Add build automations (deb and conda)

Author: imallona

.github/workflows/ci.yml

@@ -0,0 +1,100 @@
+name: build_and_test
+
+on:
+  pull_request:
+  workflow_dispatch:
+
+jobs:
+  build-and-test:
+    runs-on: ubuntu-latest
+    
+    steps:
+    - name: Checkout code
+      uses: actions/checkout@v4
+      
+    # - name: Install dependencies
+    #   run: |
+    #     sudo apt-get update
+    #     sudo apt-get install -y g++ cppcheck python3-pip
+    #     pip3 install "cmake>=4.0"
+    #     cmake --version
+        
+    - name: Set up Miniconda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        auto-update-conda: true
+        python-version: 3.12
+        channels: conda-forge,nodefaults
+        activate-environment: build-env
+
+    - name: Install build tools
+      shell: bash -l {0}
+      run: |
+        conda install -y conda-build make gxx_linux-64 cmake>=4.0
+        cmake --version
+        conda-build --version
+        
+    - name: Configure CMake
+      shell: bash -l {0}
+      run: |
+        mkdir -p build
+        cd build
+        cmake ..
+    
+    - name: Build
+      shell: bash -l {0}
+      run: |
+        cd build
+        make -j$(nproc)
+    
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        cd build
+        ctest --output-on-failure --verbose
+    
+    # - name: Run cppcheck      
+    #   uses: deep5050/cppcheck-action@main
+    #   with:
+    #     skip_preprocessor: disable
+    #     enable: all #performance,portability,warning
+    #     exclude_check: ./__tests__/exclude/
+    #     inconclusive: disable
+    #     inline_suppression: disable
+    #     force_language: c++
+    #     force: enable
+    #     max_ctu_depth: 12
+    #     platform: disable
+    #     output_file: cppcheck_report.txt
+    #     other_options: --bug-hunting --verbose
+
+    # - name: Show cppcheck report
+    #   run: |
+    #     cat cppcheck_report.txt
+
+    - name: Build Debian package
+      shell: bash -l {0}
+      run: |
+        cd build
+        cpack -G DEB
+
+    - name: Debian package as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: fastder
+        path: build/*.deb
+        # files: build/*.deb
+
+    - name: Clean previous build
+      run: rm -rf build
+      
+    - name: Build Conda package
+      shell: bash -l {0}
+      run: |
+        conda-build conda/recipe
+
+    - name: Conda package as artifact
+      uses: actions/upload-artifact@v4
+      with:
+        name: conda-package
+        path: /usr/share/miniconda3/conda-bld/*/*.tar.bz2

.gitignore

@@ -7,3 +7,5 @@ afe_data/
 afe_data_param_tuning/
 build/
 dataset1/
+.idea/
+cpp/.idea/

.idea/.gitignore

@@ -1,36 +1,48 @@
+option(CONDA_BUILD "Building inside conda-build" OFF)
+
 cmake_minimum_required(VERSION 4.0)
 project(mls)
 
 set(CMAKE_CXX_STANDARD 20)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+find_package(Threads REQUIRED)
+
 include_directories(cpp)
 
 add_library(mls_lib
         cpp/Averager.cpp
-        cpp/Averager.h
         cpp/BedGraphRow.cpp
-        cpp/BedGraphRow.h
         # cpp/integrate_sj.cpp
         cpp/Parser.cpp
-        cpp/Parser.h
         cpp/SJRow.cpp
-        cpp/SJRow.h
         cpp/StitchedER.cpp
-        cpp/StitchedER.h
         cpp/Integrator.cpp
-        cpp/Integrator.h
         cpp/GTFRow.cpp
-        cpp/GTFRow.h
-
-
 )
 
 
 add_executable(mls
         cpp/main.cpp
 )
-target_link_libraries(mls PRIVATE mls_lib)
+
+target_link_libraries(mls PRIVATE mls_lib Threads::Threads)
 
 enable_testing()
-add_subdirectory(tests)
+
+if(NOT CONDA_BUILD)
+       add_subdirectory(tests)
+endif()
+
+# packaging
+set(CPACK_PACKAGE_NAME "fastder")
+set(CPACK_PACKAGE_VENDOR "Martina Lehmann")
+set(CPACK_PACKAGE_DESCRIPTION_SUMMARY "fastder, a fast expressed regions finder")
+set(CPACK_PACKAGE_VERSION "0.0.1")
+set(CPACK_PACKAGE_CONTACT "martina.lavanya@gmail.com")
+
+# Debian-specific packaging settings
+set(CPACK_DEBIAN_PACKAGE_MAINTAINER "Martina Lehmann")
+set(CPACK_DEBIAN_PACKAGE_DEPENDS "libstdc++6")
+
+include(CPack)