deps: remove cffi dependency

.github/workflows/build.yaml

@@ -2,48 +2,100 @@ name: Python package
 
 on: [push]
 
+concurrency:
+  group: ci-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
-  build:
+  lint:
     runs-on: ubuntu-latest
-    timeout-minutes: 60
-    strategy:
-      matrix:
-        python-version: ["3.11"]
-    concurrency:
-      group: ci-${{ github.ref }}
-      cancel-in-progress: true
-
-    defaults:
-      run:
-        shell: bash -l {0}
+    timeout-minutes: 15
 
     steps:
-    - uses: actions/checkout@v2
-    
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
       with:
-        miniconda-version: "latest"
-        mamba-version: "*"
-        environment-file: conda/dev.yaml
-        channels: conda-forge,nodefaults
-        activate-environment: pyreaddbc
-        use-mamba: true
-        miniforge-variant: Mambaforge
-
+        python-version: "3.13"
+
     - name: Install dependencies
       run: |
-        # poetry config experimental.new-installer false
-        poetry config virtualenvs.create false
-        poetry build
-        poetry install
+        pip install -e .
+        pip install flake8
 
     - name: Lint with flake8
       run: |
-        # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
 
+  test:
+    name: test ${{ matrix.os }} py${{ matrix.python-version }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
+    runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies
+      run: |
+        pip install -e .
+        pip install pytest pandas
+
     - name: Test with pytest
       run: |
-        poetry run pytest -vv -k "ZIKABR21 or STPI2206 or sids" tests/
+        python -m pytest -vv -k "ZIKABR21 or STPI2206 or sids" tests/
+
+  coverage:
+    runs-on: ubuntu-latest
+    timeout-minutes: 15
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.13"
+
+    - name: Install dependencies
+      run: |
+        pip install -e .
+        pip install pytest pytest-cov pandas
+
+    - name: Run tests with coverage
+      run: |
+        python -m pytest -vv -k "ZIKABR21 or STPI2206 or sids" --cov=pyreaddbc --cov-report=xml --cov-report=term tests/
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        file: coverage.xml
+        fail_ci_if_error: false
+
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: pypa/cibuildwheel@v2.21
+        env:
+          CIBW_BUILD_VERBOSITY: 2
+
+      - name: Upload wheels as artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: cibw-wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl

.github/workflows/publish.yaml

@@ -0,0 +1,69 @@
+name: publish
+
+on:
+  push:
+    tags:
+      - '*'
+
+jobs:
+  build_wheels:
+    name: Build wheel on ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-13, macos-latest, windows-latest]
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: pypa/cibuildwheel@v2.21
+        env:
+          CIBW_BUILD_VERBOSITY: 2
+          CIBW_ARCHS_LINUX: x86_64 aarch64
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
+          path: wheelhouse/*.whl
+
+  build_sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - run: python -m pip install build && python -m build --sdist
+
+      - uses: actions/upload-artifact@v4
+        with:
+          name: sdist
+          path: dist/*.tar.gz
+
+  publish:
+    needs: [build_wheels, build_sdist]
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      id-token: write
+
+    steps:
+      - name: Download all wheels
+        uses: actions/download-artifact@v4
+        with:
+          pattern: wheels-*
+          merge-multiple: true
+          path: dist/
+
+      - name: Download source distribution
+        uses: actions/download-artifact@v4
+        with:
+          name: sdist
+          path: dist/
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.PYPIPYREADDBCTOKEN }}
+          packages_dir: dist/

.github/workflows/release.yaml

@@ -18,15 +18,14 @@ jobs:
     steps:
     - uses: actions/checkout@v2
 
-    - uses: conda-incubator/setup-miniconda@v2
+    - uses: conda-incubator/setup-miniconda@v3
       with:
-        miniconda-version: "latest"
-        mamba-version: "*"
+        miniforge-version: latest
         environment-file: conda/dev.yaml
         channels: conda-forge,nodefaults
         activate-environment: pyreaddbc
-        use-mamba: true
-        miniforge-variant: Mambaforge
+        auto-update-conda: true
+        conda-solver: libmamba
 
     - uses: actions/setup-node@v3
       with:
@@ -42,7 +41,4 @@ jobs:
       if: ${{ github.event_name == 'workflow_dispatch' }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        PYPI_TOKEN: ${{ secrets.PYPIPYREADDBCTOKEN }}
-      run: |
-        poetry config pypi-token.pypi ${PYPI_TOKEN}
-        make release
+      run: make release

.releaserc.json

@@ -59,8 +59,7 @@
     [
       "@semantic-release/exec",
       {
-        "prepareCmd": "poetry build",
-        "publishCmd": "poetry publish --build"
+        "prepareCmd": "python -m pip install build && python -m build --sdist"
       }
     ],
     [

MANIFEST.in

@@ -0,0 +1 @@
+include pyreaddbc/c-src/blast.h

Makefile

@@ -25,6 +25,10 @@ install:
 test:
 	$(PYTEST) -vv -k "ZIKABR21 or STPI2206 or sids" tests/
 
+.PHONY: coverage
+coverage:
+	$(PYTEST) -vv -k "ZIKABR21 or STPI2206 or sids" --cov=pyreaddbc --cov-report=term --cov-report=xml tests/
+
 
 .PHONY: clean-build
 clean-build: ## Remove build artifacts

conda/dev.yaml

@@ -3,7 +3,6 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - cffi
   - gcc
   - pip
   - poetry