Merge pull request #6 from phylo42/develop

Develop

Author: blinard-BIOINFO

.github/workflows/build.yml

@@ -1,75 +1,47 @@
 name: CMake
-
 on: [push]
-
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
 
 jobs:
   build:
-
     name: ${{matrix.buildname}}
-
-    runs-on: ${{matrix.os}}
-
     strategy:
       fail-fast: false
       matrix:
-        os: [ ubuntu-20.04, ubuntu-18.04, macos-10.15, macos-11.0 ]
-        include:
-          - os: ubuntu-20.04
-            buildname: 'ubuntu-20.04'
-            triplet: x64-linux
-            compiler: gcc_64
-          - os: ubuntu-18.04
-            buildname: 'ubuntu-18.04'
-            triplet: x64-linux
-            compiler: gcc_64
-          - os: macos-10.15
-            buildname: 'macos-10.15'
-            triplet: x64-osx
-            compiler: clang_64
-          - os: macos-11.0
-            buildname: 'macos-11.0'
-            triplet: x64-osx
-            compiler: clang_64
+        os: [ ubuntu-latest ] #macos-14 ]
+    runs-on: ${{matrix.os}}
     steps:
     - name: Checkout
       uses: actions/checkout@v2
       with:
         submodules: recursive
-
-    - name: (MacOS) Install dependencies
-      if: runner.os == 'macOS'
-      run: brew install boost
-
+    #- name: (MacOS) Install dependencies
+    #  if: runner.os == 'macOS'
+    #  run: brew install llvm@20 lld@20 libomp boost
     - name: (Linux) Install dependencies
       if: runner.os == 'Linux'
-      run: sudo apt-get update && sudo apt-get install -yq libboost-dev libboost-serialization-dev libboost-filesystem-dev libboost-iostreams-dev
-
-    - name: Create Build Environment
-      # Some projects don't allow in-source building, so create a separate build directory
-      # We'll use this as our working directory for all subsequent commands
-      run: cmake -E make_directory ${{runner.workspace}}/build
-
-    - name: Configure CMake
-      # Use a bash shell so we can use the same syntax for environment variable
-      # access regardless of the host operating system
+      run: sudo apt-get update && sudo apt-get install -yq libomp-dev libboost-dev libboost-serialization-dev libboost-program-options-dev libboost-filesystem-dev libboost-iostreams-dev
+    #- name: (MacOS) Configure CMake
+    #  if: runner.os == 'macOS'
+    #  shell: bash
+    #  working-directory: ${{runner.workspace}}/sherpas
+    #  run: cmake -DLDFLAGS="-L/opt/homebrew/opt/libomp/lib -L/opt/homebrew/opt/llvm/lib" -DCPPFLAGS="-I/opt/homebrew/opt/libomp/include -I/opt/homebrew/opt/llvm/include" -DCMAKE_POLICY_VERSION_MINIMUM=3.5
+    - name: (Linux) Configure CMake
+      if: runner.os == 'Linux'
       shell: bash
-      working-directory: ${{runner.workspace}}/build
-      # Note the current convention is to use the -S and -B options here to specify source 
-      # and build directories, but this is only available with CMake 3.13 and higher.  
-      # The CMake binaries on the Github Actions machines are (as of this writing) 3.12
-      run: cmake $GITHUB_WORKSPACE -DCMAKE_BUILD_TYPE=$BUILD_TYPE
-
+      working-directory: ${{runner.workspace}}/sherpas
+      run: cmake -DCMAKE_POLICY_VERSION_MINIMUM=3.5
     - name: Build
-      working-directory: ${{runner.workspace}}/build
+      working-directory: ${{runner.workspace}}/sherpas
       shell: bash
-      # Execute the build.  You can specify a specific target with "--target <NAME>"
-      run: cmake --build . --config $BUILD_TYPE --target SHERPAS
-
-    - name: Test
-      working-directory: ${{runner.workspace}}/build
+      run: make
+    - name: Test SHERPAS
+      working-directory: ${{runner.workspace}}/sherpas
       shell: bash
       run: sherpas/SHERPAS -h
+    #- name: Test XPAS-DNA (db build capacity)
+    #  working-directory: ${{runner.workspace}}/sherpas
+    #  shell: bash
+    #  run: lib/xpas/build/xpas-build-dna --help

.gitignore

@@ -2,4 +2,6 @@ recomb/src/mull-main.cpp
 recomb/src/mull.cpp
 release-build
 core
-.DS_Store
+.DS_Store
+cmake-*
+.idea