Merge pull request #231 from grahamgower/libdeflate

Add libdeflate to the wheel build.

.github/workflows/wheels.yml

@@ -39,11 +39,12 @@ jobs:
       run: |
         python -m cibuildwheel --output-dir wheelhouse
       env:
-        CIBW_SKIP: "pp* *i686*"
+        CIBW_SKIP: "pp* *i686* *musllinux*"
         CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
         CIBW_BEFORE_BUILD_LINUX: "{project}/ci/linux-deps"
         CIBW_TEST_COMMAND: "{project}/ci/test"
-        CIBW_ENVIRONMENT: "CYTHONIZE=1 LDFLAGS='-L/usr/lib64/openssl11' CPPFLAGS='-I/usr/include/openssl11' C_INCLUDE_PATH='/root/include' LIBRARY_PATH='/root/lib'"
+        CIBW_ENVIRONMENT: "CYTHONIZE=1 LIBDEFLATE=1 LDFLAGS='-L/usr/lib64/openssl11' CPPFLAGS='-I/usr/include/openssl11' C_INCLUDE_PATH='/root/include' LIBRARY_PATH='/root/lib'"
+        CIBW_REPAIR_WHEEL_COMMAND_LINUX: LD_LIBRARY_PATH='/root/lib' auditwheel repair -w {dest_dir} {wheel}
 
     - name: Build wheels for Mac OS
       if: matrix.os == 'macos-latest'
@@ -56,7 +57,11 @@ jobs:
         CIBW_BEFORE_BUILD_MACOS: "{project}/ci/osx-deps"
         CIBW_TEST_COMMAND: "{project}/ci/test"
         CIBW_TEST_SKIP: "*-macosx_arm64"
-        CIBW_ENVIRONMENT: "CYTHONIZE=1"
+        CIBW_ENVIRONMENT: "CYTHONIZE=1 LIBDEFLATE=1 C_INCLUDE_PATH='/usr/local/include' LIBRARY_PATH='/usr/local/lib'"
+        # https://cibuildwheel.readthedocs.io/en/stable/faq/#macos-passing-dyld_library_path-to-delocate
+        CIBW_REPAIR_WHEEL_COMMAND_MACOS: >
+          DYLD_LIBRARY_PATH=/usr/local/lib delocate-listdeps {wheel} &&
+          DYLD_LIBRARY_PATH=/usr/local/lib delocate-wheel --require-archs {delocate_archs} -w {dest_dir} {wheel}
         LDFLAGS: "-L/usr/local/opt/[email protected]/lib"
         CPPFLAGS: "-I/usr/local/opt/[email protected]/include"
         PKG_CONFIG_PATH: "/usr/local/opt/[email protected]/lib/pkgconfig"

ci/linux-deps

@@ -29,6 +29,13 @@ make install
 cd ..
 rm -rf curl-7.73.0
 
+curl -L -o libdeflate-v1.8.tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.8.tar.gz
+tar xzf libdeflate-v1.8.tar.gz
+cd libdeflate-1.8
+make
+make install PREFIX=/root
+cd ..
+
 cd htslib
 # configure fails with autoconf 2.71 (in /usr/local/bin), so use 2.69 (in /usr/bin)
 /usr/bin/autoconf -V

ci/osx-deps

@@ -13,6 +13,13 @@ brew install [email protected] && \
 brew link --overwrite [email protected] && \
 autoconf -V
 
+curl -L -o libdeflate-v1.8.tar.gz https://github.com/ebiggers/libdeflate/archive/refs/tags/v1.8.tar.gz
+tar xzf libdeflate-v1.8.tar.gz
+cd libdeflate-1.8
+make
+make install
+cd ..
+
 cd htslib
 autoheader
 autoconf

setup.py

@@ -54,9 +54,15 @@ def no_cythonize(extensions, **_ignore):
 sources = [x for x in sources if not x.endswith(('htsfile.c', 'tabix.c', 'bgzip.c'))]
 sources.append('cyvcf2/helpers.c')
 
+extra_libs = []
+if platform.system() != 'Darwin':
+    extra_libs.append('crypt')
+if bool(int(os.getenv("LIBDEFLATE", 0))):
+    extra_libs.append('deflate')
+
 extensions = [Extension("cyvcf2.cyvcf2",
                         ["cyvcf2/cyvcf2.pyx"] + sources,
-                        libraries=['z', 'bz2', 'lzma', 'curl', 'ssl'] + (['crypt'] if platform.system() != 'Darwin' else []),
+                        libraries=['z', 'bz2', 'lzma', 'curl', 'ssl'] + extra_libs,
                         extra_compile_args=["-Wno-sign-compare", "-Wno-unused-function",
                             "-Wno-strict-prototypes",
                             "-Wno-unused-result", "-Wno-discarded-qualifiers"],