rxn)\r\n```\r\n```\r\nFe2O3 + Fe + 0.5 O2 -> 3 Fe + 2 O2\r\n```\r\nSo this is more of a general problem anyway with using the `Reaction.get_coeff` method.\r\n\r\n@montoyjh, if your fix is working fine for the Pourbaix functionality, I don't see any problems with it.",
"> I am not an avid user of pymatgen's Pourbaix diagrams, but my first take is that this might be a misuse of the functionality of the `Reaction` class (at least from a programming point of view). If we wanted to be very proper, we should probably make a new reaction class that takes in `Species` objects instead of `Composition` objects.\r\n\r\nAgreed - an ion-compatible reaction class would more accurately model our use-case, and we're abusing the current one here in order to avoid duplicating code for stoichiometry solvers."
] | 2023-04-18T21:59:12
| 2023-06-09T05:48:13
|
2023-06-09T05:48:13Z
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NONE
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**Describe the bug**
[Related matsci post](https://matsci.org/t/47247)
The Pourbaix diagram sometimes includes the multientry with a different composition than the one initially used to generate the pourbaix diagram. This only occurs for some initial compositions. What could be the reason for this?
Also, in the example shown in the attached screenshot, the multientry includes both Fe(s) and Fe[+2] at the same time. It looks unphysical, but could this be a bug in the code?
**To Reproduce**
```py
ELEMENTS_HO = {Element("H"), Element("O")}
chem_sys = 'Fe-Ir-Li-Si-V'
pourbaix_entries = mpr.get_pourbaix_entries(chemsys=chem_sys)
pourbaix_elem = [Element(elem) for elem in chem_sys.split('-')]
conc_dict = {}
for elem in pourbaix_elem:
conc_dict[elem.symbol] = 1e-6
comp_dict = Composition({Element('Fe'): 1, Element('Ir'): 1,
Element('Li'): 2, Element('Si'): 1, Element('V'): 2, }).fractional_composition
print(comp_dict)
pbx = PourbaixDiagram(pourbaix_entries, comp_dict=comp_dict, conc_dict = conc_dict)
pbx_comp = Composition(pbx._elt_comp).fractional_composition
print(pbx_comp)
for multientry in pbx.all_entries:
entry_pbx_comp = Composition(
{elt: coeff for elt, coeff in multientry.composition.items() if elt not in ELEMENTS_HO}
).fractional_composition
if entry_pbx_comp != pbx_comp:
print(multientry)
print(entry_pbx_comp)
exit()
```
**Screenshots**
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I_kwDOACgets5j1RKk
| 2,944
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Minor modification to symmetrically distinct Miller index finder
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[
"Thanks for the detailed explanation! Sounds to me like this change makes sense. Not a surface guy myself so an important question before we change this behavior is if you could imagine this breaking any existing code? I.e. are there use cases where returning an equivalent but different set of indices might affect downstream analysis?\r\n\r\nIf not or if that risk seems small, the other important thing is adding tests that fail before this change and pass with it.",
"Thanks for the swift reply! I don't imagine this breaking anything downstream. Seems like the only other place this function is used is in `pymatgen.analysis.interfaces.substrate_analyzer` and this change doesn't affect the tests there. I added the necessary change and tests to go along with it."
] | 2023-04-19T13:29:42
| 2023-04-20T14:28:15
|
2023-04-20T14:28:15Z
|
CONTRIBUTOR
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**Is your feature request related to a problem? Please describe.**
I recently noticed that when generating symmetrically distinct Miller indices using the `get_symmetrically_miller_indices()` of `pymatgen.core.surface`, some of the Miller indices that appear when `max_index=2` weren't there for `max_index=3`. My expectation was that as you increase `max_index`, each output should build upon the previous ones, i.e. the output when `max_index=2` should be a subset of the output of `max_index=3` and so on.
After checking the symmetrically equivalent Miller indices of the missing ones by manually applying the reciprocal lattice symmetry operations to one of the missing indices, I noticed that it was equivalent to another Miller index that appears when `max_index=3`, and this particular Miller index contains a 3 in it. After looking inside the function more carefully, I pinpointed the cause to https://github.com/materialsproject/pymatgen/blob/3cfbd540006ec048008611a45d4df61be2af4aa6/pymatgen/core/surface.py#L1673
where `conv_hkl_list` is built by the cartesian product of `r` values, where the `r` runs from `-max_index` to `+max_index`. Following this, when a unique Miller is encountered, it is appended to the list of `unique_millers` and if an index is not unique, it is discarded. Naturally, the high index Miller indexes are encountered first in the iteration and added to the list of unique Millers, and some Miller indices that appear when `max_index` were to be lower are discarded.
The reason I would like to see this changed is that the equivalency between these Miller indices is not so obvious, and the companion function `get_symmetrically_equivalent_miller_indices()` from the same module only checks up to the maximum of the indices in the Miller index passed to it. For this particular case, the equivalency was between (2, 1, 0) and (3, -1, 0) for ZrTe (mp-1539), where the function in question returns (3, -1, 0) instead of the preferred (2, 1, 0). Also, the system sizes seem to be smaller with the lower index Miller indices from my limited testing (I mean, this is expected).
**Describe the solution you'd like**
I think the solution is simple and pretty straightforward to implement. After `conv_hkl_list` is initialized, we have to sort it with respect to the maximum of the absolute values of the indices it contains, in ascending order, so that lower index surfaces are iterated over first. This way, every output of the function `get_symmetrically_distinct_miller_indices()` with increasing values of `max_index` builds upon the previous output.
I have a PR ready and can proceed if you agree that this makes sense.
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For MPcules: Molecule Trajectory and graph hashes
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[
"Thanks @espottesmith! Could you briefly explain the major differences between `Trajectory` and `MoleculeOptimizeTrajectory`? I understand latter is meant to handle `Molecule`s but I'm curious what is preventing an object agnostic `Trajectory` class that handles both `Structure`s and Mols?\r\n\r\nAlso, are you anticipating a MoleculeMDTrajectory class or similar with different needs? If not, why not call it `MoleculeTrajectory` and call the other StructureTrajectory with an alias for `Trajectory` for backwards compat?",
"There's nothing preventing an agnostic Trajectory class, in principle. It just felt easier to make two versions, one that had to consider Lattices and another that doesn't. This is the same approach taken previously, e.g. for StructureGraph vs. MoleculeGraph.\r\n\r\nI don't care much about the name. MoleculeTrajectory and StructureTrajectory are fine. ",
"If there's nothing preventing it, my preference is for an agnostic `Trajectory` class as that minimizes LoC and will prevent API drift that could occur between `MoleculeTrajectory` and `StructureTrajectory` over time. But this is just one opinion. Happy to be overruled by other maintainers or arguments.",
"I would respectfully say that if that's a design pattern that you or others want to move towards, then y'all should have at it. As I said, this pattern is easier to write (in my opinion and experience), and as that implies, writing a unified interface would mean a nontrivial amount of additional work (that I don't want to do if I don't have to).",
"I agree with @janosh that it is preferable to have a single unified interface with a consistent API. Trajectories are trajectories. Whether there is a periodic boundary condition shouldn't make any difference. And I would prefer if the original contributor of the PR, i.e., @espottesmith makes the change.",
"The interface is as unified as it reasonably can be.",
"Thanks a lot, Evan! I really appreciate you going the extra mile!\r\n\r\nBtw, different topic but wanted to mention I could get behind dropping `mypy`. Sounds like you'd be in favor? 🤣 \r\nIn my personal experience, the pain `mypy` adds to developing can be too high for the number of coding errors it helps avoid. If @shyuep is not against, I'm happy to make the change.",
"For mypy, I think the general approach should be to not bother with type annotations where it is not necessary but to add them where you want a more stringent control of the types being passed. If you don't annotate, mypy will not check?",
"> If you don't annotate, mypy will not check?\r\n\r\nThat's true.\r\n\r\nBut unlike most (all?) other languages, I think the main beneficiaries of type annotations in Python are actually the users, not the developers. Tools like Sphinx automatically integrate type annos into static docs and IDEs display them on hover and when passing arguments like in this example:\r\n\r\n\r\n\r\nSo from that perspective, the more type hints the better. But the more you use them, the more `mypy` can be a nuisance.",
"Philosophically, I see type annotations as doing two things: 1. forcing developers to be more rigorous about what they intend, and 2. helping users use the code as intended. I generally think that they are most useful for primitive types, e.g., saying a generic variable name like `mode` can be a string, int or something else. It becomes messy when the types are built on objects with a hierarchy or even more complex things like lists or dicts.\r\n\r\nIt is definitely more effort than just not doing type annotations, but in the long run, it will be better. I am more fussy about type annotations for something like pymatgen/core but less for pymatgen/analysis. The more users who use a particular code, the more important it is that the types are properly specified. ",
"Stepping away from the mypy discussion, does anyone know why one of the tests failed? It failed during the dependency install, but this PR doesn't touch any of pymatgen's dependencies (at least, as far as I can remember).",
"Yeah failure is unrelated to this PR. Not sure why `phonopy` suddenly fails to install on Mac py3.8. Not holding back this PR. Haven't had time to re-review yet.",
"@espottesmith One more question. Do we need the new `use_molecule` kwarg? I just tried removing it and seeing if relying on the heuristic \"`if lattice is None` = we're handling molecules\" can work. The tests pass all still pass but maybe there's some subtlety that we're not checking for? Let me know if anything seems off to you in 4c9e24c?"
] | 2023-04-19T14:48:14
| 2023-04-25T17:46:54
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2023-04-25T17:46:54Z
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CONTRIBUTOR
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## Summary
We are nearing the inclusion of a large dataset of molecules and molecular properties to the Materials Project. This PR adds some features to pymatgen which will be useful for the molecules data pipeline in emmet, namely graph hashes and a Trajectory class that works for Molecules.
The graph hashing code, which is currently in emmet but is being moved to pymatgen because we expect it to be useful for more general users (rather than only developers), was taken (following licenses, I hope) from networkx. We took the code directly because we want to have access to a stable version of the hashing algorithm (networkx has made subtle changes to the algorithm in the past, leading to the same graphs producing different hashes).
The MoleculeOptimizeTrajectory class is basically a copy-paste of the existing Trajectory class, designed for Molecule objects rather than Structure objects. This will be important if we include geometry optimization trajectories in the new MP dataset, and/or if we want to visualize atomic motion (e.g. molecular normal modes of vibration).
## Checklist
- [X] Doc strings 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 path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [X] Tests have been added for any new functionality or bug fixes.
- [x] 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. We highly recommended installing `pre-commit` hooks. Simply Run
|
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| 1,675,745,068
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I_kwDOACgets5j4dcs
| 2,946
|
Issue with WulffShape.show(): 3D image not rendering
|
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[
"Duplicate of #2900. As a temporary workaround, try the `get_plotly()` method instead.",
"I see - using get_plotly worked! Thank you!"
] | 2023-04-19T22:53:37
| 2023-04-20T12:37:09
|
2023-04-19T23:13:17Z
|
NONE
|
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Hello!
I've been struggling with the WulffShape.show() function. I am using the exact code from the tutorial scripts from https://matgenb.materialsvirtuallab.org/2017/04/03/Slab-generation-and-Wulff-shape.html. While the script outputs information about the Wulff Construction such as the weighted surface energy and anisotropy, when calling WulffShape.show(), no 3D image is rendered in the popped-up figure. I have run this script on my computer and the computers of 2 of my colleagues. I wonder if this may be a problem with upgraded versions of Pymatgen and/or its compatibility with the latest versions of Python?
|
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I_kwDOACgets5j4ro5
| 2,947
|
UnicodeDecodeError in Structure.from_file when CifParser works
|
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[] | 2023-04-20T00:19:00
| 2023-04-20T00:47:04
|
2023-04-20T00:47:04Z
|
MEMBER
|
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The attached mCIF file downloaded straight from the Bilbao Crystallographic Server displays fine in Vesta and can be read by `CifParser` but fails in `Structure.from_file`
```py
from pymatgen.io.cif import CifParser
CifParser("./1.6_NiO.mcif") # works
Structure.from_file("./1.6_NiO.mcif") # fails
```
Error:
```py
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xd0 in position 843: invalid continuation byte
```
<details><summary>1.6_NiO.mcif</summary>
```cif
#\#CIF_2.0
# Created by the Bilbao Crystallographic Server
# http://www.cryst.ehu.es
# Date: 11/19/2017 17:05:30
# Database entry: 1.6 NiO
# Cif-like file for the case 1.6
data_5yOhtAoR
_audit_creation_date 2017-11-19
_audit_creation_method "Bilbao Crystallographic Server"
_chemical_name_systematic
;
;
_chemical_name_common ?
_chemical_formula_moiety ?
_chemical_formula_structural ?
_chemical_formula_analytical ?
_chemical_formula_iupac ?
_chemical_formula_sum 'Ni O'
_chemical_formula_weight ?
_chemical_melting_point ?
_chemical_compound_source ?
_chemical_absolute_configuration .
_citation_journal_abbrev "Physica B"
_citation_journal_volume 385�386
_citation_page_first 394
_citation_page_last ?
_citation_article_id .
_citation_year 2006
_citation_DOI 10.1016/j.physb.2006.05.082
loop_
_citation_author_name
"E. Ressouche"
"N. Kernavanois"
"L.-P. Regnault"
"J.-Y. Henry"
_atomic_positions_source_database_code_ICSD .
_atomic_positions_source_other .
_transition_temperature 523
_experiment_temperature ?
loop_
_irrep_id
_irrep_dimension
_irrep_small_dimension
_irrep_direction_type
_irrep_action
_irrep_modes_number
_irrep_presence
mL3+ 8 2 special primary . .
_exptl_crystal_magnetic_properties_details
;
SNP
arbitrary spin scale.
spins along the (11-2) direction, perpendicular to the propagation vector
monoclinic axis along (1,-1,0) direction, also perpendicular to k.
;
_active_magnetic_irreps_details
;
irrep mL3+, special direction.
a secondary weak spin component (irrep mL2+, 1dim-irrep) along the propagation vector, direction (1,1,1), is allowed and sometimes reported. Not included here.
;
_parent_space_group.name_H-M_alt 'F m -3m'
_parent_space_group.IT_number 225
_parent_space_group.transform_Pp_abc 'a,b,c;0,0,0'
loop_
_parent_propagation_vector.id
_parent_propagation_vector.kxkykz
k1 [1/2 1/2 1/2]
_parent_space_group.child_transform_Pp_abc '2a,2b,2c;0,0,0'
_space_group_magn.transform_BNS_Pp_abc 'a/4+b/4-c/2,a/4-b/4,-a/2-b/2;0,0,0'
_space_group_magn.number_BNS 15.90
_space_group_magn.name_BNS "C_c 2/c"
_space_group_magn.point_group_name "2/m1'"
_space_group_magn.point_group_number "5.2.13"
_cell_length_a 8.3500
_cell_length_b 8.3500
_cell_length_c 8.3500
_cell_angle_alpha 90.0000
_cell_angle_beta 90.0000
_cell_angle_gamma 90.0000
loop_
_space_group_symop_magn_operation.id
_space_group_symop_magn_operation.xyz
1 x,y,z,+1
2 -y+3/4,-x+3/4,-z,+1
3 -x+1/4,-y+3/4,-z,+1
4 y,x+1/2,z,+1
loop_
_space_group_symop_magn_centering.id
_space_group_symop_magn_centering.xyz
1 x,y,z,+1
2 x,y+1/4,z+3/4,+1
3 x,y+1/2,z+1/2,+1
4 x,y+3/4,z+1/4,+1
5 x+1/4,y,z+3/4,+1
6 x+1/4,y+1/4,z+1/2,+1
7 x+1/4,y+1/2,z+1/4,+1
8 x+1/4,y+3/4,z,+1
9 x+1/2,y,z+1/2,+1
10 x+1/2,y+1/4,z+1/4,+1
11 x+1/2,y+1/2,z,+1
12 x+1/2,y+3/4,z+3/4,+1
13 x+3/4,y,z+1/4,+1
14 x+3/4,y+1/4,z,+1
15 x+3/4,y+1/2,z+3/4,+1
16 x+3/4,y+3/4,z+1/2,+1
17 x+3/4,y+3/4,z,-1
18 x+3/4,y,z+3/4,-1
19 x+3/4,y+1/4,z+1/2,-1
20 x+3/4,y+1/2,z+1/4,-1
21 x,y+3/4,z+3/4,-1
22 x,y,z+1/2,-1
23 x,y+1/4,z+1/4,-1
24 x,y+1/2,z,-1
25 x+1/4,y+3/4,z+1/2,-1
26 x+1/4,y,z+1/4,-1
27 x+1/4,y+1/4,z,-1
28 x+1/4,y+1/2,z+3/4,-1
29 x+1/2,y+3/4,z+1/4,-1
30 x+1/2,y,z,-1
31 x+1/2,y+1/4,z+3/4,-1
32 x+1/2,y+1/2,z+1/2,-1
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
Ni Ni 0.00000 0.00000 0.00000 1
O O 0.75000 0.50000 0.00000 1
loop_
_atom_site_moment.label
_atom_site_moment.crystalaxis_x
_atom_site_moment.crystalaxis_y
_atom_site_moment.crystalaxis_z
_atom_site_moment.symmform
Ni 1. 1. -2. mx,mx,mz
```
</details>
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| 1,675,810,714
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PR_kwDOACgets5OuG7M
| 2,948
|
Ignore bad unicode characters in Structure.from_file()
|
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[] | 2023-04-20T00:30:39
| 2023-04-20T00:47:03
|
2023-04-20T00:47:02Z
|
MEMBER
|
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Closes #2947.
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PR_kwDOACgets5Ov0cv
| 2,949
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Minor modification for symmetrically distinct Miller index generation
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[
"Nicely done and great comments! 👍 "
] | 2023-04-20T09:16:21
| 2023-04-20T14:28:55
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2023-04-20T13:34:18Z
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CONTRIBUTOR
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Closes: https://github.com/materialsproject/pymatgen/issues/2944
Fix: `conv_hkl_list` is now sorted with respect to the maximum of the absolute values of the individual Miller indices it contains, before it is iterated over, ensuring that the unique Miller indices returned contain the lowest indices possible.
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Fixed Wulff shape for new versions of matplotlib
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2023-04-22T02:02:47Z
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Closes #2900.
Since matplotlib does not allow us to set auto_add_to_figure=True in Axes3D anymore passed ver. 3.6.0, I had to add the ax object to the Figure in order for it to properly display. Should now be backward/forward compatible for all versions of matplotlib.
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Fix ValueError when passing `selective_dynamics` to `Poscar`
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"Pls provide a unit test to confirm the new functionality. Thanks. ",
"Hi @shyuep, @janosh, I have added a unit test in `test_files/vasp`. Not sure if I put the file in the right place though. Let me know if this follows the guildlines. Thanks!",
"@chiang-yuan Thanks! The test should go into [`pymatgen/io/vasp/tests/test_inputs.py`](https://github.com/materialsproject/pymatgen/blob/51280b98a60b0dc12e1cc97d755813302a46e3bb/pymatgen/io/vasp/tests/test_inputs.py). There are some examples in there to learn from. Also, please check if you can reuse some of the existing POSCAR test files rather than adding new ones.",
"Thanks @janosh ! I followed the original style to test by comparing two primitive python lists and converted numpy array back to list to assign variables. Since the system can be large and comparing two nested python lists is somewhat tricky, (For example, `all([[True, False],[True, True]])` will give `True` rather than `False`), I suggest in the future assigning and testing all these variable as numpy array. This also aligns with `frac_coords`, `cart_coords` in the `core.structure` module."
] | 2023-04-24T01:40:33
| 2023-04-30T20:23:20
|
2023-04-30T20:23:19Z
|
CONTRIBUTOR
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Before this fix, users could not directly add a `selective_dynamics` array to create a `Poscar` object:
```python
poscar = Poscar(
structure,
selective_dynamics=boolean_array
)
```
and the code would produce an error:
```
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()
```
A similar [issue](https://matsci.org/t/got-problems-in-generating-vasp-input-files-for-structure-with-changed-selective-dynamics/38978) was reported previously about manually using `add_site_property`.
The minimal example reproducing the error and the bug fix is demonstrated in the attached notebook: [poscar_debug.md](https://github.com/materialsproject/pymatgen/files/11305634/poscar_debug.md)
## Summary
Include a summary of major changes in bullet points:
- Fixed the error where `selective_dynamics` boolean array is given for creating a `Poscar` object
- Applied similar bug fixes for `velocities` and `predictor_corrector`
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[
"@rkingsbury @shyuep I've been in that same situation and would also welcome such a change. Any reservations/things to be aware of from your side?",
"I have no reservations on enabling this. But there are two approaches to this. One is to create a ComputedEntry.from_settings factory method. This will make it explicit that the construction is different from using the `__init__` method. Anything that uses this method will by default apply the relevant VASP POTCAR settings based on the Composition.",
"I have also run into this and I agree the proposed change would be a good enhancement. I like @shyuep 's proposal. An alternate or complementary approach would be to add a kwarg to `MP2020Compatibiilty.__init__` that disables the POTCAR checks which occur at [this line](https://github.com/materialsproject/pymatgen/blob/83a87bb5039414aeb68f25162b5c1403478028d8/pymatgen/entries/compatibility.py#L944). I don't have a strong opinion as to which approach is better; perhaps the `.from_settings` method since the energy adjustments in `MP2020Compatibility` are developed for specific POTCARs.\r\n\r\nInterestingly, it appears that you might be able to bypass the POTCAR check already by specifying something other than `vasp` in `entry.parameters.software`. \r\n\r\n```\r\nif entry.parameters.get(\"software\", \"vasp\") == \"vasp\":\r\n pc = PotcarCorrection(MPRelaxSet, check_hash=self.check_potcar_hash)\r\n pc.get_correction(entry)\r\n```\r\n\r\nI haven't tried this to confirm, but if I'm right this is a bug that should be fixed in any case.",
"\r\n\r\nThanks @rkingsbury for the suggestion, Seems like the bypassing is not easy",
"> \r\n> \r\n> Thanks @rkingsbury for the suggestion, Seems like the bypassing is not easy\r\n\r\nI see, thanks for checking. It looks like this is actually bypassing the POTCAR check, but then failing the U values check. So in principle if you supplied the correct U values in your `parameters` and then used `software:foo` I think you could get around it, but obviously this is still a headache.",
"I can certainly see this being useful, although of course the checks are there for a reason -- especially, to pick one example, since MPRelaxSet itself has changed over time, it is perhaps not sufficient to say \"generated with MPRelaxSet\" for the purposes of guaranteeing compatibility. Still, sometimes...",
"Linking this to #2499 since they overlap.",
"@arosen93 I'll reply here re: #2499 as well as this issue. I'm definitely in favor of addressing this somehow. It seems to me there are two options:\r\n\r\n1. Add a `.from_settings` method that to `ComputedEntry` that adds the correct POTCAR and U settings so that the compatibility scheme can be applied, as @shyuep suggests. The concern I have with this method is that it could lead to confusing `ComputedEntry` in which the energies and the populated POTCAR / U details are not internally consistent. It would be very difficult to tell.\r\n2. Add a kwarg that bypasses the POTCAR _and the U_ checking, as @arosen93 suggested in the other issue. I would suggest this go in `MP2020Compatibility.__init__()` alongside `check_potcar_hash`. To avoid confusion with the hash kwarg and to communicate that this kwarg also bypasses U-value checking, maybe it could have a more generic name like `strict` or `check_settings`.\r\n\r\nI favor approach 2 because it is less likely to lead to confusion. A user could create some `ComputedEntry` with `strict=False` and they would have no `parameters`, signaling to any future users that those checks were bypassed when the corrections were applied.",
"Closed in fad0576eb85af458cdc18daf4df9e861c75971ed"
] | 2023-04-24T23:23:57
| 2023-07-12T23:03:17
|
2023-07-12T23:03:17Z
|
NONE
|
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**Issue**: [MP2020Compatibility](https://github.com/materialsproject/pymatgen/blob/83a87bb5039414aeb68f25162b5c1403478028d8/pymatgen/entries/compatibility.py#L821-L1097) (and all other compatibility modules) currently requires a ComputedEntry object containing VASP settings and POTCAR information to operate. This makes it inconvenient to apply corrections when only the structure and energy are available. This issue is becoming more common when dealing with large datasets (e.g., directly downloading structures from MP) and machine learning methods like M3GNet.
**Example**: M3GNet is trained on MPRelaxSet entries, but it's challenging to apply MP2020 compatibility to M3GNet predicted energies since there are no VASP settings available.
**Proposed Solution**: Add an extra key under the compatibility modules (or ComputedEntry) to simplify the process. For instance, `VASPsettings = "MPRelaxSet"` could be added. With this key, energy correction can be applied without explicitly including all VASP settings and creating a ComputedEntry.
|
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PR_kwDOACgets5PDh0O
| 2,953
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Test figure returned by WulffShape.get_plot() contains single Axes3D
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[] | 2023-04-25T00:46:03
| 2023-04-25T01:02:34
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2023-04-25T01:02:33Z
|
MEMBER
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Follow-up to #2950. Improves the `get_plot()` test to make sure a regression causing an empty figure doesn't go unnoticed again.
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PR_kwDOACgets5PHExl
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Fix `Cp2kOutput.spin_polarized()` likely not doing what author intended
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[] | 2023-04-25T14:37:59
| 2023-04-25T14:59:28
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2023-04-25T14:59:26Z
|
MEMBER
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```py
if ("UKS" or "UNRESTRICTED_KOHN_SHAM" or "LSD" or "SPIN_POLARIZED") in self.data["dft"].values():
return True
```
`"UKS" or "UNRESTRICTED_KOHN_SHAM" or "LSD" or "SPIN_POLARIZED"` short-circuits to `"UKS"` and so won't return `True` even if `"UNRESTRICTED_KOHN_SHAM"` or `"LSD"` or `"SPIN_POLARIZED"` are present.
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PR_kwDOACgets5POOj4
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`self.assertArrayEqual->assert`
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[] | 2023-04-26T17:27:50
| 2023-04-26T18:06:43
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2023-04-26T18:06:42Z
|
MEMBER
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678627b72 remove unused type ignore
484d133be ruff auto doc str format
0ba2f868d drop B031 from ruff ignore
579ac1e3e rename single-letter and non-snake-case vars
2dee11169 self.assertArrayEqual -> assert
|
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PR_kwDOACgets5PbQJN
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|
Add cell_filter_kwargs to relax method that is passed to ExpCellFilter
|
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[] | null |
[
"@yuuukuma You deleted the file `test_files/vasprun.xml.dfpt.ionic` which is causing a test to fail. Please restore it. Also, could you add/modify a test that for the new `cell_filter_kwargs`?"
] | 2023-04-29T01:26:01
| 2024-08-03T19:01:57
|
CONTRIBUTOR
|
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## Summary
Add cell_filter_kwargs to relax method that is passed to ExpCellFilter
This extension allows us to e.g. relax lattice constant along particular directions, e.g.,
```
structure.relax(cell_filter_kwargs={"mask": (1,1,0,0,0,1)}))
```
Then, the lattice is optimized only in xy-plane.
Because the change is tiny, I didn't add a unittest for it.
## Checklist
Before a pull request can be merged, the following items must be checked:
- [x] Doc strings 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 path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [ ] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
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I_kwDOACgets5kuMFT
| 2,957
|
Having trouble in merge the image to matplotlib.
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[] | null |
[
"This seems more like a support question than an issue with `pymatgen`. Such questions are better asked on https://matsci.org/c/pymatgen or in GH discussion. I'll convert this to a discussion."
] | 2023-04-30T08:26:12
| 2023-05-01T00:40:57
|
2023-05-01T00:40:57Z
|
NONE
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My code works well
```python
import matplotlib.pyplot as plt
from pymatgen.electronic_structure.plotter import BSPlotter
from pymatgen.io.vasp import Vasprun
# Extract the band structure data from the vasprun.xml file
vasprun = Vasprun("Bulk_fcc_Si_bandstructure/vasprun.xml")
band_structure = vasprun.get_band_structure()
# Use pymatgen's BSPlotter tool to create the band structure plot
plotter = BSPlotter(band_structure)
band_plot = plotter.get_plot(ylim=(-20, 40))
```
But I failed to merge the plotting into Matplotlib. Because I want to use Matplotlib to adjust the figure size, tick, font size, font, etc. My other photo has the same style but this figure. I want to unify all the figures in my article.
For example. In my note: https://github.com/Photonico/OCM_Practice/blob/main/VASP/Analysis%20for%20Bulk%20Si.ipynb
I want to make the last picture becomes unified with the former pictures.
How can I do this?
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| 1,690,776,805
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PR_kwDOACgets5Pf_SP
| 2,959
|
Bump pypa/cibuildwheel from 2.11.4 to 2.12.3
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[] | 2023-05-01T12:57:31
| 2023-05-01T13:45:08
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2023-05-01T13:45:07Z
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CONTRIBUTOR
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.11.4 to 2.12.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.12.3</h2>
<ul>
<li>🐛 Fix an import error when running on Python 3.7. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a>)</li>
</ul>
<h2>v2.12.2</h2>
<ul>
<li>🐛 Fix a bug that caused an extra empty config-setting to be passed to the backend when CIBW_BUILD_FRONTEND is set to <code>build</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1474">#1474</a>)</li>
<li>🐛 Fix a crash that occurred when overwriting an existing wheel on Windows. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1464">#1464</a>)</li>
<li>🛠 Pinned version updates, including CPython 3.10.11, 3.11.3, pip 23.1 and wheel 0.40.0.</li>
</ul>
<h2>v2.12.1</h2>
<ul>
<li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
</ul>
<h2>v2.12.0</h2>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.12.3</h3>
<p><em>19 April 2023</em></p>
<ul>
<li>🐛 Fix an import error when running on Python 3.7. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a>)</li>
</ul>
<h3>v2.12.2</h3>
<p><em>18 April 2023</em></p>
<ul>
<li>🐛 Fix a bug that caused an extra empty config-setting to be passed to the backend when CIBW_BUILD_FRONTEND is set to <code>build</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1474">#1474</a>)</li>
<li>🐛 Fix a crash that occurred when overwriting an existing wheel on Windows. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1464">#1464</a>)</li>
<li>🛠 Pinned version updates, including CPython 3.10.11, 3.11.3, pip 23.1 and wheel 0.40.0.</li>
</ul>
<h3>v2.12.1</h3>
<p><em>11 March 2023</em></p>
<ul>
<li>🐛 Fix a bug that prevented the use of CIBW_CONFIG_SETTINGS with the 'pip' build backend. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>)</li>
</ul>
<h3>v2.12.0</h3>
<p><em>16 Jan 2023</em></p>
<ul>
<li>✨ Adds support for PyPy arm64 wheels. This means that you can build PyPy wheels for Apple Silicon machines. Cross-compilation is not supported for these wheels, so you'll have to build on an Apple Silicon machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1372">#1372</a>)</li>
<li>🛠 Pinned version updates, including PyPy to v7.3.11 and setuptools to 66.0.0.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pypa/cibuildwheel/commit/5e15bb25b428e1bf2daf2215f173d2b40135f56f"><code>5e15bb2</code></a> Bump version: v2.12.3</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/52572ccdd01fcde11603283bcfda090086a7d11c"><code>52572cc</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1479">#1479</a> from henryiii/henryiii/fix/py37</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/c6027e4fc72eee01851e06b1cd173aabeb3abfe0"><code>c6027e4</code></a> docs: fix options.md typos (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1477">#1477</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/aff6dd5adc49114f1ee49c82bcb386a142fc614a"><code>aff6dd5</code></a> refactor: tomllib in _compat</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/31bd9c91743e09f5b48c4def38c255c14c00d1af"><code>31bd9c9</code></a> refactor: restore typing for non-backports</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/d996af554ae21435028e538e417e403e8db7433e"><code>d996af5</code></a> fix: restore Python 3.7 support</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/e42f243b523a93352f0686ba2f4a62b7bf5f7d34"><code>e42f243</code></a> ci: add Python 3.7</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/9f18d385cbb38b9c24f46a2c798f361ecea8fd5c"><code>9f18d38</code></a> Bump version: v2.12.2</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/dfbc6c3902b689c250f9d9dd10ce8f88db8e2b7b"><code>dfbc6c3</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1476">#1476</a> from henryiii/henryiii/chore/ruff_ex</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/8c5f89c035ba6ac81794ed5a5d6cd2110957f181"><code>8c5f89c</code></a> chore: update typing to be generic on function args</li>
<li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.11.4...v2.12.3">compare view</a></li>
</ul>
</details>
<br />
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PR_kwDOACgets5Pf_bD
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|
Bump uncertainties from 3.1.6 to 3.1.7
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[] | null |
[] | 2023-05-01T12:57:54
| 2023-05-01T13:45:48
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2023-05-01T13:45:47Z
|
CONTRIBUTOR
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Bumps [uncertainties](https://github.com/lebigot/uncertainties) from 3.1.6 to 3.1.7.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/lebigot/uncertainties/releases">uncertainties's releases</a>.</em></p>
<blockquote>
<h2>No imp deprecation warning for Python 3.4+</h2>
<p>See <a href="https://redirect.github.com/lebigot/uncertainties/issues/145">lebigot/uncertainties#145</a>.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/lebigot/uncertainties/commit/81a138c86d4582ec8eead867f499fcb4891f88d4"><code>81a138c</code></a> Fully bumped version number.</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/cfeacefe89fdb0da6bab18c90fe9949af6c4dea1"><code>cfeacef</code></a> Merge branch 'master' of github.com:lebigot/uncertainties</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/1c8678d7d133d76e7b31e8116415996599d39364"><code>1c8678d</code></a> No deprecation warning for imp for Python 3.4+.</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/210d6d9a4ffe174a92b9f5fa230ca9b8dca58000"><code>210d6d9</code></a> Fixed typos</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/5d5fc4510a5fac32bea539303be38333513ce308"><code>5d5fc45</code></a> More explicit constraint for wrap()</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/c4d9b9926ff0d1fc4009bec677f2e210dd715bdf"><code>c4d9b99</code></a> More useful target for the downloads/week badge</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/0ed11c05f2c2be74ccb6f7161e4471a9fca8c02b"><code>0ed11c0</code></a> Emphasis added for automatic differentiation</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/19e28327f5e7d530537c46348416722a6009eeb1"><code>19e2832</code></a> Made the automatic differentiation capabilities clearer</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/1cf21443b97394f5c6e141bab7e39db2a1a8b1ec"><code>1cf2144</code></a> Updated badge and link to readthedocs</li>
<li><a href="https://github.com/lebigot/uncertainties/commit/0de27bcbd4570a546e2563a0ab9cad8a8e42a6a5"><code>0de27bc</code></a> Updated from travis org to travis com.</li>
<li>Additional commits viewable in <a href="https://github.com/lebigot/uncertainties/compare/3.1.6...3.1.7">compare view</a></li>
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PR_kwDOACgets5Pf_cN
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Bump tabulate from 0.8.10 to 0.9.0
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[] | 2023-05-01T12:57:57
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2023-05-01T13:46:35Z
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CONTRIBUTOR
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Bumps [tabulate](https://github.com/astanin/python-tabulate) from 0.8.10 to 0.9.0.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/astanin/python-tabulate/blob/master/CHANGELOG">tabulate's changelog</a>.</em></p>
<blockquote>
<ul>
<li>0.9.0: Drop support for Python 2.7, 3.5, 3.6.
Migrate to pyproject.toml project layout (PEP 621).
New output formats: <code>asciidoc</code>, various <code>*grid</code> and <code>*outline</code> formats.
New output features: vertical row alignment, separating lines.
New input format: list of dataclasses (Python 3.7 or later).
Support infinite iterables as row indices.
Improve column width options.
Improve support for ANSI escape sequences and document the behavior.
Various bug fixes.</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/astanin/python-tabulate/commit/bf58e37e6b35e3cc9a0bd740f752abfd32b6e6f8"><code>bf58e37</code></a> version bump to 0.9.0, update README (Benchmark, Contributors), CHANGELOG</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/fd0a34ccf34f96820005b24c51d91d9887ec4047"><code>fd0a34c</code></a> Merge pull request <a href="https://redirect.github.com/astanin/python-tabulate/issues/201">#201</a> from astanin/dev-pep621</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/0a6554e868c7cc692d65ef80c1ca1d90ea44a610"><code>0a6554e</code></a> appveyor: upgrade setuptools before build (should fix UNKNOWN package name)</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/d99d9ae4957e60d210f4e76635999bef5fdbc947"><code>d99d9ae</code></a> ignore ImportError when importing <strong>version</strong> number</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/3e45eaccf471355ec47eb633b575086693700ecd"><code>3e45eac</code></a> update appveyor.yml to use pyproject.toml instead of setup.py</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/05e88d20cc0449ecc413dde2344f1ae5013b76cb"><code>05e88d2</code></a> fix test_cli - change script path, do not import .version if <strong>init</strong>.py is r...</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/4e2eeb1fcee4c3408c07c4255ef46f81c03a169c"><code>4e2eeb1</code></a> update tox.ini - use a virtual environment to build a source dist from the so...</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/6e378029f192c34ab156d2a75b04a04cf7ee69b9"><code>6e37802</code></a> Merge pull request <a href="https://redirect.github.com/astanin/python-tabulate/issues/179">#179</a> from KOLANYCH-libs:pyproject.toml</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/91723785940dfbf33f47d7094bc0e19437f05d2a"><code>9172378</code></a> fix tests failing after PR#183 (remove 1 space from the expected values)</li>
<li><a href="https://github.com/astanin/python-tabulate/commit/930a943887b8a269b7445fa89d4a6c88281b824b"><code>930a943</code></a> reformat with black, fix flake warnings</li>
<li>Additional commits viewable in <a href="https://github.com/astanin/python-tabulate/compare/v0.8.10...v0.9.0">compare view</a></li>
</ul>
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PR_kwDOACgets5Pf_dS
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Bump beautifulsoup4 from 4.11.1 to 4.12.2
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[] | 2023-05-01T12:57:59
| 2023-05-01T13:44:49
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2023-05-01T13:44:48Z
|
CONTRIBUTOR
|
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Bumps [beautifulsoup4](https://www.crummy.com/software/BeautifulSoup/bs4/) from 4.11.1 to 4.12.2.
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
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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Bump numpy from 1.23.2 to 1.24.3
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[] | 2023-05-01T12:58:11
| 2023-05-01T13:46:20
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Bumps [numpy](https://github.com/numpy/numpy) from 1.23.2 to 1.24.3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/numpy/numpy/releases">numpy's releases</a>.</em></p>
<blockquote>
<h2>v1.24.3</h2>
<h1>NumPy 1.24.3 Release Notes</h1>
<p>NumPy 1.24.3 is a maintenance release that fixes bugs and regressions
discovered after the 1.24.2 release. The Python versions supported by
this release are 3.8-3.11.</p>
<h2>Contributors</h2>
<p>A total of 12 people contributed to this release. People with a "+" by
their names contributed a patch for the first time.</p>
<ul>
<li>Aleksei Nikiforov +</li>
<li>Alexander Heger</li>
<li>Bas van Beek</li>
<li>Bob Eldering</li>
<li>Brock Mendel</li>
<li>Charles Harris</li>
<li>Kyle Sunden</li>
<li>Peter Hawkins</li>
<li>Rohit Goswami</li>
<li>Sebastian Berg</li>
<li>Warren Weckesser</li>
<li>dependabot[bot]</li>
</ul>
<h2>Pull requests merged</h2>
<p>A total of 17 pull requests were merged for this release.</p>
<ul>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23206">#23206</a>: BUG: fix for f2py string scalars (<a href="https://redirect.github.com/numpy/numpy/issues/23194">#23194</a>)</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23207">#23207</a>: BUG: datetime64/timedelta64 comparisons return NotImplemented</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23208">#23208</a>: MAINT: Pin matplotlib to version 3.6.3 for refguide checks</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23221">#23221</a>: DOC: Fix matplotlib error in documentation</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23226">#23226</a>: CI: Ensure submodules are initialized in gitpod.</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23341">#23341</a>: TYP: Replace duplicate reduce in ufunc type signature with reduceat.</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23342">#23342</a>: TYP: Remove duplicate CLIP/WRAP/RAISE in <code>__init__.pyi</code>.</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23343">#23343</a>: TYP: Mark <code>d</code> argument to fftfreq and rfftfreq as optional...</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23344">#23344</a>: TYP: Add type annotations for comparison operators to MaskedArray.</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23345">#23345</a>: TYP: Remove some stray type-check-only imports of <code>msort</code></li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23370">#23370</a>: BUG: Ensure like is only stripped for <code>like=</code> dispatched functions</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23543">#23543</a>: BUG: fix loading and storing big arrays on s390x</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23544">#23544</a>: MAINT: Bump larsoner/circleci-artifacts-redirector-action</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23634">#23634</a>: BUG: Ignore invalid and overflow warnings in masked setitem</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23635">#23635</a>: BUG: Fix masked array raveling when <code>order="A"</code> or <code>order="K"</code></li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23636">#23636</a>: MAINT: Update conftest for newer hypothesis versions</li>
<li><a href="https://redirect.github.com/numpy/numpy/pull/23637">#23637</a>: BUG: Fix bug in parsing F77 style string arrays.</li>
</ul>
<h2>Checksums</h2>
<h3>MD5</h3>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/numpy/numpy/commit/14bb214bca49b167abc375fa873466a811e62102"><code>14bb214</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23642">#23642</a> from charris/prepare-1.24.3-release</li>
<li><a href="https://github.com/numpy/numpy/commit/118df47ffa8f9d383145e7279cb3e640a5f91854"><code>118df47</code></a> REL: Prepare for the NumPy 1.24.3 release</li>
<li><a href="https://github.com/numpy/numpy/commit/9e2085532d10eac823301f88997524234bff1e62"><code>9e20855</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23635">#23635</a> from charris/backport-23626</li>
<li><a href="https://github.com/numpy/numpy/commit/58025a456e2d597b4fa3061433cff1e8c8cdff1d"><code>58025a4</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23637">#23637</a> from charris/backport-23470</li>
<li><a href="https://github.com/numpy/numpy/commit/d4b1eac9106bb028fdabe3964f891b090353153e"><code>d4b1eac</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23634">#23634</a> from charris/backport-23627</li>
<li><a href="https://github.com/numpy/numpy/commit/4e60648dee120a2cac1c56dce2b1e3219f62e236"><code>4e60648</code></a> Merge pull request <a href="https://redirect.github.com/numpy/numpy/issues/23636">#23636</a> from charris/backport-23596</li>
<li><a href="https://github.com/numpy/numpy/commit/a1809fc756b5f648b8e2d7b1bae465902a4b7484"><code>a1809fc</code></a> BUG: Fix bug in parsing F77 style string arrays.</li>
<li><a href="https://github.com/numpy/numpy/commit/72b506c46ac76dcee9fdadf28af0e2907c03b251"><code>72b506c</code></a> MAINT: Update conftest for hypothesis</li>
<li><a href="https://github.com/numpy/numpy/commit/7576313b26240d916b435a717eec26037e1f360e"><code>7576313</code></a> BUG: Fix masked array raveling when <code>order="A"</code> or <code>order="K"</code></li>
<li><a href="https://github.com/numpy/numpy/commit/06c26944206ac384597e54c3685706e95b882e52"><code>06c2694</code></a> BUG: Ignore invalid and overflow warnings in masked setitem</li>
<li>Additional commits viewable in <a href="https://github.com/numpy/numpy/compare/v1.23.2...v1.24.3">compare view</a></li>
</ul>
</details>
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You can trigger Dependabot actions by commenting on this PR:
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PR_kwDOACgets5Pf_ms
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Bump pandas from 1.4.4 to 2.0.1
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[] | 2023-05-01T12:58:21
| 2023-05-01T18:52:22
|
2023-05-01T18:52:21Z
|
CONTRIBUTOR
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 1.4.4 to 2.0.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
<blockquote>
<h2>Pandas 2.0.1</h2>
<p>This is a patch release in the 2.0.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0.1/whatsnew/v2.0.1.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
<h2>Pandas 2.0.0</h2>
<p>We are pleased to announce the release of pandas 2.0.0, a major release from the pandas 1 series. This release includes some new features, bug fixes, and performance improvements, as well as possible breaking changes. It is recommended that users with existing code upgrade to pandas 1.5.3 before they upgrade to pandas 2, and make sure their code does not generate FutureWarning or DeprecationWarning messages.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0/whatsnew/v2.0.0.html">whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on conda-forge and PyPI.</p>
<p>The release can be installed from PyPI</p>
<pre><code>python -m pip install --upgrade pandas==2.0.0
</code></pre>
<p>Or from conda-forge</p>
<pre><code>mamba install -c conda-forge pandas==2.0.0
</code></pre>
<p>Please report any issues with the release candidate on the <a href="https://github.com/pandas-dev/pandas/issues/new/choose">pandas issue tracker</a>.</p>
<h2>Pandas 2.0.0rc1</h2>
<p>We are pleased to announce the second release candidate for pandas 2.0.0. If all goes well, we'll release pandas 2.0.0 in about two weeks.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0/whatsnew/v2.0.0.html">whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on conda-forge and PyPI.</p>
<p>The release can be installed from PyPI</p>
<pre><code>python -m pip install --upgrade --pre pandas==2.0.0rc1
</code></pre>
<p>Or from conda-forge</p>
<pre><code>conda install -c conda-forge/label/pandas_rc pandas==2.0.0rc1
</code></pre>
<!-- raw HTML omitted -->
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<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pandas-dev/pandas/commit/37ea63d540fd27274cad6585082c91b1283f963d"><code>37ea63d</code></a> RLS: 2.0.1</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/4226ed591ea91fd255ee18f4bee1831a7b312c3b"><code>4226ed5</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52882">#52882</a> on branch 2.0.x (DOC: Update whatsnew) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/52885">#52885</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/eb4af7e05c71d98113ee04f06459899c94e3c3f4"><code>eb4af7e</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52877">#52877</a> on branch 2.0.x (BUG: Adding a columns to a Frame with Ran...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/6e7efb42908bfdbd8fcafd210fd1af8140be8df2"><code>6e7efb4</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52577">#52577</a> on branch 2.0.x (BUG: describe not respecting ArrowDtype i...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/22f9e935e15ff23e2c9333373025e1ef95323f9d"><code>22f9e93</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52867">#52867</a> on branch 2.0.x (Adjust unxfail condition for nat test for...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/7a0aa9f8b49ca404e4975fdbf9f284f09a647276"><code>7a0aa9f</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52843">#52843</a> on branch 2.0.x (BUG: pyarrow duration arrays constructed ...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/3af68dcdf70eeaade3f1e0c67e048fdaee71638c"><code>3af68dc</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52850">#52850</a> on branch 2.0.x (REGR: SeriesGroupBy.agg with multiple cat...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/d220466440f46d4cf3543fbe4b5d4bcb579b5dcf"><code>d220466</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52841">#52841</a> on branch 2.0.x (BUG: dt.round with equal/higher freq reso...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/e52861d8acf8439b6c3e0abb3ac26caa9ef40e2f"><code>e52861d</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52821">#52821</a> on branch 2.0.x (BUG: Non unitless np NaT arithmetic with ...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/fa94d3b77fe63743b04f86db42cf62c51b574ddf"><code>fa94d3b</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/52614">#52614</a>: ENH: Implement more str accessor methods for ArrowDtype (...</li>
<li>Additional commits viewable in <a href="https://github.com/pandas-dev/pandas/compare/v1.4.4...v2.0.1">compare view</a></li>
</ul>
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[] | 2023-05-01T23:57:36
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2023-05-02T14:29:16Z
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CONTRIBUTOR
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updates:
- [github.com/charliermarsh/ruff-pre-commit: v0.0.261 → v0.0.263](https://github.com/charliermarsh/ruff-pre-commit/compare/v0.0.261...v0.0.263)
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Addons in documentation
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[
"It's currently linked from the [intro page](https://pymatgen.org/introduction.html?highlight=addons) where I agree it has limited visibility. Happy to feature it more prominently if you have any ideas?",
"Ah, thanks. \r\n\r\nMaybe, we could link it here directly below or above \"Writing add-ons\": \r\n\r\n",
"Sounds good."
] | 2023-05-02T07:04:16
| 2023-05-02T15:07:19
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2023-05-02T15:07:19Z
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MEMBER
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**Describe the bug**
@janosh , I am wondering where the addons page is actually linked in the current version of the documentation? I only found it via external search.
https://pymatgen.org/addons
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PR_kwDOACgets5PmDeg
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Link /addons from new subsection on /contributing page
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[] | 2023-05-02T14:49:31
| 2023-05-02T15:07:19
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2023-05-02T15:07:17Z
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MEMBER
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Closes #2966.
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I_kwDOACgets5k51sH
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Entry sets use wrong Yb pseudo-potential
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[
"I don't really have any concerns. I think whether Yb_2 or Yb_3 depends on what you are calculating. VASP \"recommends\" Yb_2 as the PSP. See https://www.vasp.at/wiki/index.php/Available_PAW_potentials. This was probably the reason why we used that in the first place. For HT efforts, we have to select one. I am fine with switching to Yb_3 given that most Yb exists in 3+ oxidation state.",
"[This docs page](https://docs.materialsproject.org/methodology/materials-methodology/calculation-details/gga+u-calculations/pseudopotentials) needs updating. It incorrectly states we use `Yb`. It even lists \"thermo data off with Yb_2\" as the reason not to use `Yb_2` even though VASP recommends. 🤦 ",
"The docs page need to be updated for sure. But the docs seem to be based on the old HT framework at MIT. When we did MP, there was a deliberate change in PSP used. Anyway, like I said, no issue with switching to Yb3+.",
"@munrojm Change request [for docs page](https://docs.materialsproject.org/methodology/materials-methodology/calculation-details/gga+u-calculations/pseudopotentials) submitted on gitbooks.",
"@janosh merging now",
"> Although if tales are correct, @arosen93 originally brought this up with @mkhorton in Oct 2021?\r\n\r\nI don’t recall, but I believe it. The consequence of changing the MP Input Set is that current data on MP will the be inconsistent with the MP Input Set; since a lot of people generate data intentionally to be compatible with MP, this can cause a lot of downstream problems (even in this case, where the change is sensible and necessary).\r\n\r\nAround that time we were also talking about reviewing other pseudopotential choices in MP, eg some pseudopotentials we’re not used because of ghost states (perhaps Na? I forget), but these issues were later fixed in the newer 54 pseudopotentials that the MP SCAN Input Set uses. The SCAN Input Set presented an opportunity to cleanly make this change. However this was not pursued, I think more out of conservativeness than anything.\r\n\r\nAll this to say, I’m glad this change was made, but if I could offer a viewpoint to the MP team, it’s that a new data release to replace the Yb data should also be done promptly (although I realise this may not be possible!), as well as a louder mention of this change in the relevant places (eg docs changelog, or a banner on the linked docs page) might be a good idea too, to let people know this change is coming.",
"Just an FYI for everyone here that I am moving to re-calculate all the Yb compounds right now. The plan is to stop working on the current MP build to get these done and incorporated. ",
"> as well as a louder mention of this change in the relevant places (eg docs changelog, or a banner on the linked docs page) might be a good idea too, to let people know this change is coming.\r\n\r\nYes this is definitely planned! 👍 \r\n\r\n> new data release to replace the Yb data should also be done promptly (although I realise this may not be possible!)\r\n\r\nThis is also planned but the timeline is less firm.",
"Lol, simultaneous posts. 😄 \r\n\r\nI stand corrected. Timeline for updating Yb compounds is _very_ firm. 🚀 ",
"@mkhorton Any suggestions for this banner on the [PSP docs page](https://docs.materialsproject.org/methodology/materials-methodology/calculation-details/gga+u-calculations/pseudopotentials)?\r\n\r\n\r\n",
"Looks perfect :)",
"Perhaps additional information to add somewhere might simply be some screenshots or descriptions of the two relevant chemical systems to demonstrate the difference. It might help justify the change, rather than \"because we say so\", as well as point(s)-of-contact for who investigated the issue. I say this as someone who's wished this information was available with previous decisions, but where I was unable to track down additional context.",
"> ...well as point(s)-of-contact for who investigated the issue. I say this as someone who's wished this information was available with previous decisions, but where I was unable to track down additional context.\r\n\r\nDefinitely! That's the reason I tried to @-mention all people I know have knowledge of this matter in the original issue above. I made sure all places documenting this change link back to this issue so hopefully people in the future can follow the trail to determine who to contact with questions. What I wrote above is most of the context I have. Of course, others are welcome to add.\r\n\r\nAnother tidbit I learned later is that prompted by A-lab results, @mattmcdermott very recently tried to re-run a bunch of `Yb` compounds (< 10?) using `Yb` instead of `Yb_2`. All of them failed, corroborating the claim that the `Yb` PSP is not usable in high throughput.",
"@janosh yep, I ran 20ish compounds with the `Yb` pseudopotential that all failed (including Yb2O3, Yb, Yb2MoO6..) I am not a great VASP debugger, but I was usually getting `PotimErrorHandler` and `PositiveEnergyErrorHandler` in custodian. Eventually every job fizzled after reaching a maximum of 5 errors",
"Also I meant to send this earlier -- this is not the most rigorous comparison, but here is a look at the Yb-Mo-O phase diagram (GGA/GGA+U) before and after I recomputed the Yb entries with the `Yb_3` pseudopotential and applied previously fitted corrections (i.e., oxide, +U corrections). \r\n\r\nBig differences -- notably, the very common Yb2O3 moves to be stable after previously being >200 meV/atom above the hull. Also stabilizes two ternary phases and destabilizes YbMoO4 greatly\r\n\r\n\r\n\r\n\r\n",
"I don't know if I am experienced enough for this conversation, but I was able to get YbCl3 relaxation converged using `Yb_3` recently. But it is difficult to get YbCl2 converged and the formation energy is quite off from the experimental value. One possible reason our lab found might be the nonmagnetic state the system gets converged to but they should be converged to magnetic state. ",
"> I don't know if I am experienced enough for this conversation\r\n\r\nAny and all relevant anecdotes are welcome! The more data we have, the better our decisions."
] | 2023-05-02T18:16:29
| 2023-05-05T00:18:57
|
2023-05-02T18:49:16Z
|
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[The docs](https://docs.materialsproject.org/methodology/mof-methodology/calculation-parameters/psuedopotentials) are incorrect on what pseudo-potential the `EntrySet`s use for `Yb`. Docs say `Yb_3`, actual is `Yb_2`. Just to list a few:
https://github.com/materialsproject/pymatgen/blob/a7ee5adf02e0ac8c0b9e150d10f631bd61f6b5de/pymatgen/io/vasp/MPRelaxSet.yaml#L171
https://github.com/materialsproject/pymatgen/blob/a7ee5adf02e0ac8c0b9e150d10f631bd61f6b5de/pymatgen/io/vasp/MPSCANRelaxSet.yaml#L123
https://github.com/materialsproject/pymatgen/blob/a7ee5adf02e0ac8c0b9e150d10f631bd61f6b5de/pymatgen/io/vasp/MVLRelax52Set.yaml#L177
https://github.com/materialsproject/pymatgen/blob/a7ee5adf02e0ac8c0b9e150d10f631bd61f6b5de/pymatgen/io/vasp/MPAbsorptionSet.yaml#L113
The A-lab revealed that as a result of using `Yb_2` the energy on Yb compounds is off by a lot, resulting in supposedly stable things being unsynthesizable. While an unfortunate mistake, it's also great to see how experiment can help surface simulation errors. (@rekumar) (Although if tales are correct, @arosen93 originally brought this up with @mkhorton in Oct 2021?)
Planned solution is to update all input sets to actually use Yb_3. Why not `Yb` so as not to force an oxidation state? Apparently `Yb` has stability issues. Additional context in
- https://github.com/materialsproject/atomate2/pull/27#issuecomment-986306566
- https://www.vasp.at/forum/viewtopic.php?t=18367
@shyuep Any concerns on your end? We plan to highlight this change in the pymatgen release notes and in the next MP database release. Any additional venues?
Unfortunately, this comes too late for the large data set Google generated which used the current `MPRelaxSet` and `MPSCANRelaxSet` but better fix this now before another large effort gets this wrong.
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PR_kwDOACgets5PnInd
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Breaking: change `Yb` pseudo-potential on all VASP input sets from `Yb_2` to `Yb_3`
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[
"Should one mark this as a breaking change? It's a rather drastic change. ",
"Yes, this change will be highlighted in the next release notes. I'll also change the PR title to make this clearer.",
"I would suggest you document the change to Yb_3 in the input sets yaml themselves. E.g., `# May 2 2023: Changed to Yb_3 from Yb_2 as the latter gives incorrect thermodynamics for most systems with Yb3+`",
"@shyuep Excellent suggestion!"
] | 2023-05-02T18:24:12
| 2023-05-02T18:59:48
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2023-05-02T18:49:15Z
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MEMBER
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Closes #2968.
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I_kwDOACgets5lCEoV
| 2,970
|
Bug in `DictSet.kpoints` due to operator precedence
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[
"I agree. I did not write this though. I think the switch to KSPACING is relatively recent."
] | 2023-05-04T00:57:49
| 2023-05-06T14:40:43
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2023-05-06T14:40:43Z
|
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@shyuep I think there's a subtle operator precedence bug here:
https://github.com/materialsproject/pymatgen/blob/ed66c977d8c2c1168a9945d64f5d043d9263fc43/pymatgen/io/vasp/sets.py#L633-L638
`and` has higher precedence than `or` but unless I'm mistaken we actually want to evaluate the `or` first. The thing that throws me off is why this wasn't caught before.
```py
if (
self.user_incar_settings.get("KSPACING") or self._config_dict["INCAR"].get("KSPACING")
) and self.user_kpoints_settings == {}:
```
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`pytest.raises() as exc_info` has no `.exception`
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[] | 2023-05-04T01:01:17
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2023-05-06T14:40:43Z
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MEMBER
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We're misusing `pytest.raises()` in at least 4 places in 2 files. 2 Examples below where it should be
```diff
- str(context.exception)
+ str(context.value)
```
https://github.com/materialsproject/pymatgen/blob/ed66c977d8c2c1168a9945d64f5d043d9263fc43/pymatgen/io/vasp/tests/test_sets.py#L505-L516
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PR_kwDOACgets5Pufap
| 2,972
|
Revert to `Yb_2` on pre-`PBE_54` input sets
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[
"@jmmshn asked for a new release which I think we're ready for once this is merged."
] | 2023-05-04T01:11:33
| 2023-05-06T14:40:43
|
2023-05-06T14:40:42Z
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MEMBER
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Follow up to #2969.
Instead of changing from `Yb_2` to `Yb_3` everywhere, we issue a warning in pre-`PBE_54` input sets that `Yb_2` will give very bad results for most systems since Yb is usually Yb3+.
Reason: The better fix `Yb_3` only became available in the `PBE_54` set of PSPs so using it in pre-`PBE_54` input sets effectively means you can't run Yb compounds.
Closes #2970 , closes #2971.
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PR_kwDOACgets5P4S0V
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fix recursion error by adding copy and deepcopy dunder methods
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[] | 2023-05-05T17:03:29
| 2023-05-05T18:35:44
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2023-05-05T18:35:44Z
|
CONTRIBUTOR
|
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## Summary
Both copy and deepcopy are currently broken for the `InputSet` object. This PR implements dunder methods to fix both. There very well may be a more elegant solution but I couldn't find it!
- Feature 1: `__copy__` and `__deepcopy__` dunder methods
## Checklist
- [x] Doc strings have been added in 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 path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [x] Tests have been added for any new functionality or bug fixes.
- [x] All linting and tests pass.
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I_kwDOACgets5lPnvq
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|
INCAR setting error in atomate workflows
|
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[
"I think you'll have to provide more information to get useful answers. I'm converting this to a discussion since this doesn't sound like a code issue."
] | 2023-05-06T11:37:06
| 2023-05-06T17:26:10
|
2023-05-06T17:26:10Z
|
NONE
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https://github.com/materialsproject/pymatgen/blob/9c7d2bb6f8f0b21474ed39b0bb4c9dce772ac240/pymatgen/io/vasp/sets.py#L441
When I calculate a Si test by using a atomate workflow, the INCAR include MAGMOM label, and the second step calculation stop. How should I deal with this problem.
|
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PR_kwDOACgets5P61Lv
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Enable `flake8-pytest-style` via `ruff`
|
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[] | 2023-05-06T16:12:34
| 2023-05-06T17:01:48
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2023-05-06T17:01:47Z
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MEMBER
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Another small step in a larger overhaul of the testing side of `pymatgen`.
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PR_kwDOACgets5P7Nq0
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Enable all ruff pylint rules (excl. PLR)
|
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[] | 2023-05-06T23:13:40
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2023-05-06T23:54:17Z
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MEMBER
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7737862cf `ruff` select `PL` (general `pylint`), disable `PLR` (`pylint refactor`)
525fc2667 fix `PLR5501`: collapsible-else-if
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I_kwDOACgets5lV7GX
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Re-add support for the Mueller kpoint scheme
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"Yup it was removed because the server was far too fragile. Would be happy to have it back as an optional dependency."
] | 2023-05-08T13:20:13
| 2023-05-08T17:01:31
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In older versions of Pymatgen, there was a pymatgen.ext.jhu utility that would allow for generation of kpoints using the scheme from Mueller but it required access to a server (which is maybe why it was removed?).
As shown here
https://gitlab.com/muellergroup/k-pointGridGenerator there is a way to generate these kpoints without the server (but with an optional dependency). It would be a nice feature to add one day. Maybe if I discover some free time.......... logging the idea here anyway.
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PR_kwDOACgets5QBfq0
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Enable ruff rule sets ISC + ICN
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2023-05-08T19:08:40Z
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678dddc02 add ruff ICN001 (unconventional-import-alias)
2ad001e13 add ruff ISC (flake8-implicit-str-concat)
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Drop deprecated SubstrateAnalyzer + ZSLGenerator reexports
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2023-05-11T17:41:52Z
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f0f6087b3 breaking: remove deprecated re-export of SubstrateAnalyzer, ZSLGenerator from pymatgen/analysis/substrate_analyzer.py
16f6da354 drop custom `ArrayLike` fallback type, make `numpy.typing.ArrayLike` required
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`ruff` enable `flake8-pyi` + `flake8-ret`
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Fix for memory leak in pbc_shortest_vectors
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[
"Great. Thanks! I have a small request. Can you provide a simple benchmark of the difference in speed (if any) between old and new version? This is a rather core part of the code. I would want to make sure that the efficiency is not compromised.",
"I've never written a test for `cython` code. @stichri Is there a way we can ensure no regressions on mem leaks?",
"As request by @shyuep, I wrote [this very simple benchmark](https://github.com/materialsproject/pymatgen/files/11439571/benchmark.py.txt).\r\nThe idea is to assess the overall runtime impact, which I think will play out along two parameters: The relative amount of work done per call - either lots or little - and the applied periodic boundary conditions (PBC) - either in all directions or just in one direction. Generally, I'd expect the _highest impact_ from _avoided calls of `malloc`_ when doing _little work per call_ with _PBC in all directions_ and from _additional calls of `free`_ when doing _little work per call_ with _PBC in just one direction_.\r\nRunning the benchmark on my mobile AMD Ryzen 7 using **pymatgen v2023.5.8** in python 3.11 on Fedora38 in WSL2 running on Windows 11 results in:\r\n```\r\nPBC in ALL directions:\r\nfastest out of 10 runs with 100000 calls each, LITTLE WORK per call: 1.76117e+00s\r\nfastest out of 10 runs with 100 calls each, LOTS OF WORK per call: 3.22905e+00s\r\nPBC in ONE directions:\r\nfastest out of 10 runs with 100000 calls each, LITTLE WORK per call: 7.77626e-01s\r\nfastest out of 10 runs with 100 calls each, LOTS OF WORK per call: 6.76336e-01s\r\n```\r\nThe same benchmark on the same machine **with the modifications applied** results in:\r\n```\r\nPBC in ALL directions:\r\nfastest out of 10 runs with 100000 calls each, LITTLE WORK per call: 1.68359e+00s\r\nfastest out of 10 runs with 100 calls each, LOTS OF WORK per call: 3.28771e+00s\r\nPBC in ONE directions:\r\nfastest out of 10 runs with 100000 calls each, LITTLE WORK per call: 7.95001e-01s\r\nfastest out of 10 runs with 100 calls each, LOTS OF WORK per call: 7.19025e-01s\r\n```\r\nJudging from this very rough benchmarking, I would assess the _impact on runtimes_ to be _typically less than 10%_.\r\nMoreover, should that turn out to be an issue, I think this additional memory managment could be eliminated altogether when considering additional modifications; The PBC application is ultimately [controlled by a bool triplet in the passed lattice object](https://github.com/materialsproject/pymatgen/blob/c2f2d724c89fa8b73044824b2e4ae3c26938280f/pymatgen/util/coord_cython.pyx#L91), thus there should be just 8 different cases to which the `images_view` variable would be needed to be assigned to, [just as it currently is](https://github.com/materialsproject/pymatgen/blob/c2f2d724c89fa8b73044824b2e4ae3c26938280f/pymatgen/util/coord_cython.pyx#LL31C45-L31C45) for the special case of full PBCs. All the additional 7 cases could thus be hardcoded into constant module-level objects as well.\r\n\r\nRegarding additional tests for memory leaks within `cython` code as @janosh mentioned, unfortunately I wouldn't be aware of a particularly convenient way of doing it 'from the python side of things'.\r\nThat is, if I were to systematically check for these kind of errors, I would probably use (dynamical memory analysis tools like) [valgrind](https://valgrind.org/). After all, the CPython implementation is conveniently shipped with a [suppression file for false positives](https://github.com/python/cpython/blob/main/Misc/valgrind-python.supp) when running python. I guess it's always possible to script some tests that automatically do just that at the cost of pulling in potentially new dependencies like valgrind.",
"Thanks for the benchmark!",
"Thanks. Much appreciated!"
] | 2023-05-09T17:33:02
| 2023-05-10T14:20:48
|
2023-05-10T12:07:43Z
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CONTRIBUTOR
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## Summary
The `pbc_shortest_vectors` function leaks all memory allocated to store the fractional coordinates of surrounding periodic sites. As a result, memory consumption keeps creeping up when (heavily) calling the function, see [this memory profile](https://github.com/materialsproject/pymatgen/files/11433457/v2023.5.8.pdf) of a script of mine which made me aware of the problem. The suggested modifications completely eliminate the issue, [curtailing the memory consumption](https://github.com/materialsproject/pymatgen/files/11433643/fixed.pdf) of the same script.
With the suggested minimal modifications, additional memory is only allocated (and freed accordingly) when needed - that is, when periodic boundary conditions are applied selectively.
### Before
### After
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I_kwDOACgets5lsTzA
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CompleteCohp.cohp and CompleteCohp.icohp produce the same output
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[
"Totally forgot to tag @JaGeo :D ",
"Thanks for writing it down! I will work on a fix as soon as I get to it. I never use the average COHP/ICOHP. 😅 \r\n\r\n(@janosh , I am assigning myself)",
"Can be closed then, @janosh or @QuantumChemist ",
"@JaGeo Thanks. Btw, if you include \"closes #issue-number\" or \"fixes #issue-number\" in the PR description or any commit message, the issue will be auto-closed on merge.",
"@janosh Thanks and sorry!",
"@janosh I think I actually did this but it did not auto-close. Do you see what I did wrong?",
"I edited the PR description. 😄 ",
"Hey @YuanbinLiu it's fixed now :)",
"> I edited the PR description. 😄\r\n\r\n@janosh , 🙃 I see. ",
"> \r\n\r\nBrilliant! Thanks!"
] | 2023-05-11T15:58:25
| 2023-05-12T14:40:25
|
2023-05-12T14:10:17Z
|
CONTRIBUTOR
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When trying to access the cohp and the icohp feature of CompleteCohp for a COHPCAR.lobster file, one gets the same output. In the following minimal code, the sum is 0 (and also the individual entries for each energy point is 0).
## Minimal code to reproduce the issue
cohp_test = CompleteCohp.from_file(filename="path_to_files/COHPCAR.lobster", fmt = 'LOBSTER', structure_file="path_to_files/POSCAR")
cohp = cohp_test.cohp[Spin.up]
icohp = cohp_test.icohp[Spin.up]
print(sum(icohp-cohp))
|
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Fix average error
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[
"Thanks!! @JaGeo 😃 "
] | 2023-05-12T09:22:35
| 2023-05-12T14:20:11
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2023-05-12T13:40:45Z
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MEMBER
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## Summary
Closes https://github.com/materialsproject/pymatgen/issues/2985. There was a simple typo. As I usually never use the average cohp, it never even occurred to me to test it. I adapted all tests and included a test to now also test the average cohp.
I also gzipped some `COHPCARs` to start reducing test file size for the `lobster/cohp` modules.
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Doc strings
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2023-05-13T16:18:10Z
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563ffb90d improve `Transformation` `return_ranked_list` kwarg doc string
8fded9b45 fix all `ruff`-detected doc string errors in `pymatgen/core`
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Symmetry Reduction in `pymatgen.io.vasp.optics`
|
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[
"Not an expert on this but maybe @jmmshn can comment.",
"That sounds like it would work. TBH I made this with defects in mind so the K-point problem was not super bad for me.\r\nI never actually used pymatgen's generated kpoints in calculations so it might work.\r\n\r\nAlthough one problem to be aware of is that I noticed that the pymatgen generated kpoints produced density of states that are not normalized properly (saw this when I ran non-scf uniform calculations) so I would watch for that very carefully to make sure the final results for the optics spectra have the correct normalization.",
"It's not clear to me why you need the symmetry operations? Can't you just parse the k-points multiplicities from the vasprun? Then you can just use the multiplicities in your integration. All the information should already be available.",
"Sorry for the late reply I was on a lengthy family leave and had Covid for like 2 weeks right when I came back. All better now!\r\n\r\n@utf, agreed but the actual problem with using ISYM = 0 is that VASP will then choose to do some aggressive reduction in how many matrix elements are calculated in the WAVEDER (I think I will only do 0 -> VBM for one index). Then you lose the ability to tweak the Fermi-level in post-processing which was the main focus for me at the time. I poked around the VASP source code quite a bit and couldn't see an easy way of untangling this."
] | 2023-05-14T09:59:23
| 2023-07-11T21:25:16
|
CONTRIBUTOR
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Hi!
Firstly, thanks to the developers for the recent addition of the `pymatgen.io.vasp.optics` module, this is very very useful! 🙌
For large k-point meshes or large numbers of electronic bands, these functions can become slow on a desktop computer (e.g. taking ~7 minutes for a 8x8x8 kpoint mesh for a CdTe primitive cell, with 24 bands), and possibly intractable at denser kpoint meshes where spectral convergence is reached.
A primary origin of this is the fact that there is no symmetry reduction of the kpoint set, so the number of kpoints becomes very large as the k-point density is increased. In the `DielectricFunctionCalculator` class docstring, it states:
```
Currently, this Calculator only works for ``ISYM=0`` calculations since we cannot gauranttee that our
externally defined symmetry operations are the same as VASP's. This can be fixed by printing the
symmetry operators into the vasprun.xml file. If this happens in future versions of VASP,
we can dramatically speed up the calculations here by considering only the irreducible kpoints.
```
I understand the issue that VASP's symmetry operations aren't printed to the `vasprun.xml`, so the calculations must be run using `ISYM = 0` (without symmetry reduction). However, would it still be possible and useful to add an optional parameter to use `pymatgen`'s symmetry analysis tools to perform symmetry reduction of the kpoint set for _parsing_?
i..e. taking the non-symmetry-reduced VASP outputs, but then reducing to only the irreducible kpoints with appropriate kpoint weights, and then perform the post-processing (which should be greatly sped up by this)?
I believe all the functions for this are available in `pymatgen` (I'm just not totally familiar with them). This would be quite a useful addition for our workflow. Either way, it's a very useful module! 😃
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PR_kwDOACgets5Qc70L
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Suspected Typo Fix in `pymatgen.io.vasp.optics`
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[
"Thanks for the fix! 👍 This sounds sensible. We should definitely have tests for these functions."
] | 2023-05-14T10:39:43
| 2023-05-14T15:15:39
|
2023-05-14T15:15:39Z
|
CONTRIBUTOR
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Hi!
Firstly, thanks to the developers for the recent addition of the `pymatgen.io.vasp.optics` module, it's been very very useful! 🙌
This is just a small fix for a suspected typo in handling `ismear` in the `delta_func()` and `step_func()` functions. `ISMEAR` is zero for Gaussian smearing, and indeed in the docstrings for `get_epsilon()` it states: `ismear: Smearing method (only has 0:gaussian, >0:Methfessel-Paxton)`. However, in the current version of the code:
```python
def delta_func(x, ismear):
"""Replication of VASP's delta function"""
if ismear < -1:
raise ValueError("Delta function not implemented for ismear < -1")
if ismear == -1:
return step_func(x, -1) * (1 - step_func(x, -1))
if ismear < 0:
return np.exp(-(x * x)) / np.sqrt(np.pi)
return delta_methfessel_paxton(x, ismear)
```
`ismear = 0` ends up returning the Methfessel-Paxton smearing (`delta_methfessel_paxton`), however the function under `if ismear < 0` is the Gaussian smearing. `ismear` should be an integer anyway, so having `ismear < -1` raise an error and `ismear == -1` return something else, it means that the `ismear < 0` line is always skipped. This is also the case for the `step_func()` function.
I believe this is likely a small typo, and should instead by `if ismear == 0:`. I have changed it to this in this PR, and tests are passing.
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PR_kwDOACgets5QddnI
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Enable ruff doc rules in CI
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[] | 2023-05-14T20:55:24
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2023-05-14T21:30:56Z
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MEMBER
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1273014de ignore some `ruff` doc string errors and fix all remaining
a6dd53e72 `ruff` enable doc rules in pre-commit
c349a806c fix `mypy` error
dea2aa043 2nd try fix `mypy`
d3e4d2b57 prefix unused func args with underscore
f7b4a5006 `ruff` enable `flynt` rules
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Add type hints for `pymatgen.io.ase` module
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[
"Welp, sorry @janosh. I thought this would be a trivial add. But I'm not sure how to make the `mypy` overlord happy with this...",
"`mypy` can be a pain. The problem you ran into is that untyped functions are not type-checked. As soon as you add types to a function, it can surface errors that were already lurking in the code.",
"Oh and I think here you meant\r\n\r\n```diff\r\n- cls: Structure = None\r\n+ cls: type[Structure] = None\r\n```",
"Thanks!! "
] | 2023-05-16T04:38:12
| 2023-05-16T14:22:18
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2023-05-16T14:16:46Z
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MEMBER
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Pretty self-explanatory. I added type hints to `pymatgen.io.ase`.
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PR_kwDOACgets5Qn_IK
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Hide all type-hint-only imports behind `if TYPE_CHECKING`
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[
"Ci failure is due to flaky test:\r\n\r\n```py\r\n @unittest.skipIf(\r\n not SETTINGS.get(\"PMG_MAPI_KEY\") or website_down,\r\n \"PMG_MAPI_KEY environment variable not set or MP is down.\",\r\n )\r\n def test_get_snls_mp(self):\r\n with OptimadeRester(\"mp\") as optimade:\r\n structs = optimade.get_snls(elements=[\"Ga\", \"N\"], nelements=2)\r\n \r\n with OptimadeRester(\"mp\") as optimade:\r\n response_field_structs_single = optimade.get_snls(\r\n elements=[\"Ga\", \"N\"], nelements=2, additional_response_fields=\"nsites\"\r\n )\r\n response_field_structs_set = optimade.get_snls(\r\n elements=[\"Ga\", \"N\"], nelements=2, additional_response_fields={\"nsites\", \"nelements\"}\r\n )\r\n if (\"mp\" in response_field_structs_single) and (\"mp\" in response_field_structs_set):\r\n> assert len(structs[\"mp\"]) == len(response_field_structs_single[\"mp\"])\r\nE KeyError: 'mp'\r\n\r\npymatgen/ext/tests/test_optimade.py:55: KeyError\r\n```"
] | 2023-05-16T14:52:41
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4 main motivations for this change:
1. reduces chance of circular imports
2. can help contributors run tests without installing extra deps like `pymatgen.analysis.defects` if they were previously in a test's import stack but only used for type hints
3. helps with readability by clearly separating type-only imports
4. can decrease startup time since `TYPE_CHECKING=False` at run time means some modules won't have to be imported. somewhat negated by the annoyingly long import time of the std lib `typing` module itself but that has been steadily coming down with newer Python versions.
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Orbital-resolved icohplist
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"@JaGeo We're trying to move away from type hint comments:\r\n\r\n```diff\r\n- list_orb_icohp = [] # type: List[dict]\r\n+ list_orb_icohp: list[dict] = []\r\n```",
"Thanks! Will change this!",
"Locally, mypy is finally passing... ",
"Seems like most of the tests are passing now. macos tests haven't started yet.",
"MacOS tests are still queued. I will contiue on another day if something fails.",
"@janosh Finally, all tests are passing 😃",
"Thanks @JaGeo! 👍 "
] | 2023-05-16T21:23:26
| 2023-05-17T08:23:17
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2023-05-17T04:59:33Z
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## Summary
@janosh, I have added support for orbital-resolved icohplists and included tests.
(@naik-aakash , FYI. I think it should be very useful for some of our currenct projects)
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Compress all test files
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"I'm in favor of this! If someone is going to try this, I would also suggest doing some light reorganization of the test files so that it's clearer which ones go with which parts of the code. \r\n\r\nFor example, move a lot of the test files in the root directory that are associated with VASP IO into a `vasp/` subdirectory, etc. Also I believe there are some old Q-Chem test files under `qchem/` but the more relevant ones are under `molecules/new_qchem_files`. Perhaps these can be consolidated.",
"In PR #3146, I added a new `OSZCIAR_MD` to the `test_files`. @janosh you may want to include that into the compiled test files? But since now `Oszicar` can read fields dynamically in principle we can shrink two OSZICAR test files into one? I feel like there are many other duplicate test files can be shrunk into one too",
"> I feel like there are many other duplicate test files can be shrunk into one too\r\n\r\nI'm sure there are. Would be some effort to identify them but PRs welcome!\r\n\r\n",
"Can we close this now or there is more test files to be compressed or relocated that I could help with? @janosh \r\n\r\nI guess it would be good to collect all `cif` (not sure about `json`) files together and I might do this in the near future 😃 \r\n\r\nWhat about the `compress-test-files` branch?",
"i think there are a lot of uncompressed output files left. try running `compress_test_files.py` from https://github.com/materialsproject/pymatgen/pull/3132 and it should show which ones i mean.\r\n\r\n`compress-test-files` branch is super outdated but might help to keep it around for reference until we're all done"
] | 2023-05-17T16:40:04
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See https://github.com/materialsproject/foundation/pull/3#issuecomment-1544290657 and surrounding discussion for motivation.
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Re-export `SiteCollection` + `DummySpecies` from `pymatgen.core`
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ff12ac5a4 rename dict vars `d` -> `dct`
502158daa re-export `DummySpecie` + `SiteCollection` from `pymatgen.core`
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Species should parse oxi state from strings like "O2-"
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[] | 2023-05-18T00:05:57
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2023-05-18T03:32:12Z
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MEMBER
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```py
from pymatgen.core import Species
Species("O2-")
>>> ValueError: 'O2-' is not a valid Element
```
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PR_kwDOACgets5Qw3Bk
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|
`Species` parse oxi state from symbol str
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2023-05-18T03:32:10Z
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MEMBER
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Closes #2997.
```py
Species("O-").oxi_state
>>> -1
Species("Fe2+").oxi_state
>>> 2
```
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Merge `ElementBase` into `Element`?
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[
"Why was `ElementBase` created to start with, presumably for good reason? I vaguely remember this, can try and find the PR. ",
"Here's the PR: https://github.com/materialsproject/pymatgen/pull/2005 by @jmmshn.\r\n\r\nIt also lists subclasses as the reason for creating `ElementBase`.",
"I see the mention for API use. Perhaps it was used to define a class for intercalant elements? ",
"I think it was to get nested as_dict / from_dict to work properly. So the problem was that all the classes in emmet that had these classes required very custom construction and I wanted to have a a definition of these classes that behaved more like dataclasses so serialization was less troublesome. There were many times where the objects serialized only when they were top level.",
"@jmmshn Thanks for the context! I'll add this to the `ElementBase` doc str."
] | 2023-05-18T00:51:03
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2023-05-18T15:39:30Z
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MEMBER
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@shyuep Should we merge `ElementBase` into `Element`? It says `ElementBase` has no enum values so it can be subclassed but it isn't actually subclassed anywhere in `pymatgen`. Seems cleaner to only have an `Element` class.
https://github.com/materialsproject/pymatgen/blob/3d4d160941edc47d26b21457c792187256f55886/pymatgen/core/periodic_table.py#L30-L33
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Add LightStructureEnvironments.from_structure_environments() fallback value if `ce_and_neighbors` is None
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[] | 2023-05-20T15:05:36
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MEMBER
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Closes #2756.
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Support writing structures to compressed JSON (.json.gz .json.bz2 .json.xz .json.lzma)
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[
"Minimal example\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nFeO = Structure(\r\n lattice=Lattice.cubic(5),\r\n species=(\"Fe\", \"O\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\n\r\nstructure.to(\"FeO.json.gz\")\r\nstructure.to(\"FeO.json.bz2\")\r\n```",
"@ml-evs Could you have a quick look at [0357d74](https://github.com/materialsproject/pymatgen/pull/3003/commits/0357d74c5780adac3d9d4c2c293e43cc84760fd1)? The Optimade test is still flaky.",
"> @ml-evs Could you have a quick look at [0357d74](https://github.com/materialsproject/pymatgen/pull/3003/commits/0357d74c5780adac3d9d4c2c293e43cc84760fd1)? The Optimade test is still flaky.\r\n\r\nTest changes look fine, from what I can see of the failures, maybe its some interaction where each job in the build matrix is hitting MP with the same query at the same time with the same IP and one is timing out? Could just boost `OptimadeRester(\"mp\", timeout=16)` or something for the tests. I think a timeout of 5 (the current default) is equivalent to one TCP packet retry (which defaults to 3 seconds, see https://docs.python-requests.org/en/latest/user/advanced/#timeouts).\r\n\r\nEDIT: Actually this probably isn't the case as the case as you're using pytest split etc so the build is quite staggered. ",
"@ml-evs Thanks for the quick reply! If the flakiness persists, I'll try increasing the timeout."
] | 2023-05-20T15:20:42
| 2023-05-20T17:16:26
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2023-05-20T16:01:43Z
|
MEMBER
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ffae4ea4e support writing structures to compressed JSON files
ba9918395 check structure equality writing and reading from .json.gz .json.bz2 .json.xz .json.lzma
Related: #2994 helps with reducing test file sizes
|
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PR_kwDOACgets5Q9RqI
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Lookup `MPRester` API key in settings if `None` provided as arg
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"For the new Rester, reading the API key from `.pmgrc.yaml` or env variable required passing no args, i.e.\r\n\r\n```diff\r\n- MPRester(None)\r\n+ MPRester()\r\n```\r\n\r\nThanks for making the upper case work as well @ml-evs!"
] | 2023-05-21T14:56:19
| 2023-05-22T10:50:47
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2023-05-21T22:42:26Z
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CONTRIBUTOR
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## Summary
Both the new and legacy versions of `MPRester` accepted `api_key=None` to be passed as an argument, triggering a fallback to the settings version of the key. The new behavior of the dynamic `MPRester` is to attempt to use the `None` value directly, i.e., without checking for an externally configured value.
This PR simply adjusts the behavior so that `api_key=None` will still trigger a settings lookup.
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Update `.pytest-split-durations`
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5458e99bd partially update .pytest-split-durations
f9edf06a1 skip StructureTest.test_relax() if tensorflow missing
0948d7062 MoleculeGraph.find_rings() only sort cycle once
ba2d98c69 drop -x (exit on error) from pytest addopts
b48009e2a rerun pytest --store-durations --durations-path test_files/.pytest-split-durations without -x flag
f7338d2b6 fix OptimadeTest.test_get_snls_mp() by making query stricter to reduce returned payload
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Spglib unable to obtain structure space group info, during magnetic structure enumeration
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"@mkhorton, @guymoore13 have you guys seen this error before, and know a potential solution?",
"First thing I would check is your `spglib` version. What version are you running? This recently saw a 2.0 release and had a few bugs which were fixed with the latest version. ",
"I'm using spglib 2.0.2",
"For additional context, @kamronald and I sat down and checked all the obvious things. It's not environment dependent and the error occurs using both the latest v1 and v2 release of spglib. On the other hand, calling `struc.get_space_group_info()` directly on the `Structure` loaded from @kamronald's `CONTCAR` works and gives expected space group 227. So must be due to sth happening inside `MagneticStructureEnumerator` where I'm out of my depth.",
"Here's a complete repro:\r\n\r\n```py\r\nimport os\r\n\r\nfrom pymatgen.analysis.magnetism import MagneticStructureEnumerator\r\nfrom pymatgen.core import Structure\r\n\r\ndirname = os.path.dirname(__file__)\r\nstruct = Structure.from_file(f\"{dirname}/LiMnO2-CONTCAR\")\r\n\r\nstruct.get_space_group_info() # works\r\n\r\nmag_enum = MagneticStructureEnumerator(\r\n structure=struct,\r\n default_magmoms={\"Li\": 0, \"Mn\": 4, \"O\": 0},\r\n strategies=(\"ferromagnetic\", \"antiferromagnetic\"),\r\n truncate_by_symmetry=True,\r\n transformation_kwargs={\"min_cell_size\": 1, \"max_cell_size\": 1},\r\n)\r\n\r\n```\r\n\r\nNone of the `MagneticStructureEnumerator` kwargs affect the error.",
"If I remember correctly, I've had similar issues with spglib a while back, which I believe that Matt resolved.\r\n\r\nI can take a look at the issue later today, and/or you're welcome to stop by my cubicle if that's easier! Thank you for bringing this to our attention. ",
"In my local build, I encounter the error `ValueError: Unable to enumerate`. Is this the same error thrown for you both?",
"@kamronald stopped by, and we resolved the issue - at least on my machine!\r\n\r\nHe identified that `enumlib` was the source of the error (not the interface to `spglib`), so I updated and re-built the `enum.x` and `makestr.x` executables. Afterwards `MagneticStructureEnumerator` worked for me.\r\n\r\n@janosh, what do you think would be the best way to either (a) make this more clear to users, or (b) update the Python dependencies? I mention (b) because it appears that `enumlib` can be installed via conda, which may be a new feature.",
"@guymoore13 That's great!\r\n\r\nWhat exactly solved the error? Updating to a newer version of `enumlib`? If so, ideally `pymatgen` would check the version and prompt users to update if outdated.",
"@janosh Yes, I simply pulled the latest `enumlib`, and then built the corresponding fortran executables. I'm not sure if it's possible to identify the `enumlib` version from the executable(s) alone, which is why I suggested the conda install. However, I have not tried installing/building `enumlib` this way yet. ",
"I just tried installing enumlib using conda, but it\nEnumerateStructureTransformation throws the that Guy saw “ValueError:\nUnable to enumerate”. Working on installing enumlib manually right now.\n\nOn Thu, May 25, 2023 at 1:43 PM Guy Moore ***@***.***> wrote:\n\n> @janosh <https://github.com/janosh> Yes, I simply pulled the latest\n> enumlib, and then built the corresponding fortran executables. I'm not\n> sure if it's possible to identify the enumlib version from the\n> executable(s) alone, which is why I suggested the conda install. However, I\n> have not tried installing/building enumlib this way yet.\n>\n> —\n> Reply to this email directly, view it on GitHub\n> <https://github.com/materialsproject/pymatgen/issues/3006#issuecomment-1563483910>,\n> or unsubscribe\n> <https://github.com/notifications/unsubscribe-auth/AISIE7HX2EBDEYPI3FQKONTXH676FANCNFSM6AAAAAAYLDY6SE>\n> .\n> You are receiving this because you were mentioned.Message ID:\n> ***@***.***>\n>\n-- \nRonald Kam\nGraduate Student Researcher | Ceder Group\nDept. of Materials Science and Engineering\nUniversity of California, Berkeley\n",
"@kamronald You may want to check whether or not you're calling the correct executables, i.e. from a previously compiled enumlib vs. the conda package.",
"Ah, from the enumlib [README](https://github.com/msg-byu/enumlib/blob/main/README.md) it appears that their conda install only works for OSX and Linux, so it may be a safer bet to simply update the error thrown during calls to `enumlib` from `EnumerateStructureTransformation`, e.g. something like: \"Error running enumlib executable. Please make sure that enum.x and makestr.x executables are up-to-date.\" ?",
"Cool, [looks like](https://github.com/msg-byu/enumlib/issues/107) the `conda` release was prompted by @shyamd no less. 😄 ",
"Thanks all for debugging. Yes, I think the version on conda is quite old. I’ve always built from source myself (luckily this is fairly straight forward).\r\n\r\nI also briefly maintained a homebrew formula to install: https://github.com/mkhorton/homebrew-matsci/blob/master/Formula/enumlib.rb However this too would need updating.",
"> it may be a safer bet to simply update the error thrown during calls to `enumlib` from `EnumerateStructureTransformation`, e.g. something like: \"Error running enumlib executable. Please make sure that enum.x and makestr.x executables are up-to-date.\" ?\r\n\r\nHappy to take a PR for this!",
"@janosh, yes this was by no means intended as a request! \r\n\r\nFYI, it appears that @kamronald is still encountering issues besides the enumlib issue that we resolved.",
"@kamronald @janosh @guymoore13 Funny enough, I just ran into the same error originally posted by Ronald. I had installed `enumlib` through conda. However, compiling `enumlib` from scratch did not fix the problem.\r\n\r\nSo I did some experimenting with different pymatgen versions and was able to get rid of the error by downgrading to `pymatgen==2022.11.1`. Note that pymatgen v2022.11.7 does **not** work, so that might narrow down what is causing the issue.\r\n\r\nNote that if you try this yourself you will also have to downgrade to `numpy==1.19.5` due to an error about `np.int` being deprecated in 1.20 onwards. (You might also have to downgrade other things that require numpy>=1.20 like matplotlib).",
"@mattmcdermott Thank you for this information, I suspected as much. @kamronald is having issues with the ground-state enumeration with the latest `pymatgen`. It works for me, but I've been sticking with `pymatgen==2022.0.17` and `numpy==1.21.4`!",
"Thanks all for the ideas! So far @mattmcdermott 's method of using pymatgen v2022.11.7 is able to remove all the errors raised. However the enumerated structures do not match the original one, and do not seem very physical at all. I have attached them below. I'll look into it more but it's perhaps an issue with finding the primitive cell, which is performed during the enumeration (pymatgen.analysis.magnetism.analyzer.MagneticStructureEnumerator._generate_ordered_structures)\r\n[mag_enum.zip](https://github.com/materialsproject/pymatgen/files/11602211/mag_enum.zip)\r\n",
"I think I *finally* figured this one out. The enumerated structures produced within `MagneticStructureEnumerator` contain only spins on SOME sites (i.e., the magnetic species). See example, which I dumped within the method:\r\n\r\n```\r\nStructure Summary\r\nLattice\r\n abc : 6.467801905019046 9.83025604876038 6.60018016898948\r\n angles : 81.6316987446084 105.45156612496812 102.22794899018017\r\n volume : 393.5240108113061\r\n A : 5.647798 3.151958 0.0\r\n B : -5.647798 5.847555 5.526519\r\n C : 0.0 -3.6083190000000003 5.526519\r\n pbc : True True True\r\nPeriodicSite: V,spin=5 (-1.1445, 5.1737, 4.1449) [0.4730, 0.6757, 0.0743]\r\nPeriodicSite: V,spin=-5 (4.5033, 2.0217, 4.1449) [0.9730, 0.1757, 0.5743]\r\nPeriodicSite: V,spin=-5 (1.1445, 0.2175, 6.9081) [0.5270, 0.3243, 0.9257]\r\nPeriodicSite: V,spin=5 (-4.5033, 3.3695, 6.9081) [0.0270, 0.8243, 0.4257]\r\nPeriodicSite: Bi (-4.4548, 1.5653, 9.6714) [0.0334, 0.8222, 0.9278]\r\nPeriodicSite: Bi (1.1930, 2.0217, 4.1449) [0.5334, 0.3222, 0.4278]\r\nPeriodicSite: Bi (4.4548, 3.8259, 1.3816) [0.9666, 0.1778, 0.0722]\r\nPeriodicSite: Bi (-1.1930, 3.3695, 6.9081) [0.4666, 0.6778, 0.5722]\r\nPeriodicSite: O (0.2406, 1.6711, 6.3422) [0.4929, 0.4503, 0.6973]\r\nPeriodicSite: O (0.2406, 7.9750, 6.3422) [0.9929, 0.9503, 0.1973]\r\nPeriodicSite: O (0.2406, 2.3723, 1.9476) [0.3210, 0.2784, 0.0740]\r\nPeriodicSite: O (0.2406, 5.0679, 7.4741) [0.8210, 0.7784, 0.5740]\r\nPeriodicSite: O (-0.2406, 3.7201, 4.7109) [0.5071, 0.5497, 0.3027]\r\nPeriodicSite: O (-0.2406, -2.5839, 4.7109) [0.0071, 0.0497, 0.8027]\r\nPeriodicSite: O (-0.2406, 3.0189, 9.1054) [0.6790, 0.7216, 0.9260]\r\nPeriodicSite: O (-0.2406, 0.3233, 3.5789) [0.1790, 0.2216, 0.4260]\r\nPeriodicSite: O (2.1649, -0.1190, 5.5923) [0.5677, 0.1843, 0.8276]\r\nPeriodicSite: O (-3.4829, 3.0330, 5.5923) [0.0677, 0.6843, 0.3276]\r\nPeriodicSite: O (2.1649, 4.1624, 2.6975) [0.7573, 0.3740, 0.1141]\r\nPeriodicSite: O (-3.4829, 3.7060, 8.2240) [0.2573, 0.8740, 0.6141]\r\nPeriodicSite: O (-2.1649, 5.5102, 5.4608) [0.4323, 0.8157, 0.1724]\r\nPeriodicSite: O (3.4829, 2.3582, 5.4608) [0.9323, 0.3157, 0.6724]\r\nPeriodicSite: O (-2.1649, 1.2288, 8.3555) [0.2427, 0.6260, 0.8859]\r\nPeriodicSite: O (3.4829, 1.6852, 2.8290) [0.7427, 0.1260, 0.3859]\r\n```\r\n\r\nWith @lbluque's PR #2727 in November (i.e., pymatgen 2022.11.7), this means that `SpaceGroupAnalyzer` no longer assumes a default magmom of 0 on the unlabeled sites. So a smaller list of magmoms `[5,-5,-5,5]` is being passed to `spglib` and that is causing it to break and return nothing, making `SpaceGroupAnalyzer._space_group_data` empty.\r\n\r\nI fixed this locally by reverting the changes in this commit: https://github.com/materialsproject/pymatgen/pull/2727/commits/d39aa9fa3fab8a261c18bfc738b1cfe94cc0ccae\r\n\r\nSince I don't really understand the implications or why this was originally changed, maybe @lbluque @mkhorton or @janosh can comment on what we should do here?",
"Ah, that explains it. I apologise because I was aware of the issue of untagged (implicit zero) spins, because this can have other consequences too: for example, incorrect (undesired) orderings if, say, a VASP input set assumes a non-zero magmom if not otherwise specified. I did not anticipate the connection to SpacegroupAnalyzer.\r\n\r\nThe good news, I hope, is that this is an easy fix! We remove the implicit zero spins and make sure they’re explicitly specified instead.\r\n\r\nI think the original thinking behind not specifying an explicit zero is that the fallback default magmom (0.6) would not be used for other sites, which I originally thought was set for stability reasons, but having had more experience here I think the correct default/fallback magmom could probably safely be exactly 0 instead. ",
"I updated to remove implicit zero spins in #2727 following the conversation in #2725 about (breaking) changes in spglib > 2.0. [also this comment](https://github.com/spglib/spglib/issues/150#issuecomment-1180158502).\r\n\r\nIt seems now the solution is to handle cases where we need implicit zero magmoms to be set explicitly to zero (this issue), and cases where we actually do not want them at all to only obtain unique (ignoring time reversal) symmetry operations (issue #2725).\r\n\r\nI had originally suggested including a `unique` or equivalent keyword in `SpacegroupAnalyzer.get_symmetry_operations`, but perhaps can also set explicit zero spin if any site has a set spin value.",
"(also apologies that this has caused such a long-running detective effort!)",
"> (also apologies that this has caused such a long-running detective effort!)\r\n\r\nSuch is the nature of large code bases. They often involve a bit of whack-a-mole. 🐰 😄 ",
"> It seems now the solution is to handle cases where we need implicit zero magmoms to be set explicitly to zero (this issue), and cases where we actually do not want them at all to only obtain unique (ignoring time reversal) symmetry operations (issue #2725).\r\n\r\nThis context helps a ton. Thanks @lbluque.\r\n\r\n> perhaps can also set explicit zero spin if any site has a set spin value.\r\n\r\nI like this idea for the fix; seems very logical to me!\r\n\r\n> (also apologies that this has caused such a long-running detective effort!)\r\n\r\nDon't worry, it actually wasn't so bad. The hardest part was the lack of error message provided by the `spglib` call!",
"Does this fix make sense to you? https://github.com/mattmcdermott/pymatgen/commit/1e303a384940adc2f3975fa3f1daf6a8be397c1a ",
"@mattmcdermott Yes this makes sense! And thanks to @lbluque and @mkhorton for clarifying those earlier changes to SpacegroupAnalyzer!",
"I have tried implementing @mattmcdermott's changes, and now can make a MagneticStructureEnumerator instance without any raised errors! \r\n> However the enumerated structures do not match the original one, and do not seem very physical at all.\r\n\r\nHowever, the other issue that I brought up earlier about the enumerated structures being different from the original structure and being highly unphysical (ie O-O bonds being 0.3 A) still persists. :( This is from using the latest pymatgen version 2023.5.31, spglib 2.0.2, and enumlib 2.0.6. I have tried this with a different structure (attached below) and the issue remains. \r\nTo reproduce this:\r\n`struc = Structure.from_file('limno2_ortho_mp_18767.cif')`\r\n`mag_enum = MagneticStructureEnumerator(structure=struc, default_magmoms={'Li': 0, 'Mn': 4, 'O': 0}, strategies=['ferromagnetic', 'antiferromagnetic'])`\r\n\r\n\r\n[limno2_ortho_mp_18767.cif.zip](https://github.com/materialsproject/pymatgen/files/11657578/limno2_ortho_mp_18767.cif.zip)\r\n\r\n",
"@kamronald Oh yeah that looks pretty bad. There is definitely more to this bug than just what I fixed.\r\n"
] | 2023-05-23T00:27:18
| 2023-06-13T22:53:23
|
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When making an instance of MagneticStructureEnumerator, there is an error with the SpacegroupAnalyzer in determining space group number of structures enumerated using EnumerateStructureTransformation. I used the following code. Also attached are the screenshot with the errors and the CONTCAR used to generate magnetic orderings.
```
from pymatgen.core import Structure
from pymatgen.analysis.magnetism import MagneticStructureEnumerator
struc = Structure.from_file('CONTCAR')
mag_enum = MagneticStructureEnumerator(structure=struc, default_magmoms={'Li': 0, 'Mn': 4, 'O': 0}, strategies=('ferromagnetic', 'antiferromagnetic'),
truncate_by_symmetry=True, transformation_kwargs={'min_cell_size': 1, 'max_cell_size': 1})
```
[limno2_contcar.zip](https://github.com/materialsproject/pymatgen/files/11537970/limno2_contcar.zip)
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Bump requests from 2.28.1 to 2.31.0
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-05-23T05:15:49
| 2023-05-23T17:43:23
|
2023-05-23T17:43:12Z
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Bumps [requests](https://github.com/psf/requests) from 2.28.1 to 2.31.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/psf/requests/releases">requests's releases</a>.</em></p>
<blockquote>
<h2>v2.31.0</h2>
<h2>2.31.0 (2023-05-22)</h2>
<p><strong>Security</strong></p>
<ul>
<li>
<p>Versions of Requests between v2.3.0 and v2.30.0 are vulnerable to potential
forwarding of <code>Proxy-Authorization</code> headers to destination servers when
following HTTPS redirects.</p>
<p>When proxies are defined with user info (<a href="https://user:pass@proxy:8080">https://user:pass@proxy:8080</a>), Requests
will construct a <code>Proxy-Authorization</code> header that is attached to the request to
authenticate with the proxy.</p>
<p>In cases where Requests receives a redirect response, it previously reattached
the <code>Proxy-Authorization</code> header incorrectly, resulting in the value being
sent through the tunneled connection to the destination server. Users who rely on
defining their proxy credentials in the URL are <em>strongly</em> encouraged to upgrade
to Requests 2.31.0+ to prevent unintentional leakage and rotate their proxy
credentials once the change has been fully deployed.</p>
<p>Users who do not use a proxy or do not supply their proxy credentials through
the user information portion of their proxy URL are not subject to this
vulnerability.</p>
<p>Full details can be read in our <a href="https://github.com/psf/requests/security/advisories/GHSA-j8r2-6x86-q33q">Github Security Advisory</a>
and <a href="https://nvd.nist.gov/vuln/detail/CVE-2023-32681">CVE-2023-32681</a>.</p>
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<h2>v2.30.0</h2>
<h2>2.30.0 (2023-05-03)</h2>
<p><strong>Dependencies</strong></p>
<ul>
<li>
<p>⚠️ Added support for urllib3 2.0. ⚠️</p>
<p>This may contain minor breaking changes so we advise careful testing and
reviewing <a href="https://urllib3.readthedocs.io/en/latest/v2-migration-guide.html">https://urllib3.readthedocs.io/en/latest/v2-migration-guide.html</a>
prior to upgrading.</p>
<p>Users who wish to stay on urllib3 1.x can pin to <code>urllib3<2</code>.</p>
</li>
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<h2>v2.29.0</h2>
<h2>2.29.0 (2023-04-26)</h2>
<p><strong>Improvements</strong></p>
<ul>
<li>Requests now defers chunked requests to the urllib3 implementation to improve
standardization. (<a href="https://redirect.github.com/psf/requests/issues/6226">#6226</a>)</li>
<li>Requests relaxes header component requirements to support bytes/str subclasses. (<a href="https://redirect.github.com/psf/requests/issues/6356">#6356</a>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/psf/requests/blob/main/HISTORY.md">requests's changelog</a>.</em></p>
<blockquote>
<h2>2.31.0 (2023-05-22)</h2>
<p><strong>Security</strong></p>
<ul>
<li>
<p>Versions of Requests between v2.3.0 and v2.30.0 are vulnerable to potential
forwarding of <code>Proxy-Authorization</code> headers to destination servers when
following HTTPS redirects.</p>
<p>When proxies are defined with user info (<a href="https://user:pass@proxy:8080">https://user:pass@proxy:8080</a>), Requests
will construct a <code>Proxy-Authorization</code> header that is attached to the request to
authenticate with the proxy.</p>
<p>In cases where Requests receives a redirect response, it previously reattached
the <code>Proxy-Authorization</code> header incorrectly, resulting in the value being
sent through the tunneled connection to the destination server. Users who rely on
defining their proxy credentials in the URL are <em>strongly</em> encouraged to upgrade
to Requests 2.31.0+ to prevent unintentional leakage and rotate their proxy
credentials once the change has been fully deployed.</p>
<p>Users who do not use a proxy or do not supply their proxy credentials through
the user information portion of their proxy URL are not subject to this
vulnerability.</p>
<p>Full details can be read in our <a href="https://github.com/psf/requests/security/advisories/GHSA-j8r2-6x86-q33q">Github Security Advisory</a>
and <a href="https://nvd.nist.gov/vuln/detail/CVE-2023-32681">CVE-2023-32681</a>.</p>
</li>
</ul>
<h2>2.30.0 (2023-05-03)</h2>
<p><strong>Dependencies</strong></p>
<ul>
<li>
<p>⚠️ Added support for urllib3 2.0. ⚠️</p>
<p>This may contain minor breaking changes so we advise careful testing and
reviewing <a href="https://urllib3.readthedocs.io/en/latest/v2-migration-guide.html">https://urllib3.readthedocs.io/en/latest/v2-migration-guide.html</a>
prior to upgrading.</p>
<p>Users who wish to stay on urllib3 1.x can pin to <code>urllib3<2</code>.</p>
</li>
</ul>
<h2>2.29.0 (2023-04-26)</h2>
<p><strong>Improvements</strong></p>
<ul>
<li>Requests now defers chunked requests to the urllib3 implementation to improve
standardization. (<a href="https://redirect.github.com/psf/requests/issues/6226">#6226</a>)</li>
<li>Requests relaxes header component requirements to support bytes/str subclasses. (<a href="https://redirect.github.com/psf/requests/issues/6356">#6356</a>)</li>
</ul>
<h2>2.28.2 (2023-01-12)</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/psf/requests/commit/147c8511ddbfa5e8f71bbf5c18ede0c4ceb3bba4"><code>147c851</code></a> v2.31.0</li>
<li><a href="https://github.com/psf/requests/commit/74ea7cf7a6a27a4eeb2ae24e162bcc942a6706d5"><code>74ea7cf</code></a> Merge pull request from GHSA-j8r2-6x86-q33q</li>
<li><a href="https://github.com/psf/requests/commit/302225334678490ec66b3614a9dddb8a02c5f4fe"><code>3022253</code></a> test on pypy 3.8 and pypy 3.9 on windows and macos (<a href="https://redirect.github.com/psf/requests/issues/6424">#6424</a>)</li>
<li><a href="https://github.com/psf/requests/commit/b639e66c816514e40604d46f0088fbceec1a5149"><code>b639e66</code></a> test on py3.12 (<a href="https://redirect.github.com/psf/requests/issues/6448">#6448</a>)</li>
<li><a href="https://github.com/psf/requests/commit/d3d504436ef0c2ac7ec8af13738b04dcc8c694be"><code>d3d5044</code></a> Fixed a small typo (<a href="https://redirect.github.com/psf/requests/issues/6452">#6452</a>)</li>
<li><a href="https://github.com/psf/requests/commit/2ad18e0e10e7d7ecd5384c378f25ec8821a10a29"><code>2ad18e0</code></a> v2.30.0</li>
<li><a href="https://github.com/psf/requests/commit/f2629e9e3c7ce3c3c8c025bcd8db551101cbc773"><code>f2629e9</code></a> Remove strict parameter (<a href="https://redirect.github.com/psf/requests/issues/6434">#6434</a>)</li>
<li><a href="https://github.com/psf/requests/commit/87d63de8739263bbe17034fba2285c79780da7e8"><code>87d63de</code></a> v2.29.0</li>
<li><a href="https://github.com/psf/requests/commit/51716c4ef390136b0d4b800ec7665dd5503e64fc"><code>51716c4</code></a> enable the warnings plugin (<a href="https://redirect.github.com/psf/requests/issues/6416">#6416</a>)</li>
<li><a href="https://github.com/psf/requests/commit/a7da1ab3498b10ec3a3582244c94b2845f8a8e71"><code>a7da1ab</code></a> try on ubuntu 22.04 (<a href="https://redirect.github.com/psf/requests/issues/6418">#6418</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/psf/requests/compare/v2.28.1...v2.31.0">compare view</a></li>
</ul>
</details>
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| 1,722,291,178
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I_kwDOACgets5mqBPq
| 3,008
|
POSCAR is ignoring selective dynamics
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[
"Hey @SelfMade2001, the purpose of selective dynamics is to enable only certain degrees of freedom during relaxations. If you enable selective dynamics, but allow all degrees of freedom to relax, as in your first example, then selective dynamics is not used. That's why pymatgen ignores it\r\n\r\nIf that's unclear, please [see the VASP manual page on this](https://www.vasp.at/wiki/index.php/POSCAR#Full_format_specification)\r\n\r\nIn your second example, the ordering of selective dynamics tags and labels for the atomic sites is incorrect, the correct format is:\r\n\r\n> Test\r\n 1.000000000\r\n 20.0000000000000000 0.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 23.0000000000000000 0.0000000000000000\r\n 0.0000000000000000 0.0000000000000000 15.0000000000000000\r\n C H \r\n 2 1\r\nSelective dynamics\r\nCartesian\r\n 2.201545747940 2.214990562232 1.000000000000 T T T C\r\n 3.625859708182 2.193941473662 1.000000000000 T T T C\r\n 4.326973622066 3.379594386626 1.000000000000 T T T H\r\n \r\nBut again, selective dynamics won't be enabled since all sites have all degrees of freedom permitted to relax.\r\n\r\nThe reason you're getting gobbled output from pymatgen is because the elemental symbols are misplaced in the last three lines, and it expects any of the strings `(\"T\", \"True\", \"F\", \"False\")` to appear where the elemental symbols appear."
] | 2023-05-23T15:16:00
| 2024-02-13T08:20:08
|
2024-02-13T08:20:08Z
|
NONE
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I am using the pymatgen.io.vasp.inputs Module. According to the documentation (https://pymatgen.org/pymatgen.io.vasp.inputs.html) the from_file(filename) method of the Poscar class should handle selective dynamics. However it does ignore selective dynamics or read it in the wrong way.
Here is some test file called POSCAR_test:
```
Test
1.000000000
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
Cartesian
2.201545747940 2.214990562232 1.000000000000 T T T
3.625859708182 2.193941473662 1.000000000000 T T T
4.326973622066 3.379594386626 1.000000000000 T T T
```
Here is the code:
```
from pymatgen.io.vasp.inputs import Poscar
poscar = Poscar.from_file('POSCAR_test', False, False)
print(poscar)
```
The output:
```
Test
1.0
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
direct
0.1100772873970000 0.0963039374883478 0.0666666666666667 C
0.1812929854091000 0.0953887597244348 0.0666666666666667 C
0.2163486811033000 0.1469388863750435 0.0666666666666667 H
```
As you can see, selective dynamics are getting ignored, which should not be the case.
If you change the POSCAR_test to this:
```
Test
1.000000000
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
Cartesian
2.201545747940 2.214990562232 1.000000000000 C T T T
3.625859708182 2.193941473662 1.000000000000 C T T T
4.326973622066 3.379594386626 1.000000000000 H T T T
```
The output will be this:
```
Test
1.0
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
direct
0.1100772873970000 0.0963039374883478 0.0666666666666667 F T T C
0.1812929854091000 0.0953887597244348 0.0666666666666667 F T T C
0.2163486811033000 0.1469388863750435 0.0666666666666667 F T T H
```
Now the module seems to get that I want to use selective dynamics, but it sets all the x-coordinates to F and not T.
I also tried this POSCAR_test:
```
Test
1.000000000
20.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 23.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 15.0000000000000000
C H
2 1
Selective dynamics
Cartesian
2.201545747940 2.214990562232 1.000000000000 T T T C
3.625859708182 2.193941473662 1.000000000000 T T T C
4.326973622066 3.379594386626 1.000000000000 T T T H
```
which outputs the same as the first POSCAR_test, totally ignoring selective dynamics.
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PR_kwDOACgets5RLaBV
| 3,010
|
Clean up
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[] | 2023-05-23T19:38:57
| 2023-05-23T20:22:53
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2023-05-23T20:22:52Z
|
MEMBER
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742f4616e simplify: `structure.sites` -> `structure`
9eb253cd5 `ruff` unignore `SIM115`, fix `pymatgen/io/qchem/tests/test_inputs.py`
04e4fd6ee `ruff` unignore `RET501` and fix unnecessary `return None`
46ed47125 `ruff` unignore and fix `PLW3301`
6e74192ac `ruff` unignore `PLW0603` and fix use of `globals`
24f812e6a improve `TestCRESTOutput` readability
bc93f619e `ruff` unignore `PD002` (pandas don't use inplace)
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I_kwDOACgets5msryG
| 3,011
|
`AseAtomsAdaptor.get_atoms(structure, **kwargs)` compares numpy boolean array wtith python nested list.
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[
"Thanks for reporting! Minimal code to trigger the error:\r\n\r\n```py\r\nimport numpy as np\r\n\r\nfrom pymatgen.core import Lattice, Structure\r\nfrom pymatgen.io.ase import AseAtomsAdaptor\r\n\r\nstructure = Structure(\r\n lattice=Lattice.cubic(5),\r\n species=(\"Fe\", \"O\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n site_properties={\"selective_dynamics\": np.array([True, True, True])},\r\n)\r\n\r\nase_atoms = AseAtomsAdaptor.get_atoms(structure)\r\n>>> ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()\r\n```\r\n\r\nShould be easy to fix using `np.all and not np.any` instead of list comparisons."
] | 2023-05-24T00:45:42
| 2023-05-24T17:32:22
|
2023-05-24T17:32:22Z
|
CONTRIBUTOR
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**Describe the bug**
`AseAtomsAdaptor.get_atoms(structure, **kwargs)` checks numpy boolean array against python nested list. This is a bug similar to my previous PR (#2951).
https://github.com/materialsproject/pymatgen/blob/233070151070c0d839ebb23d93afc6f17540e760/pymatgen/io/ase.py#L107-L111
The `ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()` can be reproduced by reading `CONTCAR` with `selective_dynamics`.
This can be bypassed temporarily by converting `poscar.selective_dynamics` back to nested list `poscar.selective_dynamics = [list(x) for x in poscar.selective_dynamics] ` Will look into this and submit pr later.
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Fix `ValueError` when `structure.selective_dynamics` has type `np.array`
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[] | 2023-05-24T17:01:46
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2023-05-24T17:32:20Z
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Closes #3011.
71e888dd9 refactor LammpsData.get_string()
a1d3509b6 refactor ase import, AseAtomsAdaptor.get_atoms() check is_struct
a21543c71 fix ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all() when structure.selective_dynamics has type np.array
bf56232bb add cases testing selective_dynamics as list and array to test_get_structure_dyn()
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Breaking: Overhaul `class PymatgenTest`
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[
"[One thing left to do](https://github.com/materialsproject/pymatgen/pull/3014/files#diff-e9cfd9b89de7ff172f8b6e26e92bb559f6f61ae34d0ee3c08c8b06954e1f69c1R65):\r\n\r\n```\r\n# TODO (janosh): replace assert_array_almost_equal decimal kwarg with assert_allclose() atol and rtol kwargs\r\n```\r\n\r\n"
] | 2023-05-25T18:58:06
| 2023-05-25T19:17:30
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2023-05-25T19:17:28Z
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Drop unused `PymatgenTest` methods, rename existing ones from camel to snake case and replace `assert_almost_equal` with `assert_allclose` as recommended by numpy docs.
8ad0792d4 breaking: drop internally unused PymatgenTest.get_mp_structure()
868179215 breaking: drop internally unused PymatgenTest.assertDictsAlmostEqual()
62e9afc38 replace all PymatgenTest.assertArrayEqual with numpy.testing.assert_array_equal
9a1dfc179 remove PymatgenTest.assertArrayEqual() method
1462805c7 replace numpy.testing.assert_almost_equal() with numpy.testing.assert_allclose()
8a0e76e38 refactor import: from numpy.testing import assert_array_almost_equal
91013e1ad breaking: snake_case assertStrContentEqual to assert_str_content_equal
729a5dfba breaking: snake_case assertMSONable to assert_msonable
Many of the commits here are breaking but since `PymatgenTest` is only for internal use, it shouldn't matter.
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PR_kwDOACgets5RX6KD
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Optimize cython find_points_in _spheres
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[
"@lbluque NICE! Very useful for all structure manipulations! Merging as teh lint errors are unrelated to PR.",
"@stichri Since you did a great job on https://github.com/materialsproject/pymatgen/pull/2983 checking for memory leaks, would be hugely appreciated if you have the time to take these changes for a spin and let us know if you notice any issues. Always good to have another pair of eyes on performance critical code. 🙏 ",
"I quickly [tried the new code](https://github.com/materialsproject/pymatgen/files/11578536/memtest.py.txt) and it indeed looks like there is **no issue with leaking memory**:\r\n\r\n\r\n\r\nJust for curiosity's sake, I also quickly tried to look at it actually using valgrind - to that end, I:\r\n* realized the [suppression file maintained for cpython](https://github.com/python/cpython/blob/3.11/Misc/valgrind-python.supp) really does not seem to suppress anything for me when running a script containing just a single `pass` statement with python3.11\r\n* therefore generated my own suppression file for everything that happens _before_ calling `find_points_in_spheres` - by commenting out everything from line 15 on in the trial script as linked above and running\r\n ```\r\n valgrind --tool=memcheck --leak-check=full --show-leak-kinds=all --error-limit=no --gen-suppressions=all --log-file=all.log python ./memtest.py\r\n ```\r\n followed by\r\n ```\r\n cat ./all.log | ./parse_valgrind_suppressions.sh > all.supp\r\n ```\r\n using [parse_valgrind_suppressions.sh from here](https://wiki.wxwidgets.org/Parse_valgrind_suppressions.sh)\r\n* got to see valgrind's output (_of arguably false positives_) for a single call of `find_points_in_spheres` - by uncommenting line 14 in the trial script as linked above and running\r\n ```\r\n valgrind --tool=memcheck --leak-check=full --show-leak-kinds=all --track-origins=yes --suppressions=all.supp python ./memtest.py\r\n ```\r\nWhen the new code was compiled with debugging symbols, (as I've done by adding `, extra_compile_args=['-ggdb3,-O0']` on line 173 of pymatgen's setup.py,) I am ultimately left with what seems to be 32 bytes in 2 blocks worth of arguably false positives:\r\n```\r\n==20882== Memcheck, a memory error detector\r\n==20882== Copyright (C) 2002-2022, and GNU GPL'd, by Julian Seward et al.\r\n==20882== Using Valgrind-3.21.0 and LibVEX; rerun with -h for copyright info\r\n==20882== Command: python ./memtest.py\r\n==20882==\r\n==20882==\r\n==20882== HEAP SUMMARY:\r\n==20882== in use at exit: 19,679,587 bytes in 149,555 blocks\r\n==20882== total heap usage: 1,146,146 allocs, 996,591 frees, 204,187,029 bytes allocated\r\n==20882==\r\n==20882== 16 bytes in 1 blocks are still reachable in loss record 120 of 21,505\r\n==20882== at 0x484182F: malloc (vg_replace_malloc.c:431)\r\n==20882== by 0x6259E62: npy_alloc_cache_dim (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62B7AC0: PyArray_NewFromDescr_int (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BAA92: PyArray_NewLikeArrayWithShape (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BAD51: PyArray_FromArray (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BB473: PyArray_FromAny (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BB5E6: PyArray_CheckFromAny (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x63588A7: array_array (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x4A1ED89: cfunction_vectorcall_FASTCALL_KEYWORDS (methodobject.c:443)\r\n==20882== by 0x383FF5DF: __Pyx_PyObject_Call (neighbors.c:25731)\r\n==20882== by 0x383FF5DF: __Pyx__PyObject_CallOneArg (neighbors.c:25770)\r\n==20882== by 0x3841FF22: __pyx_pf_8pymatgen_12optimization_9neighbors_find_points_in_spheres.isra.0 (neighbors.c:6096)\r\n==20882== by 0x384239A5: __pyx_pw_8pymatgen_12optimization_9neighbors_1find_points_in_spheres (neighbors.c:3309)\r\n==20882==\r\n==20882== 16 bytes in 1 blocks are still reachable in loss record 121 of 21,505\r\n==20882== at 0x484182F: malloc (vg_replace_malloc.c:431)\r\n==20882== by 0x6259E62: npy_alloc_cache_dim (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62B7AC0: PyArray_NewFromDescr_int (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BAA92: PyArray_NewLikeArrayWithShape (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BAD51: PyArray_FromArray (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BB473: PyArray_FromAny (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x62BB5E6: PyArray_CheckFromAny (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x63588A7: array_array (in /home/chrs/venv3.11-pmg-neighbors/lib/python3.11/site-packages/numpy/core/_multiarray_umath.cpython-311-x86_64-linux-gnu.so)\r\n==20882== by 0x4A1ED89: cfunction_vectorcall_FASTCALL_KEYWORDS (methodobject.c:443)\r\n==20882== by 0x383FF5DF: __Pyx_PyObject_Call (neighbors.c:25731)\r\n==20882== by 0x383FF5DF: __Pyx__PyObject_CallOneArg (neighbors.c:25770)\r\n==20882== by 0x38420208: __pyx_pf_8pymatgen_12optimization_9neighbors_find_points_in_spheres.isra.0 (neighbors.c:6184)\r\n==20882== by 0x384239A5: __pyx_pw_8pymatgen_12optimization_9neighbors_1find_points_in_spheres (neighbors.c:3309)\r\n==20882==\r\n==20882== LEAK SUMMARY:\r\n==20882== definitely lost: 0 bytes in 0 blocks\r\n==20882== indirectly lost: 0 bytes in 0 blocks\r\n==20882== possibly lost: 0 bytes in 0 blocks\r\n==20882== still reachable: 32 bytes in 2 blocks\r\n==20882== suppressed: 19,679,555 bytes in 149,553 blocks\r\n==20882==\r\n==20882== For lists of detected and suppressed errors, rerun with: -s\r\n==20882== ERROR SUMMARY: 0 errors from 0 contexts (suppressed: 16378 from 15300)\r\n```\r\nNote the reported offending code lines, e.g. neighbors.c:3309, refer to c code _generated by cython_ which therefore is pretty much unreadable.\r\nSo in conclusion, I'm afraid this approach has limited utility without additional tooling (which I wouldn't be aware of) that allows to correlate the offending cython-generated code with the actual pyx-code as written by the user ...\r\n\r\nThere probably is a much better way that I'm unfortunately not aware of ... 😅",
"Damn, memory leak detection in Cython is a hell of a complex task. Thanks for taking the time and being so thorough!\r\n\r\nIf it's just 32 bytes out of 20 MiB, arguably we shouldn't sweat it. 😄 I'll just assume it's a timing issue of objects having gone out of scope but the garbage collector not having done a cleanup yet."
] | 2023-05-25T19:15:25
| 2023-05-26T19:29:33
|
2023-05-25T20:17:38Z
|
CONTRIBUTOR
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## Summary
Optimized cython code in `find_points_in_spheres`, getting ~5x faster runtime.
For example here are the runtimes for searching for all neighbors within a 5A cutoff in a 32 atom FCC (on my laptop with Intel i7 (2.8 GHz) CPU):
- version 2023.5.10: `955 µs ± 35.4 µs per loop (mean ± std. dev. of 7 runs, 1,000 loops each)`
- this PR: `115 µs ± 2.69 µs per loop (mean ± std. dev. of 7 runs, 10,000 loops each)`
## 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] Doc strings 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 path/to/file.py`](https://github.com/python/mypy) to type check your code.
- [X] Tests have been added for any new functionality or bug fixes.
- [X] All linting and tests pass.
Our CI will run all the above checks but it might be more efficient if you already fix most errors before submitting the PR. We highly recommended installing `pre-commit` hooks. Simply Run
```sh
pip install -U pre-commit
pre-commit install
```
in the repo's root directory. Once `pre-commit` has installed `git` hooks, our linters will run before every commit and abort if issues pop up.
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I_kwDOACgets5m7voM
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InputSet looks for wrong W POTCAR when using PBE_54
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[
"Yes, this is definitely true. I fixed it within the LobsterSet by replacing the standard value. \r\n\r\nSee https://github.com/materialsproject/pymatgen/blob/f90929f75b27fe1d06faa4e2a5f44654009b98b0/pymatgen/io/vasp/sets.py#L2789",
"I'm open to changing to `W_sv`. It would need adequate highlighting in the change logs and GH release language similar to #2969. Plus we'd need to [update the docs](https://docs.materialsproject.org/methodology/materials-methodology/calculation-details/gga+u-calculations/pseudopotentials) which correctly state we're using `W_pv` on pre-5.4 input sets.\r\n\r\n@mkhorton What's your take?",
"`W_sv` does not exist in pre-5.4 postcars. `W_pv` not in 5.4 potcars. There is no real alternative.",
"Yes, i thought this issue was asking about switching to `W_pv` on the input sets that are version agnostic. Some explicitly state `POTCAR_FUNCTIONAL: PBE_54`, some `POTCAR_FUNCTIONAL: PBE_52` and a few have `POTCAR_FUNCTIONAL: PBE`. I thought this was asking about the latter.\r\n\r\nhttps://github.com/materialsproject/pymatgen/blob/718c9540dff478b1713e3f4bb2bb085719c1b96f/pymatgen/io/vasp/MPRelaxSet.yaml#L83",
"Mh. I see. This would lead to errors with the pre-5.4 potcars. Also, it would not be consistent with all previous computations. \r\n\r\nIn my opinion, the MPRelaxSet itself can only be run with different potcars if you don't want to compare it to MP data.",
"I agree with @JaGeo. Basically, `MPRelaxSet` can _only_ be used with the original (not v.54) PAW PBE potentials, as that's part of its definition.\r\n\r\nAssuming the question is independent of the MP sets, which it sounds like it is, then I think it's just a matter of making sure `W_sv` isn't selected when a .54 PAW PBE potential set is requested. This wouldn't involve changing any MP input sets (you can see that [MPSCANRelaxSet](https://github.com/materialsproject/pymatgen/blob/32436a6c18332021de4238b6c76e627e7965fbaf/pymatgen/io/vasp/MPSCANRelaxSet.yaml#L120) already has `W: W_sv`).",
"Is it possible to add a warning when switching to newer potcars. It could describe the compatibility issues and the required potcar updates (e.g., for W)",
"I'm happy to help implement what everyone thinks is best. But I'm wary of warnings. In my opinion, pymatgen already issues too many warnings. If there's a sensible default where Pymatgen just does the right thing given the context, I think we should implement that.",
"> I agree with @JaGeo. Basically, `MPRelaxSet` can _only_ be used with the original (not v.54) PAW PBE potentials, as that's part of its definition.\r\n> \r\n> Assuming the question is independent of the MP sets, which it sounds like it is, then I think it's just a matter of making sure `W_sv` isn't selected when a .54 PAW PBE potential set is requested. This wouldn't involve changing any MP input sets (you can see that [MPSCANRelaxSet](https://github.com/materialsproject/pymatgen/blob/32436a6c18332021de4238b6c76e627e7965fbaf/pymatgen/io/vasp/MPSCANRelaxSet.yaml#L120) already has `W: W_sv`).\r\n\r\nI understand that for compatibility/consistency the original PBE potentials are necessary, but I don't think that's the only intended use of `MPRelaxSet`, right? If you are allowed to specify `user_potcar_functional='PBE_54'` when instantiating an MPRelaxSet, it seems like the code should automatically search for W_sv since it's the only W potential in 5.4. The user is already asking explicitly for 5.4 POTCARs so they know that they are deviating from the MP standard. So no need for a warning either, IMO.",
"Entirely agreed! Apologies if my reply wasn't clear; it was mainly meant to indicate to MP staff that the MP input sets aren't influenced by a PR addressing this issue.",
"Oh, yes, I misinterpreted that first sentence. You were stating the status quo (which we are hoping to change), not the expected behavior. Yes, this fix should definitely not affect any of the default input settings. Thanks for the rapid response!",
"Then, I think simply implementing the correct W POTCAR for the 5.4 potcars (without additional warning) sounds like the best option.",
"@janosh we can then also close this one here: https://github.com/materialsproject/pymatgen/issues/1707 😅",
"If y'all could take a very _careful_ look at #3022 to make sure, I didn't miss anything, I'd be much obliged! I'm always nervous when changing VASP input settings.",
"If I forget to respond by tomorrow, please ping me with a reminder! "
] | 2023-05-26T05:35:46
| 2023-06-01T00:41:02
|
2023-06-01T00:41:02Z
|
CONTRIBUTOR
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**Describe the bug**
When creating an input set using the PBE_54 POTCAR setting, the code looks for the non-existent W_pv POTCAR. [This has been replaced by W_sv in the 5.4 version.](https://www.vasp.at/wiki/index.php/Available_PAW_potentials#Recommended_potentials_for_DFT_calculations)
**To Reproduce**
1. Establish PBE_54 POTCAR directory
2. Set `PMG_DEFAULT_FUNCTIONAL: 'PBE_54'` in `~/.pmgrc.yaml`
3. Run the following
```
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.sets import MPStaticSet
struc = Structure.from_str(
"""
# generated using pymatgen
data_Sb2WO6
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 4.97452257
_cell_length_b 5.55751792
_cell_length_c 9.25434909
_cell_angle_alpha 83.52945128
_cell_angle_beta 90.00000000
_cell_angle_gamma 90.00000000
_symmetry_Int_Tables_number 1
_chemical_formula_structural Sb2WO6
_chemical_formula_sum 'Sb4 W2 O12'
_cell_volume 254.21595972
_cell_formula_units_Z 2
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
Sb Sb0 1 0.44927320 0.38866033 0.16812494 1
Sb Sb1 1 0.04965522 0.88677808 0.16648034 1
Sb Sb2 1 0.94927320 0.61133967 0.83187506 1
Sb Sb3 1 0.54965522 0.11322192 0.83351966 1
W W4 1 0.03740281 0.24401928 0.50864705 1
W W5 1 0.53740281 0.75598072 0.49135295 1
O O6 1 0.77952180 0.53470618 0.44201347 1
O O7 1 0.72535535 0.03497081 0.44056689 1
O O8 1 0.22535535 0.96502919 0.55943311 1
O O9 1 0.27952180 0.46529382 0.55798653 1
O O10 1 0.84957778 0.23617072 0.68715870 1
O O11 1 0.14248836 0.26735019 0.31118039 1
O O12 1 0.64248836 0.73264981 0.68881961 1
O O13 1 0.34957778 0.76382928 0.31284130 1
O O14 1 0.18624167 0.61241876 0.06049465 1
O O15 1 0.31939681 0.11002430 0.06444027 1
O O16 1 0.68624167 0.38758124 0.93950535 1
O O17 1 0.81939681 0.88997570 0.93555973 1
""", fmt='cif')
inputs = MPStaticSet(struc, user_potcar_functional = 'PBE_54')
inputs.write_input('W_bugtest')
```
**Expected behavior**
Look for W_sv POTCAR
**Environment (please supply relevant versions and platform info):**
- OS: Ubuntu 18
- 2023.3.23 via pip
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MaterialsProjectCompatibility issue deprecation warning
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[] | 2023-05-26T16:03:25
| 2023-05-26T23:04:26
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2023-05-26T23:04:24Z
|
MEMBER
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Closes #2398.
d86e0b0f8 MaterialsProjectCompatibility issue silencable deprecation warning
e7a644539 SymmetrizedStructure type hints
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"I'm super late, but I guess we need the custom json encoder (`month.json.MontyEncoder`) otherwise `site_labels` as NumPy array and `spacegroup` (as `Sequence[SymmOp]`) cannot be directly serialized in: https://github.com/materialsproject/pymatgen/blob/c76c7a671479a8752800f00d0fdf02ebf18771cb/src/pymatgen/symmetry/structure.py#L126-L134\n\nHowever currently the `kwargs` for json format in `IStructure.to` method is not passed to `json.dump`: \nhttps://github.com/materialsproject/pymatgen/blob/c76c7a671479a8752800f00d0fdf02ebf18771cb/src/pymatgen/core/structure.py#L2933-L2935\nhttps://github.com/materialsproject/pymatgen/blob/c76c7a671479a8752800f00d0fdf02ebf18771cb/src/pymatgen/core/structure.py#L2959-L2964\n\nIf we could pass the `kwargs`:\n```diff\n- json_str = json.dumps(self.as_dict())\n+ json_str = json.dumps(self.as_dict(), **kwargs)\n```\n\nThe fix then should be fairly straightforward as:\n```python\nsymmetrized_structure.to(\"dummy.json\", cls=MontyEncoder)\n```\n\nOr do you have better ideas?\n\n--\n\nEdit: I think the `SymmetrizedStructure.as_dict` method should also be fixed to be automatically MSONable as per the docs, so it's two changes needed here? What do you think?\n1. Pass `kwargs` inside the `IStructure.to` method, to be consistent with other formats\n2. Fix `SymmetrizedStructure.as_dict` method to give a really MSONable dict (would be breaking)\n"
] | 2023-05-28T23:53:11
| 2025-03-17T13:39:58
|
2025-03-17T13:39:57Z
|
MEMBER
|
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```py
from pymatgen.analysis.structure_analyzer import SpacegroupAnalyzer
from pymatgen.core import Lattice, Structure
structure = Structure(
lattice=Lattice.cubic(3),
species=("Fe", "Fe"),
coords=((0, 0, 0), (0.5, 0.5, 0.5)),
)
symmetrized_structure = SpacegroupAnalyzer(structure).get_symmetrized_structure()
symmetrized_structure.to("dummy.json")
```
raises
```py
TypeError: Object of type SymmOp is not JSON serializable
```
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| 1,730,979,297
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PR_kwDOACgets5RnlLV
| 3,019
|
Tweak variable names
|
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[] | 2023-05-29T15:58:40
| 2023-05-29T19:31:08
|
2023-05-29T19:31:07Z
|
MEMBER
|
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Also use modern `f"{float:+}"` for explicit `+` signs.
|
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PR_kwDOACgets5Ro3Gt
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|
Unignore `ruff` `PD011`
|
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[] | 2023-05-30T01:00:54
| 2023-05-30T03:00:18
|
2023-05-30T03:00:17Z
|
MEMBER
|
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c535f4979 ruff unignore PD011 (pandas-use-of-dot-values)
7d3eba415 drop .values where not needed, else replace with .to_numpy(), noqa false positives
`pandas.DataFrame().values` is deprecated and slated for removal in a future `pandas` version.
|
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PR_kwDOACgets5RpCp-
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|
Don't use `np.nan` as kwarg default, prefer `None`
|
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[
"Closing with reasoning in https://github.com/materialsproject/pymatgen/issues/2107#issuecomment-1569239404."
] | 2023-05-30T02:38:48
| 2023-05-30T22:56:46
|
2023-05-30T22:56:42Z
|
MEMBER
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Closes #2107.
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PR_kwDOACgets5RugJb
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|
Breaking: Default `user_potcar_settings` to `{"W": "W_sv"}` in all input sets if `user_potcar_functional == "PBE_54"`
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[
"Pinging @JaGeo and @arosen93 for review.",
"Actually, the PR title is inaccurate. There are input sets that don't have any restrictions on `user_potcar_settings` which I didn't touch. So far, I only changed the input sets that ensure `user_potcar_functional in (\"PBE_52\", \"PBE_54\")`. So would make sense to move this behavior up in the class hierarchy into `DictSet` where it would always apply.",
"@janosh Currently, this code here, does not work:\r\n\r\n```Python\r\nfrom pymatgen.io.vasp.sets import MPRelaxSet\r\nfrom pymatgen.core.structure import Structure\r\n\r\nstructure = Structure.from_dict({'@module': 'pymatgen.core.structure', '@class': 'Structure', 'charge': 0.0,\r\n 'lattice': {'matrix': [[2.6794492400614325, 0.0, -1.7723083848423267],\r\n [7.778511770202987e-16, 4.837013999999999,\r\n 2.9618168562654676e-16], [0.0, 0.0, 5.76034817]],\r\n 'pbc': (True, True, True), 'a': 3.21255743, 'b': 4.837013999999999,\r\n 'c': 5.76034817, 'alpha': 90.0, 'beta': 123.48244503999997, 'gamma': 90.0,\r\n 'volume': 74.65718535099107}, 'sites': [\r\n {'species': [{'element': 'W', 'oxidation_state': 4.0, 'occu': 1.0}], 'abc': [0.0, 0.5, 0.0],\r\n 'xyz': [3.8892558851014935e-16, 2.4185069999999995, 1.4809084281327338e-16], 'label': 'W4+', 'properties': {}},\r\n {'species': [{'element': 'W', 'oxidation_state': 4.0, 'occu': 1.0}], 'abc': [0.0, 0.0, 0.5],\r\n 'xyz': [0.0, 0.0, 2.880174085], 'label': 'W4+', 'properties': {}},\r\n {'species': [{'element': 'O', 'oxidation_state': -2.0, 'occu': 1.0}], 'abc': [0.292339, 0.302264, 0.7959505],\r\n 'xyz': [0.7833075113903194, 1.4620551996959996, 4.066837145169164], 'label': 'O2-', 'properties': {}},\r\n {'species': [{'element': 'O', 'oxidation_state': -2.0, 'occu': 1.0}], 'abc': [0.707661, 0.802264, 0.7040495],\r\n 'xyz': [1.896141728671114, 3.880562199695999, 2.8013767249885095], 'label': 'O2-', 'properties': {}},\r\n {'species': [{'element': 'O', 'oxidation_state': -2.0, 'occu': 1.0}], 'abc': [0.707661, 0.697736, 0.2040495],\r\n 'xyz': [1.8961417286711137, 3.3749588003039994, -0.0787973600114904], 'label': 'O2-', 'properties': {}},\r\n {'species': [{'element': 'O', 'oxidation_state': -2.0, 'occu': 1.0}], 'abc': [0.292339, 0.197736, 0.2959505],\r\n 'xyz': [0.7833075113903193, 0.9564518003039998, 1.1866630601691643], 'label': 'O2-', 'properties': {}}]})\r\nmprelax = MPRelaxSet(structure=structure, user_potcar_functional=\"PBE_54\")\r\nmprelax.write_input(\"input\")\r\n\r\n```\r\nThe current change does not seem to correctly fix the issue. ",
"Maybe `user_potcar_settings = {\"W\": \"W_sv\"}.update(user_potcar_settings) if user_potcar_settings is not None else {\"W\": \"W_sv\"}` instead? Probably there is a more compact form.",
"Hey @JaGeo, thanks for taking a look! 🙏 \r\n\r\nGood catch! Didn't want to write tests until initial feedback but I probably should have noticed this without tests. 😅 \r\n\r\n```py\r\n{\"W\": \"W_sv\"}.update(user_potcar_settings)\r\n```\r\n\r\nreturns `None` is the problem. It should have been\r\n\r\n```py\r\nuser_potcar_settings = {\"W\": \"W_sv\", **(user_potcar_settings or {})}\r\n```\r\n\r\nFix and test incoming.",
"@JaGeo I removed `self._config_dict[\"POTCAR\"].update({\"W\": \"W_sv\"})` from `LobsterSet` since that's now handled for all subclasses of `DictSet`. Is that ok?",
"> @JaGeo I removed `self._config_dict[\"POTCAR\"].update({\"W\": \"W_sv\"})` from `LobsterSet` since that's now handled for all subclasses of `DictSet`. Is that ok?\r\n\r\n@janosh yes, completely fine!"
] | 2023-05-30T21:12:53
| 2023-06-01T03:16:37
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2023-06-01T00:41:01Z
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Closes #3016, closes #1707.
Breaking: `DictSet` drop deprecated kwarg `potcar_functional: str = None`, use `user_potcar_functional: str = None` instead (in ac51e26)
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I_kwDOACgets5nUajt
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`if self.bandgap == 0` is probably not the best in `MPScanRelaxSet`
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"Makes sense to me @arosen93 . I didn't know much about the robustness of bandgap detection when I wrote this."
] | 2023-05-31T05:16:00
| 2023-06-02T15:04:31
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2023-06-02T15:04:31Z
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MEMBER
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https://github.com/materialsproject/pymatgen/blob/3c91e69838500120cf62032037324f88defcb1a4/pymatgen/io/vasp/sets.py#L949-L952
This checks if `bandgap` is strictly equal to zero, but there are likely going to be edge cases where `bandgap` is some very small value (say, 1e-6 eV) that should also be flagged as metallic. It'd probably be better to do `if self.bandgap < tol` where `tol` is something like `1e-4`.
CC @janosh, @rkingsbury
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PR_kwDOACgets5R5kIT
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Bump palettable from 3.3.0 to 3.3.3
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[
"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-06-01T12:57:29
| 2023-06-01T14:06:54
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2023-06-01T14:06:43Z
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CONTRIBUTOR
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Bumps [palettable](https://github.com/jiffyclub/palettable) from 3.3.0 to 3.3.3.
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/jiffyclub/palettable/blob/master/CHANGELOG.rst">palettable's changelog</a>.</em></p>
<blockquote>
<h2>Version 3.3.2</h2>
<ul>
<li>Set <code>python_requires</code> metadata in <code>setup.py</code></li>
</ul>
<h2>Version 3.3.1</h2>
<ul>
<li>Removed setuptools as a runtime dependency (thanks <a href="https://github.com/wch"><code>@wch</code></a> in <a href="https://redirect.github.com/jiffyclub/palettable/issues/46">#46</a>)</li>
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<details>
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<li><a href="https://github.com/jiffyclub/palettable/commit/12509bd4dc7a73a2c2c2610a779078463c1f2556"><code>12509bd</code></a> Merge pull request <a href="https://redirect.github.com/jiffyclub/palettable/issues/46">#46</a> from wch/remove-setuptools</li>
<li><a href="https://github.com/jiffyclub/palettable/commit/e12e557830e81b0c3b6633626590c9e06ed1ba28"><code>e12e557</code></a> Write colorbrewer palettes to .py and remove setuptools dependency</li>
<li><a href="https://github.com/jiffyclub/palettable/commit/7df1908b4e946aa8805b4c9aa7a3bf7717887f7a"><code>7df1908</code></a> Merge pull request <a href="https://redirect.github.com/jiffyclub/palettable/issues/40">#40</a> from asottile/patch-1</li>
<li><a href="https://github.com/jiffyclub/palettable/commit/b20cdca13647941deaaa2c4b15cdb9c56b234add"><code>b20cdca</code></a> Add setuptools as a runtime dependency</li>
<li>See full diff in <a href="https://github.com/jiffyclub/palettable/compare/v3.3.0...v3.3.3">compare view</a></li>
</ul>
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PR_kwDOACgets5R5kMM
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Bump pandas from 2.0.1 to 2.0.2
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-06-01T12:57:35
| 2023-06-01T14:06:55
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2023-06-01T14:06:44Z
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Bumps [pandas](https://github.com/pandas-dev/pandas) from 2.0.1 to 2.0.2.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pandas-dev/pandas/releases">pandas's releases</a>.</em></p>
<blockquote>
<h2>Pandas 2.0.2</h2>
<p>This is a patch release in the 2.0.x series and includes some regression and bug fixes. We recommend that all users upgrade to this version.</p>
<p>See the <a href="https://pandas.pydata.org/pandas-docs/version/2.0.2/whatsnew/v2.0.2.html">full whatsnew</a> for a list of all the changes.</p>
<p>The release will be available on the defaults and conda-forge channels:</p>
<pre><code>conda install pandas
</code></pre>
<p>Or via PyPI:</p>
<pre><code>python3 -m pip install --upgrade pandas
</code></pre>
<p>Please report any issues with the release on the <a href="https://github.com/pandas-dev/pandas/issues">pandas issue tracker</a>.</p>
<p>Thanks to all the contributors who made this release possible.</p>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/pandas-dev/pandas/commit/965ceca9fd796940050d6fc817707bba1c4f9bff"><code>965ceca</code></a> RLS: 2.0.2</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/049539b700d826f384dc23a8edcf95331ecb7147"><code>049539b</code></a> DOC: Final clean up of release notes for 2.0.2 (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53428">#53428</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/f0d09989403a8f011dbeb7e50afaa6a13358ec08"><code>f0d0998</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53413">#53413</a> on branch 2.0.x (DOC: Update release date for 2.0.2) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53424">#53424</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/12fa6c25f17d0bf7e1e9f3cfae910df663e8a93e"><code>12fa6c2</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53393">#53393</a> on branch 2.0.x (DOC: Prepare release notes for 2.0.2) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/5">#5</a>...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/776f43a7131511bc12ffe7eca039f74fa48ffb04"><code>776f43a</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53411">#53411</a> on branch 2.0.x (DOC: Fix tooltips and captions label) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/5">#5</a>...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/8fc7924fb96e9e355d02c96f63bf7ab64cf98b18"><code>8fc7924</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53382">#53382</a> on branch 2.0.x (BUG: convert_dtypes(dtype_backend="pyarro...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/258e55e07b6ab5eca4c3557587b65f2a2cce88f5"><code>258e55e</code></a> FIX: Ignore typing and numba warnings in 2.0.x (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53372">#53372</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/c8cd0277f8f889c5db7463ef7f36b495b5c9de69"><code>c8cd027</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53344">#53344</a>: BUG: Correct .type for pyarrow.map_ and pyarrow.struct ty...</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/584504c5f54a5630891077bfce2fba12ac651e00"><code>584504c</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53364">#53364</a> on branch 2.0.x (Update whatsnew) (<a href="https://redirect.github.com/pandas-dev/pandas/issues/53371">#53371</a>)</li>
<li><a href="https://github.com/pandas-dev/pandas/commit/e821e1b0b2a9d8577906092030554bfc86c0d562"><code>e821e1b</code></a> Backport PR <a href="https://redirect.github.com/pandas-dev/pandas/issues/53343">#53343</a>: REF: Use np.result_type instead of np.find_common_type (#...</li>
<li>Additional commits viewable in <a href="https://github.com/pandas-dev/pandas/compare/v2.0.1...v2.0.2">compare view</a></li>
</ul>
</details>
<br />
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Bump monty from 2022.9.9 to 2023.5.8
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] | 2023-06-01T12:57:42
| 2023-06-01T14:06:55
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2023-06-01T14:06:45Z
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CONTRIBUTOR
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Bumps [monty](https://github.com/materialsvirtuallab/monty) from 2022.9.9 to 2023.5.8.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/materialsvirtuallab/monty/releases">monty's releases</a>.</em></p>
<blockquote>
<h2>v2023.5.8</h2>
<ul>
<li>Pytorch tensor support for MontyEncoder/Decoder.</li>
</ul>
<h2>v2023.5.7</h2>
<ul>
<li>Pytorch tensor support for MontyEncoder/Decoder.</li>
</ul>
<h2>v2023.4.10</h2>
<ul>
<li>Fix for datetime support in jsanitize (<a href="https://github.com/arosen93"><code>@arosen93</code></a>).</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/materialsvirtuallab/monty/blob/master/docs_rst/changelog.rst">monty's changelog</a>.</em></p>
<blockquote>
<h2>v2023.5.8</h2>
<ul>
<li>Improved Pytorch tensor support for MontyEncoder/Decoder.</li>
<li>Bug fix to avoid torch dependency.</li>
</ul>
<h2>v2023.5.7</h2>
<ul>
<li>Pytorch tensor support for MontyEncoder/Decoder.</li>
</ul>
<h2>v2023.4.10</h2>
<ul>
<li>Fix for datetime support in jsanitize (<a href="https://github.com/arosen93"><code>@arosen93</code></a>).</li>
</ul>
<h2>v2022.9.8</h2>
<ul>
<li>Support for DataClasses in MontyEncoder, MontyDecoder and MSONable.</li>
</ul>
<h2>v2022.4.26</h2>
<ul>
<li>Fall back on json if orjson is not present. (<a href="https://github.com/munrojm"><code>@munrojm</code></a>)</li>
</ul>
<h2>v2022.3.12</h2>
<ul>
<li>Allow recursive MSON in jsanitize (<a href="https://github.com/arosen93"><code>@arosen93</code></a>)</li>
<li>Option to use orjson for faster decoding. (<a href="https://github.com/munrojm"><code>@munrojm</code></a>)</li>
</ul>
<h2>v2022.1.19</h2>
<ul>
<li>Fix ruamel.yaml backwards compatibility.</li>
</ul>
<h2>v2022.1.12</h2>
<ul>
<li>Fix decoding of dictionaries (<a href="https://github.com/arosen93"><code>@arosen93</code></a>).</li>
<li>Formal support for py3.10</li>
</ul>
<h2>v2021.12.1</h2>
<ul>
<li>Adds support for lzma/xz format in zopen (<a href="https://github.com/zhubonan"><code>@zhubonan</code></a>).</li>
</ul>
<h2>v2021.8.17</h2>
<ul>
<li>Support serialization for Pandas DataFrames (<a href="https://github.com/mkhorton"><code>@mkhorton</code></a>).</li>
</ul>
<h2>v2021.7.8</h2>
<ul>
<li>Support the specification of <code>fmt</code> keyword arg in monty.serialization
loadfn and dumpfn.</li>
</ul>
<h2>v2021.6.10</h2>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/2fcde85eaab6ab6e38e9426b64b915286ea1e3ce"><code>2fcde85</code></a> Update dev docs</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/7b6182cba39a0ae2d219960155e10c7f74d4eeb2"><code>7b6182c</code></a> Fix pylint error.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/1ef039d97e73677f5cc121d1d43d55612be836f6"><code>1ef039d</code></a> Fix linting.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/247d90ebd4f6b23682ad596c4dca89b1d0338a95"><code>247d90e</code></a> Make naming consistent with numpy.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/f1c7dc51afc2b880f8ac59b51aa2312a8f24e3e9"><code>f1c7dc5</code></a> Add support for Complex Tensors.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/bb1df7547d81b3ea6ac64d54d369644afa4a1436"><code>bb1df75</code></a> Improve torch support.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/2b1a524fbd5bf9ceb9ad11a5c9e8612891b8fe95"><code>2b1a524</code></a> Fix linting errpr.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/e2a7c46a81f305ba19afbf5d15a351d42f30ec4e"><code>e2a7c46</code></a> Add back test files.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/61272eceb36500df3b820c65b129bdbe47d5e70e"><code>61272ec</code></a> Fix CI req.</li>
<li><a href="https://github.com/materialsvirtuallab/monty/commit/55d57a5eb4025e37e9d4c1ef6ae2ac717963f4df"><code>55d57a5</code></a> Update dev docs</li>
<li>Additional commits viewable in <a href="https://github.com/materialsvirtuallab/monty/compare/v2022.9.9...v2023.5.8">compare view</a></li>
</ul>
</details>
<br />
[](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)
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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Bump plotly from 5.11.0 to 5.14.1
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-06-01T12:57:53
| 2023-06-01T14:06:56
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2023-06-01T14:06:45Z
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CONTRIBUTOR
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Bumps [plotly](https://github.com/plotly/plotly.py) from 5.11.0 to 5.14.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/releases">plotly's releases</a>.</em></p>
<blockquote>
<h2>v5.14.1</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<h2>v5.14.0</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<ul>
<li>Added option to allow passing a column name as a <code>str</code> in <code>hover_data</code> and <code>custom_data</code> in <code>plotly.express</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4083">4083</a>]</li>
</ul>
<h2>v5.13.1</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://redirect.github.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://redirect.github.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>v5.13.0</h2>
<p>See the full release announcement with graphical examples on the forum: <a href="https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205">https://community.plotly.com/t/announcing-plotly-py-5-13-0-grouped-scatter-new-markers-and-marker-angles-sankey-links-with-arrows/72205</a></p>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://redirect.github.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://redirect.github.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://redirect.github.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://redirect.github.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://redirect.github.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>v5.12.0</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6381">#6381</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
<li>Add <code>marker.cornerradius</code> attribute to <code>treemap</code> trace [<a href="https://redirect.github.com/plotly/plotly.js/pull/6351">#6351</a>]</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/plotly/plotly.py/blob/master/CHANGELOG.md">plotly's changelog</a>.</em></p>
<blockquote>
<h2>[5.14.1] - 2023-04-05</h2>
<h3>Fixed</h3>
<ul>
<li>Fixed compatibility issue with Pandas 2.0 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4103">#4103</a>]</li>
</ul>
<h2>[5.14.0] - 2023-03-29</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js from version 2.18.2 to version 2.20.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2200----2023-03-15">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>title.automargin</code> to enable automatic top and bottom margining for both container and paper referenced titles [<a href="https://redirect.github.com/plotly/plotly.js/pull/6428">#6428</a>],
with thanks to <a href="https://www.gtisoft.com/">Gamma Technologies</a> for sponsoring the related development.</li>
<li>Add <code>label</code> attribute to shapes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6454">#6454</a>], with thanks to the <a href="https://www.volkswagenag.com">Volkswagen</a> Center of Excellence for Battery Systems for sponsoring development!</li>
<li>Add <code>labelalias</code> to various axes namely cartesian, gl3d, polar, smith, ternary, carpet,
indicator and colorbar [<a href="https://redirect.github.com/plotly/plotly.js/pull/6481">#6481</a>],
this feature was anonymously sponsored: thank you to our sponsor!</li>
</ul>
</li>
<li>Key errors no longer precalculated when performing updates on plots [<a href="https://redirect.github.com/plotly/plotly.py/pull/4101">#4101</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li>Fixed an issue with characters displaying incorrectly, by adding <code>charset="utf-8"</code> to scripts in <code>to_html</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4114">#4114</a>]</li>
<li>Added <code>packaging</code> to install requirements, fixing a <code>No module named 'packaging</code> error on Python 3.6 [<a href="https://redirect.github.com/plotly/plotly.py/pull/4113">#4113</a>]</li>
</ul>
<h3>Added</h3>
<ul>
<li>Added option to allow passing a column name as a <code>str</code> in <code>hover_data</code> and <code>custom_data</code> in <code>plotly.express</code> [<a href="https://redirect.github.com/plotly/plotly.py/pull/4083">4083</a>]</li>
</ul>
<h2>[5.13.1] - 2023-02-24</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.18.0 to version 2.18.2. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2182----2023-02-15">plotly.js CHANGELOG</a> for more information. These changes are reflected in the auto-generated <code>plotly.graph_objects</code> module.</li>
<li>Updated distutils.Version to packaging.Version <a href="https://redirect.github.com/plotly/plotly.py/pull/3897">#3897</a>] and <a href="https://redirect.github.com/plotly/plotly.py/pull/4055">#4055</a>]</li>
</ul>
<h2>[5.13.0] - 2023-01-23</h2>
<h3>Updated</h3>
<ul>
<li>Updated Plotly.js to from version 2.17.1 to version 2.18.0. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2180----2023-01-19">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>sync</code> tickmode option [<a href="https://redirect.github.com/plotly/plotly.js/pull/6356">#6356</a>, <a href="https://redirect.github.com/plotly/plotly.js/pull/6443">#6443</a>], with thanks to <a href="https://github.com/filipesantiagoAM"><code>@filipesantiagoAM</code></a> and <a href="https://github.com/VictorBezak"><code>@VictorBezak</code></a> for the contribution!</li>
</ul>
</li>
<li>Build process now uses Node 18.x and version 2 lockfile (should be an invisible change for users) [<a href="https://redirect.github.com/plotly/plotly.py/pull/4034">#4034</a>]</li>
</ul>
<h3>Fixed</h3>
<ul>
<li><code>write_html()</code> now explicitly encodes output as UTF-8 because Plotly.js' bundle contains such characters [<a href="https://redirect.github.com/plotly/plotly.py/pull/4021">#4021</a>] and [<a href="https://redirect.github.com/plotly/plotly.py/pull/4022">#4022</a>]</li>
<li>fixed <code>iframe</code> renderer regression from 5.12 and also fixed error when this renderer was used in the very first cell in a notebook [<a href="https://redirect.github.com/plotly/plotly.py/pull/4036">#4036</a>]</li>
</ul>
<h2>[5.12.0] - 2023-01-12</h2>
<h3>Updated</h3>
<ul>
<li>Support for ipywidgets 8 [<a href="https://redirect.github.com/plotly/plotly.py/pull/3930">#3930</a>]</li>
<li>Updated Plotly.js to from version 2.16.1 to version 2.17.1. See the <a href="https://github.com/plotly/plotly.js/blob/master/CHANGELOG.md#2170----2022-12-22">plotly.js CHANGELOG</a> for more information. Notable changes include:
<ul>
<li>Add <code>shift</code> and <code>autoshift</code> to cartesian y axes to help avoid overlapping of multiple axes [<a href="https://redirect.github.com/plotly/plotly.js/pull/6334">#6334</a>],
with thanks to <a href="https://www.gtisoft.com">Gamma Technologies</a> for sponsoring the related development!</li>
<li>Introduce group attributes for <code>scatter</code> trace i.e. <code>alignmentgroup</code>, <code>offsetgroup</code>, <code>scattermode</code> and <code>scattergap</code> [<a href="https://redirect.github.com/plotly/plotly.js/pull/6381">#6381</a>],</li>
</ul>
</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/plotly/plotly.py/commit/f006ae830365d6735e5d6fd3c3fb46dca10f539b"><code>f006ae8</code></a> version changes for v5.14.1</li>
<li><a href="https://github.com/plotly/plotly.py/commit/cb27da7c94dac1858fc4de0ea9803b6544ac2461"><code>cb27da7</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4103">#4103</a> from kaibir/master</li>
<li><a href="https://github.com/plotly/plotly.py/commit/67e9628ee39e5b006f90a2115e8c8f1e4bc552b6"><code>67e9628</code></a> Pandas 2 compatibility: Fix a bug regarding timedelta64[ms] representation</li>
<li><a href="https://github.com/plotly/plotly.py/commit/743b52484f47c518b85a04027c1b393528f44c15"><code>743b524</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4134">#4134</a> from plotly/update-docs-version</li>
<li><a href="https://github.com/plotly/plotly.py/commit/5b7cff6100ea0931386856513541a6c4c2a5df0c"><code>5b7cff6</code></a> update docs version</li>
<li><a href="https://github.com/plotly/plotly.py/commit/c79854564c329c3f4df9a990e5bbdea95d69a109"><code>c798545</code></a> Merge pull request <a href="https://redirect.github.com/plotly/plotly.py/issues/4128">#4128</a> from plotly/release-5.14.0</li>
<li><a href="https://github.com/plotly/plotly.py/commit/31e97dc6a62131bb9b33cc3cbcb77f40dcf4cb15"><code>31e97dc</code></a> fix date</li>
<li><a href="https://github.com/plotly/plotly.py/commit/ab8687da27d7aa68757a2cb645e38eaf73e53b71"><code>ab8687d</code></a> update changelog</li>
<li><a href="https://github.com/plotly/plotly.py/commit/ac674ef4a0370d27f32f75100c9118b929a51239"><code>ac674ef</code></a> Update README.md</li>
<li><a href="https://github.com/plotly/plotly.py/commit/8a75262e4f1c1d75e5803c47aab9763f46bbaea9"><code>8a75262</code></a> version changes for v5.14.0</li>
<li>Additional commits viewable in <a href="https://github.com/plotly/plotly.py/compare/v5.11.0...v5.14.1">compare view</a></li>
</ul>
</details>
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You can trigger Dependabot actions by commenting on this PR:
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Bump pypa/cibuildwheel from 2.12.3 to 2.13.0
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] | 2023-06-01T12:57:56
| 2023-06-01T14:06:57
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2023-06-01T14:06:46Z
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CONTRIBUTOR
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.12.3 to 2.13.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p>
<blockquote>
<h2>v2.13.0</h2>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/blob/main/docs/changelog.md">pypa/cibuildwheel's changelog</a>.</em></p>
<blockquote>
<h3>v2.13.0</h3>
<p><em>28 May 2023</em></p>
<ul>
<li>
<p>✨ Adds CPython 3.12 support, under the prerelease flag <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#prerelease-pythons">CIBW_PRERELEASE_PYTHONS</a>. This version of cibuildwheel uses 3.12.0b1.</p>
<p>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.12 will be available in cibuildwheel without the flag. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</p>
</li>
<li>
<p>✨ Adds the ability to pass arguments to the container engine when the container is created, using the <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine">CIBW_CONTAINER_ENGINE</a> option. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a>)</p>
</li>
</ul>
</blockquote>
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<details>
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<li><a href="https://github.com/pypa/cibuildwheel/commit/51f5c7fe68ff24694d5a6ac0eb3ad476ddd062a8"><code>51f5c7f</code></a> Bump version: v2.13.0</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/8499628a5b38525c047996750633a7f7536ada17"><code>8499628</code></a> feat: add Python 3.12 beta 1 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1507">#1507</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/b2bc6fdda6ac2f3e9da11e69d45aba17c7ebcbbd"><code>b2bc6fd</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1499">#1499</a> from pypa/docker-flags</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/754a47388d5e2dcddc8f98e7c36dc605818caa9e"><code>754a473</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1503">#1503</a> from pypa/pre-commit-ci-update-config</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/f25c8a64f6ee92473583130e5ec30ea583b90e7b"><code>f25c8a6</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1506">#1506</a> from artfwo/patch-1</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/9b904777d4c3dd275fa23ca567c4e1ec4fa2b951"><code>9b90477</code></a> Apply suggestions from code review</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/e14b8e8e2f129cdacbd49564032a2d0579d30269"><code>e14b8e8</code></a> Add aalink to examples</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/da9be0a27b525a61e5b418a86e5526a93e349220"><code>da9be0a</code></a> [pre-commit.ci] pre-commit autoupdate</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/301dca264f3e41b1f0d07e13019fccfaaaae6273"><code>301dca2</code></a> chore: use PyPI Trusted Publisher for releases (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1500">#1500</a>)</li>
<li><a href="https://github.com/pypa/cibuildwheel/commit/c74083cfdaa286dc3a30b46c098010a60dc6429e"><code>c74083c</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1485">#1485</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.12.3...v2.13.0">compare view</a></li>
</ul>
</details>
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You can trigger Dependabot actions by commenting on this PR:
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"OK, I won't notify you again about this release, but will get in touch when a new version is available. If you'd rather skip all updates until the next major or minor version, let me know by commenting `@dependabot ignore this major version` or `@dependabot ignore this minor version`. You can also ignore all major, minor, or patch releases for a dependency by adding an [`ignore` condition](https://docs.github.com/en/code-security/supply-chain-security/configuration-options-for-dependency-updates#ignore) with the desired `update_types` to your config file.\n\nIf you change your mind, just re-open this PR and I'll resolve any conflicts on it."
] | 2023-06-01T12:58:01
| 2023-06-01T14:07:00
|
2023-06-01T14:06:47Z
|
CONTRIBUTOR
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Bumps [networkx](https://github.com/networkx/networkx) from 2.8.8 to 3.1.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a href="https://github.com/networkx/networkx/releases">networkx's releases</a>.</em></p>
<blockquote>
<h2>NetworkX 3.1</h2>
<p>No release notes provided.</p>
<h2>networkx-3.1rc0</h2>
<h2>What's Changed</h2>
<ul>
<li>Fix link in isomorphvf2.py by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6347">networkx/networkx#6347</a></li>
<li>Update precommit hooks by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6348">networkx/networkx#6348</a></li>
<li>Add clique examples and deprecate helper funtions by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6186">networkx/networkx#6186</a></li>
<li>Laplace centrality for issue 4973 by <a href="https://github.com/gaborberei"><code>@gaborberei</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/5399">networkx/networkx#5399</a></li>
<li>doc:improve doc of possible values of nodes and expected behaviour by <a href="https://github.com/tinaoberoi"><code>@tinaoberoi</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6333">networkx/networkx#6333</a></li>
<li>add OrderedGraph removal as an API change in release_3.0.rst by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6354">networkx/networkx#6354</a></li>
<li>Update release_3.0 authors (add Jim and Erik) by <a href="https://github.com/eriknw"><code>@eriknw</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6356">networkx/networkx#6356</a></li>
<li>Fix broken link nx guide by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6361">networkx/networkx#6361</a></li>
<li>Add nx-guide link in the tutorial by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6353">networkx/networkx#6353</a></li>
<li>DOC: Minor formatting fixups to get rid of doc build warnings. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6363">networkx/networkx#6363</a></li>
<li>Fix ecuation in clustering documentation by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6369">networkx/networkx#6369</a></li>
<li>Add reference to paper in vf2pp by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6373">networkx/networkx#6373</a></li>
<li>provide tikz with degrees, not radians by <a href="https://github.com/dimpase"><code>@dimpase</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6360">networkx/networkx#6360</a></li>
<li>Improve handling of create_using to allow Mixins of type Protocol by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6244">networkx/networkx#6244</a></li>
<li>Remove an instance of random.sample from a set (deprecated in Python 3.9) by <a href="https://github.com/eriknw"><code>@eriknw</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6380">networkx/networkx#6380</a></li>
<li>DOC: Add banner for user survey annoucement by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6375">networkx/networkx#6375</a></li>
<li>bump pre-commit hooks (and fix CI) by <a href="https://github.com/danieleades"><code>@danieleades</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6396">networkx/networkx#6396</a></li>
<li>Add generate / write "network text" (formerly graph_str) by <a href="https://github.com/Erotemic"><code>@Erotemic</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/5602">networkx/networkx#5602</a></li>
<li>Improve doc regular graphs by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6397">networkx/networkx#6397</a></li>
<li>Fix link vonoroi by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6398">networkx/networkx#6398</a></li>
<li>Document PageRank algo convergence condition by <a href="https://github.com/Qudirah"><code>@Qudirah</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6212">networkx/networkx#6212</a></li>
<li>Fix pre-commit on Python 3.10 by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6407">networkx/networkx#6407</a></li>
<li>DOC: list pred method for MultiDiGraphs by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6409">networkx/networkx#6409</a></li>
<li>Delete warning in approximation documentation by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6221">networkx/networkx#6221</a></li>
<li>Comment out unused unlayered dict construction. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6411">networkx/networkx#6411</a></li>
<li>Update installation test instructions by <a href="https://github.com/EricPostMaster"><code>@EricPostMaster</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6303">networkx/networkx#6303</a></li>
<li>Added new tests in test_clique.py by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6142">networkx/networkx#6142</a></li>
<li>Added test in project. Coverage up to 100. by <a href="https://github.com/Mjh9122"><code>@Mjh9122</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6196">networkx/networkx#6196</a></li>
<li>Add dispatching to more shortest path algorithms by <a href="https://github.com/eriknw"><code>@eriknw</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6415">networkx/networkx#6415</a></li>
<li>Add Plausible Analytics to our docs by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6413">networkx/networkx#6413</a></li>
<li>Fix docstring heading title. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6424">networkx/networkx#6424</a></li>
<li>Added tests to test_directed.py. by <a href="https://github.com/Mjh9122"><code>@Mjh9122</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6208">networkx/networkx#6208</a></li>
<li>Gallery example for Maximum Independent Set by <a href="https://github.com/stanyas"><code>@stanyas</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/5563">networkx/networkx#5563</a></li>
<li>spectral bisection for graphs using fiedler vector by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6404">networkx/networkx#6404</a></li>
<li>Update developer requirements by <a href="https://github.com/jarrodmillman"><code>@jarrodmillman</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6429">networkx/networkx#6429</a></li>
<li>Fix reference in line.py-inverse_line_graph by <a href="https://github.com/Blueclaus13"><code>@Blueclaus13</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6434">networkx/networkx#6434</a></li>
<li>Add project desc for visualization and ISMAGs by <a href="https://github.com/dschult"><code>@dschult</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6432">networkx/networkx#6432</a></li>
<li>Lint using Ruff by <a href="https://github.com/danieleades"><code>@danieleades</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6371">networkx/networkx#6371</a></li>
<li>add ruff commit to git-blame-ignore by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6440">networkx/networkx#6440</a></li>
<li>NXEP 0 and NXEP 1 - change status to Accepted by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/5343">networkx/networkx#5343</a></li>
<li>Bump gh-pages deploy bot version. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6446">networkx/networkx#6446</a></li>
<li>Start using ruff for pyupgrade and isort by <a href="https://github.com/MridulS"><code>@MridulS</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6441">networkx/networkx#6441</a></li>
<li>Add documentation building to contributor guide by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6437">networkx/networkx#6437</a></li>
<li>Reset deploy-action param names for latest version. by <a href="https://github.com/rossbar"><code>@rossbar</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6451">networkx/networkx#6451</a></li>
<li>Doc upgrade paley graph by <a href="https://github.com/paulitapb"><code>@paulitapb</code></a> in <a href="https://redirect.github.com/networkx/networkx/pull/6399">networkx/networkx#6399</a></li>
</ul>
<!-- raw HTML omitted -->
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<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a href="https://github.com/networkx/networkx/commit/9210d9c5bb9875caae0c7be2214abebfdd9255d2"><code>9210d9c</code></a> Designate 3.1 release</li>
<li><a href="https://github.com/networkx/networkx/commit/13ea1f11c442e80f96805af804bdf13932de8bb2"><code>13ea1f1</code></a> Prep 3.1 release</li>
<li><a href="https://github.com/networkx/networkx/commit/8776211515b2bf87f12e5222713870884ff0ec2d"><code>8776211</code></a> Draft release notes (<a href="https://redirect.github.com/networkx/networkx/issues/6621">#6621</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/7297ae8a37dd3356b64d383cb0c55735a6364bcc"><code>7297ae8</code></a> Fix typos (<a href="https://redirect.github.com/networkx/networkx/issues/6620">#6620</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/c55f87045edb25b033854f40eefab092ab9df6eb"><code>c55f870</code></a> Resolve NXEP4 with justification for not implementing it. (<a href="https://redirect.github.com/networkx/networkx/issues/6617">#6617</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/020eaf626d6252f71a75751f63c57cbcc3d55573"><code>020eaf6</code></a> Fix module docstring format for ismags reference article. (<a href="https://redirect.github.com/networkx/networkx/issues/6611">#6611</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/cf7158efc5261a49d0cf9f10a09ff51aeb831c30"><code>cf7158e</code></a> Better default alpha value for viz attributes in gexf writer (<a href="https://redirect.github.com/networkx/networkx/issues/6612">#6612</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/7366c9f5352352e562d5081cdaff042a15a73f72"><code>7366c9f</code></a> Minor docs/test maintenance (<a href="https://redirect.github.com/networkx/networkx/issues/6614">#6614</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/f26a1705f57c83838a966cc847fc52f78ff7314c"><code>f26a170</code></a> Fixed method description in ismags.py (<a href="https://redirect.github.com/networkx/networkx/issues/6600">#6600</a>)</li>
<li><a href="https://github.com/networkx/networkx/commit/6574d58a2d6d2c43692cb6919db701cc1e1ade5f"><code>6574d58</code></a> corrections to docstring of <code>weisfeiler_lehman_subgraph_hashes</code> (<a href="https://redirect.github.com/networkx/networkx/issues/6598">#6598</a>)</li>
<li>Additional commits viewable in <a href="https://github.com/networkx/networkx/compare/networkx-2.8.8...networkx-3.1">compare view</a></li>
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DOC: remove "structure" from init
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[] | 2023-06-01T17:47:35
| 2023-06-01T19:01:56
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2023-06-01T19:01:56Z
|
CONTRIBUTOR
|
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Remove superfluous structure argument docstring from `SQSTransformation` init
Ensure:
- [X] Google format doc strings added. Check with `ruff`.
- [X] Type annotations included. Check with `mypy`.
- [X] Tests added for new features/fixes.
- [X] All tests and linting pass.
Tip: Install `pre-commit` hooks to auto-check before every commit:
```sh
pip install -U pre-commit
pre-commit install
```
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PR_kwDOACgets5R7eOR
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Update `DictSet` to allow direct initialisation
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[
"Thanks!"
] | 2023-06-01T18:04:49
| 2023-06-02T01:23:49
|
2023-06-01T19:01:40Z
|
CONTRIBUTOR
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This is a quick fix to allow direct initialisation of the `DictSet` class, which was possible before but broke in https://github.com/materialsproject/pymatgen/pull/2972 due to the `Yb_2` check querying `self.CONFIG`, which is only defined if `DictSet` was being initialised from a subclass and not directly.
This fixes this behaviour by checking the `config_dict` which is a required input parameter so always defined (same as `self.CONFIG` if initialising from a subclass), and also updates this with the `user_potcar_settings` before checking, in case the user has explicitly specified to avoid the `Yb_2` `POTCAR`.
Demo in the attached notebook and PDF!
[pymatgen_DictSet_fix.zip](https://github.com/materialsproject/pymatgen/files/11628196/pymatgen_DictSet_fix.zip)
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PR_kwDOACgets5R9AA9
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Improvements to `PDPlotter`: unary plots, 2D ternaries, better defaults, and highlight entries
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[
"@janosh I think this is good to go. \r\n\r\nThe tests for `PDPlotter` have always been somewhat minimal (just checking if the functions can run); let me know if you think more is needed here.",
"@mattmcdermott Nice work! This looks like a huge improvement! Thanks for all the screenshots to showcase. You probably know test which parts of the code base in particular might benefit from more tests. Happy to wait but also happy to merge as is.",
"@janosh I think it should be okay to merge. In general, I don't think it's super useful to test Plotly plot generation (beyond the current tests, which make sure figures are generated).",
"@mattmcdermott fantastic work; thanks for this! I'm thinking about how to make similar enhancements in `PourbaixPlotter`. Do you see any opportunities for refactoring where `PDPlotter` and `PourbaixPlotter` could share some of the code you've written here?",
"Thanks for merging in my plotting updates @mattmcdermott and the improvements/extensions! Super helpful and much appreciated :)",
"Thanks for the support guys ❤️\n\n@rkingsbury I'll look into PourbaixPlotter to see if we can streamline anything!",
"Re. Pourbaix plotter, most of the plotly improvements are currently in Crystal Toolkit and quite Pourbaix-specific. I’d be very happy to see it upstreamed (removing code from Crystal Toolkit is a-ok), but I’m not sure specifically what improvements remain to be made. I think it’s pretty decent already but could likely benefit from some love too.",
"> Re. Pourbaix plotter, most of the plotly improvements are currently in Crystal Toolkit and quite Pourbaix-specific. I’d be very happy to see it upstreamed (removing code from Crystal Toolkit is a-ok), but I’m not sure specifically what improvements remain to be made. I think it’s pretty decent already but could likely benefit from some love too.\r\n\r\nAh yes, thanks for the reminder @mkhorton . Much like the PD app before this update, I know a lot of the nice Pourbaix enhancements were living in the web app (which I suppose is powered by Crystal Toolkit), so maybe it's just a matter of moving some of that back into pymatgen. If we could get similar functionality to the web within pymatgen I think that's all we need really.",
"You can use it via Crystal Toolkit too (in a standalone way eg in a notebook) so it’s there if you want it, nevertheless I think pymatgen is a better home. "
] | 2023-06-02T00:14:51
| 2023-06-05T17:47:35
|
2023-06-03T00:55:12Z
|
MEMBER
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## Summary
The `PDPlotter` class has been overdue for updates for quite some time. This PR adds missing functionality that has been living in the MP Phase Diagram app. I have also addressed some issues / requested features.
- Feature: unary (1 component) plots. Code adapted from @mkhorton.
- Feature: 2D ternary plots. Code adapted from @mkhorton. This is now the default behavior; can select from "2d" or "3d" with the `ternary_style` argument in `PDPlotter.__init__()`
- Feature: highlighting a collection of provided entries, per the suggestion by @CompRhys resolves #2402.
- Feature: color fill of facets in quaternary plots. Code adapted from @mkhorton.
- Feature: improved default layouts. Most of this is subtle. For example, I changed margins slightly, camera angles, element annotation positions, etc. I think you'll find most of these changes agreeable! (See attached images)
- Feature: new convenience wrapper for plotting entirely within the phase diagram class: `PhaseDiagram.get_plot()`.
- Fix: `PDPlotter.write_image` now works with `plotly` backend. Addresses https://github.com/materialsproject/pymatgen/issues/1966.
- Fix: With changes to defaults, the complaints addressed by @Youjin1985 are hopefully resolved #2465
- Fix: entry-ids were not displaying in `hovertext` for grand potential phase diagrams
## Checklist
- [x] Google format doc strings added. Check with `ruff`.
- [x] Type annotations included. Check with `mypy`.
- [x] Tests added for new features/fixes.
- [x] All tests and linting pass.
## Pictures
### Unary
### Binary
### Ternary (2D)
### Ternary (3D)
### Quaternary
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`site.specie` in `Structure.species` should be changed to `site.species`
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[
"Can you post the `Structure.to(\"gh-3033.json\")`? This works for me on current `master`\r\n\r\n```py\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nstructure = Structure(\r\n lattice=Lattice.cubic(3),\r\n species=(\"Fe\", \"Fe\"),\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\nstructure.species\r\n>>> [Element Fe, Element Fe]\r\n```",
"```\r\nTraceback (most recent call last):\r\n File ~/miniconda3/envs/chem/lib/python3.9/site-packages/spyder_kernels/py3compat.py:356 in compat_exec\r\n exec(code, globals, locals)\r\n File ~/Rafael_project/codes/test.py:18\r\n Structure.to(\"gh-3033.json\")\r\n File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/structure.py:2549 in to\r\n raise ValueError(f\"Invalid format: `{str(fmt)}`\")\r\nValueError: Invalid format: ``\r\n```\r\nThis is after I changed `site.specie` to `site.species` on line 240 of core/structure.py.",
"Sorry, should have been more clear. The `to` method needs to be called on the `struct` instance, not the class itself.",
"My output is:\r\n`[Comp: Fe1, Comp: Fe1]`",
"So there's no `AttributeError `?",
"Sorry, I need to clarify, there is still `AttributeError` with the original code. After I changed the code in core/structure.py the error disappeared.",
"Again, please post the structure so I can reproduce.",
"After some testing I now know why. My IDE somehow messed up the python interpreter it uses. Running your code on the command line yields no error. (#3034 as well)",
"This issue can be reproduced with the following test code:\r\n```\r\nfrom pymatgen.core import Lattice, Structure\r\n\r\nstructure = Structure(\r\n lattice=Lattice.cubic(3),\r\n species=[{\"Fe\": 0.5, \"Mn\": 0.5}, {\"Fe\": 0.5, \"Mn\": 0.5}],\r\n coords=((0, 0, 0), (0.5, 0.5, 0.5)),\r\n)\r\nprint(structure.species)\r\n```\r\n\r\nAfter changing `site.specie` to `site.species` in line 240 of core/structure.py, the output of this test code yields:\r\n```\r\n[Comp: Mn0.5 Fe0.5, Comp: Mn0.5 Fe0.5]\r\n```",
"I found that the property `species_and_occu` in class `Structure` does what I thought `species` should do. Therefore, it seems this is not a bug but a feature."
] | 2023-06-02T00:40:07
| 2023-06-06T00:42:37
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2023-06-06T00:42:37Z
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CONTRIBUTOR
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The code below
```
print(struct.species)
```
yields the error
```
File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/structure.py:248 in <listcomp>
return [site.specie for site in self]
File ~/miniconda3/envs/chem/lib/python3.9/site-packages/pymatgen/core/sites.py:75 in __getattr__
raise AttributeError(attr)
AttributeError: specie
```
The pymatgen version is 2023.5.10.
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Structures obtained from MP-API yields error when queried `species` attribute
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[
"Similar to #3033, it works for me:\r\n\r\n```py\r\nfrom mp_api.client import MPRester\r\n\r\nwith MPRester() as mpr:\r\n struct = mpr.get_structure_by_material_id(\"mp-1153\", conventional_unit_cell=True)\r\n\r\nprint(struct.species)\r\n>>> [Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element Li, Element S, Element S, Element S, Element S]\r\n```",
"Yeah, mine has `ValidationError`. Not sure what's going on though.",
"After some testing I now know why. My IDE somehow messed up the python interpreter it uses. Running your code on the command line yields no error. (#3033 as well)"
] | 2023-06-02T00:53:58
| 2023-06-02T01:58:30
|
2023-06-02T01:58:29Z
|
CONTRIBUTOR
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The code below:
```
from mp_api.client import MPRester
api_key = "*****"
with MPRester(api_key) as mpr:
struct = mpr.get_structure_by_material_id('mp-1153',
conventional_unit_cell=True)
print(struct.species)
```
yields the error
```
File pydantic/main.py:526 in pydantic.main.BaseModel.parse_obj
File pydantic/main.py:342 in pydantic.main.BaseModel.__init__
ValidationError: 1 validation error for MaterialsDoc
structure
Must provide Structure, the as_dict form, or the proper (type=value_error)
```
The pymatgen version is 2023.5.10.
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Rename VaspInputSet.(potcar_functional->user_potcar_functional) and start testing `DictSet`
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[
"Agreed."
] | 2023-06-02T01:23:19
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Follow up to #3031 adding a test to make sure we don't regress again. I just realized we had 0 tests for `DictSet` before. While writing some, I noticed `DictSet.as_dict()` is also broken. Not only since https://github.com/materialsproject/pymatgen/pull/2972, even before due to not storing the `validate_magmons` init kwarg on instances.
`VaspInputSet.potcar_functional` was renamed to `VaspInputSet.user_potcar_functional` to fix `DictSet.as_dict()` which otherwise errors
```py
NotImplementedError: Unable to automatically determine as_dict format from class. MSONAble requires all args to be present as either self.argname or self._argname
```
A `DictSet` `@property` was added aliasing `.user_potcar_functional` to `.potcar_functional` to avoid breaking changes.
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PR_kwDOACgets5R9lMd
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Don't do a hard `bandgap==0` check in the r2SCAN workflow
|
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[
"Thanks for adding those unit tests! Greatly appreciated!! "
] | 2023-06-02T04:30:45
| 2023-06-02T15:04:30
|
2023-06-02T15:04:29Z
|
MEMBER
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Closes #3023. CC'ing @janosh and @munrojm.
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PR_kwDOACgets5R9xRf
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[WIP] Run selected `deepsource.io` autofixes
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[] | 2023-06-02T05:36:00
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2023-06-02T05:44:24Z
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MEMBER
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Was just playing with things :)
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PR_kwDOACgets5SDBK1
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Simplify `dict["key"] if "key" in dict else None` to `dict.get("key")`
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[] | 2023-06-03T01:14:38
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I_kwDOACgets5nsbWs
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CI failure in `MPResterOldTest.test_pourbaix_mpr_pipeline()`
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[
"The odd thing is, I just ran this test locally and it passes.\r\n\r\n```sh\r\npytest pymatgen/ext/tests/test_matproj.py -k test_pourbaix_mpr_pipeline\r\n```",
"Hi @janosh , I'm not sure what's happening here, but in general yes, changes to the database or API pipeline could potentially trigger test failures here. In this specific case, it looks like one entry has been dropped (reducing the count of stable entries), and a different entry (`mp-996958`) is stabilized than was before.\r\n\r\nIf `mp-499` were somehow excluded from the returned data, that might explain both failures. But weirdly, `mp-499` [still appears on MP](https://materialsproject.org/materials/mp-499?material_ids=mp-499) whereas `mp-996958` does not (it's not shown in search results, and manually [entering the URL](https://materialsproject.org/materials/mp-996958) will time out)\r\n\r\nThe test also passes for me when run locally using the latest `git` pymatgen and the latest released `mp_api`\r\n\r\nI agree it would be nice to make this more robust to database changes, but I've had difficulty thinking of a good way to do so without making the test less rigorous. We could \"dumb it down\" such that we just test 1) that all the returned objects are `PourbaixEntry` type, or that there are a certain number of ions, but the total number of stable domains and the stable phases are really what define a Pourbaix Diagram, so I think it's nice to have a specific tests that verifies those."
] | 2023-06-03T17:30:02
| 2023-09-05T21:47:52
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2023-09-05T21:47:52Z
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@rkingsbury `test_pourbaix_mpr_pipeline` has [started failing recently](https://github.com/materialsproject/pymatgen/actions/runs/5161568900/jobs/9298662810#step:7:31). Based on the call to Rester and the larger than expected number of `stable_entries`, is this because of new data in MP? If so, could we refactor this test to be more robust to future data additions?
```py
def test_pourbaix_mpr_pipeline(self):
data = self.rester.get_pourbaix_entries(["Zn"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Zn": 1e-8})
pbx.find_stable_entry(10, 0)
data = self.rester.get_pourbaix_entries(["Ag", "Te"])
pbx = PourbaixDiagram(data, filter_solids=True, conc_dict={"Ag": 1e-8, "Te": 1e-8})
assert len(pbx.stable_entries) == [30]
E AssertionError: assert [29] == [30]
test_entry = pbx.find_stable_entry(8, 2)
> assert sorted(test_entry.entry_id) == ["ion-10", "mp-499"]
E AssertionError: assert ['ion-10', 'mp-996958'] == ['ion-10', 'mp-499']
```
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I_kwDOACgets5ntxx1
| 3,040
|
`LMAXMIX` should be set based on the presence of s, p, d, f electrons not based on Z
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[] | 2023-06-04T01:44:37
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2023-06-04T18:12:35Z
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MEMBER
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Currently, `LMAXMIX` is set as follows:
https://github.com/materialsproject/pymatgen/blob/67ba063073b468cb33b93f2dc3841fd6ae3941d5/pymatgen/io/vasp/sets.py#L529-L543
However, this is based on Z value and not based on the presence or lack of s, p, d, or f electrons (see [VASP manual](https://www.vasp.at/wiki/index.php/LMAXMIX)). For instance, Sr has Z > 20 but does not have d electrons. And so on. We should be checking this based on the "block" of the electrons in the `Structure` object.
See https://github.com/materialsproject/atomate2/issues/364 for a mirror of this comment and the linked PR for the fix.
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PR_kwDOACgets5SH9Jb
| 3,041
|
Fix LMAXMIX default in VASP INCAR now set based on element blocks in structure
|
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[
"I don't have a unit test for this one yet. We can copy it from the Atomate2 PR once I add it there. I have a unit test in my [Quacc code](https://github.com/Quantum-Accelerators/quacc/blob/3e2e6c2281c214ada86fcba44d43750017844a2a/tests/calculators/vasp/test_vasp.py#L63-L75), but it's not quite the same.",
"@arosen93 How's this test?\r\n\r\n\r\n```py\r\n def test_incar_lmaxmix(self):\r\n # structure containing neither f- nor d-electrons\r\n structure_f = self.get_structure(\"Si\")\r\n assert \"LMAXMIX\" not in MPRelaxSet(structure_f).incar\r\n\r\n # structure containing d-electrons but no f-electrons\r\n structure_d = self.get_structure(\"LiFePO4\")\r\n assert MPRelaxSet(structure_d).incar[\"LMAXMIX\"] == 4\r\n\r\n # structure containing f-electrons but no d-electrons\r\n structure_f = structure_d.copy()\r\n structure_f.replace_species({\"Fe\": \"La\"})\r\n assert MPRelaxSet(structure_f).incar[\"LMAXMIX\"] == 6\r\n\r\n # explicit LMAXMIX in settings overrides automatic selection\r\n structure_override = self.get_structure(\"Si\") # Iron is in the d-block\r\n set_override = MPRelaxSet(structure_override, user_incar_settings={\"LMAXMIX\": 3})\r\n assert set_override.incar[\"LMAXMIX\"] == 3\r\n```",
"Looks almost right, but La doesn't actually have f electrons. Try Ce instead.\r\n\r\n<img width=\"483\" alt=\"image\" src=\"https://github.com/materialsproject/pymatgen/assets/8674072/d4850caa-8935-4224-b151-7b47a15c76f3\">\r\n\r\nAlso, it might be worth adding a test for a structure containing d and f electrons (e.g. Fe and Ce). It should set LMAXMIX = 6.\r\n\r\nAlso also, your final test has Si in place of Fe.",
"Are you sure?\r\n\r\n```py\r\nfrom pymatgen.core import Element\r\n\r\nElement(\"La\").block\r\n>>> 'f'\r\n```",
"Ugh, it's an f-block element but has no f electrons... lol. https://en.wikipedia.org/wiki/Lanthanum. It's probably fine to let LMAXMIX = 6 here regardless.",
"> Among the lanthanides, lanthanum is exceptional as it has no 4f electrons as a single gas-phase atom. Thus it is only very weakly [paramagnetic](https://en.wikipedia.org/wiki/Paramagnetic), unlike the strongly paramagnetic later lanthanides (with the exceptions of the last two, [ytterbium](https://en.wikipedia.org/wiki/Ytterbium) and [lutetium](https://en.wikipedia.org/wiki/Lutetium), where the 4f shell is completely full).[[17]](https://en.wikipedia.org/wiki/Lanthanum#cite_note-17) However, the 4f shell of lanthanum can become partially occupied in chemical environments and participate in chemical bonding\r\n\r\nAh okay, so testing for block is the right thing to do. Carry on with La.",
"> Also also, your final test has Si in place of Fe.\r\n\r\nGood catch.\r\n\r\n> Also, it might be worth adding a test for a structure containing d and f electrons (e.g. Fe and Ce). It should set LMAXMIX = 6.\r\n\r\nWill do.",
"@arosen93 @janosh would this set LMAXMIX = 4 for Gallium (a p-block element)? Because it should according to https://www.vasp.at/forum/viewtopic.php?p=24392#p24374",
"This is an interesting point worth solidifying. In practice, I think the answer is that it depends on the pseudopotential. For instance, if one were to use `Ge`, there are no d electrons in the valence. However, if you use the (recommended) `Ge_d` then of course they are. There is never harm in \"overdoing it\" with regards to LMAXMIX, so I would agree that something like Ge should have LMAXMIX = 4 given the information in the forum post.\r\n\r\nWhat this all boils down to is that:\r\n\r\n1. The VASP manual was ambiguous, per usual.\r\n2. This merged PR should probably be undone to go back to the old way of checking based on Z.\r\n3. The decision should be made in both Pymatgen and Atomate2.\r\n\r\nDo you agree with this assessment?",
"We could also just parse the electrons included in the particular pseudopotential and set LMAXMIX according to what types of electrons are present",
"That might be smarter, albeit slightly more complex. ",
"This change should be reverted, no? @janosh ",
"> We could also just parse the electrons included in the particular pseudopotential and set LMAXMIX according to what types of electrons are present\n\n@matthewkuner are you able to submit a PR for this?",
"@janosh I may be able to do it eventually, but my bandwidth is a bit low rn. I think it is best to revert this change for the time being. ",
"Agreed. I think simplest option is to revert the LMAXMIX-related change. No need to overengineer a solution.",
"Just to confirm, you'd like to revert to this logic?\r\n\r\n```py\r\n if \"LMAXMIX\" not in settings:\r\n # contains f-electrons\r\n if any(el.Z > 56 for el in structure.composition):\r\n incar[\"LMAXMIX\"] = 6\r\n # contains d-electrons\r\n elif any(el.Z > 20 for el in structure.composition):\r\n incar[\"LMAXMIX\"] = 4\r\n```",
"@janosh that seems good to me",
"Correct. "
] | 2023-06-04T15:59:32
| 2023-07-27T18:26:57
|
2023-06-04T18:12:33Z
|
MEMBER
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Closes #3040.
@arosen93 Do you have a good test case for this by any chance?
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