release candidate 3

.github/changelog.md

@@ -1,31 +1,31 @@
 Release History
 ===============
 
-[Release 3.12.0rc1](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.12.0rc1)
+[Release 3.12.0rc3](https://github.com/GUDHI/gudhi-devel/releases/tag/tags%2Fgudhi-release-3.12.0rc3)
 -----------
 
 Release date: February 2026
 
 Below is a list of changes made since GUDHI 3.11.0:
 
-- [Čech complex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html) `[Python]`
+- [Čech complex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html) `[Python]`
      - Čech complex persistence scikit-learn like interface provides 2 new classes:
-         * [CechPersistence](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.CechPersistence) for computing the same persistent homology as the Čech complex, while being significantly smaller, using internally a [DelaunayCechComplex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_ref.html#gudhi.DelaunayCechComplex).
-         * [WeightedCechPersistence](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.WeightedCechPersistence) for computing the same persistent homology as the Weighted Čech complex, while being significantly smaller, using internally a Weighted version of [AlphaComplex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_ref.html#gudhi.AlphaComplex).
+         * [CechPersistence](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.CechPersistence) for computing the same persistent homology as the Čech complex, while being significantly smaller, using internally a [DelaunayCechComplex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_ref.html#gudhi.DelaunayCechComplex).
+         * [WeightedCechPersistence](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.WeightedCechPersistence) for computing the same persistent homology as the Weighted Čech complex, while being significantly smaller, using internally a Weighted version of [AlphaComplex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_ref.html#gudhi.AlphaComplex).
 
-- [Alpha complex dD](https://gudhi.inria.fr/doc/3.12.0rc1/class_gudhi_1_1alpha__complex_1_1_alpha__complex.html) `[C++]`
+- [Alpha complex dD](https://gudhi.inria.fr/doc/3.12.0rc3/class_gudhi_1_1alpha__complex_1_1_alpha__complex.html) `[C++]`
      - **API break:** The simplicial complex for the Alpha complex concept has been changed to
        `dimension_simplex_range` (that must returns a range of simplices of a given dimension) instead of
        `skeleton_simplex_range` (that was returning a range of simplices lower or equal to a given dimension)
 
-- [Simplex_tree](https://gudhi.inria.fr/doc/3.12.0rc1/class_gudhi_1_1_simplex__tree.html) `[C++]`
+- [Simplex_tree](https://gudhi.inria.fr/doc/3.12.0rc3/class_gudhi_1_1_simplex__tree.html) `[C++]`
      - A new iterator over the simplices of the simplicial complex that match a given dimension
 
-- [Persistence matrix](https://gudhi.inria.fr/doc/3.12.0rc1/group__persistence__matrix.html) `[C++]`
+- [Persistence matrix](https://gudhi.inria.fr/doc/3.12.0rc3/group__persistence__matrix.html) `[C++]`
      > Matrix API is in a beta version and may change in incompatible ways in the near future.
      - A new function to insert a maximal cell using swaps.
 
-- [Representations](https://gudhi.inria.fr/python/3.12.0rc1/representations.html) `[Python]`
+- [Representations](https://gudhi.inria.fr/python/3.12.0rc3/representations.html) `[Python]`
      - in metrics, `BottleneckDistance` argument `epsilon` is deprecrated and renamed `e` to be consistent with `bottleneck_distance` and `pairwise_persistence_diagram_distances`
 
 - Installation

.github/for_maintainers/new_gudhi_version_creation.md

@@ -22,7 +22,7 @@ nor [unlabelled closed PRs](https://github.com/GUDHI/gudhi-devel/pulls?q=is%3Apr
 
 ## Version file modification
 
-**Edit the file CMakeGUDHIVersion.txt**, and increment major, minor, or patch version number, in function of the version new delivery.
+**Edit the file CMakeGUDHIVersion.txt and the file pyproject.toml**, 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__

.github/next_release.md

@@ -9,24 +9,24 @@ From a user point of view, we recommend to download GUDHI user version (gudhi.3.
 
 Below is a list of changes:
 
-- [Čech complex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html) `[Python]`
+- [Čech complex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html) `[Python]`
      - Čech complex persistence scikit-learn like interface provides 2 new classes:
-         * [CechPersistence](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.CechPersistence) for computing the same persistent homology as the Čech complex, while being significantly smaller, using internally a [DelaunayCechComplex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_ref.html#gudhi.DelaunayCechComplex).
-         * [WeightedCechPersistence](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.WeightedCechPersistence) for computing the same persistent homology as the Weighted Čech complex, while being significantly smaller, using internally a Weighted version of [AlphaComplex](https://gudhi.inria.fr/python/3.12.0rc1/delaunay_complex_ref.html#gudhi.AlphaComplex).
+         * [CechPersistence](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.CechPersistence) for computing the same persistent homology as the Čech complex, while being significantly smaller, using internally a [DelaunayCechComplex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_ref.html#gudhi.DelaunayCechComplex).
+         * [WeightedCechPersistence](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_sklearn_itf_ref.html#gudhi.sklearn.WeightedCechPersistence) for computing the same persistent homology as the Weighted Čech complex, while being significantly smaller, using internally a Weighted version of [AlphaComplex](https://gudhi.inria.fr/python/3.12.0rc3/delaunay_complex_ref.html#gudhi.AlphaComplex).
 
-- [Alpha complex dD](https://gudhi.inria.fr/doc/3.12.0rc1/class_gudhi_1_1alpha__complex_1_1_alpha__complex.html) `[C++]`
+- [Alpha complex dD](https://gudhi.inria.fr/doc/3.12.0rc3/class_gudhi_1_1alpha__complex_1_1_alpha__complex.html) `[C++]`
      - **API break:** The simplicial complex for the Alpha complex concept has been changed to
        `dimension_simplex_range` (that must returns a range of simplices of a given dimension) instead of
        `skeleton_simplex_range` (that was returning a range of simplices lower or equal to a given dimension)
 
-- [Simplex_tree](https://gudhi.inria.fr/doc/3.12.0rc1/class_gudhi_1_1_simplex__tree.html) `[C++]`
+- [Simplex_tree](https://gudhi.inria.fr/doc/3.12.0rc3/class_gudhi_1_1_simplex__tree.html) `[C++]`
      - A new iterator over the simplices of the simplicial complex that match a given dimension
 
-- [Persistence matrix](https://gudhi.inria.fr/doc/3.12.0rc1/group__persistence__matrix.html) `[C++]`
+- [Persistence matrix](https://gudhi.inria.fr/doc/3.12.0rc3/group__persistence__matrix.html) `[C++]`
      > Matrix API is in a beta version and may change in incompatible ways in the near future.
      - A new function to insert a maximal cell using swaps.
 
-- [Representations](https://gudhi.inria.fr/python/3.12.0rc1/representations.html) `[Python]`
+- [Representations](https://gudhi.inria.fr/python/3.12.0rc3/representations.html) `[Python]`
      - in metrics, `BottleneckDistance` argument `epsilon` is deprecrated and renamed `e` to be consistent with `bottleneck_distance` and `pairwise_persistence_diagram_distances`
 
 - Installation

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

@@ -39,6 +39,10 @@ jobs:
           ./scripts/build_osx_universal_gmpfr.sh
           # Now the universal libraries are in $PWD/deps-uni/lib
       - name: Build python wheel
+        # Force the use of apple clang - brew clang seems problematic for universal wheel
+        env:
+          CXX: /usr/bin/clang++
+          CC: /usr/bin/clang
         run: |
           export   GMP_LIB_DIR=$PWD/deps-uni/lib
           export GMPXX_LIB_DIR=$PWD/deps-uni/lib

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

@@ -48,6 +48,9 @@ jobs:
           ./scripts/build_osx_universal_gmpfr.sh
           # Now the universal libraries are in $PWD/deps-uni/lib
       - name: Build python wheel
+        # To workaround an issue on Sonoma where mixing ar from brew install
+        env:
+          SKBUILD_CMAKE_DEFINE: "CMAKE_AR=/usr/bin/ar"
         run: |
           export   GMP_LIB_DIR=$PWD/deps-uni/lib
           export GMPXX_LIB_DIR=$PWD/deps-uni/lib

CMakeGUDHIVersion.txt

@@ -2,7 +2,7 @@
 set (GUDHI_MAJOR_VERSION 3)
 set (GUDHI_MINOR_VERSION 12)
 # GUDHI_PATCH_VERSION can be 'ZaN' for Alpha release, 'ZbN' for Beta release, 'ZrcN' for release candidate or 'Z' for a final release.
-set (GUDHI_PATCH_VERSION 0rc2)
+set (GUDHI_PATCH_VERSION 0rc3)
 set(GUDHI_VERSION ${GUDHI_MAJOR_VERSION}.${GUDHI_MINOR_VERSION}.${GUDHI_PATCH_VERSION})
 
 message(STATUS "GUDHI version : ${GUDHI_VERSION}")

pyproject.toml

@@ -28,9 +28,9 @@ wheel.packages = []
 
 [project]
 name = "gudhi"
-version = "3.12.0a1"
+version = "3.12.0rc3"
 description = "The Gudhi library is an open source library for Computational Topology and Topological Data Analysis (TDA)."
-# readme = "doc/pypi_introduction.inc"
+readme = "src/python/doc/pypi_introduction.rst"
 requires-python = ">=3.10"
 authors = [{ name = "GUDHI Editorial Board <https://gudhi.inria.fr/contact/>" }]
 classifiers = [

src/cmake/modules/GUDHI_user_version_target.cmake

@@ -45,8 +45,12 @@ add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
 add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
                    copy ${CMAKE_SOURCE_DIR}/src/Doxyfile.in ${GUDHI_USER_VERSION_DIR}/Doxyfile.in)
 
-add_custom_command(TARGET user_version PRE_BUILD COMMAND ${CMAKE_COMMAND} -E
-                   copy ${CMAKE_SOURCE_DIR}/pyproject.toml ${GUDHI_USER_VERSION_DIR}/pyproject.toml)
+# readme is not in the same place in developper and user version
+file(READ "${CMAKE_SOURCE_DIR}/pyproject.toml" PYPROJECT_TOML)
+string(REGEX REPLACE "readme = \"src/python/doc/pypi_introduction.rst\""
+                     "readme = \"python/doc/pypi_introduction.rst\"" MODIFIED_PYPROJECT_TOML "${PYPROJECT_TOML}")
+file(WRITE "${GUDHI_USER_VERSION_DIR}/pyproject.toml" "${MODIFIED_PYPROJECT_TOML}")
+
 file(GLOB_RECURSE PYTHON_FILES ${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/*)
 foreach(PYTHON_FILE ${PYTHON_FILES})
   string(REPLACE "${CMAKE_SOURCE_DIR}/${GUDHI_PYTHON_PATH}/" "" RELATIVE_PYTHON_FILE ${PYTHON_FILE})