morphio 2.7.1__tar.gz → 3.0.2__tar.gz

MorphIO-3.0.2/.github/workflows/coverage_test.yaml

@@ -0,0 +1,29 @@
+name: coverage-test
+on: [pull_request, push]
+env:
+  CC: gcc-9
+  CXX: g++-9
+
+jobs:
+    build:
+        name: coverage-test
+        runs-on: ubuntu-20.04
+        # Run on external PRs, but not internal PRs as they'll be run by the push
+        if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
+
+        steps:
+            - name: Checkout repository
+              uses: actions/checkout@v2
+            - name: Fetch repository
+              run: git fetch --prune --unshallow
+            - name: Get submodules
+              run: git submodule update --init --force --recursive
+            - name: Install packages
+              run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev lcov
+            - name: Build and run unittests
+              run: ci/coverage_test.sh
+            - name: Upload Coverage to Coveralls
+              uses: coverallsapp/github-action@master
+              with:
+                github-token: ${{ secrets.GITHUB_TOKEN }}
+                path-to-lcov: build/build-coverage/coverage.info.cleaned

MorphIO-3.0.2/.github/workflows/docstring_check.yaml

@@ -0,0 +1,22 @@
+name: docstring-check
+on:
+    push:
+
+jobs:
+  build:
+    name: docstring-check
+    runs-on: ubuntu-18.04
+    steps:
+        - name: Fetch repository
+          uses: actions/checkout@v2
+          with:
+            submodules: recursive
+        - name: Install packages
+          run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-9
+        - name: Check docstrings
+          run: |
+            export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-9.so.1
+            ci/check_generated_docstrings.sh || true
+
+            export LIBCLANG_PATH=libLLVM-10.so.1
+            ci/check_generated_docstrings.sh || true

{MorphIO-2.7.1 → MorphIO-3.0.2}/.gitignore

@@ -43,3 +43,7 @@ MorphIO.egg-info/
 .tags
 build/
 .*.swp
+*.idea
+ci/venv*
+cmake-build*
+env*

MorphIO-3.0.2/.readthedocs.yaml

@@ -0,0 +1,13 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+submodules:
+  include: all
+  recursive: true
+
+conda:
+  environment: doc/environment.yml

MorphIO-3.0.2/CMake/CodeCoverage.cmake

@@ -0,0 +1,303 @@
+# Copyright (c) 2012 - 2017, Lars Bilke
+# All rights reserved.
+#
+# Redistribution and use in source and binary forms, with or without modification,
+# are permitted provided that the following conditions are met:
+#
+# 1. Redistributions of source code must retain the above copyright notice, this
+#    list of conditions and the following disclaimer.
+#
+# 2. Redistributions in binary form must reproduce the above copyright notice,
+#    this list of conditions and the following disclaimer in the documentation
+#    and/or other materials provided with the distribution.
+#
+# 3. Neither the name of the copyright holder nor the names of its contributors
+#    may be used to endorse or promote products derived from this software without
+#    specific prior written permission.
+#
+# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+# ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+# WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+# DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+# ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+# ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+#
+# CHANGES:
+#
+# 2012-01-31, Lars Bilke
+# - Enable Code Coverage
+#
+# 2013-09-17, Joakim Söderberg
+# - Added support for Clang.
+# - Some additional usage instructions.
+#
+# 2016-02-03, Lars Bilke
+# - Refactored functions to use named parameters
+#
+# 2017-06-02, Lars Bilke
+# - Merged with modified version from github.com/ufz/ogs
+#
+#
+# USAGE:
+#
+# 1. Copy this file into your cmake modules path.
+#
+# 2. Add the following line to your CMakeLists.txt:
+#      include(CodeCoverage)
+#
+# 3. Append necessary compiler flags:
+#      APPEND_COVERAGE_COMPILER_FLAGS()
+#
+# 4. If you need to exclude additional directories from the report, specify them
+#    using the COVERAGE_LCOV_EXCLUDES variable before calling SETUP_TARGET_FOR_COVERAGE_LCOV.
+#    Example:
+#      set(COVERAGE_LCOV_EXCLUDES 'dir1/*' 'dir2/*')
+#
+# 5. Use the functions described below to create a custom make target which
+#    runs your test executable and produces a code coverage report.
+#
+# 6. Build a Debug build:
+#      cmake -DCMAKE_BUILD_TYPE=Debug ..
+#      make
+#      make my_coverage_target
+#
+
+include(CMakeParseArguments)
+
+# Check prereqs
+find_program( GCOV_PATH gcov )
+find_program( LCOV_PATH  NAMES lcov lcov.bat lcov.exe lcov.perl)
+find_program( GENHTML_PATH NAMES genhtml genhtml.perl genhtml.bat )
+find_program( GCOVR_PATH gcovr PATHS ${CMAKE_SOURCE_DIR}/scripts/test)
+find_program( SIMPLE_PYTHON_EXECUTABLE python )
+
+if(NOT GCOV_PATH)
+    message(FATAL_ERROR "gcov not found! Aborting...")
+endif() # NOT GCOV_PATH
+
+if("${CMAKE_CXX_COMPILER_ID}" MATCHES "(Apple)?[Cc]lang")
+    if("${CMAKE_CXX_COMPILER_VERSION}" VERSION_LESS 3)
+        message(FATAL_ERROR "Clang version must be 3.0.0 or greater! Aborting...")
+    endif()
+elseif(NOT CMAKE_COMPILER_IS_GNUCXX)
+    message(FATAL_ERROR "Compiler is not GNU gcc! Aborting...")
+endif()
+
+set(COVERAGE_COMPILER_FLAGS "-g -O0 --coverage -fprofile-arcs -ftest-coverage"
+    CACHE INTERNAL "")
+
+set(CMAKE_CXX_FLAGS_COVERAGE
+    ${COVERAGE_COMPILER_FLAGS}
+    CACHE STRING "Flags used by the C++ compiler during coverage builds."
+    FORCE )
+set(CMAKE_C_FLAGS_COVERAGE
+    ${COVERAGE_COMPILER_FLAGS}
+    CACHE STRING "Flags used by the C compiler during coverage builds."
+    FORCE )
+set(CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used for linking binaries during coverage builds."
+    FORCE )
+set(CMAKE_SHARED_LINKER_FLAGS_COVERAGE
+    ""
+    CACHE STRING "Flags used by the shared libraries linker during coverage builds."
+    FORCE )
+mark_as_advanced(
+    CMAKE_CXX_FLAGS_COVERAGE
+    CMAKE_C_FLAGS_COVERAGE
+    CMAKE_EXE_LINKER_FLAGS_COVERAGE
+    CMAKE_SHARED_LINKER_FLAGS_COVERAGE )
+
+if(NOT CMAKE_BUILD_TYPE STREQUAL "Debug")
+    message(WARNING "Code coverage results with an optimised (non-Debug) build may be misleading")
+endif() # NOT CMAKE_BUILD_TYPE STREQUAL "Debug"
+
+if(CMAKE_C_COMPILER_ID STREQUAL "GNU")
+    link_libraries(gcov)
+else()
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
+endif()
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# SETUP_TARGET_FOR_COVERAGE_LCOV(
+#     NAME testrunner_coverage                    # New target name
+#     EXECUTABLE testrunner -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES testrunner                     # Dependencies to build first
+# )
+function(SETUP_TARGET_FOR_COVERAGE_LCOV)
+
+    set(options NONE)
+    set(oneValueArgs NAME)
+    set(multiValueArgs EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT LCOV_PATH)
+        message(FATAL_ERROR "lcov not found! Aborting...")
+    endif() # NOT LCOV_PATH
+
+    if(NOT GENHTML_PATH)
+        message(FATAL_ERROR "genhtml not found! Aborting...")
+    endif() # NOT GENHTML_PATH
+
+    # Setup target
+    add_custom_target(${Coverage_NAME}
+
+        # Cleanup lcov
+        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -directory . --zerocounters
+        # Create baseline to make sure untouched files show up in the report
+        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -c -i -d . -o ${Coverage_NAME}.base
+
+        # Run tests
+        COMMAND ${Coverage_EXECUTABLE}
+
+        # Capturing lcov counters and generating report
+        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} --directory . --capture --output-file ${Coverage_NAME}.info
+        # add baseline counters
+        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} -a ${Coverage_NAME}.base -a ${Coverage_NAME}.info --output-file ${Coverage_NAME}.total
+        COMMAND ${LCOV_PATH} --gcov-tool ${GCOV_PATH} --remove ${Coverage_NAME}.total ${COVERAGE_LCOV_EXCLUDES} --output-file ${PROJECT_BINARY_DIR}/${Coverage_NAME}.info.cleaned
+        COMMAND ${GENHTML_PATH} -o ${Coverage_NAME} ${PROJECT_BINARY_DIR}/${Coverage_NAME}.info.cleaned
+        COMMAND ${CMAKE_COMMAND} -E remove ${Coverage_NAME}.base ${Coverage_NAME}.total
+
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        COMMENT "Resetting code coverage counters to zero.\nProcessing code coverage counters and generating report."
+    )
+
+    # Show where to find the lcov info report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Lcov code coverage info report saved in ${Coverage_NAME}.info."
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
+    )
+
+endfunction() # SETUP_TARGET_FOR_COVERAGE_LCOV
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# SETUP_TARGET_FOR_COVERAGE_GCOVR_XML(
+#     NAME ctest_coverage                    # New target name
+#     EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES executable_target         # Dependencies to build first
+# )
+function(SETUP_TARGET_FOR_COVERAGE_GCOVR_XML)
+
+    set(options NONE)
+    set(oneValueArgs NAME)
+    set(multiValueArgs EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT SIMPLE_PYTHON_EXECUTABLE)
+        message(FATAL_ERROR "python not found! Aborting...")
+    endif() # NOT SIMPLE_PYTHON_EXECUTABLE
+
+    if(NOT GCOVR_PATH)
+        message(FATAL_ERROR "gcovr not found! Aborting...")
+    endif() # NOT GCOVR_PATH
+
+    # Combine excludes to several -e arguments
+    set(GCOVR_EXCLUDES "")
+    foreach(EXCLUDE ${COVERAGE_GCOVR_EXCLUDES})
+        list(APPEND GCOVR_EXCLUDES "-e")
+        list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
+    endforeach()
+
+    add_custom_target(${Coverage_NAME}
+        # Run tests
+        ${Coverage_EXECUTABLE}
+
+        # Running gcovr
+        COMMAND ${GCOVR_PATH} --xml
+            -r ${PROJECT_SOURCE_DIR} ${GCOVR_EXCLUDES}
+            --object-directory=${PROJECT_BINARY_DIR}
+            -o ${Coverage_NAME}.xml
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        COMMENT "Running gcovr to produce Cobertura code coverage report."
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Cobertura code coverage report saved in ${Coverage_NAME}.xml."
+    )
+
+endfunction() # SETUP_TARGET_FOR_COVERAGE_GCOVR_XML
+
+# Defines a target for running and collection code coverage information
+# Builds dependencies, runs the given executable and outputs reports.
+# NOTE! The executable should always have a ZERO as exit code otherwise
+# the coverage generation will not complete.
+#
+# SETUP_TARGET_FOR_COVERAGE_GCOVR_HTML(
+#     NAME ctest_coverage                    # New target name
+#     EXECUTABLE ctest -j ${PROCESSOR_COUNT} # Executable in PROJECT_BINARY_DIR
+#     DEPENDENCIES executable_target         # Dependencies to build first
+# )
+function(SETUP_TARGET_FOR_COVERAGE_GCOVR_HTML)
+
+    set(options NONE)
+    set(oneValueArgs NAME)
+    set(multiValueArgs EXECUTABLE EXECUTABLE_ARGS DEPENDENCIES)
+    cmake_parse_arguments(Coverage "${options}" "${oneValueArgs}" "${multiValueArgs}" ${ARGN})
+
+    if(NOT SIMPLE_PYTHON_EXECUTABLE)
+        message(FATAL_ERROR "python not found! Aborting...")
+    endif() # NOT SIMPLE_PYTHON_EXECUTABLE
+
+    if(NOT GCOVR_PATH)
+        message(FATAL_ERROR "gcovr not found! Aborting...")
+    endif() # NOT GCOVR_PATH
+
+    # Combine excludes to several -e arguments
+    set(GCOVR_EXCLUDES "")
+    foreach(EXCLUDE ${COVERAGE_GCOVR_EXCLUDES})
+        list(APPEND GCOVR_EXCLUDES "-e")
+        list(APPEND GCOVR_EXCLUDES "${EXCLUDE}")
+    endforeach()
+
+    add_custom_target(${Coverage_NAME}
+        # Run tests
+        ${Coverage_EXECUTABLE}
+
+        # Create folder
+        COMMAND ${CMAKE_COMMAND} -E make_directory ${PROJECT_BINARY_DIR}/${Coverage_NAME}
+
+        # Running gcovr
+        COMMAND ${GCOVR_PATH} --html --html-details
+            -r ${PROJECT_SOURCE_DIR} ${GCOVR_EXCLUDES}
+            --object-directory=${PROJECT_BINARY_DIR}
+            -o ${Coverage_NAME}/index.html
+        WORKING_DIRECTORY ${PROJECT_BINARY_DIR}
+        DEPENDS ${Coverage_DEPENDENCIES}
+        COMMENT "Running gcovr to produce HTML code coverage report."
+    )
+
+    # Show info where to find the report
+    add_custom_command(TARGET ${Coverage_NAME} POST_BUILD
+        COMMAND ;
+        COMMENT "Open ./${Coverage_NAME}/index.html in your browser to view the coverage report."
+    )
+
+endfunction() # SETUP_TARGET_FOR_COVERAGE_GCOVR_HTML
+
+function(APPEND_COVERAGE_COMPILER_FLAGS)
+    set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${COVERAGE_COMPILER_FLAGS}")
+    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COVERAGE_COMPILER_FLAGS}")
+    message(STATUS "Appending code coverage compiler flags: ${COVERAGE_COMPILER_FLAGS}")
+endfunction() # APPEND_COVERAGE_COMPILER_FLAGS

{MorphIO-2.7.1 → MorphIO-3.0.2}/CMakeLists.txt

@@ -8,8 +8,14 @@ set(CMAKE_VERBOSE_MAKEFILE ON)
 option(BUILD_BINDINGS "Build the python bindings" ON)
 option(MorphIO_CXX_WARNINGS "Compile C++ with warnings" ON)
 option(EXTERNAL_HIGHFIVE "Use HighFive from external source" OFF)
+option(MORPHIO_TESTS "Build tests" ON)
 option(MORPHIO_USE_DOUBLE "Use doubles instead of floats" OFF)
 
+set(MORPHIO_ENABLE_COVERAGE OFF)
+if (CMAKE_BUILD_TYPE STREQUAL "Debug")
+  set(MORPHIO_ENABLE_COVERAGE ON)
+endif()
+
 if(MORPHIO_USE_DOUBLE)
   add_definitions(-DMORPHIO_USE_DOUBLE)
   message("Floating Point Type: double")
@@ -17,7 +23,8 @@ else()
   message("Floating Point Type: float")
 endif()
 
-include(${PROJECT_SOURCE_DIR}/CMake/CompilerFlags.cmake)
+set(CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/CMake)
+include(CompilerFlags)
 set(CMAKE_CXX_FLAGS "${FLAGS}")
 
 if (EXTERNAL_HIGHFIVE)
@@ -48,5 +55,8 @@ install(
   DESTINATION lib/cmake/MorphIO
   )
 
-enable_testing()
-add_subdirectory(tests)
+
+if (MORPHIO_TESTS)
+  enable_testing()
+  add_subdirectory(tests)
+endif()