[pull] master from deepmodeling:master - #5
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Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.23 to 3.0. <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>v3.0.0</h2> <p>See <a href="https://github.com/henryiii"><code>@henryiii</code></a>'s <a href="https://iscinumpy.dev/post/cibuildwheel-3-0-0/">release post</a> for more info on new features!</p> <ul> <li> <p>🌟 Adds the ability to <a href="https://cibuildwheel.pypa.io/en/stable/platforms/#ios">build wheels for iOS</a>! Set the <a href="https://cibuildwheel.pypa.io/en/stable/options/#platform"><code>platform</code> option</a> to <code>ios</code> on a Mac with the iOS toolchain to try it out! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2286">#2286</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2363">#2363</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2432">#2432</a>)</p> </li> <li> <p>🌟 Adds support for the GraalPy interpreter! Enable for your project using the <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable"><code>enable</code> option</a>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1538">#1538</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2411">#2411</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2414">#2414</a>)</p> </li> <li> <p>✨ Adds CPython 3.14 support, under the <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable"><code>enable</code> option</a> <code>cpython-prerelease</code>. This version of cibuildwheel uses 3.14.0b2. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2390">#2390</a>)</p> <p><em>While CPython is in beta, the ABI can change, so your wheels might not be compatible with the final release. For this reason, we don't recommend distributing wheels until RC1, at which point 3.14 will be available in cibuildwheel without the flag.</em> (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2390">#2390</a>)</p> </li> <li> <p>✨ Adds the <a href="https://cibuildwheel.pypa.io/en/stable/options/#test-sources">test-sources option</a>, and changes the working directory for tests. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2062">#2062</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2284">#2284</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2437">#2437</a>)</p> <ul> <li>If this option is set, cibuildwheel will copy the files and folders specified in <code>test-sources</code> into the temporary directory we run from. This is required for iOS builds, but also useful for other platforms, as it allows you to avoid placeholders.</li> <li>If this option is not set, behaviour matches v2.x - cibuildwheel will run the tests from a temporary directory, and you can use the <code>{project}</code> placeholder in the <code>test-command</code> to refer to the project directory. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2420">#2420</a>)</li> </ul> </li> <li> <p>✨ Adds <a href="https://cibuildwheel.pypa.io/en/stable/options/#dependency-versions"><code>dependency-versions</code></a> inline syntax (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2122">#2122</a>)</p> </li> <li> <p>✨ Improves support for Pyodide builds and adds the experimental <a href="https://cibuildwheel.pypa.io/en/stable/options/#pyodide-version"><code>pyodide-version</code></a> option, which allows you to specify the version of Pyodide to use for builds. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2002">#2002</a>)</p> </li> <li> <p>✨ Add <code>pyodide-prerelease</code> <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable">enable</a> option, with an early build of 0.28 (Python 3.13). (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2431">#2431</a>)</p> </li> <li> <p>✨ Adds the <a href="https://cibuildwheel.pypa.io/en/stable/options/#test-environment"><code>test-environment</code></a> option, which allows you to set environment variables for the test command. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2388">#2388</a>)</p> </li> <li> <p>✨ Adds the <a href="https://cibuildwheel.pypa.io/en/stable/options/#xbuild-tools"><code>xbuild-tools</code></a> option, which allows you to specify tools safe for cross-compilation. Currently only used on iOS; will be useful for Android in the future. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2317">#2317</a>)</p> </li> <li> <p>🛠 The default <a href="https://cibuildwheel.pypa.io/en/stable/options/#linux-image">manylinux image</a> has changed from <code>manylinux2014</code> to <code>manylinux_2_28</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2330">#2330</a>)</p> </li> <li> <p>🛠 EOL images <code>manylinux1</code>, <code>manylinux2010</code>, <code>manylinux_2_24</code> and <code>musllinux_1_1</code> can no longer be specified by their shortname. The full OCI name can still be used for these images, if you wish. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2316">#2316</a>)</p> </li> <li> <p>🛠 Invokes <code>build</code> rather than <code>pip wheel</code> to build wheels by default. You can control this via the <a href="https://cibuildwheel.pypa.io/en/stable/options/#build-frontend"><code>build-frontend</code></a> option. You might notice that you can see your build log output now! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2321">#2321</a>)</p> </li> <li> <p>🛠 Build verbosity settings have been reworked to have consistent meanings between build backends when non-zero. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2339">#2339</a>)</p> </li> <li> <p>🛠 Removed the <code>CIBW_PRERELEASE_PYTHONS</code> and <code>CIBW_FREE_THREADED_SUPPORT</code> options - these have been folded into the <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable"><code>enable</code></a> option instead. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2095">#2095</a>)</p> </li> <li> <p>🛠 Build environments no longer have setuptools and wheel preinstalled. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2329">#2329</a>)</p> </li> <li> <p>🛠 Use the standard Schema line for the integrated JSONSchema. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2433">#2433</a>)</p> </li> <li> <p>⚠️ Dropped support for building Python 3.6 and 3.7 wheels. If you need to build wheels for these versions, use cibuildwheel v2.23.3 or earlier. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2282">#2282</a>)</p> </li> <li> <p>⚠️ The minimum Python version required to run cibuildwheel is now Python 3.11. You can still build wheels for Python 3.8 and newer. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1912">#1912</a>)</p> </li> <li> <p>⚠️ 32-bit Linux wheels no longer built by default - the <a href="https://cibuildwheel.pypa.io/en/stable/options/#archs">arch</a> was removed from <code>"auto"</code>. It now requires explicit <code>"auto32"</code>. Note that modern manylinux images (like the new default, <code>manylinux_2_28</code>) do not have 32-bit versions. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2458">#2458</a>)</p> </li> <li> <p>⚠️ PyPy wheels no longer built by default, due to a change to our options system. To continue building PyPy wheels, you'll now need to set the <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable"><code>enable</code> option</a> to <code>pypy</code> or <code>pypy-eol</code>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2095">#2095</a>)</p> </li> <li> <p>⚠️ Dropped official support for Appveyor. If it was working for you before, it will probably continue to do so, but we can't be sure, because our CI doesn't run there anymore. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2386">#2386</a>)</p> </li> <li> <p>📚 A reorganisation of the docs, and numerous updates. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2280">#2280</a>)</p> </li> <li> <p>📚 Use Python 3.14 color output in docs CLI output. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2407">#2407</a>)</p> </li> <li> <p>📚 Docs now primarily use the pyproject.toml name of options, rather than the environment variable name. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2389">#2389</a>)</p> </li> <li> <p>📚 README table now matches docs and auto-updates. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2427">#2427</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2428">#2428</a>)</p> </li> </ul> <h2>v3.0.0rc3</h2> <p>Not yet released, but available for testing.</p> <p>Note - when using a beta version, be sure to check the <a href="https://cibuildwheel.pypa.io/en/latest/">latest docs</a>, rather than the stable version, which is still on v2.X.</p> <!-- raw HTML omitted --> <p>If you've used previous versions of the beta:</p> <ul> <li>⚠️ Previous betas of v3.0 changed the working directory for tests. This has been rolled back to the v2.x behaviour, so you might need to change configs if you adapted to the beta 1 or 2 behaviour. See [issue <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2406">#2406</a>](<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2406">pypa/cibuildwheel#2406</a>) for more information.</li> <li>⚠️ GraalPy shipped with the identifier <code>gp242-*</code> in previous betas, this has been changed to <code>gp311_242-*</code> to be consistent with other interpreters, and to fix a bug with GraalPy and project requires-python detection. If you were using GraalPy, you might need to update your config to use the new identifier.</li> <li>⚠️ <code>test-sources</code> now uses <code>project</code> directory instead of the <code>package</code> directory (matching the docs).</li> <li>⚠️ 32-bit linux builds were removed from <code>"auto"</code> (the default), now require <code>"auto32"</code> or explicit archs, as modern manylinux images (including our new default) do not support them.</li> </ul> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </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>v2.23.0</h3> <p><em>1 March 2025</em></p> <ul> <li>✨ Adds official support for the new GitHub Actions Arm runners. In fact these worked out-of-the-box, now we include them in our tests and example configs. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2135">#2135</a> via <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2281">#2281</a>)</li> <li>✨ Adds support for building PyPy 3.11 wheels (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2268">#2268</a> via <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2281">#2281</a>)</li> <li>🛠 Adopts the beta pypa/manylinux image for armv7l builds (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2269">#2269</a> via <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2281">#2281</a>)</li> <li>🛠 Dependency updates, including Pyodide 0.27 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2117">#2117</a> and <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2281">#2281</a>)</li> </ul> <h3>v2.22.0</h3> <p><em>23 November 2024</em></p> <ul> <li>🌟 Added a new <code>CIBW_ENABLE</code>/<code>enable</code> feature that replaces <code>CIBW_FREETHREADED_SUPPORT</code>/<code>free-threaded-support</code> and <code>CIBW_PRERELEASE_PYTHONS</code> with a system that supports both. In cibuildwheel 3, this will also include a PyPy setting and the deprecated options will be removed. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2048">#2048</a>)</li> <li>🌟 <a href="https://peps.python.org/pep-0735/">Dependency groups</a> are now supported for tests. Use <code>CIBW_TEST_GROUPS</code>/<code>test-groups</code> to specify groups in <code>[dependency-groups]</code> for testing. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2063">#2063</a>)</li> <li>🌟 Support for the experimental Ubuntu-based ARMv7l manylinux image (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2052">#2052</a>)</li> <li>✨ Show a warning when cibuildwheel is run from Python 3.10 or older; cibuildwheel 3.0 will require Python 3.11 or newer as host (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2050">#2050</a>)</li> <li>🐛 Fix issue with stderr interfering with checking the docker version (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2074">#2074</a>)</li> <li>🛠 Python 3.9 is now used in <code>CIBW_BEFORE_ALL</code>/<code>before-all</code> on linux, replacing 3.8, which is now EoL (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2043">#2043</a>)</li> <li>🛠 Error messages for producing a pure-Python wheel are slightly more informative (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2044">#2044</a>)</li> <li>🛠 Better error when <code>uname -m</code> fails on ARM (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2049">#2049</a>)</li> <li>🛠 Better error when repair fails and docs for abi3audit on Windows (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2058">#2058</a>)</li> <li>🛠 Better error when <code>manylinux-interpreters ensure</code> fails (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2066">#2066</a>)</li> <li>🛠 Update Pyodide to 0.26.4, and adapt to the unbundled pyodide-build (now 0.29) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2090">#2090</a>)</li> <li>🛠 Now cibuildwheel uses dependency-groups for development dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2064">#2064</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2085">#2085</a>)</li> <li>📚 Docs updates and tidy ups (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2061">#2061</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2067">#2067</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2072">#2072</a>)</li> </ul> <h3>v2.21.3</h3> <p><em>9 October 2024</em></p> <ul> <li>🛠 Update CPython 3.13 to 3.13.0 final release (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2032">#2032</a>)</li> <li>📚 Docs updates and tidy ups (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2035">#2035</a>)</li> </ul> <h3>v2.21.2</h3> <p><em>2 October 2024</em></p> <ul> <li>✨ Adds support for building 32-bit armv7l wheels on musllinux. On a Linux system with emulation set up, set <a href="https://cibuildwheel.pypa.io/en/stable/options/#archs">CIBW_ARCHS</a> to <code>armv7l</code> on Linux to try it out if you're interested! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2017">#2017</a>)</li> <li>🐛 Fix Linux Podman builds on some systems (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2016">#2016</a>)</li> <li>✨ Adds official support for running on Python 3.13 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2026">#2026</a>)</li> <li>🛠 Update CPython 3.13 to 3.13.0rc3 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2029">#2029</a>)</li> </ul> <p>Note: the default <a href="https://cibuildwheel.pypa.io/en/stable/options/#linux-image">manylinux image</a> is <strong>scheduled to change</strong> from <code>manylinux2014</code> to <code>manylinux_2_28</code> in a cibuildwheel release on or after <strong>6th May 2025</strong> - you can set the value now to avoid getting upgraded if you want. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1992">#1992</a>)</p> <h3>v2.21.1</h3> <p><em>16 September 2024</em></p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/5f22145df44122af0f5a201f93cf0207171beca7"><code>5f22145</code></a> Bump version: v3.0.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/a73177515a438c947d6e6e7a7356dfe67991d740"><code>a731775</code></a> Docs: mobile layout fix (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2466">#2466</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/ff86a6457781e53a6edbb60d3c2677c64be4f282"><code>ff86a64</code></a> docs: add tips for numpy (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2465">#2465</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/6f5e480fec0d367f9230ee0be4bcb56136eeec43"><code>6f5e480</code></a> chore: use pip's groups in CI (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2463">#2463</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3c5ff0988806752c5a6502c845f9edc2d98095d6"><code>3c5ff09</code></a> Bump version: v3.0.0rc3</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/1b9a56e01487f7fd9146e622505ea22d4d35e954"><code>1b9a56e</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2455">#2455</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/aa9fe2a24edd67db40cbd394e4621a479e9e69f1"><code>aa9fe2a</code></a> ci: use uv python for docs (binary b1) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2462">#2462</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/e188d9e26007031c475bb5293b90c5f386ecb439"><code>e188d9e</code></a> feat: remove 32-bit linux from auto arch, fix auto32 on linux aarch64 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2458">#2458</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3fa7bd1e72c565f4efc61363db6b2f14dbdbb198"><code>3fa7bd1</code></a> ci: fix cirrus and reduce rebuilds (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2460">#2460</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/c6368be701a99f8315656f925236dbcec5b9b9c2"><code>c6368be</code></a> Move to the <code>OS-latest</code> image tags on Azure Pipelines (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2461">#2461</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.23...v3.0">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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This PR fixes the error in UT where the argument of `xp.reshape` should be a tuple, not a list. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Style** - Standardized the use of tuple syntax for shape arguments in array reshaping operations throughout the application, replacing previous list-based syntax. This change ensures consistency and aligns with best practices for array manipulation. No functional behavior is affected. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
This brings ~10% speedup for the training of DPA3 model with 24 thin layers and dynamic sel (average training time: 0.6891 s/batch vs 0.7635 s/batch, batch size = auto:128). <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Updated the shape and indexing conventions for edge and angle index arrays and tensors across multiple components, standardizing them to column-major format for improved consistency. - Adjusted initialization and handling of index arrays/tensors to match the new conventions in both NumPy and PyTorch implementations. - Updated relevant method calls and internal logic to align with the revised index shapes and access patterns. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/pre-commit/mirrors-clang-format: v20.1.5 → v20.1.6](pre-commit/mirrors-clang-format@v20.1.5...v20.1.6) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
pop unnecessary item when wrapping model with `jit.to_static`, so we can support se_e2_a/dpa2/dpa3 without extra modification. @njzjz can you give some suggestions for better code improvements? The current approach of fetching data via `self.get_data` isn't very concise. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved compatibility by dynamically matching label input specifications to available label keys during model compilation when CINN is enabled. This prevents errors caused by mismatched label keys at runtime. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: HydrogenSulfate <490868991@qq.com> Co-authored-by: coderabbitai[bot] <136622811+coderabbitai[bot]@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
1. get local rank from `PADDLE_LOCAL_RANK` environment variable instead of `get_rank()`(which will return global rank). 2. disable gradient synchronization in forward-backward and synchronize manually before optimizer update 4. update parallel training tutorial(multi-node multi-GPU) in document <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved gradient synchronization in distributed training for multi-process setups. - Updated local rank assignment to use environment variables for enhanced compatibility. - **Documentation** - Added an example using `mpirun` and a sample shell script to the parallel training guide for distributed training launch. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: HydrogenSulfate <490868991@qq.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
fix #4212 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Refactor** - Improved the logic for accumulating and reporting training time during model training, resulting in clearer and more consistent step counting and average time logging. <!-- 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>
adapt preparing input spec in paddle backend to support `loc_mapping` for dpa3 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added support for dynamic neighbor and angle selection, enabling flexible graph-based computations. - Introduced options for local atom index mapping and alternative edge feature initialization. - Added exponential switch function for neighbor smoothing. - Introduced JIT-compiled SiLUT activation with higher-order gradient support, configurable via environment variable. - New utility functions for aggregation and graph index computation. - **Improvements** - Enhanced documentation for descriptor parameters. - Defaulted local mapping to enabled for relevant descriptors. - Improved device handling and tensor operations for better compatibility and clarity. - **Bug Fixes** - Simplified test skipping logic to rely on a unified flag. - **Chores** - Refactored and clarified internal logic for smoother weight and switch function computations. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.11.13 → v0.12.0](astral-sh/ruff-pre-commit@v0.11.13...v0.12.0) - [github.com/pycqa/flake8: 7.2.0 → 7.3.0](PyCQA/flake8@7.2.0...7.3.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
(cherry picked from commit 2433566) <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **Bug Fixes** - Improved the reliability of neighbor selection for angle calculations, ensuring more accurate identification of neighbors within the angular cutoff radius. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Enhanced support for optional fitting and atomic parameters during calculations. - **Tests** - Added tests to verify correct handling of models with multiple fitting and atomic parameters, ensuring consistent results under atom permutation. <!-- 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>
#4563 Signed-off-by: Chun Cai <amoycaic@gmail.com>
It has been moved to PyPI. See https://github.com/mpi4py/mpi4py/releases/tag/4.1.0 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Removed use of a custom package index for installing certain dependencies in the build and test configurations. * Updated workflow and build settings to use the default package index for installations. * Improved environment variable handling to preserve existing paths during testing. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu>
`jaxlib.xla_extension` has been removed in recent versions of JAX. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Refactor** * Improved exception handling by updating error type checks and removing an unnecessary dependency. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…ynamic shape (#4826) Add flag `CINN_ALLOW_DYNAMIC_SHAPE` for allow compiling dynamic input shape, if set to `0` or `False`, performance might be slightly enhanced for fixed shape. We set default value to `True` for compativility. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit ## Summary by CodeRabbit * **New Features** * Added support for the "paddle" backend, including updated help and error messages to reflect new output file formats. * Introduced a new environment variable to control dynamic shape support for the CINN compiler, allowing users to choose between improved compatibility or enhanced performance. * **Improvements** * Enhanced training setup to conditionally enable or disable dynamic shape support based on user configuration. * Updated documentation to guide users on configuring CINN compilation for fixed or dynamic input shapes during training. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.0 → v0.12.1](astral-sh/ruff-pre-commit@v0.12.0...v0.12.1) - [github.com/pre-commit/mirrors-clang-format: v20.1.6 → v20.1.7](pre-commit/mirrors-clang-format@v20.1.6...v20.1.7) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.1 → v0.12.2](astral-sh/ruff-pre-commit@v0.12.1...v0.12.2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
…le & support TF tensor fitting trainable (#4793) 1. For dpmodel, pt, and pd, pass the trainable parameter to the layer (not actually used in this PR). 2. For JAX, support the `trainable` parameter in the layer. 3. "trainable" is now serialized in dpmodel, tf, pt, pd, etc. 4. Support trainable in TF dipole & polar fitting. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit ## Summary by CodeRabbit - **New Features** - Added a `trainable` parameter to numerous model components, descriptors, embedding and fitting networks, and attention layers, allowing users to enable or disable parameter trainability. - Ensured consistent propagation of the `trainable` flag across submodules and layers in PyTorch, TensorFlow, and JAX backends. - Enhanced serialization and deserialization processes to include the `trainable` attribute, maintaining trainability settings during model save and load. - Implemented conditional parameter wrapping in the JAX backend to differentiate trainable parameters from fixed variables. - **Tests** - Updated test configurations to include the `trainable` flag, validating behavior with non-trainable components. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn> Signed-off-by: Jinzhe Zeng <njzjz@qq.com> Co-authored-by: Duo <50307526+iProzd@users.noreply.github.com>
support running `input_torch_dynamic.json` with paddle backend(including CINN) TODO list: - [x] PaddlePaddle/Paddle#73601 - [x] PaddlePaddle/Paddle#73622 - [x] PaddlePaddle/Paddle#73737 - [x] PaddlePaddle/Paddle#73747 - [x] PaddlePaddle/Paddle#73809 - [x] PaddlePaddle/Paddle#73761 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit ## Summary by CodeRabbit * **Bug Fixes** * Resolved issues with tensor shape and indexing consistency, preventing assertion errors during model execution. * Improved handling of default tensor initialization to avoid JIT assertion issues. * **Refactor** * Standardized tensor dimension handling and broadcasting for improved clarity and maintainability. * Enhanced code readability with clearer indexing conventions and formatting. * Updated aggregation logic for safer and more efficient tensor operations. * **New Features** * Added an option to control graph index mapping behavior for greater flexibility in advanced use cases. * **Tests** * Introduced comprehensive tests validating descriptor model consistency with dynamic selection enabled. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added support for displaying "observed-type" information in the model reporting tool, showing element types observed during training for single-task and multi-task models. - **Tests** - Updated tests to verify correct reporting of observed types for both single-task and multi-task models. - **Documentation** - Updated documentation to include the new "observed-type" attribute in model information display, with examples and explanations. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Duo <50307526+iProzd@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <jinzhe.zeng@rutgers.edu> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit - **New Features** - Added the ability to evaluate and retrieve the output of the last hidden layer in fitting neural networks, providing access to intermediate model outputs. - Extended evaluation interfaces to support fetching intermediate fitting outputs for both standard and mixed-type models. - **Improvements** - Enhanced output dictionaries to optionally include intermediate network outputs when enabled, allowing for more detailed inspection during evaluation. - **Tests** - Introduced tests to verify correctness and consistency of fitting last layer evaluations across supported model types. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
As reported by #4837 (comment), the pytorch in the cuda 11 image is currently cuda12. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Cleaned up documentation formatting by removing unnecessary blank lines for improved readability and consistency. * **Refactor** * Improved Docker installation process to better manage PyTorch backend selection for CUDA 11 environments. <!-- end of auto-generated comment: release notes by coderabbit.ai --> --------- Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.2 → v0.12.3](astral-sh/ruff-pre-commit@v0.12.2...v0.12.3) - [github.com/pre-commit/mirrors-clang-format: v20.1.7 → v20.1.8](pre-commit/mirrors-clang-format@v20.1.7...v20.1.8) - [github.com/scop/pre-commit-shfmt: v3.11.0-1 → v3.12.0-1](scop/pre-commit-shfmt@v3.11.0-1...v3.12.0-1) <!--pre-commit.ci end--> --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
dict.insert will not replace old value of the key value while lammps reallocate will keep old value in old address. This may cause dict always use the initial value of some keys. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Improved handling of communication settings to ensure that updates to existing entries are correctly applied, preventing potential issues with outdated or duplicate information during tensor communication. <!-- end of auto-generated comment: release notes by coderabbit.ai -->
<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.3 → v0.12.4](astral-sh/ruff-pre-commit@v0.12.3...v0.12.4) - [github.com/scop/pre-commit-shfmt: v3.12.0-1 → v3.12.0-2](scop/pre-commit-shfmt@v3.12.0-1...v3.12.0-2) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 3.0 to 3.1. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p> <blockquote> <h2>v3.1.0</h2> <ul> <li>🌟 CPython 3.14 wheels are now built by default - without the <code>"cpython-prerelease"</code> <code>enable</code> set. It's time to build and upload these wheels to PyPI! This release includes CPython 3.14.0rc1, which is guaranteed to be ABI compatible with the final release. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2507">#2507</a>) Free-threading is no longer experimental in 3.14, so you have to skip it explicitly with <code>'cp31?t-*'</code> if you don't support it yet. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2503">#2503</a>)</li> <li>🌟 Adds the ability to <a href="https://cibuildwheel.pypa.io/en/stable/platforms/#android">build wheels for Android</a>! Set the <a href="https://cibuildwheel.pypa.io/en/stable/options/#platform"><code>platform</code> option</a> to <code>android</code> on Linux or macOS to try it out! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2349">#2349</a>)</li> <li>🌟 Adds Pyodide 0.28, which builds 3.13 wheels (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2487">#2487</a>)</li> <li>✨ Support for 32-bit <code>manylinux_2_28</code> (now a consistent default) and <code>manylinux_2_34</code> added (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2500">#2500</a>)</li> <li>🛠 Improved summary, will also use markdown summary output on GHA (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2469">#2469</a>)</li> <li>🛠 The riscv64 images now have a working default (as they are now part of pypy/manylinux), but are still experimental (and behind an <code>enable</code>) since you can't push them to PyPI yet (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2506">#2506</a>)</li> <li>🛠 Fixed a typo in the 3.9 MUSL riscv64 identifier (<code>cp39-musllinux_ricv64</code> -> <code>cp39-musllinux_riscv64</code>) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2490">#2490</a>)</li> <li>🛠 Mistyping <code>--only</code> now shows the correct possibilities, and even suggests near matches on Python 3.14+ (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2499">#2499</a>)</li> <li>🛠 Only support one output from the repair step on linux like other platforms; auditwheel fixed this over four years ago! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2478">#2478</a>)</li> <li>🛠 We now use pattern matching extensively (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2434">#2434</a>)</li> <li>📚 We now have platform maintainers for our special platforms and interpreters! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2481">#2481</a>)</li> </ul> <h2>v3.0.1</h2> <ul> <li>🛠 Updates CPython 3.14 prerelease to 3.14.0b3 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2471">#2471</a>)</li> <li>✨ Adds a CPython 3.14 prerelease iOS build (only when prerelease builds are <a href="https://cibuildwheel.pypa.io/en/stable/options/#enable">enabled</a>) (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2475">#2475</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>v2.23.1</h3> <p><em>15 March 2025</em></p> <ul> <li>⚠️ Added warnings when the shorthand values <code>manylinux1</code>, <code>manylinux2010</code>, <code>manylinux_2_24</code>, and <code>musllinux_1_1</code> are used to specify the images in linux builds. The shorthand to these (unmaintainted) images will be removed in v3.0. If you want to keep using these images, explicitly opt-in using the full image URL, which can be found in <a href="https://github.com/pypa/cibuildwheel/blob/v2.23.1/cibuildwheel/resources/pinned_docker_images.cfg">this file</a>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2312">#2312</a>)</li> <li>🛠 Dependency updates, including a manylinux update which fixes an <a href="https://redirect.github.com/pypa/cibuildwheel/issues/2303">issue with rustup</a>. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2315">#2315</a>)</li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/e6de07ed3921b51089aae6981989889cf1eddd0c"><code>e6de07e</code></a> Bump version: v3.1.1</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/2ca692b1e55a1f924bfb460099c9d7e015671a8d"><code>2ca692b</code></a> docs: iOS typo fix in docs (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2510">#2510</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/1ac7fa7f004958fbde774ee89523c446a5d99934"><code>1ac7fa7</code></a> fix: report defects in logs and HTML summaries (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2512">#2512</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/ffd835cef18fa11522f608fc0fa973b89f5ddc87"><code>ffd835c</code></a> Bump version: v3.1.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/3e2a9aa6e85824999f897fc2c060ca12a5113ef6"><code>3e2a9aa</code></a> fix: regenerate schema</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/10c727eed9fc962f75d33d472272e3ad78c3e707"><code>10c727e</code></a> feat: Python 3.14rc1 build by default (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2507">#2507</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f628c9dd23fe6e263cb91cef755a51a0af3bcddc"><code>f628c9d</code></a> [pre-commit.ci] pre-commit autoupdate (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2505">#2505</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/0f487ee2cb00876d95290da49d04208c91237857"><code>0f487ee</code></a> feat: add support for building Android wheels (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2349">#2349</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/e2e24882d8422e974295b1b9079d4ce80a5098a4"><code>e2e2488</code></a> feat: add default riscv64 images (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2506">#2506</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/a8bff94dbb5f3a4a914e29cf8353c2f6f1b9ab8b"><code>a8bff94</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/2504">#2504</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v3.0...v3.1">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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<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.12.4 → v0.12.5](astral-sh/ruff-pre-commit@v0.12.4...v0.12.5) - [github.com/njzjz/mirrors-bibtex-tidy: v1.13.0 → v1.14.0](njzjz/mirrors-bibtex-tidy@v1.13.0...v1.14.0) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Remove version `>=a.b.crc0` from dependencies. The stable version should be preferred. This prevents the installation of TensorFlow 2.20.0rc0, which breaks the CI. However, the incompatibility should still be fixed in the future. TensorFlow 2.20.0rc0 removes the version information from the header files. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated version requirements for TensorFlow and myst-nb packages to use stable releases instead of release candidate versions in build and documentation workflows. * Adjusted dependency handling for TensorFlow CPU to ensure stable versions are used during build processes. <!-- end of auto-generated comment: release notes by coderabbit.ai --> Signed-off-by: Jinzhe Zeng <jinzhe.zeng@ustc.edu.cn>
…ed. (#4854) feat: add Mean absolute percentage error (MAPE) loss for property prediction <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **New Features** * Added support for the Mean Absolute Percentage Error (MAPE) as a selectable loss function and metric. * **Documentation** * Updated user-facing documentation to include "mape" as an option for loss function selection. <!-- 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>
…#5103) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pytorch/pytorch/releases">torch's releases</a>.</em></p> <blockquote> <h2>PyTorch 2.9.1 Release, bug fix release</h2> <p>This release is meant to fix the following issues (regressions / silent correctness):</p> <h3>Tracked Regressions</h3> <p>Significant Memory Regression in F.conv3d with bfloat16 Inputs in PyTorch 2.9.0 (<a href="https://redirect.github.com/pytorch/pytorch/issues/166643">#166643</a>) This release provides work around this issue. If you are impacted please install nvidia-cudnn package version 9.15+ from pypi. (<a href="https://redirect.github.com/pytorch/pytorch/pull/166480">#166480</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/167111">#167111</a>)</p> <h3>Torch.compile</h3> <p>Fix Inductor bug when compiling Gemma (<a href="https://redirect.github.com/pytorch/pytorch/pull/165601">#165601</a>) Fix InternalTorchDynamoError in bytecode_transformation (<a href="https://redirect.github.com/pytorch/pytorch/pull/166036">#166036</a>) Fix silent correctness error_on_graph_break bug where non-empty checkpoint results in unwanted graph break resumption (<a href="https://redirect.github.com/pytorch/pytorch/pull/166586">#166586</a>) Improve performance by avoiding recompilation with mark_static_address with cudagraphs (<a href="https://redirect.github.com/pytorch/pytorch/pull/162208">#162208</a>) Improve performance by caching get_free_symbol_uses in torch inductor (<a href="https://redirect.github.com/pytorch/pytorch/pull/166338">#166338</a>) Fix fix registration design for inductor graph partition for vLLM (<a href="https://redirect.github.com/pytorch/pytorch/pull/166458">#166458</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/165815">#165815</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/165514">#165514</a>) Fix warning spamming in torch.compile (<a href="https://redirect.github.com/pytorch/pytorch/pull/166993">#166993</a>) Fix exception related to uninitialized tracer_output variable (<a href="https://redirect.github.com/pytorch/pytorch/pull/163169">#163169</a>) Fix crash in torch.bmm and torch.compile with PyTorch release 2.9.0 (<a href="https://redirect.github.com/pytorch/pytorch/pull/166457">#166457</a>)</p> <h3>Other</h3> <p>Fix warning spamming on new APIs to control TF32 behavior (<a href="https://redirect.github.com/pytorch/pytorch/pull/166956">#166956</a>) Fix distributed crash with non-contiguous gather inputs (<a href="https://redirect.github.com/pytorch/pytorch/pull/166181">#166181</a>) Fix indexing on large tensor causes invalid configuration argument (<a href="https://redirect.github.com/pytorch/pytorch/pull/166974">#166974</a>) Fix numeric issue in CUDNN_ATTENTION (<a href="https://redirect.github.com/pytorch/pytorch/pull/166912">#166912</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/166570">#166570</a>) Fix symmetric memory issue with fused_scaled_matmul_reduce_scatter (<a href="https://redirect.github.com/pytorch/pytorch/pull/165086">#165086</a>) Improve libtorch stable ABI documentation (<a href="https://redirect.github.com/pytorch/pytorch/pull/163899">#163899</a>) Fix image display on pypi project description section (<a href="https://redirect.github.com/pytorch/pytorch/pull/166404">#166404</a>)</p> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytorch/pytorch/blob/main/RELEASE.md">torch's changelog</a>.</em></p> <blockquote> <h1>Releasing PyTorch</h1> <!-- raw HTML omitted --> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-compatibility-matrix">Release Compatibility Matrix</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorch-cuda-support-matrix">PyTorch CUDA Support Matrix</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-cadence">Release Cadence</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#general-overview">General Overview</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#frequently-asked-questions">Frequently Asked Questions</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cutting-a-release-branch-preparations">Cutting a release branch preparations</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cutting-release-branches">Cutting release branches</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorchpytorch"><code>pytorch/pytorch</code></a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorch-ecosystem-libraries">PyTorch ecosystem libraries</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#making-release-branch-specific-changes-for-pytorch">Making release branch specific changes for PyTorch</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#making-release-branch-specific-changes-for-ecosystem-libraries">Making release branch specific changes for ecosystem libraries</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#running-launch-execution-team-core-xfn-sync">Running Launch Execution team Core XFN sync</a></li> <li><a href="#drafting-rcs-release-candidates-for-pytorch-and-domain-libraries">Drafting RCs (https://github.com/pytorch/pytorch/blob/main/Release Candidates) for PyTorch and domain libraries</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-candidate-storage">Release Candidate Storage</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-candidate-health-validation">Release Candidate health validation</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cherry-picking-fixes">Cherry Picking Fixes</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#how-to-do-cherry-picking">How to do Cherry Picking</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cherry-picking-reverts">Cherry Picking Reverts</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#preparing-and-creating-final-release-candidate">Preparing and Creating Final Release Candidate</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#promoting-rcs-to-stable">Promoting RCs to Stable</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#additional-steps-to-prepare-for-release-day">Additional Steps to prepare for release day</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#modify-release-matrix">Modify release matrix</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#open-google-colab-issue">Open Google Colab issue</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-releases">Patch Releases</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-criteria">Patch Release Criteria</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-process">Patch Release Process</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-process-description">Patch Release Process Description</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#triage">Triage</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#issue-tracker-for-patch-releases">Issue Tracker for Patch releases</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#building-a-release-schedule--cherry-picking">Building a release schedule / cherry picking</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#building-binaries--promotion-to-stable">Building Binaries / Promotion to Stable</a></li> </ul> </li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#hardware--software-support-in-binary-build-matrix">Hardware / Software Support in Binary Build Matrix</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#python">Python</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#accelerator-software">Accelerator Software</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#special-support-cases">Special support cases</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#operating-systems">Operating Systems</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#submitting-tutorials">Submitting Tutorials</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#special-topics">Special Topics</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#updating-submodules-for-a-release">Updating submodules for a release</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#triton-dependency-for-the-release">Triton dependency for the release</a></li> </ul> </li> </ul> <!-- raw HTML omitted --> <h2>Release Compatibility Matrix</h2> <p>Following is the Release Compatibility Matrix for PyTorch releases:</p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytorch/pytorch/commit/d38164a545b4a4e4e0cf73ce67173f70574890b6"><code>d38164a</code></a> Enable Doc builds for: Minor Releases RCs. Minor and Patch Releases final RC ...</li> <li><a href="https://github.com/pytorch/pytorch/commit/b002562550577a09038c40c0e04ae18a54c8f12b"><code>b002562</code></a> Add doc for Symmetric Memory (<a href="https://redirect.github.com/pytorch/pytorch/issues/167477">#167477</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/5811a8d7da873dd699ff6687092c225caffcf1bb"><code>5811a8d</code></a> [cuDNN][SDPA][Convolution] Expose cuDNN runtime version in CUDA hooks (<a href="https://redirect.github.com/pytorch/pytorch/issues/167327">#167327</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/f36c764ca475ea382ee4af6ff8bc807a9bd89876"><code>f36c764</code></a> [dynamo][ez] Initialize tracer_output to None by default. (<a href="https://redirect.github.com/pytorch/pytorch/issues/167366">#167366</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/6877288115e10776d9ee74d4e86dafdc1556d5bc"><code>6877288</code></a> Change forkserver test to only run below 3.13.8 (<a href="https://redirect.github.com/pytorch/pytorch/issues/167361">#167361</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/9976b77abbb6e920684f899c539101e4b412f911"><code>9976b77</code></a> Cherry-pick LibTorch Stable ABI documentation (<a href="https://redirect.github.com/pytorch/pytorch/issues/167112">#167112</a> <a href="https://redirect.github.com/pytorch/pytorch/issues/166661">#166661</a> <a href="https://redirect.github.com/pytorch/pytorch/issues/163899">#163899</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/167">#167</a>...</li> <li><a href="https://github.com/pytorch/pytorch/commit/e6bcbbe17c64a2fd9e660324bbdfc5c32cd560a8"><code>e6bcbbe</code></a> [Inductor] No longer throw error in bmm out_dtype lowering due to tem… (<a href="https://redirect.github.com/pytorch/pytorch/issues/166922">#166922</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/8f658d7599a9cf5e12d749c6c140457cd6f05978"><code>8f658d7</code></a> don't produce invalid grid configs (<a href="https://redirect.github.com/pytorch/pytorch/issues/166973">#166973</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/167158">#167158</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/3d27d955fd257283b4adfad635a7ed240ff83489"><code>3d27d95</code></a> [GraphPartition] cache get_free_symbol_uses (<a href="https://redirect.github.com/pytorch/pytorch/issues/166338">#166338</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/166994">#166994</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/a06141f73d603084910db381504b7c41eedb7210"><code>a06141f</code></a> Delete deprecated fp32 precision warnings (<a href="https://redirect.github.com/pytorch/pytorch/issues/166956">#166956</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/166998">#166998</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pytorch/pytorch/compare/v2.8.0...v2.9.1">compare view</a></li> </ul> </details> <br /> Dependabot will resolve any conflicts with this PR as long as you don't alter it yourself. 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Bumps [actions/upload-artifact](https://github.com/actions/upload-artifact) from 5 to 6. <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>v6.0.0</h2> <h2>v6 - What's new</h2> <blockquote> <p>[!IMPORTANT] actions/upload-artifact@v6 now runs on Node.js 24 (<code>runs.using: node24</code>) and requires a minimum Actions Runner version of 2.327.1. If you are using self-hosted runners, ensure they are updated before upgrading.</p> </blockquote> <h3>Node.js 24</h3> <p>This release updates the runtime to Node.js 24. v5 had preliminary support for Node.js 24, however this action was by default still running on Node.js 20. Now this action by default will run on Node.js 24.</p> <h2>What's Changed</h2> <ul> <li>Upload Artifact Node 24 support by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/719">actions/upload-artifact#719</a></li> <li>fix: update <code>@actions/artifact</code> for Node.js 24 punycode deprecation by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/744">actions/upload-artifact#744</a></li> <li>prepare release v6.0.0 for Node.js 24 support by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/upload-artifact/pull/745">actions/upload-artifact#745</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/upload-artifact/compare/v5.0.0...v6.0.0">https://github.com/actions/upload-artifact/compare/v5.0.0...v6.0.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/upload-artifact/commit/b7c566a772e6b6bfb58ed0dc250532a479d7789f"><code>b7c566a</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/745">#745</a> from actions/upload-artifact-v6-release</li> <li><a href="https://github.com/actions/upload-artifact/commit/e516bc8500aaf3d07d591fcd4ae6ab5f9c391d5b"><code>e516bc8</code></a> docs: correct description of Node.js 24 support in README</li> <li><a href="https://github.com/actions/upload-artifact/commit/ddc45ed9bca9b38dbd643978d88e3981cdc91415"><code>ddc45ed</code></a> docs: update README to correct action name for Node.js 24 support</li> <li><a href="https://github.com/actions/upload-artifact/commit/615b319bd27bb32c3d64dca6b6ed6974d5fbe653"><code>615b319</code></a> chore: release v6.0.0 for Node.js 24 support</li> <li><a href="https://github.com/actions/upload-artifact/commit/017748b48f8610ca8e6af1222f4a618e84a9c703"><code>017748b</code></a> Merge pull request <a href="https://redirect.github.com/actions/upload-artifact/issues/744">#744</a> from actions/fix-storage-blob</li> <li><a href="https://github.com/actions/upload-artifact/commit/38d4c7997f5510fcc41fc4aae2a6b97becdbe7fc"><code>38d4c79</code></a> chore: rebuild dist</li> <li><a href="https://github.com/actions/upload-artifact/commit/7d27270e0cfd253e666c44abac0711308d2d042f"><code>7d27270</code></a> chore: add missing license cache files for <code>@actions/core</code>, <code>@actions/io</code>, and mi...</li> <li><a href="https://github.com/actions/upload-artifact/commit/5f643d3c9475505ccaf26d686ffbfb71a8387261"><code>5f643d3</code></a> chore: update license files for <code>@actions/artifact</code><a href="https://github.com/5"><code>@5</code></a>.0.1 dependencies</li> <li><a href="https://github.com/actions/upload-artifact/commit/1df1684032c88614064493e1a0478fcb3583e1d0"><code>1df1684</code></a> chore: update package-lock.json with <code>@actions/artifact</code><a href="https://github.com/5"><code>@5</code></a>.0.1</li> <li><a href="https://github.com/actions/upload-artifact/commit/b5b1a918401ee270935b6b1d857ae66c85f3be6f"><code>b5b1a91</code></a> fix: update <code>@actions/artifact</code> to ^5.0.0 for Node.js 24 punycode fix</li> <li>Additional commits viewable in <a href="https://github.com/actions/upload-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. 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Bumps [actions/download-artifact](https://github.com/actions/download-artifact) from 6 to 7. <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>v7.0.0</h2> <h2>v7 - What's new</h2> <blockquote> <p>[!IMPORTANT] actions/download-artifact@v7 now runs on Node.js 24 (<code>runs.using: node24</code>) and requires a minimum Actions Runner version of 2.327.1. If you are using self-hosted runners, ensure they are updated before upgrading.</p> </blockquote> <h3>Node.js 24</h3> <p>This release updates the runtime to Node.js 24. v6 had preliminary support for Node 24, however this action was by default still running on Node.js 20. Now this action by default will run on Node.js 24.</p> <h2>What's Changed</h2> <ul> <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/download-artifact/pull/440">actions/download-artifact#440</a></li> <li>Download Artifact Node24 support by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/415">actions/download-artifact#415</a></li> <li>fix: update <code>@actions/artifact</code> to fix Node.js 24 punycode deprecation by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/451">actions/download-artifact#451</a></li> <li>prepare release v7.0.0 for Node.js 24 support by <a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> in <a href="https://redirect.github.com/actions/download-artifact/pull/452">actions/download-artifact#452</a></li> </ul> <h2>New Contributors</h2> <ul> <li><a href="https://github.com/patrikpolyak"><code>@patrikpolyak</code></a> made their first contribution in <a href="https://redirect.github.com/actions/download-artifact/pull/440">actions/download-artifact#440</a></li> <li><a href="https://github.com/salmanmkc"><code>@salmanmkc</code></a> made their first contribution in <a href="https://redirect.github.com/actions/download-artifact/pull/415">actions/download-artifact#415</a></li> </ul> <p><strong>Full Changelog</strong>: <a href="https://github.com/actions/download-artifact/compare/v6.0.0...v7.0.0">https://github.com/actions/download-artifact/compare/v6.0.0...v7.0.0</a></p> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/actions/download-artifact/commit/37930b1c2abaa49bbe596cd826c3c89aef350131"><code>37930b1</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/452">#452</a> from actions/download-artifact-v7-release</li> <li><a href="https://github.com/actions/download-artifact/commit/72582b9e0acd370909e83fa4a1fd0fca3ad452d8"><code>72582b9</code></a> doc: update readme</li> <li><a href="https://github.com/actions/download-artifact/commit/0d2ec9d4cbcefe257d822f108de2a1f15f8da9f6"><code>0d2ec9d</code></a> chore: release v7.0.0 for Node.js 24 support</li> <li><a href="https://github.com/actions/download-artifact/commit/fd7ae8fda6dc16277a9ffbc91cdb0eedf156e912"><code>fd7ae8f</code></a> Merge pull request <a href="https://redirect.github.com/actions/download-artifact/issues/451">#451</a> from actions/fix-storage-blob</li> <li><a href="https://github.com/actions/download-artifact/commit/d484700543354b15886d6a52910cf61b7f1d2b27"><code>d484700</code></a> chore: restore minimatch.dep.yml license file</li> <li><a href="https://github.com/actions/download-artifact/commit/03a808050efe42bb6ad85281890afd4e4546672c"><code>03a8080</code></a> chore: remove obsolete dependency license files</li> <li><a href="https://github.com/actions/download-artifact/commit/56fe6d904b0968950f8b68ea17774c54973ed5e2"><code>56fe6d9</code></a> chore: update <code>@actions/artifact</code> license file to 5.0.1</li> <li><a href="https://github.com/actions/download-artifact/commit/8e3ebc4ab4d2e095e5eb44ba1a4a53b6b03976ad"><code>8e3ebc4</code></a> chore: update package-lock.json with <code>@actions/artifact</code><a href="https://github.com/5"><code>@5</code></a>.0.1</li> <li><a href="https://github.com/actions/download-artifact/commit/1e3c4b4d4906c98ab57453c24efefdf16c078044"><code>1e3c4b4</code></a> fix: update <code>@actions/artifact</code> to ^5.0.0 for Node.js 24 punycode fix</li> <li><a href="https://github.com/actions/download-artifact/commit/458627d354794c71bc386c8d5839d20b5885fe2a"><code>458627d</code></a> chore: use local <code>@actions/artifact</code> package for Node.js 24 testing</li> <li>Additional commits viewable in <a href="https://github.com/actions/download-artifact/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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<!--pre-commit.ci start--> updates: - [github.com/astral-sh/ruff-pre-commit: v0.14.8 → v0.14.9](astral-sh/ruff-pre-commit@v0.14.8...v0.14.9) <!--pre-commit.ci end--> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
The previous value was MSE. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Fixed RMSE metric calculations to correctly display square-root values for energy, force, virial, and atom-related loss measurements, ensuring accurate performance metrics reporting. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…el (#5091) - Add try-catch block for loading frozen models - Use strict=False when state_dict keys don't match - Log warnings for model state_dict mismatches - Prevent crashes when loading models with different architectures" Fix bug in #5090 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Frozen model loading now uses non‑strict mode; missing or unexpected parameters are logged as warnings instead of causing failure. * **Tests** * Added an end-to-end test covering conversion and loading of frozen models from external formats. * Test I/O standardized to UTF‑8; teardown extended to remove generated artifacts. * **New Files** * Added a JSON test model configuration for validation and training workflows. <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** * Updated CUDA testing environment to a newer runtime version for improved compatibility and stability. * Added installation of the NVIDIA cuBLAS package in CUDA tests to ensure required GPU math libraries are available. <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 <jinzhe.zeng@ustc.edu.cn>
1. Allow backend-convert from pt to tf with `atom_exclude_types` 2. Fix bug in `get_sel_type` method of pt model (by calling `fitting.reinit_exclude` in atomic model init). Fix #5096 <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Fitting now reinitializes exclusion/selection settings during model initialization and after type-map changes; deserialization injects selection info when atom exclusions exist to ensure correct selection behavior. * **Tests** * Added unit and cross-backend tests to verify atom-exclude → selection computation and parity between backends; expanded coverage for exclusion scenarios. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
… backends (#5094) For dpmodel and JAX, previously it returns str, but the type hint is dict. For PyTorch and Paddle, previously it returns dict, but the type hint is str. Now, all backends return dict, and the type hints are also dict. Add a test to test it. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Corrected method return type annotations to improve code accuracy and consistency across inference modules. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
`case_embd` was supported but the JAX backend was not touched. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Bug Fixes** * Ensured the case_embd parameter is consistently converted and handled during fitting, improving compatibility across array backends and preventing mis-coercion. * **Tests** * Adjusted test setup to reset the default computation graph before enabling eager execution, stabilizing related test runs. <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 <jinzhe.zeng@ustc.edu.cn>
This pull request refactors several test files to update import paths for the `expand_sys_str` utility and related modules, reflecting a migration away from the `deepmd.tf` namespace. Additionally, it temporarily skips a test due to compatibility issues with numpy 2.4 and improves file cleanup logic in one test. The main themes are import path updates and test maintenance. **Import path updates:** * Updated imports of `expand_sys_str` in multiple test files (`test_descriptor.py`, `test_embedding_net.py`, `test_model.py`, `test_saveload_dpa1.py`, `test_saveload_se_e2_a.py`, `test_sampler.py`) to use `deepmd.common` instead of `deepmd.tf.common`. [[1]](diffhunk://#diff-026c6e70e7f5fd37843904e99c43910d638b0da8607e1bc0ab84702f256f3264R16-R18) [[2]](diffhunk://#diff-026c6e70e7f5fd37843904e99c43910d638b0da8607e1bc0ab84702f256f3264L34-L36) [[3]](diffhunk://#diff-9d16c9bf54ca3ba29bd1045d492b6a4eb11956305c05631ac8691fe681271535R21-R23) [[4]](diffhunk://#diff-9d16c9bf54ca3ba29bd1045d492b6a4eb11956305c05631ac8691fe681271535L37-L39) [[5]](diffhunk://#diff-a3bf7b66e3c105cf0d73116440343c6b0be07ff6246557f04f6707bec0e21af3R22-R24) [[6]](diffhunk://#diff-a3bf7b66e3c105cf0d73116440343c6b0be07ff6246557f04f6707bec0e21af3L35-L37) [[7]](diffhunk://#diff-0d7e97b8c00caf452b143cae472e2fa0a97473ba4b685f588bb60c21c504b934R16-R18) [[8]](diffhunk://#diff-0d7e97b8c00caf452b143cae472e2fa0a97473ba4b685f588bb60c21c504b934L35-L37) [[9]](diffhunk://#diff-74518d33e0df93e8af8027509351b11fbbe1f32b8c84f6d3a165e1df0953048fR16-R18) [[10]](diffhunk://#diff-74518d33e0df93e8af8027509351b11fbbe1f32b8c84f6d3a165e1df0953048fL35-L37) [[11]](diffhunk://#diff-fd952e5725b949f09ee868247a1a5b0b1b383a25b096766fa994a102a3aeca31R16-R24) * Changed import of `DeepmdDataSystem` in `test_sampler.py` from `deepmd.tf.utils.data_system` to `deepmd.utils.data_system`. **Test maintenance and compatibility:** * Temporarily skipped the `test_sampler_debug_info` test in `test_sampler.py` due to issues with numpy 2.4. * Enhanced file cleanup in `test_training.py` by checking for file existence before attempting to remove files or directories. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Tests** * Improved test robustness by adding existence checks before file cleanup operations to prevent errors. * Temporarily skipped one test due to numpy compatibility issues. * **Chores** * Reorganized internal module imports for improved code structure. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai --> Related PR: <PaddlePaddle/Paddle#77013>
Previously, it was in `ruff.lint.exclude`, so exclusions were not applied to `ruff format`. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Chores** * Updated development tooling configuration to enhance code quality standards and consistency checks. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
Update the DeepModeling domain from deepmodeling.org to deepmodeling.com. The former is no longer used. Generated by the task: njzjz-bot/njzjz-bot#23. <!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Documentation** * Updated documentation links to the correct domain across getting started guides and installation instructions. <sub>✏️ Tip: You can customize this high-level summary in your review settings.</sub> <!-- end of auto-generated comment: release notes by coderabbit.ai -->
…#5114) Updates the requirements on [torch](https://github.com/pytorch/pytorch) to permit the latest version. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pytorch/pytorch/releases">torch's releases</a>.</em></p> <blockquote> <h2>PyTorch 2.9.1 Release, bug fix release</h2> <p>This release is meant to fix the following issues (regressions / silent correctness):</p> <h3>Tracked Regressions</h3> <p>Significant Memory Regression in F.conv3d with bfloat16 Inputs in PyTorch 2.9.0 (<a href="https://redirect.github.com/pytorch/pytorch/issues/166643">#166643</a>) This release provides work around this issue. If you are impacted please install nvidia-cudnn package version 9.15+ from pypi. (<a href="https://redirect.github.com/pytorch/pytorch/pull/166480">#166480</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/167111">#167111</a>)</p> <h3>Torch.compile</h3> <p>Fix Inductor bug when compiling Gemma (<a href="https://redirect.github.com/pytorch/pytorch/pull/165601">#165601</a>) Fix InternalTorchDynamoError in bytecode_transformation (<a href="https://redirect.github.com/pytorch/pytorch/pull/166036">#166036</a>) Fix silent correctness error_on_graph_break bug where non-empty checkpoint results in unwanted graph break resumption (<a href="https://redirect.github.com/pytorch/pytorch/pull/166586">#166586</a>) Improve performance by avoiding recompilation with mark_static_address with cudagraphs (<a href="https://redirect.github.com/pytorch/pytorch/pull/162208">#162208</a>) Improve performance by caching get_free_symbol_uses in torch inductor (<a href="https://redirect.github.com/pytorch/pytorch/pull/166338">#166338</a>) Fix fix registration design for inductor graph partition for vLLM (<a href="https://redirect.github.com/pytorch/pytorch/pull/166458">#166458</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/165815">#165815</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/165514">#165514</a>) Fix warning spamming in torch.compile (<a href="https://redirect.github.com/pytorch/pytorch/pull/166993">#166993</a>) Fix exception related to uninitialized tracer_output variable (<a href="https://redirect.github.com/pytorch/pytorch/pull/163169">#163169</a>) Fix crash in torch.bmm and torch.compile with PyTorch release 2.9.0 (<a href="https://redirect.github.com/pytorch/pytorch/pull/166457">#166457</a>)</p> <h3>Other</h3> <p>Fix warning spamming on new APIs to control TF32 behavior (<a href="https://redirect.github.com/pytorch/pytorch/pull/166956">#166956</a>) Fix distributed crash with non-contiguous gather inputs (<a href="https://redirect.github.com/pytorch/pytorch/pull/166181">#166181</a>) Fix indexing on large tensor causes invalid configuration argument (<a href="https://redirect.github.com/pytorch/pytorch/pull/166974">#166974</a>) Fix numeric issue in CUDNN_ATTENTION (<a href="https://redirect.github.com/pytorch/pytorch/pull/166912">#166912</a>) (<a href="https://redirect.github.com/pytorch/pytorch/pull/166570">#166570</a>) Fix symmetric memory issue with fused_scaled_matmul_reduce_scatter (<a href="https://redirect.github.com/pytorch/pytorch/pull/165086">#165086</a>) Improve libtorch stable ABI documentation (<a href="https://redirect.github.com/pytorch/pytorch/pull/163899">#163899</a>) Fix image display on pypi project description section (<a href="https://redirect.github.com/pytorch/pytorch/pull/166404">#166404</a>)</p> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/pytorch/pytorch/blob/main/RELEASE.md">torch's changelog</a>.</em></p> <blockquote> <h1>Releasing PyTorch</h1> <!-- raw HTML omitted --> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-compatibility-matrix">Release Compatibility Matrix</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorch-cuda-support-matrix">PyTorch CUDA Support Matrix</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-cadence">Release Cadence</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#general-overview">General Overview</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#frequently-asked-questions">Frequently Asked Questions</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cutting-a-release-branch-preparations">Cutting a release branch preparations</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cutting-release-branches">Cutting release branches</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorchpytorch"><code>pytorch/pytorch</code></a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#pytorch-ecosystem-libraries">PyTorch ecosystem libraries</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#making-release-branch-specific-changes-for-pytorch">Making release branch specific changes for PyTorch</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#making-release-branch-specific-changes-for-ecosystem-libraries">Making release branch specific changes for ecosystem libraries</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#running-launch-execution-team-core-xfn-sync">Running Launch Execution team Core XFN sync</a></li> <li><a href="#drafting-rcs-release-candidates-for-pytorch-and-domain-libraries">Drafting RCs (https://github.com/pytorch/pytorch/blob/main/Release Candidates) for PyTorch and domain libraries</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-candidate-storage">Release Candidate Storage</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#release-candidate-health-validation">Release Candidate health validation</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cherry-picking-fixes">Cherry Picking Fixes</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#how-to-do-cherry-picking">How to do Cherry Picking</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#cherry-picking-reverts">Cherry Picking Reverts</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#preparing-and-creating-final-release-candidate">Preparing and Creating Final Release Candidate</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#promoting-rcs-to-stable">Promoting RCs to Stable</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#additional-steps-to-prepare-for-release-day">Additional Steps to prepare for release day</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#modify-release-matrix">Modify release matrix</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#open-google-colab-issue">Open Google Colab issue</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-releases">Patch Releases</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-criteria">Patch Release Criteria</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-process">Patch Release Process</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#patch-release-process-description">Patch Release Process Description</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#triage">Triage</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#issue-tracker-for-patch-releases">Issue Tracker for Patch releases</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#building-a-release-schedule--cherry-picking">Building a release schedule / cherry picking</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#building-binaries--promotion-to-stable">Building Binaries / Promotion to Stable</a></li> </ul> </li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#hardware--software-support-in-binary-build-matrix">Hardware / Software Support in Binary Build Matrix</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#python">Python</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#accelerator-software">Accelerator Software</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#special-support-cases">Special support cases</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#operating-systems">Operating Systems</a></li> </ul> </li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#submitting-tutorials">Submitting Tutorials</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#special-topics">Special Topics</a> <ul> <li><a href="https://github.com/pytorch/pytorch/blob/main/#updating-submodules-for-a-release">Updating submodules for a release</a></li> <li><a href="https://github.com/pytorch/pytorch/blob/main/#triton-dependency-for-the-release">Triton dependency for the release</a></li> </ul> </li> </ul> <!-- raw HTML omitted --> <h2>Release Compatibility Matrix</h2> <p>Following is the Release Compatibility Matrix for PyTorch releases:</p> <!-- raw HTML omitted --> </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pytorch/pytorch/commit/d38164a545b4a4e4e0cf73ce67173f70574890b6"><code>d38164a</code></a> Enable Doc builds for: Minor Releases RCs. Minor and Patch Releases final RC ...</li> <li><a href="https://github.com/pytorch/pytorch/commit/b002562550577a09038c40c0e04ae18a54c8f12b"><code>b002562</code></a> Add doc for Symmetric Memory (<a href="https://redirect.github.com/pytorch/pytorch/issues/167477">#167477</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/5811a8d7da873dd699ff6687092c225caffcf1bb"><code>5811a8d</code></a> [cuDNN][SDPA][Convolution] Expose cuDNN runtime version in CUDA hooks (<a href="https://redirect.github.com/pytorch/pytorch/issues/167327">#167327</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/f36c764ca475ea382ee4af6ff8bc807a9bd89876"><code>f36c764</code></a> [dynamo][ez] Initialize tracer_output to None by default. (<a href="https://redirect.github.com/pytorch/pytorch/issues/167366">#167366</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/6877288115e10776d9ee74d4e86dafdc1556d5bc"><code>6877288</code></a> Change forkserver test to only run below 3.13.8 (<a href="https://redirect.github.com/pytorch/pytorch/issues/167361">#167361</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/9976b77abbb6e920684f899c539101e4b412f911"><code>9976b77</code></a> Cherry-pick LibTorch Stable ABI documentation (<a href="https://redirect.github.com/pytorch/pytorch/issues/167112">#167112</a> <a href="https://redirect.github.com/pytorch/pytorch/issues/166661">#166661</a> <a href="https://redirect.github.com/pytorch/pytorch/issues/163899">#163899</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/167">#167</a>...</li> <li><a href="https://github.com/pytorch/pytorch/commit/e6bcbbe17c64a2fd9e660324bbdfc5c32cd560a8"><code>e6bcbbe</code></a> [Inductor] No longer throw error in bmm out_dtype lowering due to tem… (<a href="https://redirect.github.com/pytorch/pytorch/issues/166922">#166922</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/8f658d7599a9cf5e12d749c6c140457cd6f05978"><code>8f658d7</code></a> don't produce invalid grid configs (<a href="https://redirect.github.com/pytorch/pytorch/issues/166973">#166973</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/167158">#167158</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/3d27d955fd257283b4adfad635a7ed240ff83489"><code>3d27d95</code></a> [GraphPartition] cache get_free_symbol_uses (<a href="https://redirect.github.com/pytorch/pytorch/issues/166338">#166338</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/166994">#166994</a>)</li> <li><a href="https://github.com/pytorch/pytorch/commit/a06141f73d603084910db381504b7c41eedb7210"><code>a06141f</code></a> Delete deprecated fp32 precision warnings (<a href="https://redirect.github.com/pytorch/pytorch/issues/166956">#166956</a>) (<a href="https://redirect.github.com/pytorch/pytorch/issues/166998">#166998</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pytorch/pytorch/compare/v2.8.0...v2.9.1">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. 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<!-- This is an auto-generated comment: release notes by coderabbit.ai --> ## Summary by CodeRabbit * **Documentation** * Updated installation and contributor guides to reference the master development flow and revised download/setup instructions. * Clarified contributor workflow to create and use new branches instead of working directly on the old development branch. * **Chores** * CI/CD workflows and deployment now target the master branch for pushes; Pages deployment triggers on master. * Removed obsolete automation/autoupdate settings and explicit branch targets from config. <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 <njzjz@qq.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>
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