Merge branch 'master' into master

.github/workflows/test_and_deploy.yml

@@ -0,0 +1,122 @@
+# Based on the workflow from https://github.com/biotite-dev/biotite/
+# contributed by Daniel Farrell (danpf) and published under the same license
+
+name: "CI & CD"
+
+on:
+  workflow_dispatch:
+  pull_request:
+  release:
+    types:
+    - published
+
+env:
+  CIBW_BUILD: cp39-* cp310-* cp311-*
+  CIBW_ARCHS_LINUX: "x86_64"
+  CIBW_ARCHS_MACOS: "x86_64 arm64"
+  CIBW_ARCHS_WINDOWS: "x86 AMD64"
+  # Skip musllinux because it takes too long to compile on GHA
+  # since it is emulated. (6+ hours)
+  # *note* most of the build time is actually numpy for musllinux
+  CIBW_SKIP: "*musllinux* *-manylinux_i686 *-musllinux_i686 *-win32 pp*"
+  CIBW_TEST_EXTRAS: test
+  CIBW_TEST_COMMAND: pytest {project} --durations=50
+  CIBW_DEPENDENCY_VERSIONS: "pinned"
+  # Runtime too long due to architecture emulation
+  CIBW_TEST_SKIP: "*-macosx_arm64"
+
+
+jobs:
+  test-and-build:
+    name: "Build & Test"
+    strategy:
+      matrix:
+        os: [ubuntu-20.04, windows-2019, macos-11]
+
+    runs-on: ${{ matrix.os }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Set up QEMU
+        if: runner.os == 'Linux'
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: all
+
+      - name: Build & (optionally) test wheels
+        uses: pypa/cibuildwheel@v2.12.1
+
+      - uses: actions/upload-artifact@v3
+        with:
+          name: dist
+          path: ./wheelhouse/*.whl
+          if-no-files-found: error
+
+
+  make-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+      with:
+        fetch-depth: 0
+        submodules: true
+    - name: Build source distribution
+      run: pipx run build --sdist
+    - uses: actions/upload-artifact@v3
+      with:
+        name: dist
+        path: dist/*.tar.gz
+        if-no-files-found: error
+
+
+  make-doc:
+    name: Build documentation
+
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: hydride
+          auto-update-conda: true
+          python-version: '3.11'
+      - name: Installing dependencies
+        run: conda install -c conda-forge sphinx cython numpy numpydoc biotite
+      - name: Building documentation
+        run: sphinx-build ./doc ./build/doc
+      - name: Zipping documentation
+        run: cd .//build; zip -r doc.zip doc; cd ..
+      - uses: actions/upload-artifact@v3
+        with:
+          name: doc
+          path: build//doc.zip
+          if-no-files-found: error
+
+
+  upload:
+    name: Upload to GitHub Releases & PyPI
+    permissions:
+      contents: write
+    needs: [test-and-build, make-sdist, make-doc]
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/download-artifact@v3
+    - name: List distributions to be uploaded
+      run: ls dist
+    - name: Upload to GitHub Releases
+      uses: softprops/action-gh-release@de2c0eb89ae2a093876385947365aca7b0e5f844
+      if: github.event_name == 'release' && github.event.action == 'published'
+      with:
+        files: |
+          dist//*
+          doc//*
+    - name: Upload to PyPI
+      uses: pypa/gh-action-pypi-publish@c7f29f7adef1a245bd91520e94867e5c6eedddcc
+      if: github.event_name == 'release' && github.event.action == 'published'
+      with:
+        password: ${{ secrets.PYPI_TOKEN }}

pyproject.toml

@@ -1,10 +1,51 @@
+[project]
+name = "hydride"
+authors = [
+    {name = "The 'Hydride' contributors"},
+]
+description = "Adding hydrogen atoms to molecular models"
+readme = "README.rst"
+requires-python = ">=3.7"
+license = {file = "LICENSE.rst"}
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: MacOS",
+    "Operating System :: Microsoft :: Windows",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: Implementation :: CPython",
+    "Topic :: Scientific/Engineering :: Bio-Informatics"
+]
+dependencies = [
+    "biotite >= 0.35",
+    "numpy >= 1.14.5",
+]
+dynamic = ["version"]
+
+[project.urls]
+homepage = "https://hydride.biotite-python.org"
+repository = "https://github.com/biotite-dev/hydride"
+documentation = "https://hydride.biotite-python.org"
+
+[project.optional-dependencies]
+test = [
+  "pytest",
+]
+
+[project.scripts]
+hydride = "hydride.cli:main"
+
 [build-system]
 # Minimum requirements for the build system to execute.
 requires = [
     "setuptools >= 0.30",
     "wheel >= 0.30",
     "biotite >= 0.37",
-    "numpy >= 1.14, <= 1.21",
+    "oldest-supported-numpy",
     "msgpack >= 0.5.6",
     "cython >= 0.29"
-]
+]