DoubleHelixApp · teepean · Nov 6, 2024 · Nov 6, 2024
diff --git a/.github/workflows/compile-and-publish.yml b/.github/workflows/compile-and-publish.yml
@@ -1,16 +1,11 @@
 name: Compile and publish MSYS2 Dependencies
-
 on:
   release:
     branches: [ "main" ]
     types: [ published ]
-
 permissions:
   contents: read
-
 jobs:
-  # Builds on MSYS2 and upload a wheels artifact to be 
-  # released on PyPI
   build:
     runs-on: windows-latest
     steps:
@@ -19,8 +14,8 @@ jobs:
     - name: Set up MSYS2
       uses: msys2/setup-msys2@v2
       with:
-        msystem: UCRT64
-        update: false
+        msystem: ucrt64
+        update: true
         install: >-
           git
           autotools
@@ -32,6 +27,19 @@ jobs:
           python
           python-pip
           mingw-w64-ucrt-x86_64-tools-git
+          mingw-w64-ucrt-x86_64-toolchain
+          mingw-w64-ucrt-x86_64-curl
+          mingw-w64-ucrt-x86_64-libdeflate
+          mingw-w64-ucrt-x86_64-bzip2
+          mingw-w64-ucrt-x86_64-zlib
+          mingw-w64-ucrt-x86_64-xz
+          mingw-w64-ucrt-x86_64-openssl
+          mingw-w64-ucrt-x86_64-libtre-git
+          mingw-w64-ucrt-x86_64-libiconv
+          mingw-w64-ucrt-x86_64-libsystre
+          mingw-w64-ucrt-x86_64-libwinpthread
+          mingw-w64-ucrt-x86_64-ncurses
+          mingw-w64-ucrt-x86_64-autotools
     - name: Clone repositories
       shell: msys2 {0}
       run: |
@@ -42,7 +50,7 @@ jobs:
     - name: Compile htslib
       shell: msys2 {0}
       run: |
-        export PATH=$PATH:/mingw64/bin
+        export PATH=$PATH:/ucrt64/bin
         pushd .
         cd htslib
         autoreconf -i
@@ -52,7 +60,7 @@ jobs:
     - name: Compile samtools
       shell: msys2 {0}
       run: |
-        export PATH=$PATH:/mingw64/bin
+        export PATH=$PATH:/ucrt64/bin
         pushd .
         cd samtools
         autoheader
@@ -63,7 +71,7 @@ jobs:
     - name: Compile bcftools
       shell: msys2 {0}
       run: |
-        export PATH=$PATH:/mingw64/bin
+        export PATH=$PATH:/ucrt64/bin
         pushd .
         cd bcftools
         autoheader
@@ -74,18 +82,23 @@ jobs:
     - name: Compile bwa
       shell: msys2 {0}
       run: |
-        export PATH=$PATH:/mingw64/bin
+        # Temporarily switch to MSYS for bwa compilation
+        export MSYSTEM=MSYS
+        export PATH=/usr/bin:$PATH
         pushd .
         cd bwa
         make -j32
         popd      
     - name: Compile minimap2
       shell: msys2 {0}
       run: |
-        export PATH=$PATH:/mingw64/bin
+        # Switch back to UCRT64 for minimap2
+        export MSYSTEM=UCRT64
+        export PATH=$PATH:/ucrt64/bin
         pushd .
         cd minimap2
         make -j32
+        popd
     - name: Scan imports
       shell: msys2 {0}
       run: |
@@ -107,7 +120,6 @@ jobs:
         path: dist/
         retention-days: 1
 
-  # Publish Job
   pypi-publish:
     name: Upload release to PyPI
     runs-on: ubuntu-latest
@@ -123,4 +135,4 @@ jobs:
         name: wheels
         path: ./dist/
     - name: Publish package distributions to PyPI
-      uses: pypa/gh-action-pypi-publish@release/v1
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/testbuild.yml b/.github/workflows/testbuild.yml
@@ -0,0 +1,106 @@
+name: Compile and publish MSYS2 Dependencies
+on:
+  release:
+    branches: [ "main" ]
+    types: [ published ]
+permissions:
+  contents: read
+jobs:
+  build:
+    runs-on: windows-latest
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v4
+    - name: Set up MSYS2
+      uses: msys2/setup-msys2@v2
+      with:
+        msystem: ucrt64
+        update: true
+        install: >-
+          git
+          autotools
+          gcc
+          zlib-devel
+          libbz2-devel
+          liblzma-devel
+          ncurses-devel
+          python
+          python-pip
+          mingw-w64-ucrt-x86_64-tools-git
+          mingw-w64-ucrt-x86_64-toolchain
+          mingw-w64-ucrt-x86_64-curl
+          mingw-w64-ucrt-x86_64-libdeflate
+          mingw-w64-ucrt-x86_64-bzip2
+          mingw-w64-ucrt-x86_64-zlib
+          mingw-w64-ucrt-x86_64-xz
+          mingw-w64-ucrt-x86_64-openssl
+          mingw-w64-ucrt-x86_64-libtre-git
+          mingw-w64-ucrt-x86_64-libiconv
+          mingw-w64-ucrt-x86_64-libsystre
+          mingw-w64-ucrt-x86_64-libwinpthread
+          mingw-w64-ucrt-x86_64-ncurses
+          mingw-w64-ucrt-x86_64-autotools
+    - name: Clone repositories
+      shell: msys2 {0}
+      run: |
+        python -m pip install requests
+        python make_clone_script.py $GITHUB_REF > clone_script.sh
+        chmod +x clone_script.sh
+        ./clone_script.sh
+    - name: Compile htslib
+      shell: msys2 {0}
+      run: |
+        export PATH=$PATH:/ucrt64/bin
+        pushd .
+        cd htslib
+        autoreconf -i
+        ./configure
+        make -j32
+        popd
+    - name: Compile samtools
+      shell: msys2 {0}
+      run: |
+        export PATH=$PATH:/ucrt64/bin
+        pushd .
+        cd samtools
+        autoheader
+        autoconf -Wno-syntax
+        ./configure
+        make -j32
+        popd
+    - name: Compile bcftools
+      shell: msys2 {0}
+      run: |
+        export PATH=$PATH:/ucrt64/bin
+        pushd .
+        cd bcftools
+        autoheader
+        autoconf -Wno-syntax
+        ./configure
+        make -j32
+        popd
+    - name: Compile bwa
+      shell: msys2 {0}
+      run: |
+        # Temporarily switch to MSYS for bwa compilation
+        export MSYSTEM=MSYS
+        export PATH=/usr/bin:$PATH
+        pushd .
+        cd bwa
+        make -j32
+        popd      
+    - name: Compile minimap2
+      shell: msys2 {0}
+      run: |
+        # Switch back to UCRT64 for minimap2
+        export MSYSTEM=UCRT64
+        export PATH=$PATH:/ucrt64/bin
+        pushd .
+        cd minimap2
+        make -j32
+        popd
+    - name: Scan imports
+      shell: msys2 {0}
+      run: |
+        python -m pip install pefile
+        python import_scanner.py
diff --git a/make_clone_script.py b/make_clone_script.py
@@ -13,7 +13,7 @@ def print_clone_script(tag:str):
         "htslib": "git clone --depth 1 --recurse-submodules --branch {version} https://github.com/samtools/htslib",
         "samtools": "git clone --depth 1 --recurse-submodules --branch {version} https://github.com/samtools/samtools",
         "bcftools": "git clone --depth 1 --recurse-submodules --branch {version} https://github.com/samtools/bcftools",
-        "bwa": "git clone --depth 1 --recurse-submodules --branch {version} https://github.com/lh3/bwa",
+        "bwa": "git clone --depth 1 --recurse-submodules --branch cygwin https://github.com/WGSExtract/bwa/tree/cygwin",
         "minimap2": "git clone --depth 1 --recurse-submodules --branch {version} https://github.com/lh3/minimap2",
     }