try to update htslib

brentp · Aug 22, 2023 · 4e939e4 · 4e939e4
1 parent ea49bf4
commit 4e939e4
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Showing 5 changed files with 5 additions and 4 deletions.
diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -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

diff --git a/MANIFEST.in b/MANIFEST.in
@@ -10,3 +10,4 @@ include htslib/*.h
 include htslib/htslib/*.h
 include htslib/cram/*.c
 include htslib/cram/*.h
+include htslib/htscodecs/htscodecs/varint.h
diff --git a/htslib b/htslib
diff --git a/requirements.txt b/requirements.txt
@@ -1,4 +1,4 @@
-cython>=0.23.3
+cython>=0.23.3,<3.0.0
 numpy
 coloredlogs
 click
diff --git a/setup.py b/setup.py
@@ -48,7 +48,7 @@ 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']]
 # 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')