Try setting up CI for Python bindings tests (#180)

.github/workflows/flatgfa-py.yml

@@ -0,0 +1,148 @@
+# This file is autogenerated by maturin v1.5.1
+# To update, run
+#
+#    maturin generate-ci github --pytest -m flatgfa-py/Cargo.toml -o .github/workflows/flatgfa-py.yml
+#
+name: flatgfa-py CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    paths:
+      - "flatgfa-py/**"
+
+permissions:
+  contents: read
+
+jobs:
+  linux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path flatgfa-py/Cargo.toml
+          sccache: "true"
+          manylinux: auto
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'x86_64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install flatgfa --find-links dist --force-reinstall
+          pip install pytest
+          cd flatgfa-py && pytest
+
+  windows:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: windows-latest
+            target: x64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+          architecture: ${{ matrix.platform.target }}
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path flatgfa-py/Cargo.toml
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-windows-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ !startsWith(matrix.platform.target, 'aarch64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install flatgfa --find-links dist --force-reinstall
+          pip install pytest
+          cd flatgfa-py && pytest
+
+  macos:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: macos-latest
+            target: x86_64
+          - runner: macos-latest
+            target: aarch64
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --manifest-path flatgfa-py/Cargo.toml
+          sccache: "true"
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-macos-${{ matrix.platform.target }}
+          path: dist
+      - name: pytest
+        if: ${{ startsWith(matrix.platform.target, 'aarch64') }}
+        shell: bash
+        run: |
+          set -e
+          pip install flatgfa --find-links dist --force-reinstall
+          pip install pytest
+          cd flatgfa-py && pytest
+
+  sdist:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Build sdist
+        uses: PyO3/maturin-action@v1
+        with:
+          command: sdist
+          args: --out dist --manifest-path flatgfa-py/Cargo.toml
+      - name: Upload sdist
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-sdist
+          path: dist
+
+  release:
+    name: Release
+    runs-on: ubuntu-latest
+    if: "startsWith(github.ref, 'refs/tags/')"
+    needs: [linux, windows, macos, sdist]
+    steps:
+      - uses: actions/download-artifact@v4
+      - name: Publish to PyPI
+        uses: PyO3/maturin-action@v1
+        env:
+          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
+        with:
+          command: upload
+          args: --non-interactive --skip-existing wheels-*/*

flatgfa-py/pyproject.toml

@@ -1,3 +1,22 @@
+[project]
+name = "flatgfa"
+version = "0.1.0"
+description = "efficient processing of pangenomes in Graphical Fragment Assembly (GFA) format"
+readme = "README.md"
+requires-python = ">=3.8"
+license = "MIT"
+keywords = ["genomics", "pangenomics", "gfa"]
+classifiers = [
+    "Scientific/Engineering :: Bio-Informatics",
+    "OSI Approved :: MIT License",
+]
+
+[project.urls]
+repository = "https://github.com/cucapra/pollen"
+
+[project.optional-dependencies]
+test = ["pytest"]
+
 [build-system]
 requires = ["maturin>=1.0,<2.0"]
 build-backend = "maturin"