From 0ba7fed1faafbbd394399137bf210c7d2edda36c Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 31 Jul 2024 02:48:43 -0400 Subject: [PATCH 1/7] fix:fix LAMMPS MPI tests with mpi4py 4.0.0 (#4032) The previous code works with mpi4py<4 but fails with mpi4py 4.0.0. I don't know what breaking change was made. ## Summary by CodeRabbit - **Bug Fixes** - Optimized potential energy calculation in the LAMMPS simulation by restricting evaluation to the master process, reducing unnecessary computations. - **Chores** - Improved control flow for better performance in parallel execution contexts. Signed-off-by: Jinzhe Zeng (cherry picked from commit 1e7223666d58fca7ae131b0415706ccaf69a4f08) --- source/lmp/tests/run_mpi_pair_deepmd.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/lmp/tests/run_mpi_pair_deepmd.py b/source/lmp/tests/run_mpi_pair_deepmd.py index b27774ce11..0c4291ab3a 100644 --- a/source/lmp/tests/run_mpi_pair_deepmd.py +++ b/source/lmp/tests/run_mpi_pair_deepmd.py @@ -54,8 +54,8 @@ ) lammps.pair_coeff("* *") lammps.run(0) -pe = lammps.eval("pe") if rank == 0: + pe = lammps.eval("pe") arr = [pe] np.savetxt(output, np.array(arr)) MPI.Finalize() From 8dc6bfe1f504a1b15728cdae983b152621b61525 Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Fri, 25 Oct 2024 04:18:38 -0400 Subject: [PATCH 2/7] ci: bump tensorflow/build image to 2.18 (#4252) Fix the CI error. ## Summary by CodeRabbit - **Chores** - Updated TensorFlow build version from 2.15 to 2.18 in the C library build workflow. This change ensures compatibility with the latest TensorFlow features and improvements during the library's build process. Signed-off-by: Jinzhe Zeng (cherry picked from commit a66afd34ec81187dc196b0557bd672bf39da8fc7) --- .github/workflows/package_c.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/package_c.yml b/.github/workflows/package_c.yml index e932dd0eba..e58b8452d2 100644 --- a/.github/workflows/package_c.yml +++ b/.github/workflows/package_c.yml @@ -11,7 +11,7 @@ jobs: strategy: matrix: include: - - tensorflow_build_version: "2.15" + - tensorflow_build_version: "2.18" tensorflow_version: "" filename: libdeepmd_c.tar.gz - tensorflow_build_version: "2.14" From bde3c8d048c4ac818519d661e4d4f7ce95be791b Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 5 Aug 2024 21:33:48 +0000 Subject: [PATCH 3/7] build(deps): bump pypa/cibuildwheel from 2.19 to 2.20 (#4045) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.19 to 2.20.
Release notes

Sourced from pypa/cibuildwheel's releases.

Version 2.20.0

  • 🌟 CPython 3.13 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.13.0rc1, which is guaranteed to be ABI compatible with the final release. Free-threading is still behind a flag/config option. (#1950)
  • ✨ Provide a CIBW_ALLOW_EMPTY environment variable as an alternative to the command line flag. (#1937)
  • 🐛 Don't use uv on PyPy3.8 on Windows, it stopped working starting in 0.2.25. Note that PyPy 3.8 is EoL. (#1868)
  • 🛠 Set the VSCMD_ARG_TGT_ARCH variable based on target arch. (#1876)
  • 🛠 Undo cleaner output on pytest 8-8.2 now that 8.3 is out. (#1943)
  • 📚 Update examples to use Python 3.12 on host (cibuildwheel will require Python 3.11+ on the host machine starting in October 2024) (#1919)

Version 2.19.2

  • 🐛 Update manylinux2014 pins to versions that support past-EoL CentOS 7 mirrors. (#1917)
  • 🐛 Support --no-isolation with build[uv] build-frontend. (#1889)
  • 🛠 Provide attestations for releases at https://github.com/pypa/cibuildwheel/attestations. (#1916)
  • 🛠 Provide CPython 3.13.0b3. (#1913)
  • 🛠 Remove some workarounds now that pip 24.1 is available. (#1891, #1892)
  • 📚 Remove nosetest from our docs. (#1821)
  • 📚 Document the macOS ARM workaround for 3.8 on GHA. (#1871)
  • 📚 GitLab CI + macOS is now a supported platform with an example. (#1911)

Version 2.19.1

  • 🐛 Don't require setup-python on GHA for Pyodide (#1868)
  • 🐛 Specify full python path for uv (fixes issue in 0.2.10 & 0.2.11) (#1881)
  • 🛠 Update for pip 24.1b2 on CPython 3.13. (#1879)
  • 🛠 Fix a warning in our schema generation script. (#1866)
  • 🛠 Cleaner output on pytest 8-8.2. (#1865)
Changelog

Sourced from pypa/cibuildwheel's changelog.

title: Changelog

Changelog

v2.20.0

  • 🌟 CPython 3.13 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.13.0rc1, which is guaranteed to be ABI compatible with the final release. Free-threading is still behind a flag/config option. (#1950)
  • ✨ Provide a CIBW_ALLOW_EMPTY environment variable as an alternative to the command line flag. (#1937)
  • 🐛 Don't use uv on PyPy3.8 on Windows, it stopped working starting in 0.2.25. Note that PyPy 3.8 is EoL. (#1868)
  • 🛠 Set the VSCMD_ARG_TGT_ARCH variable based on target arch. (#1876)
  • 🛠 Undo cleaner output on pytest 8-8.2 now that 8.3 is out. (#1943)
  • 📚 Update examples to use Python 3.12 on host (cibuildwheel will require Python 3.11+ on the host machine starting in October 2024) (#1919)

v2.19.2

  • 🐛 Update manylinux2014 pins to versions that support past-EoL CentOS 7 mirrors. (#1917)
  • 🐛 Support --no-isolation with build[uv] build-frontend. (#1889)
  • 🛠 Provide attestations for releases at https://github.com/pypa/cibuildwheel/attestations. (#1916)
  • 🛠 Provide CPython 3.13.0b3. (#1913)
  • 🛠 Remove some workarounds now that pip 21.1 is available. (#1891, #1892)
  • 📚 Remove nosetest from our docs. (#1821)
  • 📚 Document the macOS ARM workaround for 3.8 on GHA. (#1871)
  • 📚 GitLab CI + macOS is now a supported platform with an example. (#1911)

v2.19.1

  • 🐛 Don't require setup-python on GHA for Pyodide (#1868)
  • 🐛 Specify full python path for uv (fixes issue in 0.2.10 & 0.2.11) (#1881)
  • 🛠 Update for pip 24.1b2 on CPython 3.13. (#1879)
  • 🛠 Fix a warning in our schema generation script. (#1866)
  • 🛠 Cleaner output on pytest 8-8.2. (#1865)

v2.19.0

See the release post for more info on new features!

  • 🌟 Add Pyodide platform. Set with --platform pyodide or CIBW_PLATFORM: pyodide on Linux with a host Python 3.12 to build WebAssembly wheels. Not accepted on PyPI currently, but usable directly in a website using Pyodide, for live docs, etc. (#1456, #1859)
  • 🌟 Add build[uv] backend, which will take a pre-existing uv install (or install cibuildwheel[uv]) and use uv for all environment setup and installs on Python 3.8+. This is significantly faster in most cases. (#1856)
  • ✨ Add free-threaded macOS builds and update CPython to 3.13.0b2. (#1854)
  • 🐛 Issue copying a wheel to a non-existent output dir fixed. (#1851, #1862)
  • 🐛 Better determinism for the test environment seeding. (#1835)
  • 🛠 VIRTUAL_ENV variable now set. (#1842)
  • 🛠 Remove a pip<21.3 workaround. (#1842)
  • 🛠 Error handling was refactored to use exceptions. (#1719)
  • 🛠 Hardcoded paths in tests avoided. (#1834)

... (truncated)

Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=pypa/cibuildwheel&package-manager=github_actions&previous-version=2.19&new-version=2.20)](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) ---
Dependabot commands and options
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 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)
## Summary by CodeRabbit - **Chores** - Updated the `cibuildwheel` GitHub Action to version `v2.20`, potentially enhancing the build process for Python projects with new features and improvements. Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (cherry picked from commit 35ef72117359ffbcd3d3143ed513e0a65246d103) --- .github/workflows/build_wheel.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index e203737424..7fa58dbe76 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -77,7 +77,7 @@ jobs: rm -rf .git if: matrix.dp_pkg_name == 'deepmd-kit-cu11' - name: Build wheels - uses: pypa/cibuildwheel@v2.19 + uses: pypa/cibuildwheel@v2.20 env: CIBW_BUILD_VERBOSITY: 1 CIBW_ARCHS: all From f71e77c0e57dea4ea35cf3d9e7c128c8b469e0e4 Mon Sep 17 00:00:00 2001 From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com> Date: Mon, 16 Sep 2024 14:48:20 -0400 Subject: [PATCH 4/7] build(deps): bump pypa/cibuildwheel from 2.20 to 2.21 (#4127) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Bumps [pypa/cibuildwheel](https://github.com/pypa/cibuildwheel) from 2.20 to 2.21.
Release notes

Sourced from pypa/cibuildwheel's releases.

v2.21.0

  • ⚠️ Update CPython 3.12 to 3.12.6, which changes the macOS minimum deployment target on CPython 3.12 from macOS 10.9 to macOS 10.13 (#1998)
  • 🛠 Changes the behaviour when inheriting config-settings in TOML overrides - rather than extending each key, which is rarely useful, individual keys will override previously set values. (#1803)
  • 🛠 Update CPython 3.13 to 3.13.0rc2 (#1998)
  • ✨ Adds support for multiarch OCI images (#1961)
  • 🐛 Fixes some bugs building Linux wheels on macOS. (#1961)
  • ⚠️ Changes the minimum version of Docker/Podman to Docker API version 1.43, Podman API version 3. The only mainstream runner this should affect is Travis Graviton2 runners - if so you can upgrade your version of Docker. (#1961)
Changelog

Sourced from pypa/cibuildwheel's changelog.

title: Changelog

Changelog

v2.21.0

13 September 2024

  • ⚠️ Update CPython 3.12 to 3.12.6, which changes the macOS minimum deployment target on CPython 3.12 from macOS 10.9 to macOS 10.13 (#1998)
  • 🛠 Changes the behaviour when inheriting config-settings in TOML overrides - rather than extending each key, which is rarely useful, individual keys will override previously set values. (#1803)
  • 🛠 Update CPython 3.13 to 3.13.0rc2 (#1998)
  • ✨ Adds support for multiarch OCI images (#1961)
  • 🐛 Fixes some bugs building Linux wheels on macOS. (#1961)
  • ⚠️ Changes the minimum version of Docker/Podman to Docker API version 1.43, Podman API version 3. The only mainstream runner this should affect is Travis Graviton2 runners - if so you can upgrade your version of Docker. (#1961)

v2.20.0

4 August 2024

  • 🌟 CPython 3.13 wheels are now built by default - without the CIBW_PRERELEASE_PYTHONS flag. It's time to build and upload these wheels to PyPI! This release includes CPython 3.13.0rc1, which is guaranteed to be ABI compatible with the final release. Free-threading is still behind a flag/config option. (#1950)
  • ✨ Provide a CIBW_ALLOW_EMPTY environment variable as an alternative to the command line flag. (#1937)
  • 🐛 Don't use uv on PyPy3.8 on Windows, it stopped working starting in 0.2.25. Note that PyPy 3.8 is EoL. (#1868)
  • 🛠 Set the VSCMD_ARG_TGT_ARCH variable based on target arch. (#1876)
  • 🛠 Undo cleaner output on pytest 8-8.2 now that 8.3 is out. (#1943)
  • 📚 Update examples to use Python 3.12 on host (cibuildwheel will require Python 3.11+ on the host machine starting in October 2024) (#1919)

v2.19.2

2 July 2024

  • 🐛 Update manylinux2014 pins to versions that support past-EoL CentOS 7 mirrors. (#1917)
  • 🐛 Support --no-isolation with build[uv] build-frontend. (#1889)
  • 🛠 Provide attestations for releases at https://github.com/pypa/cibuildwheel/attestations. (#1916)
  • 🛠 Provide CPython 3.13.0b3. (#1913)
  • 🛠 Remove some workarounds now that pip 21.1 is available. (#1891, #1892)
  • 📚 Remove nosetest from our docs. (#1821)
  • 📚 Document the macOS ARM workaround for 3.8 on GHA. (#1871)
  • 📚 GitLab CI + macOS is now a supported platform with an example. (#1911)

v2.19.1

13 June 2024

  • 🐛 Don't require setup-python on GHA for Pyodide (#1868)
  • 🐛 Specify full python path for uv (fixes issue in 0.2.10 & 0.2.11) (#1881)

... (truncated)

Commits

[![Dependabot compatibility score](https://dependabot-badges.githubapp.com/badges/compatibility_score?dependency-name=pypa/cibuildwheel&package-manager=github_actions&previous-version=2.20&new-version=2.21)](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) ---
Dependabot commands and options
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 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)
Signed-off-by: dependabot[bot] Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> (cherry picked from commit 0c59ef3d2a898e98bc72a22a1469067b4f648452) --- .github/workflows/build_wheel.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index 7fa58dbe76..19be29fe9f 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -77,7 +77,7 @@ jobs: rm -rf .git if: matrix.dp_pkg_name == 'deepmd-kit-cu11' - name: Build wheels - uses: pypa/cibuildwheel@v2.20 + uses: pypa/cibuildwheel@v2.21 env: CIBW_BUILD_VERBOSITY: 1 CIBW_ARCHS: all From 7ceb809bcddd8449ceb8b4f3e16c70dc0d0507ac Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 23 Oct 2024 10:12:56 -0400 Subject: [PATCH 5/7] ci: limit downloaded files in build_docker (#4242) This download-artifact step fails randomly. Limiting the files to download should reduce the possibility of failure. ## Summary by CodeRabbit - **New Features** - Enhanced artifact downloading patterns for improved specificity in the build process. - Expanded artifact access during the PyPI index build. - **Improvements** - Maintained job structure and dependencies for consistent build and deployment processes. - Defined permissions for critical jobs to ensure secure operations. Signed-off-by: Jinzhe Zeng (cherry picked from commit 8e777859c7f17e8812e4ed25237ca6b4f7cc04a3) --- .github/workflows/build_wheel.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index 19be29fe9f..9e5cf15c45 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -137,6 +137,7 @@ jobs: - uses: actions/download-artifact@v4 with: path: source/install/docker/dist + pattern: cibw-*-manylinux_x86_64-cu${{ matrix.cuda_version }}* merge-multiple: true - name: Log in to the Container registry uses: docker/login-action@v3 @@ -169,6 +170,7 @@ jobs: - uses: actions/download-artifact@v4 with: path: dist/packages + pattern: cibw-* merge-multiple: true - uses: actions/setup-python@v5 name: Install Python From e9a45c2e850a23f52955f99208105d535ad23ea7 Mon Sep 17 00:00:00 2001 From: Anyang Peng <137014849+anyangml@users.noreply.github.com> Date: Wed, 3 Jul 2024 12:02:52 +0800 Subject: [PATCH 6/7] fix: pin uv version to 0.2.18 (#3946) ## Summary by CodeRabbit - **Chores** - Updated the URL for downloading the `uv` installer script in the build workflow configuration. (cherry picked from commit ec1cf86cde7d248c509bbfcff8c7b7c6968efe28) --- .github/workflows/build_wheel.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index 9e5cf15c45..af2797a271 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -66,7 +66,7 @@ jobs: # https://github.com/pypa/setuptools_scm/issues/480 fetch-depth: 0 - name: Install uv - run: curl -LsSf https://astral.sh/uv/install.sh | sh + run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.2.18/uv-installer.sh | sh if: runner.os != 'Linux' - uses: docker/setup-qemu-action@v3 name: Setup QEMU From 7e1dfd396266a7cef30c61aaf928533b44356ead Mon Sep 17 00:00:00 2001 From: Jinzhe Zeng Date: Wed, 10 Jul 2024 21:17:41 -0400 Subject: [PATCH 7/7] ci(deps): bump uv to 0.2.24 (#3964) Bump uv to [0.2.24](https://github.com/astral-sh/uv/releases/tag/0.2.24), which adds retry on connection reset network errors. Let's see if this fixes the network issue. ## Summary by CodeRabbit - **Chores** - Updated the build configuration to download the latest version (0.2.24) of `uv`. Signed-off-by: Jinzhe Zeng (cherry picked from commit bd02cccd4335b70443e66dcc0fba3bc9e35ca436) --- .github/workflows/build_wheel.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build_wheel.yml b/.github/workflows/build_wheel.yml index af2797a271..4cebac9ab5 100644 --- a/.github/workflows/build_wheel.yml +++ b/.github/workflows/build_wheel.yml @@ -66,7 +66,7 @@ jobs: # https://github.com/pypa/setuptools_scm/issues/480 fetch-depth: 0 - name: Install uv - run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.2.18/uv-installer.sh | sh + run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/0.2.24/uv-installer.sh | sh if: runner.os != 'Linux' - uses: docker/setup-qemu-action@v3 name: Setup QEMU