Merge pull request #388 from glotzerlab/test-python-3.13

Support Python 3.13
glotzerlab · Sep 6, 2024 · 26b6bfb · 26b6bfb
2 parents 2d1e71f + 1b4ff6d
commit 26b6bfb
Show file tree

Hide file tree

Showing 16 changed files with 110 additions and 139 deletions.
diff --git a/.clang-tidy b/.clang-tidy
@@ -14,4 +14,6 @@ Checks: 'bugprone-*,
          -readability-function-cognitive-complexity,
          -cert-dcl37-c,
          -cert-dcl51-cpp,
-         -bugprone-narrowing-conversions'
+         -bugprone-narrowing-conversions,
+         -misc-include-cleaner,
+         '
diff --git a/.github/requirements-test.in b/.github/requirements-test.in
@@ -1,3 +1,3 @@
-cython == 3.0.8
-numpy == 1.26.4
-pytest == 8.2.0
+cython == 3.0.11
+numpy == 2.1.1
+pytest == 8.3.2
diff --git a/.github/requirements-test.txt b/.github/requirements-test.txt
@@ -1,18 +1,18 @@
-#
-# This file is autogenerated by pip-compile with Python 3.12
-# by the following command:
-#
-#    pip-compile requirements-test.in
-#
-cython==3.0.8
+# This file was autogenerated by uv via the following command:
+#    uv pip compile -p 3.10.1 requirements-test.in
+cython==3.0.11
     # via -r requirements-test.in
+exceptiongroup==1.2.2
+    # via pytest
 iniconfig==2.0.0
     # via pytest
-numpy==1.26.4
+numpy==2.1.1
     # via -r requirements-test.in
-packaging==24.0
+packaging==24.1
     # via pytest
 pluggy==1.5.0
     # via pytest
-pytest==8.2.0
+pytest==8.3.2
     # via -r requirements-test.in
+tomli==2.0.1
+    # via pytest
diff --git a/.github/workflows/build_wheels.yaml b/.github/workflows/build_wheels.yaml
@@ -15,9 +15,6 @@ on:
 
   workflow_dispatch:
 
-env:
-  UV_VERSION: 0.2.2
-
 jobs:
   build_wheels:
     name: Build wheels [${{ matrix.python.version }}, ${{ matrix.os.base }}-${{ matrix.os.arch }}]
@@ -40,25 +37,25 @@ jobs:
           arch: 'x86_64'
 
         python:
-        - version: 'cp39'
-          oldest_numpy: '1.21.6'
         - version: 'cp310'
           oldest_numpy: '1.21.6'
         - version: 'cp311'
           oldest_numpy: '1.23.2'
         - version: 'cp312'
           oldest_numpy: '1.26.2'
+        - version: 'cp313'
+          oldest_numpy: '2.1.1'
 
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.20.0
+        uses: pypa/cibuildwheel@bd033a44476646b606efccdd5eed92d5ea1d77ad # v2.20.0
         env:
           CIBW_BUILD: "${{ matrix.python.version }}-*"
           CIBW_TEST_REQUIRES: pytest==8.2.1 numpy==${{ matrix.python.oldest_numpy }}
 
-      - uses: actions/upload-artifact@v4.4.0
+      - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
           name: dist-python-${{ matrix.python.version }}-${{ matrix.os.base }}-${{ matrix.os.arch }}
           path: ./wheelhouse/*.whl
@@ -67,23 +64,21 @@ jobs:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
-      - uses: actions/setup-python@v5.2.0
-        name: Install Python
+      - name: Set up Python
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
-          python-version: '3.12'
-
-      - name: Install uv
-        run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${{ env.UV_VERSION }}/uv-installer.sh | bash
-
-      - name: Install build
-        run: 'uv pip install -r .github/requirements-build-sdist.txt --only-binary :all: --system --reinstall'
+          python-version: 3.12
+      - name: Set up Python environment
+        uses: glotzerlab/workflows/setup-uv@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+        with:
+          lockfile: ".github/requirements-build-sdist.txt"
 
       - name: Build sdist
         run: python -m build --sdist --outdir dist/ .
 
-      - uses: actions/upload-artifact@v4.4.0
+      - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
           name: dist-sdist
           path: dist/*.tar.gz
@@ -95,7 +90,7 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4.1.8
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
           merge-multiple: 'true'
           pattern: dist-*
@@ -107,15 +102,15 @@ jobs:
       - name: Upload to PyPI
         # upload to PyPI on every tag starting with 'v'
         if: startsWith(github.ref, 'refs/tags/v')
-        uses: pypa/gh-action-pypi-publish@v1.10.0
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}
 
       - name: Upload to TestPyPI
         # otherwise, upload to TestPyPi
         if: ${{ !startsWith(github.ref, 'refs/tags/v') && (github.event_name != 'pull_request' || (github.event.pull_request.head.repo.full_name == github.repository && github.actor != 'dependabot[bot]')) }}
-        uses: pypa/gh-action-pypi-publish@v1.10.0
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1
         with:
           user: __token__
           password: ${{ secrets.TEST_PYPI_API_TOKEN }}

diff --git a/.github/workflows/release.yaml b/.github/workflows/release.yaml
@@ -28,7 +28,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
         with:
           fetch-depth: 0
           submodules: true
@@ -63,7 +63,7 @@ jobs:
       - name: Tar source
         run: tar -cvJf "${name}-${tag:1}.tar.xz" "${name}-${tag:1}"
 
-      - uses: actions/upload-artifact@v4.4.0
+      - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4.4.0
         with:
           name: release
           path: |
@@ -77,12 +77,12 @@ jobs:
 
     steps:
       - name: Download artifacts
-        uses: actions/download-artifact@v4.1.8
+        uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         with:
           name: release
 
       - name: Create release
-        uses: softprops/action-gh-release@v2
+        uses: softprops/action-gh-release@c062e08bd532815e2082a85e87e3ef29c3e6d191 # v2.0.8
         if: startsWith(github.ref, 'refs/tags/v')
         with:
           files: "*.tar.*"

diff --git a/.github/workflows/stale.yaml b/.github/workflows/stale.yaml
@@ -8,28 +8,4 @@ on:
 
 jobs:
   stale:
-    runs-on: ubuntu-latest
-    steps:
-    - uses: actions/stale@v9.0.0
-      with:
-        days-before-close: 10
-        stale-issue-label: stale
-        stale-pr-label: stale
-        exempt-issue-labels: essential
-        exempt-pr-labels: essential
-
-        days-before-issue-stale: 170
-        stale-issue-message: >
-          This issue has been automatically marked as stale because it has not had
-          recent activity. It will be closed if no further activity occurs.
-        close-issue-message: >
-          This issue has been automatically closed because it has not had
-          recent activity.
-
-        days-before-pr-stale: 20
-        stale-pr-message: >
-          This pull request has been automatically marked as stale because it has not had
-          recent activity. It will be closed if no further activity occurs.
-        close-pr-message: >
-          This pull request has been automatically closed because it has not had
-          recent activity.
+    uses: glotzerlab/workflows/.github/workflows/stale.yaml@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
diff --git a/.github/workflows/style_check.yaml b/.github/workflows/style_check.yaml
@@ -13,27 +13,24 @@ on:
 
   workflow_dispatch:
 
-env:
-  UV_VERSION: 0.2.2
-
 jobs:
   clang-tidy:
     name: Run clang-tidy
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python
-        uses: actions/setup-python@v5.2.0
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: 3.12
-      - name: Install uv
-        run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${{ env.UV_VERSION }}/uv-installer.sh | bash
-      - name: Install prereqs
-        run: 'uv pip install -r .github/requirements-test.txt --only-binary :all: --system --reinstall'
+      - name: Set up Python environment
+        uses: glotzerlab/workflows/setup-uv@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+        with:
+          lockfile: ".github/requirements-test.txt"
       - name: Configure
         run: cmake -B build
       - name: Execute clang-tidy
-        run: clang-tidy-14 -p=build gsd/*.c gsd/*.h scripts/*.cc --quiet --warnings-as-errors="*"
+        run: clang-tidy-18 -p=build gsd/*.c gsd/*.h scripts/*.cc --quiet --warnings-as-errors="*"
 
   # This job is used to provide a single requirement for branch merge conditions.
   checks_complete:

diff --git a/.github/workflows/unit_test.yaml b/.github/workflows/unit_test.yaml
@@ -17,36 +17,30 @@ defaults:
   run:
     shell: bash
 
-env:
-  UV_VERSION: 0.2.2
-
 jobs:
   unit_test:
     name: Unit test [py${{ matrix.python }} ${{ matrix.c_compiler }} ${{ matrix.os }}]
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: false
       matrix:
         include:
         ##############
         # Windows
         - os: windows-2019
           python: '3.12'
         - os: windows-2022
-          python: '3.12'
+          python: '3.13.0-rc.1'
         ##############
         # Mac
         # macos-x86_64
         - os: macos-13
           python: '3.12'
         # macos-arm64
         - os: macos-14
-          python: '3.12'
+          python: '3.13.0-rc.1'
         ##############
         # Ubuntu 24.04
-        - os: ubuntu-24.04
-          python: '3.9'
-          c_compiler: gcc-13
-          cxx_compiler: g++-14
         - os: ubuntu-24.04
           python: '3.10'
           c_compiler: gcc-14
@@ -63,12 +57,12 @@ jobs:
           python: '3.12'
           c_compiler: clang-18
           cxx_compiler: clang++-18
+        - os: ubuntu-24.04
+          python: '3.13.0-rc.1'
+          c_compiler: clang-18
+          cxx_compiler: clang++-18
         ##############
         # Ubuntu 22.04
-        - os: ubuntu-22.04
-          python: '3.9'
-          c_compiler: gcc-11
-          cxx_compiler: g++-11
         - os: ubuntu-22.04
           python: '3.10'
           c_compiler: gcc-12
@@ -87,10 +81,6 @@ jobs:
           cxx_compiler: clang++-15
         ##############
         # Ubuntu 20.04
-        - os: ubuntu-20.04
-          python: '3.9'
-          c_compiler: gcc-10
-          cxx_compiler: g++-10
         - os: ubuntu-20.04
           python: '3.10'
           c_compiler: clang-10
@@ -105,17 +95,17 @@ jobs:
           cxx_compiler: clang++-12
 
     steps:
-      - uses: actions/checkout@v4.1.7
+      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
         with:
           path: code
       - name: Set up Python
-        uses: actions/setup-python@v5.2.0
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python }}
-      - name: Install uv
-        run: curl --proto '=https' --tlsv1.2 -LsSf https://github.com/astral-sh/uv/releases/download/${{ env.UV_VERSION }}/uv-installer.sh | bash
-      - name: Install prereqs
-        run: 'uv pip install -r code/.github/requirements-test.txt --only-binary :all: --system --reinstall'
+      - name: Set up Python environment
+        uses: glotzerlab/workflows/setup-uv@ae7e7c6931098a313ef8069ef04b88a55c3a40f6 # 0.3.0
+        with:
+          lockfile: "code/.github/requirements-test.txt"
       - name: Set Linux compiler
         if: ${{ startsWith(matrix.os, 'ubuntu') }}
         run: |

diff --git a/.gitignore b/.gitignore
@@ -3,8 +3,10 @@ __pycache__
 *.pyc
 *.pyo
 *.so
+.cache
 fl.c
 build
+compile_commands.json
 devdoc
 dist
 gsd.egg-info
-Original file line number
+Diff line change
@@ Expand Up / @@ -3,8 +3,10 @@ __pycache__ @@
     *.pyc
     *.pyo
     *.so
+    .cache
     fl.c
     build
+    compile_commands.json
     devdoc
     dist
     gsd.egg-info
@@ Expand Down @@