Api/gamma

.github/workflows/c-cpp.yml

@@ -16,35 +16,53 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
+    - uses: s-weigand/setup-conda@v1
+      with: 
+        activate-conda: true
+        update-conda: true
+    - run: conda --version
+    - run: which python
     - name: dependencies
-      run: sudo apt-get install coreutils build-essential gcc-12 g++-12 gfortran-12 libgsl-dev libgslcblas0 qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools dvipng lcov cmake texlive texlive-latex-extra texlive-luatex -y
+      run: |
+        sudo apt-get install coreutils build-essential gcc-12 g++-12 gfortran-12 libgsl-dev libgslcblas0 qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools dvipng lcov cmake texlive texlive-latex-extra texlive-luatex -y
+        conda env create -f pymarty-conda-env.yml
+        source ${CONDA_PREFIX}/bin/activate pymarty
     - name: configure
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         mkdir build
         cd build
         export CXX=g++-12
         export CC=gcc-12
         export FC=gfortran-12
-        cmake ..
+        cmake .. -DFORCE_PYMARTY_CONFIG=1
     - name: make
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         make
     - name: install
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         sudo make install
     - name: test
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
         ctest --output-on-failure
   build-and-test-ubuntu-gcc9:
     runs-on: ubuntu-20.04
     steps:
     - uses: actions/checkout@v3
+    - uses: s-weigand/setup-conda@v1
+      with: 
+        activate-conda: true
+        update-conda: true
     - name: dependencies
-      run: sudo apt-get install coreutils build-essential gcc-9 g++-9 gfortran-9 libgsl-dev libgslcblas0 qt5-default dvipng lcov cmake texlive texlive-latex-extra texlive-luatex -y
+      run: |
+        sudo apt-get install coreutils build-essential gcc-9 g++-9 gfortran-9 libgsl-dev libgslcblas0 qt5-default dvipng lcov cmake texlive texlive-latex-extra texlive-luatex -y
     - name: configure
       run: |
         mkdir build
@@ -70,10 +88,18 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v3
+    - uses: s-weigand/setup-conda@v1
+      with: 
+        activate-conda: true
+        update-conda: true
     - name: dependencies
-      run: sudo apt-get install coreutils build-essential clang gfortran libgsl-dev libgslcblas0 qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools dvipng cmake lcov texlive texlive-latex-extra texlive-luatex -y
+      run: |
+        sudo apt-get install coreutils build-essential clang gfortran libgsl-dev libgslcblas0 qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools dvipng cmake lcov texlive texlive-latex-extra texlive-luatex -y
+        conda env create -f pymarty-conda-env.yml
+        source ${CONDA_PREFIX}/bin/activate pymarty
     - name: configure
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         mkdir build
         cd build
         export CXX=clang++
@@ -82,21 +108,28 @@ jobs:
         cmake ..
     - name: make
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         make
     - name: install
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         sudo make install
     - name: test
       run: |
+        source ${CONDA_PREFIX}/bin/activate pymarty
         cd build
         export LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/usr/local/lib
         ctest --output-on-failure
   build-and-test-macos:
     runs-on: macos-latest
     steps:
     - uses: actions/checkout@v3
+    - uses: s-weigand/setup-conda@v1
+      with: 
+        activate-conda: true
+        update-conda: true
     - name: dependencies
       run: |
         brew install coreutils gcc@12 gsl qt5 cmake lcov imagemagick texlive octave pkg-config

.gitignore

@@ -2,3 +2,4 @@ marty_env.sh
 build/*
 .vscode
 *.sw[p-z]
+*.so

CMakeLists.txt

@@ -13,6 +13,25 @@ set(LLVM_COMPILERS 0)
 set(REQUIRED_COMPILER_VERSION 0)
 set(IDENTICAL_COMPILER_VERSION 0)
 
+# Config for Pymarty
+if (NOT PYMARTY_PYTHON_VERSION)
+    find_package(Python COMPONENTS Interpreter Development)
+else()
+    find_package(Python EXACT ${PYMARTY_PYTHON_VERSION} COMPONENTS Interpreter Development)
+    set(PYBIND11_PYTHON_VERSION ${PYMARTY_PYTHON_VERSION} CACHE STRING "")
+endif()
+find_package(pybind11 CONFIG)
+
+if (Python_FOUND AND pybind11_FOUND)
+    set(CONFIGURE_PYMARTY ON)
+else()
+    message(WARNING "Cannot configure pybindings for MARTY. Python or pybind11 are missing.")
+    set(CONFIGURE_PYMARTY OFF)
+endif()
+if (FORCE_PYMARTY_CONFIG AND (NOT CONFIGURE_PYMARTY))
+    message(FATAL_ERROR "The variable FORCE_PYMARTY_CONFIG was set to 1 but pymarty cannot be configured, aborting configuration.")
+endif()
+
 find_package(GSL REQUIRED)
 
 # Dependencies for GRAFED
@@ -94,10 +113,18 @@ include_directories(${CMAKE_CURRENT_SOURCE_DIR}/src)
 add_subdirectory(dep)
 add_subdirectory(src)
 add_subdirectory(examples)
+if (CONFIGURE_PYMARTY)
+    add_subdirectory(python)
+endif()
+
 add_subdirectory(tests)
 
 install(TARGETS marty marty-static csl csl-static marty-lha marty-lha-static marty-gamma-api
     DESTINATION lib)
+if (CONFIGURE_PYMARTY)
+    install(PROGRAMS "$<TARGET_FILE:_pymarty>"
+        DESTINATION lib)
+endif()
 install(DIRECTORY src/
     DESTINATION include
     FILES_MATCHING PATTERN *.h)

pymarty-conda-env.yml

@@ -0,0 +1,11 @@
+name: pymarty
+channels:
+  - defaults
+dependencies:
+  - ipython
+  - matplotlib
+  - numpy
+  - pybind11
+  - pytest
+  - python
+  - scipy

python/.gitignore

@@ -0,0 +1,5 @@
+__pycache__
+*checkpoint.ipynb
+*.egg-info
+build
+tests/conftest.py

python/CMakeLists.txt

@@ -0,0 +1,13 @@
+enable_testing()
+
+include(Pytest.cmake)
+
+pytest_discover_tests(
+    WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+    TEST_PREFIX "PYUNITTEST_"
+    TEST_SUFFIX ""
+    # XML_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR}/report
+)
+
+set(PYMARTY_PATH ${CMAKE_CURRENT_SOURCE_DIR}/src)
+configure_file(tests/conftest.py.in ${CMAKE_CURRENT_SOURCE_DIR}/tests/conftest.py @ONLY)

python/Pytest.cmake

@@ -0,0 +1,139 @@
+# Distributed under the OSI-approved BSD 3-Clause License.
+
+#[=======================================================================[.rst:
+Pytest
+----------
+
+This module defines functions to help integrate Pytest scripts into CMake.
+
+.. command:: pytest_discover_tests
+
+  Automatically add tests with CTest by querying the compiled test executable
+  for available tests::
+
+    pytest_discover_tests([EXTRA_ARGS arg1...]
+                         [WORKING_DIRECTORY dir]
+                         [TEST_PREFIX prefix]
+                         [TEST_SUFFIX suffix]
+                         [XML_OUTPUT_DIR dir]
+    )
+
+  ``pytest_discover_tests()`` will collect all pytest test cases and register
+  commands that execute them through CTest.
+
+  The main advantage of using this instead of just calling pytest directly is
+  that you can synchronize filtering and other configuration within CMake. The
+  only disadvantage of using this however is that pytest does test collection
+  whether or not test filtering is used, so this can add significant overhead.
+
+  The options are:
+
+  ``EXTRA_ARGS arg1...``
+    Any extra arguments to pass on the command line to pytest
+
+  ``COLLECTION_ARGS arg1...``
+    Extra arguments to pass to pytest during test case collection
+
+  ``EXECUTION_ARGS arg1...``
+    Extra arguments to pass to pytest during test case execution
+
+  ``WORKING_DIRECTORY dir``
+    Specifies the directory in which to run test case collection and test case
+    execution.  If this
+    option is not provided, the current source directory is used.
+
+  ``TEST_PREFIX prefix``
+    Specifies a ``prefix`` to be prepended to the name of each discovered test
+    case.  This can be useful when using multiple test folders and there are
+    potentially clashing test names, it can also make test filtering in presets
+    easier. If this option is not provided then the prefix is empty.
+
+  ``TEST_SUFFIX suffix``
+    Similar to ``TEST_PREFIX`` except the ``suffix`` is appended to the name of
+    every discovered test case.  Both ``TEST_PREFIX`` and ``TEST_SUFFIX`` may
+    be specified.
+
+  ``XML_OUTPUT_DIR dir``
+
+    If specified, the parameter is passed along with ``--junitxml=<test name>``
+    to test executable. The actual file name is the same as the test target,
+    including prefix and suffix.
+
+#]=======================================================================]
+
+cmake_policy(PUSH)
+
+#------------------------------------------------------------------------------
+function(pytest_discover_tests)
+
+cmake_parse_arguments(
+    ""
+    ""
+    "TEST_PREFIX;TEST_SUFFIX;WORKING_DIRECTORY;XML_OUTPUT_DIR"
+    "EXTRA_ARGS;COLLECTION_ARGS;EXECUTION_ARGS"
+    ${ARGN}
+  )
+
+  # Default settings
+  if(NOT _WORKING_DIRECTORY)
+    set(_WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+  endif()
+
+  # https://docs.pytest.org/en/6.2.x/example/pythoncollection.html#finding-out-what-is-collected
+  set(pytest_collection_args --collect-only -q ${_EXTRA_ARGS} ${_COLLECTION_ARGS})
+  set(pytest_execution_args ${_EXTRA_ARGS} ${_EXECUTION_ARGS})
+  set(pytest_base_command pytest)
+
+  execute_process(
+    COMMAND ${pytest_base_command} ${pytest_collection_args}
+    WORKING_DIRECTORY ${_WORKING_DIRECTORY}
+    OUTPUT_VARIABLE pytest_collect_output
+    OUTPUT_STRIP_TRAILING_WHITESPACE
+    RESULT_VARIABLE pytest_collect_result
+  )
+  if(NOT ${pytest_collect_result} EQUAL 0)
+    message(WARNING "Error running Pytest discovery, tests for the python API will not be ran...")
+    return()
+  endif()
+
+  # Splits lines into a list variable
+  string(REPLACE [[;]] [[\;]] pytest_collect_output "${pytest_collect_output}")
+  string(REPLACE "\n" ";" pytest_collect_output "${pytest_collect_output}")
+
+  set(pytest_testcase_regex "([^:]+)(::([^:]+))?::([^:]+)")
+
+  foreach(test_case ${pytest_collect_output})
+    string(REGEX MATCHALL ${pytest_testcase_regex} test_case_match "${test_case}")
+
+    if(test_case_match)
+      set(test_case_file ${CMAKE_MATCH_1})
+      set(test_case_class ${CMAKE_MATCH_3})
+      set(test_case_func ${CMAKE_MATCH_4})
+
+      if(test_case_class)
+        set(test_case_name "${_TEST_PREFIX}${test_case_class}.${test_case_func}${_TEST_SUFFIX}")
+      else()
+        set(test_case_name "${_TEST_PREFIX}${test_case_func}${_TEST_SUFFIX}")
+      endif()
+
+      if(_XML_OUTPUT_DIR)
+        set(pytest_local_args --junitxml=${_XML_OUTPUT_DIR}/${test_case_name}.xml)
+      endif()
+
+      add_test(
+        NAME "${test_case_name}"
+        COMMAND ${pytest_base_command}
+                ${test_case} ${pytest_execution_args} ${pytest_local_args}
+        WORKING_DIRECTORY ${_WORKING_DIRECTORY}
+      )
+      # Pytest Exit code 5 means all tests were deselected
+      set_tests_properties("${test_case_name}" PROPERTIES SKIP_RETURN_CODE 5)
+    endif()
+
+  endforeach()
+
+endfunction()
+
+#------------------------------------------------------------------------------
+
+cmake_policy(POP)

python/README.md

@@ -0,0 +1 @@
+# PyMarty