morphio 2.2.0__tar.gz → 2.5.0__tar.gz

{MorphIO-2.2.0 → MorphIO-2.5.0}/.clang-format

@@ -1,62 +1,91 @@
 ---
-AccessModifierOffset: -4
+AccessModifierOffset: -2
+AlignAfterOpenBracket: Align
 AlignConsecutiveAssignments: false
 AlignConsecutiveDeclarations: false
 AlignEscapedNewlinesLeft: true
 AlignOperands: true
 AlignTrailingComments: true
 AllowAllParametersOfDeclarationOnNextLine: true
-AllowShortFunctionsOnASingleLine: Inline
+AllowShortBlocksOnASingleLine: false
+AllowShortCaseLabelsOnASingleLine: false
+AllowShortFunctionsOnASingleLine: Empty
 AllowShortIfStatementsOnASingleLine: false
 AllowShortLoopsOnASingleLine: false
 AlwaysBreakBeforeMultilineStrings: true
 AlwaysBreakTemplateDeclarations: true
 BasedOnStyle: WebKit
-BinPackParameters: true
+BinPackArguments: false
+BinPackParameters: false
 BraceWrapping:
   AfterClass: true
   AfterControlStatement: false
-  AfterEnum: true
-  AfterFunction: true
+  AfterEnum: false
+  AfterExternBlock: false
+  AfterFunction: false
   AfterNamespace: false
-  AfterStruct: true
-  AfterUnion: true
+  AfterStruct: false
+  AfterUnion: false
   BeforeCatch: false
   BeforeElse: false
 BreakBeforeBraces: Custom
 BreakBeforeBinaryOperators: false
 BreakBeforeTernaryOperators: true
 BreakConstructorInitializersBeforeComma: true
+BreakStringLiterals: true
+ColumnLimit: 100
+CommentPragmas: '^ IWYU pragma:'
 ConstructorInitializerAllOnOneLineOrOnePerLine: false
 ConstructorInitializerIndentWidth: 4
 ContinuationIndentWidth: 4
 Cpp11BracedListStyle: true
+DerivePointerAlignment: false
 DerivePointerBinding: true
 ExperimentalAutoDetectBinPacking: false
+FixNamespaceComments: true
+ForEachMacros: [ foreach, ]
+IncludeCategories:
+  - Regex: '^"(llvm|llvm-c|clang|clang-c)/'
+    Priority: 2
+  - Regex: '^(<|"(gtest|isl|json)/)'
+    Priority: 3
+  - Regex: '.*'
+    Priority: 1
+IncludeIsMainRegex: '$'
 IndentCaseLabels: false
-IndentFunctionDeclarationAfterType: true
-IndentWidth:     4
+IndentWidth: 4
+IndentWrappedFunctionNames: false
 KeepEmptyLinesAtTheStartOfBlocks: false
 Language: Cpp
 MaxEmptyLinesToKeep: 2
 NamespaceIndentation: None
+PenaltyBreakAssignment: 40
 PenaltyBreakBeforeFirstCallParameter: 100
 PenaltyBreakComment: 60
 PenaltyBreakFirstLessLess: 120
 PenaltyBreakString: 1000
 PenaltyExcessCharacter: 1000000
 PenaltyReturnTypeOnItsOwnLine: 200
+PointerAlignment: Left
 PointerBindsToType: true
+ReflowComments: true
 SortIncludes: true
-SpaceAfterControlStatementKeyword: true
+SpaceAfterCStyleCast: true
+SpaceAfterTemplateKeyword: true
 SpaceBeforeAssignmentOperators: true
+SpaceBeforeCpp11BracedList: false
+SpaceBeforeCtorInitializerColon: false
+SpaceBeforeInheritanceColon: false
 SpaceBeforeParens: ControlStatements
+SpaceBeforeRangeBasedForLoopColon: true
 SpaceInEmptyParentheses: false
-SpacesBeforeTrailingComments: 1
+SpacesBeforeTrailingComments: 2
 SpacesInAngles: false # '< ' style
+SpacesInContainerLiterals: false
 SpacesInCStyleCastParentheses: false
 SpacesInParentheses: false # '(' style
+SpacesInSquareBrackets: false
 Standard: Cpp11
-TabWidth:        4
-UseTab:          Never
+TabWidth: 4
+UseTab: Never
 ...

MorphIO-2.5.0/.github/workflows/clang_format_check.yaml

@@ -0,0 +1,17 @@
+name: clang-format-check
+on:
+    pull_request:
+
+jobs:
+  build:
+    name: clang-format-check
+    runs-on: ubuntu-18.04
+    steps:
+        - name: Fetch repository
+          uses: actions/checkout@v1
+        - name: Install apt
+          run: sudo apt-get update -y
+        - name: Install packages
+          run: sudo apt-get install python3-venv
+        - name: check_clang_format
+          run: ci/check_clang_format.sh

MorphIO-2.5.0/.github/workflows/publish-sdist-wheels.yml

@@ -0,0 +1,99 @@
+name: Publish sdist and wheels macos-manylinux
+
+on:
+  push:
+    tags:
+      - 'v[0-9]+.[0-9]+.[0-9]+'
+
+env:
+  CIBW_MANYLINUX_X86_64_IMAGE: manylinux2014
+  MACOSX_DEPLOYMENT_TARGET: '10.13'
+  CIBW_BUILD_VERBOSITY: 2
+  # Only build on Python 3.x
+  CIBW_BUILD: 'cp3?-*'
+  CIBW_SKIP: 'cp35-* cp39-* *-manylinux_i686'
+  CIBW_BEFORE_TEST: pip install nose mock h5py numpy
+  CIBW_TEST_COMMAND: nosetests -s -v -P {project}/tests
+
+jobs:
+  build_wheels:
+    name: Build wheels on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-18.04, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          submodules: 'true'
+
+      - uses: actions/setup-python@v2
+        name: Install Python
+        with:
+          python-version: '3.7'
+
+      - name: Install cibuildwheel
+        run: |
+          python -m pip install cibuildwheel==1.6.4
+      - name: Build wheels on Linux
+        if: runner.os == 'Linux'
+        env:
+          CIBW_BEFORE_BUILD: 'yum update -y; yum -y install hdf5-devel'
+        run: |
+          python -m cibuildwheel --output-dir dist
+      - name: Build wheels Mac OS
+        if: runner.os == 'macOS'
+        env:
+          CIBW_BEFORE_BUILD: |
+            brew update
+            brew unlink gcc@8 gcc@9
+            brew install cmake
+            brew install hdf5
+        run: |
+          python -m cibuildwheel --output-dir dist
+      - name: Store wheel as artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: dist
+          path: dist
+
+  build_sdist:
+    name: Build sdist
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      - name: Set up Python 3.6
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.6
+      - name: Build a source tarball
+        run:
+          python setup.py sdist
+      - name: Store sdist as artifact
+        uses: actions/upload-artifact@v2
+        with:
+          name: dist
+          path: dist
+
+  upload_wheels:
+    runs-on: ubuntu-latest
+    needs: [build_wheels, build_sdist]
+    name: Upload wheels to PyPI
+    steps:
+      - name: Download artifacts produced during the build_wheels and build_sdist jobs
+        uses: actions/download-artifact@v2
+        with:
+          name: dist
+          path: dist
+
+      - name: Display structure of downloaded files
+        run: ls -R
+        working-directory: dist
+
+      - name: Publish package to PyPI
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.PYPI_PASSWORD }}
+          packages_dir: dist/

MorphIO-2.5.0/.github/workflows/run-tests.yml

@@ -0,0 +1,44 @@
+name: Run tests
+on:
+    pull_request:
+
+jobs:
+  build:
+    name: Run tests on ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        compiler:
+          - CC: clang
+            CXX: clang++
+          - CC: gcc
+            CXX: g++
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          submodules: 'true'
+
+      - name: Install packages on Linux
+        if: runner.os == 'Linux'
+        run: sudo apt-get update && sudo apt-get install build-essential libhdf5-dev
+
+      - name: Install packages on MacOS
+        if: runner.os == 'macOS'
+        run: |
+            brew update
+            brew unlink gcc@8 gcc@9  # work around for https://github.com/actions/virtual-environments/issues/2391
+            brew install cmake || true  # macos image has cmake installed, but a new version may exist; ignore it if so
+            brew install hdf5
+
+      - name: Build and run unittests
+        env:
+          CC: ${{ matrix.compiler.CC }}
+          CXX: ${{ matrix.compiler.CXX }}
+        run: |
+          ./ci/python_test.sh
+          ./ci/cpp_test.sh
+          ./ci/cpp_test.sh "-DMORPHIO_USE_DOUBLE=ON"

{MorphIO-2.2.0 → MorphIO-2.5.0}/.gitignore

@@ -1,9 +1,12 @@
 # Python wheels
 *.whl
 
+.eggs/
 bin/
 src/version.cpp
 morphio.egg-info/
+MorphIO.egg-info/
+.venv
 
 *.pyc
 

{MorphIO-2.2.0 → MorphIO-2.5.0}/.gitmodules

@@ -10,6 +10,3 @@
 [submodule "3rdparty/GSL_LITE"]
 	path = 3rdparty/GSL_LITE
 	url = https://github.com/martinmoene/gsl-lite.git
-[submodule "multibuild"]
-	path = multibuild
-	url = https://github.com/matthew-brett/multibuild.git

MorphIO-2.5.0/.travis.yml

@@ -0,0 +1,60 @@
+jobs:
+  include:
+    - os: linux
+      dist: xenial
+      env:
+        CXX: g++
+        CC: gcc
+    - os: linux
+      dist: xenial
+      env:
+        CXX: clang++
+        CC: clang
+
+    - os: osx
+      osx_image: xcode10.1
+      language: generic
+      env:
+        CXX: clang++
+        CC: clang
+    - os: osx
+      osx_image: xcode10.1
+      language: generic
+      env:
+        CXX: g++
+        CC: gcc
+
+    - os: windows
+      language: c++
+      env:
+        - MINCONDA_VERSION="latest"
+        - CMAKE_GENERATOR="Visual Studio 15 2017 Win64"
+        - TESTS_TARGET="RUN_TESTS";
+      install:
+        - choco install --yes miniconda3
+        - source C:/Tools/miniconda3/Scripts/activate
+        - conda config --set always_yes yes --set changeps1 no
+        - conda update -q conda
+        - conda install -c conda-forge hdf5
+
+addons:
+  homebrew:
+    packages:
+    - hdf5
+  apt:
+    packages:
+    - libhdf5-dev
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+
+language: python
+python:
+  - 3.7
+
+install: skip
+
+script:
+  - ./ci/python_test.sh
+  - ./ci/cpp_test.sh

{MorphIO-2.2.0 → MorphIO-2.5.0}/3rdparty/CMakeLists.txt

@@ -1,10 +1,13 @@
 find_package(HDF5 REQUIRED)
-add_library(HighFive INTERFACE)
-target_include_directories(HighFive SYSTEM INTERFACE
-    HighFive/include/
-    ${HDF5_INCLUDE_DIRS})
-target_link_libraries(HighFive INTERFACE
-    ${HDF5_C_LIBRARIES})
+
+if (NOT EXTERNAL_HIGHFIVE)
+  set(HIGHFIVE_EXAMPLES OFF CACHE BOOL "" FORCE)
+  set(HIGHFIVE_UNIT_TESTS OFF CACHE BOOL "" FORCE)
+  set(HIGHFIVE_USE_BOOST OFF CACHE BOOL "" FORCE)
+  set(HIGHFIVE_USE_INSTALL_DEPS ON CACHE BOOL "" FORCE)
+  add_subdirectory(HighFive)
+  target_include_directories(HighFive SYSTEM INTERFACE)
+endif()
 
 add_subdirectory(GSL_LITE)
 target_include_directories(gsl-lite SYSTEM INTERFACE)

MorphIO-2.2.0/CMakeLists.txt → MorphIO-2.5.0/CMake/CompilerFlags.cmake

@@ -1,14 +1,7 @@
-cmake_minimum_required(VERSION 3.2)
-project(MorphIO VERSION 2.0.0)
-
-set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
-set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
-set(CMAKE_VERBOSE_MAKEFILE ON)
-
-option(BUILD_BINDINGS "Build the python bindings" ON)
-option(${PROJECT_NAME}_CXX_WARNINGS "Compile C++ with warnings" ON)
 # Taken from https://github.com/BlueBrain/hpc-coding-conventions/blob/master/cpp/cmake/bob.cmake#L192-L255
-if(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+if (WIN32)
+  set(FLAGS "${FLAGS} /DH5_BUILT_AS_DYNAMIC_LIB /EHsc /D_USE_MATH_DEFINES")
+elseif(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   if(${PROJECT_NAME}_CXX_WARNINGS)
     set(FLAGS "${FLAGS} -Werror -Weverything")
     # Using std=c++11, no need for 98 compat
@@ -75,28 +68,3 @@ elseif(${CMAKE_CXX_COMPILER_ID} STREQUAL "Intel")
 else()
   message(WARNING "Unexpected compiler type ${CMAKE_CXX_COMPILER_ID}")
 endif()
-
-set(CMAKE_CXX_FLAGS "${FLAGS}")
-
-add_subdirectory(3rdparty)
-add_subdirectory(src)
-
-if(BUILD_BINDINGS)
-  add_subdirectory(binds/python)
-endif(BUILD_BINDINGS)
-
-install(
-  DIRECTORY include/morphio
-  DESTINATION include
-  )
-
-install(
-  EXPORT MorphIOTargets
-  NAMESPACE MorphIO::
-  DESTINATION lib/cmake/MorphIO
-  )
-
-install(
-  FILES ${CMAKE_CURRENT_LIST_DIR}/CMake/MorphIOConfig.cmake
-  DESTINATION lib/cmake/MorphIO
-  )

{MorphIO-2.2.0 → MorphIO-2.5.0}/CMake/MorphIOConfig.cmake

@@ -1,5 +1,6 @@
 include(CMakeFindDependencyMacro)
 
 find_dependency(gsl-lite)
+find_dependency(HighFive)
 
 include("${CMAKE_CURRENT_LIST_DIR}/MorphIOTargets.cmake")

MorphIO-2.5.0/CMakeLists.txt

@@ -0,0 +1,52 @@
+cmake_minimum_required(VERSION 3.2)
+project(MorphIO VERSION 2.0.0)
+
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+set(CMAKE_VERBOSE_MAKEFILE ON)
+
+option(BUILD_BINDINGS "Build the python bindings" ON)
+option(${PROJECT_NAME}_CXX_WARNINGS "Compile C++ with warnings" ON)
+option(EXTERNAL_HIGHFIVE "Use HighFive from external source" OFF)
+option(MORPHIO_USE_DOUBLE "Use doubles instead of floats" OFF)
+
+if(MORPHIO_USE_DOUBLE)
+  add_definitions(-DMORPHIO_USE_DOUBLE)
+  message("Floating Point Type: double")
+else()
+  message("Floating Point Type: float")
+endif()
+
+include(${PROJECT_SOURCE_DIR}/CMake/CompilerFlags.cmake)
+set(CMAKE_CXX_FLAGS "${FLAGS}")
+
+if (EXTERNAL_HIGHFIVE)
+  find_package(HighFive REQUIRED)
+endif()
+set(MORPHIO_INCLUDE_DIR ${PROJECT_SOURCE_DIR}/include/)
+
+add_subdirectory(3rdparty)
+add_subdirectory(src)
+
+if(BUILD_BINDINGS)
+  add_subdirectory(binds/python)
+endif(BUILD_BINDINGS)
+
+install(
+  DIRECTORY ${MORPHIO_INCLUDE_DIR}
+  DESTINATION include
+  )
+
+install(
+  EXPORT MorphIOTargets
+  NAMESPACE MorphIO::
+  DESTINATION lib/cmake/MorphIO
+  )
+
+install(
+  FILES ${CMAKE_CURRENT_LIST_DIR}/CMake/MorphIOConfig.cmake
+  DESTINATION lib/cmake/MorphIO
+  )
+
+enable_testing()
+add_subdirectory(tests)

MorphIO-2.5.0/CONTRIBUTING.md

@@ -0,0 +1,140 @@
+# Contribution Guide
+
+We would love for you to contribute to the MorphIO project and help make it better than it is today.
+As a contributor, here are the guidelines we would like you to follow:
+
+ - [Question or Problem?](#got-a-question)
+ - [Issues and Bugs](#found-a-bug)
+ - [Feature Requests](#missing-a-feature)
+ - [Submissions](#submission-guidelines)
+ - [Development Guidelines](#development)
+ - [Release Procedure](#release)
+
+# Got a Question?
+
+Please do not hesitate to raise an issue on [github project page][github].
+
+# Found a Bug?
+
+If you find a bug in the source code, you can help us by [submitting an issue](#issues)
+to our [GitHub Repository][github]. Even better, you can [submit a Pull Request](#pull-requests) with a fix.
+
+#  Missing a Feature?
+
+You can *request* a new feature by [submitting an issue](#issues) to our GitHub Repository.
+If you would like to *implement* a new feature, please submit an issue with a proposal for your 
+work first, to be sure that we can use it.
+
+Please consider what kind of change it is:
+
+* For a **Major Feature**, first open an issue and outline your proposal so that it can be
+discussed. This will also allow us to better coordinate our efforts, prevent duplication of work,
+and help you to craft the change so that it is successfully accepted into the project.
+* **Small Features** can be crafted and directly [submitted as a Pull Request](#pull-requests).
+
+# Submission Guidelines
+
+## Issues
+
+Before you submit an issue, please search the issue tracker, maybe an issue for your problem
+already exists and the discussion might inform you of workarounds readily available.
+
+We want to fix all the issues as soon as possible, but before fixing a bug we need to reproduce
+and confirm it. In order to reproduce bugs we will need as much information as possible, and
+preferably with an example.
+
+## Pull Requests
+
+When you wish to contribute to the code base, please consider the following guidelines:
+
+* Make a [fork](https://guides.github.com/activities/forking/) of this repository.
+* Make your changes in your fork, in a new git branch:
+
+     ```shell
+     git checkout -b my-fix-branch master
+     ```
+* Create your patch, **including appropriate Python test cases**.
+  Please check the coding [conventions](#coding-conventions) for more information.
+* Run the full test suite, and ensure that all tests pass.
+* Commit your changes using a descriptive commit message.
+
+     ```shell
+     git commit -a
+     ```
+* Push your branch to GitHub:
+
+    ```shell
+    git push origin my-fix-branch
+    ```
+* In GitHub, send a Pull Request to the `master` branch of the upstream repository of the relevant component.
+* If we suggest changes then:
+  * Make the required updates.
+  * Re-run the test suites to ensure tests are still passing.
+  * Rebase your branch and force push to your GitHub repository (this will update your Pull Request):
+
+       ```shell
+        git rebase master -i
+        git push -f
+       ```
+
+That’s it! Thank you for your contribution!
+
+### After your pull request is merged
+
+After your pull request is merged, you can safely delete your branch and pull the changes from
+the main (upstream) repository:
+
+* Delete the remote branch on GitHub either through the GitHub web UI or your local shell as follows:
+
+    ```shell
+    git push origin --delete my-fix-branch
+    ```
+* Check out the master branch:
+
+    ```shell
+    git checkout master -f
+    ```
+* Delete the local branch:
+
+    ```shell
+    git branch -D my-fix-branch
+    ```
+* Update your master with the latest upstream version:
+
+    ```shell
+    git pull --ff upstream master
+    ```
+
+[github]: https://github.com/BlueBrain/MorphIO
+
+# Development Environment
+
+Please make sure to install the project requirements,
+see the [dependencies](./README.md#dependencies) section in top README.
+
+This section applies to both Python versions 2 and 3.
+
+## Setup
+
+It is recommended to use `virtualenv` to develop in a sandbox environment:
+
+```
+virtualenv venv
+. venv/bin/activate
+pip install -r tests/requirement_tests.txt
+```
+
+## Build
+
+Run the following command to build incrementally the project: `pip install -e .`
+
+## Test
+
+Run the following command to run the Python unit-tests: `nosetests`
+
+## Coding conventions
+
+The code coverage of the Python unit-tests may not decrease over time.
+It means that every change must go with their corresponding Python unit-tests to
+validate the library behavior as well as to demonstrate the API usage. 
+