merge devel to master (v3.1.2) #5088
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 3.1 to 3.2. <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>v3.2.0</h2> <ul> <li>✨ Adds GraalPy v25 (Python 3.12) support (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2597">#2597</a>)</li> <li>🛠 Update to CPython 3.14.0rc3 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2602">#2602</a>)</li> <li>🛠 Adds CPython 3.14.0 prerelease support for Android, and a number of improvements to Android builds (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2568">#2568</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2591">#2591</a>)</li> <li>🛠 Improvements to testing on Android, passing environment markers when installing the venv, and providing more debug output when build-verbosity is set (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2575">#2575</a>)</li> <li>⚠️ PyPy 3.10 was moved to <code>pypy-eol</code> in the <code>enable</code> option, as it is now end-of-life. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2521">#2521</a>)</li> <li>📚 Docs improvements (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2574">#2574</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2601">#2601</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2598">#2598</a>)</li> </ul> <h2>v3.1.4</h2> <ul> <li>✨ Add a <code>--clean-cache</code> command to clean up our cache (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2489">#2489</a>)</li> <li>🛠 Update Python to 3.14rc2 and other patch version bumps (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2542">#2542</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2556">#2556</a>)</li> <li>🛠 Update Pyodide to 0.28.2 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2562">#2562</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2558">#2558</a>)</li> <li>🐛 Fix resolution with <code>pyodide-build</code> when <code>dependency-versions</code> is set (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2548">#2548</a>)</li> <li>🐛 Set <code>CMAKE_FIND_ROOT_PATH_MODE_PACKAGE</code> to <code>BOTH</code> on Android (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2547">#2547</a>)</li> <li>🐛 Add <code>patchelf</code> dependency for platforms that can build Android wheels (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2552">#2552</a>)</li> <li>🐛 Ignore empty values for <code>CIBW_ARCHS</code> like most other environment variables (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2541">#2541</a>)</li> <li>💼 The <code>color</code> and <code>suggest_on_error</code> argparse options are now default in 3.14rc1+ (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2554">#2554</a>)</li> <li>💼 Use the virtualenv release URL instead of blob URL (should be more robust) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2555">#2555</a>)</li> <li>🧪 For iOS, lowering to macos-14 is needed for now due to issues with GitHub's runner images (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2557">#2557</a>)</li> <li>🧪 Split out platforms iOS and Android in our tests (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2519">#2519</a>)</li> <li>🧪 Fix and enable doctests (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2546">#2546</a>)</li> <li>📚 Improve our docs on free-threading (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2549">#2549</a>)</li> </ul> <h2>v3.1.3</h2> <ul> <li>🐛 Fix bug where "latest" dependencies couldn't update to pip 25.2 on Windows (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2537">#2537</a>)</li> <li>🧪 Use pytest-rerunfailures to improve some of our iOS/Android tests (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2527">#2527</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2539">#2539</a>)</li> <li>🧪 Remove some GraalPy Windows workarounds in our tests (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2501">#2501</a>)</li> </ul> <h2>v3.1.2</h2> <ul> <li>⚠️ Add an error if <code>CIBW_FREE_THREADING_SUPPORT</code> is set; you are likely missing 3.13t wheels, please use the <code>enable</code>/<code>CIBW_ENABLE</code> (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2520">#2520</a>)</li> <li>🛠 <code>riscv64</code> now enabled if you target that architecture, it's now supported on PyPI (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2509">#2509</a>)</li> <li>🛠 Add warning when using <code>cpython-experimental-riscv64</code> (no longer needed) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2526">#2526</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2528">#2528</a>)</li> <li>🛠 iOS versions bumped, fixing issues with 3.14 (now RC 1) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2530">#2530</a>)</li> <li>🐛 Fix bug in Android running wheel from our GitHub Action (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2517">#2517</a>)</li> <li>🐛 Fix warning when using <code>test-skip</code> of <code>"*-macosx_universal2:arm64"</code> (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2522">#2522</a>)</li> <li>🐛 Fix incorrect number of wheels reported in logs, again (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2517">#2517</a>)</li> <li>📚 We welcome our Android platform maintainer (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2516">#2516</a>)</li> </ul> <h2>v3.1.1</h2> <ul> <li>🐛 Fix a bug showing an incorrect wheel count at the end of execution, and misrepresenting test-only runs in the GitHub Action summary (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2512">#2512</a>)</li> <li>📚 Docs fix (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2510">#2510</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>v2.23.2</h3> <p><em>24 March 2025</em></p> <ul> <li>🐛 Workaround an issue with pyodide builds when running cibuildwheel with a Python that was installed via UV (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2328">#2328</a> via <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2331">#2331</a>)</li> <li>🛠 Dependency updates, including a manylinux update that fixes an <a href="https://redirect.github.com/pypa/manylinux/issues/1760">'undefined symbol' error</a> in gcc-toolset (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2334">#2334</a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/7c619efba910c04005a835b110b057fc28fd6e93"><code>7c619ef</code></a> Bump version: v3.2.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/bbebb68339e0aee225907d52767bd4a0423be7e4"><code>bbebb68</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2603">#2603</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/5bbeaf830fbc45f506c78995a91508753a80a2c2"><code>5bbeaf8</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2604">#2604</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/7a67c6b5a9b98a3ac8c63ce05cbbf0665ea19ea7"><code>7a67c6b</code></a> Add GraalPy 25 and remove workarounds for that version. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2597">#2597</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/b8a4fbc237c513da28f6df5eb6443d63ee9c2275"><code>b8a4fbc</code></a> Improve information about configuration overriding (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2598">#2598</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/70de033a7ff4087510bb4cd5f0b5e0b6328390a4"><code>70de033</code></a> Replace the <code>macos-13</code> images with the <code>macos-15-intel</code> images (GHA) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2601">#2601</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/ce4c16f88f17ab1f5711ab46e1bc6c796cd97fe1"><code>ce4c16f</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2602">#2602</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/66490f05369c9df86f605f2e87725dde3de6816c"><code>66490f0</code></a> Add CMAKE_CROSSCOMPILING_EMULATOR to Android CMake toolchain (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2591">#2591</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/77b9e35d7c4c367d5e2838147a7a456fee55c7a6"><code>77b9e35</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2594">#2594</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/39e9da06c5d3f3a360ec315ce12252eb84e34e8c"><code>39e9da0</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2593">#2593</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v3.1...v3.2">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>
## Summary This PR bumps the CMake minimum required version from 3.16 to 3.25.2 across the repository to support the `RUN_OUTPUT_STDOUT_VARIABLE` option used in `source/cmake/Findtensorflow.cmake`. ## Background PR deepmodeling#4890 introduced the use of `RUN_OUTPUT_STDOUT_VARIABLE` in the `try_run()` command within `source/cmake/Findtensorflow.cmake` (line 297). This CMake feature was added in CMake 3.25, but the minimum required version was still set to 3.16, which would cause build failures on systems with older CMake versions. Additionally, CMake 3.25.0 and 3.25.1 contain a bug (https://gitlab.kitware.com/cmake/cmake/-/issues/24275), so the minimum version is set to 3.25.2 to avoid this issue. ## Changes This PR updates the CMake version requirements consistently across all build configuration files: - **Main CMakeLists.txt**: Updated base requirement and conditional requirements for CUDA/ROCM variants - **Python build configuration** (`backend/read_env.py`): Updated version requirements for CPU, CUDA, and ROCM variants - **Documentation** (`doc/install/install-from-source.md`): Simplified to state that CMake 3.25.2+ is required for all platforms - **Test and example CMakeLists**: Updated all test directories and example projects to require CMake 3.25.2 for consistency ### Files Modified - `source/CMakeLists.txt` - `backend/read_env.py` - `doc/install/install-from-source.md` - `source/lib/src/gpu/CMakeLists.txt` - `source/lib/tests/CMakeLists.txt` - `source/api_c/tests/CMakeLists.txt` - `source/api_cc/tests/CMakeLists.txt` - `source/lmp/plugin/CMakeLists.txt` - `examples/infer_water/CMakeLists.txt` ## Impact Users will need CMake 3.25.2 or later to build DeePMD-kit from source. CMake 3.25.2 was released in March 2022, so it should be widely available. Users can easily install or upgrade CMake via pip: ```bash pip install -U cmake ``` Fixes the issue where builds would fail with CMake versions between 3.16 and 3.24 due to the use of `RUN_OUTPUT_STDOUT_VARIABLE`, and avoids the bug present in CMake 3.25.0 and 3.25.1. <!-- START COPILOT CODING AGENT SUFFIX --> <details> <summary>Original prompt</summary> > > ---- > > *This section details on the original issue you should resolve* > > <issue_title>[BUG] CMake minimal version should be bumped to 3.25</issue_title> > <issue_description>### Bug summary > > deepmodeling#4890 uses `RUN_OUTPUT_STDOUT_VARIABLE` which is new in CMake 3.25. Thus, the CMake minimal version should be bumped to 3.25 in CMakeLists.txt, read_env.py, and the documentation. > > ### DeePMD-kit Version > > devel > > ### Backend and its version > > - > > ### How did you download the software? > > Built from source > > ### Input Files, Running Commands, Error Log, etc. > > As above. > > ### Steps to Reproduce > > As above. > > ### Further Information, Files, and Links > > _No response_</issue_description> > > ## Comments on the Issue (you are @copilot in this section) > > <comments> > </comments> > </details> Fixes deepmodeling#5000 <!-- START COPILOT CODING AGENT TIPS --> --- 💬 Share your feedback on Copilot coding agent for the chance to win a $200 gift card! Click [here](https://survey3.medallia.com/?EAHeSx-AP01bZqG0Ld9QLQ) to start the survey. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]>
…odeling#5002) per https://github.blog/changelog/2025-09-19-github-actions-macos-13-runner-image-is-closing-down/ <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated macOS build matrix in CI to use macOS 15 Intel runners for x86_64 wheel builds, keeping Python versions and other matrix settings unchanged. * No user-facing changes; application behavior remains the same. This update only affects build infrastructure, improving reliability and maintaining platform coverage. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
<!--pre-commit.ci start--> updates: - [github.com/PyCQA/isort: 6.0.1 → 6.1.0](PyCQA/isort@6.0.1...6.1.0) - [github.com/astral-sh/ruff-pre-commit: v0.13.2 → v0.13.3](astral-sh/ruff-pre-commit@v0.13.2...v0.13.3) - https://github.com/pylint-dev/pylint/: v3.3.8 → v3.3.9 <!--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/PyCQA/isort: 6.1.0 → 7.0.0](PyCQA/isort@6.1.0...7.0.0) - [github.com/astral-sh/ruff-pre-commit: v0.13.3 → v0.14.0](astral-sh/ruff-pre-commit@v0.13.3...v0.14.0) - https://github.com/pylint-dev/pylint/: v3.3.9 → v4.0.0 <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [github/codeql-action](https://github.com/github/codeql-action) from 3 to 4. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/github/codeql-action/releases">github/codeql-action's releases</a>.</em></p> <blockquote> <h2>v3.30.8</h2> <h1>CodeQL Action Changelog</h1> <p>See the <a href="https://github.com/github/codeql-action/releases">releases page</a> for the relevant changes to the CodeQL CLI and language packs.</p> <h2>3.30.8 - 10 Oct 2025</h2> <p>No user facing changes.</p> <p>See the full <a href="https://github.com/github/codeql-action/blob/v3.30.8/CHANGELOG.md">CHANGELOG.md</a> for more information.</p> <h2>v3.30.7</h2> <h1>CodeQL Action Changelog</h1> <p>See the <a href="https://github.com/github/codeql-action/releases">releases page</a> for the relevant changes to the CodeQL CLI and language packs.</p> <h2>3.30.7 - 06 Oct 2025</h2> <p>No user facing changes.</p> <p>See the full <a href="https://github.com/github/codeql-action/blob/v3.30.7/CHANGELOG.md">CHANGELOG.md</a> for more information.</p> <h2>v3.30.6</h2> <h1>CodeQL Action Changelog</h1> <p>See the <a href="https://github.com/github/codeql-action/releases">releases page</a> for the relevant changes to the CodeQL CLI and language packs.</p> <h2>3.30.6 - 02 Oct 2025</h2> <ul> <li>Update default CodeQL bundle version to 2.23.2. <a href="https://redirect.github.com/github/codeql-action/pull/3168">#3168</a></li> </ul> <p>See the full <a href="https://github.com/github/codeql-action/blob/v3.30.6/CHANGELOG.md">CHANGELOG.md</a> for more information.</p> <h2>v3.30.5</h2> <h1>CodeQL Action Changelog</h1> <p>See the <a href="https://github.com/github/codeql-action/releases">releases page</a> for the relevant changes to the CodeQL CLI and language packs.</p> <h2>3.30.5 - 26 Sep 2025</h2> <ul> <li>We fixed a bug that was introduced in <code>3.30.4</code> with <code>upload-sarif</code> which resulted in files without a <code>.sarif</code> extension not getting uploaded. <a href="https://redirect.github.com/github/codeql-action/pull/3160">#3160</a></li> </ul> <p>See the full <a href="https://github.com/github/codeql-action/blob/v3.30.5/CHANGELOG.md">CHANGELOG.md</a> for more information.</p> <h2>v3.30.4</h2> <h1>CodeQL Action Changelog</h1> <p>See the <a href="https://github.com/github/codeql-action/releases">releases page</a> for the relevant changes to the CodeQL CLI and language packs.</p> <h2>3.30.4 - 25 Sep 2025</h2> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/github/codeql-action/blob/main/CHANGELOG.md">github/codeql-action's changelog</a>.</em></p> <blockquote> <h2>3.29.4 - 23 Jul 2025</h2> <p>No user facing changes.</p> <h2>3.29.3 - 21 Jul 2025</h2> <p>No user facing changes.</p> <h2>3.29.2 - 30 Jun 2025</h2> <ul> <li>Experimental: When the <code>quality-queries</code> input for the <code>init</code> action is provided with an argument, separate <code>.quality.sarif</code> files are produced and uploaded for each language with the results of the specified queries. Do not use this in production as it is part of an internal experiment and subject to change at any time. <a href="https://redirect.github.com/github/codeql-action/pull/2935">#2935</a></li> </ul> <h2>3.29.1 - 27 Jun 2025</h2> <ul> <li>Fix bug in PR analysis where user-provided <code>include</code> query filter fails to exclude non-included queries. <a href="https://redirect.github.com/github/codeql-action/pull/2938">#2938</a></li> <li>Update default CodeQL bundle version to 2.22.1. <a href="https://redirect.github.com/github/codeql-action/pull/2950">#2950</a></li> </ul> <h2>3.29.0 - 11 Jun 2025</h2> <ul> <li>Update default CodeQL bundle version to 2.22.0. <a href="https://redirect.github.com/github/codeql-action/pull/2925">#2925</a></li> <li>Bump minimum CodeQL bundle version to 2.16.6. <a href="https://redirect.github.com/github/codeql-action/pull/2912">#2912</a></li> </ul> <h2>3.28.21 - 28 July 2025</h2> <p>No user facing changes.</p> <h2>3.28.20 - 21 July 2025</h2> <ul> <li>Remove support for combining SARIF files from a single upload for GHES 3.18, see <a href="https://github.blog/changelog/2024-05-06-code-scanning-will-stop-combining-runs-from-a-single-upload/">the changelog post</a>. <a href="https://redirect.github.com/github/codeql-action/pull/2959">#2959</a></li> </ul> <h2>3.28.19 - 03 Jun 2025</h2> <ul> <li>The CodeQL Action no longer includes its own copy of the extractor for the <code>actions</code> language, which is currently in public preview. The <code>actions</code> extractor has been included in the CodeQL CLI since v2.20.6. If your workflow has enabled the <code>actions</code> language <em>and</em> you have pinned your <code>tools:</code> property to a specific version of the CodeQL CLI earlier than v2.20.6, you will need to update to at least CodeQL v2.20.6 or disable <code>actions</code> analysis.</li> <li>Update default CodeQL bundle version to 2.21.4. <a href="https://redirect.github.com/github/codeql-action/pull/2910">#2910</a></li> </ul> <h2>3.28.18 - 16 May 2025</h2> <ul> <li>Update default CodeQL bundle version to 2.21.3. <a href="https://redirect.github.com/github/codeql-action/pull/2893">#2893</a></li> <li>Skip validating SARIF produced by CodeQL for improved performance. <a href="https://redirect.github.com/github/codeql-action/pull/2894">#2894</a></li> <li>The number of threads and amount of RAM used by CodeQL can now be set via the <code>CODEQL_THREADS</code> and <code>CODEQL_RAM</code> runner environment variables. If set, these environment variables override the <code>threads</code> and <code>ram</code> inputs respectively. <a href="https://redirect.github.com/github/codeql-action/pull/2891">#2891</a></li> </ul> <h2>3.28.17 - 02 May 2025</h2> <ul> <li>Update default CodeQL bundle version to 2.21.2. <a href="https://redirect.github.com/github/codeql-action/pull/2872">#2872</a></li> </ul> <h2>3.28.16 - 23 Apr 2025</h2> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/github/codeql-action/commit/a841c540b73bac7685691a2f930006ba52db3645"><code>a841c54</code></a> Scratch <code>uploadSpecifiedFiles</code> tests, make <code>uploadPayload</code> tests instead</li> <li><a href="https://github.com/github/codeql-action/commit/aeb12f6eaaa7419b7170f27dc3e2b5710203ff2d"><code>aeb12f6</code></a> Merge branch 'main' into redsun82/skip-sarif-upload-tests</li> <li><a href="https://github.com/github/codeql-action/commit/6fd4ceb7bbb8ec2746fd4d3a64b77787dffd9afc"><code>6fd4ceb</code></a> Merge pull request <a href="https://redirect.github.com/github/codeql-action/issues/3189">#3189</a> from github/henrymercer/download-codeql-rate-limit</li> <li><a href="https://github.com/github/codeql-action/commit/196a3e577b477ffb129cb35c7ed3ba72e6e2dbe7"><code>196a3e5</code></a> Merge pull request <a href="https://redirect.github.com/github/codeql-action/issues/3188">#3188</a> from github/mbg/telemetry/partial-config</li> <li><a href="https://github.com/github/codeql-action/commit/98abb870dcd6421594724ae220643e13baf90298"><code>98abb87</code></a> Add configuration error for rate limited CodeQL download</li> <li><a href="https://github.com/github/codeql-action/commit/bdd2cdf891a0a89c6680bd54c9ba63c80e440f75"><code>bdd2cdf</code></a> Also include <code>language</code> in error status report for <code>start-proxy</code>, if available</li> <li><a href="https://github.com/github/codeql-action/commit/fb148789ab863424b005147b4b018fe5691e5ccc"><code>fb14878</code></a> Include <code>languages</code> in <code>start-proxy</code> telemetry</li> <li><a href="https://github.com/github/codeql-action/commit/2ff418f28a66dd71cd80701e95ec26db12875f15"><code>2ff418f</code></a> Parse <code>language</code> before calling <code>getCredentials</code></li> <li>See full diff in <a href="https://github.com/github/codeql-action/compare/v3...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 [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) from 6 to 7. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/astral-sh/setup-uv/releases">astral-sh/setup-uv's releases</a>.</em></p> <blockquote> <h2>v7.0.0 🌈 node24 and a lot of bugfixes</h2> <h2>Changes</h2> <p>This release comes with a load of bug fixes and a speed up. Because of switching from node20 to node24 it is also a breaking change. If you are running on GitHub hosted runners this will just work, if you are using self-hosted runners make sure, that your runners are up to date. If you followed the normal installation instructions your self-hosted runner will keep itself updated.</p> <p>This release also removes the deprecated input <code>server-url</code> which was used to download uv releases from a different server. The <a href="https://github.com/astral-sh/setup-uv?tab=readme-ov-file#manifest-file">manifest-file</a> input supersedes that functionality by adding a flexible way to define available versions and where they should be downloaded from.</p> <h3>Fixes</h3> <ul> <li>The action now respects when the environment variable <code>UV_CACHE_DIR</code> is already set and does not overwrite it. It now also finds <a href="https://docs.astral.sh/uv/reference/settings/#cache-dir">cache-dir</a> settings in config files if you set them.</li> <li>Some users encountered problems that <a href="https://github.com/astral-sh/setup-uv?tab=readme-ov-file#disable-cache-pruning">cache pruning</a> took forever because they had some <code>uv</code> processes running in the background. Starting with uv version <code>0.8.24</code> this action uses <code>uv cache prune --ci --force</code> to ignore the running processes</li> <li>If you just want to install uv but not have it available in path, this action now respects <code>UV_NO_MODIFY_PATH</code></li> <li>Some other actions also set the env var <code>UV_CACHE_DIR</code>. This action can now deal with that but as this could lead to unwanted behavior in some edgecases a warning is now displayed.</li> </ul> <h3>Improvements</h3> <p>If you are using minimum version specifiers for the version of uv to install for example</p> <pre lang="toml"><code>[tool.uv] required-version = ">=0.8.17" </code></pre> <p>This action now detects that and directly uses the latest version. Previously it would download all available releases from the uv repo to determine the highest matching candidate for the version specifier, which took much more time.</p> <p>If you are using other specifiers like <code>0.8.x</code> this action still needs to download all available releases because the specifier defines an upper bound (not 0.9.0 or later) and "latest" would possibly not satisfy that.</p> <h2>🚨 Breaking changes</h2> <ul> <li>Use node24 instead of node20 <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/608">#608</a>)</li> <li>Remove deprecated input server-url <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/607">#607</a>)</li> </ul> <h2>🐛 Bug fixes</h2> <ul> <li>Respect UV_CACHE_DIR and cache-dir <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/612">#612</a>)</li> <li>Use --force when pruning cache <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/611">#611</a>)</li> <li>Respect UV_NO_MODIFY_PATH <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/603">#603</a>)</li> <li>Warn when <code>UV_CACHE_DIR</code> has changed <a href="https://github.com/jamesbraza"><code>@jamesbraza</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/601">#601</a>)</li> </ul> <h2>🚀 Enhancements</h2> <ul> <li>Shortcut to latest version for minimum version specifier <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/598">#598</a>)</li> </ul> <h2>🧰 Maintenance</h2> <ul> <li>Bump dependencies <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/613">#613</a>)</li> <li>Fix test-uv-no-modify-path <a href="https://github.com/eifinger"><code>@eifinger</code></a> (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/604">#604</a>)</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/astral-sh/setup-uv/commit/3259c6206f993105e3a61b142c2d97bf4b9ef83d"><code>3259c62</code></a> Bump deps (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/633">#633</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/bf8e8ed895b7f686f85839659243f31a7df4a977"><code>bf8e8ed</code></a> Split up documentation (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/632">#632</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/9c6b5e9fb575cac8e82bb437dd7fc25a094bd85d"><code>9c6b5e9</code></a> Add resolution-strategy input to support oldest compatible version selection ...</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/a5129e99f44f5d2ba22cdc54770745bd6f0d9c33"><code>a5129e9</code></a> Add copilot-instructions.md (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/630">#630</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/d18bcc753ac29c1ed721aa4a812a90eb937852d6"><code>d18bcc7</code></a> Add value of UV_PYTHON_INSTALL_DIR to path (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/628">#628</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/bd1f875aba1ebb6d38211b773b094ad1dcca58df"><code>bd1f875</code></a> Set output venv when activate-environment is used (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/627">#627</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/1a91c3851df47749b241e3c5c696350957c93ff0"><code>1a91c38</code></a> chore: update known checksums for 0.9.2 (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/626">#626</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/c79f606987cb4a0f3d1a95a3e44bcebfb0a9b303"><code>c79f606</code></a> chore: update known checksums for 0.9.1 (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/625">#625</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/e0249f159931b41f44fc8208c9b4cff085288cc9"><code>e0249f1</code></a> Fall back to PR for updating known versions (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/623">#623</a>)</li> <li><a href="https://github.com/astral-sh/setup-uv/commit/6d2eb15b4979924f7be71aa06908c6211f80ac88"><code>6d2eb15</code></a> Cache python installs (<a href="https://redirect.github.com/astral-sh/setup-uv/issues/621">#621</a>)</li> <li>Additional commits viewable in <a href="https://github.com/astral-sh/setup-uv/compare/v6...v7">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. 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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>
add compression support for se_e3_tebd <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added TEBD-style descriptor support, optional runtime compression, and a Python-callable tabulation operation with autograd. - **Performance Improvements** - Shared/global tabulation tables and shared embeddings to reduce redundant table builds and improve CPU/GPU throughput. - **Reliability** - Validation and guards around enabling compression and runtime dispatch to prevent misconfiguration. - **Tests** - New CPU/GPU unit and integration tests for forward/backward TEBD paths. - **Documentation** - Docs updated to state model compression is supported. <!-- 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>
auto detect cuda version, if >= 13.0, set c++17 fix issue deepmodeling#5016 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Build now detects the installed CUDA Toolkit version and adjusts configuration accordingly. * Automatically selects C++17 for host/device compilation when CUDA Toolkit 13.0+ is present. * Emits clearer build status messages showing detected CUDA version and chosen C++ standard. * Maintains existing version checks and does not change runtime behavior or public APIs. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: OutisLi <[email protected]> Co-authored-by: Copilot <[email protected]> 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 * **Documentation** * Updated model compression documentation to clarify dependency requirements and specify that compression is supported only under particular input mode configurations, providing clearer implementation guidance for users. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…#5025) Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 5 to 6. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/actions/download-artifact/releases">actions/download-artifact's releases</a>.</em></p> <blockquote> <h2>v6.0.0</h2> <h2>What's Changed</h2> <p><strong>BREAKING CHANGE:</strong> this update supports Node <code>v24.x</code>. This is not a breaking change per-se but we're treating it as such.</p> <ul> <li>Update README for download-artifact v5 changes by <a href="https://github.com/yacaovsnc"><code>@yacaovsnc</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/417">actions/download-artifact#417</a></li> <li>Update README with artifact extraction details by <a href="https://github.com/yacaovsnc"><code>@yacaovsnc</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/424">actions/download-artifact#424</a></li> <li>Readme: spell out the first use of GHES by <a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/431">actions/download-artifact#431</a></li> <li>Bump <code>@actions/artifact</code> to <code>v4.0.0</code></li> <li>Prepare <code>v6.0.0</code> by <a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/438">actions/download-artifact#438</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> made their first contribution in <a href="https://redirect.github.com/actions/download-artifact/pull/431">actions/download-artifact#431</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v5...v6.0.0">https://github.com/actions/download-artifact/compare/v5...v6.0.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/download-artifact/commit/018cc2cf5baa6db3ef3c5f8a56943fffe632ef53"><code>018cc2c</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/438">#438</a> from actions/danwkennedy/prepare-6.0.0</li> <li><a href="https://github.com/actions/download-artifact/commit/815651c680ffe1c95719d0ed08aba1a2f9d5c177"><code>815651c</code></a> Revert "Remove <code>github.dep.yml</code>"</li> <li><a href="https://github.com/actions/download-artifact/commit/bb3a066a8babc8ed7b3e4218896c548fe34e7115"><code>bb3a066</code></a> Remove <code>github.dep.yml</code></li> <li><a href="https://github.com/actions/download-artifact/commit/fa1ce46bbd11b8387539af12741055a76dfdf804"><code>fa1ce46</code></a> Prepare <code>v6.0.0</code></li> <li><a href="https://github.com/actions/download-artifact/commit/4a24838f3d5601fd639834081e118c2995d51e1c"><code>4a24838</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/431">#431</a> from danwkennedy/patch-1</li> <li><a href="https://github.com/actions/download-artifact/commit/5e3251c4ff5a32e4cf8dd4adaee0e692365237ae"><code>5e3251c</code></a> Readme: spell out the first use of GHES</li> <li><a href="https://github.com/actions/download-artifact/commit/abefc31eafcfbdf6c5336127c1346fdae79ff41c"><code>abefc31</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/424">#424</a> from actions/yacaovsnc/update_readme</li> <li><a href="https://github.com/actions/download-artifact/commit/ac43a6070aa7db8a41e756e7a2846221edca7027"><code>ac43a60</code></a> Update README with artifact extraction details</li> <li><a href="https://github.com/actions/download-artifact/commit/de96f4613b77ec03b5cf633e7c350c32bd3c5660"><code>de96f46</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/417">#417</a> from actions/yacaovsnc/update_readme</li> <li><a href="https://github.com/actions/download-artifact/commit/7993cb44e9052f2f08f9b828ae5ef3ecca7d2ac7"><code>7993cb4</code></a> Remove migration guide for artifact download changes</li> <li>Additional commits viewable in <a href="https://github.com/actions/download-artifact/compare/v5...v6">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>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.0 → v0.14.2](astral-sh/ruff-pre-commit@v0.14.0...v0.14.2) - https://github.com/pylint-dev/pylint/: v4.0.0 → v4.0.2 <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
) Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 4 to 5. <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>v5.0.0</h2> <h2>What's Changed</h2> <p><strong>BREAKING CHANGE:</strong> this update supports Node <code>v24.x</code>. This is not a breaking change per-se but we're treating it as such.</p> <ul> <li>Update README.md by <a href="https://github.com/GhadimiR"><code>@GhadimiR</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/681">actions/upload-artifact#681</a></li> <li>Update README.md by <a href="https://github.com/nebuk89"><code>@nebuk89</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/712">actions/upload-artifact#712</a></li> <li>Readme: spell out the first use of GHES by <a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/727">actions/upload-artifact#727</a></li> <li>Update GHES guidance to include reference to Node 20 version by <a href="https://github.com/patrikpolyak"><code>@patrikpolyak</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/725">actions/upload-artifact#725</a></li> <li>Bump <code>@actions/artifact</code> to <code>v4.0.0</code></li> <li>Prepare <code>v5.0.0</code> by <a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/734">actions/upload-artifact#734</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/GhadimiR"><code>@GhadimiR</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/681">actions/upload-artifact#681</a></li> <li><a href="https://github.com/nebuk89"><code>@nebuk89</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/712">actions/upload-artifact#712</a></li> <li><a href="https://github.com/danwkennedy"><code>@danwkennedy</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/727">actions/upload-artifact#727</a></li> <li><a href="https://github.com/patrikpolyak"><code>@patrikpolyak</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/725">actions/upload-artifact#725</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v4...v5.0.0">https://github.com/actions/upload-artifact/compare/v4...v5.0.0</a></p> <h2>v4.6.2</h2> <h2>What's Changed</h2> <ul> <li>Update to use artifact 2.3.2 package & prepare for new upload-artifact release by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/685">actions/upload-artifact#685</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/685">actions/upload-artifact#685</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v4...v4.6.2">https://github.com/actions/upload-artifact/compare/v4...v4.6.2</a></p> <h2>v4.6.1</h2> <h2>What's Changed</h2> <ul> <li>Update to use artifact 2.2.2 package by <a href="https://github.com/yacaovsnc"><code>@yacaovsnc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/673">actions/upload-artifact#673</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v4...v4.6.1">https://github.com/actions/upload-artifact/compare/v4...v4.6.1</a></p> <h2>v4.6.0</h2> <h2>What's Changed</h2> <ul> <li>Expose env vars to control concurrency and timeout by <a href="https://github.com/yacaovsnc"><code>@yacaovsnc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/662">actions/upload-artifact#662</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v4...v4.6.0">https://github.com/actions/upload-artifact/compare/v4...v4.6.0</a></p> <h2>v4.5.0</h2> <h2>What's Changed</h2> <ul> <li>fix: deprecated <code>Node.js</code> version in action by <a href="https://github.com/hamirmahal"><code>@hamirmahal</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/578">actions/upload-artifact#578</a></li> <li>Add new <code>artifact-digest</code> output by <a href="https://github.com/bdehamer"><code>@bdehamer</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/656">actions/upload-artifact#656</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/hamirmahal"><code>@hamirmahal</code></a> made their first contribution in <a href="https://redirect.github.com/actions/upload-artifact/pull/578">actions/upload-artifact#578</a></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/330a01c490aca151604b8cf639adc76d48f6c5d4"><code>330a01c</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/734">#734</a> from actions/danwkennedy/prepare-5.0.0</li> <li><a href="https://github.com/actions/upload-artifact/commit/03f282445299bbefc96171af272a984663b63a26"><code>03f2824</code></a> Update <code>github.dep.yml</code></li> <li><a href="https://github.com/actions/upload-artifact/commit/905a1ecb5915b264cbc519e4eb415b5d82916018"><code>905a1ec</code></a> Prepare <code>v5.0.0</code></li> <li><a href="https://github.com/actions/upload-artifact/commit/2d9f9cdfa99fedaddba68e9b5b5c281eca26cc63"><code>2d9f9cd</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/725">#725</a> from patrikpolyak/patch-1</li> <li><a href="https://github.com/actions/upload-artifact/commit/9687587dec67f2a8bc69104e183d311c42af6d6f"><code>9687587</code></a> Merge branch 'main' into patch-1</li> <li><a href="https://github.com/actions/upload-artifact/commit/2848b2cda0e5190984587ec6bb1f36730ca78d50"><code>2848b2c</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/727">#727</a> from danwkennedy/patch-1</li> <li><a href="https://github.com/actions/upload-artifact/commit/9b511775fd9ce8c5710b38eea671f856de0e70a7"><code>9b51177</code></a> Spell out the first use of GHES</li> <li><a href="https://github.com/actions/upload-artifact/commit/cd231ca1eda77976a84805c4194a1954f56b0727"><code>cd231ca</code></a> Update GHES guidance to include reference to Node 20 version</li> <li><a href="https://github.com/actions/upload-artifact/commit/de65e23aa2b7e23d713bb51fbfcb6d502f8667d8"><code>de65e23</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/712">#712</a> from actions/nebuk89-patch-1</li> <li><a href="https://github.com/actions/upload-artifact/commit/8747d8cd7632611ad6060b528f3e0f654c98869c"><code>8747d8c</code></a> Update README.md</li> <li>Additional commits viewable in <a href="https://github.com/actions/upload-artifact/compare/v4...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>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.2 → v0.14.3](astral-sh/ruff-pre-commit@v0.14.2...v0.14.3) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…eepmodeling#5036) NVCC compilation errors with gcc-14 and C++11. Cases in other repos: https://gitlab.archlinux.org/archlinux/packaging/packages/cuda/-/issues/12 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Improved GPU build configuration to better support newer compiler versions (GCC/Clang 14+) and preserve user-specified C++ standards during compilation. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
…ems list (deepmodeling#5033) ### Description This PR modifies the `process_systems` utility function to change how it handles list inputs. Previously, if the `systems` argument was a `str`, the function would recursively search that path for systems. However, if `systems` was a `list`, the function would return the list as-is, assuming it was already a complete list of system paths. This update unifies the logic. The function now treats *every* string path—whether it's a single `str` input or an item within a `list`—as a directory to be recursively searched. It also refactors the internal logic to first normalize the input into a list of paths and then process them uniformly, improving code clarity and maintainability. ### Motivation and Justification The original implementation's inconsistent handling of `str` versus `list` inputs caused two significant problems: 1. **Broken JSON Configurations:** A very common use case, specifying a single data directory in `input.json` like `"systems": ["/path/to/training_data"]`, would fail. The function would not search inside `/path/to/training_data` for the actual system directories (e.g., `set.000`, `set.001`, etc.). 2. **Inability to Aggregate Data:** It was impossible for users to combine multiple datasets by providing a list of top-level directories, such as `"systems": ["/path/to/dataset_A", "/path/to/dataset_B"]`. This change solves both problems by ensuring that paths provided in a list are searched recursively, just as a single string path would be. ### Benefits * **Fixes Bug:** Correctly processes the common configuration of a single-item list in `input.json`. * **Enables Data Aggregation:** Users can now successfully provide a list of multiple data directories to be searched and combined. * **Improves Consistency:** The function's behavior is now intuitive and consistent, regardless of whether the user provides a single `str` or a `list[str]`. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Documentation** * Clarified how training/validation system paths may be specified: a single system directory or a parent directory to recursively discover systems; lists of paths are explicitly supported and processed per-item. * **Improvements** * Input handling for system paths enhanced to accept multiple paths and consolidate discovered systems, with expanded pattern-based discovery for more flexible data input. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
Accelerate data loading in training phase. Up to 40x acceleration for small descriptors with lower CPU usage. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Single-frame loading API and improved mixed-type atomic system support. * Platform-aware cache size exposed for tuning. * **Performance Improvements** * Memory-mapped data access with cached file handles. * Concurrent loading of frame data for better multi-core utilization. * **Bug Fixes** * Standardized frame keys and reshaping for consistent downstream behavior. * **Tests** * Updated tests to include polarizability in batch key handling. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
Bug fix when type num in training system is less than type map. Fix issue deepmodeling#5042 @ <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Refactor** * Optimized internal atom-type mapping to make data import and processing more efficient. * Maintains identical behavior and output formats; no changes to public interfaces or exported declarations. * Improves performance and observability during data handling without altering results or user-facing functionality. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.3 → v0.14.4](astral-sh/ruff-pre-commit@v0.14.3...v0.14.4) - [github.com/pre-commit/mirrors-clang-format: v21.1.2 → v21.1.5](pre-commit/mirrors-clang-format@v21.1.2...v21.1.5) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
I found that the inference time per atom very weird using small models (both DPA3-L3 and DPA1 attn0) on very large systems (more than 1000 atoms): <img width="1034" height="695" alt="截屏2025-11-11 17 52 32" src="https://github.com/user-attachments/assets/71b12719-ee74-4f2b-bb50-9f5f7031ee16" /> Through profilling, I found some unnecessary memory allocation matters for keys not in the model outputs (such as hessian). After fix, the inference time seems good: <img width="1067" height="693" alt="截屏2025-11-11 17 56 26" src="https://github.com/user-attachments/assets/0fe6d430-3daa-43cd-b245-0889cd1311a8" /> <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Refactor** * Improved internal handling of output definitions in model inference to ensure proper filtering for models without Hessian support. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…sts and bias standard tests (deepmodeling#5049) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Tests** * Improved test isolation by resetting the TensorFlow default graph before and after affected tests to ensure a clean graph state between runs. * Adjusted test modules to import the TensorFlow environment wrapper used in tests. * No changes to test assertions or runtime behavior beyond lifecycle improvements. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
## Summary - add a regression test that reproduces the original atom-type remapping failure when the training system contains fewer atom types than the provided type_map - ensure the fix from commit 4ec0437 remains covered going forward <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Tests** * Added unit tests for DeepmdData that validate atom-type remapping, handling of unused types, and correct loading/formatting of type arrays. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…ion (deepmodeling#5040) ## Overview This PR introduces performance optimizations for data loading and statistics computation in deepmd-kit. The changes focus on multi-threading parallelization, memory-mapped I/O, and efficient filesystem operations. ## Changes Summary ### 1. Multi-threaded Statistics Computation (`deepmd/pt/utils/stat.py`) - Introduced `ThreadPoolExecutor` for parallel processing of multiple datasets - Refactored `make_stat_input` to use thread pool with 256 workers - Created `_process_one_dataset` helper function for individual dataset processing - Significantly accelerates statistics computation for multi-system datasets ### 2. Efficient System Path Lookup (`deepmd/common.py`) - Optimized `expand_sys_str` to use `rglob("type.raw")` instead of `rglob("*")` + filtering - Added `parent` property to `DPOSPath` and `DPH5Path` classes in `deepmd/utils/path.py` - **Performance**: 10x speedup for system discovery (as noted in commit message) ### 3. Memory-mapped Data Loading (`deepmd/utils/data.py`) - Added `_get_nframes` method to read numpy file headers without loading data - Modified `get_numb_batch` to use the new method instead of loading entire dataset - Uses `np.lib.format.read_magic` and `read_array_header_*` to extract shape information - Reduces memory consumption for large datasets ### 4. Parallel Statistics File Loading (`deepmd/utils/env_mat_stat.py`) - Implemented `ThreadPoolExecutor` for parallel loading of stat files - Added `_load_stat_file` static method with error handling - Uses 128 worker threads for I/O-bound operations - Enhanced file format validation and malformed file handling ## Performance Impact | Component | Before | After | Improvement | |-----------|--------|-------|-------------| | System path lookup | O(n) file traversal | O(k) direct match | 10x faster | | Statistics computation | Sequential processing | 256-thread parallel | Significant | | Data loading | Full dataset load | Header-only read | Memory efficient | | Statistics loading | Sequential file I/O | 128-thread parallel | Significant | ## Compatibility ✅ **Backward Compatible**: All API interfaces remain unchanged ✅ **Data Format**: No changes to data file formats ✅ **Functionality**: All existing features work normally <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Performance Improvements** * Optimized frame detection to avoid loading complete datasets during initialization, enhancing startup performance for large data files. * Improved support for multiple data format variants with more efficient metadata reading. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…ations (deepmodeling#5055) - Introduced the SiLU (Sigmoid Linear Unit) activation function with corresponding gradient and second derivative calculations. - Updated the activation function mapping to include SiLU, enhancing the flexibility of activation functions available in the DPTabulate class. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Added support for the SiLU (Swish) activation across runtime computations and gradients. * **Tests** * Expanded test coverage to validate all supported activations (tanh, gelu, relu, relu6, softplus, sigmoid, silu) and their first/second derivatives across execution paths. * **Documentation** * Updated activation references and lists to include SiLU among supported options. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.4 → v0.14.5](astral-sh/ruff-pre-commit@v0.14.4...v0.14.5) - https://github.com/pylint-dev/pylint/: v4.0.2 → v4.0.3 <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…5052) Updates LAMMPS version reference from `stable_22Jul2025_update1` to `stable_22Jul2025_update2` across build scripts, documentation, and Python package configuration. ### Changes - Build configuration scripts: `.devcontainer/build_cxx.sh`, `source/install/{build_cc.sh, build_from_c.sh, build_lammps.sh, test_cc.sh, test_cc_local.sh}` - Installation documentation: `doc/install/install-lammps.md` - Python package configuration: `pyproject.toml` (updated `lammps[mpi]` dependency to `~=2025.7.22.2.0` and CI environment variables for macOS and Linux) All references to the LAMMPS version tag have been updated consistently across the repository, following the pattern from commit 0fe38c8. - Fixes deepmodeling#5051 <!-- START COPILOT CODING AGENT SUFFIX --> <details> <summary>Original prompt</summary> > > ---- > > *This section details on the original issue you should resolve* > > <issue_title>Bump LAMMPS version to stable_22Jul2025_update2</issue_title> > <issue_description>### Summary > > Bump LAMMPS version to stable_22Jul2025_update2. > > ### Detailed Description > > Follow the style of deepmodeling#4955 (0fe38c8). > > ### Further Information, Files, and Links > > _No response_</issue_description> > > ## Comments on the Issue (you are @copilot in this section) > > <comments> > </comments> > </details> - Fixes deepmodeling#5051 <!-- START COPILOT CODING AGENT TIPS --> --- 💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more [Copilot coding agent tips](https://gh.io/copilot-coding-agent-tips) in the docs. --------- Co-authored-by: copilot-swe-agent[bot] <[email protected]> Co-authored-by: njzjz <[email protected]>
…netuning process (deepmodeling#4928) In finetuing process, the computation of fitting stat is skipped in previous code. There are two situations: 1. Finetuning from pretrained model's branch: it means pretrained model also has `fparam` or `aparam` which has the same meaning of finetuning task. The key `fparam_avg`/`fparam_inv_std`/ `aparam_avg`/`aparam_inv_std` load from the pretrained model. It is correct. 2. Finetuning using RANDOM fitting. The fitting stat should be calculated in this situation. But the computation of fitting stat is skipped now. There is some error. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** - Automatic computation of input statistics is now performed during bias adjustment in "set-by-statistic" mode; public API extended to support computing fitting input statistics. * **Tests** - Training tests now compare additional parameter categories to the random-finetuned baseline. - Added test-only batching configuration for data-statistics and new unit tests validating fitting input-statistics calculation. <!-- 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>
…d using share fitting. (deepmodeling#5038) In this PR: 1. Support writing fitting stat to `stat_file` and loading fitting stat from `stat_file` 2. Ensure the fitting stat calculate is correct when using `default_fparam` 3. Support sharing fitting stat when using `share_fitting` in multitask mode. 4. Print the process of calculating fitting stat to the board via `log.info`. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Default frame parameters auto-fill missing samples and are exposed via a new accessor. * Compute/load/save per-parameter statistics to/from optional stat files. * Multitask training adds probability-weighted parameter sharing and propagates default fparam into data requirements. * Statistic items support scalar scaling for aggregation. * **Refactor** * Parameter-sharing and statistic-propagation flows reorganized for consistent buffering and persistence. * **Tests** * New tests and test data for stats computation, persistence, and multitask sharing. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Chenqqian Zhang <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Update the DeepModeling email from [email protected] to [email protected]. The former is no longer used. Generated by the task: njzjz-bot/njzjz-bot#17. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Documentation** * Updated contact email address in contributing guidelines. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Improved dependency management automation for Python packages. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <[email protected]>
This will make the CI more robust, i.e., new TF/PT versions will not break the CI until we bump the version. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Added CPU-optimized build support for PyTorch and TensorFlow. * Platform-specific dependency resolution for Linux x86_64, macOS, and other architectures. * **Chores** * Updated build configuration to use configurable dependency groups and conditional pins for CPU vs GPU builds. * Adjusted CI/build selection logic to better handle CPU-targeted packaging across environments. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- 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> Co-authored-by: Copilot <[email protected]>
….11,>=0.5 to >=0.5,!=0.6.0,<0.12 (deepmodeling#5076) 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>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Improved model type detection to also recognize "polarizability" as equivalent to "polar", ensuring models that report polarizability are correctly handled during inference and expanding compatibility with additional model variants. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
Fix "No space left on device" <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Enhanced build process optimization for improved workflow performance. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…eepmodeling#5075) 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>
Horovod has not released a new version for a long time. The PR to support TF 2.20 (horovod/horovod#4302) has never been merged, I think it has been dead, <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Simplified test workflow by removing specific installation steps. * **Documentation** * Added compatibility warning regarding Horovod and TensorFlow support in installation guide. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
This pull request updates PaddlePaddle dependencies to nightly builds and refactors device handling throughout the codebase to support more flexible device selection (including XPU), improves compatibility, and adds better flag management for tests. The most significant changes are grouped below. **Dependency Updates:** * Updated PaddlePaddle and PaddlePaddle-GPU installation in `.github/workflows/test_python.yml` and `.github/workflows/test_cuda.yml` to use nightly builds (`3.3.0.dev20251204`) from new package URLs, improving access to the latest features and fixes. [[1]](diffhunk://#diff-6d72d7142742932ca8c930aa674e12e3cf6c528566c88ab43f5cdb3169075f2fL50-R50) [[2]](diffhunk://#diff-896a3c7f7278514eba7e2573f009d6739b3de6d4e1ece4b756e04cdbe5c3f3caL35-R35) **Device Handling Refactor:** * Replaced usage of `paddle.device.cuda.device_count()` and related CUDA-specific APIs with more general `paddle.device.device_count()` and `paddle.device.empty_cache()` in multiple locations, enabling support for devices beyond CUDA (e.g., XPU). [[1]](diffhunk://#diff-e3f56cd14511cf86a0db88d6d9ee5b08cf45374edfdef0625a0f519d94c58507L217-R217) [[2]](diffhunk://#diff-c42cc453489450e30747781035e34ce592843893004b24481df3802b4fd6fa34L39-R39) [[3]](diffhunk://#diff-c42cc453489450e30747781035e34ce592843893004b24481df3802b4fd6fa34L54-R54) [[4]](diffhunk://#diff-e678abb052b278f8a479f8d13b839a9ec0effd9923478a850bc13758f918e1e9L32-R35) [[5]](diffhunk://#diff-03ca05b7d964e1dd8ec22a81aff2d76b61b9f9b36111e384f177a04cc5a02f1eL9-R10) * Updated logic for setting and retrieving device information in `deepmd/pd/utils/env.py` to use `paddle.device.get_device()`, ensuring correct device assignment for both CPU and GPU/XPU scenarios. **Device Compatibility Improvements:** * Enhanced `get_generator` in `deepmd/pd/utils/utils.py` to support XPU devices and added a warning for unsupported device types, improving compatibility and error messaging. **Test Flag Management:** * Added explicit management of the `FLAGS_use_stride_kernel` Paddle flag in `source/tests/pd/test_multitask.py` to ensure proper test isolation and restore flag values after tests. [[1]](diffhunk://#diff-ad724907bbb8b6260857768d8f1fc7f0f2122b6b86c010efaf66f22f87c4170dR236-R242) [[2]](diffhunk://#diff-ad724907bbb8b6260857768d8f1fc7f0f2122b6b86c010efaf66f22f87c4170dR280-R288) * Set `FLAGS_use_stride_compute_kernel` environment variable to `0` in workflow files to control kernel usage during tests. [[1]](diffhunk://#diff-6d72d7142742932ca8c930aa674e12e3cf6c528566c88ab43f5cdb3169075f2fR64) [[2]](diffhunk://#diff-896a3c7f7278514eba7e2573f009d6739b3de6d4e1ece4b756e04cdbe5c3f3caR63) **Distributed Training Check:** * Improved NCCL initialization check in distributed training setup to handle cases where NCCL is not compiled, preventing assertion errors. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit ## Release Notes * **New Features** * Added support for XPU device accelerators. * **Refactor** * Improved device detection and initialization to support non-CUDA backends and multiple device types with device-agnostic APIs. * **Chores** * Updated testing workflows and dependencies. * Enhanced test compatibility for non-GPU environments. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…=2.18,<2.21 (deepmodeling#5074) Updates the requirements on [tensorflow-cpu](https://github.com/tensorflow/tensorflow) to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/tensorflow/tensorflow/releases">tensorflow-cpu's releases</a>.</em></p> <blockquote> <h2>TensorFlow 2.20.0</h2> <h1>Release 2.20.0</h1> <h2>TensorFlow</h2> <h3>Breaking Changes</h3> <ul> <li>The <code>tensorflow-io-gcs-filesystem</code> package is now optional, due its uncertain, and limited support. To install it alongside <code>tensorflow</code>, run <code>pip install "tensorflow[gcs-filesystem]"</code>.</li> </ul> <h3>Major Features and Improvements</h3> <ul> <li><code>tf.data</code> <ul> <li>Adds <code>autotune.min_parallelism</code> to <code>tf.data.Options</code> to enable faster input pipeline warm up.</li> </ul> </li> <li><code>tf.lite</code> <ul> <li>tf.lite will be deprecated, in favor of the new repo <a href="https://github.com/google-ai-edge/LiteRT">https://github.com/google-ai-edge/LiteRT</a>.</li> <li>The duplicated source will also be removed from the TF repo.</li> </ul> </li> </ul> <h2>Thanks to our Contributors</h2> <p>This release contains contributions from many people at Google, as well as:</p> <p>1ndig0, 372046933, abhinav, afzpatel, Akhil Goel, Alain Carlucci, Aleksei, Alen Huang, Alex, Amrinfathima-Mcw, Aravindh Balaji, Armand Picard, Aseem Athale, Ashiq Imran, Assoap, Chao, Chase Riley Roberts, Chenhao Jiang, chunhsue, chuntl, Chunyu Jin, Corentin Kerisit, Crefeda Rodrigues, dependabot[bot], Dragan Mladjenovic, Elen Kalda, Felix Thomasmathibalan, gabeweisz, Gauri Deshpande, Georg Stefan Schmid, Guozhong Zhuang, Harsha H S, Harshith_N, Hugo Mano, Ian Tayler Lessa, Jack Wolfard, James Ward, Jane Liu, Jaroslav Sevcik, JD, Jerry-Ge, Jian Li, Jinzhe Zeng, jiunkaiy, Johannes Reifferscheid, johnnkp, junweifu, Kanvi Khanna, Kasper Nielsen, Linzb-Xyz, Luke Hutton, Mahmoud Abuzaina, Mathew Odden, Michael Platings, misterBart, Mitchell Ludwig, Mmakevic-Amd, mraunak, NamanAgarwal0905, Namrata-Ibm, Neuropilot-Captain, nhatle, Nicholas Wilson, Nikhil Shinde, Olli Lupton, Patrick J. Lopresti, Pavel Emeliyanenko, Pearu Peterson, pemeliya, Peng Sun, Philipp Hack, Pratham-Mcw, RahulSudarMCW, RakshithGB, Rakshithgb-Fujitsu, RuslanSemchenko, Ruturaj Vaidya, Sachin Muradi, sandeepgupta12, SaoirseARM, Sergey Kozub, Sevin Fide Varoglu, Shanbin Ke, Shaogang Wang, Shraiysh Vaishay, Siddhartha Menon, spiao, Swatheesh Muralidharan, Tai Ly, Terry Sun, Thibaut Goetghebuer-Planchon, Thomas Dickerson, Tilak, Tj Xu, Trevor Morris, tyb0807, vfdev, Wei Wang, wokron, wondertx, Xuefei Jiang, Yaowei Zhou, Zentrik, Ziyun Cheng, Zoranjovanovic-Ns</p> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/tensorflow/tensorflow/blob/master/RELEASE.md">tensorflow-cpu's changelog</a>.</em></p> <blockquote> <h1>Release 2.20.0</h1> <h2>TensorFlow</h2> <h3>Breaking Changes</h3> <ul> <li>The <code>tensorflow-io-gcs-filesystem</code> package is now optional, due its uncertain, and limited support. To install it alongside <code>tensorflow</code>, run <code>pip install "tensorflow[gcs-filesystem]"</code>.</li> </ul> <h3>Major Features and Improvements</h3> <ul> <li><code>tf.data</code> <ul> <li>Adds <code>autotune.min_parallelism</code> to <code>tf.data.Options</code> to enable faster input pipeline warm up.</li> </ul> </li> <li><code>tf.lite</code> <ul> <li>LiteRT announced a <a href="https://developers.googleblog.com/en/litert-maximum-performance-simplified/">new release</a> at Google IO ‘25 that improves upon TFLite, particularly in terms of NPU and GPU hardware acceleration and performance for on-device ML and AI applications. The APIs are available in Kotlin and C++.</li> <li>Additionally, LiteRT code base will decouple from TensorFlow repository, and <code>tf.lite</code> will be removed in future TensorFlow Python package. More details to follow in future release notes.</li> <li>Migrate to LiteRT for continued updates; the new repo can be found at <a href="https://github.com/google-ai-edge/LiteRT">https://github.com/google-ai-edge/LiteRT</a>. For more information and NPU EAP signup, reach out to the team at: <a href="https://g.co/ai/LiteRT-NPU-EAP">g.co/ai/LiteRT-NPU-EAP</a>.</li> </ul> </li> </ul> <h2>Thanks to our Contributors</h2> <p>This release contains contributions from many people at Google, as well as:</p> <p>1ndig0, 372046933, abhinav, afzpatel, Akhil Goel, Alain Carlucci, Aleksei, Alen Huang, Alex, Amrinfathima-Mcw, Aravindh Balaji, Armand Picard, Aseem Athale, Ashiq Imran, Assoap, Chao, Chase Riley Roberts, Chenhao Jiang, chunhsue, chuntl, Chunyu Jin, Corentin Kerisit, Crefeda Rodrigues, dependabot[bot], Dragan Mladjenovic, Elen Kalda, Felix Thomasmathibalan, gabeweisz, Gauri Deshpande, Georg Stefan Schmid, Guozhong Zhuang, Harsha H S, Harshith_N, Hugo Mano, Ian Tayler Lessa, Jack Wolfard, James Ward, Jane Liu, Jaroslav Sevcik, JD, Jerry-Ge, Jian Li, Jinzhe Zeng, jiunkaiy, Johannes Reifferscheid, johnnkp, junweifu, Kanvi Khanna, Kasper Nielsen, Linzb-Xyz, Luke Hutton, Mahmoud Abuzaina, Mathew Odden, Michael Platings, misterBart, Mitchell Ludwig, Mmakevic-Amd, mraunak, NamanAgarwal0905, Namrata-Ibm, Neuropilot-Captain, nhatle, Nicholas Wilson, Nikhil Shinde, Olli Lupton, Patrick J. Lopresti, Pavel Emeliyanenko, Pearu Peterson, pemeliya, Peng Sun, Philipp Hack, Pratham-Mcw, RahulSudarMCW, RakshithGB, Rakshithgb-Fujitsu, RuslanSemchenko, Ruturaj Vaidya, Sachin Muradi, sandeepgupta12, SaoirseARM, Sergey Kozub, Sevin Fide Varoglu, Shanbin Ke, Shaogang Wang, Shraiysh Vaishay, Siddhartha Menon, spiao, Swatheesh Muralidharan, Tai Ly, Terry Sun, Thibaut Goetghebuer-Planchon, Thomas Dickerson, Tilak, Tj Xu, Trevor Morris, tyb0807, vfdev, Wei Wang, wokron, wondertx, Xuefei Jiang, Yaowei Zhou, Zentrik, Ziyun Cheng, Zoranjovanovic-Ns</p> <h1>Release 2.19.1</h1> <h3>Bug Fixes and Other Changes</h3> <ul> <li>Fix save_model.save for Serving embedding and add SparseCore Reshard.</li> </ul> <h1>Release 2.19.0</h1> <h2>TensorFlow</h2> <h3>Breaking Changes</h3> <ul> <li><code>LiteRT</code>, a.k.a. <code>tf.lite</code>: <ul> <li>C++ API: <ul> <li>The public constants <code>tflite::Interpreter:kTensorsReservedCapacity</code> and <code>tflite::Interpreter:kTensorsCapacityHeadroom</code> are now const references, rather than <code>constexpr</code> compile-time constants. (This is to enable better API compatibility for TFLite in Play services while preserving the implementation flexibility to change the values of these constants in the future.)</li> </ul> </li> <li>Python API: <ul> <li><code>tf.lite.Interpreter</code> gives deprecation warning redirecting to its new location at <code>ai_edge_litert.interpreter</code>, as the API <code>tf.lite.Interpreter</code> will be deleted in TF 2.20. See the <a href="https://ai.google.dev/edge/litert/migration">migration guide</a> for details.</li> </ul> </li> </ul> </li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/tensorflow/tensorflow/commit/72fbba3d20f4616d7312b5e2b7f79daf6e82f2fa"><code>72fbba3</code></a> Merge pull request <a href="https://redirect.github.com/tensorflow/tensorflow/issues/98438">#98438</a> from tensorflow-jenkins/version-numbers-2.20.0-17429</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/bf5899deaf70fa45173c5c7b8dc9ace8824dc980"><code>bf5899d</code></a> Update version numbers to 2.20.0</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/a80fbfe0eb3d71986a6ba06c6275180761d549e6"><code>a80fbfe</code></a> Merge pull request <a href="https://redirect.github.com/tensorflow/tensorflow/issues/97728">#97728</a> from tensorflow/r2.20-b0b73e1d3b4</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/b2eeb62c6bc5e93f57140690d5f5dab132fd6dc7"><code>b2eeb62</code></a> Fix release wheels build.</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/2272fa9f3573d54674c9fcfd1185943b6d11ebe5"><code>2272fa9</code></a> Merge pull request <a href="https://redirect.github.com/tensorflow/tensorflow/issues/97519">#97519</a> from rtg0795/r2.20</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/2cbf40e81cdbe77245062fc1e0bd9e45af648402"><code>2cbf40e</code></a> Refresh lock files</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/89106da7a82e3415e5b12ec36238b9882bb513f5"><code>89106da</code></a> Update keras in requirements.in and setup.py.tpl</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/ea85f434bce2ab4a1334ad552de13c537a55dd29"><code>ea85f43</code></a> Merge pull request <a href="https://redirect.github.com/tensorflow/tensorflow/issues/97305">#97305</a> from rtg0795/r2.20</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/58d26a9207e4147cb8b7e70d01775a03b9f1c106"><code>58d26a9</code></a> Update BUILD files with dependencies</li> <li><a href="https://github.com/tensorflow/tensorflow/commit/de4ccfbc3aae6914401afa3d255e90bb6dac53c0"><code>de4ccfb</code></a> Merge pull request <a href="https://redirect.github.com/tensorflow/tensorflow/issues/97302">#97302</a> from rtg0795/r2.20</li> <li>Additional commits viewable in <a href="https://github.com/tensorflow/tensorflow/compare/v2.18.0...v2.20.0">compare view</a></li> </ul> </details> <br /> 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> Co-authored-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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| TORCH_LIBRARY_FRAGMENT(deepmd, m) { | ||
| m.def("tabulate_fusion_se_t", tabulate_fusion_se_t); | ||
| } | ||
| TORCH_LIBRARY_FRAGMENT(deepmd, m) { |
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Pull request overview
This is a large merge from the devel branch to master, consolidating multiple features and improvements. The PR includes:
- New tabulation operations for SE_T_TEBD descriptor compression
- Support for additional activation functions (silu/swish)
- Enhanced test infrastructure with conditional framework skipping
- Multi-task training improvements with shared fitting statistics
- Build system updates (CMake and LAMMPS versions)
- Test isolation improvements with TensorFlow graph resets
Reviewed changes
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Show a summary per file
| File | Description |
|---|---|
| source/tests/tf/test_out_bias_std.py | Adds setUp/tearDown with TF graph reset for test isolation |
| source/tests/tf/test_nvnmd_entrypoints.py | Adds TF graph reset in tearDown |
| source/tests/pt/test_training.py | Updates fine-tuning test to handle fparam/aparam in fitting_net, adds data_stat_nbatch config |
| source/tests/pt/test_tabulate_fusion_se_t_tebd.py | New comprehensive test file for SE_T_TEBD tabulation operations |
| source/tests/pt/test_tabulate.py | Refactors to test multiple activation functions with subtests |
| source/tests/pt/test_model_compression_se_e3_tebd.py | New test suite for SE_E3_TEBD model compression scenarios |
| source/tests/pt/test_model_compression_se_atten.py | New test suite for SE_ATTEN model compression with various configurations |
| source/tests/pt/test_loss_tensor.py | Adds atom_polarizability to reshaping logic |
| source/tests/pt/test_fitting_stat.py | Major expansion with multi-task fitting stat tests and file I/O validation |
| source/tests/pt/model/test_descriptor_dpa2.py | Adds type_embd_data to state dict translation |
| source/tests/pt/model/test_descriptor_dpa1.py | Adds type_embd_data to state dict handling |
| source/tests/pd/* | Multiple Paddle test files with framework availability checks and flag management |
| source/tests/common/test_deepmd_data.py | New test for type_map remapping with unused types |
| source/tests/init.py | Adds environment-based Paddle/TF import ordering |
| source/op/tf/unaggregated_grad.cc | Implements silu activation gradient and hessian |
| source/op/pt/tabulate_multi_device.cc | Implements SE_T_TEBD tabulation ops (forward, grad, grad_grad) |
| source/lmp/tests/* | Multiple LAMMPS test files with conditional framework skipping |
| source/lib/src/tabulate.cc | CPU implementation of SE_T_TEBD tabulation kernels |
| source/lib/src/gpu/CMakeLists.txt | CMake updates for CUDA 13.0+ and gcc-14 compatibility |
| source/lib/include/tabulate.h | Header declarations for SE_T_TEBD functions |
| source/install/* | Updates LAMMPS version to stable_22Jul2025_update2, conditional framework builds |
| source/api_cc/tests/test_read_file_to_string.cc | Adds conditional TF skip |
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## master #5088 +/- ##
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Files 708 709 +1
Lines 69911 72508 +2597
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Dec 10, 2025
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