From e0f2cc59f72901118f6d4a58f59889358af19960 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 15 Mar 2023 09:40:16 +0800
Subject: [PATCH 01/13] Bump actions/checkout from 2 to 3 (#2381)
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
3.
<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>v3.0.0</h2>
<ul>
<li>Updated to the node16 runtime by default
<ul>
<li>This requires a minimum <a
href="https://github.com/actions/runner/releases/tag/v2.285.0">Actions
Runner</a> version of v2.285.0 to run, which is by default available in
GHES 3.4 or later.</li>
</ul>
</li>
</ul>
<h2>v2.6.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Add backports to v2 branch by <a
href="https://github.com/cory-miller"><code>@​cory-miller</code></a> in
<a
href="https://redirect.github.com/actions/checkout/pull/1040">actions/checkout#1040</a>
<ul>
<li>Includes backports from the following changes: <a
href="https://redirect.github.com/actions/checkout/pull/964">actions/checkout#964</a>,
<a
href="https://redirect.github.com/actions/checkout/pull/1002">actions/checkout#1002</a>,
<a
href="https://redirect.github.com/actions/checkout/pull/1029">actions/checkout#1029</a></li>
<li>Upgraded the licensed version to match what is used in v3.</li>
</ul>
</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2.5.0...v2.6.0">https://github.com/actions/checkout/compare/v2.5.0...v2.6.0</a></p>
<h2>v2.5.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update <code>@​actions/core</code> to 1.10.0 by <a
href="https://github.com/rentziass"><code>@​rentziass</code></a> in <a
href="https://redirect.github.com/actions/checkout/pull/962">actions/checkout#962</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2...v2.5.0">https://github.com/actions/checkout/compare/v2...v2.5.0</a></p>
<h2>v2.4.2</h2>
<h2>What's Changed</h2>
<ul>
<li>Add set-safe-directory input to allow customers to take control. (<a
href="https://redirect.github.com/actions/checkout/issues/770">#770</a>)
by <a
href="https://github.com/TingluoHuang"><code>@​TingluoHuang</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/776">actions/checkout#776</a></li>
<li>Prepare changelog for v2.4.2. by <a
href="https://github.com/TingluoHuang"><code>@​TingluoHuang</code></a>
in <a
href="https://redirect.github.com/actions/checkout/pull/778">actions/checkout#778</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/actions/checkout/compare/v2...v2.4.2">https://github.com/actions/checkout/compare/v2...v2.4.2</a></p>
<h2>v2.4.1</h2>
<ul>
<li>Fixed an issue where checkout failed to run in container jobs due to
the new git setting <code>safe.directory</code></li>
</ul>
<h2>v2.4.0</h2>
<ul>
<li>Convert SSH URLs like <code>org-&lt;ORG_ID&gt;@github.com:</code> to
<code>https://github.com/</code> - <a
href="https://redirect.github.com/actions/checkout/pull/621">pr</a></li>
</ul>
<h2>v2.3.5</h2>
<p>Update dependencies</p>
<h2>v2.3.4</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/379">Add
missing <code>await</code>s</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/360">Swap
to Environment Files</a></li>
</ul>
<h2>v2.3.3</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/345">Remove
Unneeded commit information from build logs</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/326">Add
Licensed to verify third party dependencies</a></li>
</ul>
<h2>v2.3.2</h2>
<p><a href="https://redirect.github.com/actions/checkout/pull/320">Add
Third Party License Information to Dist Files</a></p>
<h2>v2.3.1</h2>
<p><a href="https://redirect.github.com/actions/checkout/pull/284">Fix
default branch resolution for .wiki and when using SSH</a></p>
<!-- 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>v3.1.0</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/939">Use
<code>@​actions/core</code> <code>saveState</code> and
<code>getState</code></a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/922">Add
<code>github-server-url</code> input</a></li>
</ul>
<h2>v3.0.2</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/770">Add
input <code>set-safe-directory</code></a></li>
</ul>
<h2>v3.0.1</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/762">Fixed an
issue where checkout failed to run in container jobs due to the new git
setting <code>safe.directory</code></a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/744">Bumped
various npm package versions</a></li>
</ul>
<h2>v3.0.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/689">Update to
node 16</a></li>
</ul>
<h2>v2.3.1</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/284">Fix
default branch resolution for .wiki and when using SSH</a></li>
</ul>
<h2>v2.3.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/278">Fallback to
the default branch</a></li>
</ul>
<h2>v2.2.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/258">Fetch all
history for all tags and branches when fetch-depth=0</a></li>
</ul>
<h2>v2.1.1</h2>
<ul>
<li>Changes to support GHES (<a
href="https://redirect.github.com/actions/checkout/pull/236">here</a>
and <a
href="https://redirect.github.com/actions/checkout/pull/248">here</a>)</li>
</ul>
<h2>v2.1.0</h2>
<ul>
<li><a
href="https://redirect.github.com/actions/checkout/pull/191">Group
output</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/199">Changes to
support GHES alpha release</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/184">Persist
core.sshCommand for submodules</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/163">Add
support ssh</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/179">Convert
submodule SSH URL to HTTPS, when not using SSH</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/157">Add
submodule support</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/144">Follow
proxy settings</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/141">Fix
ref for pr closed event when a pr is merged</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/128">Fix
issue checking detached when git less than 2.22</a></li>
</ul>
<h2>v2.0.0</h2>
<ul>
<li><a href="https://redirect.github.com/actions/checkout/pull/108">Do
not pass cred on command line</a></li>
<li><a href="https://redirect.github.com/actions/checkout/pull/107">Add
input persist-credentials</a></li>
<li><a
href="https://redirect.github.com/actions/checkout/pull/104">Fallback to
REST API to download repo</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/ac593985615ec2ede58e132d2e21d2b1cbd6127c"><code>ac59398</code></a>
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/issues/1057">#1057</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/3ba5ee6fac7e0e30e2ea884e236f282d3a775891"><code>3ba5ee6</code></a>
Add in explicit reference to private checkout options (<a
href="https://redirect.github.com/actions/checkout/issues/1050">#1050</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/885641592076c27bfb56c028cd5612cdad63e16d"><code>8856415</code></a>
Implement branch list using callbacks from exec function (<a
href="https://redirect.github.com/actions/checkout/issues/1045">#1045</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/755da8c3cf115ac066823e79a1e1788f8940201b"><code>755da8c</code></a>
3.2.0 (<a
href="https://redirect.github.com/actions/checkout/issues/1039">#1039</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/26d48e8ea150211a9bc3b1f0c20448599687d926"><code>26d48e8</code></a>
Update <code>@​actions/io</code> to 1.1.2 (<a
href="https://redirect.github.com/actions/checkout/issues/1029">#1029</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/bf085276cecdb0cc76fbbe0687a5a0e786646936"><code>bf08527</code></a>
wrap pipeline commands for submoduleForeach in quotes (<a
href="https://redirect.github.com/actions/checkout/issues/964">#964</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/5c3ccc22eb2c950a0fa5bc7c47190d8e3f7e681a"><code>5c3ccc2</code></a>
Replace datadog/squid with ubuntu/squid Docker image (<a
href="https://redirect.github.com/actions/checkout/issues/1002">#1002</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/1f9a0c22da41e6ebfa534300ef656657ea2c6707"><code>1f9a0c2</code></a>
README - fix status badge (<a
href="https://redirect.github.com/actions/checkout/issues/967">#967</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/8230315d06ad95c617244d2f265d237a1682d445"><code>8230315</code></a>
Add workflow to update a main version (<a
href="https://redirect.github.com/actions/checkout/issues/942">#942</a>)</li>
<li><a
href="https://github.com/actions/checkout/commit/93ea575cb5d8a053eaa0ac8fa3b40d7e05a33cc8"><code>93ea575</code></a>
Prepare release v3.1.0 (<a
href="https://redirect.github.com/actions/checkout/issues/940">#940</a>)</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/checkout/compare/v2...v3">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/checkout&package-manager=github_actions&previous-version=2&new-version=3)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

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

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index bb34fe0bf6..cd4dd728b3 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -33,7 +33,7 @@ jobs:
             platform_id: manylinux_aarch64
             dp_variant: cpu
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
         with:
           submodules: true
           # https://github.com/pypa/setuptools_scm/issues/480
diff --git a/.github/workflows/package_c.yml b/.github/workflows/package_c.yml
index e57c0a30e1..0a0d16816f 100644
--- a/.github/workflows/package_c.yml
+++ b/.github/workflows/package_c.yml
@@ -9,7 +9,7 @@ jobs:
     name: Build C library
     runs-on: ubuntu-22.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Package C library
         run: ./source/install/docker_package_c.sh
       - name: Test C library

From 55cf6b4dcd9c35a755ad91cd80bd85981d3fc61d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 15 Mar 2023 09:40:50 +0800
Subject: [PATCH 02/13] Bump pypa/cibuildwheel from 2.11.3 to 2.12.1 (#2382)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from
2.11.3 to 2.12.1.
<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>v2.12.1</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>
<h2>v2.11.4</h2>
<ul>
<li>🐛 Fix a bug that caused missing wheels on Windows when a test was
skipped using CIBW_TEST_SKIP (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1377">#1377</a>)</li>
<li>🛠 Updates CPython 3.11 to 3.11.1 (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1371">#1371</a>)</li>
<li>🛠 Updates PyPy 3.7 to 3.7.10, except on macOS which remains on 7.3.9
due to a bug. (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1371">#1371</a>)</li>
<li>📚 Added a reference to abi3audit to the docs (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1347">#1347</a>)</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>v2.12.1</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>
<h3>v2.11.4</h3>
<p><em>24 Dec 2022</em></p>
<ul>
<li>🐛 Fix a bug that caused missing wheels on Windows when a test was
skipped using CIBW_TEST_SKIP (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1377">#1377</a>)</li>
<li>🛠 Updates CPython 3.11 to 3.11.1 (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1371">#1371</a>)</li>
<li>🛠 Updates PyPy to 7.3.10, except on macOS which remains on 7.3.9 due
to a bug on that platform. (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1371">#1371</a>)</li>
<li>📚 Added a reference to abi3audit to the docs (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1347">#1347</a>)</li>
</ul>
</blockquote>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/02ad79a31bf7aa0eee07f690509048d2fb9fd445"><code>02ad79a</code></a>
Bump version: v2.12.1</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/1d6ee75d21e2d39eeff59a101efbdff3f926060d"><code>1d6ee75</code></a>
Merge pull request <a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1430">#1430</a>
from henryiii/henryiii/fix/pipconfigopts</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/0b1b539450d86f7be21182225467c24303b687f7"><code>0b1b539</code></a>
[Bot] Update dependencies (<a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1425">#1425</a>)</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/2e48667e29fa128d96738dd6bb585aaab232b580"><code>2e48667</code></a>
refactor: use frontend instead of plural</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/c6818608d23a2f54b26e48b22c28fceb40ce2c57"><code>c681860</code></a>
fix: pip config options were broken</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/7190b1a6a7be78508bc9a75badd370ec33018880"><code>7190b1a</code></a>
Merge pull request <a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1428">#1428</a>
from henryiii/henryiii/ci/appveyor</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/16380b855562429b51e9ac36f6dd57094121c4b4"><code>16380b8</code></a>
Update CI table</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/94efa61f7667e9451d24b5ce8265b0afaaead76a"><code>94efa61</code></a>
ci: fix appveyor (Python 3.8+ needed for macOS)</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/acdbe87e3d002598b10435bb6f17bae758418ba8"><code>acdbe87</code></a>
Merge pull request <a
href="https://redirect.github.com/pypa/cibuildwheel/issues/1427">#1427</a>
from pypa/pre-commit-ci-update-config</li>
<li><a
href="https://github.com/pypa/cibuildwheel/commit/49b736d1c725bda880a31df86e46a3d1a09d92b8"><code>49b736d</code></a>
[pre-commit.ci] pre-commit autoupdate</li>
<li>Additional commits viewable in <a
href="https://github.com/pypa/cibuildwheel/compare/v2.11.3...v2.12.1">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=pypa/cibuildwheel&package-manager=github_actions&previous-version=2.11.3&new-version=2.12.1)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

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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/build_wheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index cd4dd728b3..911673f96d 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -42,7 +42,7 @@ jobs:
         name: Setup QEMU
         if: matrix.platform_id == 'manylinux_aarch64'
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.11.3
+        uses: pypa/cibuildwheel@v2.12.1
         env:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_ARCHS: all

From c22f0447da8f3b90a77c7e5e1003b7a6497363af Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 15 Mar 2023 09:41:13 +0800
Subject: [PATCH 03/13] Bump docker/metadata-action from 3.3.0 to 4.3.0 (#2383)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps
[docker/metadata-action](https://github.com/docker/metadata-action) from
3.3.0 to 4.3.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/docker/metadata-action/releases">docker/metadata-action's
releases</a>.</em></p>
<blockquote>
<h2>v4.3.0</h2>
<ul>
<li>Provide outputs as env vars by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/257">#257</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v4.2.0...v4.3.0">https://github.com/docker/metadata-action/compare/v4.2.0...v4.3.0</a></p>
<h2>v4.2.0</h2>
<ul>
<li>Add <code>tz</code> attribute to handlebar date function by <a
href="https://github.com/chroju"><code>@​chroju</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/251">#251</a>)</li>
<li>Bump minimatch from 3.0.4 to 3.1.2 (<a
href="https://redirect.github.com/docker/metadata-action/issues/242">#242</a>)</li>
<li>Bump csv-parse from 5.3.1 to 5.3.3 (<a
href="https://redirect.github.com/docker/metadata-action/issues/245">#245</a>)</li>
<li>Bump json5 from 2.2.0 to 2.2.3 (<a
href="https://redirect.github.com/docker/metadata-action/issues/252">#252</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v4.1.1...v4.2.0">https://github.com/docker/metadata-action/compare/v4.1.1...v4.2.0</a></p>
<h2>v4.1.1</h2>
<ul>
<li>Revert changes to set associated head sha on pull request event by
<a href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/239">#239</a>)
<ul>
<li>User can still set associated head sha on PR by setting the env var
<code>DOCKER_METADATA_PR_HEAD_SHA=true</code></li>
</ul>
</li>
<li>Bump csv-parse from 5.3.0 to 5.3.1 (<a
href="https://redirect.github.com/docker/metadata-action/issues/237">#237</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v4.1.0...v4.1.1">https://github.com/docker/metadata-action/compare/v4.1.0...v4.1.1</a></p>
<h2>v4.1.0</h2>
<ul>
<li>Do not trim whitespace for <code>sep-tags</code> and
<code>sep-labels</code> inputs by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/233">#233</a>)</li>
<li>Set associated head sha on pull request event by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/234">#234</a>)</li>
<li>Remove workaround for <code>setOutput</code> by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/236">#236</a>)</li>
<li>Bump <code>@​actions/github</code> from 5.0.1 to 5.1.1 (<a
href="https://redirect.github.com/docker/metadata-action/issues/208">#208</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/232">#232</a>)</li>
<li>Bump <code>@​actions/core</code> from 1.6.0 to 1.10.0 (<a
href="https://redirect.github.com/docker/metadata-action/issues/209">#209</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/216">#216</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/226">#226</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/231">#231</a>)</li>
<li>Bump csv-parse from 5.0.4 to 5.3.0 (<a
href="https://redirect.github.com/docker/metadata-action/issues/210">#210</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/221">#221</a>)</li>
<li>Bump moment from 2.29.3 to 2.29.4 (<a
href="https://redirect.github.com/docker/metadata-action/issues/220">#220</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v4.0.1...v4.1.0">https://github.com/docker/metadata-action/compare/v4.0.1...v4.1.0</a></p>
<h2>v4.0.1</h2>
<ul>
<li>Sanitize tag earlier by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/203">#203</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v4.0.0...v4.0.1">https://github.com/docker/metadata-action/compare/v4.0.0...v4.0.1</a></p>
<h2>v4.0.0</h2>
<ul>
<li>Node 16 as default runtime by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/176">#176</a>)
<ul>
<li>This requires a minimum <a
href="https://github.com/actions/runner/releases/tag/v2.285.0">Actions
Runner</a> version of v2.285.0, which is by default available in GHES
3.4 or later.</li>
</ul>
</li>
<li>Do not sanitize before pattern matching by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/201">#201</a>)
<ul>
<li>Breaking change with <code>type=match</code> pattern matching</li>
</ul>
</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/metadata-action/compare/v3.8.0...v4.0.0">https://github.com/docker/metadata-action/compare/v3.8.0...v4.0.0</a></p>
<h2>v3.8.0</h2>
<ul>
<li>Add attribute to enable/disable images by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/193">#193</a>)</li>
<li>Add <code>is_default_branch</code> global expression by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/192">#192</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/197">#197</a>
<a
href="https://redirect.github.com/docker/metadata-action/issues/198">#198</a>)</li>
<li>Update fixtures (dev) by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/metadata-action/issues/190">#190</a>)</li>
<li>Bump semver from 7.3.5 to 7.3.7 (<a
href="https://redirect.github.com/docker/metadata-action/issues/185">#185</a>)</li>
<li>Bump moment from 2.29.2 to 2.29.3 (<a
href="https://redirect.github.com/docker/metadata-action/issues/187">#187</a>)</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Upgrade guide</summary>
<p><em>Sourced from <a
href="https://github.com/docker/metadata-action/blob/master/UPGRADE.md">docker/metadata-action's
upgrade guide</a>.</em></p>
<blockquote>
<h1>Upgrade notes</h1>
<h2>v2 to v3</h2>
<ul>
<li>Repository has been moved to docker org. Replace
<code>crazy-max/ghaction-docker-meta@v2</code>
with <code>docker/metadata-action@v4</code></li>
<li>The default bake target has been changed:
<code>ghaction-docker-meta</code> &gt;
<code>docker-metadata-action</code></li>
</ul>
<h2>v1 to v2</h2>
<ul>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#inputs">inputs</a>
<ul>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-sha"><code>tag-sha</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-edge--tag-edge-branch"><code>tag-edge</code>
/ <code>tag-edge-branch</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-semver"><code>tag-semver</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-match--tag-match-group"><code>tag-match</code>
/ <code>tag-match-group</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-latest"><code>tag-latest</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-schedule"><code>tag-schedule</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#tag-custom--tag-custom-only"><code>tag-custom</code>
/ <code>tag-custom-only</code></a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#label-custom"><code>label-custom</code></a></li>
</ul>
</li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#basic-workflow">Basic
workflow</a></li>
<li><a
href="https://github.com/docker/metadata-action/blob/master/#semver-workflow">Semver
workflow</a></li>
</ul>
<h3>inputs</h3>
<table>
<thead>
<tr>
<th>New</th>
<th>Unchanged</th>
<th>Removed</th>
</tr>
</thead>
<tbody>
<tr>
<td><code>tags</code></td>
<td><code>images</code></td>
<td><code>tag-sha</code></td>
</tr>
<tr>
<td><code>flavor</code></td>
<td><code>sep-tags</code></td>
<td><code>tag-edge</code></td>
</tr>
<tr>
<td><code>labels</code></td>
<td><code>sep-labels</code></td>
<td><code>tag-edge-branch</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-semver</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-match</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-match-group</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-latest</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-schedule</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-custom</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>tag-custom-only</code></td>
</tr>
<tr>
<td></td>
<td></td>
<td><code>label-custom</code></td>
</tr>
</tbody>
</table>
<h4><code>tag-sha</code></h4>
<pre lang="yaml"><code>tags: |
  type=sha
</code></pre>
<h4><code>tag-edge</code> / <code>tag-edge-branch</code></h4>
<pre lang="yaml"><code>tags: |
  # default branch
&lt;/tr&gt;&lt;/table&gt;
</code></pre>
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/docker/metadata-action/commit/507c2f2dc502c992ad446e3d7a5dfbe311567a96"><code>507c2f2</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/metadata-action/issues/257">#257</a>
from crazy-max/env-output</li>
<li><a
href="https://github.com/docker/metadata-action/commit/04861f5102fc7042b8529e3f426856244a8cfba2"><code>04861f5</code></a>
update generated content</li>
<li><a
href="https://github.com/docker/metadata-action/commit/6729545cde76a1fb0fc1133c68fa5af1181f7e68"><code>6729545</code></a>
Provide outputs as env vars</li>
<li><a
href="https://github.com/docker/metadata-action/commit/05d22bf31770de02e20c67c70365453e00227f61"><code>05d22bf</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/metadata-action/issues/256">#256</a>
from crazy-max/fix-readme</li>
<li><a
href="https://github.com/docker/metadata-action/commit/70b403b46b081a6f32f3ebe072afd18ebfa4ce38"><code>70b403b</code></a>
Fix README</li>
<li><a
href="https://github.com/docker/metadata-action/commit/9e6ae02878038daef2841c9e4bb61e486c726684"><code>9e6ae02</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/metadata-action/issues/252">#252</a>
from docker/dependabot/npm_and_yarn/json5-2.2.3</li>
<li><a
href="https://github.com/docker/metadata-action/commit/3d239e8b8ac4bbf4cc24920f391d8f08d44b839e"><code>3d239e8</code></a>
Bump json5 from 2.2.0 to 2.2.3</li>
<li><a
href="https://github.com/docker/metadata-action/commit/7cb52e275081c4e9294d257dd188716a82c82670"><code>7cb52e2</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/metadata-action/issues/251">#251</a>
from chroju/set_timezone</li>
<li><a
href="https://github.com/docker/metadata-action/commit/90a1d5cf2150f6b10fc688351279736c24eedf25"><code>90a1d5c</code></a>
Add tz attribute to handlebar date function</li>
<li><a
href="https://github.com/docker/metadata-action/commit/c98ac5e987c125fe23d39b3cecb9ac130a108e27"><code>c98ac5e</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/metadata-action/issues/249">#249</a>
from crazy-max/fix-readme</li>
<li>Additional commits viewable in <a
href="https://github.com/docker/metadata-action/compare/98669ae865ea3cffbcbaa878cf57c20bbf1c6c38...507c2f2dc502c992ad446e3d7a5dfbe311567a96">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=docker/metadata-action&package-manager=github_actions&previous-version=3.3.0&new-version=4.3.0)](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
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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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Signed-off-by: dependabot[bot] <support@github.com>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
---
 .github/workflows/build_wheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index 911673f96d..b318f2c0e4 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -103,7 +103,7 @@ jobs:
 
       - name: Extract metadata (tags, labels) for Docker
         id: meta
-        uses: docker/metadata-action@98669ae865ea3cffbcbaa878cf57c20bbf1c6c38
+        uses: docker/metadata-action@507c2f2dc502c992ad446e3d7a5dfbe311567a96
         with:
           images: ghcr.io/deepmodeling/deepmd-kit
 

From ebca80fc858450899113f91a38547156692a686d Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 15 Mar 2023 09:43:52 +0800
Subject: [PATCH 04/13] Bump actions/upload-artifact from 2 to 3 (#2384)

Bumps
[actions/upload-artifact](https://github.com/actions/upload-artifact)
from 2 to 3.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/actions/upload-artifact/releases">actions/upload-artifact's
releases</a>.</em></p>
<blockquote>
<h2>v3.0.0</h2>
<h2>What's Changed</h2>
<ul>
<li>Update default runtime to node16 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/293">#293</a>)</li>
<li>Update package-lock.json file version to 2 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/302">#302</a>)</li>
</ul>
<h3>Breaking Changes</h3>
<p>With the update to Node 16, all scripts will now be run with Node 16
rather than Node 12.</p>
<h2>v2.3.1</h2>
<p>Fix for empty fails on Windows failing on upload <a
href="https://redirect.github.com/actions/upload-artifact/issues/281">#281</a></p>
<h2>v2.3.0 Upload Artifact</h2>
<ul>
<li>Optimizations for faster uploads of larger files that are already
compressed</li>
<li>Significantly improved logging when there are chunked uploads</li>
<li>Clarifications in logs around the upload size and prohibited
characters that aren't allowed in the artifact name or any uploaded
files</li>
<li>Various other small bugfixes &amp; optimizations</li>
</ul>
<h2>v2.2.4</h2>
<ul>
<li>Retry on HTTP 500 responses from the service</li>
</ul>
<h2>v2.2.3</h2>
<ul>
<li>Fixes for proxy related issues</li>
</ul>
<h2>v2.2.2</h2>
<ul>
<li>Improved retryability and error handling</li>
</ul>
<h2>v2.2.1</h2>
<ul>
<li>Update used actions/core package to the latest version</li>
</ul>
<h2>v2.2.0</h2>
<ul>
<li>Support for artifact retention</li>
</ul>
<h2>v2.1.4</h2>
<ul>
<li>Add Third Party License Information</li>
</ul>
<h2>v2.1.3</h2>
<ul>
<li>Use updated version of the <code>@action/artifact</code> NPM
package</li>
</ul>
<h2>v2.1.2</h2>
<ul>
<li>Increase upload chunk size from 4MB to 8MB</li>
<li>Detect case insensitive file uploads</li>
</ul>
<h2>v2.1.1</h2>
<ul>
<li>Fix for certain symlinks not correctly being identified as
directories before starting uploads</li>
</ul>
<h2>v2.1.0</h2>
<ul>
<li>Support for uploading artifacts with multiple paths</li>
<li>Support for using exclude paths</li>
<li>Updates to dependencies</li>
</ul>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/actions/upload-artifact/commit/0b7f8abb1508181956e8e162db84b466c27e18ce"><code>0b7f8ab</code></a>
ci(github): update action/download-artifact from v1 to v3 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/312">#312</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/013d2b89baa2f354c5ffec54c68bec4ab39a2534"><code>013d2b8</code></a>
Create devcontainer for codespaces + update all dev dependencies (<a
href="https://redirect.github.com/actions/upload-artifact/issues/375">#375</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/055b8b3f04a4a7ed853f2c6ab04256f83e4874dc"><code>055b8b3</code></a>
Bump Actions NPM dependencies (<a
href="https://redirect.github.com/actions/upload-artifact/issues/374">#374</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/7a5d4831f75130126bffffb8443b412485f7b836"><code>7a5d483</code></a>
ci(github): update action/checkout from v2 to v3 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/315">#315</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/e0057a5b76f2fdad976135e8dd7b691e632b9056"><code>e0057a5</code></a>
README: Bump actions/checkout to v3 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/352">#352</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/7fe6c13ac83e8572a115d6d5e45afc880cc4fe7e"><code>7fe6c13</code></a>
Update to latest <code>actions/publish-action</code> (<a
href="https://redirect.github.com/actions/upload-artifact/issues/363">#363</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/83fd05a356d7e2593de66fc9913b3002723633cb"><code>83fd05a</code></a>
Bump actions-core to v1.10.0 (<a
href="https://redirect.github.com/actions/upload-artifact/issues/356">#356</a>)</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/3cea5372237819ed00197afe530f5a7ea3e805c8"><code>3cea537</code></a>
Merge pull request <a
href="https://redirect.github.com/actions/upload-artifact/issues/327">#327</a>
from actions/robherley/artifact-1.1.0</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/849aa7758a428ee22be38de371b49c8bd57c4b9d"><code>849aa77</code></a>
nvm use 12 &amp; npm run release</li>
<li><a
href="https://github.com/actions/upload-artifact/commit/4d3986961d0423ba9a593efb490a2960eb65f43b"><code>4d39869</code></a>
recompile with correct ncc version</li>
<li>Additional commits viewable in <a
href="https://github.com/actions/upload-artifact/compare/v2...v3">compare
view</a></li>
</ul>
</details>
<br />


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score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=actions/upload-artifact&package-manager=github_actions&previous-version=2&new-version=3)](https://docs.github.com/en/github/managing-security-vulnerabilities/about-dependabot-security-updates#about-compatibility-scores)

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<br />

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

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index b318f2c0e4..53131f540a 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -48,7 +48,7 @@ jobs:
           CIBW_ARCHS: all
           CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.platform_id }}
           DP_VARIANT: ${{ matrix.dp_variant }}
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
   build_sdist:
diff --git a/.github/workflows/package_c.yml b/.github/workflows/package_c.yml
index 0a0d16816f..6cc5ed8dc8 100644
--- a/.github/workflows/package_c.yml
+++ b/.github/workflows/package_c.yml
@@ -16,7 +16,7 @@ jobs:
         run: ./source/install/docker_test_package_c.sh
       # for download and debug
       - name: Upload artifact
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           path: ./libdeepmd_c.tar.gz
       - name: Release

From 12d56779c31f73dfe9fb253c62b619eb942d547e Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Wed, 15 Mar 2023 09:44:04 +0800
Subject: [PATCH 05/13] Bump docker/build-push-action from 2.5.0 to 4.0.0
 (#2385)
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Bumps
[docker/build-push-action](https://github.com/docker/build-push-action)
from 2.5.0 to 4.0.0.
<details>
<summary>Release notes</summary>
<p><em>Sourced from <a
href="https://github.com/docker/build-push-action/releases">docker/build-push-action's
releases</a>.</em></p>
<blockquote>
<h2>v4.0.0</h2>
<blockquote>
<p><strong>Note</strong></p>
<p>Buildx v0.10 enables support for a minimal <a
href="https://slsa.dev/provenance/">SLSA Provenance</a> attestation,
which requires support for <a
href="https://github.com/opencontainers/image-spec">OCI-compliant</a>
multi-platform images. This may introduce issues with registry and
runtime support (e.g. <a
href="https://redirect.github.com/docker/buildx/issues/1533">Google
Cloud Run and AWS Lambda</a>). You can optionally disable the default
provenance attestation functionality using <code>provenance:
false</code>.</p>
</blockquote>
<ul>
<li>Revert disable provenance by default if not set by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> in <a
href="https://redirect.github.com/docker/build-push-action/pull/784">docker/build-push-action#784</a></li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.3.1...v4.0.0">https://github.com/docker/build-push-action/compare/v3.3.1...v4.0.0</a></p>
<h2>v3.3.1</h2>
<ul>
<li>Disable provenance by default if not set by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/781">#781</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.3.0...v3.3.1">https://github.com/docker/build-push-action/compare/v3.3.0...v3.3.1</a></p>
<h2>v3.3.0</h2>
<blockquote>
<p><strong>Note</strong></p>
<p>Buildx v0.10 enables support for a minimal <a
href="https://slsa.dev/provenance/">SLSA Provenance</a> attestation,
which requires support for <a
href="https://github.com/opencontainers/image-spec">OCI-compliant</a>
multi-platform images. This may introduce issues with registry and
runtime support (e.g. <a
href="https://redirect.github.com/docker/buildx/issues/1533">Google
Cloud Run and AWS Lambda</a>). You can optionally disable the default
provenance attestation functionality using <code>provenance:
false</code>.</p>
</blockquote>
<ul>
<li>Add <code>attests</code>, <code>provenance</code> and
<code>sbom</code> inputs by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/746">#746</a>
<a
href="https://redirect.github.com/docker/build-push-action/issues/759">#759</a>)</li>
<li>Log GitHub Actions runtime token access controls by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/707">#707</a>)</li>
<li>Examples moved to <a
href="https://docs.docker.com/build/ci/github-actions/examples/">docs
website</a> by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/718">#718</a>)</li>
<li>Bump minimatch from 3.0.4 to 3.1.2 (<a
href="https://redirect.github.com/docker/build-push-action/issues/732">#732</a>)</li>
<li>Bump csv-parse from 5.3.0 to 5.3.3 (<a
href="https://redirect.github.com/docker/build-push-action/issues/729">#729</a>)</li>
<li>Bump json5 from 2.2.0 to 2.2.3 (<a
href="https://redirect.github.com/docker/build-push-action/issues/749">#749</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.2.0...v3.3.0">https://github.com/docker/build-push-action/compare/v3.2.0...v3.3.0</a></p>
<h2>v3.2.0</h2>
<ul>
<li>Remove workaround for <code>setOutput</code> by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/704">#704</a>)</li>
<li>Docs: fix Git context link and add more details about subdir support
by <a href="https://github.com/crazy-max"><code>@​crazy-max</code></a>
(<a
href="https://redirect.github.com/docker/build-push-action/issues/685">#685</a>)</li>
<li>Docs: named context by <a
href="https://github.com/baibaratsky"><code>@​baibaratsky</code></a> and
<a href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/665">#665</a>)</li>
<li>Bump <code>@​actions/core</code> from 1.9.0 to 1.10.0 (<a
href="https://redirect.github.com/docker/build-push-action/issues/667">#667</a>
<a
href="https://redirect.github.com/docker/build-push-action/issues/695">#695</a>)</li>
<li>Bump <code>@​actions/github</code> from 5.0.3 to 5.1.1 (<a
href="https://redirect.github.com/docker/build-push-action/issues/696">#696</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.1.1...v3.2.0">https://github.com/docker/build-push-action/compare/v3.1.1...v3.2.0</a></p>
<h2>v3.1.1</h2>
<ul>
<li>Fix GitHub token not passed with Git context if subdir defined by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/663">#663</a>)</li>
<li>Replace deprecated <code>fs.rmdir</code> with <code>fs.rm</code> by
<a href="https://github.com/bendrucker"><code>@​bendrucker</code></a>
(<a
href="https://redirect.github.com/docker/build-push-action/issues/657">#657</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.1.0...v3.1.1">https://github.com/docker/build-push-action/compare/v3.1.0...v3.1.1</a></p>
<h2>v3.1.0</h2>
<ul>
<li><code>no-cache-filters</code> input by <a
href="https://github.com/crazy-max"><code>@​crazy-max</code></a> (<a
href="https://redirect.github.com/docker/build-push-action/issues/653">#653</a>)</li>
<li>Bump <code>@​actions/github</code> from 5.0.1 to 5.0.3 (<a
href="https://redirect.github.com/docker/build-push-action/issues/619">#619</a>)</li>
<li>Bump <code>@​actions/core</code> from 1.6.0 to 1.9.0 (<a
href="https://redirect.github.com/docker/build-push-action/issues/620">#620</a>
<a
href="https://redirect.github.com/docker/build-push-action/issues/637">#637</a>)</li>
<li>Bump csv-parse from 5.0.4 to 5.3.0 (<a
href="https://redirect.github.com/docker/build-push-action/issues/623">#623</a>
<a
href="https://redirect.github.com/docker/build-push-action/issues/650">#650</a>)</li>
</ul>
<p><strong>Full Changelog</strong>: <a
href="https://github.com/docker/build-push-action/compare/v3.0.0...v3.1.0">https://github.com/docker/build-push-action/compare/v3.0.0...v3.1.0</a></p>
<!-- raw HTML omitted -->
</blockquote>
<p>... (truncated)</p>
</details>
<details>
<summary>Commits</summary>
<ul>
<li><a
href="https://github.com/docker/build-push-action/commit/3b5e8027fcad23fda98b2e3ac259d8d67585f671"><code>3b5e802</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/build-push-action/issues/784">#784</a>
from crazy-max/enable-provenance</li>
<li><a
href="https://github.com/docker/build-push-action/commit/02d3266a89e5dfed960723e6127886a5adc7eb2f"><code>02d3266</code></a>
update generated content</li>
<li><a
href="https://github.com/docker/build-push-action/commit/f403dafe18abeb00b9d5976ab285a9f457520f29"><code>f403daf</code></a>
revert disable provenance by default if not set</li>
<li><a
href="https://github.com/docker/build-push-action/commit/1104d471370f9806843c095c1db02b5a90c5f8b6"><code>1104d47</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/build-push-action/issues/781">#781</a>
from crazy-max/disable-provenance</li>
<li><a
href="https://github.com/docker/build-push-action/commit/838bf90c88a4d6a02272e7afa2e4e2227b96f2dc"><code>838bf90</code></a>
update generated content</li>
<li><a
href="https://github.com/docker/build-push-action/commit/337a09d182ee8c86aa958168dc985219e49e4b3b"><code>337a09d</code></a>
disable provenance by default if not set</li>
<li><a
href="https://github.com/docker/build-push-action/commit/37abcedcc1da61a57767b7588cb9d03eb57e28b3"><code>37abced</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/build-push-action/issues/760">#760</a>
from crazy-max/test-envs</li>
<li><a
href="https://github.com/docker/build-push-action/commit/67109bc4b2230dc1ac72d54058d11285dc26bd87"><code>67109bc</code></a>
test: move envs to jest config</li>
<li><a
href="https://github.com/docker/build-push-action/commit/d1b0eb0a29d50896608d0b3a0fd3c012fef617d8"><code>d1b0eb0</code></a>
Merge pull request <a
href="https://redirect.github.com/docker/build-push-action/issues/759">#759</a>
from crazy-max/fix-provenance-input</li>
<li><a
href="https://github.com/docker/build-push-action/commit/a0635fe7cdb196c0c076b004dfdc1cab820ef1d4"><code>a0635fe</code></a>
update generated content</li>
<li>Additional commits viewable in <a
href="https://github.com/docker/build-push-action/compare/ad44023a93711e3deb337508980b4b5e9bcdc5dc...3b5e8027fcad23fda98b2e3ac259d8d67585f671">compare
view</a></li>
</ul>
</details>
<br />


[![Dependabot compatibility
score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=docker/build-push-action&package-manager=github_actions&previous-version=2.5.0&new-version=4.0.0)](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 ignore this major version` will close this PR and stop
Dependabot creating any more for this major version (unless you reopen
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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/build_wheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index 53131f540a..a20f867e69 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -108,7 +108,7 @@ jobs:
           images: ghcr.io/deepmodeling/deepmd-kit
 
       - name: Build and push Docker image
-        uses: docker/build-push-action@ad44023a93711e3deb337508980b4b5e9bcdc5dc
+        uses: docker/build-push-action@3b5e8027fcad23fda98b2e3ac259d8d67585f671
         with:
           context: source/install/docker
           push: ${{ github.repository_owner == 'deepmodeling' && github.event_name == 'push' }}

From c762e0cda0ea28d88562a1da9404fab1893aca41 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Tue, 14 Mar 2023 21:46:14 -0400
Subject: [PATCH 06/13] fix the version of pypa/gh-action-pypi-publish (#2389)

The error was found when v2.2.0 was released. I have manually uploaded
v2.2.0 to PyPI.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 .github/workflows/build_wheel.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml
index a20f867e69..c497e86e1d 100644
--- a/.github/workflows/build_wheel.yml
+++ b/.github/workflows/build_wheel.yml
@@ -79,7 +79,7 @@ jobs:
         with:
           name: artifact
           path: dist
-      - uses: pypa/gh-action-pypi-publish@v4
+      - uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

From dfe2a00e7ebe209dab42c4a4987703bfe6cebc4c Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 00:40:00 -0400
Subject: [PATCH 07/13] link op library with protobuf (#2391)

---
 source/op/CMakeLists.txt | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/source/op/CMakeLists.txt b/source/op/CMakeLists.txt
index fdc7fa7ea2..059e72b9a8 100644
--- a/source/op/CMakeLists.txt
+++ b/source/op/CMakeLists.txt
@@ -56,6 +56,9 @@ add_library(${LIB_DEEPMD_OP} MODULE ${OP_SRC} ${OP_REMAPPER_SRC})
 # link: libdeepmd libtensorflow_cc libtensorflow_framework
 target_link_libraries(${LIB_DEEPMD_OP} PRIVATE TensorFlow::tensorflow_framework)
 target_link_libraries(${LIB_DEEPMD_OP} PRIVATE ${LIB_DEEPMD})
+if(Protobuf_LIBRARY)
+  target_link_libraries(${LIB_DEEPMD_OP} PRIVATE ${Protobuf_LIBRARY})
+endif()
 if(APPLE)
   set_target_properties(
     ${LIB_DEEPMD_OP} PROPERTIES INSTALL_RPATH

From d06580f21b9210acd50b30e77ae871ba51784262 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 00:40:12 -0400
Subject: [PATCH 08/13] atype_filter should have the shape of nloc (#2390)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 deepmd/fit/ener.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

diff --git a/deepmd/fit/ener.py b/deepmd/fit/ener.py
index d65a3a984b..53c3b1d468 100644
--- a/deepmd/fit/ener.py
+++ b/deepmd/fit/ener.py
@@ -549,13 +549,14 @@ def build(
                 aparam = tf.reshape(aparam, [-1, self.numb_aparam * natoms[0]])
 
         atype_nall = tf.reshape(atype, [-1, natoms[1]])
-        atype_filter = tf.cast(atype_nall >= 0, GLOBAL_TF_FLOAT_PRECISION)
+        self.atype_nloc = tf.slice(
+            atype_nall, [0, 0], [-1, natoms[0]]
+        )  ## lammps will make error
+        atype_filter = tf.cast(self.atype_nloc >= 0, GLOBAL_TF_FLOAT_PRECISION)
+        self.atype_nloc = tf.reshape(self.atype_nloc, [-1])
         # prevent embedding_lookup error,
         # but the filter will be applied anyway
-        atype_nall = tf.clip_by_value(atype_nall, 0, self.ntypes - 1)
-        self.atype_nloc = tf.reshape(
-            tf.slice(atype_nall, [0, 0], [-1, natoms[0]]), [-1]
-        )  ## lammps will make error
+        self.atype_nloc = tf.clip_by_value(self.atype_nloc, 0, self.ntypes - 1)
         if type_embedding is not None:
             atype_embed = tf.nn.embedding_lookup(type_embedding, self.atype_nloc)
         else:

From e200d287ed0cbc6a1f1a2e15eeae562a535947bb Mon Sep 17 00:00:00 2001
From: Duo <50307526+iProzd@users.noreply.github.com>
Date: Thu, 16 Mar 2023 09:36:31 +0800
Subject: [PATCH 09/13] Fix incompatibility after fixing the incontinuity of
 se_atten (#2397)

Add `set_davg_zero` para in `se_atten` with default value True. This
will fix incompatibility after fixing the incontinuity of se_atten.
#2393 #2394

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 deepmd/descriptor/se_atten.py | 11 ++++++++++-
 deepmd/utils/argcheck.py      |  4 ++++
 2 files changed, 14 insertions(+), 1 deletion(-)

diff --git a/deepmd/descriptor/se_atten.py b/deepmd/descriptor/se_atten.py
index 356c1fae2b..ba8fa9adfa 100644
--- a/deepmd/descriptor/se_atten.py
+++ b/deepmd/descriptor/se_atten.py
@@ -1,3 +1,4 @@
+import warnings
 from typing import (
     List,
     Optional,
@@ -67,6 +68,8 @@ class DescrptSeAtten(DescrptSeA):
     exclude_types : List[List[int]]
             The excluded pairs of types which have no interaction with each other.
             For example, `[[0, 1]]` means no interaction between type 0 and type 1.
+    set_davg_zero
+            Set the shift of embedding net input to zero.
     activation_function
             The activation function in the embedding net. Supported options are |ACTIVATION_FN|
     precision
@@ -97,6 +100,7 @@ def __init__(
         trainable: bool = True,
         seed: Optional[int] = None,
         type_one_side: bool = True,
+        set_davg_zero: bool = True,
         exclude_types: List[List[int]] = [],
         activation_function: str = "tanh",
         precision: str = "default",
@@ -107,6 +111,11 @@ def __init__(
         attn_mask: bool = False,
         multi_task: bool = False,
     ) -> None:
+        if not set_davg_zero:
+            warnings.warn(
+                "Set 'set_davg_zero' False in descriptor 'se_atten' "
+                "may cause unexpected incontinuity during model inference!"
+            )
         DescrptSeA.__init__(
             self,
             rcut,
@@ -119,7 +128,7 @@ def __init__(
             seed=seed,
             type_one_side=type_one_side,
             exclude_types=exclude_types,
-            set_davg_zero=True,
+            set_davg_zero=set_davg_zero,
             activation_function=activation_function,
             precision=precision,
             uniform_seed=uniform_seed,
diff --git a/deepmd/utils/argcheck.py b/deepmd/utils/argcheck.py
index 93135304a9..ca9afd43ac 100644
--- a/deepmd/utils/argcheck.py
+++ b/deepmd/utils/argcheck.py
@@ -325,6 +325,7 @@ def descrpt_se_atten_args():
     doc_precision = f"The precision of the embedding net parameters, supported options are {list_to_doc(PRECISION_DICT.keys())} Default follows the interface precision."
     doc_trainable = "If the parameters in the embedding net is trainable"
     doc_seed = "Random seed for parameter initialization"
+    doc_set_davg_zero = "Set the normalization average to zero. This option should be set when `se_atten` descriptor or `atom_ener` in the energy fitting is used"
     doc_exclude_types = "The excluded pairs of types which have no interaction with each other. For example, `[[0, 1]]` means no interaction between type 0 and type 1."
     doc_attn = "The length of hidden vectors in attention layers"
     doc_attn_layer = "The number of attention layers"
@@ -361,6 +362,9 @@ def descrpt_se_atten_args():
         Argument(
             "exclude_types", list, optional=True, default=[], doc=doc_exclude_types
         ),
+        Argument(
+            "set_davg_zero", bool, optional=True, default=True, doc=doc_set_davg_zero
+        ),
         Argument("attn", int, optional=True, default=128, doc=doc_attn),
         Argument("attn_layer", int, optional=True, default=2, doc=doc_attn_layer),
         Argument("attn_dotr", bool, optional=True, default=True, doc=doc_attn_dotr),

From 27f21d14a44adce48a70ef53eb7228dc62378b2e Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 21:37:22 -0400
Subject: [PATCH 10/13] support mixed natoms training (#2366)

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 deepmd/utils/data.py              | 10 +++++-
 deepmd/utils/neighbor_stat.py     |  4 +--
 doc/model/train-se-atten.md       |  6 ++--
 source/op/neighbor_stat.cc        |  2 ++
 source/tests/common.py            | 55 ++++++++++++++++++++++++++++++-
 source/tests/test_virtual_type.py | 32 ++++++++++++++++++
 6 files changed, 103 insertions(+), 6 deletions(-)

diff --git a/deepmd/utils/data.py b/deepmd/utils/data.py
index 537c5b4868..66870e85b2 100644
--- a/deepmd/utils/data.py
+++ b/deepmd/utils/data.py
@@ -91,6 +91,10 @@ def __init__(
                 self.type_idx_map = np.array(
                     sorter[np.searchsorted(type_map, self.type_map, sorter=sorter)]
                 )
+                # padding for virtual atom
+                self.type_idx_map = np.append(
+                    self.type_idx_map, np.array([-1], dtype=np.int32)
+                )
             self.type_map = type_map
         if type_map is None and self.type_map is None and self.mixed_type:
             raise RuntimeError("mixed_type format must have type_map!")
@@ -489,8 +493,12 @@ def _load_set(self, set_name: DPPath):
                 [(real_type == i).sum(axis=-1) for i in range(self.get_ntypes())],
                 dtype=np.int32,
             ).T
+            ghost_nums = np.array(
+                [(real_type == -1).sum(axis=-1)],
+                dtype=np.int32,
+            ).T
             assert (
-                atom_type_nums.sum(axis=-1) == natoms
+                atom_type_nums.sum(axis=-1) + ghost_nums.sum(axis=-1) == natoms
             ).all(), "some types in 'real_atom_types.npy' of set {} are not contained in {} types!".format(
                 set_name, self.get_ntypes()
             )
diff --git a/deepmd/utils/neighbor_stat.py b/deepmd/utils/neighbor_stat.py
index b07614fd57..eebe33d7a0 100644
--- a/deepmd/utils/neighbor_stat.py
+++ b/deepmd/utils/neighbor_stat.py
@@ -69,8 +69,8 @@ def builder():
             t_natoms = place_holders["natoms_vec"]
             if self.one_type:
                 # all types = 0, natoms_vec = [natoms, natoms, natoms]
-                t_type = tf.zeros_like(t_type, dtype=tf.int32)
-                t_natoms = tf.repeat(t_natoms[0], 3)
+                t_type = tf.clip_by_value(t_type, -1, 0)
+                t_natoms = tf.tile(t_natoms[0:1], [3])
 
             _max_nbor_size, _min_nbor_dist = op_module.neighbor_stat(
                 place_holders["coord"],
diff --git a/doc/model/train-se-atten.md b/doc/model/train-se-atten.md
index e91ae646c4..8b006346a9 100644
--- a/doc/model/train-se-atten.md
+++ b/doc/model/train-se-atten.md
@@ -103,11 +103,13 @@ ID             | Property                         | File                | Requir
 ----------     | -------------------------------- | ------------------- | -------------------- | -----------------------  | -----------
 /              | Atom type indexes (place holder) | type.raw            | Required             | Natoms                   | All zeros to fake the type input
 type_map       | Atom type names                  | type_map.raw        | Required             | Ntypes                   | Atom names that map to atom type contained in all the frames, which is unnecessart to be contained in the periodic table
-type           | Atom type indexes of each frame  | real_atom_types.npy | Required             | Nframes \* Natoms        | Integers that describe atom types in each frame, corresponding to indexes in type_map
+type           | Atom type indexes of each frame  | real_atom_types.npy | Required             | Nframes \* Natoms        | Integers that describe atom types in each frame, corresponding to indexes in type_map. `-1` means virtual atoms.
 
 With these edited files, one can put together frames with the same `Natoms`, instead of the same formula (like `H2O`). Note that this `mixed_type` format only supports `se_atten` descriptor.
 
-The API to generate or transfer to `mixed_type` format will be uploaded on [dpdata](https://github.com/deepmodeling/dpdata) soon for a more convenient experience.
+To put frames with different `Natoms` into the same system, one can pad systems by adding virtual atoms whose type is `-1`. Virtual atoms do not contribute to any fitting property, so the atomic property of virtual atoms (e.g. forces) should be given zero.
+
+The API to generate or transfer to `mixed_type` format is available on [dpdata](https://github.com/deepmodeling/dpdata) for a more convenient experience.
 
 ## Training example
 Here we upload the AlMgCu example shown in the paper, you can download it here:
diff --git a/source/op/neighbor_stat.cc b/source/op/neighbor_stat.cc
index 6c58096824..ba067786f9 100644
--- a/source/op/neighbor_stat.cc
+++ b/source/op/neighbor_stat.cc
@@ -180,8 +180,10 @@ class NeighborStatOp : public OpKernel {
 
 #pragma omp parallel for
     for (int ii = 0; ii < nloc; ii++) {
+      if (d_type[ii] < 0) continue;  // virtual atom
       for (int jj = 0; jj < d_nlist_r[ii].size(); jj++) {
         int type = d_type[d_nlist_r[ii][jj]];
+        if (type < 0) continue;  // virtual atom
         max_nbor_size[ii * ntypes + type] += 1;
         compute_t rij[3] = {
             d_coord3[d_nlist_r[ii][jj] * 3 + 0] - d_coord3[ii * 3 + 0],
diff --git a/source/tests/common.py b/source/tests/common.py
index d0dd2d2608..8fc303c1d7 100644
--- a/source/tests/common.py
+++ b/source/tests/common.py
@@ -85,9 +85,62 @@ def gen_data_mixed_type(nframes=1):
     )
 
 
-def gen_data(nframes=1, mixed_type=False):
+def gen_data_virtual_type(nframes=1, nghost=4):
+    tmpdata = Data(rand_pert=0.1, seed=1, nframes=nframes)
+    sys = dpdata.LabeledSystem()
+    real_type_map = ["foo", "bar"]
+    sys.data["atom_names"] = ["X"]
+    sys.data["coords"] = tmpdata.coord
+    sys.data["atom_types"] = np.concatenate(
+        [
+            np.zeros_like(tmpdata.atype),
+            np.zeros([nghost], dtype=np.int32),
+        ],
+        axis=0,
+    )
+    sys.data["cells"] = tmpdata.cell
+    nframes = tmpdata.nframes
+    natoms = tmpdata.natoms
+    sys.data["coords"] = np.concatenate(
+        [
+            sys.data["coords"].reshape([nframes, natoms, 3]),
+            np.zeros([nframes, nghost, 3]),
+        ],
+        axis=1,
+    )
+    sys.data["cells"] = sys.data["cells"].reshape([nframes, 3, 3])
+    sys.data["energies"] = np.zeros([nframes, 1])
+    sys.data["forces"] = np.zeros([nframes, natoms + nghost, 3])
+    sys.to_deepmd_npy("system_mixed_type", prec=np.float64)
+    np.savetxt("system_mixed_type/type_map.raw", real_type_map, fmt="%s")
+    np.save(
+        "system_mixed_type/set.000/real_atom_types.npy",
+        np.concatenate(
+            [
+                tmpdata.atype.reshape(1, -1).repeat(nframes, 0),
+                np.full([nframes, nghost], -1, dtype=np.int32),
+            ],
+            axis=1,
+        ),
+    )
+    np.save("system_mixed_type/set.000/fparam.npy", tmpdata.fparam)
+    np.save(
+        "system_mixed_type/set.000/aparam.npy",
+        np.concatenate(
+            [
+                tmpdata.aparam.reshape([nframes, natoms, 2]),
+                np.zeros([nframes, nghost, 2]),
+            ],
+            axis=1,
+        ),
+    )
+
+
+def gen_data(nframes=1, mixed_type=False, virtual_type=False):
     if not mixed_type:
         gen_data_type_specific(nframes)
+    elif virtual_type:
+        gen_data_virtual_type(nframes)
     else:
         gen_data_mixed_type(nframes)
 
diff --git a/source/tests/test_virtual_type.py b/source/tests/test_virtual_type.py
index 575f6dc768..98ab84cf93 100644
--- a/source/tests/test_virtual_type.py
+++ b/source/tests/test_virtual_type.py
@@ -4,15 +4,26 @@
 
 import numpy as np
 from common import (
+    gen_data,
+    j_loader,
     tests_path,
 )
 
+from deepmd.common import (
+    j_must_have,
+)
 from deepmd.infer import (
     DeepPot,
 )
 from deepmd.utils.convert import (
     convert_pbtxt_to_pb,
 )
+from deepmd.utils.data_system import (
+    DeepmdDataSystem,
+)
+from deepmd.utils.neighbor_stat import (
+    NeighborStat,
+)
 
 
 class TestVirtualType(unittest.TestCase):
@@ -106,3 +117,24 @@ def test_infer_mixed_type(self):
         np.testing.assert_almost_equal(v1, v2)
         np.testing.assert_almost_equal(ae1[:nloc], ae2[nghost:])
         np.testing.assert_almost_equal(av1[:nloc], av2[nghost:])
+
+
+class TestTrainVirtualType(unittest.TestCase):
+    def setUp(self) -> None:
+        gen_data(mixed_type=True, virtual_type=True)
+
+    def test_data_mixed_type(self):
+        jfile = "water_se_atten_mixed_type.json"
+        jdata = j_loader(jfile)
+
+        systems = j_must_have(jdata, "systems")
+        batch_size = 1
+        test_size = 1
+        rcut = j_must_have(jdata["model"]["descriptor"], "rcut")
+        type_map = j_must_have(jdata["model"], "type_map")
+
+        data = DeepmdDataSystem(systems, batch_size, test_size, rcut, type_map=type_map)
+        data.get_batch()
+        # neighbor stat
+        nei_stat = NeighborStat(len(type_map), rcut, one_type=True)
+        min_nbor_dist, max_nbor_size = nei_stat.get_stat(data)

From 5fe6e5756a5731171d8a4b4c54945164c9f9b9a4 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 22:27:15 -0400
Subject: [PATCH 11/13] support mixed systems training (#2372)

With the new option, a batch of data could come from all systems with
different numbers of atoms and is generated and padded into a mixed
system on the fly.

This PR is independent of #2366, which provides a manual way to use
mixed systems. In theory #2366 should have better performance and this
PR is more convenient.

---------

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 deepmd/utils/argcheck.py             |   3 +-
 deepmd/utils/data_system.py          | 106 ++++++++++++++++++++++++++-
 examples/nopbc/mixed/input.json      |  71 ++++++++++++++++++
 source/tests/test_deepmd_data_sys.py |  24 ++++++
 4 files changed, 201 insertions(+), 3 deletions(-)
 create mode 100644 examples/nopbc/mixed/input.json

diff --git a/deepmd/utils/argcheck.py b/deepmd/utils/argcheck.py
index ca9afd43ac..9fb977e5eb 100644
--- a/deepmd/utils/argcheck.py
+++ b/deepmd/utils/argcheck.py
@@ -976,7 +976,8 @@ def training_data_args():  # ! added by Ziyao: new specification style for data
 - list: the length of which is the same as the {link_sys}. The batch size of each system is given by the elements of the list.\n\n\
 - int: all {link_sys} use the same batch size.\n\n\
 - string "auto": automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than 32.\n\n\
-- string "auto:N": automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.'
+- string "auto:N": automatically determines the batch size so that the batch_size times the number of atoms in the system is no less than N.\n\n\
+- string "mixed:N": the batch data will be sampled from all systems and merged into a mixed system with the batch size N. Only support the se_atten descriptor.'
     doc_auto_prob_style = 'Determine the probability of systems automatically. The method is assigned by this key and can be\n\n\
 - "prob_uniform"  : the probability all the systems are equal, namely 1.0/self.get_nsystems()\n\n\
 - "prob_sys_size" : the probability of a system is proportional to the number of batches in the system\n\n\
diff --git a/deepmd/utils/data_system.py b/deepmd/utils/data_system.py
index 28dc799bf8..d87219fcc9 100644
--- a/deepmd/utils/data_system.py
+++ b/deepmd/utils/data_system.py
@@ -112,6 +112,7 @@ def __init__(
         # batch size
         self.batch_size = batch_size
         is_auto_bs = False
+        self.mixed_systems = False
         if isinstance(self.batch_size, int):
             self.batch_size = self.batch_size * np.ones(self.nsystems, dtype=int)
         elif isinstance(self.batch_size, str):
@@ -121,9 +122,16 @@ def __init__(
                 rule = 32
                 if len(words) == 2:
                     rule = int(words[1])
+                self.batch_size = self._make_auto_bs(rule)
+            elif "mixed" == words[0]:
+                self.mixed_systems = True
+                if len(words) == 2:
+                    rule = int(words[1])
+                else:
+                    raise RuntimeError("batch size must be specified for mixed systems")
+                self.batch_size = rule * np.ones(self.nsystems, dtype=int)
             else:
                 raise RuntimeError("unknown batch_size rule " + words[0])
-            self.batch_size = self._make_auto_bs(rule)
         elif isinstance(self.batch_size, list):
             pass
         else:
@@ -361,7 +369,7 @@ def _get_sys_probs(self, sys_probs, auto_prob_style):  # depreciated
             prob = self._process_sys_probs(sys_probs)
         return prob
 
-    def get_batch(self, sys_idx: Optional[int] = None):
+    def get_batch(self, sys_idx: Optional[int] = None) -> dict:
         # batch generation style altered by Ziyao Li:
         # one should specify the "sys_prob" and "auto_prob_style" params
         # via set_sys_prob() function. The sys_probs this function uses is
@@ -375,9 +383,36 @@ def get_batch(self, sys_idx: Optional[int] = None):
             The index of system from which the batch is get.
             If sys_idx is not None, `sys_probs` and `auto_prob_style` are ignored
             If sys_idx is None, automatically determine the system according to `sys_probs` or `auto_prob_style`, see the following.
+            This option does not work for mixed systems.
+
+        Returns
+        -------
+        dict
+            The batch data
         """
         if not hasattr(self, "default_mesh"):
             self._make_default_mesh()
+        if not self.mixed_systems:
+            b_data = self.get_batch_standard(sys_idx)
+        else:
+            b_data = self.get_batch_mixed()
+        return b_data
+
+    def get_batch_standard(self, sys_idx: Optional[int] = None) -> dict:
+        """Get a batch of data from the data systems in the standard way.
+
+        Parameters
+        ----------
+        sys_idx : int
+            The index of system from which the batch is get.
+            If sys_idx is not None, `sys_probs` and `auto_prob_style` are ignored
+            If sys_idx is None, automatically determine the system according to `sys_probs` or `auto_prob_style`, see the following.
+
+        Returns
+        -------
+        dict
+            The batch data
+        """
         if sys_idx is not None:
             self.pick_idx = sys_idx
         else:
@@ -390,6 +425,73 @@ def get_batch(self, sys_idx: Optional[int] = None):
         b_data["default_mesh"] = self.default_mesh[self.pick_idx]
         return b_data
 
+    def get_batch_mixed(self) -> dict:
+        """Get a batch of data from the data systems in the mixed way.
+
+        Returns
+        -------
+        dict
+            The batch data
+        """
+        # mixed systems have a global batch size
+        batch_size = self.batch_size[0]
+        batch_data = []
+        for _ in range(batch_size):
+            self.pick_idx = dp_random.choice(np.arange(self.nsystems), p=self.sys_probs)
+            bb_data = self.data_systems[self.pick_idx].get_batch(1)
+            bb_data["natoms_vec"] = self.natoms_vec[self.pick_idx]
+            bb_data["default_mesh"] = self.default_mesh[self.pick_idx]
+            batch_data.append(bb_data)
+        b_data = self._merge_batch_data(batch_data)
+        return b_data
+
+    def _merge_batch_data(self, batch_data: List[dict]) -> dict:
+        """Merge batch data from different systems.
+
+        Parameters
+        ----------
+        batch_data : list of dict
+            A list of batch data from different systems.
+
+        Returns
+        -------
+        dict
+            The merged batch data.
+        """
+        b_data = {}
+        max_natoms = max(bb["natoms_vec"][0] for bb in batch_data)
+        # natoms_vec
+        natoms_vec = np.zeros(2 + self.get_ntypes(), dtype=int)
+        natoms_vec[0:3] = max_natoms
+        b_data["natoms_vec"] = natoms_vec
+        # real_natoms_vec
+        real_natoms_vec = np.vstack([bb["natoms_vec"] for bb in batch_data])
+        b_data["real_natoms_vec"] = real_natoms_vec
+        # type
+        type_vec = np.full((len(batch_data), max_natoms), -1, dtype=int)
+        for ii, bb in enumerate(batch_data):
+            type_vec[ii, : bb["type"].shape[1]] = bb["type"][0]
+        b_data["type"] = type_vec
+        # default_mesh
+        default_mesh = np.mean([bb["default_mesh"] for bb in batch_data], axis=0)
+        b_data["default_mesh"] = default_mesh
+        # other data
+        data_dict = self.get_data_dict(0)
+        for kk, vv in data_dict.items():
+            if kk not in batch_data[0]:
+                continue
+            b_data["find_" + kk] = batch_data[0]["find_" + kk]
+            if not vv["atomic"]:
+                b_data[kk] = np.concatenate([bb[kk] for bb in batch_data], axis=0)
+            else:
+                b_data[kk] = np.zeros(
+                    (len(batch_data), max_natoms * vv["ndof"] * vv["repeat"]),
+                    dtype=batch_data[0][kk].dtype,
+                )
+                for ii, bb in enumerate(batch_data):
+                    b_data[kk][ii, : bb[kk].shape[1]] = bb[kk][0]
+        return b_data
+
     # ! altered by Marián Rynik
     def get_test(self, sys_idx: Optional[int] = None, n_test: int = -1):  # depreciated
         """Get test data from the the data systems.
diff --git a/examples/nopbc/mixed/input.json b/examples/nopbc/mixed/input.json
new file mode 100644
index 0000000000..ab49b4e442
--- /dev/null
+++ b/examples/nopbc/mixed/input.json
@@ -0,0 +1,71 @@
+{
+  "_comment": " model parameters",
+  "model": {
+    "type_map": [
+      "C",
+      "H",
+      "O"
+    ],
+    "descriptor": {
+      "type": "se_atten",
+      "sel": 120,
+      "rcut_smth": 1.00,
+      "rcut": 6.00,
+      "neuron": [
+        25,
+        50,
+        100
+      ],
+      "resnet_dt": false,
+      "axis_neuron": 12,
+      "seed": 1,
+      "_comment": " that's all"
+    },
+    "fitting_net": {
+      "neuron": [
+        240,
+        240,
+        240
+      ],
+      "resnet_dt": true,
+      "seed": 1,
+      "_comment": " that's all"
+    },
+    "_comment": " that's all"
+  },
+
+  "learning_rate": {
+    "type": "exp",
+    "decay_steps": 4000,
+    "start_lr": 0.001,
+    "stop_lr": 3.51e-8,
+    "_comment": "that's all"
+  },
+
+  "loss": {
+    "type": "ener",
+    "start_pref_e": 0.02,
+    "limit_pref_e": 1,
+    "start_pref_f": 1000,
+    "limit_pref_f": 1,
+    "start_pref_v": 0,
+    "limit_pref_v": 0,
+    "_comment": " that's all"
+  },
+
+  "training": {
+    "training_data": {
+      "systems": "../data/",
+      "batch_size": "mixed:4",
+      "_comment": "that's all"
+    },
+    "numb_steps": 4000000,
+    "seed": 10,
+    "disp_file": "lcurve.out",
+    "disp_freq": 100,
+    "save_freq": 1000,
+    "_comment": "that's all"
+  },
+
+  "_comment": "that's all"
+}
diff --git a/source/tests/test_deepmd_data_sys.py b/source/tests/test_deepmd_data_sys.py
index d24291114d..9df48c3f57 100644
--- a/source/tests/test_deepmd_data_sys.py
+++ b/source/tests/test_deepmd_data_sys.py
@@ -7,6 +7,9 @@
 from deepmd.env import (
     GLOBAL_NP_FLOAT_PRECISION,
 )
+from deepmd.utils import (
+    random,
+)
 from deepmd.utils.data_system import (
     DeepmdDataSystem,
 )
@@ -398,3 +401,24 @@ def test_sys_prob_floating_point_error(self):
         ]
         ds = DeepmdDataSystem(self.sys_name, 3, 2, 2.0, sys_probs=sys_probs)
         self.assertEqual(ds.sys_probs.size, len(sys_probs))
+
+    def test_get_mixed_batch(self):
+        """test get_batch with mixed system."""
+        batch_size = "mixed:3"
+        test_size = 2
+
+        ds = DeepmdDataSystem(self.sys_name, batch_size, test_size, 2.0)
+        ds.add("test", self.test_ndof, atomic=True, must=True)
+        ds.add("null", self.test_ndof, atomic=True, must=False)
+        random.seed(114514)
+        # with this seed, the batch is fixed, with natoms 3, 6, 6
+        data = ds.get_batch()
+        np.testing.assert_equal(data["natoms_vec"], np.array([6, 6, 6, 0, 0]))
+        np.testing.assert_equal(data["real_natoms_vec"][:, 0], np.array([3, 6, 6]))
+        np.testing.assert_equal(data["type"][0, 3:6], np.array([-1, -1, -1]))
+        np.testing.assert_equal(data["coord"][0, 9:18], np.zeros(9))
+        for kk in ("test", "null"):
+            np.testing.assert_equal(
+                data[kk][0, 3 * self.test_ndof : 6 * self.test_ndof],
+                np.zeros(3 * self.test_ndof),
+            )

From 7920cfe4b801817fe27de4d9defc2a631059b314 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 23:31:49 -0400
Subject: [PATCH 12/13] fix pdf docs (#2401)

It looks that the documentation is broken

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 deepmd/descriptor/se_a.py      | 4 ++--
 deepmd/descriptor/se_a_mask.py | 4 ++--
 deepmd/fit/ener.py             | 8 ++++----
 deepmd/utils/network.py        | 4 ++--
 doc/conf.py                    | 4 ++++
 5 files changed, 14 insertions(+), 10 deletions(-)

diff --git a/deepmd/descriptor/se_a.py b/deepmd/descriptor/se_a.py
index d49c329353..2bff523608 100644
--- a/deepmd/descriptor/se_a.py
+++ b/deepmd/descriptor/se_a.py
@@ -96,8 +96,8 @@ class DescrptSeA(DescrptSe):
     .. math::
         (\mathcal{G}^i)_j = \mathcal{N}(s(r_{ji}))
 
-    :math:`\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}` takes first :math:`M_2`$` columns of
-    :math:`\mathcal{G}^i`$`. The equation of embedding network :math:`\mathcal{N}` can be found at
+    :math:`\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}` takes first :math:`M_2` columns of
+    :math:`\mathcal{G}^i`. The equation of embedding network :math:`\mathcal{N}` can be found at
     :meth:`deepmd.utils.network.embedding_net`.
 
     Parameters
diff --git a/deepmd/descriptor/se_a_mask.py b/deepmd/descriptor/se_a_mask.py
index 00b23232f1..93256e3910 100644
--- a/deepmd/descriptor/se_a_mask.py
+++ b/deepmd/descriptor/se_a_mask.py
@@ -70,8 +70,8 @@ class DescrptSeAMask(DescrptSeA):
     .. math::
         (\mathcal{G}^i)_j = \mathcal{N}(s(r_{ji}))
 
-    :math:`\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}` takes first :math:`M_2`$` columns of
-    :math:`\mathcal{G}^i`$`. The equation of embedding network :math:`\mathcal{N}` can be found at
+    :math:`\mathcal{G}^i_< \in \mathbb{R}^{N \times M_2}` takes first :math:`M_2` columns of
+    :math:`\mathcal{G}^i`. The equation of embedding network :math:`\mathcal{N}` can be found at
     :meth:`deepmd.utils.network.embedding_net`.
     Specially for descriptor se_a_mask is a concise implementation of se_a.
     The difference is that se_a_mask only considered a non-pbc system.
diff --git a/deepmd/fit/ener.py b/deepmd/fit/ener.py
index 53c3b1d468..c9f70117f7 100644
--- a/deepmd/fit/ener.py
+++ b/deepmd/fit/ener.py
@@ -59,9 +59,9 @@ class EnerFitting(Fitting):
         \mathbf{y}=\mathcal{L}(\mathbf{x};\mathbf{w},\mathbf{b})=
             \boldsymbol{\phi}(\mathbf{x}^T\mathbf{w}+\mathbf{b})
 
-    where :math:`\mathbf{x} \in \mathbb{R}^{N_1}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}`
+    where :math:`\mathbf{x} \in \mathbb{R}^{N_1}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}`
     is the output vector. :math:`\mathbf{w} \in \mathbb{R}^{N_1 \times N_2}` and
-    :math:`\mathbf{b} \in \mathbb{R}^{N_2}`$` are weights and biases, respectively,
+    :math:`\mathbf{b} \in \mathbb{R}^{N_2}` are weights and biases, respectively,
     both of which are trainable if `trainable[i]` is `True`. :math:`\boldsymbol{\phi}`
     is the activation function.
 
@@ -71,9 +71,9 @@ class EnerFitting(Fitting):
         \mathbf{y}=\mathcal{L}^{(n)}(\mathbf{x};\mathbf{w},\mathbf{b})=
             \mathbf{x}^T\mathbf{w}+\mathbf{b}
 
-    where :math:`\mathbf{x} \in \mathbb{R}^{N_{n-1}}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}`
+    where :math:`\mathbf{x} \in \mathbb{R}^{N_{n-1}}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}`
     is the output scalar. :math:`\mathbf{w} \in \mathbb{R}^{N_{n-1}}` and
-    :math:`\mathbf{b} \in \mathbb{R}`$` are weights and bias, respectively,
+    :math:`\mathbf{b} \in \mathbb{R}` are weights and bias, respectively,
     both of which are trainable if `trainable[n]` is `True`.
 
     Parameters
diff --git a/deepmd/utils/network.py b/deepmd/utils/network.py
index e5ce249f45..a718da0b26 100644
--- a/deepmd/utils/network.py
+++ b/deepmd/utils/network.py
@@ -144,9 +144,9 @@ def embedding_net(
             \boldsymbol{\phi}(\mathbf{x}^T\mathbf{w}+\mathbf{b}), & \text{otherwise} \\
         \end{cases}
 
-    where :math:`\mathbf{x} \in \mathbb{R}^{N_1}`$` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}`
+    where :math:`\mathbf{x} \in \mathbb{R}^{N_1}` is the input vector and :math:`\mathbf{y} \in \mathbb{R}^{N_2}`
     is the output vector. :math:`\mathbf{w} \in \mathbb{R}^{N_1 \times N_2}` and
-    :math:`\mathbf{b} \in \mathbb{R}^{N_2}`$` are weights and biases, respectively,
+    :math:`\mathbf{b} \in \mathbb{R}^{N_2}` are weights and biases, respectively,
     both of which are trainable if `trainable` is `True`. :math:`\boldsymbol{\phi}`
     is the activation function.
 
diff --git a/doc/conf.py b/doc/conf.py
index e338274f0e..2fd0dcdc33 100644
--- a/doc/conf.py
+++ b/doc/conf.py
@@ -305,6 +305,10 @@ def setup(app):
     "fontpkg": r"""
 \usepackage{fontspec}
 \setmainfont{Symbola}
+""",
+    "preamble": r"""
+\usepackage{enumitem}
+\setlistdepth{99}
 """,
 }
 

From afa27d753baeaf7ec34c818a975b0ef580cb4052 Mon Sep 17 00:00:00 2001
From: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
Date: Wed, 15 Mar 2023 23:47:15 -0400
Subject: [PATCH 13/13] clean old handlers before adding new one (#2400)

It's not a problem for production, but during tests there might be
multiple handlers added.

Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
---
 deepmd/loggers/loggers.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/deepmd/loggers/loggers.py b/deepmd/loggers/loggers.py
index bb2e5f2dad..4249d7fb3d 100644
--- a/deepmd/loggers/loggers.py
+++ b/deepmd/loggers/loggers.py
@@ -229,6 +229,8 @@ def set_log_handles(
 
     ch.setLevel(level)
     ch.addFilter(_AppFilter())
+    # clean old handlers before adding new one
+    root_log.handlers.clear()
     root_log.addHandler(ch)
 
     # * add file handler ***************************************************************