v0.2.19 #668
Merged
v0.2.19 #668
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
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. 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>
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>
Now the PyMatgenStructureFormat doesn't support the <kbd>from_system</kbd> method. This PR adds this method, enabling users to convert the <kbd>pymatgen.core.Structure</kbd> to the dpdata format, which is convenient when you use <kbd>pymatgen.transformations</kbd> to build the atomic model. --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/pre-commit-hooks: v4.5.0 → v4.6.0](pre-commit/pre-commit-hooks@v4.5.0...v4.6.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.7 → v0.4.1](astral-sh/ruff-pre-commit@v0.3.7...v0.4.1) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Add function description on `system.py/check_type_map`
Fix the warning below:
```
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:6
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:6: DeprecationWarning: invalid escape sequence '\|'
latt_patt = "\|\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)\s+([0-9]{1,}[.][0-9]*)"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:7
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:7: DeprecationWarning: invalid escape sequence '\|'
pos_patt_first = "\|\s+[0-9]{1,}[:]\s\w+\s(\w+)(\s.*[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)(\s+[-]?[0-9]{1,}[.][0-9]*)"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:8
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:8: DeprecationWarning: invalid escape sequence '\s'
pos_patt_other = "\s+[a][t][o][m]\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+([-]?[0-9]{1,}[.][0-9]*)\s+(\w{1,2})"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:9
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:9: DeprecationWarning: invalid escape sequence '\|'
force_patt = "\|\s+[0-9]{1,}\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:10
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/fhi_aims/output.py:10: DeprecationWarning: invalid escape sequence '\s'
eng_patt = "Total energy uncorrected.*([-]?[0-9]{1,}[.][0-9]*[E][+-][0-9]{1,})\s+eV"
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:41
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:41: DeprecationWarning: invalid escape sequence '\s'
while len(re.split("\s+", lines[blk_idx])) == 0:
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:44
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:44: DeprecationWarning: invalid escape sequence '\s'
if len(re.split("\s+", lines[blk_idx])) == 0 or lines[blk_idx] == "":
../../../../../opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:332
/opt/hostedtoolcache/Python/3.11.9/x64/lib/python3.11/site-packages/dpdata/abacus/scf.py:332: DeprecationWarning: invalid escape sequence '\s'
if len(re.split("\s+", geometry_inlines[iline])) >= 3:
```
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.1 → v0.4.2](astral-sh/ruff-pre-commit@v0.4.1...v0.4.2) <!--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]>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced a new command-line interface for easier interaction with the application. - **Tests** - Added tests to verify the correct version output from the new command-line interface. <!-- 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>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.4.2 → v0.4.3](astral-sh/ruff-pre-commit@v0.4.2...v0.4.3) <!--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** - Added new elements to the periodic table: Rf, Db, Sg, Bh, Hs, Mt, Ds, Rg, Cn, Nh, Fl, Mc, Lv, Ts, Og. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
Do a benchmark before working on deepmodeling#526 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Introduced benchmark tests for import functionality and command line interface operations. - **Tests** - Added new benchmark tests to assess performance improvements. - **Chores** - Integrated `pytest` and `pytest-codspeed` into the project for enhanced testing capabilities. <!-- 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>
Fix deepmodeling#526. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Removed unnecessary import statements and restructured import handling for improved code organization and readability. - Reorganized imports within functions to localize dependencies and enhance code modularity. - **New Features** - Introduced conditional imports based on `TYPE_CHECKING` for better resource management and efficiency. - Added a new method `from_dict` to the `System` class for constructing instances from a data dictionary. - **Chores** - Updated linting rules in `pyproject.toml` to include `TID253` for banned module-level imports. - Modified import statements in test files to comply with the new linting rules for better code quality. - **Style** - Added `# noqa: TID253` comments to specific import statements to adhere to new linting rules and ensure clean code styling. <!-- 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>
I give up fix type annotations in all files, but it's meaningful to fix the top-module files `dpdata/*.py`. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added `name` property to `DPDataCalculator` class. - Introduced assertion for `rdkit_mol` in bond order system. - **Improvements** - Enhanced type hinting across various functions and methods. - Added decorators and type assertion checks for better code validation. - **Maintenance** - Introduced a GitHub Actions workflow for running Pyright type checker. - Updated dependencies and configurations in `pyproject.toml`. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]>
Try to fix deepmodeling#657 automatically
<!--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>
add functions to convert from others formats to ASE traj format <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced system and labeled system handling with new parameters and functionalities. - Improved stress calculations by modifying method parameters. - **Bug Fixes** - Corrected return types for several methods to ensure consistency and reliability. - **Tests** - Added new test cases to validate system setups and trajectory file operations. - **Chores** - Updated Python version matrix in workflow to include only version 3.11. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <[email protected]> Signed-off-by: C. Thang Nguyen <[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]>
deepmodeling#667) - add UT to detect the issue. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved the logic for replicating atom types in the system, ensuring more accurate replication behavior. - **Tests** - Added new tests to verify the replication of atom types, enhancing test coverage and reliability. <!-- 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: v0.4.5 → 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>
CodSpeed Performance ReportCongrats! CodSpeed is installed 🎉
You will start to see performance impacts in the reports once the benchmarks are run from your default branch.
|
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
No description provided.