Merge release workflow updates

.cirrus.yml

@@ -17,7 +17,7 @@ build_wheels_task:
 
     - name: Build ARM macOS wheels
       macos_instance:
-        image: ghcr.io/cirruslabs/macos-ventura-base:latest
+        image: ghcr.io/cirruslabs/macos-sonoma-base:latest
       env:
         CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
 
@@ -26,11 +26,17 @@ build_wheels_task:
   env:
     CIRRUS_CLONE_DEPTH: 1
 
+    VENV: $HOME/relenv
+    PATH: $VENV/bin:$PATH
+
     CIBW_SKIP: "*-musllinux_*"
+    CIBW_BUILD_VERBOSITY: 1
+
     CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
 
   install_script: |
-    python3 -m pip install cibuildwheel==2.16.2
+    python3 -m venv $VENV
+    pip3 install cibuildwheel==2.17.0
 
   build_script: |
     cibuildwheel

.github/workflows/release.yaml

@@ -18,11 +18,13 @@ jobs:
         os: [ubuntu, macos]
         build: ["cp36-* cp37-* cp38-* cp39-*", "cp310-* cp311-* cp312-*"]
         x64image: [manylinux_2_28]
+        nametag: [none]
 
         include:
           - os: ubuntu
             build: "cp38-manylinux_x86_64"
             x64image: manylinux2014
+            nametag: focal
 
     steps:
       - name: Checkout pysam
@@ -32,7 +34,8 @@ jobs:
         uses: pypa/[email protected]
         env:
           CIBW_BUILD: ${{ matrix.build }}
-          CIBW_SKIP: "*musllinux*"
+          CIBW_SKIP: "*-musllinux_*"
+          CIBW_BUILD_VERBOSITY: 1
 
           CIBW_ARCHS_LINUX: x86_64
           CIBW_ARCHS_MACOS: x86_64
@@ -41,42 +44,46 @@ jobs:
           CIBW_MANYLINUX_I686_IMAGE:    manylinux2014
           CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
 
+      - name: Check wheelhouse
+        run:  devtools/artifactname.py wheelhouse/*.whl >> $GITHUB_ENV
+        env:
+          NAMETAG: ${{ matrix.nametag }}
+
       - name: Upload artifacts
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
+          name: ${{ env.artifactname }}
           path: wheelhouse/*.whl
 
   build_sdist:
-    runs-on: ${{ matrix.os }}-latest
-    strategy:
-      matrix:
-        os: [ubuntu, macos]
-        python-version: [3.9]
+    runs-on: ubuntu-latest
+    env:
+      job_python_version: "3.10"
 
     steps:
       - name: Checkout pysam
         uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ env.job_python_version }}
         uses: actions/setup-python@v5
         with:
-          python-version: ${{ matrix.python-version }}
+          python-version: ${{ env.job_python_version }}
 
       - name: Install prerequisite Python libraries
-        run:  pip install cython pytest pytest-pep8
+        run:  pip install cython
 
       - name: Install build prerequisites
-        if:   runner.os == 'Linux'
         run: |
           sudo apt-get update
           sudo apt-get install -q --no-install-recommends --no-install-suggests libcurl4-openssl-dev
 
       - name: Create source distribution
-        run:  python setup.py sdist
+        run:  python setup.py sdist --owner=root --group=root
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
-          path: dist/*.tar.gz
+          name: sdist
+          path: dist/pysam-*.tar.gz
 
   upload_pypi:
     needs: [build_wheels, build_sdist]
@@ -88,9 +95,9 @@ jobs:
 
     steps:
       - name: Get artifacts
-        uses: actions/download-artifact@v3
+        uses: actions/download-artifact@v4
         with:
-          name: artifact
+          merge-multiple: true
           path: dist
 
       - name: Publish distribution to Test PyPI

devtools/artifactname.py

@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+
+import os
+import re
+import sys
+
+pattern = re.compile(r'-cp([^-]*)-cp[^-]*-([^_]*)[0-9_]*_([^.]*)')
+vers = set()
+plats = set()
+arches = set()
+
+for fname in sys.argv[1:]:
+    m = pattern.search(fname)
+    vers.add(int(m[1]))
+    plats.add(m[2])
+    arches.add(m[3])
+
+plat = '-'.join(sorted(plats))
+arch = '-'.join(sorted(arches))
+ver  = '-'.join(map(str, sorted(vers)))
+
+tag = os.environ.get('NAMETAG', 'none')
+tag = f'-{tag}' if tag != 'none' else ''
+
+print(f'artifactname=wheels-{plat}-{arch}-{ver}{tag}')

devtools/install-prerequisites.sh

@@ -3,26 +3,26 @@
 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
+    dnf -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-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
+        yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-devel samtools bcftools htslib-tools
     else
         echo Installing non-test prerequisites via yum...
-        yum -y install zlib-devel bzip2-devel xz-devel curl-devel
+        yum -y install zlib-devel bzip2-devel xz-devel curl-devel openssl-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
+    apt-get install -y --no-install-recommends --no-install-suggests libcurl4-openssl-dev libssl-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
+    apk add zlib-dev bzip2-dev xz-dev curl-dev openssl-dev
 
 elif test -x ${HOMEBREW_PREFIX-/usr/local}/bin/brew; then
     echo Installing prerequisites via brew...