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pysam-developers / pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.
https://pysam.readthedocs.io/en/latest/
MIT License
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Add ``htslib/hts_probe_cc.sh`` to sdist #1247

Closed nsoranzo closed 4 months ago

nsoranzo commented 9 months ago

Otherwise the before-build command make -C {project}/htslib distclean from pyproject.toml fail with:

      + sh -c 'make -C /project/htslib distclean'
  Makefile:142: htscodecs.mk: No such file or directory
  make: Entering directory `/project/htslib'
  echo '# Default htscodecs.mk generated by Makefile' > htscodecs.mk
  echo 'include $(HTSPREFIX)htscodecs_bundled.mk' >> htscodecs.mk
  ./hts_probe_cc.sh 'gcc' '-g -Wall -O2 -fvisibility=hidden ' '-fvisibility=hidden' >> htscodecs.mk
  /bin/sh: ./hts_probe_cc.sh: No such file or directory
  make: *** [htscodecs.mk] Error 127
  make: Leaving directory `/project/htslib'
nsoranzo commented 4 months ago

This is not needed any more after commit 8ab52871e6d97755cae625742db6a1243ff5c243, closing.

jmarshall commented 4 months ago

Yes, we don’t use _hts_probecc.sh during building so we don’t really want to use it just for cleaning, so as you noticed I wanted to fix this in a different way. Thanks for reporting the problem!