Multiple enhancements

- Added Pfasum substitution matrices. 
- New dissimilarity measure.
- Added AVX512 support.
- Added gzipped inputs support.
- Added distance-based prefiltering in MST Prim's algorithm.
- Fix in MedoidTrees - full FAMSA executed always when subtree size is smaller then `-sample_size` parameter.
- Automatic deployment of Windows releases.

Author: agudys

.github/workflows/deploy.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
-    runs-on: [self-hosted, kmer-db, '${{ matrix.machine }}']
+    runs-on: [self-hosted, famsa, '${{ matrix.machine }}']
 
     steps:
     - name: clean
@@ -24,6 +24,22 @@ jobs:
       with:
         submodules: recursive
 
+  ########################################################################################
+  checkout-windows:
+    name: checkout (Windows)
+    strategy:
+      matrix:
+        machine: [x64_windows]
+    runs-on: [self-hosted, famsa, '${{ matrix.machine }}']
+    
+    steps:
+    - name: clean
+      run: Remove-Item -Path "${{ github.workspace }}/*" -Recurse -Force 
+
+    - uses: actions/checkout@v4
+      with:
+        submodules: recursive
+    
 ########################################################################################
   make:
     name: Make
@@ -33,35 +49,62 @@ jobs:
       matrix:
         machine: [x64_linux]
         platform: [avx2]
-        compiler: [g++-13]
-        static: [true]
+        compiler: [13]
         include:
-        - {machine: arm64_linux, platform: arm8, compiler: g++-12, static: true}
-        - {machine: x64_mac, platform: avx2, compiler: g++-13, static: false}
-        - {machine: arm64_mac, platform: m1, compiler: g++-13, static: false}
+        - {machine: arm64_linux, platform: arm8, compiler: 12}
+        - {machine: x64_mac, platform: avx2, compiler: 13}
+        - {machine: arm64_mac, platform: m1, compiler: 13}
 
     runs-on: [self-hosted, famsa, '${{ matrix.machine }}']  
 
     steps:
     - name: make 
-      run: make -j32 CXX=${{matrix.compiler}} STATIC_LINK=${{ matrix.static }} PLATFORM=${{ matrix.platform }}
+      run: gmake -j32 CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} STATIC_LINK=true PLATFORM=${{ matrix.platform }}
     - name: tar artifacts
-      run: tar -cvzf famsa.tar.gz famsa LICENSE
+      run: tar -cvzf famsa.tar.gz LICENSE -C ./bin famsa 
+
+
+########################################################################################
+  make-windows:
+    name: Make (Windows)
+    needs: checkout-windows
+    strategy:
+      fail-fast: false
+      matrix:
+        machine: [x64_windows]
+     
+    runs-on: [self-hosted, famsa, '${{ matrix.machine }}']  
+
+    env:
+      MSBUILD: "C:/Microsoft Visual Studio/2022/Community/MSBuild/Current/Bin/MSBuild.exe"
+        
+    steps:
+    - name: make 
+      run: | 
+        & "$env:MSBUILD" FAMSA.sln /p:Configuration=Release /p:Platform=x64 /m
+    - name: tar artifacts
+      run: tar -cvzf famsa.tar.gz LICENSE -C ./x64/Release famsa.exe 
 
 
 ########################################################################################
   help:
     name: Print usage
-    needs: make
+    needs: 
+      - make
+      - make-windows
     strategy:
       fail-fast: false
       matrix:
         machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
+        exec: [./bin/famsa]
+        include:
+          - {machine: x64_windows, exec: ./x64/Release/famsa.exe}
+        
     runs-on: [self-hosted, famsa, '${{ matrix.machine }}']
 
     steps:
     - name: help
-      run: ./famsa
+      run: ${{ matrix.exec }}
 
 ########################################################################################
   upload:
@@ -70,7 +113,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        machine: [x64_linux, x64_mac, arm64_linux, arm64_mac]
+        machine: [x64_linux, x64_mac, arm64_linux, arm64_mac, x64_windows]
     runs-on: [self-hosted, famsa, '${{ matrix.machine }}']
 
     steps:

.github/workflows/main.yml

@@ -9,45 +9,53 @@ on:
 
 jobs:
 
-  make-tests:
+ ########################################################################################
+  make:
     name: Make
     strategy:
+      fail-fast: false
       matrix:
         machine: [ubuntu-latest, macOS-13]
-    runs-on: ['${{ matrix.machine }}']
-    
-    env: 
-      REF_DIR: ./test/adeno_fiber
-      INPUT: ./test/adeno_fiber/adeno_fiber
- 
+        include:
+        - {machine: ubuntu-latest, gmake_install_command: 'gmake --version', compiler: 12}
+        - {machine: macOS-13, gmake_install_command: 'brew install make && gmake --version', compiler: 12}
+        
+    runs-on: ['${{ matrix.machine }}']   
+
     steps:
     - uses: actions/checkout@v4
       with:
         submodules: recursive
-    - name: make
-      run: |
-        g++ --version
-        make -j
-        
-    - name: copy sl->slink references
-      run: |
-        cp ./test/adeno_fiber/sl.fasta ./test/adeno_fiber/slink.fasta
-        cp ./test/hemopexin/medoid-sl.fasta ./test/hemopexin/medoid-slink.fasta  
+
+    - name: install gmake
+      run: ${{ matrix.gmake_install_command }}    
 
+    - name: get tags
+      run: | 
+        cd ./libs/igraph
+        git fetch --prune --unshallow
+        echo exit code $?
+        git tag --list
+      continue-on-error: true 
+      
+    - name: make
+      run: | 
+        gmake -j CXX=g++-${{matrix.compiler}} CC=gcc-${{matrix.compiler}} STATIC_LINK=true PLATFORM=avx2
+        cp ./bin/famsa ./famsa
     - name: tar artifacts
-      run: tar -cvf famsa.tar ./famsa ./test   
+      run: tar -cvf famsa.tar ./famsa ./test/adeno_fiber/* ./test/hemopexin/*
 
     - uses: actions/upload-artifact@v4
       with:
         name: executable-artifact-${{ matrix.machine }}
         path: ./famsa.tar    
-      
-    
+        
+   
   ########################################################################################    
 
   full-tree:
     name: Full tree (adeno-fiber)
-    needs: make-tests
+    needs: make
     strategy:
       fail-fast: false
       matrix: