Merge branch 'GUDHI:master' into persistence_matrix

.circleci/config.yml

@@ -6,7 +6,7 @@ jobs:
   examples:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -25,7 +25,7 @@ jobs:
 
   tests:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -44,7 +44,7 @@ jobs:
 
   debug_tests:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -63,7 +63,7 @@ jobs:
 
   utils:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -82,7 +82,7 @@ jobs:
 
   python:
     docker:
-      - image: gudhi/ci_for_gudhi:latest
+      - image: gudhi/ci_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -118,7 +118,7 @@ jobs:
 
   doxygen:
     docker:
-      - image: gudhi/doxygen_for_gudhi:latest
+      - image: gudhi/doxygen_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -148,7 +148,7 @@ jobs:
 
   bibliography:
     docker:
-      - image: gudhi/doxygen_for_gudhi:latest
+      - image: gudhi/doxygen_for_gudhi:2024.06.01
     steps:
       - checkout
       - run:
@@ -172,7 +172,7 @@ jobs:
   examples_without_cgal_eigen:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image_without_cgal
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -191,7 +191,7 @@ jobs:
 
   tests_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -210,7 +210,7 @@ jobs:
 
   utils_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -229,7 +229,7 @@ jobs:
 
   python_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -252,7 +252,7 @@ jobs:
 
   examples_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -271,7 +271,7 @@ jobs:
 
   tests_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -290,7 +290,7 @@ jobs:
 
   utils_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:
@@ -309,7 +309,7 @@ jobs:
 
   python_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:latest
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
     steps:
       - checkout
       - run:

.github/code_conventions.md

@@ -18,7 +18,6 @@
 * Example files should be called `example_[what_it_is].cpp`. E.g. `example_sparsify_point_set.cpp`
 
 ### In CMakeLists.txt files:
-* The name of the "project" should be in this form: `Package_[tests|examples|…]`. E.g. `project(Simplex_tree_examples)`.
 * The name if each "target" (first parameter of add_executable) should be in this form: `Package_{name of the cpp file without extension}`. E.g `add_executable(Subsampling_test_sparsify_point_set test_sparsify_point_set.cpp)`.
 
 ### Code style

.github/next_release.md

@@ -7,6 +7,10 @@ Below is a list of changes made since GUDHI 3.9.0:
 - [Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_sklearn_itf_ref.html)
      - Rips complex persistence scikit-learn like interface
 
+- Installation
+     - CGAL ≥ 5.1.0 is now required (was ≥ 4.11.0).
+     - Eigen3 ≥ 3.3.0 is now required (was ≥ 3.1.0).
+
 - [Module](link)
      - **...**
 

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

@@ -7,7 +7,7 @@ jobs:
     name: build pip wheel
     runs-on: ubuntu-latest
     # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
-    container: gudhi/pip_for_gudhi:2023.12.01
+    container: gudhi/pip_for_gudhi:2024.06.01
     steps:
       # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
       - uses: actions/checkout@v3

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

@@ -9,7 +9,7 @@ jobs:
     name: build pip wheel
     runs-on: ubuntu-latest
     # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
-    container: gudhi/pip_for_gudhi:2023.12.01
+    container: gudhi/pip_for_gudhi:2024.06.01
     steps:
       # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
       - uses: actions/checkout@v3

azure-pipelines.yml

@@ -61,6 +61,8 @@ jobs:
         python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
         # No PyKeOps on windows, let's workaround this one.
         for /F "tokens=*" %%A in (ext\gudhi-deploy\test-requirements.txt) do python -m pip install  %%A
+        # Only vcpkg release libs for CI
+        echo.set(VCPKG_BUILD_TYPE release)>> C:\vcpkg\triplets\x64-windows.cmake
         vcpkg install boost-filesystem:x64-windows boost-test:x64-windows boost-program-options:x64-windows tbb:x64-windows eigen3:x64-windows cgal:x64-windows
         choco install -y ninja --force --force-dependencies
       displayName: 'Install build dependencies'

src/Alpha_complex/benchmark/CMakeLists.txt

@@ -1,9 +1 @@
-project(Alpha_complex_benchmark)
-
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-  add_executable(Alpha_complex_3d_benchmark Alpha_complex_3d_benchmark.cpp)
-  target_link_libraries(Alpha_complex_3d_benchmark ${CGAL_LIBRARY})
-  if(TARGET TBB::tbb)
-    target_link_libraries(Alpha_complex_3d_benchmark TBB::tbb)
-  endif()
-endif ()
+add_executable_with_targets(Alpha_complex_3d_benchmark Alpha_complex_3d_benchmark.cpp CGAL::CGAL Eigen3::Eigen TBB::tbb)

src/Alpha_complex/doc/Intro_alpha_complex.h

@@ -163,7 +163,6 @@ Table of Contents
  * In the following example, the value is given by the user as argument of the program.
  *
  * \section weightedversion Weighted specific version
- * <b>Requires:</b> \ref eigen &ge; 3.1.0 and \ref cgal &ge; 5.1.0.
  * 
  * A weighted version for Alpha complex is available (cf. Alpha_complex). It is like a usual Alpha complex, but based
  * on a <a href="https://doc.cgal.org/latest/Triangulation/index.html#TriangulationSecRT">CGAL regular triangulation</a> instead

src/Alpha_complex/example/CMakeLists.txt

@@ -1,18 +1,9 @@
-project(Alpha_complex_examples)
-
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
-  add_executable ( Alpha_complex_example_from_points Alpha_complex_from_points.cpp )
-  target_link_libraries(Alpha_complex_example_from_points  ${CGAL_LIBRARY})
-  add_executable ( Alpha_complex_example_from_off Alpha_complex_from_off.cpp )
-  target_link_libraries(Alpha_complex_example_from_off ${CGAL_LIBRARY})
-  add_executable ( Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp )
-  target_link_libraries(Alpha_complex_example_fast_from_off ${CGAL_LIBRARY})
-  if(TARGET TBB::tbb)
-    target_link_libraries(Alpha_complex_example_from_points TBB::tbb)
-    target_link_libraries(Alpha_complex_example_from_off TBB::tbb)
-    target_link_libraries(Alpha_complex_example_fast_from_off TBB::tbb)
-  endif()
+add_executable_with_targets(Alpha_complex_example_from_points Alpha_complex_from_points.cpp CGAL::CGAL Eigen3::Eigen TBB::tbb)
+add_executable_with_targets(Alpha_complex_example_from_off Alpha_complex_from_off.cpp CGAL::CGAL Eigen3::Eigen TBB::tbb)
+add_executable_with_targets(Alpha_complex_example_fast_from_off Fast_alpha_complex_from_off.cpp CGAL::CGAL Eigen3::Eigen TBB::tbb)
+add_executable_with_targets(Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp CGAL::CGAL Eigen3::Eigen TBB::tbb)
 
+if (TARGET CGAL::CGAL AND TARGET Eigen3::Eigen)
   add_test(NAME Alpha_complex_example_from_points COMMAND $<TARGET_FILE:Alpha_complex_example_from_points>)
 
   add_test(NAME Alpha_complex_example_from_off_60 COMMAND $<TARGET_FILE:Alpha_complex_example_from_off>
@@ -44,32 +35,16 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
         ${CMAKE_CURRENT_BINARY_DIR}/fastalphaoffreader_result_32.txt ${CMAKE_CURRENT_BINARY_DIR}/alphaoffreader_for_doc_32.txt)
     set_tests_properties(Alpha_complex_example_fast_from_off_32_diff_files PROPERTIES DEPENDS Alpha_complex_example_fast_from_off_32) 
   endif()
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 4.11.0)
+  add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $<TARGET_FILE:Weighted_alpha_complex_example_from_points>)
+endif()
 
-if (NOT CGAL_VERSION VERSION_LESS 4.11.0)
-  add_executable ( Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp )
-  target_link_libraries(Alpha_complex_example_weighted_3d_from_points  ${CGAL_LIBRARY})
-  if(TARGET TBB::tbb)
-    target_link_libraries(Alpha_complex_example_weighted_3d_from_points TBB::tbb)
-  endif()
+add_executable_with_targets(Alpha_complex_example_weighted_3d_from_points Weighted_alpha_complex_3d_from_points.cpp CGAL::CGAL TBB::tbb)
+add_executable_with_targets(Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp CGAL::CGAL TBB::tbb)
+
+if (TARGET CGAL::CGAL)
   add_test(NAME Alpha_complex_example_weighted_3d_from_points
           COMMAND $<TARGET_FILE:Alpha_complex_example_weighted_3d_from_points>)
 
-  add_executable ( Alpha_complex_example_3d_from_points Alpha_complex_3d_from_points.cpp )
-  target_link_libraries(Alpha_complex_example_3d_from_points  ${CGAL_LIBRARY})
-  if(TARGET TBB::tbb)
-    target_link_libraries(Alpha_complex_example_3d_from_points TBB::tbb)
-  endif()
   add_test(NAME Alpha_complex_example_3d_from_points
           COMMAND $<TARGET_FILE:Alpha_complex_example_3d_from_points>)
-
-endif(NOT CGAL_VERSION VERSION_LESS 4.11.0)
-
-if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
-  add_executable ( Weighted_alpha_complex_example_from_points Weighted_alpha_complex_from_points.cpp )
-  target_link_libraries(Weighted_alpha_complex_example_from_points  ${CGAL_LIBRARY})
-  if(TARGET TBB::tbb)
-    target_link_libraries(Weighted_alpha_complex_example_from_points TBB::tbb)
-  endif()
-  add_test(NAME Weighted_alpha_complex_example_from_points COMMAND $<TARGET_FILE:Weighted_alpha_complex_example_from_points>)
-endif(NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
+endif()

src/Alpha_complex/include/gudhi/Alpha_complex.h

@@ -98,7 +98,6 @@ template<typename D> struct Is_Epeck_D<CGAL::Epeck_d<D>> { static const bool val
  * [10^12,10^12+10^6]. Using `CGAL::Epick_d` makes the computations slightly faster, and the combinatorics are still
  * exact, but the computation of filtration values can exceptionally be arbitrarily bad. In all cases, we still
  * guarantee that the output is a valid filtration (faces have a filtration value no larger than their cofaces).
- * - For performances reasons, it is advised to use `Alpha_complex` with \ref cgal &ge; 5.0.0.
  */
 template<class Kernel = CGAL::Epeck_d<CGAL::Dynamic_dimension_tag>, bool Weighted = false>
 class Alpha_complex {
@@ -256,8 +255,8 @@ class Alpha_complex {
     #endif
 
 #if CGAL_VERSION_NR < 1050101000
-    // Make compilation fail if weighted and CGAL < 5.1
-    static_assert(!Weighted, "Weighted Alpha_complex is only available for CGAL >= 5.1");
+    // Make compilation fail if weighted and CGAL < 5.1.0
+    static_assert(!Weighted, "Weighted Alpha_complex is only available for CGAL >= 5.1.0");
 #endif
 
     auto first = std::begin(points);