From 2d27e36d902763dbe295eccf89c9afa8eaadb4d8 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 3 Apr 2024 14:38:53 -0400
Subject: [PATCH 1/5] Bump actions/checkout from 2 to 4 (#631)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps [actions/checkout](https://github.com/actions/checkout) from 2 to
4.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/releases">actions/checkout's
releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update default runtime to node20 by <a
href="https://github.com/takost"><code>@​takost</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1436">actions/checkout#1436</a></li>
<li>Support fetching without the --progress option by <a
href="https://github.com/simonbaird"><code>@​simonbaird</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li>
<li>Release 4.0.0 by <a
href="https://github.com/takost"><code>@​takost</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1447">actions/checkout#1447</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/takost"><code>@​takost</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1436">actions/checkout#1436</a></li>
<li><a
href="https://github.com/simonbaird"><code>@​simonbaird</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1067">actions/checkout#1067</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v3...v4.0.0">https://github.com/actions/checkout/compare/v3...v4.0.0</a></p>
<h2>v3.6.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Mark test scripts with Bash'isms to be run via Bash by <a
href="https://github.com/dscho"><code>@​dscho</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1377">actions/checkout#1377</a></li>
<li>Add option to fetch tags even if fetch-depth &gt; 0 by <a
href="https://github.com/RobertWieczoreck"><code>@​RobertWieczoreck</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li>
<li>Release 3.6.0 by <a
href="https://github.com/luketomlinson"><code>@​luketomlinson</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a
href="https://github.com/RobertWieczoreck"><code>@​RobertWieczoreck</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/579">actions/checkout#579</a></li>
<li><a
href="https://github.com/luketomlinson"><code>@​luketomlinson</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1437">actions/checkout#1437</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v3.5.3...v3.6.0">https://github.com/actions/checkout/compare/v3.5.3...v3.6.0</a></p>
<h2>v3.5.3</h2>
<h2>What's Changed</h2>
<ul>
<li>Fix: Checkout Issue in self hosted runner due to faulty submodule
check-ins by <a
href="https://github.com/megamanics"><code>@​megamanics</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li>
<li>Fix typos found by codespell by <a
href="https://github.com/DimitriPapadopoulos"><code>@​DimitriPapadopoulos</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li>
<li>Add support for sparse checkouts by <a
href="https://github.com/dscho"><code>@​dscho</code></a> and <a
href="https://github.com/dfdez"><code>@​dfdez</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li>
<li>Release v3.5.3 by <a
href="https://github.com/TingluoHuang"><code>@​TingluoHuang</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/1376">actions/checkout#1376</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a
href="https://github.com/megamanics"><code>@​megamanics</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1196">actions/checkout#1196</a></li>
<li><a
href="https://github.com/DimitriPapadopoulos"><code>@​DimitriPapadopoulos</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1287">actions/checkout#1287</a></li>
<li><a href="https://github.com/dfdez"><code>@​dfdez</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1369">actions/checkout#1369</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v3...v3.5.3">https://github.com/actions/checkout/compare/v3...v3.5.3</a></p>
<h2>v3.5.2</h2>
<h2>What's Changed</h2>
<ul>
<li>Fix: Use correct API url / endpoint in GHES by <a
href="https://github.com/fhammerl"><code>@​fhammerl</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1289">actions/checkout#1289</a>
based on <a
href="https://redirect.github.com/actions/checkout/issues/1286">#1286</a>
by <a href="https://github.com/1newsr"><code>@​1newsr</code></a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v3.5.1...v3.5.2">https://github.com/actions/checkout/compare/v3.5.1...v3.5.2</a></p>
<h2>v3.5.1</h2>
<h2>What's Changed</h2>
<ul>
<li>Improve checkout performance on Windows runners by upgrading
<code>@​actions/github</code> dependency by <a
href="https://github.com/BrettDong"><code>@​BrettDong</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a href="https://github.com/BrettDong"><code>@​BrettDong</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/checkout/pull/1246">actions/checkout#1246</a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Changelog</summary>
<p><em>Sourced from <a
href="https://github.com/actions/checkout/blob/main/CHANGELOG.md">actions/checkout's
changelog</a>.</em></p>
<blockquote>
<h1>Changelog</h1>
<h2>v4.1.2</h2>
<ul>
<li>Fix: Disable sparse checkout whenever <code>sparse-checkout</code>
option is not present <a
href="https://github.com/dscho"><code>@​dscho</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1598">actions/checkout#1598</a></li>
</ul>
<h2>v4.1.1</h2>
<ul>
<li>Correct link to GitHub Docs by <a
href="https://github.com/peterbe"><code>@​peterbe</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/1511">actions/checkout#1511</a></li>
<li>Link to release page from what's new section by <a
href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1514">actions/checkout#1514</a></li>
</ul>
<h2>v4.1.0</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/1396">Add
support for partial checkout filters</a></li>
</ul>
<h2>v4.0.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1067">Support
fetching without the --progress option</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1436">Update to
node20</a></li>
</ul>
<h2>v3.6.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1377">Fix: Mark
test scripts with Bash'isms to be run via Bash</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/579">Add
option to fetch tags even if fetch-depth &gt; 0</a></li>
</ul>
<h2>v3.5.3</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1196">Fix:
Checkout fail in self-hosted runners when faulty submodule are
checked-in</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/1287">Fix
typos found by codespell</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/1369">Add
support for sparse checkouts</a></li>
</ul>
<h2>v3.5.2</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/1289">Fix
api endpoint for GHES</a></li>
</ul>
<h2>v3.5.1</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/1246">Fix
slow checkout on Windows</a></li>
</ul>
<h2>v3.5.0</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/1237">Add
new public key for known_hosts</a></li>
</ul>
<h2>v3.4.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1209">Upgrade
codeql actions to v2</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1210">Upgrade
dependencies</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1225">Upgrade
<code>@​actions/io</code></a></li>
</ul>
<h2>v3.3.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1045">Implement
branch list using callbacks from exec function</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/1050">Add
in explicit reference to private checkout options</a></li>
<li>[Fix comment typos (that got added in <a
href="https://redirect.github.com/actions/checkout/issues/770">#770</a>)](<a
href="https://redirect.github.com/actions/checkout/pull/1057">actions/checkout#1057</a>)</li>
</ul>
<h2>v3.2.0</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/942">Add
GitHub Action to perform release</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/967">Fix
status badge</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1002">Replace
datadog/squid with ubuntu/squid Docker image</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/964">Wrap
pipeline commands for submoduleForeach in quotes</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/1029">Update
<code>@​actions/io</code> to 1.1.2</a></li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/checkout/commit/b4ffde65f46336ab88eb53be808477a3936bae11"><code>b4ffde6</code></a>
Link to release page from what's new section (<a
href="https://redirect.github.com/actions/checkout/issues/1514">#1514</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/8530928916aaef40f59e6f221989ccb31f5759e7"><code>8530928</code></a>
Correct link to GitHub Docs (<a
href="https://redirect.github.com/actions/checkout/issues/1511">#1511</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/7cdaf2fbc075e6f3b9ca94cfd6cec5adc8a75622"><code>7cdaf2f</code></a>
Update CODEOWNERS to Launch team (<a
href="https://redirect.github.com/actions/checkout/issues/1510">#1510</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/8ade135a41bc03ea155e62e844d188df1ea18608"><code>8ade135</code></a>
Prepare 4.1.0 release (<a
href="https://redirect.github.com/actions/checkout/issues/1496">#1496</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/c533a0a4cfc4962971818edcfac47a2899e69799"><code>c533a0a</code></a>
Add support for partial checkout filters (<a
href="https://redirect.github.com/actions/checkout/issues/1396">#1396</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/72f2cec99f417b1a1c5e2e88945068983b7965f9"><code>72f2cec</code></a>
Update README.md for V4 (<a
href="https://redirect.github.com/actions/checkout/issues/1452">#1452</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/3df4ab11eba7bda6032a0b82a6bb43b11571feac"><code>3df4ab1</code></a>
Release 4.0.0 (<a
href="https://redirect.github.com/actions/checkout/issues/1447">#1447</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/8b5e8b768746b50394015010d25e690bfab9dfbc"><code>8b5e8b7</code></a>
Support fetching without the --progress option (<a
href="https://redirect.github.com/actions/checkout/issues/1067">#1067</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/97a652b80035363df47baee5031ec8670b8878ac"><code>97a652b</code></a>
Update default runtime to node20 (<a
href="https://redirect.github.com/actions/checkout/issues/1436">#1436</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/f43a0e5ff2bd294095638e18286ca9a3d1956744"><code>f43a0e5</code></a>
Release 3.6.0 (<a
href="https://redirect.github.com/actions/checkout/issues/1437">#1437</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/checkout/compare/v2...v4">compare
view</a></li>
</ul>
</details>
<br />


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You can trigger Dependabot actions by commenting on this PR:
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---
 .github/workflows/test.yml        | 2 +-
 .github/workflows/test_import.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 3e88b72b..32e5fde6 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
         python-version: ["3.7", "3.8", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     # set up conda
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
diff --git a/.github/workflows/test_import.yml b/.github/workflows/test_import.yml
index b04d05cd..9f1f7d8e 100644
--- a/.github/workflows/test_import.yml
+++ b/.github/workflows/test_import.yml
@@ -8,7 +8,7 @@ jobs:
   build:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - uses: actions/setup-python@v2
       with:
         python-version: '3.9'

From 38691462dbbca535115804ad413fe380a2b483d5 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 3 Apr 2024 14:43:07 -0400
Subject: [PATCH 2/5] Bump actions/setup-python from 2 to 5 (#630)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps [actions/setup-python](https://github.com/actions/setup-python)
from 2 to 5.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/setup-python/releases">actions/setup-python's
releases</a>.</em></p>
<blockquote>
<h2>v5.0.0</h2>
<h2>What's Changed</h2>
<p>In scope of this release, we update node version runtime from node16
to node20 (<a
href="https://redirect.github.com/actions/setup-python/pull/772">actions/setup-python#772</a>).
Besides, we update dependencies to the latest versions.</p>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0">https://github.com/actions/setup-python/compare/v4.8.0...v5.0.0</a></p>
<h2>v4.8.0</h2>
<h2>What's Changed</h2>
<p>In scope of this release we added support for GraalPy (<a
href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a>).
You can use this snippet to set up GraalPy:</p>
<pre lang="yaml"><code>steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
  with:
    python-version: 'graalpy-22.3'
- run: python my_script.py
</code></pre>
<p>Besides, the release contains such changes as:</p>
<ul>
<li>Trim python version when reading from file by <a
href="https://github.com/FerranPares"><code>@​FerranPares</code></a> in
<a
href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
<li>Use non-deprecated versions in examples by <a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
<li>Change deprecation comment to past tense by <a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/723">actions/setup-python#723</a></li>
<li>Bump <code>@​babel/traverse</code> from 7.9.0 to 7.23.2 by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/743">actions/setup-python#743</a></li>
<li>advanced-usage.md: Encourage the use actions/checkout@v4 by <a
href="https://github.com/cclauss"><code>@​cclauss</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/729">actions/setup-python#729</a></li>
<li>Examples now use checkout@v4 by <a
href="https://github.com/simonw"><code>@​simonw</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/738">actions/setup-python#738</a></li>
<li>Update actions/checkout to v4 by <a
href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
in <a
href="https://redirect.github.com/actions/setup-python/pull/761">actions/setup-python#761</a></li>
</ul>
<h2>New Contributors</h2>
<ul>
<li><a
href="https://github.com/FerranPares"><code>@​FerranPares</code></a>
made their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/628">actions/setup-python#628</a></li>
<li><a href="https://github.com/timfel"><code>@​timfel</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/694">actions/setup-python#694</a></li>
<li><a
href="https://github.com/jeffwidman"><code>@​jeffwidman</code></a> made
their first contribution in <a
href="https://redirect.github.com/actions/setup-python/pull/724">actions/setup-python#724</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4...v4.8.0">https://github.com/actions/setup-python/compare/v4...v4.8.0</a></p>
<h2>v4.7.1</h2>
<h2>What's Changed</h2>
<ul>
<li>Bump word-wrap from 1.2.3 to 1.2.4 by <a
href="https://github.com/dependabot"><code>@​dependabot</code></a> in <a
href="https://redirect.github.com/actions/setup-python/pull/702">actions/setup-python#702</a></li>
<li>Add range validation for toml files by <a
href="https://github.com/dmitry-shibanov"><code>@​dmitry-shibanov</code></a>
in <a
href="https://redirect.github.com/actions/setup-python/pull/726">actions/setup-python#726</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/setup-python/compare/v4...v4.7.1">https://github.com/actions/setup-python/compare/v4...v4.7.1</a></p>
<h2>v4.7.0</h2>
<p>In scope of this release, the support for reading python version from
pyproject.toml was added (<a
href="https://redirect.github.com/actions/setup-python/pull/669">actions/setup-python#669</a>).</p>
<pre lang="yaml"><code>      - name: Setup Python
        uses: actions/setup-python@v4
&lt;/tr&gt;&lt;/table&gt;
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/setup-python/commit/82c7e631bb3cdc910f68e0081d67478d79c6982d"><code>82c7e63</code></a>
Documentation changes for avoiding rate limit issues on GHES (<a
href="https://redirect.github.com/actions/setup-python/issues/835">#835</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/10aa35afd7f071e70ffaa122e3d7c6ffcb5f7ed1"><code>10aa35a</code></a>
feat: fallback to raw endpoint for manifest when rate limit is reached
(<a
href="https://redirect.github.com/actions/setup-python/issues/766">#766</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/9a7ac94420f42ee15fc60ab88d0dca4be1fd5757"><code>9a7ac94</code></a>
Bump undici from 5.27.2 to 5.28.3 (<a
href="https://redirect.github.com/actions/setup-python/issues/817">#817</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/871daa956ca9ea99f3c3e30acb424b7960676734"><code>871daa9</code></a>
Fix the &quot;Specifying multiple Python/PyPy versions&quot; link (<a
href="https://redirect.github.com/actions/setup-python/issues/782">#782</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/2f078955e4d0f34cc7a8b0108b2eb7bbe154438e"><code>2f07895</code></a>
Fix broken README.md link (<a
href="https://redirect.github.com/actions/setup-python/issues/793">#793</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/e9d6f990972a57673cdb72ec29e19d42ba28880f"><code>e9d6f99</code></a>
Replace setup-python@v4 by setup-python@v5 in README (<a
href="https://redirect.github.com/actions/setup-python/issues/776">#776</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/0a5c61591373683505ea898e09a3ea4f39ef2b9c"><code>0a5c615</code></a>
Update action to node20 (<a
href="https://redirect.github.com/actions/setup-python/issues/772">#772</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/0ae58361cdfd39e2950bed97a1e26aa20c3d8955"><code>0ae5836</code></a>
Add example of GraalPy to docs (<a
href="https://redirect.github.com/actions/setup-python/issues/773">#773</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/b64ffcaf5b410884ad320a9cfac8866006a109aa"><code>b64ffca</code></a>
update actions/checkout to v4 (<a
href="https://redirect.github.com/actions/setup-python/issues/761">#761</a>)</li>
<li><a
href="https://github.com/actions/setup-python/commit/8d2896179abf658742de432b3f203d2c2d86a587"><code>8d28961</code></a>
Examples now use checkout@v4 (<a
href="https://redirect.github.com/actions/setup-python/issues/738">#738</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/setup-python/compare/v2...v5">compare
view</a></li>
</ul>
</details>
<br />


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`@dependabot rebase`.

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<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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</details>

Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/test.yml        | 2 +-
 .github/workflows/test_import.yml | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 32e5fde6..e4d9a91f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -15,7 +15,7 @@ jobs:
     - uses: actions/checkout@v4
     # set up conda
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     # install rdkit and openbabel
diff --git a/.github/workflows/test_import.yml b/.github/workflows/test_import.yml
index 9f1f7d8e..6ab0dbe2 100644
--- a/.github/workflows/test_import.yml
+++ b/.github/workflows/test_import.yml
@@ -9,7 +9,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
-    - uses: actions/setup-python@v2
+    - uses: actions/setup-python@v5
       with:
         python-version: '3.9'
         architecture: 'x64'

From 17fe0aa1381937144224995ce51575acf8c8ff30 Mon Sep 17 00:00:00 2001
From: m0sey <61280022+MoseyQAQ@users.noreply.github.com>
Date: Fri, 5 Apr 2024 22:34:05 +0800
Subject: [PATCH 3/5] PyMatgenStructureFormat with from_system method (#626)

Now the PyMatgenStructureFormat doesn't support the
<kbd>from_system</kbd> method.
This PR adds this method, enabling users to convert the
<kbd>pymatgen.core.Structure</kbd> to the dpdata format, which is
convenient when you use <kbd>pymatgen.transformations</kbd> to build the
atomic model.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 dpdata/plugins/pymatgen.py   | 18 ++++++++++++++++++
 dpdata/pymatgen/structure.py | 24 ++++++++++++++++++++++++
 tests/test_from_pymatgen.py  | 30 ++++++++++++++++++++++++++++++
 tests/test_to_pymatgen.py    |  4 ++--
 4 files changed, 74 insertions(+), 2 deletions(-)
 create mode 100644 dpdata/pymatgen/structure.py
 create mode 100644 tests/test_from_pymatgen.py

diff --git a/dpdata/plugins/pymatgen.py b/dpdata/plugins/pymatgen.py
index 82b64e71..e7e527ff 100644
--- a/dpdata/plugins/pymatgen.py
+++ b/dpdata/plugins/pymatgen.py
@@ -1,11 +1,29 @@
 import numpy as np
 
 import dpdata.pymatgen.molecule
+import dpdata.pymatgen.structure
 from dpdata.format import Format
 
 
 @Format.register("pymatgen/structure")
 class PyMatgenStructureFormat(Format):
+    def from_system(self, structure, **kwargs) -> dict:
+        """Convert pymatgen.core.Structure to System.
+
+        Parameters
+        ----------
+        structure : pymatgen.core.Structure
+            a Pymatgen Structure, containing a structure
+        **kwargs : dict
+            other parameters
+
+        Returns
+        -------
+        dict
+            data dict
+        """
+        return dpdata.pymatgen.structure.from_system_data(structure)
+
     def to_system(self, data, **kwargs):
         """Convert System to Pymatgen Structure obj."""
         structures = []
diff --git a/dpdata/pymatgen/structure.py b/dpdata/pymatgen/structure.py
new file mode 100644
index 00000000..b6c148da
--- /dev/null
+++ b/dpdata/pymatgen/structure.py
@@ -0,0 +1,24 @@
+import numpy as np
+
+try:
+    from pymatgen.core import Structure  # noqa: F401
+except ImportError:
+    pass
+
+
+def from_system_data(structure) -> dict:
+    symbols = [site.species_string for site in structure]
+    atom_names = list(structure.symbol_set)
+    atom_numbs = [symbols.count(symbol) for symbol in atom_names]
+    atom_types = np.array([atom_names.index(symbol) for symbol in symbols]).astype(int)
+    coords = structure.cart_coords
+    cells = structure.lattice.matrix
+
+    info_dict = {
+        "atom_names": atom_names,
+        "atom_numbs": atom_numbs,
+        "atom_types": atom_types,
+        "coords": np.array([coords]),
+        "cells": np.array([cells]),
+    }
+    return info_dict
diff --git a/tests/test_from_pymatgen.py b/tests/test_from_pymatgen.py
new file mode 100644
index 00000000..d3ddbe3e
--- /dev/null
+++ b/tests/test_from_pymatgen.py
@@ -0,0 +1,30 @@
+import os
+import unittest
+
+from comp_sys import CompSys
+from context import dpdata
+
+try:
+    from pymatgen.core import Structure  # noqa: F401
+
+    exist_module = True
+except Exception:
+    exist_module = False
+
+
+@unittest.skipIf(not exist_module, "skip pymatgen")
+class TestFormPytmatgen(unittest.TestCase, CompSys):
+    def setUp(self):
+        structure = Structure.from_file(os.path.join("poscars", "POSCAR.P42nmc"))
+        self.system_1 = dpdata.System(structure, fmt="pymatgen/structure")
+        self.system_2 = dpdata.System(
+            os.path.join("poscars", "POSCAR.P42nmc"), fmt="poscar"
+        )
+        self.places = 6
+        self.e_places = 6
+        self.f_places = 6
+        self.v_places = 6
+
+
+if __name__ == "__main__":
+    unittest.main()
diff --git a/tests/test_to_pymatgen.py b/tests/test_to_pymatgen.py
index d5815396..b55443d4 100644
--- a/tests/test_to_pymatgen.py
+++ b/tests/test_to_pymatgen.py
@@ -5,7 +5,7 @@
 from context import dpdata
 
 try:
-    from pymatgen import Structure  # noqa: F401
+    from pymatgen.core import Structure  # noqa: F401
 
     exist_module = True
 except Exception:
@@ -19,7 +19,7 @@ def setUp(self):
         system_1.from_lammps_lmp(
             os.path.join("poscars", "conf.lmp"), type_map=["O", "H"]
         )
-        system_1.to_pymatgen_structure()[0].to("poscar", "tmp.POSCAR")
+        system_1.to_pymatgen_structure()[0].to(filename="tmp.POSCAR", fmt="poscar")
         self.system_1 = system_1
         self.system_2 = dpdata.System("tmp.POSCAR")
         self.places = 6

From a5c0252eeb008659428e682a1b891da5800eedee Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 9 Apr 2024 08:31:00 +0800
Subject: [PATCH 4/5] [pre-commit.ci] pre-commit autoupdate (#634)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/pre-commit/pre-commit-hooks: v4.5.0 →
v4.6.0](https://github.com/pre-commit/pre-commit-hooks/compare/v4.5.0...v4.6.0)
<!--pre-commit.ci end-->

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 .pre-commit-config.yaml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index a7a2afa8..c199c7ad 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     # there are many log files in tests
     # TODO: seperate py files and log files

From 4bf2f57ba43d92a3ccce41e815eff28c7a98250f Mon Sep 17 00:00:00 2001
From: "njzjz-bot[bot]" <48687836+njzjz-bot@users.noreply.github.com>
Date: Fri, 12 Apr 2024 21:34:53 -0400
Subject: [PATCH 5/5] feat(build): Add Git archives version files

When downloading the source code of a branch or a release from GitHub or the mirror, there is no Git version information, making setuptools-scm unable to read the version. The alternative way is to add a git archive file supported by setuptools-scm. See:
* https://setuptools-scm.readthedocs.io/en/latest/usage/#git-archives (available in setuptools-scm 7.0.0)
* https://git-scm.com/docs/git-archive#Documentation/git-archive.txt-export-subst
* https://docs.github.com/en/repositories/working-with-files/using-files/downloading-source-code-archives

Generated by the task: https://github.com/njzjz-bot/njzjz-bot/issues/4.
---
 .git_archival.txt | 4 ++++
 .gitattributes    | 1 +
 pyproject.toml    | 2 +-
 3 files changed, 6 insertions(+), 1 deletion(-)
 create mode 100644 .git_archival.txt
 create mode 100644 .gitattributes

diff --git a/.git_archival.txt b/.git_archival.txt
new file mode 100644
index 00000000..8fb235d7
--- /dev/null
+++ b/.git_archival.txt
@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$
diff --git a/.gitattributes b/.gitattributes
new file mode 100644
index 00000000..00a7b00c
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/pyproject.toml b/pyproject.toml
index 8fe408eb..3f09801a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools>=61", "setuptools_scm[toml]>=6.2"]
+requires = ["setuptools>=61", "setuptools_scm[toml]>=7"]
 build-backend = "setuptools.build_meta"
 
 [project]