merge upstream

GUDHI · Feb 5, 2025 · 5b4b9e2 · 5b4b9e2
2 parents 5ee81bc + 9b26cab
commit 5b4b9e2
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diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -5,7 +5,7 @@ jobs:
   examples:
     docker:
       # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_circleci_image
-      - image: gudhi/ci_for_gudhi:2024.10.01
+      - image: gudhi/ci_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -24,7 +24,7 @@ jobs:
 
   tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.10.01
+      - image: gudhi/ci_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -43,7 +43,7 @@ jobs:
 
   debug_tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.10.01
+      - image: gudhi/ci_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -62,7 +62,7 @@ jobs:
 
   utils:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.10.01
+      - image: gudhi/ci_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -81,7 +81,7 @@ jobs:
 
   python:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.10.01
+      - image: gudhi/ci_for_gudhi:2024.12.01
     resource_class: large # Delaunay complex requires about 5 Gb of RAM to compile
     steps:
       - checkout
@@ -100,13 +100,13 @@ jobs:
             cd version
             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
+            python setup.py build_ext --inplace
             ctest --output-on-failure
             make sphinx
             cp -R sphinx /tmp/sphinx
-            python3 setup.py install
-            python3 setup.py clean --all
-            python3 -B -m pytest test/*.py --cov-report html --cov=gudhi
+            python setup.py install
+            python setup.py clean --all
+            python -B -m pytest test/*.py --cov-report html --cov=gudhi
             cp -R htmlcov /tmp/htmlcov
       - store_artifacts:
           path: /tmp/sphinx
@@ -117,7 +117,7 @@ jobs:
 
   doxygen:
     docker:
-      - image: gudhi/doxygen_for_gudhi:2024.10.01
+      - image: gudhi/doxygen_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -137,7 +137,7 @@ jobs:
             cd build
             cmake -DWITH_GUDHI_THIRD_PARTY=OFF ..
             make doxygen
-            grep warning doxygen.log
+            grep warning doxygen.log || true # No need to test the result of this command
             cp doxygen.log html/
             cp -R html /tmp/doxygen
 
@@ -147,7 +147,7 @@ jobs:
 
   bibliography:
     docker:
-      - image: gudhi/doxygen_for_gudhi:2024.10.01
+      - image: gudhi/doxygen_for_gudhi:2024.12.01
     steps:
       - checkout
       - run:
@@ -170,7 +170,7 @@ 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:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -189,7 +189,7 @@ jobs:
 
   tests_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -208,7 +208,7 @@ jobs:
 
   utils_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -227,7 +227,7 @@ jobs:
 
   python_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -242,14 +242,14 @@ jobs:
             cd build
             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
+            python setup.py build_ext --inplace
             ctest --output-on-failure
 
   ### With all third parties, except CGAL
 
   examples_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -260,15 +260,22 @@ jobs:
       - run:
           name: Build and test examples without cgal
           command: |
+            cur_dir=`pwd`
+            cd /eigen-3.4.0
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
+            cmake ..
+            make install
+            cd $cur_dir
+            mkdir build
+            cd build
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
             make all
             ctest --output-on-failure
 
   tests_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -279,15 +286,22 @@ jobs:
       - run:
           name: Build and test unitary tests without cgal
           command: |
+            cur_dir=`pwd`
+            cd /eigen-3.4.0
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
+            cmake ..
+            make install
+            cd $cur_dir
+            mkdir build
+            cd build
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=OFF -DWITH_GUDHI_PYTHON=OFF ..
             make all
             ctest --output-on-failure
 
   utils_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -298,15 +312,22 @@ jobs:
       - run:
           name: Build and test utilities without cgal
           command: |
+            cur_dir=`pwd`
+            cd /eigen-3.4.0
             mkdir build
             cd build
-            cmake -DCMAKE_BUILD_TYPE=Release -DEIGEN3_INCLUDE_DIR=/eigen-3.3.9 -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF ..
+            cmake ..
+            make install
+            cd $cur_dir
+            mkdir build
+            cd build
+            cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_EXAMPLE=OFF -DWITH_GUDHI_TEST=OFF -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=OFF ..
             make all
             ctest --output-on-failure
 
   python_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.12.01
     steps:
       - checkout
       - run:
@@ -317,11 +338,18 @@ jobs:
       - run:
           name: Build and test python module without cgal
           command: |
+            cur_dir=`pwd`
+            cd /eigen-3.4.0
             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 ..
+            cmake ..
+            make install
+            cd $cur_dir
+            mkdir build
+            cd build
+            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
+            python setup.py build_ext --inplace
             ctest --output-on-failure
 
 workflows:

diff --git a/.github/code_conventions.md b/.github/code_conventions.md
@@ -6,6 +6,7 @@
 * The classes and functions of a package should be in a sub-namespace of the `Gudhi` namespace. The sub-namespace names are in lowercase and use underscore separators. E.g. `Gudhi::package_name::`
 * Concepts are named with camel case starting with uppercase. E.g. `PersistentHomology` for the concept of Persitence homology.
 * Classes start with an uppercase letter and use underscore separators. E.g. `Skeleton_blocker_contractor`.
+* Constant iterators are preferably named as `*_const_iterator`. E.g. `Vertex_const_iterator`.
 * Member functions and free functions are in lowercase and use underscore separators. E.g. `int num_vertices()`.
 * Constants and macros are in uppercase.
 * Macros should begin with the prefix `GUDHI_`.

diff --git a/.github/next_release.md b/.github/next_release.md
@@ -12,6 +12,9 @@ Below is a list of changes:
           * Delaunay Čech complex (using minimal enclosing ball)
           * Alpha complex (moved in this new section)
 
+- [Persistence graphical tools](https://gudhi.inria.fr/python/latest/persistence_graphical_tools_user.html)
+     - Can now handle scikit-learn like interfaces outputs as inputs
+
 - [Module](link)
      - **...**
 

diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
@@ -2,19 +2,14 @@ name: pip build linux
 
 on: [push, pull_request]
 
-# Temporary workaround to allow node16
-env:
-  ACTIONS_ALLOW_USE_UNSECURE_NODE_VERSION: true
-
 jobs:
   build:
     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:2024.10.02
+    container: gudhi/pip_for_gudhi:2024.12.02
     steps:
-      # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       - name: Build wheel for Python 3.9
@@ -37,8 +32,7 @@ jobs:
           $PYTHON39/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON39/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Upload linux python wheel
-        # Should use actions/upload-artifact@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: linux python wheel
           path: build_39/src/python/wheelhouse/*.whl
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
@@ -9,10 +9,9 @@ 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:2024.10.02
+    container: gudhi/pip_for_gudhi:2024.12.02
     steps:
-      # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           submodules: true
       # Python 3.8 specific case where NumPy 2.x will not be supported

diff --git a/src/Persistence_matrix/concept/PersistenceMatrixColumn.h b/src/Persistence_matrix/concept/PersistenceMatrixColumn.h
@@ -242,18 +242,19 @@ class PersistenceMatrixColumn :
 
   /**
    * @brief Reorders the column with the given map of row indices. Also changes the column index stored in the
-   * entries if row access is enabled and @p columnIndex is not -1.
+   * entries if row access is enabled and @p columnIndex is not the @ref Matrix::get_null_value "null index".
    *
    * Only useful for @ref basematrix "base" and @ref boundarymatrix "boundary matrices" using lazy swaps.
    * 
    * @tparam Row_index_map Map with an %at() method.
    * @param valueMap Map such that `valueMap.at(i)` indicates the new row index of the entry
    * at current row index `i`.
-   * @param columnIndex New @ref MatIdx column index of the column. If -1, the index does not change. Ignored if
-   * the row access is not enabled. Default value: -1.
+   * @param columnIndex New @ref MatIdx column index of the column. If @ref Matrix::get_null_value "null index",
+   * the index does not change. Ignored if the row access is not enabled.
+   * Default value: @ref Matrix::get_null_value "null index".
    */
   template <class Row_index_map>
-  void reorder(const Row_index_map& valueMap, [[maybe_unused]] Index columnIndex = -1);
+  void reorder(const Row_index_map& valueMap, [[maybe_unused]] Index columnIndex = Matrix::get_null_value<Index>());
   /**
    * @brief Zeros/empties the column.
    * 
@@ -275,11 +276,12 @@ class PersistenceMatrixColumn :
   void clear(ID_index rowIndex);
 
   /**
-   * @brief Returns the row index of the pivot. If the column does not have a pivot, returns -1.
+   * @brief Returns the row index of the pivot. If the column does not have a pivot,
+   * returns @ref Matrix::get_null_value "null index".
    *
    * Only useful for @ref boundarymatrix "boundary" and @ref chainmatrix "chain matrices".
    * 
-   * @return Row index of the pivot or -1.
+   * @return Row index of the pivot or @ref Matrix::get_null_value "null index".
    */
   ID_index get_pivot();
   /**
@@ -429,7 +431,7 @@ class PersistenceMatrixColumn :
   /**
    * @brief Adds a copy of the given entry at the end of the column. It is therefore assumed that the row index
    * of the entry is higher than the current pivot of the column. Not available for @ref chainmatrix "chain matrices"
-   * and is only needed for @ref rumatrix "RU matrices".
+   * and is only needed for @ref boundarymatrix "RU matrices".
    * 
    * @param entry Entry to push back.
    */