python-pysam fails to build with Python 3.10.0b1: gcc -pthread -Wno-unused-result -Wsign-compare -DDYNAMIC_ANNOTATIONS_ENABLED=1 -DNDEBUG -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-p rotector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIF Y_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -fexceptions -g -grecord-gcc-switches -pi pe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fstack-protector-strong -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -D_GNU_SOURCE -fPIC -fwrapv -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-st rong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fPIC -I/builddir/build/BUILD/pysam-0.16.0.1/htslib -I/builddir/build/BUILD/pysam-0. 16.0.1/samtools -I/builddir/build/BUILD/pysam-0.16.0.1/samtools/lz4 -I/builddir/build/BUILD/pysam-0.16.0.1/bcftools -I/builddir/build/BUILD/pysam-0.16.0.1/pysam -I/builddir/build/BUILD/pysam-0.16.0.1 -I/usr/include/python3.10 -c pysam/libchtslib.c -o build/temp.linux-x86_64-3.10/pysam/libchtslib.o -Wno-unused -Wno-strict-prototypes -Wno-sign-compare -Wno-error=declaration-after-statement pysam/libchtslib.c: In function ‘__Pyx_call_return_trace_func’: pysam/libchtslib.c:1273:15: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘use_tracing’; did you mean ‘tracing’? 1273 | tstate->use_tracing = 0; | ^~~~~~~~~~~ | tracing pysam/libchtslib.c:1279:15: error: ‘PyThreadState’ {aka ‘struct _ts’} has no member named ‘use_tracing’; did you mean ‘tracing’? 1279 | tstate->use_tracing = 1; | ^~~~~~~~~~~ | tracing ... See https://bugs.python.org/issue43760 For the build logs, see: https://copr-be.cloud.fedoraproject.org/results/@python/python3.10/fedora-rawhide-x86_64/02175078-python-pysam/ For all our attempts to build python-pysam with Python 3.10, see: https://copr.fedorainfracloud.org/coprs/g/python/python3.10/package/python-pysam/ Testing and mass rebuild of packages is happening in copr. You can follow these instructions to test locally in mock if your package builds with Python 3.10: https://copr.fedorainfracloud.org/coprs/g/python/python3.10/ Let us know here if you have any questions. Python 3.10 will be included in Fedora 35. To make that update smoother, we're building Fedora packages with early pre-releases of Python 3.10. A build failure prevents us from testing all dependent packages (transitive [Build]Requires), so if this package is required a lot, it's important for us to get it fixed soon. We'd appreciate help from the people who know this package best, but if you don't want to work on this now, let us know so we can try to work around it on our side.
The underlying problem is in Cython, not pysam, and has been reported upstream as <https://github.com/cython/cython/issues/4153>.
Fixed in https://src.fedoraproject.org/rpms/Cython/pull-request/30