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: 1.59.0
 
     - 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
-
+
 # 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()
 

README.md

@@ -17,7 +17,7 @@ This documentation outlines the necessary and optional [dependencies](#dependenc
 Dependencies installation
 -------------------------
 
-**PURIFY** is written in `C++11`. Pre-requisites and dependencies are listed in following and minimal versions required are tested against `Travis CI` meaning that they come natively with OSX and the Ubuntu Trusty release. These are also the default ones fetched by `CMake` (an internet connection is required for this).
+**PURIFY** is written in `C++11`. Pre-requisites and dependencies are listed in following and minimal versions required are meaning that they come natively with OSX and the Ubuntu Trusty release. These are also the default ones fetched by `CMake` (an internet connection is required for this).
 
 `C++` minimal dependencies:
 
@@ -51,31 +51,47 @@ Dependencies installation
 Installing and building PURIFY
 -------------------------------------
 
-**PURIFY** can be installed through the software packet manager on Linux Debian distributions:
+To build Purify:
 
-```
-apt-get install purify
-```
+1. Install [TensorFlow C API](https://www.tensorflow.org/install/lang_c)
+1. Clone the UCL fork of cppflow and create a conan package using
 
-Alternatively, you can build **PURIFY** entirely from the source code. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/purify):
+    ``` bash
+    git clone [email protected]:UCL/cppflow.git
+    conan create ./cppflow/ -pr:h=default -pr:b=default
+    ```
 
-```
-git clone https://github.com/astro-informatics/purify.git
-```
+1. Clone sopt and create a conan package using
+
+    ``` bash
+    git clone [email protected]:astro-informatics/sopt.git
+    conan create ./sopt/ --build missing -s compiler.libcxx=libstdc++11 -o cppflow=on  -pr:h=default -pr:b=default
+    ```
 
-Then, the program can be built with standard `CMake` command:
+1. Once the mandatory dependencies are present, `git clone` from the [GitHub repository](https://github.com/astro-informatics/purify):
 
-```
-cd /path/to/code
-mkdir build
-cd build
-cmake -DCMAKE_BUILD_TYPE=Release ..
-make
-```
+    ``` bash
+    git clone https://github.com/astro-informatics/purify.git
+    ```
+
+1. Then, the program can be built using Conan:
+
+    ``` bash
+    cd /path/to/code
+    mkdir build
+    conan install .. --build missing -pr:h=default -pr:b=default
+        conan build ..
+    ```
+
+    You can turn the various options on and off by adding flags to the `conan install` command, e.g.
+
+    ```bash
+    conan install .. --build missing -o cppflow=on -o openmp=on -o mpi=off -pr:h=default -pr:b=default
+    ```
 
 To test everything went all right:
 
-```
+``` bash
 cd /path/to/code/build
 ctest .
 ```