Merge main, retrigger build

agriyakhetarpal · Nov 29, 2024 · fd3e01c · fd3e01c
2 parents 1dc3a0f + fdd1570
commit fd3e01c
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Showing 19 changed files with 254 additions and 981 deletions.
diff --git a/.github/workflows/emscripten.yml b/.github/workflows/emscripten.yml
@@ -29,54 +29,29 @@ env:
 jobs:
   build_wasm_emscripten:
     name: Build PyWavelets for Pyodide
-    runs-on: ubuntu-latest
-    # Uncomment the following line to test changes on a fork
-    # if: github.repository == 'PyWavelets/pywt'
+    runs-on: ubuntu-22.04
+    # Comment out the following line to test changes on a fork
+    if: github.repository == 'PyWavelets/pywt'
     steps:
       - name: Check out repository
         uses: actions/checkout@v4
 
-      - name: Set up Python 3.11
-        id: setup-python
-        uses: actions/setup-python@v5
-        with:
-          python-version: "3.11.2"
-
-      - name: Install prerequisites
-        run: |
-          python -m pip install pyodide-build "pydantic<2"
-          echo EMSCRIPTEN_VERSION=$(pyodide config get emscripten_version) >> $GITHUB_ENV
-
-      - name: Set up Emscripten toolchain
-        uses: mymindstorm/setup-emsdk@v14
-        with:
-          version: ${{ env.EMSCRIPTEN_VERSION }}
-          actions-cache-folder: emsdk-cache
-
-      - name: Set up Node.js
-        uses: actions/[email protected]
-        with:
-          node-version: "18"
-
-      - name: Build PyWavelets
-        run: |
-          pyodide build
-
-      - name: Install and test wheel
-        run: |
-          pyodide venv .venv-pyodide
-          source .venv-pyodide/bin/activate
-          pip install dist/*.whl
-          pushd demo
-          pip install matplotlib pytest
-          python -c "import pywt; print(pywt.__version__)"
-          pytest --pyargs pywt -m "not slow"
+      - name: Build and test PyWavelets
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
+        env:
+          CIBW_PLATFORM: pyodide
+          CIBW_TEST_REQUIRES: pytest matplotlib
+          CIBW_TEST_COMMAND: python -c "import pywt; pywt.test(extra_argv=['-m', 'not slow'])"
 
         # https://anaconda.org/scientific-python-nightly-wheels/pywavelets
         # WARNING: this job will overwrite existing wheels.
-      - name: Push to Anaconda PyPI index
-        if: (github.repository == 'PyWavelets/pywt') && (github.event_name == 'push' && github.ref == 'refs/heads/main') || (github.event_name == 'workflow_dispatch' && github.event.inputs.push_wheels == 'true') || (github.event_name == 'schedule')
-        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # v0.5.0
+      - name: Push wheels to Anaconda PyPI index
+        if: >-
+          (github.repository == 'PyWavelets/pywt') &&
+          (github.event_name == 'push' && github.ref == 'refs/heads/main') ||
+          (github.event_name == 'workflow_dispatch' && github.event.inputs.push_wheels == 'true') ||
+          (github.event_name == 'schedule')
+        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b # v0.6.1
         with:
-          artifacts_path: dist/
+          artifacts_path: wheelhouse/
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}
diff --git a/.github/workflows/tests.yml b/.github/workflows/tests.yml
@@ -37,7 +37,7 @@ jobs:
         MINIMUM_REQUIREMENTS: [0]
         USE_SCIPY: [0]
         USE_SDIST: [0]
-        REFGUIDE_CHECK: [0]
+        REFGUIDE_CHECK: [1]
         PIP_FLAGS: [""]
         OPTIONS_NAME: ["default"]
         include:
@@ -105,7 +105,7 @@ jobs:
                 python -m build --sdist
                 pip install dist/pyw*.tar.gz -v
             elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-                pip install sphinx numpydoc
+                pip install sphinx numpydoc scipy-doctest
                 pip install . -v
             else
                 pip install . -v
@@ -129,16 +129,53 @@ jobs:
               pytest --pyargs pywt
               python ../pywt/tests/test_doc.py
           elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-              # Run doctests and check if the refguide contains entries from __all__
-              python util/refguide_check.py --doctests
+              # doctest docstrings
+              pytest --doctest-modules --pyargs pywt -v  --doctest-collect=api
               # Run Sphinx HTML docs builder, converting warnings to errors
+              # Move back out of demo/ to root directory
+              cd ..
               pip install -r util/readthedocs/requirements.txt
-              sphinx-build -b html -W --keep-going -d _build/doctrees . doc/source doc/build
+              sphinx-build -b html -W --keep-going -d _build/doctrees doc/source doc/build
           else
               pytest --pyargs pywt
           fi
           popd
 
+  test_pywavelets_linux_free_threaded:
+    name: linux-cp313t-with-scipy
+    runs-on: ubuntu-latest
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails
+      fail-fast: false
+
+    steps:
+      - name: Checkout PyWavelets
+        uses: actions/checkout@v4
+
+      # TODO: replace with setup-python when there is support
+      - uses: deadsnakes/action@e640ac8743173a67cca4d7d77cd837e514bf98e8 # v3.2.0
+        with:
+          python-version: "3.13-dev"
+          nogil: true
+
+      - name: Build package
+        run: |
+          which python
+          python --version
+          pip install --upgrade pip build
+          # We need nightly wheels for free-threaded support and latest fixes
+          pip install --pre -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple cython numpy scipy
+          pip install pytest meson-python ninja
+          pip install . -v --no-build-isolation
+
+      - name: Run tests
+        env:
+          PYTHON_GIL: 0
+        run: |
+          # Move out of source directory to avoid finding local pywt
+          cd demo
+          pytest --pyargs pywt
+
   test_pywavelets_macos:
     name: macos-cp${{ matrix.python-version }}-${{ matrix.OPTIONS_NAME }}
     runs-on: macos-latest
@@ -203,7 +240,7 @@ jobs:
                 python -m build --sdist
                 pip install pywavelets* -v
             elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-                pip install sphinx numpydoc
+                pip install sphinx numpydoc scipy-doctest
                 pip install . -v
             else
                 pip install . -v
@@ -221,7 +258,9 @@ jobs:
               pytest --pyargs pywt
               python ../pywt/tests/test_doc.py
           elif [ "${REFGUIDE_CHECK}" == "1" ]; then
-              python util/refguide_check.py --doctests
+              # doctests docstrings
+              pytest --doctest-modules --pyargs pywt -v  --doctest-collect=api
+              pytest --doctest-modules --pyargs pywt.data -v
           else
               pytest --pyargs pywt
           fi

diff --git a/.github/workflows/wheel_tests_and_release.yml b/.github/workflows/wheel_tests_and_release.yml
@@ -34,7 +34,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        cibw_python: ["cp310", "cp311", "cp312"]
+        cibw_python: ["cp310", "cp311", "cp312", "cp313", "cp313t"]
         cibw_arch: ["x86_64"]
     steps:
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
@@ -44,16 +44,29 @@ jobs:
         name: Install Python
         with:
           python-version: "3.10"
+
+      - name: Install build deps; set CIBW environment variables
+        if: ${{ matrix.cibw_python }} == "cp313t"
+        run: |
+          PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
+          CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
+                     pip install numpy pytest meson-python ninja"
+          NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
+          echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BEFORE_TEST=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BUILD_FRONTEND=$NO_BUILD_ISOLATION" >> "$GITHUB_ENV"
+
       - name: Build the wheel
-        uses: pypa/cibuildwheel@8d945475ac4b1aac4ae08b2fd27db9917158b6ce # 2.17.0
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         with:
           output-dir: dist
         env:
           CIBW_BUILD: ${{ matrix.cibw_python }}-*
           CIBW_ARCHS_LINUX: ${{ matrix.cibw_arch }}
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
-          CIBW_MUSLLINUX_X86_64_IMAGE: musllinux_1_1
-      - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+          CIBW_MUSLLINUX_X86_64_IMAGE: musllinux_1_2
+          CIBW_FREE_THREADED_SUPPORT: True
+      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
         with:
           name: wheels_linux_${{ matrix.cibw_arch }}_${{ matrix.cibw_python }}
           path: ./dist/*.whl
@@ -66,7 +79,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest]
-        cibw_python: ["cp310", "cp311", "cp312"]
+        cibw_python: ["cp310", "cp311", "cp312", "cp313"]
         cibw_arch: ["aarch64"]
     steps:
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
@@ -80,16 +93,17 @@ jobs:
         uses: docker/setup-qemu-action@v3
         with:
           platforms: arm64
+
       - name: Build the wheel
-        uses: pypa/cibuildwheel@8d945475ac4b1aac4ae08b2fd27db9917158b6ce # 2.17.0
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         with:
           output-dir: dist
         env:
           CIBW_BUILD: ${{ matrix.cibw_python }}-*
           CIBW_ARCHS_LINUX: ${{ matrix.cibw_arch }}
           CIBW_MANYLINUX_AARCH64_IMAGE: manylinux2014
-          CIBW_MUSLLINUX_AARCH64_IMAGE: musllinux_1_1
-      - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+          CIBW_MUSLLINUX_AARCH64_IMAGE: musllinux_1_2
+      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
         with:
           name: wheels_linux_${{ matrix.cibw_arch }}_${{ matrix.cibw_python }}
           path: ./dist/*.whl
@@ -102,13 +116,16 @@ jobs:
       matrix:
         # macos-13 is the last runner that supports Intel (x86_64) architecture
         os: [macos-13, macos-14]
-        cibw_python: ["cp310", "cp311", "cp312"]
+        cibw_python: ["cp310", "cp311", "cp312", "cp313", "cp313t"]
         cibw_arch: ["x86_64", "arm64"]
         exclude:
           - os: macos-14
             cibw_arch: "x86_64"
           - os: macos-13
             cibw_arch: "arm64"
+          - os: macos-13
+            cibw_arch: "x86_64"
+            cibw_python: "cp313t"
     steps:
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
@@ -119,9 +136,20 @@ jobs:
         with:
           python-version: "3.12"
 
+      - name: Install build deps; set CIBW environment variables
+        if: ${{ matrix.cibw_python }} == "cp313t"
+        run: |
+          PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
+          CIBW_DEPS="pip install --pre -i $PYPI_URL cython scipy &&\
+                     pip install numpy pytest meson-python ninja"
+          NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
+          echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BEFORE_TEST=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BUILD_FRONTEND=$NO_BUILD_ISOLATION" >> "$GITHUB_ENV"
+
       - name: Build wheels for CPython (macOS) (x86_64)
         if: matrix.cibw_arch == 'x86_64'
-        uses: pypa/cibuildwheel@8d945475ac4b1aac4ae08b2fd27db9917158b6ce # 2.17.0
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         with:
           output-dir: dist
         env:
@@ -130,14 +158,15 @@ jobs:
 
       - name: Build wheels for CPython (macOS) (arm64)
         if: matrix.cibw_arch == 'arm64'
-        uses: pypa/cibuildwheel@8d945475ac4b1aac4ae08b2fd27db9917158b6ce # 2.17.0
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         with:
           output-dir: dist
         env:
           CIBW_BUILD: ${{ matrix.cibw_python }}-*
           CIBW_ARCHS_MACOS: ${{ matrix.cibw_arch }}
+          CIBW_FREE_THREADED_SUPPORT: True
 
-      - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
         with:
           name: wheels_macos_${{ matrix.cibw_arch }}_${{ matrix.cibw_python }}
           path: ./dist/*.whl
@@ -151,7 +180,7 @@ jobs:
       matrix:
         os: [windows-latest]
         cibw_arch: ["AMD64", "x86"]
-        cibw_python: ["cp310", "cp311", "cp312"]
+        cibw_python: ["cp310", "cp311", "cp312", "cp313", "cp313t"]
     steps:
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
@@ -174,15 +203,28 @@ jobs:
         with:
           architecture: x64
 
+      - name: Install build deps; set CIBW environment variables
+        if: ${{ matrix.cibw_python }} == "cp313t"
+        shell: bash -el {0}
+        run: |
+          PYPI_URL="https://pypi.anaconda.org/scientific-python-nightly-wheels/simple"
+          CIBW_DEPS="pip install --pre -i $PYPI_URL cython numpy &&\
+                     pip install pytest meson-python ninja"
+          NO_BUILD_ISOLATION="pip; args: --no-build-isolation"
+          echo "CIBW_BEFORE_BUILD=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BEFORE_TEST=$CIBW_DEPS" >> "$GITHUB_ENV"
+          echo "CIBW_BUILD_FRONTEND=$NO_BUILD_ISOLATION" >> "$GITHUB_ENV"
+
       - name: Build Windows wheels for CPython
-        uses: pypa/cibuildwheel@8d945475ac4b1aac4ae08b2fd27db9917158b6ce # 2.17.0
+        uses: pypa/cibuildwheel@7940a4c0e76eb2030e473a5f864f291f63ee879b # v2.21.3
         with:
           output-dir: dist
         env:
           CIBW_BUILD: ${{ matrix.cibw_python }}-*
           CIBW_ARCHS_WINDOWS: ${{ matrix.cibw_arch }}
+          CIBW_FREE_THREADED_SUPPORT: True
 
-      - uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      - uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4.4.3
         with:
           name: wheels_windows_${{ matrix.cibw_arch }}_${{ matrix.cibw_python }}
           path: ./dist/*.whl
@@ -216,7 +258,7 @@ jobs:
           pip install twine
           pip install cython numpy build
 
-      - uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      - uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         id: download
         with:
           pattern: "wheels_*"
@@ -237,7 +279,7 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.TWINE_TOKEN }}
 
       - name: Github release
-        uses: softprops/action-gh-release@9d7c94cfd0a1f3ed45544c887983e9fa900f0564 # v2.0.4
+        uses: softprops/action-gh-release@e7a8f85e1c67a31e6ed99a94b41bd0b71bbee6b8 # v2.0.9
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_REPOSITORY: ${{ github.repository }}
@@ -263,15 +305,15 @@ jobs:
         with:
           fetch-depth: 0
 
-      - uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      - uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
         id: download
         with:
           pattern: "wheels_*"
           path: dist/
           merge-multiple: true
 
       - name: Push to Anaconda PyPI index
-        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # v0.5.0
+        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b # v0.6.1
         with:
           artifacts_path: dist/
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_ORG_UPLOAD_TOKEN }}