Replace AppVeyor for GitHub Actions workflow for Windows builds

Author: jkbonfield

.appveyor.yml

@@ -18,7 +18,7 @@ ref=''
 [ -z "$ref" ] && repository='https://github.com/samtools/htslib.git'
 
 set -x
-git clone --recurse-submodules --shallow-submodules --depth=1 ${ref:+--branch="$branch"} "$repository" "$localdir"
+git clone --recurse-submodules --shallow-submodules --depth=2 ${ref:+--branch="$branch"} "$repository" "$localdir"
 
 # NB: "samtools" as the owner/organisation, not the repo name
 if [ "x$owner" = "xsamtools" -a -z "$ref" -a "x$htslib_PR" != "x" ]

.ci_helpers/clone

@@ -10,3 +10,46 @@
 .git*           export-ignore
 .ci_helpers     export-ignore
 README.md       export-ignore
+
+# Prevent Windows cr-lf endings
+test/**       	       -text
+test/**.out		text
+test/**.bed		text
+test/**.vcf		text
+test/**.sam		text
+test/**.c		text
+test/**.pl		text
+test/**.sh		text
+test/**.reg		text
+test/**.23andme		text
+test/**.chain		text
+test/**.cmd		text
+test/**.chk		text
+test/**.fa		text
+test/**.fai		text
+test/**.gen		text
+test/**.gen6		text
+test/**.gff		text
+test/**.gff3		text
+test/**.hap		text
+test/**.haps		text
+test/**.hdr		text
+test/**.legend		text
+test/**.ori		text
+test/**.pairs		text
+test/**.ped		text
+test/**.ploidy		text
+test/**.ref		text
+test/**.rev		text
+test/**.rgs		text
+test/**.sample		text
+test/**.samples		text
+test/**.samples[234]	text
+test/**.smpl		text
+test/**.tab		text
+test/**.tsv		text
+test/**.txt		text
+test/create-bam-test	text
+test/csq/make-csq-test	text
+test/csq/make-csq-test-by-region	text
+test/csq/sort-csq	text

.gitattributes

@@ -0,0 +1,52 @@
+name: Windows/MinGW-W64 CI
+on: [push, pull_request]
+
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.event.pull_request.head.sha }}
+    - name: Set up MSYS2 MinGW-W64
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: mingw64
+        update: false
+        install: >-
+          mingw-w64-x86_64-toolchain
+          mingw-w64-x86_64-autotools
+          mingw-w64-x86_64-curl
+          mingw-w64-x86_64-libdeflate
+          mingw-w64-x86_64-tools-git
+          mingw-w64-x86_64-zlib
+          mingw-w64-x86_64-bzip2
+          mingw-w64-x86_64-xz
+    - name: Clone htslib
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        htslib_pr=`git log -2 --format='%s' | sed -n 's/.*htslib#\([0-9]*\).*/\1/p'`
+        .ci_helpers/clone ${GITHUB_REPOSITORY_OWNER} htslib htslib ${GITHUB_HEAD_REF:-$GITHUB_REF_NAME} $htslib_pr
+        pushd .
+        cd htslib
+        autoreconf -i
+        popd
+    - name: Compile bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        autoheader
+        autoconf -Wno-syntax
+        ./configure --enable-werror
+        make -j4
+    - name: Check bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH="$PATH:/mingw64/bin:/c/Program Files/Git/bin"
+        export MSYSTEM=MINGW64
+        make check
+