merge devel to master (v0.13.0) #1676
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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 > 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 > 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 /> [](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 it. 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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 </tr></table> </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 "Specifying multiple Python/PyPy versions" 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 /> [](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 it. You can achieve the same result by closing it manually - `@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 Dependabot creating any more for this major version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this minor version` will close this PR and stop Dependabot creating any more for this minor version (unless you reopen the PR or upgrade to it yourself) - `@dependabot ignore this dependency` will close this PR and stop Dependabot creating any more for this dependency (unless you reopen the PR or upgrade to it yourself) </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
… to run different system at one single iteration model_devi step. (deepmodeling#1513) 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 <[email protected]>
Signed-off-by: Jinzhe Zeng <[email protected]>
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: njzjz-bot/njzjz-bot#4.
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.5 → v0.3.7](astral-sh/ruff-pre-commit@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>
Signed-off-by: Jinzhe Zeng <[email protected]>
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Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.3](astral-sh/ruff-pre-commit@v0.4.1...v0.4.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
Avoid `SyntaxWarning: invalid escape sequence '\{'`
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **Refactor**
- Improved string formatting in the generator for consistency.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
Co-authored-by: Han Wang <[email protected]>
See: - deepmodeling/deepmd-kit#3477 - deepmodeling/deepmd-kit#3753 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Removed the `"set_prefix": "set"` attribute across various JSON and YAML configuration files, streamlining data handling and batch processing setups. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
Follow up deepmodeling#1533 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Updated string formatting across various modules to use f-strings for improved readability and consistency in error messages, log entries, and data output. - **Style** - Enhanced string interpolation methods from older formatting styles to modern f-string syntax across the application, ensuring uniformity and clearer code presentation. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…eling#1544) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Improved efficiency in model name processing within the model deviation functionality. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Han Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
reopen PR deepmodeling#1541 due to branch is deleted add a new key in `param.json` file ``` "train_backend": "pytorch"/"tensorflow", ``` relate to this issue deepmodeling#1462 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Improved model management by dynamically generating model suffixes based on the selected backend, enhancing compatibility. - **Enhancements** - Updated model-related functions to incorporate backend-specific model suffixes for accurate file handling during training processes. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: C. Thang Nguyen <[email protected]> Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
```
/home/runner/work/dpgen/dpgen/dpgen/auto_test/Gamma.py:389: SyntaxWarning: invalid escape sequence '\('
upper = re.search("variable N equal count\(all\)", contents[ii])
```
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **Bug Fixes**
- Improved the reliability of the Gamma module by correcting a regular
expression pattern. This change ensures more accurate data parsing and
handling.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
Signed-off-by: Jinzhe Zeng <[email protected]>
fixes deepmodeling#1553 Co-authored-by: Han Wang <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.4 → v0.4.5](astral-sh/ruff-pre-commit@v0.4.4...v0.4.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Simplified and streamlined the submission processes for various job types, improving efficiency and reducing redundancy. - Centralized API version checking with a new utility function, enhancing maintainability and consistency across the application. - **Bug Fixes** - Improved error handling for API versions below 1.0, ensuring clearer and more consistent error messages. - **New Features** - Introduced a new function for API version validation, ensuring compatibility and proper error handling. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.5 → v0.4.7](astral-sh/ruff-pre-commit@v0.4.5...v0.4.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.7 → v0.4.8](astral-sh/ruff-pre-commit@v0.4.7...v0.4.8) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.8 → v0.4.10](astral-sh/ruff-pre-commit@v0.4.8...v0.4.10) <!--pre-commit.ci end--> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.10 → v0.5.0](astral-sh/ruff-pre-commit@v0.4.10...v0.5.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
I am going to use DP-GEN to develop models trained by other MLP software. This may or may not be merged into the main branch, but I think a general `mlp_engine` option can be added anyway. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced handling for multiple ML potential engines with specialized training argument functions. - **Improvements** - Enhanced training initialization by splitting into common and engine-specific functions. - Improved error handling for unsupported ML potential engines. - **Bug Fixes** - Corrected logic to differentiate between `dp` and other engine values during training and model initialization. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Removing ref-names is now suggested by setuptools-scm, per https://setuptools-scm.readthedocs.io/en/latest/usage/#git-archives, as it may lead to the git archive checksum changing. Generated by the task: njzjz-bot/njzjz-bot#6.
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.0 → v0.5.1](astral-sh/ruff-pre-commit@v0.5.0...v0.5.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Renamed internal function `make_train_dp` to `run_train_dp` for better clarity and consistency within the codebase. (Note: This change does not impact end-user functionalities directly.) <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.5 → v0.5.6](astral-sh/ruff-pre-commit@v0.5.5...v0.5.6) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
See readthedocs/sphinx_rtd_theme#1571 (comment) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Updated the version constraint for the `sphinx_rtd_theme` package to ensure compatibility, enhancing project stability and performance. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Streamlined dependency management by removing outdated comments and constraints from the project configuration. This change may allow for compatibility with newer versions of the `numpy` library. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.6 → v0.5.7](astral-sh/ruff-pre-commit@v0.5.6...v0.5.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.5.7 → v0.6.1](astral-sh/ruff-pre-commit@v0.5.7...v0.6.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.1 → v0.6.2](astral-sh/ruff-pre-commit@v0.6.1...v0.6.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
My suggestion:
- Separate VASP and ABACUS into separated functions (and may be
separated files). This will helpful to someone who want to implement a
new DFT engine and also convenient for maintain.
<!-- This is an auto-generated comment: release notes by coderabbit.ai
-->
## Summary by CodeRabbit
- **New Features**
- Enhanced the `pert_scaled` function to support different
initialization styles ("VASP" or "ABACUS").
- **Refactor**
- Improved loop logic and file handling for better performance and
reliability in perturbation processes.
- Streamlined the `make_vasp_relax` and `make_scale` functions for
improved readability and clarity.
- Simplified the construction of perturbation commands in the
`pert_scaled` function.
<!-- end of auto-generated comment: release notes by coderabbit.ai -->
---------
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Chores** - Improved code readability and maintainability through cleanup and simplification of functions. - Streamlined file path construction using the modern `Path` API. - Removed unnecessary operations related to file handling and training resources. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: C. Thang Nguyen <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.2 → v0.6.3](astral-sh/ruff-pre-commit@v0.6.2...v0.6.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Updated data representation to enhance classification and processing of information. - **Bug Fixes** - Improved data structure to ensure better interpretation and utilization in subsequent operations. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Co-authored-by: Han Wang <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.3 → v0.6.4](astral-sh/ruff-pre-commit@v0.6.3...v0.6.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
Update DeepModeling URLs for domain migration. Generated by the task: njzjz-bot/njzjz-bot#8.
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.4 → v0.6.5](astral-sh/ruff-pre-commit@v0.6.4...v0.6.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
ut failure caused by deepmodeling/dpdata#725 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved handling of edge cases in coordinate and energy tests, enhancing test robustness for zero values. - Added conditional checks to ensure accurate comparisons in energy calculations. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: Han Wang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.5 → v0.6.7](astral-sh/ruff-pre-commit@v0.6.5...v0.6.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]>
…epmodeling#1641) 1. make default deepmd_version setting be consistent with the doc 2. add StreamHandlers to root logger to make the screen output complete <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Updated versioning information for improved clarity. - Added a versioning element in the configuration for tracking and compatibility. - **Bug Fixes** - Enhanced logging configuration to improve message handling and visibility during runtime. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Scott Wu <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.7 → v0.6.8](astral-sh/ruff-pre-commit@v0.6.7...v0.6.8) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/pre-commit-hooks: v4.6.0 → v5.0.0](pre-commit/pre-commit-hooks@v4.6.0...v5.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.6.8 → v0.6.9](astral-sh/ruff-pre-commit@v0.6.8...v0.6.9) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.6.9 → v0.7.0](astral-sh/ruff-pre-commit@v0.6.9...v0.7.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…g#1659) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Updated the version constraint for the `pymatgen-analysis-defects` package, enabling access to newer features and fixes. - **Bug Fixes** - Commented out failing assertions in test methods to address issues with structure comparisons, indicating a need for future fixes. - **Chores** - Minor updates to the test files to manage test assertions effectively. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.7.2](astral-sh/ruff-pre-commit@v0.7.0...v0.7.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
) Compared to `sphinx-rtd-theme`, `sphinx-book-theme` is a clean and modern Sphinx theme. Generated by the task: njzjz-bot/njzjz-bot#11. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Updated documentation theme to `sphinx_book_theme`, enhancing visual presentation. - Introduced options for light and dark logo images in the documentation. - **Bug Fixes** - Updated dependency versions to ensure compatibility and improved functionality. - **Documentation** - Enhanced configuration settings for better theme management in the documentation. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.2 → v0.7.3](astral-sh/ruff-pre-commit@v0.7.2...v0.7.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Removed unused import statements and commented out assertions related to the `Incar` class in test methods, addressing previous test failures. - **Tests** - Adjusted test methods to exclude checks for the `Incar` data structure, streamlining the testing framework. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
deepmodeling#1662 was wrongly merged into master. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced input generation for LAMMPS to accommodate electron temperature settings. - Added a new parameter, `use_ele_temp`, for improved flexibility in input handling. - **Bug Fixes** - Ensured correct retrieval and passing of the `use_ele_temp` value during model deviation tasks. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added support for the "jax" backend, allowing users to work with model files using the new `.savedmodel` suffix. - **Bug Fixes** - Updated error messages to include "jax" in the list of supported backends, improving clarity for users encountering unsupported backend issues. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.3 → v0.7.4](astral-sh/ruff-pre-commit@v0.7.3...v0.7.4) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]>
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