Use Conan for installing dependencies

.clang-format-ignore

@@ -0,0 +1,2 @@
+#ignore .in.h template files
+**/*.in.h

.github/workflows/cmake.yml

@@ -4,15 +4,27 @@ on:
   push:
     branches: [ development ]
   pull_request:
-    branches: [ development ]
+    # CI runs when new commits are pushed or when draft PR is marked ready for review
+    types: [opened, synchronize, reopened, ready_for_review]
+  workflow_dispatch:
+    inputs:
+      debug_enabled:
+        description: 'Run the build with tmate debugging enabled (https://github.com/marketplace/actions/debugging-with-tmate)'
+        required: false
+        default: false
 
 env:
   # Customize the CMake build type here (Release, Debug, RelWithDebInfo, etc.)
   BUILD_TYPE: Release
-  OMP_NUM_THREADS: 4
+  OMP_NUM_THREADS: 2
+  CONAN_PRINT_RUN_COMMANDS: 1
+  CONAN_CPU_COUNT: 2
+  CONAN_SKIP_BROKEN_SYMLINKS_CHECK: 'True'
 
 jobs:
   build:
+    # Skip CI if PR is a draft
+    if: github.event.pull_request.draft == false
     name: ${{matrix.os}}-${{matrix.cxx}}-mpi:${{matrix.mpi}}-openmp:${{matrix.omp}}
     # The CMake configure and build commands are platform agnostic and should work equally
     # well on Windows or Mac.  You can convert this to a matrix build if you need
@@ -29,51 +41,96 @@ jobs:
             - ubuntu-20.04
             - macos-11
           cc:
-            - gcc-9
+            - gcc-10
             - clang
           cxx:
-            - g++-9
+            - g++-10
             - clang++
           mpi:
-            - "ON"
-            - "OFF"
+            - "on"
+            - "off"
           omp:
-            - "ON"
-            - "OFF"
+            - "on"
+            - "off"
           exclude:
-            - cc: gcc-9
+            - cc: gcc-10
               cxx: clang++
             - cc: clang
-              cxx: g++-9
+              cxx: g++-10
             - os: ubuntu-20.04
               cc: clang
               cxx: clang++
+            - os: macos-11
+              mpi: "on"
+            - cxx: clang++
+              omp: "on"
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
+      with:
+        submodules: recursive
+
+   # Enable tmate debugging of manually-triggered workflows if the input option was provided
+    - name: Setup tmate session
+      uses: mxschmitt/action-tmate@v3
+      if: ${{ github.event_name == 'workflow_dispatch' && github.event.inputs.debug_enabled }}
 
     - name: Install Dependencies on Ubunutu
       if: ${{ contains(matrix.os, 'ubuntu') }}
-      run: sudo apt install libfftw3-dev libtiff5-dev openmpi-bin libopenmpi-dev libboost-all-dev libeigen3-dev libyaml-cpp-dev ccache libcfitsio-dev casacore-dev
+      run: |
+        sudo apt update
+        sudo apt install openmpi-bin libopenmpi-dev ccache casacore-dev
 
     - name: Install Dependencies on MacOS
       if: ${{ contains(matrix.os, 'macos') }}
-      run: brew install fftw libtiff open-mpi boost libyaml cfitsio ccache
+      run: |
+        # Brew update has bugs but we don't seem to be affected, see
+        # https://github.com/actions/setup-python/issues/577
+        # brew update is very slow because it's updating a lot of unrelated packages
+        # workflow seems to run fine with default versions
+        # brew update
+        brew install open-mpi libomp ccache
+        echo "CMAKE_PREFIX_PATH=/usr/local/opt/libomp" >> $GITHUB_ENV
+
+    - name: Install Tensorflow API on Ubuntu
+      # TODO could this be combined with mac version somehow? if/else?
+      if: ${{ contains(matrix.os, 'ubuntu') }}
+      uses: UCL/install-tensorflow-action@main
+      with:
+        version: 2.11.0
+        os: linux
+
+    - name: Install Tensorflow API on MacOS
+      if: ${{ contains(matrix.os, 'macos') }}
+      uses: UCL/install-tensorflow-action@main
+      with:
+        version: 2.11.0
+        os: darwin
+
+    - name: Select Python 3.10
+      # otherwise turtlebrowser/[email protected] fails on macos-12
+      # ref: https://github.com/turtlebrowser/get-conan/issues/4
+      uses: actions/setup-python@v4
+      with:
+        python-version: '3.10'
+
+    - name: Install Conan
+      id: conan
+      uses: turtlebrowser/get-conan@main
+      with:
+        version: 1.60.1
 
     - name: Prepare ccache timestamp
       id: ccache_cache_timestamp
-      shell: cmake -P {0}
-      run: |
-        string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC)
-        message("::set-output name=timestamp::${current_date}")
+      run: echo "{date_and_time}={$(date +'%Y-%m-%d-%H;%M;%S')}" >> $GITHUB_OUTPUT
     - name: Set ccache cache directory
       shell: bash
       run: echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}"
     - name: Cache ccache files
-      uses: actions/cache@v2
+      uses: actions/cache@v3
       with:
         path: ${{runner.workspace}}/.ccache
-        key: ${{matrix.os}}-${{matrix.cxx}}-${{matrix.mpi}}-${{matrix.omp}}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
+        key: ${{matrix.os}}-${{matrix.cxx}}-${{matrix.mpi}}-${{matrix.omp}}-${{ steps.ccache_cache_timestamp.outputs.date_and_time }}
         restore-keys: |
           ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}-${{ matrix.omp }}
           ${{ matrix.os }}-${{ matrix.cxx }}-${{ matrix.mpi }}
@@ -83,21 +140,28 @@ jobs:
 #    - name: Clear ccache
 #      run: ccache --clear
 
-    - name: Configure CMake
-      # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.
-      # See https://cmake.org/cmake/help/latest/variable/CMAKE_BUILD_TYPE.html?highlight=cmake_build_type
-      run: |
-        cmake -B ${{github.workspace}}/build -DCMAKE_BUILD_TYPE=${{env.BUILD_TYPE}} \
-        -DCMAKE_C_COMPILER_LAUNCHER=ccache -DCMAKE_CXX_COMPILER_LAUNCHER=ccache \
-        -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \
-        -Ddompi=${{matrix.mpi}} -Dopenmp=${{matrix.omp}}
+    - name: create sopt package on gcc
+      if: ${{ contains(matrix.cxx, 'g++-10') }}
+      run: conan create ${{github.workspace}}/sopt --build missing -s:b compiler.libcxx=libstdc++11 -o:b mpi=${{matrix.mpi}} -o:b openmp=${{matrix.omp}}  -pr:h=default -pr:b=default
+
+    - name: create sopt package on apple-clang
+      if: ${{ contains(matrix.cxx, 'clang++') }}
+      run: conan create ${{github.workspace}}/sopt --build missing -o:b mpi=${{matrix.mpi}} -o:b openmp=${{matrix.omp}}  -pr:h=default -pr:b=default
+
+    - name: Conan install on gcc
+      if: ${{ contains(matrix.cxx, 'g++-10') }}
+      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build -s compiler.libcxx=libstdc++11 --build missing  -o mpi=${{matrix.mpi}} -o openmp=${{matrix.omp}}  -pr:h=default -pr:b=default
+
+    - name: Conan install on apple-clang
+      if: ${{ contains(matrix.cxx, 'clang++') }}
+      run: conan install ${{github.workspace}} -if ${{github.workspace}}/build --build missing  -o mpi=${{matrix.mpi}} -o openmp=${{matrix.omp}}  -pr:h=default -pr:b=default
 
     - name: Build
       # Build your program with the given configuration
-      run: cmake --build ${{github.workspace}}/build --config ${{env.BUILD_TYPE}} --parallel 2
+      run: conan build ${{github.workspace}} -bf ${{github.workspace}}/build
 
     - name: Test
       working-directory: ${{github.workspace}}/build
       # Execute tests defined by the CMake configuration.
       # See https://cmake.org/cmake/help/latest/manual/ctest.1.html for more detail
-      run: ctest -C ${{env.BUILD_TYPE}}
+      run: ctest -C ${{env.BUILD_TYPE}} --output-on-failure

.github/workflows/documentation.yml

@@ -3,15 +3,17 @@ name: Documentation
 on:
   push:
     branches: [ development ]
-  
+
 jobs:
   make-documentation:
     runs-on: ubuntu-20.04
     steps:
-    
+
       - name: Install dependencies
-        run: sudo apt install libfftw3-dev libtiff5-dev libboost-all-dev libeigen3-dev libyaml-cpp-dev libcfitsio-dev casacore-dev doxygen graphviz
-
+        run: |
+            sudo apt install libfftw3-dev libtiff5-dev libboost-all-dev libeigen3-dev libyaml-cpp-dev libcfitsio-dev casacore-dev doxygen graphviz
+            pip install conan
+
       - name: Pull sopt repo and build docs
         run : |
           git clone https://github.com/astro-informatics/sopt.git
@@ -23,21 +25,23 @@ jobs:
 
       - name: Check out Purify
         uses: actions/checkout@v2
- 
+
       - name: Configure and build docs
         run: | 
           mkdir build
           cd build
+          conan install ..
           cmake .. \
           -Ddompi=OFF \
           -Dopenmp=OFF \
           -Ddocs=ON \
           -Dweb=ON 
           make docweb VERBOSE=1
-        
+
       - name: Deploy to GH pages
         if: ${{github.event_name == 'push'}}
         uses: JamesIves/[email protected]
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: build/cpp/docs/html # The folder the action should deploy.
+

.github/workflows/linting.yml

@@ -3,28 +3,27 @@ name: Linting
 on:
   push:
     branches: [ development ]
-  pull-request:
-    branches: [development]    
+  pull_request:
+    branches: [development]
+
 
-
 jobs:
   linting:
     runs-on: ubuntu-20.04
     steps:
       - name: Checkout repo
-        uses: actions/checkout@v2
-
-
-      - name: Install dependencies
-        run: |
-          sudo apt install clang-format
-
+        uses: actions/checkout@v3
+
 # Check code meets Google C++ style guide https://google.github.io/styleguide/cppguide.html
       - name: Run linting
-        run: | 
-          find ../ -regex '.*\.\(cc\|h\)' -not -iname '*.in.h' | xargs -I{} -P 10 clang-format -i -style=file {}; git diff
-
+        uses: DoozyX/[email protected]
+        with:
+          source: '.'
+          extensions: 'h,cc'
+          clangFormatVersion: 16
+          inplace: True
+
       - name: Report results
-        run: | 
+        run: |
           git diff --exit-code || (echo '## NOTE: your code is not linted properly - please commit the suggested changes'; false)
- 
+

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "sopt"]
+	path = sopt
+	url = https://github.com/astro-informatics/sopt.git

CMakeLists.txt

@@ -3,6 +3,7 @@ project(Purify C CXX)
 
 # Location of extra cmake includes for the project
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake_files)
+list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/build)
 
 # Downloads and installs GreatCMakeCookOff
 # It contains a number of cmake recipes
@@ -19,6 +20,7 @@ option(docimg         "Enable CImg"                                     off)
 option(docasa         "Enable CASA"                                     off)
 option(docs           "Build documentation"                             off)
 option(coverage       "Build coverage"                                  off)
+option(cppflow        "Build with TensorFlow interface"                 off)
 
 if(NOT CMAKE_BUILD_TYPE)
   message(STATUS "Setting build type to 'Relese' as none was specified.")
@@ -30,8 +32,12 @@ message(STATUS "Building purify in ${CMAKE_BUILD_TYPE} mode")
 include(version)
 set(Sopt_GIT_TAG "development" CACHE STRING "Branch/tag when downloading sopt")
 
-# we are doing c++11
-include(AddCPP11Flags)
+## we are doing c++11
+#include(AddCPP11Flags)
+# c++17 is required when using cppflow with learned algorithms
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
 
 # sets up rpath so libraries can be found
 include(rpath)
@@ -52,7 +58,7 @@ endif()
 
 if(tests)  # Adds ctest
   enable_testing()
-  find_package(Catch 2.3.0 EXACT)
+  find_package(Catch)
   include(AddCatchTest)
 endif()