.flake8

@@ -5,14 +5,24 @@ exclude =
 
 max-line-length = 120
 ignore =
-    E203  # whitespace before ':'
-    E266  # too many leading '#' for block comment
-    E501  # line too long
-    W503  # line break before binary operator
+    # whitespace before ':'
+    E203
+    # too many leading '#' for block comment
+    E266
+    # line too long
+    E501
+    # line break before binary operator
+    W503
 select =
-    C  # mccabe complexity
-    E  # pycodestyle
-    F  # pyflakes error
-    W  # pyflakes warning
-    B  # bugbear
-    B950  # line exceeds max-line-length + 10%
+    # mccabe complexity
+    C
+    # pycodestyle
+    E
+    # pyflakes error
+    F
+    # pyflakes warning
+    W
+    # bugbear
+    B
+    # line exceeds max-line-length + 10%
+    B950

.github/workflows/python-build-wheels.yml

@@ -0,0 +1,88 @@
+name: Build wheels
+
+on: [workflow_dispatch]
+
+jobs:
+  make_sdist:
+    name: Make SDist
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0  # Optional, use if you use setuptools_scm
+        submodules: true  # Optional, use if you have submodules
+
+    - name: Install dependencies
+      run: python -m pip install cython numpy pysam
+
+    - name: Build SDist
+      run: pipx run build --sdist
+
+    - uses: actions/upload-artifact@v4
+      with:
+        name: cibw-sdist
+        path: dist/*.tar.gz
+
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # macos-13 is an intel runner, macos-14 is apple silicon
+        os: [ubuntu-latest]
+        #, windows-latest, macos-13, macos-14]
+        python-version: [ "3.11" ] # "3.7", "3.8", "3.9", "3.10",
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      # - name: Build wheels
+      #   uses: pypa/cibuildwheel@v2.21.0
+      #   # uses: pypa/cibuildwheel@v2.17.0
+      #   # env:
+      #   #   CIBW_SOME_OPTION: value
+      #   #    ...
+      #   # with:
+      #   #   package-dir: .
+      #   #   output-dir: wheelhouse
+      #   #   config-file: "{package}/pyproject.toml"
+
+      - name: Install cibuildwheel
+        run: python -m pip install cibuildwheel==2.22.0
+
+      - name: Build wheels
+        run: python -m cibuildwheel --output-dir dist
+        # to supply options, put them in 'env', like:
+        env:
+          #CIBW_BUILD_FRONTEND: "pip; args: --no-build-isolation"
+          CIBW_BUILD_FRONTEND: "build; args: --no-isolation"
+          CIBW_BEFORE_ALL: "yum install bzip2-devel xz-devel -y;"
+
+          # we have to recompile pysam so that repairwheel can later find various libraries (libssl, libnghttp2, etc)
+          #CIBW_BEFORE_ALL: "yum install bzip2-devel xz-devel openssl-devel openldap-devel krb5-devel libssh-devel libnghttp2-devel -y;"
+          CIBW_BEFORE_BUILD: "python -m pip install setuptools cython numpy pysam --no-binary pysam" 
+
+          # skip building 32-bit wheels (i686)
+          CIBW_ARCHS_LINUX: "auto64"
+
+          # we could use 2_28 to download pysam's wheel instead of compiling it ;
+          # HOWEVER THAT DIDN'T WORK BECAUSE PYSAM DEPENDS ON LIBSSL, LIBNGHTTP2, ETC, WHICH CANNOT BE FOUND
+          # SO WE ARE BACK TO COMPILING PYSAM'S WHEEL (no-binary pysam)
+          # CIBW_MANYLINUX_X86_64_IMAGE: "manylinux_2_28"
+
+          ## skip building pypy and musllinux
+          CIBW_SKIP: pp* *musllinux*
+
+          #CIBW_REPAIR_WHEEL_COMMAND: 'auditwheel -v repair -w {dest_dir} {wheel}'
+
+          #PIP_NO_CACHE_DIR: "false"
+          #PIP_NO_BUILD_ISOLATION: "false"
+          #PIP_NO_BINARY: "pysam"
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}-${{ strategy.job-index }}
+          path: ./dist/*.whl

.github/workflows/python-publish-test.yml

@@ -1,32 +1,51 @@
-
-# This workflows will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
 name: Publish Python Package to Test PyPI
 
 on:
-  release:
-    types: [prereleased]
+  # release:
+  #   types: [published]
+  workflow_dispatch:
 
 jobs:
-  deploy:
-
+  publish_all:
+    name: Publish wheels and sdist to Test PyPI
+
+    # if: github.event_name == 'release' && github.event.action == 'published'
+
+    environment: testpypi
+    permissions:
+      id-token: write
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine cython numpy pysam
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist
-        twine upload --repository-url https://test.pypi.org/legacy/ dist/*
+      - uses: dawidd6/action-download-artifact@v7
+        with:
+          # Required, if the repo is private a Personal Access Token with `repo` scope is needed or GitHub token in a job where the permissions `action` scope set to `read`
+          #github_token: ${{secrets.GITHUB_TOKEN}}
+          # Optional, workflow file name or ID
+          # If not specified, will be inferred from run_id (if run_id is specified), or will be the current workflow
+          workflow: python-build-wheels.yml
+          # Optional, the status or conclusion of a completed workflow to search for
+          # Can be one of a workflow conclusion:
+          #   "failure", "success", "neutral", "cancelled", "skipped", "timed_out", "action_required"
+          # Or a workflow status:
+          #   "completed", "in_progress", "queued"
+          # Use the empty string ("") to ignore status or conclusion in the search
+          workflow_conclusion: success
+
+      - name: Publish sdist 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: cibw-sdist
+          repository-url: https://test.pypi.org/legacy/
+
+      - name: Publish wheels 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: cibw-wheels-ubuntu-latest-0
+          repository-url: https://test.pypi.org/legacy/
+
+
+
+
+
+
+

.github/workflows/python-publish.yml

@@ -1,31 +1,48 @@
-# This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
-
-name: Upload Python Package
+name: Publish Python Package to PyPI
 
 on:
-  release:
-    types: [created]
+  # release:
+  #   types: [published]
+  workflow_dispatch:
 
 jobs:
-  deploy:
-
+  publish_all:
+    name: Publish wheels and sdist to  PyPI
+
+    # if: github.event_name == 'release' && github.event.action == 'published'
+
+    environment: pypi
+    permissions:
+      id-token: write
     runs-on: ubuntu-latest
-
     steps:
-    - uses: actions/checkout@v2
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: '3.x'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install setuptools wheel twine cython pysam numpy
-    - name: Build and publish
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        python setup.py sdist
-        twine upload dist/*
+      - uses: dawidd6/action-download-artifact@v7
+        with:
+          # Required, if the repo is private a Personal Access Token with `repo` scope is needed or GitHub token in a job where the permissions `action` scope set to `read`
+          #github_token: ${{secrets.GITHUB_TOKEN}}
+          # Optional, workflow file name or ID
+          # If not specified, will be inferred from run_id (if run_id is specified), or will be the current workflow
+          workflow: python-build-wheels.yml
+          # Optional, the status or conclusion of a completed workflow to search for
+          # Can be one of a workflow conclusion:
+          #   "failure", "success", "neutral", "cancelled", "skipped", "timed_out", "action_required"
+          # Or a workflow status:
+          #   "completed", "in_progress", "queued"
+          # Use the empty string ("") to ignore status or conclusion in the search
+          workflow_conclusion: success
+
+      - name: Publish sdist 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: cibw-sdist
+
+      - name: Publish wheels 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: cibw-wheels-ubuntu-latest-0
+
+
+
+
+
+

.github/workflows/python-package.yml → .github/workflows/python-test.yml

@@ -1,17 +1,21 @@
 # This workflow will install Python dependencies, run tests and lint with a variety of Python versions
 # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
 
-name: Python package
-
-on: push
-
+name: Test build, lint and test
+on:
+  push:
+    branches: [ master ]
+    tags:
+      - "v*"  # Tag events matching v*, i.e. v1.0, v20.15.10
+  pull_request:
+    branches: [ master ]
 jobs:
   build:
 
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2
@@ -21,10 +25,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip wheel setuptools
-        pip install numpy cython pysam
-        pip install -r requirements-dev.txt
-        pip install -e .
+        python -m pip install --upgrade pip wheel setuptools build 
+        pip install cython pysam numpy
+        pip install -e .[test] --no-build-isolation -v -v 
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
@@ -35,3 +38,6 @@ jobs:
       run: |
         pip install pytest
         pytest
+
+
+