[r2] v2.2.10 #3648

njzjz · 2024-04-06T07:10:29Z

Collect the following PRs:

Deprecate per discussion. --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 5c545f7) --------- When cherry-pick from devel, PyTorch and v3 specific documentation are removed. Signed-off-by: Jinzhe Zeng <[email protected]>

…ing#3237) [A segfault](https://github.com/deepmodeling/deepmd-kit/actions/runs/7782245372/job/21218255452) sometimes appears in the tests after deepmodeling#3223. The reason is that the required shape of the electric field is set to nall * 3 in the C interface, but a vector of nloc * 3 is given in the tests and lammps and used in the C++ interface. It was not caught before, as the program didn't write to these addresses (only reading it usually won't cause a segfault, unless the address is invalid). Perhaps fix deepmodeling#2895. --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit e281a8c)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.1.14 → v0.2.0](astral-sh/ruff-pre-commit@v0.1.14...v0.2.0)  --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 37cdccf)

We don't need to pin them to a specific tag. This can close deepmodeling#3230. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 1c8d635)

(cherry picked from commit a7153b1)

…modeling#3254) To have the same behavior between TF and PT. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit dc63793) Signed-off-by: Jinzhe Zeng <[email protected]>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.0 → v0.2.1](astral-sh/ruff-pre-commit@v0.2.0...v0.2.1) - [github.com/scop/pre-commit-shfmt: v3.7.0-4 → v3.8.0-1](scop/pre-commit-shfmt@v3.7.0-4...v3.8.0-1)  Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit 1bdc60d)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.1 → v0.2.2](astral-sh/ruff-pre-commit@v0.2.1...v0.2.2) - [github.com/Lucas-C/pre-commit-hooks: v1.5.4 → v1.5.5](Lucas-C/pre-commit-hooks@v1.5.4...v1.5.5)  --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 4b994df) Signed-off-by: Jinzhe Zeng <[email protected]>

…update (deepmodeling#3312) Bumps the npm_and_yarn group with 1 update in the /source/nodejs directory: [ip](https://github.com/indutny/node-ip). Updates `ip` from 2.0.0 to 2.0.1 <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/indutny/node-ip/commit/3b0994a74eca51df01f08c40d6a65ba0e1845d04"><code>3b0994a</code></a> 2.0.1</li> <li><a href="https://github.com/indutny/node-ip/commit/32f468f1245574785ec080705737a579be1223aa"><code>32f468f</code></a> lib: fixed CVE-2023-42282 and added unit test</li> <li>See full diff in <a href="https://github.com/indutny/node-ip/compare/v2.0.0...v2.0.1">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=ip&package-manager=npm_and_yarn&previous-version=2.0.0&new-version=2.0.1)](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) You can disable automated security fix PRs for this repo from the [Security Alerts page](https://github.com/deepmodeling/deepmd-kit/network/alerts). </details> Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Han Wang <[email protected]> (cherry picked from commit 4956864)

Fix deepmodeling#3256. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit d629616)

Fix a bug caused by the breaking change in Keras 3 (shipped by TF 2.16). --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 473cc0a) Signed-off-by: Jinzhe Zeng <[email protected]>

Redundant setup was removed. The setup has already been executed in the initial lines of post_force, along with subsequent calculations. Reinitialization will lead to an error. (cherry picked from commit 254afc8)

The atom->image of the wannier centroid should be set to the same as its real counterpart when assigning the position. --------- Co-authored-by: Yifan Li李一帆 <[email protected]> (cherry picked from commit b1de9e6)

Fix deepmodeling#2265. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 84d0576) Signed-off-by: Jinzhe Zeng <[email protected]>

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 54efc03)

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 7af9e20) Signed-off-by: Jinzhe Zeng <[email protected]>

Fix deepmodeling#3168. deepmodeling#3172 didn't fix deepmodeling#3168. The environmental variable `SETUPTOOLS_SCM_PRETEND_VERSION` works. I don't know what's wrong with the previous one. In this PR, I deleted the `.git` directory for `deepmd-kit-cu11`, which will throw an error if it doesn't work. --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit bd79dec)

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 268a0fc) Signed-off-by: Jinzhe Zeng <[email protected]>

Signed-off-by: Duo <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]> (cherry picked from commit fd82f04) -------- Code for PyTorch is removed. Signed-off-by: Jinzhe Zeng <[email protected]>

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 804848a)

Fix deepmodeling#3272. Apply implementation of deepmodeling#3271 into TF. Confirm consistent results on `examples/water`, `examples/nopbc`, and ANI-1x (deepmodeling#1624). 80x speed up: ![image](https://github.com/deepmodeling/deepmd-kit/assets/9496702/85aa1fed-e3c0-4cb6-9082-db45c9a03f9d) --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 02080db) --------- Cleanup for r2. Signed-off-by: Jinzhe Zeng <[email protected]>

…ng#3446) Bumps [softprops/action-gh-release](https://github.com/softprops/action-gh-release) from 1 to 2. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/softprops/action-gh-release/releases">softprops/action-gh-release's releases</a>.</em></p> <blockquote> <h2>v2.0.0</h2> <ul> <li>update actions.yml declaration to node20 to address warnings</li> </ul> </blockquote> </details> <details> <summary>Changelog</summary> <p><em>Sourced from <a href="https://github.com/softprops/action-gh-release/blob/master/CHANGELOG.md">softprops/action-gh-release's changelog</a>.</em></p> <blockquote> <h2>0.1.12</h2> <ul> <li>fix bug leading to empty strings subsituted for inputs users don't provide breaking api calls <a href="https://redirect.github.com/softprops/action-gh-release/pull/144">#144</a></li> </ul> </blockquote> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/softprops/action-gh-release/commit/d99959edae48b5ffffd7b00da66dcdb0a33a52ee"><code>d99959e</code></a> prep release</li> <li><a href="https://github.com/softprops/action-gh-release/commit/0e39c679e8bac647fe5ad41070fe2295b0393d58"><code>0e39c67</code></a> make pattern error opt in (<a href="https://redirect.github.com/softprops/action-gh-release/issues/417">#417</a>)</li> <li><a href="https://github.com/softprops/action-gh-release/commit/20e085ccc73308c2c8e43ab8da4f8d7ecbb94d4e"><code>20e085c</code></a> kick off 2.0.1 release</li> <li><a href="https://github.com/softprops/action-gh-release/commit/9f5c4d39bc56b5ed07f92f260dd05d33000058a6"><code>9f5c4d3</code></a> update changelog</li> <li><a href="https://github.com/softprops/action-gh-release/commit/0bea76b22707a1871a52b97e07c80657071adb76"><code>0bea76b</code></a> Add support for make_latest property (<a href="https://redirect.github.com/softprops/action-gh-release/issues/304">#304</a>)</li> <li><a href="https://github.com/softprops/action-gh-release/commit/762fe13dfbc8921c36ebb81da5626a394a6a5b95"><code>762fe13</code></a> typo in changelog</li> <li><a href="https://github.com/softprops/action-gh-release/commit/c0f2569fb90b35a0e2b043535a5778f437ec86ea"><code>c0f2569</code></a> remove unused script</li> <li><a href="https://github.com/softprops/action-gh-release/commit/5743e060246b253faba6cb8e051511b63e7639c9"><code>5743e06</code></a> update changelog</li> <li><a href="https://github.com/softprops/action-gh-release/commit/fe71fd3b919b0ad8636bb9a2930b15466814fbb7"><code>fe71fd3</code></a> Don't swallow errors (<a href="https://redirect.github.com/softprops/action-gh-release/issues/384">#384</a>)</li> <li><a href="https://github.com/softprops/action-gh-release/commit/9150ab13f3b0f0b7df0b9979d0e04968f5844d96"><code>9150ab1</code></a> rebuild and update changelog</li> <li>Additional commits viewable in <a href="https://github.com/softprops/action-gh-release/compare/v1...v2">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=softprops/action-gh-release&package-manager=github_actions&previous-version=1&new-version=2)](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> Co-authored-by: Han Wang <[email protected]> (cherry picked from commit 4c84514)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.2.2 → v0.3.2](astral-sh/[email protected]) - [github.com/pre-commit/mirrors-clang-format: v17.0.6 → v18.1.1](pre-commit/[email protected])  --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit da68686) Signed-off-by: Jinzhe Zeng <[email protected]>

This week, a random segfault occurred in GHA when using `-fsanitize=leak`. It seems related to actions/runner-images#9491. Workaround: actions/runner-images#9491 (comment) See also: https://stackoverflow.com/questions/77894856/possible-bug-in-gcc-sanitizers Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 487f85c) Signed-off-by: Jinzhe Zeng <[email protected]>

This pull request fixes the broken symlink for `dpplugin.so` on macOS. It should point to `libdeepmd_lmp.so` but point to `libdeepmd_lmp.dylib` instead. ### Details The `libdeepmd_lmp` is a shared module. https://github.com/deepmodeling/deepmd-kit/blob/b875ea8f6661b6e1567537ead7e2b4a8b14ea113/source/lmp/plugin/CMakeLists.txt#L72 The build target name on macOS is `libdeepmd_lmp.so`. Because on macOS, the `CMAKE_SHARED_MODULE_SUFFIX` (`.so`) is different from `CMAKE_SHARED_LIBRARY_SUFFIX` (`.dynlib`). As a result, in previous versions, on macOS the symbolic link `dpplugin.so` was pointed to `libdeepmd_lmp.dylib`, which does not exist. One can check the conda-forge builds to confirm (e.g., [osx-arm64/deepmd-kit-2.2.9-cpu_py311hf5376d5_mpi_openmpi_0.conda](https://anaconda.org/conda-forge/deepmd-kit/2.2.9/download/osx-arm64/deepmd-kit-2.2.9-cpu_py311hf5376d5_mpi_openmpi_0.conda)). (cherry picked from commit abf3477)

updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.2 → v0.3.3](astral-sh/ruff-pre-commit@v0.3.2...v0.3.3)  Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit 2851fb9)

) Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.16 to 2.17. <details> <summary>Release notes</summary> <p><em>Sourced from <a href="https://github.com/pypa/cibuildwheel/releases">pypa/cibuildwheel's releases</a>.</em></p> <blockquote> <h2>v2.17.0</h2> <ul> <li>🌟 Adds the ability to inherit configuration in TOML overrides. This makes certain configurations much simpler. If you're overriding an option like <code>before-build</code> or <code>environment</code>, and you just want to add an extra command or environment variable, you can just append (or prepend) to the previous config. See <a href="https://cibuildwheel.pypa.io/en/stable/options/#inherit">the docs</a> for more information. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1730">#1730</a>)</li> <li>🌟 Adds official support for native arm64 macOS GitHub runners. To use them, just specify <code>macos-14</code> as an <code>os</code> of your job in your workflow file. You can also keep <code>macos-13</code> in your build matrix to build x86_64. Check out the new <a href="https://cibuildwheel.pypa.io/en/stable/setup/#github-actions">GitHub Actions example config</a>.</li> <li>✨ You no longer need to specify <code>--platform</code> to run cibuildwheel locally! Instead it will detect your platform automatically. This was a safety feature, no longer necessary. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1727">#1727</a>)</li> <li>🛠 Removed setuptools and wheel pinned versions. This only affects old-style projects without a <code>pyproject.toml</code>, projects with <code>pyproject.toml</code> are already getting fresh versions of their <code>build-system.requires</code> installed into an isolated environment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1725">#1725</a>)</li> <li>🛠 Improve how the GitHub Action passes arguments (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1757">#1757</a>)</li> <li>🛠 Remove a system-wide install of pipx in the GitHub Action (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1745">#1745</a>)</li> <li>🐛 No longer will cibuildwheel override the PIP_CONSTRAINT environment variable when using the <code>build</code> frontend. Instead it will be extended. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1675">#1675</a>)</li> <li>🐛 Fix a bug where building and testing both x86_86 and arm64 wheels on the same runner caused the wrong architectures in the test environment (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1750">#1750</a>)</li> <li>🐛 Fix a bug that prevented testing a CPython 3.8 wheel targeting macOS 11+ on x86_64 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1768">#1768</a>)</li> <li>📚 Moved the docs onto the official PyPA domain - they're now available at <a href="https://cibuildwheel.pypa.io">https://cibuildwheel.pypa.io</a> . (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1775">#1775</a>)</li> <li>📚 Docs and examples improvements (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1762">#1762</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1734">#1734</a>)</li> </ul> <h2>v2.16.5</h2> <ul> <li>🐛 Fix an incompatibility with the GitHub Action and new GitHub Runner images for Windows that bundle Powershell 7.3+ (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1741">#1741</a>)</li> <li>🛠 Preliminary support for new <code>macos-14</code> arm64 runners (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1743">#1743</a>)</li> </ul> <h2>v2.16.4</h2> <p>🛠 Update manylinux pins to upgrade from a problematic PyPy version. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1737">#1737</a>)</p> <h2>v2.16.3</h2> <ul> <li>🐛 Fix a bug when building from sdist, where relative paths to files in the package didn't work because the working directory was wrong (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1687">#1687</a>)</li> <li>🛠 Adds the ability to disable mounting the host filesystem in containers to <code>/host</code>, through the <code>disable_host_mount</code> suboption on <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#container-engine"><code>CIBW_CONTAINER_ENGINE</code></a>.</li> <li>📚 A lot of docs improvements! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1708">#1708</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1705">#1705</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1686">#1686</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1679">#1679</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1667">#1667</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1665">#1665</a>)</li> </ul> <h2>v2.16.2</h2> <ul> <li>🛠 Updates CPython 3.12 version to 3.12.0, final release (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1635">#1635</a>)</li> <li>✨ Adds a debug option <a href="https://cibuildwheel.readthedocs.io/en/stable/options/#cibw_debug_keep_container"><code>CIBW_DEBUG_KEEP_CONTAINER</code></a> to stop cibuildwheel deleting build containers after the build finishes. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1620">#1620</a>)</li> <li>📚 Adds support for <code>[tool.cibuildwheel]</code> checking by adding a schema compatible with the <a href="https://github.com/abravalheri/validate-pyproject/">validate-pyproject</a> tool (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1622">#1622</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1628">#1628</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1629">#1629</a>)</li> <li>🐛 Fix parsing of <code>CIBW_CONTAINER_ENGINE</code> and <code>CIBW_BUILD_FRONTEND</code> options to not break arguments on <code>:</code> characters (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1621">#1621</a>)</li> <li>🐛 Fix the evaluation order of <code>CIBW_ENVIRONMENT</code> and <code>CIBW_ENVIRONMENT_PASS</code> so that <code>CIBW_ENVIRONMENT</code> assignments can reference environment variables passed through from the host machine. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1617">#1617</a>)</li> <li>🛠 Supports manylinux images' deferred installation of interpreters through the <code>manylinux-interpreters</code> tool (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1630">#1630</a>)</li> </ul> <h2>v2.16.1</h2> <ul> <li>🛠 Updates the prerelease CPython 3.12 version to 3.12.0rc3 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1625">#1625</a>)</li> <li>🛠 Only calls <code>linux32</code> in containers when necessary (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1599">#1599</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> <hr /> <h2>title: Changelog</h2> <h1>Changelog</h1> <h3>v2.17.0</h3> <p><em>11 March 2024</em></p> <ul> <li>🌟 Adds the ability to inherit configuration in TOML overrides. This makes certain configurations much simpler. If you're overriding an option like <code>before-build</code> or <code>environment</code>, and you just want to add an extra command or environment variable, you can just append (or prepend) to the previous config. See <a href="https://cibuildwheel.pypa.io/en/stable/options/#inherit">the docs</a> for more information. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1730">#1730</a>)</li> <li>🌟 Adds official support for native arm64 macOS GitHub runners. To use them, just specify <code>macos-14</code> as an <code>os</code> of your job in your workflow file. You can also keep <code>macos-13</code> in your build matrix to build x86_64. Check out the new <a href="https://cibuildwheel.pypa.io/en/stable/setup/#github-actions">GitHub Actions example config</a>.</li> <li>✨ You no longer need to specify <code>--platform</code> to run cibuildwheel locally! Instead it will detect your platform automatically. This was a safety feature, no longer necessary. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1727">#1727</a>)</li> <li>🛠 Removed setuptools and wheel pinned versions. This only affects old-style projects without a <code>pyproject.toml</code>, projects with <code>pyproject.toml</code> are already getting fresh versions of their <code>build-system.requires</code> installed into an isolated environment. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1725">#1725</a>)</li> <li>🛠 Improve how the GitHub Action passes arguments (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1757">#1757</a>)</li> <li>🛠 Remove a system-wide install of pipx in the GitHub Action (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1745">#1745</a>)</li> <li>🐛 No longer will cibuildwheel override the PIP_CONSTRAINT environment variable when using the <code>build</code> frontend. Instead it will be extended. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1675">#1675</a>)</li> <li>🐛 Fix a bug where building and testing both x86_86 and arm64 wheels on the same runner caused the wrong architectures in the test environment (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1750">#1750</a>)</li> <li>🐛 Fix a bug that prevented testing a CPython 3.8 wheel targeting macOS 11+ on x86_64 (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1768">#1768</a>)</li> <li>📚 Moved the docs onto the official PyPA domain - they're now available at <a href="https://cibuildwheel.pypa.io">https://cibuildwheel.pypa.io</a> . (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1775">#1775</a>)</li> <li>📚 Docs and examples improvements (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1762">#1762</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1734">#1734</a>)</li> </ul> <h3>v2.16.5</h3> <p><em>30 January 2024</em></p> <ul> <li>🐛 Fix an incompatibility with the GitHub Action and new GitHub Runner images for Windows that bundle Powershell 7.3+ (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1741">#1741</a>)</li> <li>🛠 Preliminary support for new <code>macos-14</code> arm64 runners (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1743">#1743</a>)</li> </ul> <h3>v2.16.4</h3> <p><em>28 January 2024</em></p> <ul> <li>🛠 Update manylinux pins to upgrade from a problematic PyPy version. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1737">#1737</a>)</li> </ul> <h3>v2.16.3</h3> <p><em>26 January 2024</em></p> <ul> <li>🐛 Fix a bug when building from sdist, where relative paths to files in the package didn't work because the working directory was wrong (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1687">#1687</a>)</li> <li>🛠 Adds the ability to disable mounting the host filesystem in containers to <code>/host</code>, through the <code>disable_host_mount</code> suboption on <a href="https://cibuildwheel.pypa.io/en/stable/options/#container-engine"><code>CIBW_CONTAINER_ENGINE</code></a>.</li> <li>📚 A lot of docs improvements! (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1708">#1708</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1705">#1705</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1686">#1686</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1679">#1679</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1667">#1667</a>, <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1665">#1665</a>)</li> </ul> <h3>v2.16.2</h3> <p><em>3 October 2023</em></p> <ul> <li>🛠 Updates CPython 3.12 version to 3.12.0, final release (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1635">#1635</a>)</li> <li>✨ Adds a debug option <a href="https://cibuildwheel.pypa.io/en/stable/options/#cibw_debug_keep_container"><code>CIBW_DEBUG_KEEP_CONTAINER</code></a> to stop cibuildwheel deleting build containers after the build finishes. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1620">#1620</a>)</li> </ul>  </blockquote> <p>... (truncated)</p> </details> <details> <summary>Commits</summary> <ul> <li><a href="https://github.com/pypa/cibuildwheel/commit/8d945475ac4b1aac4ae08b2fd27db9917158b6ce"><code>8d94547</code></a> Bump version: v2.17.0</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/ca06deb26f92b2b2c6019a3bc223875215fe4cf2"><code>ca06deb</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1775">#1775</a> from pypa/doc-domain</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/f7e19222253830775777d4dc7e8cf56aa098d97f"><code>f7e1922</code></a> CirrusCI fixes (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1786">#1786</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/0d8e919dfc5b7631e641377671db317556dcc7ef"><code>0d8e919</code></a> [Bot] Update dependencies (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1784">#1784</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/022de07dc13bb25455653a082449a0c038632ac0"><code>022de07</code></a> Merge pull request <a href="https://redirect.github.com/pypa/cibuildwheel/issues/1785">#1785</a> from pypa/revert-1783</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/920f574191fe30782d55398b7a0e70d62c999024"><code>920f574</code></a> Remove manylinux1 docker pin</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/5c06f3c28934b3830d065b17ab853c4465ce6623"><code>5c06f3c</code></a> docs: Add how to run tests in development (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1698">#1698</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/e2a0839555d4d2ffd366ac4cd933262f5974fd10"><code>e2a0839</code></a> fix: set SYSTEM_VERSION_COMPAT=0 during pip install on macos (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1768">#1768</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/87fff7728267ddada9c54df079e5864e5c5e5dfb"><code>87fff77</code></a> chore(deps): bump the actions group with 1 update (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1776">#1776</a>)</li> <li><a href="https://github.com/pypa/cibuildwheel/commit/8ef9486aab2cc0aea71870a765265e294d84a679"><code>8ef9486</code></a> Add <code>pedalboard</code> to projects.yml. (<a href="https://redirect.github.com/pypa/cibuildwheel/issues/1781">#1781</a>)</li> <li>Additional commits viewable in <a href="https://github.com/pypa/cibuildwheel/compare/v2.16...v2.17">compare view</a></li> </ul> </details> <br /> [![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=pypa/cibuildwheel&package-manager=github_actions&previous-version=2.16&new-version=2.17)](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> (cherry picked from commit be95d09)

Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit 145f501) Signed-off-by: Jinzhe Zeng <[email protected]>

Fix deepmodeling#3509. Note: 0 atoms in a processor with the PyTorch backend is currently broken. I commented with a TODO tag. --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit fb61efb) Signed-off-by: Jinzhe Zeng <[email protected]>

updates: - [github.com/astral-sh/ruff-pre-commit: v0.3.4 → v0.3.5](astral-sh/ruff-pre-commit@v0.3.4...v0.3.5)  Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit cb08410)

…pmodeling#3632) Currently, `se_atten_v2` is always masked to zero when `exclude_types` is given. However, for the no neighbor case, the placeholder for a virtual neighbor is `davg`. This causes discontinuity when `set_davg_zero` is not set. This PR uses `davg` for masking. In production, we usually use `set_davg_zero` along with `exclude_types`, so it hasn't caused a real problem. I notice PT hasn't implemented `se_atten_v2` or `exclude_types`, but we need attention in the future. --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit 63601b0)

To solve this issue: deepmodeling#3641 --------- Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: robinzyb <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 181b631)

Replace quick_start.ipynb with a new version. Aligned English tutorial with Chinese version(https://nb.bohrium.dp.tech/detail/3313403083) in structure and content. --------- Signed-off-by: Xu zhangmancang <[email protected]> Co-authored-by: Mancn <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit edb9da8)

deepmd/infer/model_devi.py

@@ -33,8 +33,7 @@
    real_f: Optional[np.ndarray] = None,
    relative: Optional[float] = None,
    atomic: Literal[False] = False,
-) -> Tuple[np.ndarray, np.ndarray, np.ndarray]:
-    ...
+) -> Tuple[np.ndarray, np.ndarray, np.ndarray]: ...


deepmd/infer/model_devi.py

@@ -44,8 +43,7 @@
    relative: Optional[float] = None,
    *,
    atomic: Literal[True],
-) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]:
-    ...
+) -> Tuple[np.ndarray, np.ndarray, np.ndarray, np.ndarray]: ...


codecov · 2024-04-06T07:17:11Z

Codecov Report

Attention: Patch coverage is 93.22382% with 33 lines in your changes are missing coverage. Please review.

Project coverage is 81.52%. Comparing base (29a0387) to head (128b6c7).

Files	Patch %	Lines
source/api_c/include/deepmd.hpp	86.04%	4 Missing and 8 partials ⚠️
source/api_c/src/c_api.cc	77.27%	5 Missing and 5 partials ⚠️
source/api_cc/src/DeepPot.cc	78.94%	2 Missing and 2 partials ⚠️
source/ipi/driver.cc	0.00%	3 Missing ⚠️
deepmd/fit/ener.py	71.42%	2 Missing ⚠️
deepmd/entrypoints/freeze.py	80.00%	1 Missing ⚠️
deepmd_utils/entrypoints/doc.py	0.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##               r2    #3648      +/-   ##
==========================================
+ Coverage   76.21%   81.52%   +5.30%     
==========================================
  Files         277      342      +65     
  Lines       25639    33844    +8205     
  Branches     1605     2872    +1267     
==========================================
+ Hits        19542    27590    +8048     
- Misses       5225     5371     +146     
- Partials      872      883      +11

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This seems to fix the GPG key error posted at deepmodeling#3325 (comment). See https://almalinux.org/blog/2023-12-20-almalinux-8-key-update/ Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit d7a4f72)

…conda docs (deepmodeling#3462) Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Chun Cai <[email protected]> (cherry picked from commit 80b6900) Signed-off-by: Jinzhe Zeng <[email protected]>

* fix NeighborStat Signed-off-by: Jinzhe Zeng <[email protected]> * mixed_type Signed-off-by: Jinzhe Zeng <[email protected]> --------- Signed-off-by: Jinzhe Zeng <[email protected]>

njzjz · 2024-04-06T07:58:09Z

Important

DO NOT SQUASH!

njzjz · 2024-04-06T08:23:57Z

We may consider setting r2 as the default branch... The master branch will not be updated until v3.0.0 is released.

wanghan-iapcm · 2024-04-06T13:32:03Z

We may consider setting r2 as the default branch... The master branch will not be updated until v3.0.0 is released.

@njzjz default changed to r2.

njzjz and others added 30 commits April 6, 2024 01:43

pin docker actions to major versions (deepmodeling#3238)

d3efb98

We don't need to pin them to a specific tag. This can close deepmodeling#3230. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 1c8d635)

issue template: change TF version to backend version (deepmodeling#3244)

e354960

(cherry picked from commit a7153b1)

tf: support checkpoint path (instead of directory) in dp freeze (deep…

b476890

…modeling#3254) To have the same behavior between TF and PT. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit dc63793) Signed-off-by: Jinzhe Zeng <[email protected]>

tf: add fparam/aparam support for finetune (deepmodeling#3313)

cdb7fb2

Fix deepmodeling#3256. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit d629616)

bump python to 3.12 in the test environment (deepmodeling#3343)

afac0c0

Fix a bug caused by the breaking change in Keras 3 (shipped by TF 2.16). --------- Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 473cc0a) Signed-off-by: Jinzhe Zeng <[email protected]>

fix_dplr.cpp delete redundant setup (deepmodeling#3344)

61c1b8d

Redundant setup was removed. The setup has already been executed in the initial lines of post_force, along with subsequent calculations. Reinitialization will lead to an error. (cherry picked from commit 254afc8)

fix_dplr.cpp set atom->image when pre_force (deepmodeling#3345)

fe8056d

The atom->image of the wannier centroid should be set to the same as its real counterpart when assigning the position. --------- Co-authored-by: Yifan Li李一帆 <[email protected]> (cherry picked from commit b1de9e6)

docs: apply type_one_side=True to se_a and se_r (deepmodeling#3364)

1bf218d

Fix deepmodeling#2265. Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 84d0576) Signed-off-by: Jinzhe Zeng <[email protected]>

bump scikit-build-core to 0.8 (deepmodeling#3369)

c877479

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 54efc03)

bump LAMMPS to stable_2Aug2023_update3 (deepmodeling#3399)

2408b47

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 7af9e20) Signed-off-by: Jinzhe Zeng <[email protected]>

ban print (deepmodeling#3415)

0eede70

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 268a0fc) Signed-off-by: Jinzhe Zeng <[email protected]>

Add max_ckpt_keep for trainer (deepmodeling#3441)

3509b20

Signed-off-by: Duo <[email protected]> Co-authored-by: Jinzhe Zeng <[email protected]> (cherry picked from commit fd82f04) -------- Code for PyTorch is removed. Signed-off-by: Jinzhe Zeng <[email protected]>

fix: do not install tf-keras for cu11 (deepmodeling#3444)

4ac18c7

Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit 804848a)

ci: add linter for markdown, yaml, CSS (deepmodeling#3574)

065ba3e

Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> (cherry picked from commit 145f501) Signed-off-by: Jinzhe Zeng <[email protected]>

pre-commit-ci bot and others added 4 commits April 6, 2024 03:05

njzjz added this to the v2.2.10 milestone Apr 6, 2024

github-actions bot added Python Core CUDA ROCM OP C++ LAMMPS Docs Examples i-PI C labels Apr 6, 2024

njzjz marked this pull request as draft April 6, 2024 07:16

github-advanced-security bot found potential problems Apr 6, 2024

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njzjz and others added 3 commits April 6, 2024 03:24

fix AlmaLinux GPG key error (deepmodeling#3326)

6cc02ad

This seems to fix the GPG key error posted at deepmodeling#3325 (comment). See https://almalinux.org/blog/2023-12-20-almalinux-8-key-update/ Signed-off-by: Jinzhe Zeng <[email protected]> (cherry picked from commit d7a4f72)

docs: add deprecation notice for the official conda channel and more …

d47e43d

…conda docs (deepmodeling#3462) Signed-off-by: Jinzhe Zeng <[email protected]> Co-authored-by: Chun Cai <[email protected]> (cherry picked from commit 80b6900) Signed-off-by: Jinzhe Zeng <[email protected]>

[r2] fix NeighborStat (#207)

128b6c7

* fix NeighborStat Signed-off-by: Jinzhe Zeng <[email protected]> * mixed_type Signed-off-by: Jinzhe Zeng <[email protected]> --------- Signed-off-by: Jinzhe Zeng <[email protected]>

njzjz marked this pull request as ready for review April 6, 2024 07:56

njzjz requested a review from wanghan-iapcm April 6, 2024 08:02

wanghan-iapcm approved these changes Apr 6, 2024

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njzjz merged commit f8a0b31 into deepmodeling:r2 Apr 6, 2024
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njzjz deleted the r2-2.2.10 branch April 6, 2024 18:46

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[r2] v2.2.10 #3648

[r2] v2.2.10 #3648

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[r2] v2.2.10 #3648

[r2] v2.2.10 #3648

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