Add release download and windows compilation workflow tests

.github/workflows/build.yml

@@ -13,14 +13,26 @@ on:
 name: Build 
 
 jobs:
-  build_and_test:
+  download_and_test_ubuntu:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v4
+      - name: Download Release Binaries
+        run: |
+          curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Linux_x86-64.zip &&
+          unzip trimal.zip && mv trimAl_Linux_x86-64/* source/
+      - name: Test trimal for Linux x86_64
+        run: file source/trimal && file source/readal && file source/statal && ./scripts/generate_trimmed_msas.sh &&
+          ./scripts/compare_trimmed_msas.sh
+
+  build_and_test_ubuntu:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
         arch: [x86_64, aarch64]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Build trimal for Linux x86_64
         if: matrix.arch == 'x86_64'
         run: cd source && make all && file trimal && file readal && file statal &&
@@ -41,3 +53,56 @@ jobs:
           run: |
             cd /trimal/source && make all && file trimal && file readal && file statal &&
             cd .. && ./scripts/generate_trimmed_msas.sh && ./scripts/compare_trimmed_msas.sh
+
+  download_and_test_windows:
+      runs-on: windows-2022
+      steps:
+      - uses: actions/checkout@v4
+      - name: Download Release Binaries
+        run: |
+          curl -L -o trimal.zip https://github.com/inab/trimal/releases/download/v1.5.0/trimAl_Windows_x86-64.zip
+
+      - name: Unzip Binaries
+        run: |
+          powershell -Command "Expand-Archive -Path trimal.zip -DestinationPath ."
+
+      - name: Verify Binaries
+        run: |
+          Move-Item -Path .\trimal.exe -Destination .\source\
+          Get-Command .\source\trimal.exe
+
+      - name: Run generate_trimmed_msas.ps1
+        run: |
+          powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1
+
+      - name: Run compare_trimmed_msas.ps1
+        run: |
+          powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1
+
+  build_and_test_windows:
+      runs-on: windows-2022
+      steps:
+        - uses: actions/checkout@v4
+        - name: Set up MSYS2
+          uses: msys2/setup-msys2@v2
+          with:
+            msystem: MINGW64
+            update: true
+            install: >-
+              make
+              mingw-w64-x86_64-gcc
+              file
+        - name: Build trimal for Windows x86_64
+          run: |
+            cd source
+            make -f makefile.Windows
+            file trimal.exe
+            file readal.exe
+            file statal.exe
+        - name: Run generate_trimmed_msas.ps1
+          run: |
+            powershell -ExecutionPolicy Bypass -File .\scripts\generate_trimmed_msas.ps1
+
+        - name: Run compare_trimmed_msas.ps1
+          run: |
+            powershell -ExecutionPolicy Bypass -File .\scripts\compare_trimmed_msas.ps1

.gitignore

@@ -2,4 +2,5 @@
 source/readal
 source/statal
 source/trimal
-docs/build
+docs/build
+scripts/dummy-file.txt

scripts/compare_trimmed_msas.ps1

@@ -0,0 +1,44 @@
+# Define methods
+$methods = "gappyout", "strict", "strictplus", "automated1", "nogaps", "noallgaps"
+
+# Compare files
+foreach ($method in $methods) {
+    $files = Get-ChildItem -Path "test_msas\$method" -Filter *.fasta
+    foreach ($file in $files) {
+        $msa_filename = $file.Name
+        $test_file = $file.FullName
+        $reference_file = Join-Path -Path "dataset\trimmed_msas\$method" -ChildPath $msa_filename
+
+        if (-Not (Test-Path $reference_file)) {
+            Write-Output "Reference file $reference_file does not exist."
+            exit 1
+        }
+
+        if (-Not (Test-Path $test_file)) {
+            Write-Output "Test file $test_file does not exist."
+            exit 1
+        }
+
+        $test_content = Get-Content $test_file
+        $reference_content = Get-Content $reference_file
+
+        # Check if both files are empty
+        if ($test_content.Count -eq 0 -and $reference_content.Count -eq 0) {
+            Write-Output "Both $test_file and $reference_file are empty and considered equal."
+            continue
+        }
+
+        # Compare contents
+        $result = Compare-Object $test_content $reference_content -SyncWindow 0
+        if ($result) {
+            Write-Output "Files $test_file and $reference_file differ."
+            exit 1
+        }
+        else {
+            Write-Output "Compared $test_file and $reference_file"
+        }
+    }
+}
+
+# Remove test_msas directory
+Remove-Item -Recurse -Force test_msas