chore: CI for windows

.github/actions/build-gk/action.yaml

@@ -38,12 +38,26 @@ runs:
 
     - name: create build env
       if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
-      shell: bash -l -e {0}
+      shell: bash
       run: |
+        set -e
+        if [[ "$RUNNER_OS" != "Windows" ]]; then
+          source ${HOME}/.bash_profile 2>/dev/null || true
+        fi
+        # Determine env directory
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+          ENV_DIR="$MAMBA_ROOT_PREFIX/envs/build"
+        else
+          ENV_DIR="${HOME}/micromamba/envs/build"
+        fi
         set -x
-        # boa required for the mambabuild subcommand
-        if [ ! -d "${HOME}/micromamba/envs/build" ]; then
-          micromamba create -yqn build -c conda-forge boa==0.17.0 mamba==1.5.8 conda=24.5 ccache
+        if [ ! -d "$ENV_DIR" ]; then
+          # boa required for the mambabuild subcommand
+          PKGS="boa==0.17.0 mamba==1.5.8 conda=24.5"
+          if [[ "$RUNNER_OS" != "Windows" ]]; then
+            PKGS="$PKGS ccache"
+          fi
+          micromamba create -yqn build -c conda-forge $PKGS
         fi
         set +x
 
@@ -53,7 +67,7 @@ runs:
         env: build
 
     - name: save mamba gk ccache
-      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' && runner.os != 'Windows' }}
       id: save_mamba_gk_ccache
       uses: actions/cache@v4
       with:
@@ -65,9 +79,10 @@ runs:
           ~/.ccache
 
     - name: set compiler cache size
-      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
-      shell: bash -l -e {0}
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' && runner.os != 'Windows' }}
+      shell: bash
       run: |
+        source ${HOME}/.bash_profile 2>/dev/null || true
         set -x
         micromamba activate build
         ccache -M 100M
@@ -76,14 +91,24 @@ runs:
 
     - if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       name: build conda package
-      shell: bash -l -e {0}
+      shell: bash
       run: |
+        set -e
+        if [[ "$RUNNER_OS" != "Windows" ]]; then
+          source ${HOME}/.bash_profile 2>/dev/null || true
+        fi
         set -x
-        micromamba activate build
-        mkdir ~/conda-bld
-        conda mambabuild --croot ~/conda-bld -q --no-test conda-recipe
-        conda build --croot ~/conda-bld purge
-        conda clean -it
+        mkdir -p ~/conda-bld
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+          micromamba run -n build conda mambabuild --croot ~/conda-bld -q --no-test conda-recipe
+          micromamba run -n build conda build --croot ~/conda-bld purge
+          micromamba run -n build conda clean -it
+        else
+          micromamba activate build
+          conda mambabuild --croot ~/conda-bld -q --no-test conda-recipe
+          conda build --croot ~/conda-bld purge
+          conda clean -it
+        fi
 
     - name: cache mamba env
       if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}

.github/actions/configure-conda/action.yaml

@@ -7,17 +7,29 @@ inputs:
 runs:
   using: "composite"
   steps:
-    - shell: bash -l -e {0}
+    - shell: bash
       run: |
-        source ${HOME}/.bash_profile # for macos
-        set -x
-        if [ ! -e "${HOME}/.condarc" ]; then
+        set -eo pipefail
+        # Determine condarc location and how to run conda commands
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+          CONDARC="$USERPROFILE/.condarc"
+          PKGS_ROOT="$MAMBA_ROOT_PREFIX"
+          RUN_PREFIX="micromamba run -n ${{ inputs.env }}"
+        else
+          source ${HOME}/.bash_profile 2>/dev/null || true  # for macos
+          CONDARC="${HOME}/.condarc"
+          PKGS_ROOT="${HOME}/micromamba"
           micromamba activate ${{ inputs.env }}
-          conda config --set always_yes yes --set changeps1 no --set auto_update_conda no
+          RUN_PREFIX=""
+        fi
+
+        set -x
+        if [ ! -e "$CONDARC" ]; then
+          $RUN_PREFIX conda config --set always_yes yes --set changeps1 no --set auto_update_conda no
           # cache additional pkgs separately from docker pre-install
-          conda config --prepend pkgs_dirs ${HOME}/micromamba/envs/${{ inputs.env }}/pkgs
+          $RUN_PREFIX conda config --prepend pkgs_dirs "$PKGS_ROOT/envs/${{ inputs.env }}/pkgs"
           # fallback to docker pre-installed packages
-          conda config --append pkgs_dirs ${HOME}/micromamba/pkgs
-          conda config --prepend channels conda-forge
+          $RUN_PREFIX conda config --append pkgs_dirs "$PKGS_ROOT/pkgs"
+          $RUN_PREFIX conda config --prepend channels conda-forge
         fi
         set +x

.github/actions/curl-meta-yaml/action.yaml

@@ -3,8 +3,9 @@ description: 'Download meta.yaml from the conda-forge GK feedstock'
 runs:
   using: "composite"
   steps:
-    - shell: bash -l -e {0}
+    - shell: bash
       run: |
+        set -euo pipefail
         # Fail if on main branch and conda-recipe/meta.yaml exists
         if [[ "${GITHUB_REF_NAME}" == "main" && -f "conda-recipe/meta.yaml" ]]; then
           echo "ERROR: conda-recipe/meta.yaml should not be committed to main. Failing build."

.github/actions/install-mamba/action.yaml

@@ -1,22 +1,43 @@
 name: 'Install Mamba'
-description: 'Install Mamba'
+description: 'Install micromamba'
 inputs:
   installer-url:
     description: 'Installer URL'
     required: true
 runs:
   using: "composite"
   steps:
-    - shell: bash -l -e {0}
+    - shell: bash
       run: |
-        set -x
-        if [ ! -e ${HOME}/bin/micromamba ]; then
-          echo "Downloading ${{inputs.installer-url}}"
-          curl --retry 5 -Lfs "${{ inputs.installer-url }}" | tar -xvj -C ${HOME}/ bin/micromamba
+        set -eux
+        if [[ "$RUNNER_OS" == "Windows" ]]; then
+          MAMBA_DIR="$USERPROFILE/micromamba"
+          MAMBA_EXE="$MAMBA_DIR/micromamba.exe"
+          if [ ! -e "$MAMBA_EXE" ]; then
+            echo "Downloading ${{ inputs.installer-url }}"
+            ARCHIVE="$RUNNER_TEMP/micromamba.tar.bz2"
+            EXTRACT_DIR="$RUNNER_TEMP/micromamba-extract"
+            curl --retry 5 -Lfs -o "$ARCHIVE" "${{ inputs.installer-url }}"
+            mkdir -p "$EXTRACT_DIR" "$MAMBA_DIR"
+            # Git Bash tar can't handle Windows drive-letter paths (the colon
+            # is interpreted as a remote host separator), so use 7z instead.
+            7z x "$ARCHIVE" -o"$EXTRACT_DIR" -y > /dev/null
+            7z x "$EXTRACT_DIR"/*.tar -o"$EXTRACT_DIR" -y > /dev/null
+            cp "$EXTRACT_DIR/Library/bin/micromamba.exe" "$MAMBA_EXE"
+            [ -e "$MAMBA_EXE" ] || { echo "micromamba.exe not found after extraction"; exit 1; }
+            echo "micromamba installed at $MAMBA_EXE"
+          fi
+          # Add to PATH and set MAMBA_ROOT_PREFIX for subsequent steps
+          echo "$MAMBA_DIR" >> "$GITHUB_PATH"
+          echo "MAMBA_ROOT_PREFIX=$MAMBA_DIR" >> "$GITHUB_ENV"
+        else
+          if [ ! -e ${HOME}/bin/micromamba ]; then
+            echo "Downloading ${{ inputs.installer-url }}"
+            curl --retry 5 -Lfs "${{ inputs.installer-url }}" | tar -xvj -C ${HOME}/ bin/micromamba
+          fi
+          # `command -vp` and `hash` don't work on macos for some reason
+          if ! grep -F "bin/micromamba shell hook -s posix" ${HOME}/.bash_profile >/dev/null 2>&1 ; then
+            echo "Adding micromamba init to bash profile"
+            echo "$(~/bin/micromamba shell hook -s posix)" >> ${HOME}/.bash_profile
+          fi
         fi
-        # `command -vp` and `hash` don't work on macos for some reason
-        if ! grep -F "bin/micromamba shell hook -s posix" ${HOME}/.bash_profile >/dev/null 2>&1 ; then
-          echo "Adding micromamba init to bash profile"
-          echo "$(~/bin/micromamba shell hook -s posix)" >> ${HOME}/.bash_profile
-        fi
-        set +x

.github/workflows/build-wheels.yaml

@@ -125,6 +125,112 @@ jobs:
           path: wheelhouse/*.whl
 
 
+  build-wheel-windows:
+    name: Build windows wheels
+    runs-on: windows-2022
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: try to restore the windows wheels cache
+        id: restore_windows_wheels
+        uses: actions/cache/restore@v4
+        with:
+          key: windows-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          path: wheelhouse/*.whl
+
+      # skip remaining steps on cache hit
+
+      - if: ${{ steps.restore_windows_wheels.outputs.cache-hit != 'true' }}
+        name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.12'
+
+
+      - if: ${{ steps.restore_windows_wheels.outputs.cache-hit != 'true' }}
+        name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.23.3
+
+      - if: ${{ steps.restore_windows_wheels.outputs.cache-hit != 'true' }}
+        name: Build wheels
+        run: python -m cibuildwheel --output-dir wheelhouse && dir wheelhouse\
+        env:
+          GK_BUILD_WHEELS: "1"
+          CIBW_BUILD: "cp310-* cp311-* cp312-* cp313-*"
+          CIBW_ARCHS_WINDOWS: AMD64
+          CIBW_ENVIRONMENT_PASS_WINDOWS: GK_BUILD_WHEELS
+          CIBW_ENVIRONMENT_WINDOWS: >-
+            INCLUDE="C:\\vcpkg\\installed\\x64-windows-static\\include"
+            LIB="C:\\vcpkg\\installed\\x64-windows-static\\lib"
+          CIBW_BEFORE_BUILD_WINDOWS: vcpkg install zlib:x64-windows-static
+          CIBW_BUILD_VERBOSITY: "3"
+
+      - if: ${{ steps.restore_windows_wheels.outputs.cache-hit != 'true' }}
+        name: cache windows wheels
+        uses: actions/cache/save@v4
+        with:
+          key: ${{ steps.restore_windows_wheels.outputs.cache-primary-key }}
+          path: wheelhouse/*.whl
+
+
+  test-wheel-windows:
+    needs: build-wheel-windows
+    name: Test wheels on windows / Python ${{ matrix.pyver }}
+    runs-on: windows-2022
+    strategy:
+      matrix:
+        include:
+          - {"pyver": "3.10", "pyvershort": "310"}
+          - {"pyver": "3.11", "pyvershort": "311"}
+          - {"pyver": "3.12", "pyvershort": "312"}
+          - {"pyver": "3.13", "pyvershort": "313"}
+
+    steps:
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.pyver }}
+
+      - uses: actions/checkout@v4
+
+      - name: Download built wheels
+        uses: actions/cache/restore@v4
+        with:
+          key: windows-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          path: wheelhouse/*.whl
+          fail-on-cache-miss: true
+
+      - name: Install wheel
+        shell: bash
+        run: |
+          wheel=$(ls wheelhouse/*cp${{ matrix.pyvershort }}*win*.whl | head -1)
+          echo "Installing wheel: $wheel"
+          pip install "$wheel"
+
+      # separate step from above b/c GITHUB_PATH updates don't take effect until the next step
+      - name: Verify GK loads
+        shell: bash
+        run: |
+          cd "$RUNNER_TEMP"
+          python -c "import genome_kit; print(genome_kit.__version__)"
+
+      - name: Run unit tests
+        shell: bash
+        run: |
+          # Run from a temp dir so that the local genome_kit/ source folder
+          # doesn't shadow the installed wheel.
+          test_dir="$RUNNER_TEMP/gk_tests"
+          mkdir -p "$test_dir"
+          cp -r tests "$test_dir/tests"
+          cd "$test_dir"
+          for f in tests/test_*.py; do
+            module="tests.$(basename "$f" .py)"
+            echo "Running: $module"
+            CI=1 python -m unittest "$module" || exit $?
+          done
+
+
   test-wheel-macos:
     needs: build-wheel-macos
     name: Test wheels on ${{ matrix.os }}
@@ -215,6 +321,14 @@ jobs:
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
+#      - name: Restore the windows wheels cache
+#        id: restore_windows_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: windows-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          path: wheelhouse/*.whl
+#          fail-on-cache-miss: true
+#
 #      - name: Debug see what's in wheelhouse dir
 #        run: |
 #          set -euxo pipefail
@@ -231,7 +345,7 @@ jobs:
 
   publish-to-pypi:
     name: Publish to PyPI
-    needs: [build-wheel-linux, test-wheel-macos]
+    needs: [build-wheel-linux, test-wheel-macos, test-wheel-windows]
     runs-on: ubuntu-latest
 
     environment:
@@ -268,6 +382,14 @@ jobs:
           path: wheelhouse/*.whl
           fail-on-cache-miss: true
 
+      - name: Restore the windows wheels cache
+        id: restore_windows_wheels
+        uses: actions/cache/restore@v4
+        with:
+          key: windows-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+          path: wheelhouse/*.whl
+          fail-on-cache-miss: true
+
       - name: Publish distribution to PyPI
         # don't use a version tag with 3rd party actions
         uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc