morphio 2.0.7__tar.gz → 2.1.3__tar.gz

MorphIO-2.1.3/.clang-format

@@ -0,0 +1,62 @@
+---
+AccessModifierOffset: -4
+AlignConsecutiveAssignments: false
+AlignConsecutiveDeclarations: false
+AlignEscapedNewlinesLeft: true
+AlignOperands: true
+AlignTrailingComments: true
+AllowAllParametersOfDeclarationOnNextLine: true
+AllowShortFunctionsOnASingleLine: Inline
+AllowShortIfStatementsOnASingleLine: false
+AllowShortLoopsOnASingleLine: false
+AlwaysBreakBeforeMultilineStrings: true
+AlwaysBreakTemplateDeclarations: true
+BasedOnStyle: WebKit
+BinPackParameters: true
+BraceWrapping:
+  AfterClass: true
+  AfterControlStatement: false
+  AfterEnum: true
+  AfterFunction: true
+  AfterNamespace: false
+  AfterStruct: true
+  AfterUnion: true
+  BeforeCatch: false
+  BeforeElse: false
+BreakBeforeBraces: Custom
+BreakBeforeBinaryOperators: false
+BreakBeforeTernaryOperators: true
+BreakConstructorInitializersBeforeComma: true
+ConstructorInitializerAllOnOneLineOrOnePerLine: false
+ConstructorInitializerIndentWidth: 4
+ContinuationIndentWidth: 4
+Cpp11BracedListStyle: true
+DerivePointerBinding: true
+ExperimentalAutoDetectBinPacking: false
+IndentCaseLabels: false
+IndentFunctionDeclarationAfterType: true
+IndentWidth:     4
+KeepEmptyLinesAtTheStartOfBlocks: false
+Language: Cpp
+MaxEmptyLinesToKeep: 2
+NamespaceIndentation: None
+PenaltyBreakBeforeFirstCallParameter: 100
+PenaltyBreakComment: 60
+PenaltyBreakFirstLessLess: 120
+PenaltyBreakString: 1000
+PenaltyExcessCharacter: 1000000
+PenaltyReturnTypeOnItsOwnLine: 200
+PointerBindsToType: true
+SortIncludes: true
+SpaceAfterControlStatementKeyword: true
+SpaceBeforeAssignmentOperators: true
+SpaceBeforeParens: ControlStatements
+SpaceInEmptyParentheses: false
+SpacesBeforeTrailingComments: 1
+SpacesInAngles: false # '< ' style
+SpacesInCStyleCastParentheses: false
+SpacesInParentheses: false # '(' style
+Standard: Cpp11
+TabWidth:        4
+UseTab:          Never
+...

MorphIO-2.1.3/.gitignore

@@ -0,0 +1,42 @@
+# Python wheels
+*.whl
+
+bin/
+src/version.cpp
+morphio.egg-info/
+
+*.pyc
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app
+
+# Custom
+.tags
+build/
+.*.swp

MorphIO-2.1.3/.gitmodules

@@ -0,0 +1,15 @@
+[submodule "3rdparty/HighFive"]
+	path = 3rdparty/HighFive
+	url = https://github.com/BlueBrain/HighFive.git
+[submodule "3rdparty/pybind11"]
+	path = 3rdparty/pybind11
+	url = https://github.com/pybind/pybind11.git
+[submodule "3rdparty/lexertl"]
+	path = 3rdparty/lexertl
+	url = https://github.com/wizmer/lexertl.git
+[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-2.1.3/.travis.yml

@@ -0,0 +1,38 @@
+matrix:
+  include:
+    - os: linux
+      dist: xenial
+      sudo: required
+      env:
+        CXX: g++
+        CC: gcc
+    - os: linux
+      dist: xenial
+      sudo: required
+      env:
+        CXX: clang++
+        CC: clang
+
+cache:
+  directories:
+    - $HOME/.cache/pip
+    # - $HOME/Library/Caches/Homebrew
+language: python
+sudo: required
+python:
+  - 3.7
+
+before_install:
+  - if [ $TRAVIS_OS_NAME = linux ]; then sudo apt-get install libhdf5-dev; else brew install hdf5; fi
+  - pip install virtualenv
+  - virtualenv env && source env/bin/activate
+install:
+  - pip install --upgrade pip
+  - pip install .
+script:
+  # Need to concatenate all commands with otherwise Travis only looks at the output code of the last command
+
+  # Testing compilation with warning as error
+  - rm -rf build; mkdir build && pushd build && cmake .. && make -j && popd &&
+    pip install -r tests/requirement_tests.txt &&
+    nosetests

MorphIO-2.1.3/3rdparty/CMakeLists.txt

@@ -0,0 +1,19 @@
+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})
+
+add_subdirectory(GSL_LITE)
+target_include_directories(gsl-lite SYSTEM INTERFACE)
+
+add_library(lexertl INTERFACE)
+target_include_directories(lexertl SYSTEM INTERFACE lexertl)
+
+if(BUILD_BINDINGS)
+  add_subdirectory(pybind11)
+  target_include_directories(pybind11 SYSTEM INTERFACE
+    pybind11)
+endif()

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/.appveyor.yml

@@ -3,6 +3,7 @@ image:
 - Visual Studio 2017
 - Visual Studio 2015
 test: off
+skip_branch_with_pr: true
 build:
   parallel: true
 platform:
@@ -41,13 +42,14 @@ install:
     if ($env:PYTHON) {
       if ($env:PLATFORM -eq "x64") { $env:PYTHON = "$env:PYTHON-x64" }
       $env:PATH = "C:\Python$env:PYTHON\;C:\Python$env:PYTHON\Scripts\;$env:PATH"
-      pip install --disable-pip-version-check --user --upgrade pip wheel
-      pip install pytest numpy
+      python -W ignore -m pip install --upgrade pip wheel
+      python -W ignore -m pip install pytest numpy --no-warn-script-location
     } elseif ($env:CONDA) {
       if ($env:CONDA -eq "27") { $env:CONDA = "" }
       if ($env:PLATFORM -eq "x64") { $env:CONDA = "$env:CONDA-x64" }
       $env:PATH = "C:\Miniconda$env:CONDA\;C:\Miniconda$env:CONDA\Scripts\;$env:PATH"
       $env:PYTHONHOME = "C:\Miniconda$env:CONDA"
+      conda --version
       conda install -y -q pytest numpy scipy
     }
 - ps: |
@@ -60,6 +62,7 @@ build_script:
     -DPYBIND11_WERROR=ON
     -DDOWNLOAD_CATCH=ON
     -DCMAKE_SUPPRESS_REGENERATION=1
+    .
 - set MSBuildLogger="C:\Program Files\AppVeyor\BuildAgent\Appveyor.MSBuildLogger.dll"
 - cmake --build . --config %CONFIG% --target pytest -- /m /v:m /logger:%MSBuildLogger%
 - cmake --build . --config %CONFIG% --target cpptest -- /m /v:m /logger:%MSBuildLogger%

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/.gitignore

@@ -27,6 +27,7 @@ MANIFEST
 *.py[co]
 *.egg-info
 *~
+.*.swp
 .DS_Store
 /dist
 /build

MorphIO-2.1.3/3rdparty/pybind11/.gitmodules

@@ -0,0 +1,3 @@
+[submodule "tools/clang"]
+	path = tools/clang
+	url = ../../wjakob/clang-cindex-python3

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/.travis.yml

@@ -1,6 +1,4 @@
 language: cpp
-dist: trusty
-sudo: false
 matrix:
   include:
   # This config does a few things:
@@ -10,16 +8,17 @@ matrix:
   # - Makes sure that everything still works without optional deps (numpy/scipy/eigen) and
   #   also tests the automatic discovery functions in CMake (Python version, C++ standard).
   - os: linux
-    env: STYLE DOCS PIP
+    dist: xenial # Necessary to run doxygen 1.8.15
+    name: Style, docs, and pip
     cache: false
     before_install:
     - pyenv global $(pyenv whence 2to3)  # activate all python versions
     - PY_CMD=python3
-    - $PY_CMD -m pip install --user --upgrade pip wheel
-    install:
-    - $PY_CMD -m pip install --user --upgrade sphinx sphinx_rtd_theme breathe flake8 pep8-naming pytest
-    - curl -fsSL ftp://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.12.linux.bin.tar.gz | tar xz
-    - export PATH="$PWD/doxygen-1.8.12/bin:$PATH"
+    - $PY_CMD -m pip install --user --upgrade pip wheel setuptools
+    install: # Breathe does not yet support Sphinx 2
+    - $PY_CMD -m pip install --user --upgrade "sphinx<2" sphinx_rtd_theme breathe flake8 pep8-naming pytest
+    - curl -fsSL https://sourceforge.net/projects/doxygen/files/rel-1.8.15/doxygen-1.8.15.linux.bin.tar.gz/download | tar xz
+    - export PATH="$PWD/doxygen-1.8.15/bin:$PATH"
     script:
     - tools/check-style.sh
     - flake8
@@ -32,62 +31,119 @@ matrix:
       diff -rq $installed ./include/pybind11
     - |
       # Barebones build
-      cmake -DCMAKE_BUILD_TYPE=Debug -DPYBIND11_WERROR=ON -DDOWNLOAD_CATCH=ON
+      cmake -DCMAKE_BUILD_TYPE=Debug -DPYBIND11_WERROR=ON -DDOWNLOAD_CATCH=ON -DPYTHON_EXECUTABLE=$(which $PY_CMD) .
       make pytest -j 2
       make cpptest -j 2
   # The following are regular test configurations, including optional dependencies.
   # With regard to each other they differ in Python version, C++ standard and compiler.
   - os: linux
+    dist: trusty
+    name: Python 2.7, c++11, gcc 4.8
     env: PYTHON=2.7 CPP=11 GCC=4.8
     addons:
       apt:
-        packages: [cmake=2.\*, cmake-data=2.\*]
+        packages:
+          - cmake=2.\*
+          - cmake-data=2.\*
   - os: linux
+    dist: trusty
+    name: Python 3.6, c++11, gcc 4.8
     env: PYTHON=3.6 CPP=11 GCC=4.8
     addons:
       apt:
-        sources: [deadsnakes]
-        packages: [python3.6-dev python3.6-venv, cmake=2.\*, cmake-data=2.\*]
-  - sudo: true
-    services: docker
+        sources:
+          - deadsnakes
+        packages:
+          - python3.6-dev
+          - python3.6-venv
+          - cmake=2.\*
+          - cmake-data=2.\*
+  - os: linux
+    dist: trusty
     env: PYTHON=2.7 CPP=14 GCC=6 CMAKE=1
-  - sudo: true
-    services: docker
-    env: PYTHON=3.5 CPP=14 GCC=6 DEBUG=1
-  - sudo: true
+    name: Python 2.7, c++14, gcc 4.8, CMake test
+    addons:
+      apt:
+        sources:
+          - ubuntu-toolchain-r-test
+        packages:
+          - g++-6
+  - os: linux
+    dist: trusty
+    name: Python 3.5, c++14, gcc 6, Debug build
+    # N.B. `ensurepip` could be installed transitively by `python3.5-venv`, but
+    # seems to have apt conflicts (at least for Trusty). Use Docker instead.
     services: docker
+    env: DOCKER=debian:stretch PYTHON=3.5 CPP=14 GCC=6 DEBUG=1
+  - os: linux
+    dist: xenial
     env: PYTHON=3.6 CPP=17 GCC=7
+    name: Python 3.6, c++17, gcc 7
+    addons:
+      apt:
+        sources:
+          - deadsnakes
+          - ubuntu-toolchain-r-test
+        packages:
+          - g++-7
+          - python3.6-dev
+          - python3.6-venv
   - os: linux
-    env: PYTHON=3.6 CPP=17 CLANG=5.0
+    dist: xenial
+    env: PYTHON=3.6 CPP=17 CLANG=7
+    name: Python 3.6, c++17, Clang 7
     addons:
       apt:
-        sources: [deadsnakes, llvm-toolchain-trusty-5.0, ubuntu-toolchain-r-test]
-        packages: [python3.6-dev python3.6-venv clang-5.0 llvm-5.0-dev, lld-5.0]
+        sources:
+          - deadsnakes
+          - llvm-toolchain-xenial-7
+        packages:
+          - python3.6-dev
+          - python3.6-venv
+          - clang-7
+          - libclang-7-dev
+          - llvm-7-dev
+          - lld-7
+          - libc++-7-dev
+          - libc++abi-7-dev  # Why is this necessary???
   - os: osx
+    name: Python 2.7, c++14, AppleClang 7.3, CMake test
     osx_image: xcode7.3
     env: PYTHON=2.7 CPP=14 CLANG CMAKE=1
   - os: osx
+    name: Python 3.7, c++14, AppleClang 9, Debug build
     osx_image: xcode9
-    env: PYTHON=3.6 CPP=14 CLANG DEBUG=1
+    env: PYTHON=3.7 CPP=14 CLANG DEBUG=1
   # Test a PyPy 2.7 build
   - os: linux
+    dist: trusty
     env: PYPY=5.8 PYTHON=2.7 CPP=11 GCC=4.8
+    name: PyPy 5.8, Python 2.7, c++11, gcc 4.8
     addons:
       apt:
-        packages: [libblas-dev, liblapack-dev, gfortran]
+        packages:
+          - libblas-dev
+          - liblapack-dev
+          - gfortran
   # Build in 32-bit mode and tests against the CMake-installed version
-  - sudo: true
+  - os: linux
+    dist: trusty
     services: docker
-    env: ARCH=i386 PYTHON=3.5 CPP=14 GCC=6 INSTALL=1
+    env: DOCKER=i386/debian:stretch PYTHON=3.5 CPP=14 GCC=6 INSTALL=1
+    name: Python 3.4, c++14, gcc 6, 32-bit
     script:
       - |
-        $SCRIPT_RUN_PREFIX sh -c "set -e
-        cmake ${CMAKE_EXTRA_ARGS} -DPYBIND11_INSTALL=1 -DPYBIND11_TEST=0
-        make install
-        cp -a tests /pybind11-tests
-        mkdir /build-tests && cd /build-tests
-        cmake ../pybind11-tests ${CMAKE_EXTRA_ARGS} -DPYBIND11_WERROR=ON
-        make pytest -j 2"
+        # Consolidated 32-bit Docker Build + Install
+        set -ex
+        $SCRIPT_RUN_PREFIX sh -c "
+          set -ex
+          cmake ${CMAKE_EXTRA_ARGS} -DPYBIND11_INSTALL=1 -DPYBIND11_TEST=0 .
+          make install
+          cp -a tests /pybind11-tests
+          mkdir /build-tests && cd /build-tests
+          cmake ../pybind11-tests ${CMAKE_EXTRA_ARGS} -DPYBIND11_WERROR=ON
+          make pytest -j 2"
+        set +ex
 cache:
   directories:
   - $HOME/.local/bin
@@ -97,6 +153,7 @@ cache:
 before_install:
 - |
   # Configure build variables
+  set -ex
   if [ "$TRAVIS_OS_NAME" = "linux" ]; then
     if [ -n "$CLANG" ]; then
       export CXX=clang++-$CLANG CC=clang-$CLANG
@@ -107,18 +164,16 @@ before_install:
       fi
       export CXX=g++-$GCC CC=gcc-$GCC
     fi
-    if [ "$GCC" = "6" ]; then DOCKER=${ARCH:+$ARCH/}debian:stretch
-    elif [ "$GCC" = "7" ]; then DOCKER=debian:buster EXTRA_PACKAGES+=" catch" DOWNLOAD_CATCH=OFF
-    fi
   elif [ "$TRAVIS_OS_NAME" = "osx" ]; then
     export CXX=clang++ CC=clang;
   fi
   if [ -n "$CPP" ]; then CPP=-std=c++$CPP; fi
   if [ "${PYTHON:0:1}" = "3" ]; then PY=3; fi
   if [ -n "$DEBUG" ]; then CMAKE_EXTRA_ARGS+=" -DCMAKE_BUILD_TYPE=Debug"; fi
+  set +ex
 - |
   # Initialize environment
-  set -e
+  set -ex
   if [ -n "$DOCKER" ]; then
     docker pull $DOCKER
 
@@ -138,7 +193,7 @@ before_install:
       PY_CMD=python$PYTHON
       if [ "$TRAVIS_OS_NAME" = "osx" ]; then
         if [ "$PY" = "3" ]; then
-          brew update && brew install python$PY;
+          brew update && brew upgrade python
         else
           curl -fsSL https://bootstrap.pypa.io/get-pip.py | $PY_CMD - --user
         fi
@@ -147,13 +202,15 @@ before_install:
     if [ "$PY" = 3 ] || [ -n "$PYPY" ]; then
       $PY_CMD -m ensurepip --user
     fi
+    $PY_CMD --version
     $PY_CMD -m pip install --user --upgrade pip wheel
   fi
-  set +e
+  set +ex
 install:
 - |
   # Install dependencies
-  set -e
+  set -ex
+  cmake --version
   if [ -n "$DOCKER" ]; then
     if [ -n "$DEBUG" ]; then
       PY_DEBUG="python$PYTHON-dbg python$PY-scipy-dbg"
@@ -165,32 +222,21 @@ install:
         libeigen3-dev libboost-dev cmake make ${EXTRA_PACKAGES} && break; done"
   else
 
-    if [ "$CLANG" = "5.0" ]; then
-      if ! [ -d ~/.local/include/c++/v1 ]; then
-        # Neither debian nor llvm provide a libc++ 5.0 deb; luckily it's fairly quick
-        # to build, install (and cache), so do it ourselves:
-        git clone --depth=1 https://github.com/llvm-mirror/llvm.git llvm-source
-        git clone https://github.com/llvm-mirror/libcxx.git llvm-source/projects/libcxx -b release_50
-        git clone https://github.com/llvm-mirror/libcxxabi.git llvm-source/projects/libcxxabi -b release_50
-        mkdir llvm-build && cd llvm-build
-        # Building llvm requires a newer cmake than is provided by the trusty container:
-        CMAKE_VER=cmake-3.8.0-Linux-x86_64
-        curl https://cmake.org/files/v3.8/$CMAKE_VER.tar.gz | tar xz
-        ./$CMAKE_VER/bin/cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=~/.local ../llvm-source
-        make -j2 install-cxxabi install-cxx
-        cp -a include/c++/v1/*cxxabi*.h ~/.local/include/c++/v1
-        cd ..
-      fi
-      export CXXFLAGS="-isystem $HOME/.local/include/c++/v1 -stdlib=libc++"
-      export LDFLAGS="-L$HOME/.local/lib -fuse-ld=lld-$CLANG"
-      export LD_LIBRARY_PATH="$HOME/.local/lib${LD_LIBRARY_PATH:+:$LD_LIBRARY_PATH}"
-      if [ "$CPP" = "-std=c++17" ]; then CPP="-std=c++1z"; fi
+    if [ "$CLANG" = "7" ]; then
+      export CXXFLAGS="-stdlib=libc++"
     fi
 
     export NPY_NUM_BUILD_JOBS=2
     echo "Installing pytest, numpy, scipy..."
-    ${PYPY:+travis_wait 30} $PY_CMD -m pip install --user --upgrade pytest numpy scipy \
-        ${PYPY:+--extra-index-url https://imaginary.ca/trusty-pypi}
+    local PIP_CMD=""
+    if [ -n $PYPY ]; then
+      # For expediency, install only versions that are available on the extra index.
+      travis_wait 30 \
+        $PY_CMD -m pip install --user --upgrade --extra-index-url https://imaginary.ca/trusty-pypi \
+          pytest numpy==1.15.4 scipy==1.2.0
+    else
+      $PY_CMD -m pip install --user --upgrade pytest numpy scipy
+    fi
     echo "done."
 
     mkdir eigen
@@ -198,16 +244,37 @@ install:
         tar --extract -j --directory=eigen --strip-components=1
     export CMAKE_INCLUDE_PATH="${CMAKE_INCLUDE_PATH:+$CMAKE_INCLUDE_PATH:}$PWD/eigen"
   fi
-  set +e
+  set +ex
 script:
-- $SCRIPT_RUN_PREFIX cmake ${CMAKE_EXTRA_ARGS}
-    -DPYBIND11_PYTHON_VERSION=$PYTHON
-    -DPYBIND11_CPP_STANDARD=$CPP
-    -DPYBIND11_WERROR=${WERROR:-ON}
-    -DDOWNLOAD_CATCH=${DOWNLOAD_CATCH:-ON}
-- $SCRIPT_RUN_PREFIX make pytest -j 2
-- $SCRIPT_RUN_PREFIX make cpptest -j 2
-- if [ -n "$CMAKE" ]; then $SCRIPT_RUN_PREFIX make test_cmake_build; fi
+- |
+  # CMake Configuration
+  set -ex
+  $SCRIPT_RUN_PREFIX cmake ${CMAKE_EXTRA_ARGS} \
+    -DPYBIND11_PYTHON_VERSION=$PYTHON \
+    -DPYBIND11_CPP_STANDARD=$CPP \
+    -DPYBIND11_WERROR=${WERROR:-ON} \
+    -DDOWNLOAD_CATCH=${DOWNLOAD_CATCH:-ON} \
+    .
+  set +ex
+- |
+  # pytest
+  set -ex
+  $SCRIPT_RUN_PREFIX make pytest -j 2 VERBOSE=1
+  set +ex
+- |
+  # cpptest
+  set -ex
+  $SCRIPT_RUN_PREFIX make cpptest -j 2
+  set +ex
+- |
+  # CMake Build Interface
+  set -ex
+  if [ -n "$CMAKE" ]; then $SCRIPT_RUN_PREFIX make test_cmake_build; fi
+  set +ex
 after_failure: cat tests/test_cmake_build/*.log*
 after_script:
-- if [ -n "$DOCKER" ]; then docker stop "$containerid"; docker rm "$containerid"; fi
+- |
+  # Cleanup (Docker)
+  set -ex
+  if [ -n "$DOCKER" ]; then docker stop "$containerid"; docker rm "$containerid"; fi
+  set +ex

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/CMakeLists.txt

@@ -38,6 +38,8 @@ set(PYTHON_INCLUDE_DIRS ${PYTHON_INCLUDE_DIRS} CACHE INTERNAL "")
 set(PYTHON_LIBRARIES ${PYTHON_LIBRARIES} CACHE INTERNAL "")
 set(PYTHON_MODULE_PREFIX ${PYTHON_MODULE_PREFIX} CACHE INTERNAL "")
 set(PYTHON_MODULE_EXTENSION ${PYTHON_MODULE_EXTENSION} CACHE INTERNAL "")
+set(PYTHON_VERSION_MAJOR ${PYTHON_VERSION_MAJOR} CACHE INTERNAL "")
+set(PYTHON_VERSION_MINOR ${PYTHON_VERSION_MINOR} CACHE INTERNAL "")
 
 # NB: when adding a header don't forget to also add it to setup.py
 set(PYBIND11_HEADERS

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/CONTRIBUTING.md

@@ -27,6 +27,8 @@ adhere to the following rules to make the process as smooth as possible:
   do add value by themselves.
 * Add tests for any new functionality and run the test suite (``make pytest``)
   to ensure that no existing features break.
+* Please run ``flake8`` and ``tools/check-style.sh`` to check your code matches
+  the project style. (Note that ``check-style.sh`` requires ``gawk``.)
 * This project has a strong focus on providing general solutions using a
   minimal amount of code, thus small pull requests are greatly preferred.
 

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/README.md

@@ -51,7 +51,6 @@ pybind11 can map the following core C++ features to Python
 - Custom operators
 - Single and multiple inheritance
 - STL data structures
-- Iterators and ranges
 - Smart pointers with reference counting like ``std::shared_ptr``
 - Internal references with correct reference counting
 - C++ classes with virtual (and pure virtual) methods can be extended in Python
@@ -98,7 +97,7 @@ In addition to the core functionality, pybind11 provides some extra goodies:
 1. Clang/LLVM 3.3 or newer (for Apple Xcode's clang, this is 5.0.0 or newer)
 2. GCC 4.8 or newer
 3. Microsoft Visual Studio 2015 Update 3 or newer
-4. Intel C++ compiler 16 or newer (15 with a [workaround](https://github.com/pybind/pybind11/issues/276))
+4. Intel C++ compiler 17 or newer (16 with pybind11 v2.0 and 15 with pybind11 v2.0 and a [workaround](https://github.com/pybind/pybind11/issues/276))
 5. Cygwin/GCC (tested on 2.5.1)
 
 ## About

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/docs/advanced/cast/eigen.rst

@@ -275,7 +275,7 @@ Vectors versus column/row matrices
 Eigen and numpy have fundamentally different notions of a vector.  In Eigen, a
 vector is simply a matrix with the number of columns or rows set to 1 at
 compile time (for a column vector or row vector, respectively).  Numpy, in
-contast, has comparable 2-dimensional 1xN and Nx1 arrays, but *also* has
+contrast, has comparable 2-dimensional 1xN and Nx1 arrays, but *also* has
 1-dimensional arrays of size N.
 
 When passing a 2-dimensional 1xN or Nx1 array to Eigen, the Eigen type must

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/docs/advanced/cast/overview.rst

@@ -131,6 +131,8 @@ as arguments and return values, refer to the section on binding :ref:`classes`.
 +------------------------------------+---------------------------+-------------------------------+
 | ``std::vector<T>``                 | STL dynamic array         | :file:`pybind11/stl.h`        |
 +------------------------------------+---------------------------+-------------------------------+
+| ``std::deque<T>``                  | STL double-ended queue    | :file:`pybind11/stl.h`        |
++------------------------------------+---------------------------+-------------------------------+
 | ``std::valarray<T>``               | STL value array           | :file:`pybind11/stl.h`        |
 +------------------------------------+---------------------------+-------------------------------+
 | ``std::list<T>``                   | STL linked list           | :file:`pybind11/stl.h`        |

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/docs/advanced/cast/stl.rst

@@ -5,7 +5,7 @@ Automatic conversion
 ====================
 
 When including the additional header file :file:`pybind11/stl.h`, conversions
-between ``std::vector<>``/``std::list<>``/``std::array<>``,
+between ``std::vector<>``/``std::deque<>``/``std::list<>``/``std::array<>``,
 ``std::set<>``/``std::unordered_set<>``, and
 ``std::map<>``/``std::unordered_map<>`` and the Python ``list``, ``set`` and
 ``dict`` data structures are automatically enabled. The types ``std::pair<>``
@@ -175,9 +175,6 @@ in Python, and to define a set of available operations, e.g.:
         }, py::keep_alive<0, 1>()) /* Keep vector alive while iterator is used */
         // ....
 
-Please take a look at the :ref:`macro_notes` before using the
-``PYBIND11_MAKE_OPAQUE`` macro.
-
 .. seealso::
 
     The file :file:`tests/test_opaque_types.cpp` contains a complete

{MorphIO-2.0.7 → MorphIO-2.1.3}/3rdparty/pybind11/docs/advanced/cast/strings.rst

@@ -58,7 +58,9 @@ Passing bytes to C++
 --------------------
 
 A Python ``bytes`` object will be passed to C++ functions that accept
-``std::string`` or ``char*`` *without* conversion.
+``std::string`` or ``char*`` *without* conversion.  On Python 3, in order to
+make a function *only* accept ``bytes`` (and not ``str``), declare it as taking
+a ``py::bytes`` argument.
 
 
 Returning C++ strings to Python