Merge pull request #53 from etowahadams/etowahadams/pypi

feat: Publish to PyPI

Author: TimoLassmann

.github/workflows/wheels.yml

@@ -14,6 +14,15 @@ on:
       - 'pyproject.toml'
       - '.github/workflows/wheels.yml'
   workflow_dispatch:
+    inputs:
+      publish_target:
+        description: "Publish target (manual runs only)"
+        required: true
+        default: "none"
+        type: choice
+        options:
+          - none
+          - testpypi
 
 jobs:
   build_wheels:
@@ -25,9 +34,9 @@ jobs:
         include:
           - os: ubuntu-latest
             cibw_archs: "x86_64"
-          - os: macos-latest
+          - os: macos-14
             cibw_archs: "x86_64"
-          - os: macos-latest
+          - os: macos-14
             cibw_archs: "arm64"
 
     steps:
@@ -122,7 +131,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest, macos-14]
         python-version: ['3.9', '3.10', '3.11', '3.12']
 
     steps:
@@ -144,12 +153,17 @@ jobs:
         echo "=== Available wheels ==="
         ls -la wheelhouse/*.whl
         
+        # Determine the distribution name from the wheel filenames (PEP 427)
+        # e.g. kalign_test-3.4.5-...whl -> kalign-test
+        DIST_NAME="$(ls wheelhouse/*.whl | head -n 1 | xargs basename | cut -d- -f1 | tr '_' '-')"
+        echo "=== Detected dist name: ${DIST_NAME} ==="
+
         echo "=== Installing wheel ==="
-        pip install --find-links wheelhouse/ kalign --force-reinstall
+        pip install --find-links wheelhouse/ "${DIST_NAME}" --force-reinstall
         
         # Check what got installed
         echo "=== Checking installed packages ==="
-        pip list | grep kalign || true
+        pip list | grep -E 'kalign' || true
         
         # Check the kalign module structure
         echo "=== Checking kalign module ==="
@@ -209,6 +223,10 @@ jobs:
     needs: [build_wheels, build_sdist, test_install]
     runs-on: ubuntu-latest
     if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write
+    environment:
+      name: pypi
 
     steps:
     - name: Download all artifacts
@@ -218,9 +236,30 @@ jobs:
         merge-multiple: true
         path: dist/
 
-    - name: Publish to PyPI
+    - name: Publish to PyPI (trusted publishing)
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        packages_dir: dist/
+
+  upload_testpypi:
+    name: Upload to TestPyPI
+    needs: [build_wheels, build_sdist, test_install]
+    runs-on: ubuntu-latest
+    if: github.event_name == 'workflow_dispatch' && inputs.publish_target == 'testpypi'
+
+    steps:
+    - name: Download all artifacts
+      uses: actions/download-artifact@v4
+      with:
+        pattern: cibw-*
+        merge-multiple: true
+        path: dist/
+
+    - name: Publish to TestPyPI (API token)
       uses: pypa/gh-action-pypi-publish@release/v1
       with:
         user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
-        packages_dir: dist/
+        password: ${{ secrets.TEST_PYPI_API_TOKEN }}
+        packages_dir: dist/
+        repository-url: https://test.pypi.org/legacy/
+        verbose: true

README-python.md

@@ -32,8 +32,9 @@ For bioinformatics ecosystem integration:
 ```bash
 pip install kalign[biopython]    # + Biopython integration
 pip install kalign[skbio]        # + scikit-bio integration  
-pip install kalign[all]          # Everything
 pip install kalign[io]           # I/O helpers with Biopython
+pip install kalign[analysis]     # + pandas + matplotlib analysis/visualization helpers
+pip install kalign[all]          # Biopython + scikit-bio + pandas + matplotlib
 ```
 
 ## Quick Start
@@ -66,7 +67,7 @@ ATCGATC-ATCG
 
 - **[📖 Quick Start Guide](python-docs/python-quickstart.md)** - Get up and running in minutes
 - **[🔧 API Reference](python-docs/python-api.md)** - Complete function documentation  
-- **[🌐 Ecosystem Integration](python-docs/python-ecosystem.md)** - Biopython, scikit-bio, pandas integration
+- **[🌐 Ecosystem Integration](python-docs/python-ecosystem.md)** - Biopython, scikit-bio, pandas, and matplotlib integration
 - **[⚡ Performance Tuning](python-docs/python-performance.md)** - Optimization and benchmarking
 - **[🛠️ Troubleshooting Guide](python-docs/python-troubleshooting.md)** - Common issues and solutions
 
@@ -580,4 +581,4 @@ See the [LICENSE](../COPYING) file for details.
 
 ---
 
-**Made with ❤️ by the Kalign community** | **Star ⭐ us on GitHub if you find Kalign useful!**
+**Made with ❤️ by the Kalign community** | **Star ⭐ us on GitHub if you find Kalign useful!**

README.md

@@ -243,6 +243,48 @@ cmake -DBUILD_PYTHON_MODULE=ON ..
 make
 ```
 
+### Cutting a New Python Release (PyPI)
+
+This repo is set up to publish to PyPI from GitHub Actions on version tags (`v*`) via `.github/workflows/wheels.yml`.
+
+1) Bump versions
+- Update the Python package version in `pyproject.toml` (`[project].version`).
+- Update the C/C++ library version in `CMakeLists.txt` (`KALIGN_LIBRARY_VERSION_{MAJOR,MINOR,PATCH}`).
+- (Optional but recommended) Add an entry to `ChangeLog`.
+
+2) Sanity check locally (recommended)
+```bash
+python -m venv .venv
+source .venv/bin/activate
+python -m pip install -U pip build twine
+python -m build
+twine check dist/*
+```
+
+3) Configure trusted publishing on PyPI
+- Add this GitHub repo/workflow as a trusted publisher in the PyPI project settings.
+- Configure it to match the workflow/environment used in `.github/workflows/wheels.yml` (environment `pypi`).
+
+4) Tag and push
+```bash
+git tag vX.Y.Z
+git push origin vX.Y.Z
+```
+
+That tag push triggers the wheel + sdist build, install tests, and then uploads to PyPI.
+
+#### Testing publishing on TestPyPI (optional)
+
+If you want to test the publishing pipeline without uploading to the real PyPI project, this repo also supports a manual TestPyPI publish:
+
+1) Create a TestPyPI API token and add it as the GitHub secret `TEST_PYPI_API_TOKEN`.
+2) Run the GitHub Actions workflow **Build Python Wheels** manually and set `publish_target = testpypi`.
+
+To install from TestPyPI while resolving dependencies from PyPI:
+```bash
+pip install -i https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple <package-name>
+```
+
 ## Performance
 
 ### Benchmark Results

pyproject.toml

@@ -10,8 +10,9 @@ build-backend = "scikit_build_core.build"
 name = "kalign"
 version = "3.4.5"
 description = "Python wrapper for the Kalign multiple sequence alignment engine"
-readme = "README.md"
-license = {text = "GPL-3.0-or-later"}
+readme = "README-python.md"
+license = "GPL-3.0-or-later"
+license-files = ["COPYING"]
 authors = [
     {name = "Timo Lassmann", email = "timo.lassmann@telethonkids.org.au"}
 ]
@@ -30,7 +31,6 @@ keywords = [
 classifiers = [
     "Development Status :: 5 - Production/Stable",
     "Intended Audience :: Science/Research",
-    "License :: OSI Approved :: GNU General Public License v3 or later (GPLv3+)",
     "Operating System :: OS Independent",
     "Programming Language :: C",
     "Programming Language :: C++",
@@ -46,12 +46,7 @@ classifiers = [
 ]
 requires-python = ">=3.9"
 dependencies = [
-    "biopython>=1.85",
-    "matplotlib>=3.9.4",
     "numpy>=1.19.0",
-    "pandas>=2.3.0",
-    "rich>=14.0.0",
-    "scikit-bio>=0.6.3",
 ]
 
 [project.scripts]
@@ -62,7 +57,8 @@ kalign = "kalign.cli:main"
 biopython = ["biopython>=1.85"]
 skbio = ["scikit-bio>=0.6.3"]
 io = ["biopython>=1.85"]  # For I/O helper functions
-all = ["biopython>=1.85", "scikit-bio>=0.6.3"]
+analysis = ["pandas>=2.3.0", "matplotlib>=3.9.4"]
+all = ["biopython>=1.85", "scikit-bio>=0.6.3", "pandas>=2.3.0", "matplotlib>=3.9.4"]
 
 # Development dependencies
 dev = [

python-docs/python-quickstart.md

@@ -31,7 +31,13 @@ pip install kalign[biopython]
 # For scikit-bio integration
 pip install kalign[skbio]
 
-# For everything
+# For file I/O helpers (Biopython-backed)
+pip install kalign[io]
+
+# For pandas + matplotlib analysis/visualization helpers
+pip install kalign[analysis]
+
+# For all optional ecosystem integrations
 pip install kalign[all]
 ```
 
@@ -597,7 +603,7 @@ aligned, stats, outliers = quality_control_alignment(sequences, ids)
 
 Now that you're familiar with the basics, explore these advanced topics:
 
-1. **[Ecosystem Integration Guide](python-ecosystem.md)** - Deep dive into Biopython and scikit-bio integration
+1. **[Ecosystem Integration Guide](python-ecosystem.md)** - Deep dive into Biopython, scikit-bio, pandas, and matplotlib integration
 2. **[Performance Tuning Guide](python-performance.md)** - Optimize for large-scale alignments
 3. **[API Reference](python-api.md)** - Complete function documentation
 4. **[Troubleshooting Guide](python-troubleshooting.md)** - Common issues and solutions
@@ -623,4 +629,4 @@ help(kalign.align)
 help(kalign.utils.alignment_stats)
 ```
 
-Happy aligning! 🧬✨
+Happy aligning! 🧬✨

python-kalign/__init__.py

@@ -12,7 +12,12 @@
 
 from . import _core, io, utils
 
-__version__ = "3.4.5"
+try:
+    from importlib.metadata import PackageNotFoundError, version as _dist_version
+
+    __version__ = _dist_version("kalign")
+except Exception:
+    __version__ = "3.4.5"
 __author__ = "Timo Lassmann"
 __email__ = "timo.lassmann@telethonkids.org.au"