feat: support python 313 (wip)

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

@@ -24,23 +24,26 @@ runs:
       id: restore_gk_pkg
       uses: actions/cache/restore@v4
       with:
-        key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+        key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
         path: |
           ~/conda-bld
 
+      # skip remaining steps (except configure-conda) on cache hit
+
     - name: install mamba
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       uses: ./.github/actions/install-mamba
       with:
         installer-url: https://micro.mamba.pm/api/micromamba/${{ inputs.platform }}/1.5.8
 
     - name: create build env
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       shell: bash -l -e {0}
       run: |
         set -x
+        # boa required for the mambabuild subcommand
         if [ ! -d "${HOME}/micromamba/envs/build" ]; then
-          micromamba create -yqn build -c conda-forge \
-            boa==0.17.0 mamba==1.5.8 conda=24.5 \
-            ccache
+          micromamba create -yqn build -c conda-forge boa==0.17.0 mamba==1.5.8 conda=24.5 ccache
         fi
         set +x
 
@@ -50,6 +53,7 @@ runs:
         env: build
 
     - name: save mamba gk ccache
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_mamba_gk_ccache
       uses: actions/cache@v4
       with:
@@ -61,6 +65,7 @@ runs:
           ~/.ccache
 
     - name: set compiler cache size
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       shell: bash -l -e {0}
       run: |
         set -x
@@ -81,6 +86,7 @@ runs:
         conda clean -it
 
     - name: cache mamba env
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_mamba_cache
       uses: actions/cache/save@v4
       with:
@@ -91,9 +97,10 @@ runs:
           ~/bin/micromamba
 
     - name: cache gk package tarballs
+      if: ${{ steps.restore_gk_pkg.outputs.cache-hit != 'true' }}
       id: save_gk_pkg
       uses: actions/cache/save@v4
       with:
-        key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+        key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
         path: |
           ~/conda-bld

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

@@ -5,21 +5,41 @@ runs:
   steps:
     - shell: bash -l -e {0}
       run: |
+        # Fail if on main branch and conda-recipe/meta.yaml exists
+        if [[ "${GITHUB_REF_NAME}" == "main" && -f "conda-recipe/meta.yaml" ]]; then
+          echo "ERROR: conda-recipe/meta.yaml should not be committed to main. Failing build."
+          exit 1
+        fi
+
         set -x
         mkdir -p conda-recipe
-        curl -s -L -o conda-recipe/meta.yaml https://raw.githubusercontent.com/conda-forge/genomekit-feedstock/main/recipe/meta.yaml
+
+        # If meta.yaml exists, use it (to allow quick iteration in feature branches)
+        if [[ -f "conda-recipe/meta.yaml" ]]; then
+          echo "WARN: Using existing conda-recipe/meta.yaml"
+        else
+          curl -s -L -o conda-recipe/meta.yaml https://raw.githubusercontent.com/conda-forge/genomekit-feedstock/main/recipe/meta.yaml
+        fi
+
         export GK_VERSION=$(grep "version = " setup.py | awk -F'"' '{print $2}')
 
         export OS_TYPE=$(uname)
-        # - replace the (non-existent) tarball with local path
-        # - remove the related sha for that tarball
-        # - build for all locally allowed versions of python (conda-recipe/conda_build_config.yaml)
-        # - set the version to the local release-please version (for docs and docker publish)
         if [[ "$OS_TYPE" == "Darwin" ]]; then
-          sed -i '' -E "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1; /sha256: /d; /skip: true /d;s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+          SED_CMD="sed -i '' -E"
         else
-          sed -i -e    "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1; /sha256: /d; /skip: true /d;s/{% set version = \".\+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+          SED_CMD="sed -i"
         fi
+        # replace the (non-existent) tarball with local path
+        $SED_CMD "s|url: https://github.com/deepgenomics/GenomeKit/archive/refs/tags/v.*$|path: ../|1" conda-recipe/meta.yaml
+        # remove the related sha for that tarball
+        $SED_CMD "/sha256: /d" conda-recipe/meta.yaml
+        # build for all locally allowed versions of python (conda-recipe/conda_build_config.yaml)
+        $SED_CMD "/skip: true /d" conda-recipe/meta.yaml
+        # set the version to the local release-please version (for docs and docker publish)
+        $SED_CMD "s/{% set version = \".+\" %}/{% set version = \"${GK_VERSION}\" %}/" conda-recipe/meta.yaml
+        # avoid error "No module named 'setup'" due to "from setup import c_ext" in setup.py
+        # See if this can be removed
+        # $SED_CMD "s/script: {{ PYTHON }} -m pip install --no-deps --ignore-installed ./script: PYTHONPATH=. {{ PYTHON }} -m pip install --no-deps --ignore-installed ./" conda-recipe/meta.yaml
 
-        head -10 conda-recipe/meta.yaml
+        head -40 conda-recipe/meta.yaml
         set +x

.github/workflows/build-wheels.yaml

@@ -5,12 +5,14 @@ on:
   push:
     # only build+push docker on release-please tags
     tags: [ "v*" ]
+    branches:
+      - feat/py313
     paths:
     - ".github/actions/**"
     - ".github/workflows/**"
     - "genome_kit/**"
     - "setup.py"
-    - "_pyproject.toml"
+    - "pyproject.toml"
     - "setup/**"
     - "src/**"
     - "tests/**"
@@ -33,20 +35,16 @@ jobs:
         id: restore_linux_wheels
         uses: actions/cache/restore@v4
         with:
-          key: linux-wheels-${{ matrix.arch }}-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: linux-wheels-${{ matrix.arch }}-${{ 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_linux_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
         name: Install cibuildwheel
@@ -57,19 +55,19 @@ jobs:
         run: python -m cibuildwheel --output-dir wheelhouse && ls -l wheelhouse/
         env:
           GK_BUILD_WHEELS: "1"
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-*"
           CIBW_ARCHS_LINUX: ${{ matrix.arch }}
           CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
           CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
           CIBW_ENVIRONMENT_PASS_LINUX: GK_BUILD_WHEELS
           CIBW_SKIP: "*-musllinux_*"
 
       - if: ${{ steps.restore_linux_wheels.outputs.cache-hit != 'true' }}
-        name: Test wheels across Python 3.9–3.12
+        name: Test wheels across Python 3.9–3.13
         run: |
           set -euxo pipefail
 
-          for PYVER in 3.9 3.10 3.11 3.12; do
+          for PYVER in 3.9 3.10 3.11 3.12 3.13; do
             PYVER_SHORT=${PYVER/./}
             echo "Testing on Python $PYVER"
 
@@ -106,20 +104,16 @@ jobs:
         id: restore_macos_wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-wheels-${{ 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_macos_wheels.outputs.cache-hit != 'true' }}
-        name: Rename pyproject.toml
-        run: mv _pyproject.toml pyproject.toml
-
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.12'
+          python-version: '3.13'
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: Install cibuildwheel
@@ -131,7 +125,7 @@ jobs:
         env:
           GK_BUILD_WHEELS: "1"
           CIBW_ARCHS_MACOS: x86_64 arm64
-          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
+          CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-* cp313-macosx_arm64"
 
       - if: ${{ steps.restore_macos_wheels.outputs.cache-hit != 'true' }}
         name: cache macos wheels
@@ -154,6 +148,7 @@ jobs:
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.10", "pyvershort": "310"}
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.11", "pyvershort": "311"}
           - {"os": "macos-14", "arch": "arm64", "pyver": "3.12", "pyvershort": "312"}
+          - {"os": "macos-14", "arch": "arm64", "pyver": "3.13", "pyvershort": "313"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.9", "pyvershort": "39"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.10", "pyvershort": "310"}
           - {"os": "macos-13", "arch": "x86_64", "pyver": "3.11", "pyvershort": "311"}
@@ -170,7 +165,7 @@ jobs:
       - name: Download built wheels
         uses: actions/cache/restore@v4
         with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+          key: macos-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
 
@@ -212,23 +207,23 @@ jobs:
 #        id: restore_linux_intel_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-x86_64-${{ 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: Restore the linux arm wheels cache
 #        id: restore_linux_arm_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: linux-wheels-aarch64-${{ 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: Restore the macos wheels cache
 #        id: restore_macos_wheels
 #        uses: actions/cache/restore@v4
 #        with:
-#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
+#          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
 #          path: wheelhouse/*.whl
 #          fail-on-cache-miss: true
 #
@@ -246,48 +241,48 @@ jobs:
 #          verbose: 'true'
 #          skip-existing: 'true'
 
-  publish-to-pypi:
-    name: Publish to PyPI
-    needs: [build-wheel-linux, test-wheel-macos]
-    runs-on: ubuntu-latest
-
-    environment:
-      name: pypi
-      url: https://pypi.org/p/genomekit
-
-    permissions:
-      id-token: write  # mandatory for trusted publishing
-
-    steps:
-      - uses: actions/checkout@v4
-
-      - name: Restore the linux intel wheels cache
-        id: restore_linux_intel_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: linux-wheels-x86_64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
-          path: wheelhouse/*.whl
-          fail-on-cache-miss: true
-
-      - name: Restore the linux arm wheels cache
-        id: restore_linux_arm_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: linux-wheels-aarch64-${{ 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: Restore the macos wheels cache
-        id: restore_macos_wheels
-        uses: actions/cache/restore@v4
-        with:
-          key: macos-wheels-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', '_pyproject.toml', 'setup.py', 'setup/**') }}
-          path: wheelhouse/*.whl
-          fail-on-cache-miss: true
-
-      - name: Publish distribution to PyPI
-        # don't use a version tag with 3rd party actions
-        uses: pypa/gh-action-pypi-publish@76f52bc884231f62b9a034ebfe128415bbaabdfc
-        with:
-          packages-dir: wheelhouse
-          verbose: 'true'
+#  publish-to-pypi:
+#    name: Publish to PyPI
+#    needs: [build-wheel-linux, test-wheel-macos]
+#    runs-on: ubuntu-latest
+#
+#    environment:
+#      name: pypi
+#      url: https://pypi.org/p/genomekit
+#
+#    permissions:
+#      id-token: write  # mandatory for trusted publishing
+#
+#    steps:
+#      - uses: actions/checkout@v4
+#
+#      - name: Restore the linux intel wheels cache
+#        id: restore_linux_intel_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: linux-wheels-x86_64-${{ 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: Restore the linux arm wheels cache
+#        id: restore_linux_arm_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: linux-wheels-aarch64-${{ hashFiles('.github/workflows/build-wheels.yaml', '.github/actions/**', 'src/**', 'genome_kit/**', 'pyproject.toml', 'setup.py', 'setup/**') }}
+#          path: wheelhouse/*.whl
+#          fail-on-cache-miss: true
+#
+#      - name: Restore the macos wheels cache
+#        id: restore_macos_wheels
+#        uses: actions/cache/restore@v4
+#        with:
+#          key: macos-wheels-${{ 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
+#        with:
+#          packages-dir: wheelhouse
+#          verbose: 'true'

.github/workflows/dockerize.yaml

@@ -39,7 +39,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true

.github/workflows/publish-docs.yaml

@@ -40,7 +40,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true

.github/workflows/run-tests.yaml

@@ -39,6 +39,8 @@ jobs:
           - {"pyver-short": "311", "python-version": "3.11", "platform": "osx-64", "runs-on": "macos-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "linux-64", "runs-on": "ubuntu-latest"}
           - {"pyver-short": "312", "python-version": "3.12", "platform": "osx-64", "runs-on": "macos-latest"}
+          - {"pyver-short": "313", "python-version": "3.13", "platform": "linux-64", "runs-on": "ubuntu-latest"}
+          - {"pyver-short": "313", "python-version": "3.13", "platform": "osx-64", "runs-on": "macos-latest"}
     runs-on: ${{ matrix.runs-on }}
     steps:
       - uses: actions/checkout@v4
@@ -61,7 +63,7 @@ jobs:
         id: restore_gk_pkg
         uses: actions/cache/restore@v4
         with:
-          key: mamba-env-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
+          key: gk-tarballs-${{ runner.os }}-${{ runner.arch }}-${{ hashFiles('.github/workflows/run-tests.yaml', '.github/actions/**', 'conda-recipe/**', 'src/**', 'genome_kit/**', 'setup.py', 'setup/**', 'tests/**') }}
           path: |
             ~/conda-bld
           fail-on-cache-miss: true
@@ -74,10 +76,12 @@ jobs:
       - name: create test env
         shell: bash -l -e {0}
         run: |
+          # boa required for the mambabuild subcommand
           set -x
+          # inconsistently got "coverage 7.9.1 is not supported on this platform" so removed
+          # (not needed?)
           if [ ! -d "${HOME}/micromamba/envs/test" ]; then
-            micromamba create -yqn test -c conda-forge \
-              boa==0.16.0 mamba==1.5.7 conda==24.1.2 coverage
+            micromamba create -yqn test -c conda-forge boa==0.16.0 mamba==1.5.7 conda==24.1.2
           fi
           set +x