Warning patrol and description wordsmithing

.github/workflows/release.yaml

@@ -1,4 +1,4 @@
-name: Publish pysam wheels to PyPI and TestPyPI
+name: Publish wheels
 
 on:
   push:
@@ -12,7 +12,6 @@ on:
 
 jobs:
   build_wheels:
-    name: Build wheels on ${{ matrix.os }} for ${{ matrix.build }}
     runs-on: ${{ matrix.os }}-latest
     strategy:
       matrix:
@@ -22,7 +21,9 @@ jobs:
 
         include:
           - os: macos
-            build: "cp36-* cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*"
+            #build: "cp36-* cp37-* cp38-* cp39-* cp310-* cp311-* cp312-*"
+            # (also undo CIBW_ARCHS_LINUX below)
+            build: "cp310-* cp311-*"
 
           - os: ubuntu
             build: "cp38-manylinux_x86_64"
@@ -44,7 +45,7 @@ jobs:
           CIBW_BUILD: ${{ matrix.build }}
           CIBW_SKIP: "*musllinux*"
 
-          CIBW_ARCHS_LINUX: auto aarch64
+          CIBW_ARCHS_LINUX: x86_64
           CIBW_ARCHS_MACOS: x86_64 arm64
 
           CIBW_MANYLINUX_X86_64_IMAGE:  ${{ matrix.x64image }}
@@ -110,11 +111,8 @@ jobs:
         if: github.event_name == 'push'
         uses: pypa/gh-action-pypi-publish@release/v1
         with:
-          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

pyproject.toml

@@ -2,7 +2,7 @@
 name = "pysam"
 description = "pysam - a python module for reading, manipulating and writing genomic data sets."
 license = { text = "MIT License" }
-version = "0.22.0rc1"
+version = "0.22.0rc2"
 authors = [
  { name = "Andreas Heger", email = "[email protected]"}
 ]

pysam/version.py

@@ -1,5 +1,5 @@
 # pysam versioning information
-__version__ = "0.22.0rc1"
+__version__ = "0.22.0rc2"
 
 __samtools_version__ = "1.18"
 __bcftools_version__ = "1.18"

setup.py

@@ -1,23 +1,21 @@
 #! /usr/bin/python
 
-'''pysam - a python module for reading, manipulating and writing
+'''pysam --- a Python module 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.
+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 the htslib C-API as
-using cython and a high-level API for convenient access to the data
-within standard genomic file formats.
+This module provides a low-level wrapper around HTSlib's C API using Cython
+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
-
+https://pysam.readthedocs.io
 '''
 
 import collections
@@ -677,6 +675,7 @@ def prebuild_libcsamtools(ext, force):
     'version': get_pysam_version(),
     'description': "pysam",
     'long_description': __doc__,
+    'long_description_content_type': "text/x-rst",
     'author': "Andreas Heger",
     'author_email': "[email protected]",
     'license': "MIT",