Add Github actions builds for Linux and Mac OS

.github/workflows/linux-build.yml

@@ -0,0 +1,126 @@
+name: Linux CI
+on: [push, pull_request]
+
+jobs:
+  build-linux:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        # Fully declare each matrix entry here, as otherwise it's possible
+        # to get unexpected results due to the way the entries get expanded
+        # (See https://magmanu.github.io/blog/tech/matrices-github-actions/)
+        include:
+          # x86-64, clang, configure
+          - os: ubuntu-latest
+            use-configure: use-configure
+            htssrc: hidden-htslib
+            compiler: clang
+            sanitize: no-sanitize
+
+          # x86-64, gcc, configure, sanitize
+          - os: ubuntu-latest
+            use-configure: use-configure
+            htssrc: hidden-htslib
+            compiler: gcc
+            sanitize: sanitize
+
+          # x86-64, gcc, no configure, run extra checks
+          - os: ubuntu-latest
+            use-configure: no-configure
+            htssrc: htslib
+            compiler: gcc
+            sanitize: no-sanitize
+
+          # arm, gcc, configure
+          - os: ubuntu-24.04-arm
+            use-configure: use-configure
+            htssrc: hidden-htslib
+            compiler: gcc
+            sanitize: no-sanitize
+
+    defaults:
+      run:
+        working-directory: ./bcftools
+
+    steps:
+    - name: Checkout
+      # This is actions/checkout@v6.0.2
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+      with:
+        persist-credentials: false
+        path: bcftools
+
+    - name: Run apt
+      working-directory: .
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y --no-install-suggests --no-install-recommends autoconf automake make ${{ matrix.compiler }} perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev libdeflate-dev libperl-dev libgsl0-dev libio-pty-perl
+
+    - name: Clone htslib
+      working-directory: .
+      run: |
+        mkdir -p ${{ matrix.htssrc }}
+        htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+        ./bcftools/.ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib ${{ matrix.htssrc }} ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+    - name: Set build options
+      run: |
+        cc='clang'
+        configure_opts='--enable-werror --enable-perl-filters --enable-libgsl'
+        cflags='-g -O3'
+        ldflags=''
+
+        if [ '${{ matrix.sanitize }}' = 'sanitize' ] ; then
+          cflags="-g -Og -fsanitize=address,undefined -Wno-format-truncation -Wno-format-overflow -DHTS_ALLOW_UNALIGNED=0"
+          ldflags='-fsanitize=address,undefined'
+        fi
+
+        echo "cc=${cc}" >> "$GITHUB_ENV"
+        echo "configure_opts=${configure_opts}" >> "$GITHUB_ENV"
+        echo "cflags=${cflags}" >> "$GITHUB_ENV"
+        echo "ldflags=${ldflags}" >> "$GITHUB_ENV"
+
+    - name: Build htslib
+      working-directory: ${{ matrix.htssrc }}
+      run: |
+        htsdir="`realpath ..`/installed-htslib"
+        echo "htsdir=${htsdir}" >> "$GITHUB_ENV"
+
+        autoreconf -i
+        { ./configure --prefix="$htsdir" ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} ||
+          { cat config.log ; false ; } ; } &&
+        make -j 5 &&
+        make install
+
+    - name: Configure bcftools
+      if: ${{ matrix.use-configure == 'use-configure' }}
+      run: |
+        autoreconf -i
+
+        with_htslib="--with-htslib=$htsdir"
+        ldflags="${ldflags:+$ldflags }-Wl,-rpath=${htsdir}/lib"
+
+        printf "\nRunning ./configure ${with_htslib} ${configure_opts}${cc:+ CC='$cc'}${cflags:+ CFLAGS='$cflags'}${ldflags:+ LDFLAGS='$ldflags'} ...\n\n"
+
+        { ./configure $with_htslib ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} &&
+          { grep -qE 'CFLAGS *=.*-Werror' config.mk ||
+            { printf "\nStopping as -Werror was not set.\n" 1>&2 ; false ; } ;
+          } ;
+        } || { printf "\n### config.log content follows...\n\n" 1>&2 ; cat config.log ; false ; }
+
+    - name: Compile bcftools
+      run: |
+        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
+          make -j5
+        else
+          make -j5 ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
+        fi
+
+    - name: Check
+      run: |
+        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
+          make check BGZIP=$htsdir/bin/bgzip TABIX=$htsdir/bin/tabix
+        else
+          make check ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
+        fi

.github/workflows/macos-build.yml

@@ -0,0 +1,112 @@
+name: Mac OS CI
+on: [push, pull_request]
+
+jobs:
+  build-macos:
+    runs-on: macos-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        # Fully declare each matrix entry here, as otherwise it's possible
+        # to get unexpected results due to the way the entries get expanded
+        # (See https://magmanu.github.io/blog/tech/matrices-github-actions/)
+        include:
+          # configure
+          - use-configure: use-configure
+            htssrc: hidden-htslib
+            sanitize: no-sanitize
+
+          # make only
+          - use-configure: no-configure
+            htssrc: htslib
+            sanitize: no-sanitize
+
+          # configure, sanitize
+          - use-configure: use-configure
+            htssrc: hidden-htslib
+            sanitize: sanitize
+
+    defaults:
+      run:
+        working-directory: ./bcftools
+
+    steps:
+    - name: Checkout
+      # This is actions/checkout@v6.0.2
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
+      with:
+        persist-credentials: false
+        path: bcftools
+
+    - name: Install autotools
+      working-directory: .
+      run: |
+        brew install autoconf automake libtool
+
+    - name: Clone htslib
+      working-directory: .
+      run: |
+        mkdir -p ${{ matrix.htssrc }}
+        htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+        ./bcftools/.ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib ${{ matrix.htssrc }} ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+
+    - name: Set build options
+      run: |
+        cc='clang'
+        configure_opts='--enable-werror'
+        cflags='-g -O3 -arch arm64 -arch x86_64'
+        ldflags='-arch arm64 -arch x86_64'
+
+        if [ '${{ matrix.sanitize }}' = 'sanitize' ] ; then
+          cflags="-g -Og -fsanitize=address,undefined -Wno-format-truncation -Wno-format-overflow -arch arm64 -arch x86_64 -DHTS_ALLOW_UNALIGNED=0"
+          ldflags='-fsanitize=address,undefined -arch arm64 -arch x86_64'
+        fi
+
+        echo "cc=${cc}" >> "$GITHUB_ENV"
+        echo "configure_opts=${configure_opts}" >> "$GITHUB_ENV"
+        echo "cflags=${cflags}" >> "$GITHUB_ENV"
+        echo "ldflags=${ldflags}" >> "$GITHUB_ENV"
+
+    - name: Build htslib
+      working-directory: ${{ matrix.htssrc }}
+      run: |
+        htsdir="`realpath ..`/installed-htslib"
+        echo "htsdir=${htsdir}" >> "$GITHUB_ENV"
+
+        autoreconf -i
+        { ./configure --prefix="$htsdir" ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} ||
+          { cat config.log ; false ; } ; } &&
+        make -j 5 &&
+        make install
+
+    - name: Configure bcftools
+      if: ${{ matrix.use-configure == 'use-configure' }}
+      run: |
+        autoreconf -i
+
+        with_htslib="--with-htslib=$htsdir"
+        ldflags="${ldflags:+$ldflags }-Wl,-rpath,${htsdir}/lib"
+
+        printf "\nRunning ./configure ${with_htslib} ${configure_opts}${cc:+ CC='$cc'}${cflags:+ CFLAGS='$cflags'}${ldflags:+ LDFLAGS='$ldflags'} ...\n\n"
+
+        { ./configure $with_htslib ${configure_opts} ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags"} ${ldflags:+LDFLAGS="$ldflags"} &&
+          { grep -qE 'CFLAGS *=.*-Werror' config.mk ||
+            { printf "\nStopping as -Werror was not set.\n" 1>&2 ; false ; } ;
+          } ;
+        } || { printf "\n### config.log content follows...\n\n" 1>&2 ; cat config.log ; false ; }
+
+    - name: Compile bcftools
+      run: |
+        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
+          make -j5
+        else
+          make -j5 ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
+        fi
+
+    - name: Check
+      run: |
+        if [ '${{ matrix.use-configure }}' = 'use-configure' ] ; then
+          make check BGZIP=$htsdir/bin/bgzip TABIX=$htsdir/bin/tabix
+        else
+          make check ${cc:+CC="$cc"} ${cflags:+CFLAGS="$cflags -Werror"}
+        fi

.github/workflows/windows-build.yml

@@ -2,11 +2,12 @@ name: Windows/MinGW-W64 CI
 on: [push, pull_request]
 
 jobs:
-  build:
+  build-windows:
     runs-on: windows-latest
     steps:
     - name: Checkout
-      uses: actions/checkout@v4
+      # This is actions/checkout@v6.0.2
+      uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd
       with:
         ref: ${{ github.event.pull_request.head.sha }}
     - name: Set up MSYS2 MinGW-W64
@@ -23,6 +24,7 @@ jobs:
           mingw-w64-x86_64-zlib
           mingw-w64-x86_64-bzip2
           mingw-w64-x86_64-xz
+          mingw-w64-x86_64-gsl
     - name: Clone htslib
       shell: msys2 {0}
       run: |
@@ -41,7 +43,7 @@ jobs:
         export MSYSTEM=MINGW64
         autoheader
         autoconf -Wno-syntax
-        ./configure --enable-werror
+        ./configure --enable-werror --enable-libgsl
         make -j4
     - name: Check bcftools
       shell: msys2 {0}

config.mk.in

@@ -61,10 +61,10 @@ PLUGIN_EXT = @PLUGIN_EXT@
 @Hsource@HTSLIB_LIB = $(HTSLIB) $(HTSLIB_static_LIBS)
 @Hsource@HTSLIB_DLL = $(HTSDIR)/@HTSLIB_DLL@
 @Hsource@HTSLIB_LDFLAGS = $(HTSLIB_static_LDFLAGS)
-@Hsource@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS)
+@Hsource@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_DLL) $(ALL_LIBS) $(GSL_LIBS)
 @Hsource@BGZIP = $(HTSDIR)/bgzip
 @Hsource@TABIX = $(HTSDIR)/tabix
 HTSLIB_CPPFLAGS = @HTSLIB_CPPFLAGS@
 @Hinstall@HTSLIB_LDFLAGS = @HTSLIB_LDFLAGS@
 @Hinstall@HTSLIB_LIB = -lhts
-@Hinstall@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_LDFLAGS) $(HTSLIB_LIB) $(ALL_LIBS)
+@Hinstall@W32_PLUGIN_LIBS = libbcftools.a $(HTSLIB_LDFLAGS) $(HTSLIB_LIB) $(ALL_LIBS) $(GSL_LIBS)

hex.h

@@ -53,9 +53,9 @@
  *              If the buffer size is not sufficient, then the return value is the number of characters required for
  *              buffer string, including the terminating null byte.
  */
-static inline size_t hex_uint64_t(uint64_t n, char *str)
+static inline size_t hex_uint64_t(uint64_t n, char str[static 17])
 {
-    return sprintf(str, "%016" PRIx64, n);
+    return snprintf(str, 17, "%016" PRIx64, n);
 }
 
 /** @brief Parses a 16 chars hexadecimal string and returns the code.