Merge pull request #1131 from VincentRouvreau/symbolic_links_for_setu…

…p_py

Symbolic links for cython and pybind11 compilation

.github/for_maintainers/new_gudhi_version_creation.md

@@ -25,7 +25,7 @@ nor [unlabelled closed PRs](https://github.com/GUDHI/gudhi-devel/pulls?q=is%3Apr
 **Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the version new delivery.
 ```bash
 # cf. .gitignore - ignore this if it is a fresh clone version
-rm -rf data/points/COIL_database/lucky_cat.off_dist data/points/COIL_database/lucky_cat.off_sc.dot data/points/KleinBottle5D.off_dist data/points/KleinBottle5D.off_sc.dot data/points/human.off_dist data/points/human.off_sc.off data/points/human.off_sc.txt src/python/test/__pycache__ src/python/gudhi/*.cpp
+rm -rf data/points/COIL_database/lucky_cat.off_dist data/points/COIL_database/lucky_cat.off_sc.dot data/points/KleinBottle5D.off_dist data/points/KleinBottle5D.off_sc.dot data/points/human.off_dist data/points/human.off_sc.off data/points/human.off_sc.txt src/python/test/__pycache__
 ```
 
 Checkin the modifications, build and test the version:
@@ -154,4 +154,4 @@ Send version mail to the following lists :
 
 **Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the future version (something like `3.X+1.0a0`).
 
-Reset [.github/next_release.md](.github/next_release.md) with [.github/for_maintainers/next_release_template.md](.github/for_maintainers/next_release_template.md).
+Reset [.github/next_release.md](.github/next_release.md) with [.github/for_maintainers/next_release_template.md](.github/for_maintainers/next_release_template.md).

.github/workflows/pip-packaging-linux.yml

@@ -19,7 +19,6 @@ jobs:
       # numpy~=1.21.4 means any numpy=1.21.*, but also numpy>=1.21.4 (numpy~=1.21 do not work as it means any numpy==1.*)
       - name: Build wheel for Python 3.8
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_38
           cd build_38
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON38/bin/python ..
@@ -38,7 +37,6 @@ jobs:
           $PYTHON38/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.9
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_39
           cd build_39
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON39/bin/python ..
@@ -61,7 +59,6 @@ jobs:
           $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.10
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_310
           cd build_310
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON310/bin/python ..
@@ -80,7 +77,6 @@ jobs:
           $PYTHON310/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.11
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_311
           cd build_311
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON311/bin/python ..
@@ -99,7 +95,6 @@ jobs:
           $PYTHON311/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Build wheel for Python 3.12
         run: |
-          rm -rf src/python/gudhi/*.cpp
           mkdir build_312
           cd build_312
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON312/bin/python ..

.gitignore

@@ -1,9 +1,6 @@
 # Classical CMake build directory
 /*build*
 
-# Generated by Cython
-src/python/gudhi/*.cpp
-
 # Generated by tests
 data/points/COIL_database/lucky_cat.off_dist
 data/points/COIL_database/lucky_cat.off_sc.dot

src/python/CMakeLists.txt

@@ -56,6 +56,17 @@ function( add_gudhi_py_test THE_TEST )
   endif()
 endfunction( add_gudhi_py_test )
 
+function( add_gudhi_symbolic_links GLOBBING_EXPRESSION )
+  # No symbolic links if build in sources (aka. 'cmake .' in sources)
+  if (CMAKE_CURRENT_SOURCE_DIR STREQUAL CMAKE_CURRENT_BINARY_DIR)
+    return()
+  endif()
+  file(GLOB GUDHI_GLOB_FILES RELATIVE ${CMAKE_CURRENT_SOURCE_DIR} ${GLOBBING_EXPRESSION})
+  foreach(GUDHI_GLOB_FILENAME ${GUDHI_GLOB_FILES})
+    file(CREATE_LINK "${CMAKE_CURRENT_SOURCE_DIR}/${GUDHI_GLOB_FILENAME}" "${CMAKE_CURRENT_BINARY_DIR}/${GUDHI_GLOB_FILENAME}" SYMBOLIC)
+  endforeach()
+endfunction( add_gudhi_symbolic_links )
+
 # Set gudhi.__debug_info__
 # WARNING : to be done before setup.py.in configure_file
 function( add_gudhi_debug_info DEBUG_INFO )
@@ -382,6 +393,14 @@ file(COPY "gudhi/flag_filtration" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/gudhi
 # Some files for pip package
 file(COPY "pyproject.toml" DESTINATION "${CMAKE_CURRENT_BINARY_DIR}/")
 
+# Symbolic links to cython and Pybind11 sources to be built. "MAKE_DIRECTORY gudhi" must be done before
+add_gudhi_symbolic_links("gudhi/*.pxd")
+add_gudhi_symbolic_links("gudhi/*.pyx")
+add_gudhi_symbolic_links("gudhi/*.cc")
+add_gudhi_symbolic_links("gudhi/clustering/_tomato.cc")
+add_gudhi_symbolic_links("gudhi/hera/*.cc")
+add_gudhi_symbolic_links("gudhi/datasets/generators/_points.cc")
+
 add_custom_command(
     OUTPUT gudhi.so
     WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -438,7 +457,7 @@ add_test(NAME random_cubical_complex_persistence_example_py_test
 
 add_gudhi_py_test(test_cubical_complex)
 
-# Datasets are fetched for these tests 
+# Datasets are fetched for these tests
 if(SKLEARN_FOUND AND WITH_GUDHI_REMOTE_TEST)
   add_gudhi_py_test(test_sklearn_cubical_persistence)
 
@@ -574,7 +593,7 @@ if(SKLEARN_FOUND)
     add_gudhi_py_test(test_sklearn_rips_persistence)
   endif()
 
-  # Datasets are fetched for these tests 
+  # Datasets are fetched for these tests
   if(WITH_GUDHI_REMOTE_TEST)
     add_test(NAME rips_complex_sklearn_itf_py_test
              WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
@@ -690,4 +709,4 @@ if(MATPLOTLIB_FOUND)
 endif()
 
 # Set missing or not modules
-set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")
+set(GUDHI_MODULES ${GUDHI_MODULES} "python" CACHE INTERNAL "GUDHI_MODULES")

src/python/setup.py.in

@@ -17,7 +17,7 @@ import pybind11
 cython_modules = [@GUDHI_CYTHON_MODULES@]
 pybind11_modules = [@GUDHI_PYBIND11_MODULES@]
 
-source_dir='@CMAKE_CURRENT_SOURCE_DIR@/gudhi/'
+source_dir='gudhi/'
 extra_compile_args=[@GUDHI_PYTHON_EXTRA_COMPILE_ARGS@]
 extra_link_args=[@GUDHI_PYTHON_EXTRA_LINK_ARGS@]
 libraries=[@GUDHI_PYTHON_LIBRARIES@]