From bff4e0f4998c76bae0943fc39bdfa3d82d128179 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 3 Apr 2024 08:34:22 +0800
Subject: [PATCH 01/11] [pre-commit.ci] pre-commit autoupdate (#1499)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.4 →
v0.3.5](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.4...v0.3.5)
<!--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 60b576273..d1f8d1449 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.4
+    rev: v0.3.5
     hooks:
     - id: ruff
       args: ["--fix"]

From 53668e67c626e43ee1ac11ab728b07a354a706ba 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 08:30:50 +0800
Subject: [PATCH 02/11] [pre-commit.ci] pre-commit autoupdate (#1504)
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 d1f8d1449..c61a7fea0 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 d78d8ef2e4810b3c1448d8e0c13ab2d0aad35659 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 10 Apr 2024 02:59:07 -0400
Subject: [PATCH 03/11] build(deps): bump actions/checkout from 2 to 4 (#1509)
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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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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---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
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and block automerging
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Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/release.yml | 4 ++--
 .github/workflows/test.yml    | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index d40539314..9867c7508 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -9,7 +9,7 @@ jobs:
   conda-publish:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: publish-to-conda
       uses: felix5572/conda-publish-action@v1.9
       with:
@@ -39,7 +39,7 @@ jobs:
         # IMPORTANT: this permission is mandatory for trusted publishing
         id-token: write
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup python
       uses: actions/setup-python@v4
       with:
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 716008b30..29ad46dd4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -12,7 +12,7 @@ jobs:
         python-version: ["3.9", "3.12"]
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v2
       with:

From d28dbe619e6323e3f417df78c17d427b0a6dce93 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 10 Apr 2024 02:59:18 -0400
Subject: [PATCH 04/11] build(deps): bump actions/setup-python from 2 to 5
 (#1508)
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 />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/setup-python&package-manager=github_actions&previous-version=2&new-version=5)](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`.

[//]: # (dependabot-automerge-start)
[//]: # (dependabot-automerge-end)

---

<details>
<summary>Dependabot commands and options</summary>
<br />

You can trigger Dependabot actions by commenting on this PR:
- `@dependabot rebase` will rebase this PR
- `@dependabot recreate` will recreate this PR, overwriting any edits
that have been made to it
- `@dependabot merge` will merge this PR after your CI passes on it
- `@dependabot squash and merge` will squash and merge this PR after
your CI passes on it
- `@dependabot cancel merge` will cancel a previously requested merge
and block automerging
- `@dependabot reopen` will reopen this PR if it is closed
- `@dependabot close` will close this PR and stop Dependabot recreating
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- `@dependabot show <dependency name> ignore conditions` will show all
of the ignore conditions of the specified dependency
- `@dependabot ignore this major version` will close this PR and stop
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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/release.yml | 2 +-
 .github/workflows/test.yml    | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 9867c7508..445588380 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -41,7 +41,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Setup python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: 3.x
         architecture: x64
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 29ad46dd4..72cc38d6f 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -14,7 +14,7 @@ jobs:
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies

From db13fa6ad4c20f029ae0949231da2632032266cf Mon Sep 17 00:00:00 2001
From: DULinhan <dulh20@mails.tsinghua.edu.cn>
Date: Fri, 12 Apr 2024 17:42:43 -0400
Subject: [PATCH 05/11] Modify the post_fp_cp2k function to generate
 multisystem data. Allows to run different system at one single iteration
 model_devi step. (#1513)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Modify the post_fp_cp2k function to generate multisystem data. Allows to
run different system at one single iteration model_devi step.

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Yifan Li李一帆 <yifanl0716@gmail.com>
---
 dpgen/generator/run.py          | 16 +++++++---------
 pyproject.toml                  |  3 ++-
 tests/generator/test_post_fp.py |  2 +-
 3 files changed, 10 insertions(+), 11 deletions(-)

diff --git a/dpgen/generator/run.py b/dpgen/generator/run.py
index 6d9f1c4e4..7e8bfdce6 100644
--- a/dpgen/generator/run.py
+++ b/dpgen/generator/run.py
@@ -4437,20 +4437,18 @@ def post_fp_cp2k(iter_index, jdata, rfailed=None):
         sys_output = glob.glob(os.path.join(work_path, "task.%s.*/output" % ss))
         sys_output.sort()
         tcount += len(sys_output)
-        all_sys = None
+        all_sys = dpdata.MultiSystems(type_map=jdata["type_map"])
         for oo in sys_output:
-            _sys = dpdata.LabeledSystem(oo, fmt="cp2k/output")
-            # _sys.check_type_map(type_map = jdata['type_map'])
-            if all_sys is None:
-                all_sys = _sys
-            else:
-                all_sys.append(_sys)
+            _sys = dpdata.LabeledSystem(
+                oo, fmt="cp2kdata/e_f", type_map=jdata["type_map"]
+            )
+            all_sys.append(_sys)
+            icount += 1
 
-        icount += len(all_sys)
         if (all_sys is not None) and (len(all_sys) > 0):
             sys_data_path = os.path.join(work_path, "data.%s" % ss)
             all_sys.to_deepmd_raw(sys_data_path)
-            all_sys.to_deepmd_npy(sys_data_path, set_size=len(sys_output))
+            all_sys.to_deepmd_npy(sys_data_path)
 
     if tcount == 0:
         rfail = 0.0
diff --git a/pyproject.toml b/pyproject.toml
index 4832355af..301a7d373 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -19,7 +19,8 @@ classifiers = [
 ]
 dependencies = [
     'numpy>=1.14.3',
-    'dpdata>=0.2.16',
+    'dpdata>=0.2.17',
+    'cp2kdata>=0.6.6',
     'pymatgen>=2022.11.1',
     'ase',
     'monty>2.0.0',
diff --git a/tests/generator/test_post_fp.py b/tests/generator/test_post_fp.py
index a4f6adc5f..72251328d 100644
--- a/tests/generator/test_post_fp.py
+++ b/tests/generator/test_post_fp.py
@@ -281,7 +281,7 @@ def setUp(self):
         post_fp(0, jdata)
         self.system_1 = dpdata.LabeledSystem("iter.000000/orig", fmt="deepmd/raw")
         self.system_2 = dpdata.LabeledSystem(
-            "iter.000000/02.fp/data.000", fmt="deepmd/raw"
+            "iter.000000/02.fp/data.000/C2H2N2", fmt="deepmd/raw"
         )
 
 

From 4424fa7951c379a808346f5c32242316ba4ce347 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Fri, 12 Apr 2024 22:59:45 -0400
Subject: [PATCH 06/11] remove conda directory since not being maintained
 (#1516)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 .github/workflows/release.yml | 26 ---------------
 conda/conda_build_config.yaml |  5 ---
 conda/construct.yaml          | 18 -----------
 conda/meta.yaml               | 60 -----------------------------------
 4 files changed, 109 deletions(-)
 delete mode 100644 conda/conda_build_config.yaml
 delete mode 100644 conda/construct.yaml
 delete mode 100644 conda/meta.yaml

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
index 445588380..6b713e876 100644
--- a/.github/workflows/release.yml
+++ b/.github/workflows/release.yml
@@ -6,32 +6,6 @@ on:
       - 'v*'
 
 jobs:
-  conda-publish:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/checkout@v4
-    - name: publish-to-conda
-      uses: felix5572/conda-publish-action@v1.9
-      with:
-        subdir: 'conda'
-        anacondatoken: ${{ secrets.ANACONDA_TOKEN }}
-        platforms: 'noarch'
-  construct-and-publish:
-    runs-on: ubuntu-latest
-    needs: conda-publish
-    steps:
-    - uses: actions/checkout@master
-    - uses: s-weigand/setup-conda@v1
-    - run: conda install constructor jinja2 -y
-    - run: constructor ./conda
-    - name: Upload to release
-      uses: softprops/action-gh-release@master
-      if: startsWith(github.ref, 'refs/tags/')
-      with:
-        files: dpgen-*.sh
-        repository: ${{ env.GITHUB_REPOSITORY }}
-      env:
-        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
   release-to-pypi:
     name: Release to pypi
     runs-on: ubuntu-latest
diff --git a/conda/conda_build_config.yaml b/conda/conda_build_config.yaml
deleted file mode 100644
index 9c44fb84b..000000000
--- a/conda/conda_build_config.yaml
+++ /dev/null
@@ -1,5 +0,0 @@
-channel_sources:
-  - defaults
-  - conda-forge
-channel_targets:
-  - deepmodeling
diff --git a/conda/construct.yaml b/conda/construct.yaml
deleted file mode 100644
index 83c1b0822..000000000
--- a/conda/construct.yaml
+++ /dev/null
@@ -1,18 +0,0 @@
-{% set version = os.popen('git describe --tags --abbrev=0').read().strip('\n').lstrip('v').replace('-', '_') %}
-
-name: dpgen
-version: {{ version }}
-
-channels:
-  - defaults
-  - conda-forge
-  - deepmodeling
-
-specs:
-  - python 3.9
-  - pip
-  - dpgen {{ version }}
-
-ignore_duplicate_files: True
-
-license_file: ../LICENSE
diff --git a/conda/meta.yaml b/conda/meta.yaml
deleted file mode 100644
index b7541087d..000000000
--- a/conda/meta.yaml
+++ /dev/null
@@ -1,60 +0,0 @@
-{% set name = "dpgen" %}
-{% set version = os.popen('git describe --tags --abbrev=0').read().strip('\n').lstrip('v').replace('-', '_') %}
-
-package:
-  name: {{ name|lower }}
-  version: {{ version }}
-
-source:
-  path: ..
-
-build:
-  number: 0
-  noarch: python
-  script: python -m pip install --no-deps --ignore-installed .
-
-requirements:
-  build:
-    - git
-  host:
-    - python >=3.6
-    - pip
-    - setuptools_scm
-    - dargs
-    - paramiko
-    - requests
-    - dpdata
-    - dpdispatcher
-    - ase
-    - GromacsWrapper
-    - custodian
-    - netCDF4
-
-  run:
-    - python >=3.6
-    - dargs
-    - paramiko
-    - requests
-    - dpdata
-    - dpdispatcher
-    - pymatgen
-    - ase
-    - GromacsWrapper
-    - custodian
-    - netCDF4
-
-test:
-  imports:
-    - dpgen
-
-about:
-  home: https://github.com/deepmodeling/dpgen
-  license: LGPL-3.0
-  license_family: LGPL
-  license_file: LICENSE
-  doc_url: https://github.com/deepmodeling/dpgen
-  dev_url: https://github.com/deepmodeling/dpgen
-
-extra:
-  recipe-maintainers:
-    - felix5572

From ccab7fb2cb12b36e0624eddbb146c105aabb0c42 Mon Sep 17 00:00:00 2001
From: "A bot of @njzjz" <48687836+njzjz-bot@users.noreply.github.com>
Date: Fri, 12 Apr 2024 23:00:50 -0400
Subject: [PATCH 07/11] feat(build): Add Git archives version files (#1517)

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 000000000..8fb235d70
--- /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 000000000..00a7b00c9
--- /dev/null
+++ b/.gitattributes
@@ -0,0 +1 @@
+.git_archival.txt  export-subst
diff --git a/pyproject.toml b/pyproject.toml
index 301a7d373..d5997f6a6 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]

From 9c5566a900bf4bfc8c49af91bd5fd9f3af2d653a Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Tue, 16 Apr 2024 04:30:07 -0400
Subject: [PATCH 08/11] ci: setup uv (#1522)

pip: 91 s

![image](https://github.com/deepmodeling/dpgen/assets/9496702/937071b5-d0f1-4963-914f-aab200a3d2ad)

uv: 1 s + 34 s

![image](https://github.com/deepmodeling/dpgen/assets/9496702/9d27d164-e835-4f0a-b56d-bc45dff6a06b)
---
 .github/workflows/test.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 72cc38d6f..ac61619b4 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -17,8 +17,9 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+    - run: pip install uv
     - name: Install dependencies
-      run: pip install -e .[test]
+      run: uv pip install --system -e .[test]
     - name: Test
       run: coverage run --source=./dpgen -m unittest -v && coverage report
     - uses: codecov/codecov-action@v4

From 7d6eed4e2273f4bccbbb9fad55c4fc9536c11fb5 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Tue, 16 Apr 2024 16:30:50 +0800
Subject: [PATCH 09/11] [pre-commit.ci] pre-commit autoupdate (#1521)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.5 →
v0.3.7](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.5...v0.3.7)
<!--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 c61a7fea0..6b52b1535 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.5
+    rev: v0.3.7
     hooks:
     - id: ruff
       args: ["--fix"]

From c0faa58d58ecca9b123ae681fe304a83f8e53f42 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Thu, 18 Apr 2024 22:41:01 -0400
Subject: [PATCH 10/11] docs: setup uv for readthedocs (#1524)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 .readthedocs.yaml | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index 46c022414..bfcccb534 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -10,15 +10,14 @@ build:
   os: ubuntu-22.04
   tools:
     python: "3.10"
-
+  jobs:
+    post_create_environment:
+      - pip install uv
+    post_install:
+      - VIRTUAL_ENV=$READTHEDOCS_VIRTUALENV_PATH uv pip install -r doc/requirements.txt
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
    configuration: doc/conf.py
 
 # If using Sphinx, optionally build your docs in additional formats such as PDF
 formats: all
-
-# Optionally declare the Python requirements required to build your docs
-python:
-   install:
-   - requirements: doc/requirements.txt

From b6714208fb3048f42d40df86255f5fa08a71da1d Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 22 Apr 2024 18:58:24 -0400
Subject: [PATCH 11/11] [pre-commit.ci] pre-commit autoupdate (#1530)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.3.7 →
v0.4.1](https://github.com/astral-sh/ruff-pre-commit/compare/v0.3.7...v0.4.1)
<!--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 6b52b1535..19e94fd61 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -28,7 +28,7 @@ repos:
 
 # Python
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.3.7
+    rev: v0.4.1
     hooks:
     - id: ruff
       args: ["--fix"]