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BROKEN: try to update htslib #278

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BROKEN: try to update htslib #278

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41b6719
try to update htslib
brentp Aug 22, 2023
7ce7827
Add additional htscodecs sources
ccwang002 Aug 22, 2023
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2 changes: 1 addition & 1 deletion .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,7 @@ jobs:
cd htslib
autoheader && autoconf && autoreconf --install
./configure --enable-s3 --disable-lzma --disable-bz2
make
make version.h && make
cd ..
CYTHONIZE=1 python setup.py build_ext -i
- name: Test
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2 changes: 2 additions & 0 deletions MANIFEST.in
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Expand Up @@ -10,3 +10,5 @@ include htslib/*.h
include htslib/htslib/*.h
include htslib/cram/*.c
include htslib/cram/*.h
include htslib/htscodecs/htscodecs/*.h
include htslib/htscodecs/htscodecs/*.c
2 changes: 1 addition & 1 deletion htslib
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Submodule htslib updated 174 files
2 changes: 1 addition & 1 deletion requirements.txt
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@@ -1,4 +1,4 @@
cython>=0.23.3
cython>=0.23.3,<3.0.0
numpy
coloredlogs
click
15 changes: 13 additions & 2 deletions setup.py
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Expand Up @@ -48,7 +48,17 @@ def no_cythonize(extensions, **_ignore):
if not any(e in x for e in ['irods', 'plugin'])
]
sources += glob.glob('htslib/cram/*.c')
sources += glob.glob('htslib/htscodecs/htscodecs/*.c')
sources += ['htslib/htscodecs/htscodecs/%s' % s for s in ['rle.c', 'arith_dynamic.c', 'pack.c', 'utils.c',
'htscodecs.c', 'fqzcomp_qual.c',
'rANS_static.c',
'rANS_static4x16pr.c',
'rANS_static32x16pr.c',
'rANS_static32x16pr_avx2.c',
'rANS_static32x16pr_avx512.c',
'rANS_static32x16pr_sse4.c',
'rANS_static32x16pr_neon.c',
]]

# Exclude the htslib sources containing main()'s
sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]
sources.append('cyvcf2/helpers.c')
Expand All @@ -65,7 +75,8 @@ def no_cythonize(extensions, **_ignore):
extra_compile_args=["-Wno-sign-compare", "-Wno-unused-function",
"-Wno-strict-prototypes",
"-Wno-unused-result", "-Wno-discarded-qualifiers"],
include_dirs=['htslib', 'cyvcf2', np.get_include()])]
library_dirs=['htslib', 'htslib/htscodecs/htscodecs'],
include_dirs=['htslib', 'cyvcf2', 'htslib/htscodecs/htscodecs', np.get_include()])]


CYTHONIZE = bool(int(os.getenv("CYTHONIZE", 0)))
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