Merge branch 'master' into piyumal

Author: piyumalanthony

.github/workflows/ci.yaml

@@ -49,17 +49,19 @@ jobs:
       run: |
         mkdir build
         cd build
-        cmake .. -DIQTREE_FLAGS=static -DCMAKE_C_COMPILER=$(which gcc-${{ matrix.gcc-version }}) -DCMAKE_CXX_COMPILER=$(which g++-${{ matrix.gcc-version }})
+        cmake .. -DCMAKE_POLICY_VERSION_MINIMUM=3.5 -DIQTREE_FLAGS=static -DCMAKE_C_COMPILER=$(which gcc-${{ matrix.gcc-version }}) -DCMAKE_CXX_COMPILER=$(which g++-${{ matrix.gcc-version }})
         make -j
-        file iqtree2 | grep x86-64
+        make package
+        file iqtree3 | grep x86-64
+        file iqtree*.tar.gz | grep gzip
 
     - name: Upload Built Binary
       # Only upload for one of the gcc & cmake tests
       if: ${{ matrix.upload }}
       uses: actions/upload-artifact@v4
       with:
         name: Linux x86-64
-        path: build/iqtree2
+        path: build/iqtree*.tar.gz
         if-no-files-found: error
 
   build-linux-aarch64:
@@ -83,13 +85,15 @@ jobs:
            cd build
            cmake .. -DIQTREE_FLAGS=static
            make -j
-           file iqtree2 | grep aarch64
+           make package
+           file iqtree3 | grep aarch64
+           file iqtree*.tar.gz | grep gzip
 
        - name: Upload Built Binary
          uses: actions/upload-artifact@v4
          with:
            name: Linux AArch64
-           path: build/iqtree2
+           path: build/iqtree*.tar.gz
            if-no-files-found: error
 
   build-macos-x86_64:
@@ -110,18 +114,19 @@ jobs:
           set -x
           mkdir build
           cd build
-          export LDFLAGS="-L/usr/local/opt/libomp/lib"
           export CPPFLAGS="-I/usr/local/opt/libomp/include"
           export CXXFLAGS="-I/usr/local/opt/libomp/include"
           cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
-          gmake -j
-          file iqtree2 | grep x86_64
+          make -j
+          make package
+          file iqtree3 | grep x86_64
+          file iqtree*.zip | grep Zip
           
       - name: Upload Built Binary
         uses: actions/upload-artifact@v4
         with:
           name: Mac x86-64
-          path: build/iqtree2
+          path: build/iqtree*.zip
           if-no-files-found: error
 
   build-macos-arm:
@@ -142,18 +147,19 @@ jobs:
           set -x
           mkdir build
           cd build
-          export LDFLAGS="-L/opt/homebrew/opt/libomp/lib"
           export CPPFLAGS="-I/opt/homebrew/opt/libomp/include"
           export CXXFLAGS="-I/opt/homebrew/opt/libomp/include"
           cmake .. -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++
-          gmake -j
-          file iqtree2 | grep arm64
+          make -j
+          make package
+          file iqtree3 | grep arm64
+          file iqtree*.zip | grep Zip
 
       - name: Upload Built Binary
         uses: actions/upload-artifact@v4
         with:
           name: Mac Arm
-          path: build/iqtree2
+          path: build/iqtree*.zip
           if-no-files-found: error
 
   compile-mac-universal:
@@ -164,22 +170,33 @@ jobs:
       - build-macos-arm
 
     steps:
-      - name: Download Artifacts
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Download Mac x86-64 Artifact
         uses: actions/download-artifact@v4
         with:
-          pattern: Mac *
-
+          name: Mac x86-64
+          path: x86
+        
+      - name: Download Mac Arm Artifact
+        uses: actions/download-artifact@v4
+        with:
+          name: Mac Arm
+          path: arm
+    
       - name: Combine Artifacts
-        run: lipo -create -output iqtree2 "Mac x86-64/iqtree2" "Mac Arm/iqtree2"
-
-      - name: Check Architectures
-        run: lipo -archs iqtree2
-
+        run: |
+          chmod +x test_scripts/make_universal.sh 
+          file1=$(ls x86/iqtree*.zip)
+          file2=$(ls arm/iqtree*.zip)
+          test_scripts/make_universal.sh "$file1" "$file2"
+          
       - name: Upload Built Binary
         uses: actions/upload-artifact@v4
         with:
           name: Mac Universal
-          path: iqtree2
+          path: iqtree*.zip
           if-no-files-found: error
 
   build-windows-x86-64:
@@ -221,20 +238,23 @@ jobs:
             -DCMAKE_MAKE_PROGRAM=mingw32-make ^
             -DBoost_INCLUDE_DIR=${{steps.install-boost.outputs.BOOST_ROOT}}/include ^
             -DBoost_LIBRARY_DIRS=${{steps.install-boost.outputs.BOOST_ROOT}}/lib ^
-            -DIQTREE_FLAGS="cpp14" ..
+            -DCMAKE_POLICY_VERSION_MINIMUM=3.5 ^
+            -DIQTREE_FLAGS="static cpp14" ..
           make -j
+          make package
         env:
           BOOST_ROOT: ${{ steps.install-boost.outputs.BOOST_ROOT }}
 
       - name: Check File Arch
         shell: bash
         run: |
           cd build
-          file iqtree2.exe | grep x86-64
+          file iqtree3.exe | grep x86-64
+          file iqtree*.zip
 
       - name: Upload Built Binary
         uses: actions/upload-artifact@v4
         with:
           name: Windows x86-64
-          path: build/iqtree2.exe
+          path: build/iqtree*.zip
           if-no-files-found: error