Merge release workflow revamp and package metadata updates

.github/workflows/release.yaml

@@ -1,4 +1,4 @@
-name: Publish pysam wheels to PyPI and TestPyPI
+name: Publish wheels
 
 on:
   push:
@@ -12,77 +12,52 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }} for ${{ matrix.cibw_archs }}
-    runs-on: ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-10.15]  # windows-2019,
-        cibw_archs: [auto]
-        cibw_build: ['cp37-* cp38-* cp39-* cp310-* cp311-*']
+        os: [ubuntu]
+        build: ["cp36-* cp37-*", "cp38-* cp39-*", "cp310-* cp311-*", "cp312-*"]
+        x64image: [manylinux_2_28]
+
         include:
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp36-*
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp37-*
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp38-*
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp39-*
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp310-*
-           - os: ubuntu-latest
-             cibw_archs: aarch64
-             cibw_build: cp311-*
+          - os: macos
+            build: "cp36-* cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*"
+
+          - os: ubuntu
+            build: "cp38-manylinux_x86_64"
+            x64image: manylinux2014
+
     steps:
       - name: Checkout pysam
         uses: actions/checkout@v3
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v4
-        with:
-          python-version: '3.8'
-
       - name: Set up QEMU
-        if: ${{ matrix.cibw_archs == 'aarch64' }}
-        uses: docker/setup-qemu-action@v1
-
-      - name: Install prerequisite Python libraries
-        run:  |
-          python -m pip install --upgrade pip
-          pip install cython pytest pytest-pep8
-
-      - name: Build wheels for linux
         if:   runner.os == 'Linux'
-        uses: pypa/[email protected]
+        uses: docker/setup-qemu-action@v2
+        with:
+          platforms: arm64
+
+      - name: Build wheels
+        uses: pypa/[email protected]
         env:
-          CIBW_BUILD: ${{ matrix.cibw_build }}
+          CIBW_BUILD: ${{ matrix.build }}
           CIBW_SKIP: "*musllinux*"
-          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_24
-          CIBW_MANYLINUX_I686_IMAGE: manylinux_2_24
-          CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_24
-          CIBW_BEFORE_BUILD: apt-get update && apt-get install -y libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev && pip install cython
-          CIBW_ARCHS: ${{ matrix.cibw_archs }}
-
-      - name: Build wheels for macos
-        if:   runner.os != 'Linux'
-        uses: pypa/[email protected]
-        env:
-          CIBW_BUILD: ${{ matrix.cibw_build }}
-          CIBW_BEFORE_BUILD: pip install cython
-          CIBW_ARCHS: ${{ matrix.cibw_archs }}
+
+          CIBW_ARCHS_LINUX: auto aarch64
+          CIBW_ARCHS_MACOS: x86_64 arm64
+
+          CIBW_MANYLINUX_X86_64_IMAGE:  ${{ matrix.x64image }}
+          CIBW_MANYLINUX_I686_IMAGE:    manylinux2014
+          CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
+
+          CIBW_TEST_SKIP: "*-*linux_i686 *-*linux_aarch64 *-macosx_arm64"
 
       - name: Upload artifacts
         uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
 
   build_sdist:
-
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
@@ -115,28 +90,26 @@ jobs:
           path: dist/*.tar.gz
 
   upload_pypi:
-
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
+    environment: ${{ github.event_name == 'release' && 'pypi' || 'testpypi' }}
+
+    permissions:
+      id-token: write
 
     steps:
-      - name: Get Artifacts
+      - name: Get artifacts
         uses: actions/download-artifact@v3
         with:
           name: artifact
           path: dist
 
       - name: Publish distribution to Test PyPI
-        if: github.event_name == 'push' && startsWith(github.event.ref, 'refs/tags/v')
-        uses: pypa/gh-action-pypi-publish@master
+        if: github.event_name == 'push'
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          user: __token__
-          password: ${{ secrets.TEST_PYPI_API_TOKEN }}
-          repository_url: https://test.pypi.org/legacy/
+          repository-url: https://test.pypi.org/legacy/
 
       - name: Publish distribution to PyPI
         if: github.event_name == 'release' && github.event.action == 'published'
-        uses: pypa/gh-action-pypi-publish@master
-        with:
-          password: ${{ secrets.PYPI_API_TOKEN }}
-
+        uses: pypa/gh-action-pypi-publish@release/v1

devtools/install-prerequisites.sh

@@ -0,0 +1,34 @@
+#!/bin/sh -e
+
+if test -x /usr/bin/dnf; then
+    echo Installing prerequisites via dnf...
+    dnf -y install epel-release
+    dnf -y install zlib-devel bzip2-devel xz-devel curl-devel samtools bcftools htslib-tools
+
+elif test -x /usr/bin/yum; then
+    if yum -y install epel-release; then
+        echo Installing prerequisites via yum...
+        yum -y install zlib-devel bzip2-devel xz-devel curl-devel samtools bcftools htslib-tools
+    else
+        echo Installing non-test prerequisites via yum...
+        yum -y install zlib-devel bzip2-devel xz-devel curl-devel
+    fi
+
+elif test -d /etc/dpkg; then
+    echo Installing prerequisites via apt-get...
+    apt-get update
+    apt-get install -y --no-install-recommends --no-install-suggests libcurl4-openssl-dev zlib1g-dev libbz2-dev liblzma-dev samtools bcftools tabix
+
+elif test -x /sbin/apk; then
+    echo Installing non-test prerequisites via apk...
+    apk update
+    apk add zlib-dev bzip2-dev xz-dev curl-dev
+
+elif test -x ${HOMEBREW_PREFIX-/usr/local}/bin/brew; then
+    echo Installing prerequisites via brew...
+    HOMEBREW_NO_AUTO_UPDATE=1 brew install -q samtools bcftools
+    brew unlink xz || true
+
+else
+    echo No package manager detected
+fi

pyproject.toml

@@ -1,8 +1,7 @@
 [project]
 name = "pysam"
-description = "pysam - a python module for reading, manipulating and writing genomic data sets."
+description = "Package for reading, manipulating, and writing genomic data"
 license = { text = "MIT License" }
-version = "0.21.0"
 authors = [
  { name = "Andreas Heger", email = "[email protected]"}
 ]
@@ -11,12 +10,23 @@ requires-python = ">=3.6"
 dynamic = [
     "classifiers",
     "readme",
+    "version",
 ]
 
+[project.urls]
+"Documentation" = "https://pysam.readthedocs.io/en/stable/"
+"Release notes" = "https://pysam.readthedocs.io/en/stable/release.html"
+
 [build-system]
 requires = ["setuptools>=59.0", "Cython>=0.29.12,<4"]
 build-backend = "setuptools.build_meta:__legacy__"
 
+[tool.cibuildwheel]
+before-all = "{project}/devtools/install-prerequisites.sh"
+
+test-requires = ["pytest"]
+test-command = "REF_PATH=: pytest {project}/tests"
+
 [tool.tox]
 legacy_tox_ini = """
     [tox]

setup.py

@@ -1,23 +1,16 @@
 #! /usr/bin/python
 
-'''pysam - a python module for reading, manipulating and writing
+'''pysam --- a Python package for reading, manipulating, and writing
 genomic data sets.
 
-pysam is a lightweight wrapper of the htslib C-API and provides
-facilities to read and write SAM/BAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ
-files as well as access to the command line functionality of the
-samtools and bcftools packages. The module supports compression and
-random access through indexing.
-
-This module provides a low-level wrapper around the htslib C-API as
-using cython and a high-level API for convenient access to the data
-within standard genomic file formats.
-
-See:
-http://www.htslib.org
-https://github.com/pysam-developers/pysam
-http://pysam.readthedocs.org/en/stable
+pysam is a lightweight wrapper of the HTSlib API and provides facilities
+to read and write SAM/BAM/CRAM/VCF/BCF/BED/GFF/GTF/FASTA/FASTQ files
+as well as access to the command-line functionality of samtools and bcftools.
+The module supports compression and random access through indexing.
 
+This module provides a low-level wrapper around HTSlib's C API using Cython
+and a high-level API for convenient access to the data within standard genomic
+file formats.
 '''
 
 import collections
@@ -675,8 +668,9 @@ def prebuild_libcsamtools(ext, force):
 metadata = {
     'name': "pysam",
     'version': get_pysam_version(),
-    'description': "pysam",
+    'description': "Package for reading, manipulating, and writing genomic data",
     'long_description': __doc__,
+    'long_description_content_type': "text/x-rst",
     'author': "Andreas Heger",
     'author_email': "[email protected]",
     'license': "MIT",