Dysgu dev

.github/workflows/main.yml

@@ -10,18 +10,22 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-20.04, macOS-13]
+        os: [ubuntu-20.04, macOS-14]
         #os: [ubuntu-latest, macOS-11]
 
     steps:
       - uses: actions/checkout@v4
       - name: Set correct paths for Homebrew on macOS
-        if: matrix.os == 'macOS-13'
+        if: matrix.os == 'macOS-14'
         run: |
-          BREW_PREFIX=$(brew --prefix)
+          export BREW_PREFIX="$(brew --prefix)"
+          export PREFIX="$(brew --prefix)"
           export PATH="$BREW_PREFIX/bin:$PATH"
           export LIBRARY_PATH="$BREW_PREFIX/lib:$LIBRARY_PATH"
           export PKG_CONFIG_PATH="$BREW_PREFIX/lib/pkgconfig:$PKG_CONFIG_PATH"
+          export MACOSX_DEPLOYMENT_TARGET=14.0
+          echo "MACOSX_DEPLOYMENT_TARGET=14.0" >> $GITHUB_ENV
+          brew install libomp
       - name: Install project dependencies
         run: which python; python -m pip install -r requirements.txt
       - name: Build wheels
@@ -32,16 +36,19 @@ jobs:
           CIBW_ARCHS_MACOS: "x86_64 arm64"
           CIBW_ARCHS_LINUX: "auto"
           CIBW_BEFORE_ALL_MACOS: |
-            bash ci/osx-deps
-          CIBW_BEFORE_ALL_LINUX: bash ci/manylinux-deps
+            sudo bash ci/osx-deps
+          CIBW_BEFORE_ALL_LINUX: |
+            bash ci/manylinux-deps
           CIBW_BEFORE_BUILD_MACOS: |
             ln -s /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11/cpython/longintrepr.h /Library/Frameworks/Python.framework/Versions/3.11/include/python3.11
             which python3
             python3 -m pip install -r requirements.txt
           CIBW_BEFORE_BUILD_LINUX: pip install -r requirements.txt
-          CIBW_REPAIR_WHEEL_COMMAND_MACOS: delocate-wheel --require-archs x86_64 -w {dest_dir} -v {wheel} --require-target-macos-version 13.0
+          CIBW_REPAIR_WHEEL_COMMAND_MACOS: |
+            delocate-wheel -w {dest_dir} -v {wheel} --require-target-macos-version 14.0
           CIBW_TEST_SKIP: "*-macosx_arm64"
-          CIBW_TEST_REQUIRES: cython click>=8.0 numpy scipy pandas pysam>=0.22.0 networkx>=2.4 scikit-learn>=0.22 sortedcontainers lightgbm
+          CIBW_TEST_REQUIRES: |
+            cython click>=8.0 numpy scipy pandas pysam>=0.22.0 networkx>=2.4 scikit-learn>=0.22 sortedcontainers lightgbm
           CIBW_TEST_COMMAND: dysgu test --verbose
 
       - uses: actions/upload-artifact@v4

ci/osx-deps

@@ -1,15 +1,32 @@
 #!/bin/bash
 
-git clone --depth 1 https://github.com/ebiggers/libdeflate.git && \
-    cd libdeflate && CFLAGS+=' -fPIC -O3 ' cmake -B build && CFLAGS+=' -fPIC -O3 ' cmake --build build && \
-    cp build/libdeflate.a /usr/local/lib && cp libdeflate.h /usr/local/include && cd ../
+
+BREW_PREFIX="$(brew --prefix)"
+
+export MACOSX_DEPLOYMENT_TARGET=14.0
+export CFLAGS="${CFLAGS} -mmacosx-version-min=14.0"
+export CPPFLAGS="${CXXFLAGS} -mmacosx-version-min=14.0 -I${BREW_PREFIX}/include "
+export LDFLAGS="${LDFLAGS} -mmacosx-version-min=14.0 -L${BREW_PREFIX}/lib"
+
+git clone --depth 1 https://github.com/ebiggers/libdeflate.git
+cd libdeflate
+CFLAGS+=" -fPIC -O3 " cmake -B build
+CFLAGS+=" -fPIC -O3 " cmake --build build
+cp build/libdeflate.a ${BREW_PREFIX}/lib
+cp libdeflate.h ${BREW_PREFIX}/include
+cd ../
 
 cd ./dysgu
-wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.17/htslib-1.17.tar.bz2
+wget -O htslib.tar.bz2 https://github.com/samtools/htslib/releases/download/1.21/htslib-1.21.tar.bz2
 ls -lh
 tar -xvf htslib.tar.bz2
-mv htslib-1.17 htslib && rm htslib.tar.bz2
+mv htslib-1.21 htslib && rm htslib.tar.bz2
 cd htslib
 
-./configure --enable-libcurl --enable-s3 --enable-lzma --enable-bz2 --with-libdeflate
-make && make install
+./configure \
+ --enable-libcurl \
+ --enable-s3 \
+ --enable-lzma \
+ --enable-bz2 \
+ --with-libdeflate
+sudo make && make install