Begin packaging effort

hpc4cmb · Dec 31, 2024 · d9665c5 · d9665c5
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,9 @@
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
@@ -0,0 +1,112 @@
+# Deploy tagged releases.
+
+name:  Deploy Release
+
+on:
+  push:
+    tags:
+      - '*'
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  TWINE_USERNAME: __token__
+  TWINE_PASSWORD: ${{ secrets.TWINE_TOKEN }}
+
+jobs:
+  build_wheels:
+    name: Build wheel for cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails.  Useful for
+      # debugging multiple problems in parallel.
+      fail-fast: false
+      matrix:
+        include:
+          # Linux 64 bit manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 39
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 310
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 311
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 312
+            builder: manylinux
+
+          # MacOS x86_64.  The macos-13 runner is the last
+          # Intel-based runner version.  At some point we'll
+          # need to switch to macos-latest and test cross compiling.
+          - os: macos-13
+            arch: x86_64
+            python: 310
+            builder: macosx
+            deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 311
+            builder: macosx
+            deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 312
+            builder: macosx
+            deploy: 13.0
+
+          # MacOS arm64
+          - os: macos-latest
+            arch: arm64
+            python: 310
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 311
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 312
+            builder: macosx
+            deploy: 14.0
+    env:
+      CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+      CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
+      CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.builder }}2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX:
+      CIBW_ENVIRONMENT_MACOS: >
+        MACOSX_DEPLOYMENT_TARGET=${{ matrix.deploy }}
+      CIBW_BEFORE_BUILD_LINUX: ./packaging/wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./packaging/wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: export OMP_NUM_THREADS=1
+      CIBW_TEST_COMMAND: python3 -c 'import flacarray.tests; flacarray.tests.run()'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install twine cibuildwheel==2.20.0
+
+      - name: Build wheel
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - name: Upload to PyPI
+        run: |
+          python -m twine upload wheelhouse/flacarray*cp${{ matrix.python }}-${{ matrix.builder }}*${{ matrix.arch }}*.whl
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -0,0 +1,106 @@
+# In general, we try to run on:
+# - The oldest supported python
+# - The latest stable python that is the common default on most systems and conda
+# - (During transitions) The newly released bleeding edge python
+
+name:  Run Test Suite
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    name: Tests on ${{ matrix.arch }} with Conda Python-${{ matrix.python }}
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            python: "3.9"
+            arch: Linux-x86_64
+            ompdisable: 0
+          - os: ubuntu-latest
+            python: "3.10"
+            arch: Linux-x86_64
+            ompdisable: 0
+          - os: ubuntu-latest
+            python: "3.12"
+            arch: Linux-x86_64
+            ompdisable: 0
+          - os: macos-latest
+            python: "3.10"
+            arch: MacOSX-x86_64
+            ompdisable: 1
+          - os: macos-latest
+            python: "3.12"
+            arch: MacOSX-x86_64
+            ompdisable: 1
+          - os: macos-latest
+            python: "3.10"
+            arch: MacOSX-arm64
+            ompdisable: 1
+          - os: macos-latest
+            python: "3.12"
+            arch: MacOSX-arm64
+            ompdisable: 1
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Conda Base
+        run: |
+          sudo rm -rf /usr/share/miniconda \
+            && sudo rm -rf /usr/local/miniconda \
+            && curl -SL -o miniforge.sh https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-${{ matrix.arch }}.sh \
+            && bash miniforge.sh -b -f -p ~/conda \
+            && source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && conda update -n base --yes conda
+
+      - name: Check Conda Config
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && conda info \
+            && conda list \
+            && conda config --show-sources \
+            && conda config --show
+
+      - name: Install Dependencies
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && conda install --file packaging/conda_build_requirements.txt
+
+      - name: Install
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && pip install .
+
+      - name: Run Serial Tests
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && export OMP_NUM_THREADS=2 \
+            && python3 -c 'import flacarray.tests; flacarray.tests.run()'
+
+      - name: Run MPI Tests
+        run: |
+          source ~/conda/etc/profile.d/conda.sh \
+            && conda activate base \
+            && export OMP_NUM_THREADS=1 \
+            && mpirun -np 2 python -c 'import flacarray.tests; flacarray.tests.run()'
diff --git a/.github/workflows/wheels.yml b/.github/workflows/wheels.yml
@@ -0,0 +1,108 @@
+
+name:  Test Binary Wheels
+
+on: workflow_dispatch
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build_wheels:
+    name: Build wheel for cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      # Ensure that a wheel builder finishes even if another fails.  Useful for
+      # debugging multiple problems in parallel.
+      fail-fast: false
+      matrix:
+        include:
+          # Linux 64 bit manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 39
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 310
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 311
+            builder: manylinux
+          - os: ubuntu-latest
+            arch: x86_64
+            python: 312
+            builder: manylinux
+
+          # MacOS x86_64.  The macos-13 runner is the last
+          # Intel-based runner version.  At some point we'll
+          # need to switch to macos-latest and test cross compiling.
+          - os: macos-13
+            arch: x86_64
+            python: 310
+            builder: macosx
+            deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 311
+            builder: macosx
+            deploy: 13.0
+          - os: macos-13
+            arch: x86_64
+            python: 312
+            builder: macosx
+            deploy: 13.0
+
+          # MacOS arm64
+          - os: macos-latest
+            arch: arm64
+            python: 310
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 311
+            builder: macosx
+            deploy: 14.0
+          - os: macos-latest
+            arch: arm64
+            python: 312
+            builder: macosx
+            deploy: 14.0
+    env:
+      CIBW_BUILD: cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+      CIBW_MANYLINUX_X86_64_IMAGE: ${{ matrix.builder }}2014
+      CIBW_MANYLINUX_I686_IMAGE: ${{ matrix.builder }}2014
+      CIBW_BUILD_VERBOSITY: 3
+      CIBW_ENVIRONMENT_LINUX:
+      CIBW_ENVIRONMENT_MACOS: >
+        MACOSX_DEPLOYMENT_TARGET=${{ matrix.deploy }}
+      CIBW_BEFORE_BUILD_LINUX: ./packaging/wheels/install_deps_linux.sh
+      CIBW_BEFORE_BUILD_MACOS: ./packaging/wheels/install_deps_osx.sh
+      CIBW_BEFORE_TEST: export OMP_NUM_THREADS=2
+      CIBW_TEST_COMMAND_LINUX: >
+        python -c 'import flacarray.tests; flacarray.tests.run()'
+      CIBW_TEST_COMMAND_MACOS: >
+        python -c 'import flacarray.tests; flacarray.tests.run()'
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        name: Install Python
+        with:
+          python-version: '3.10'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==2.20.0
+
+      - name: Build wheel
+        run: |
+          python -m cibuildwheel --output-dir wheelhouse
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels_cp${{ matrix.python }}-${{ matrix.builder }}_${{ matrix.arch }}
+          path: ./wheelhouse/flacarray*cp${{ matrix.python }}-${{ matrix.builder }}*${{ matrix.arch }}*.whl
diff --git a/.gitignore b/.gitignore
@@ -19,7 +19,6 @@ lib64/
 parts/
 sdist/
 var/
-wheels/
 share/python-wheels/
 *.egg-info/
 .installed.cfg

diff --git a/packaging/conda_build_requirements.txt b/packaging/conda_build_requirements.txt
@@ -0,0 +1,8 @@
+c_compiler
+cmake
+cython
+meson
+meson-python
+libflac
+h5py
+zarr
diff --git a/packaging/pip_build_requirements.txt b/packaging/pip_build_requirements.txt
@@ -0,0 +1,7 @@
+cmake
+cython
+meson
+meson-python
+libflac
+h5py
+zarr
-Original file line number
+Diff line change
@@ Expand Up / @@ -19,7 +19,6 @@ lib64/ @@
     parts/
     sdist/
     var/
-    wheels/
     share/python-wheels/
     *.egg-info/
     .installed.cfg
@@ Expand Down @@