From 624e95b874661d93cdd572ef83c7cfdf58351b88 Mon Sep 17 00:00:00 2001
From: James Bonfield <jkb@sanger.ac.uk>
Date: Mon, 24 Jun 2024 11:50:11 +0100
Subject: [PATCH] Add Windows CI via github actions

Also amend .gitattributes file for more Windows text-mode removal as
for some reason the GitHub Actions git is much more likely to use
CR-LF line endings.

Added libdeflate to the windows build.

Corrected test/header_syms.pl to work on windows line endings.
---
 .gitattributes                      | 11 ++++++++
 .github/workflows/windows-build.yml | 40 +++++++++++++++++++++++++++++
 test/header_syms.pl                 |  1 +
 3 files changed, 52 insertions(+)
 create mode 100644 .github/workflows/windows-build.yml

diff --git a/.gitattributes b/.gitattributes
index 5d9850bc7..2d5a80e04 100644
--- a/.gitattributes
+++ b/.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
diff --git a/.github/workflows/windows-build.yml b/.github/workflows/windows-build.yml
new file mode 100644
index 000000000..c9c18461b
--- /dev/null
+++ b/.github/workflows/windows-build.yml
@@ -0,0 +1,40 @@
+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: >-
+          git
+          zlib-devel
+          libbz2-devel
+          liblzma-devel
+          mingw-w64-x86_64-toolchain
+          mingw-w64-x86_64-autotools
+          mingw-w64-x86_64-tools-git
+          mingw-w64-x86_64-libdeflate
+    - name: Compile htslib
+      shell: msys2 {0}
+      run: |
+        export PATH=/mingw64/bin:$PATH
+        export MSYSTEM=MINGW64
+        autoreconf -i
+        ./configure
+        make -j6
+    - name: Check Htslib
+      shell: msys2 {0}
+      run: |
+        export PATH=/mingw64/bin:$PATH
+        export MSYSTEM=MINGW64
+        make test-shlib-exports && make check
+
diff --git a/test/header_syms.pl b/test/header_syms.pl
index fe5128a78..a8d4a885c 100755
--- a/test/header_syms.pl
+++ b/test/header_syms.pl
@@ -60,6 +60,7 @@ sub extract_symbols {
 
     open(my $f, '<', $file) || die "Couldn't open $file : $!\n";
     my $text = <$f>;
+    $text =~ tr/\r//d;
     close($f) || die "Error reading $file : $!\n";
 
     # Get rid of comments