Release 1.21

.cirrus.yml

@@ -35,21 +35,22 @@ compile_template: &COMPILE
     if test "$USE_CONFIG" = "yes"; then
       MAKE_OPTS=
       autoreconf -i
-      eval ./configure --enable-plugins --enable-werror $CONFIG_OPTS CFLAGS=\"-g -O3 $CFLAGS\" || \
+      eval ./configure --enable-plugins --enable-werror $CONFIG_OPTS CFLAGS=\"$CFLAGS\" || \
         ( cat config.log; false )
     else
       MAKE_OPTS=-e
     fi
+    make cc-version $MAKE_OPTS
     if test "x$DO_MAINTAINER_CHECKS" = "xyes"; then
-      make maintainer-check
+      make maintainer-check $MAKE_OPTS
     fi
     make -j 4 $MAKE_OPTS
 
 test_template: &TEST
   test_script: |
-    make test-shlib-exports
-    make test
-    if test "x$DO_UNTRACKED_FILE_CHECK" = "xyes"; then make check-untracked ; fi
+    make test-shlib-exports $MAKE_OPTS
+    make test $MAKE_OPTS
+    if test "x$DO_UNTRACKED_FILE_CHECK" = "xyes"; then make check-untracked $MAKE_OPTS ; fi
 
 #--------------------------------------------------
 # Task: linux builds.
@@ -71,10 +72,14 @@ gcc_task:
        DO_MAINTAINER_CHECKS: yes
        DO_UNTRACKED_FILE_CHECK: yes
        USE_CONFIG: no
+       CFLAGS: -g -O2 -Wall -Werror -fvisibility=hidden
     - environment:
        USE_CONFIG: yes
-       CFLAGS: -std=c99 -pedantic -Wformat=2
+       # ubsan is incompatible with some -Wformat opts so we do that on clang.
+       CFLAGS: -g -O3 -fsanitize=address,undefined -DHTS_ALLOW_UNALIGNED=0 -Wno-format-truncation -Wno-format-overflow
+       LDFLAGS: -fsanitize=address,undefined
        USE_LIBDEFLATE: yes
+       UBSAN_OPTIONS: print_stacktrace=1:halt_on_error=1
 
   install_script: |
     apt-get update
@@ -105,11 +110,12 @@ ubuntu_task:
   matrix:
     - environment:
        USE_CONFIG: yes
+       CFLAGS: -g -O3
        DO_UNTRACKED_FILE_CHECK: yes
     - environment:
+       # Cirrus-CI's clang isn't installed with ubsan, so we do that in gcc
        USE_CONFIG: yes
-       CFLAGS: -g -Wall -O3 -fsanitize=address
-       LDFLAGS: -fsanitize=address
+       CFLAGS: -g -O3 -std=c99 -pedantic -Wall -Wformat -Wformat=2
        USE_LIBDEFLATE: yes
 
   # NB: we could consider building a docker image with these
@@ -137,7 +143,7 @@ rocky_task:
     LC_ALL: C
     CIRRUS_CLONE_DEPTH: 1
     USE_CONFIG: yes
-    CFLAGS: -std=gnu90
+    CFLAGS: -g -O3 -std=gnu90 -Wall -Wformat -Wformat=2 -Wextra -Wno-sign-compare -Wno-unused-parameter -Wno-missing-field-initializers
 
   # NB: we could consider building a docker image with these
   # preinstalled and specifying that instead, to speed up testing.
@@ -182,11 +188,10 @@ arm_ubuntu_task:
 macosx_task:
   name: macosx + clang
   macos_instance:
-    image: ghcr.io/cirruslabs/macos-ventura-base:latest
+    image: ghcr.io/cirruslabs/macos-runner:sonoma
 
   environment:
     CC: clang
-    CFLAGS: "-Wall -arch arm64 -arch x86_64"
     LDFLAGS: "-arch arm64 -arch x86_64"
     LIBDEFLATE_CFLAGS: "-arch arm64 -arch x86_64"
     LC_ALL: C
@@ -195,9 +200,11 @@ macosx_task:
   matrix:
     - environment:
        USE_CONFIG: no
+       CFLAGS: "-g -O3 -Wall -Werror -arch arm64 -arch x86_64"
     - environment:
        USE_CONFIG: yes
        USE_LIBDEFLATE: yes
+       CFLAGS: "-g -O3 -Wall -arch arm64 -arch x86_64"
 
   package_install_script: |
     HOMEBREW_NO_AUTO_UPDATE=1 brew install autoconf automake libtool xz git \

.gitattributes

@@ -24,3 +24,14 @@ test/index_dos.sam -text
 # Remove the text attribute from various faidx test files
 test/faidx/faidx*.fa* -text
 test/faidx/fastqs*.fq* -text
+test/fastq/*.fa -text
+test/fastq/*.fq -text
+*.tst -text
+*.out -text
+*.crai    -text
+*.bai     -text
+*.csi     -text
+*.gzi     -text
+*.bcf     -text
+*.sam     -text
+*.sam.gz  -text

.github/workflows/windows-build.yml

@@ -0,0 +1,41 @@
+name: Windows/MinGW-W64 CI
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        submodules: true
+    - name: Set up MSYS2 MinGW-W64
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: mingw64
+        update: false
+        install: >-
+          mingw-w64-x86_64-autotools
+          mingw-w64-x86_64-bzip2
+          mingw-w64-x86_64-curl
+          mingw-w64-x86_64-libdeflate
+          mingw-w64-x86_64-toolchain
+          mingw-w64-x86_64-tools-git
+          mingw-w64-x86_64-xz
+          mingw-w64-x86_64-zlib
+    - name: Compile htslib
+      shell: msys2 {0}
+      run: |
+        export PATH="/mingw64/bin:$PATH:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        autoreconf -i
+        ./configure --enable-werror
+        make cc-version
+        make -j6
+    - name: Check Htslib
+      shell: msys2 {0}
+      run: |
+        export PATH="/mingw64/bin:$PATH:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        make test-shlib-exports && make check
+

.gitignore

@@ -45,8 +45,9 @@ shlib-exports-*.txt
 /bgzip
 /htsfile
 /tabix
+/test/*/FAIL*
+/test/bgzf_boundaries/*.tmp.*
 /test/faidx/*.tmp*
-/test/faidx/FAIL*
 /test/fieldarith
 /test/hfile
 /test/hts_endian
@@ -56,7 +57,6 @@ shlib-exports-*.txt
 /test/plugins-dlhts
 /test/sam
 /test/tabix/*.tmp.*
-/test/tabix/FAIL*
 /test/test-bcf-sr
 /test/test-bcf-translate
 /test/test-bcf_set_variant_type
@@ -66,8 +66,10 @@ shlib-exports-*.txt
 /test/test_index
 /test/test_introspection
 /test/test_kfunc
+/test/test_khash
 /test/test_kstring
 /test/test_mod
+/test/test_nibbles
 /test/test-parse-reg
 /test/test_realn
 /test/test-regidx