Merge branch 'GUDHI:master' into simplex_tree_filtration_value_genera…

…lization
hschreiber · Sep 3, 2024 · 7555436 · 7555436
2 parents df5a510 + 2a89fd5
commit 7555436
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -100,7 +100,7 @@ jobs:
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF -DUSER_VERSION_DIR=version ..
             make user_version
             cd version
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 -DWITH_GUDHI_REMOTE_TEST=ON .
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON .
             cd python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
@@ -243,7 +243,7 @@ jobs:
           command: |
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON ..
             cd src/python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure
@@ -323,7 +323,7 @@ jobs:
           command: |
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=ON ..
             cd src/python
             python3 setup.py build_ext --inplace
             ctest --output-on-failure

diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md
@@ -32,7 +32,7 @@ Checkin the modifications, build and test the version:
 ```bash
 git submodule update --init
 rm -rf build; mkdir build; cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_REMOTE_TEST=ON -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON  -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_REMOTE_TEST=ON -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON  -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ ..
 make user_version
 date +"%d-%m-%Y-%T" > gudhi.@GUDHI_VERSION@/timestamp.txt
 tar -czvf gudhi.@GUDHI_VERSION@.tar.gz gudhi.@GUDHI_VERSION@
@@ -54,7 +54,7 @@ mkdir gudhi.doc.@GUDHI_VERSION@
 ```bash
 cd gudhi.@GUDHI_VERSION@
 rm -rf build; mkdir build; cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_EXAMPLE=ON ..
 make doxygen && grep warning doxygen.log
 ```
 

diff --git a/.github/next_release.md b/.github/next_release.md
@@ -18,6 +18,9 @@ Below is a list of changes:
 - [Module](link)
      - **...**
 
+- Installation
+     - CMake &ge; 3.15 is now required (was &ge; 3.8).
+
 - Miscellaneous
      - The [list of bugs that were solved](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.11.0+is%3Aclosed) is available on GitHub.
 

diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
@@ -21,7 +21,7 @@ jobs:
         run: |
           mkdir build_39
           cd build_39
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON39/bin/python ..
           cd src/python
           $PYTHON39/bin/python -m build -n -w
           auditwheel repair dist/*.whl

diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
@@ -46,7 +46,7 @@ jobs:
           python --version
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
+          cmake -DCMAKE_BUILD_TYPE=Release ..
           cd src/python
           python -m build -n -w
           export PATH="$PATH:`python -m site --user-base`/bin"

diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
@@ -22,7 +22,7 @@ jobs:
           rm -rf src/python/gudhi/*.cpp
           mkdir build_38
           cd build_38
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON38/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON38/bin/python ..
           cd src/python
           $PYTHON38/bin/python -m build -n -w
           auditwheel repair dist/*.whl
@@ -41,7 +41,7 @@ jobs:
           rm -rf src/python/gudhi/*.cpp
           mkdir build_39
           cd build_39
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON39/bin/python ..
           cd src/python
           $PYTHON39/bin/python -m build -n -w
           auditwheel repair dist/*.whl
@@ -64,7 +64,7 @@ jobs:
           rm -rf src/python/gudhi/*.cpp
           mkdir build_310
           cd build_310
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON310/bin/python ..
           cd src/python
           $PYTHON310/bin/python -m build -n -w
           auditwheel repair dist/*.whl
@@ -83,7 +83,7 @@ jobs:
           rm -rf src/python/gudhi/*.cpp
           mkdir build_311
           cd build_311
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON311/bin/python ..
           cd src/python
           $PYTHON311/bin/python -m build -n -w
           auditwheel repair dist/*.whl
@@ -102,7 +102,7 @@ jobs:
           rm -rf src/python/gudhi/*.cpp
           mkdir build_312
           cd build_312
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON312/bin/python ..
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON312/bin/python ..
           cd src/python
           $PYTHON312/bin/python -m build -n -w
           auditwheel repair dist/*.whl

diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
@@ -42,7 +42,7 @@ jobs:
           python --version
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
+          cmake -DCMAKE_BUILD_TYPE=Release ..
           cd src/python
           python -m build -n -w
       - name: Install and test python wheel
@@ -112,7 +112,7 @@ jobs:
           python --version
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
+          cmake -DCMAKE_BUILD_TYPE=Release ..
           cd src/python
           python -m build -n -w
       # Test ABI compatibility with numpy 1.X

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.8)
+cmake_minimum_required(VERSION 3.15)
 
 project(GUDHIdev)
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -8,6 +8,10 @@ jobs:
     variables:
       pythonVersion: "3.9"
       cmakeBuildType: Release
+      gudhiCmakeOptions: -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON
+      # On this VM, 2 versions of python are installed. Default Python_FIND_FRAMEWORK is FIRST, which means asks frameworks first
+      # LAST means consult frameworks in last resort, use the PATH first
+      extraCmakeOptions: -DPython_FIND_FRAMEWORK=LAST
 
     steps:
       # Use a specific Python version
@@ -29,7 +33,8 @@ jobs:
       - bash: |
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE:STRING=$(cmakeBuildType) -GNinja -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON ..
+          which python
+          cmake -DCMAKE_BUILD_TYPE:STRING=$(cmakeBuildType) $(extraCmakeOptions) -GNinja $(gudhiCmakeOptions) ..
           ninja
           ninja doxygen
           ctest --output-on-failure
@@ -44,7 +49,11 @@ jobs:
     variables:
       pythonVersion: "3.9"
       cmakeVcpkgFlags: -DVCPKG_TARGET_TRIPLET=x64-windows -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake
-      cmakeFlags: -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF
+      # WITH_GUDHI_PYTHON=OFF on purpose. It is set to ON on a second cmake call
+      gudhiCmakeOptions: -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF
+      # On this VM, 2 versions of python are installed. Default Python_FIND_REGISTRY is FIRST, which means asks registry first
+      # LAST means consult registry in last resort, use the standard libraries or headers first
+      extraCmakeOptions: -DPython_FIND_REGISTRY=LAST
 
     steps:
       # Use a specific Python version
@@ -69,16 +78,16 @@ jobs:
           IF %ERRORLEVEL% NEQ 0 EXIT 1
         displayName: "Install build dependencies"
       - script: |
-          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvarsall.bat" amd64
+          call "C:\Program Files\Microsoft Visual Studio\2022\Enterprise\VC\Auxiliary\Build\vcvars64.bat"
           mkdir build
           cd build
-          cmake -DCMAKE_BUILD_TYPE=Release -G "Ninja" -DFORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT=ON $(cmakeVcpkgFlags) $(cmakeFlags) ..
+          cmake -DCMAKE_BUILD_TYPE=Release -G "Ninja" -DFORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT=ON $(cmakeVcpkgFlags) $(gudhiCmakeOptions) ..
           IF %ERRORLEVEL% NEQ 0 EXIT 1
           ninja
           IF %ERRORLEVEL% NEQ 0 EXIT 1
           ctest --output-on-failure -C Release -E diff_files
           IF %ERRORLEVEL% NEQ 0 EXIT 1
-          cmake  -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON .
+          cmake $(extraCmakeOptions) -DWITH_GUDHI_PYTHON=ON -DWITH_GUDHI_REMOTE_TEST=ON .
           IF %ERRORLEVEL% NEQ 0 EXIT 1
           cd src\python
           copy "C:\vcpkg\installed\x64-windows\bin\mpfr*.dll" ".\gudhi\"

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,4 +1,4 @@
-cmake_minimum_required(VERSION 3.8)
+cmake_minimum_required(VERSION 3.15)
 
 project(GUDHI)
 

diff --git a/src/cmake/modules/GUDHI_third_party_libraries.cmake b/src/cmake/modules/GUDHI_third_party_libraries.cmake
@@ -134,23 +134,27 @@ add_definitions( -DBOOST_SYSTEM_NO_DEPRECATED )
 
 if (WITH_GUDHI_PYTHON)
   # Find the correct Python interpreter.
-  # Can be set with -DPYTHON_EXECUTABLE=/usr/bin/python3 or -DPython_ADDITIONAL_VERSIONS=3 for instance.
-  find_package( PythonInterp )
-
+  # Can be set with -DPython_EXECUTABLE=/usr/bin/python3 for instance.
+  # Default Python_FIND_STRATEGY to LOCATION: Stops lookup as soon as a version satisfying version constraints is founded
+  # (as opposed to VERSION: Try to find the most recent version in all specified locations.)
+  cmake_policy(SET CMP0094 NEW)
+  # Should be Development.Module (Development also includes Development.Embed) but it would require cmake 3.18. TODO in a later version
+  find_package( Python COMPONENTS Interpreter Development NumPy)
+
   # find_python_module tries to import module in Python interpreter and to retrieve its version number
   # returns ${PYTHON_MODULE_NAME_UP}_VERSION and ${PYTHON_MODULE_NAME_UP}_FOUND
   function( find_python_module PYTHON_MODULE_NAME )
     string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
     execute_process(
-            COMMAND ${PYTHON_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
+            COMMAND ${Python_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}; print(${PYTHON_MODULE_NAME}.__version__)"
             RESULT_VARIABLE PYTHON_MODULE_RESULT
             OUTPUT_VARIABLE PYTHON_MODULE_VERSION
             ERROR_VARIABLE PYTHON_MODULE_ERROR)
     if(PYTHON_MODULE_RESULT EQUAL 0)
       # Remove all carriage returns as it can be multiline
       string(REGEX REPLACE "\n" " " PYTHON_MODULE_VERSION "${PYTHON_MODULE_VERSION}")
       message ("++ Python module ${PYTHON_MODULE_NAME} - Version ${PYTHON_MODULE_VERSION} found")
-  
+
       set(${PYTHON_MODULE_NAME_UP}_VERSION ${PYTHON_MODULE_VERSION} PARENT_SCOPE)
       set(${PYTHON_MODULE_NAME_UP}_FOUND TRUE PARENT_SCOPE)
     else()
@@ -167,7 +171,7 @@ if (WITH_GUDHI_PYTHON)
   function( find_python_module_no_version PYTHON_MODULE_NAME )
     string(TOUPPER ${PYTHON_MODULE_NAME} PYTHON_MODULE_NAME_UP)
     execute_process(
-            COMMAND ${PYTHON_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}"
+            COMMAND ${Python_EXECUTABLE}  -c "import ${PYTHON_MODULE_NAME}"
             RESULT_VARIABLE PYTHON_MODULE_RESULT
             ERROR_VARIABLE PYTHON_MODULE_ERROR)
     if(PYTHON_MODULE_RESULT EQUAL 0)
@@ -181,8 +185,8 @@ if (WITH_GUDHI_PYTHON)
       set(${PYTHON_MODULE_NAME_UP}_FOUND FALSE PARENT_SCOPE)
     endif()
   endfunction( find_python_module_no_version )
-  
-  if( PYTHONINTERP_FOUND )
+
+  if( TARGET Python::Interpreter )
     find_python_module("cython")
     find_python_module("pytest")
     find_python_module("matplotlib")
@@ -202,19 +206,11 @@ if (WITH_GUDHI_PYTHON)
     find_python_module_no_version("sphinxcontrib.bibtex")
     find_python_module("networkx")
   endif()
-  
+
   if(NOT GUDHI_PYTHON_PATH)
     message(FATAL_ERROR "ERROR: GUDHI_PYTHON_PATH is not valid.")
   endif(NOT GUDHI_PYTHON_PATH)
-  
+
   option(WITH_GUDHI_PYTHON_RUNTIME_LIBRARY_DIRS "Build with setting runtime_library_dirs. Useful when setting rpath is not allowed" ON)
-
-  if(PYTHONINTERP_FOUND AND CYTHON_FOUND)
-    if(SPHINX_FOUND)
-      # Documentation generation is available through sphinx
-      #find_program( SPHINX_PATH sphinx-build )
-      # Calling sphinx-build may use a different version of python and fail
-      set(SPHINX_PATH "${PYTHON_EXECUTABLE}" "-m" "sphinx.cmd.build")
-    endif(SPHINX_FOUND)
-  endif(PYTHONINTERP_FOUND AND CYTHON_FOUND)
+
 endif (WITH_GUDHI_PYTHON)
diff --git a/src/common/doc/installation.h b/src/common/doc/installation.h
@@ -6,7 +6,7 @@
  * 
  * \section compiling Compiling
  * The library uses c++17 and requires <a target="_blank" href="https://www.boost.org/">Boost</a>  &ge; 1.71.0
- * and <a target="_blank" href="https://cmake.org/">CMake</a> &ge; 3.8.
+ * and <a target="_blank" href="https://cmake.org/">CMake</a> &ge; 3.15.
  * It is a multi-platform library and compiles on Linux, Mac OSX and Visual Studio 2017.
  * 
  * \subsection utilities Utilities and examples