Merge branch 'GUDHI:master' into simplex_tree_filtration_value_genera…

…lization
hschreiber · Nov 27, 2024 · b202391 · b202391
2 parents bcdad85 + 7bd2ecc
commit b202391
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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:2024.09.01
+      - image: gudhi/ci_for_gudhi:2024.10.01
     steps:
       - checkout
       - run:
@@ -24,7 +24,7 @@ jobs:
 
   tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.09.01
+      - image: gudhi/ci_for_gudhi:2024.10.01
     steps:
       - checkout
       - run:
@@ -43,7 +43,7 @@ jobs:
 
   debug_tests:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.09.01
+      - image: gudhi/ci_for_gudhi:2024.10.01
     steps:
       - checkout
       - run:
@@ -62,7 +62,7 @@ jobs:
 
   utils:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.09.01
+      - image: gudhi/ci_for_gudhi:2024.10.01
     steps:
       - checkout
       - run:
@@ -81,7 +81,7 @@ jobs:
 
   python:
     docker:
-      - image: gudhi/ci_for_gudhi:2024.09.01
+      - image: gudhi/ci_for_gudhi:2024.10.01
     resource_class: large # Delaunay complex requires about 5 Gb of RAM to compile
     steps:
       - checkout
@@ -117,7 +117,7 @@ jobs:
 
   doxygen:
     docker:
-      - image: gudhi/doxygen_for_gudhi:2024.06.01
+      - image: gudhi/doxygen_for_gudhi:2024.10.01
     steps:
       - checkout
       - run:
@@ -147,7 +147,7 @@ jobs:
 
   bibliography:
     docker:
-      - image: gudhi/doxygen_for_gudhi:2024.06.01
+      - image: gudhi/doxygen_for_gudhi:2024.10.01
     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:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -189,7 +189,7 @@ jobs:
 
   tests_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -208,7 +208,7 @@ jobs:
 
   utils_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -227,7 +227,7 @@ jobs:
 
   python_without_cgal_eigen:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -249,7 +249,7 @@ jobs:
 
   examples_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -268,7 +268,7 @@ jobs:
 
   tests_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -287,7 +287,7 @@ jobs:
 
   utils_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:
@@ -306,7 +306,7 @@ jobs:
 
   python_without_cgal:
     docker:
-      - image: gudhi/ci_for_gudhi_wo_cgal:2024.06.01
+      - image: gudhi/ci_for_gudhi_wo_cgal:2024.10.01
     steps:
       - checkout
       - run:

diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
@@ -11,7 +11,7 @@ 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:2024.06.02
+    container: gudhi/pip_for_gudhi:2024.10.02
     steps:
       # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
       - uses: actions/checkout@v3

diff --git a/.github/workflows/pip-packaging-linux.yml b/.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:2024.06.02
+    container: gudhi/pip_for_gudhi:2024.10.02
     steps:
       # Should use actions/checkout@v4, but requires node20, not available for quay.io/pypa/manylinux2014_x86_64
       - uses: actions/checkout@v3
@@ -111,6 +111,24 @@ jobs:
           $PYTHON312/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
           $PYTHON312/bin/python -m pytest -v src/python/test/test_cubical_complex.py
           $PYTHON312/bin/python -m pytest -v src/python/test/test_rips_complex.py
+      - name: Build wheel for Python 3.13
+        run: |
+          mkdir build_313
+          cd build_313
+          cmake -DCMAKE_BUILD_TYPE=Release -DPython_EXECUTABLE=$PYTHON313/bin/python ..
+          cd src/python
+          $PYTHON313/bin/python -m build -n -w
+          auditwheel repair dist/*.whl
+      - name: Install and test wheel for Python 3.13
+        run: |
+          $PYTHON313/bin/python -m pip install --user pytest build_313/src/python/dist/*.whl
+          $PYTHON313/bin/python -m pip install numpy~=1.26.0
+          $PYTHON313/bin/python -c "import gudhi; print(gudhi.__version__)"
+          $PYTHON313/bin/python -m pytest -v src/python/test/test_alpha_complex.py
+          $PYTHON313/bin/python -m pytest -v src/python/test/test_delaunay_complex.py
+          $PYTHON313/bin/python -m pytest -v src/python/test/test_bottleneck_distance.py
+          $PYTHON313/bin/python -m pytest -v src/python/test/test_cubical_complex.py
+          $PYTHON313/bin/python -m pytest -v src/python/test/test_rips_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__
@@ -121,3 +139,4 @@ jobs:
           $PYTHON38/bin/python -m twine upload build_310/src/python/wheelhouse/*.whl
           $PYTHON38/bin/python -m twine upload build_311/src/python/wheelhouse/*.whl
           $PYTHON38/bin/python -m twine upload build_312/src/python/wheelhouse/*.whl
+          $PYTHON38/bin/python -m twine upload build_313/src/python/wheelhouse/*.whl
diff --git a/README.md b/README.md
@@ -1,9 +1,5 @@
-
-[![OSx and Win on Azure](https://dev.azure.com/GUDHI/gudhi-devel/_apis/build/status/GUDHI.gudhi-devel?branchName=master)](https://dev.azure.com/GUDHI/gudhi-devel/_build/latest?definitionId=1&branchName=master)
-[![Linux on CircleCI](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master.svg?style=svg)](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master)
-[![Anaconda Cloud](https://anaconda.org/conda-forge/gudhi/badges/version.svg)](https://anaconda.org/conda-forge/gudhi)
-[![Anaconda downloads](https://anaconda.org/conda-forge/gudhi/badges/downloads.svg)](https://anaconda.org/conda-forge/gudhi)
-
+| [![OSx and Win on Azure](https://dev.azure.com/GUDHI/gudhi-devel/_apis/build/status/GUDHI.gudhi-devel?branchName=master)](https://dev.azure.com/GUDHI/gudhi-devel/_build/latest?definitionId=1&branchName=master) [![Linux on CircleCI](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master.svg?style=svg)](https://circleci.com/gh/GUDHI/gudhi-devel/tree/master) | [![Anaconda Cloud](https://anaconda.org/conda-forge/gudhi/badges/version.svg)](https://anaconda.org/conda-forge/gudhi) ![Conda Downloads](https://img.shields.io/conda/d/conda-forge/gudhi) | ![PyPI - Version](https://img.shields.io/pypi/v/gudhi) ![PyPI - Downloads](https://img.shields.io/pypi/dm/gudhi) |
+| --- | --- | --- |
 
 ![GUDHI](src/common/doc/Gudhi_banner.png "Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding")
 

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -4,7 +4,7 @@ jobs:
     timeoutInMinutes: 0
     cancelTimeoutInMinutes: 60
     pool:
-      vmImage: macOS-latest
+      vmImage: macOS-13
     variables:
       pythonVersion: "3.9"
       cmakeBuildType: Release

diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/Chain_matrix.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/Chain_matrix.h
@@ -913,24 +913,28 @@ inline void Chain_matrix<Master_matrix>::print() const
 {
   std::cout << "Column Matrix:\n";
   if constexpr (!Master_matrix::Option_list::has_map_column_container) {
-    for (ID_index i = 0; i < pivotToColumnIndex_.size() && pivotToColumnIndex_[i] != static_cast<Index>(-1); ++i) {
+    for (ID_index i = 0; i < pivotToColumnIndex_.size(); ++i) {
       Index pos = pivotToColumnIndex_[i];
-      const Column& col = matrix_[pos];
-      for (const auto& entry : col) {
-        std::cout << entry.get_row_index() << " ";
+      if (pos != static_cast<Index>(-1)){
+        const Column& col = matrix_[pos];
+        for (const auto& entry : col) {
+          std::cout << entry.get_row_index() << " ";
+        }
+        std::cout << "(" << i << ", " << pos << ")\n";
       }
-      std::cout << "(" << i << ", " << pos << ")\n";
     }
     if constexpr (Master_matrix::Option_list::has_row_access) {
       std::cout << "\n";
       std::cout << "Row Matrix:\n";
-      for (ID_index i = 0; i < pivotToColumnIndex_.size() && pivotToColumnIndex_[i] != static_cast<Index>(-1); ++i) {
+      for (ID_index i = 0; i < pivotToColumnIndex_.size(); ++i) {
         Index pos = pivotToColumnIndex_[i];
-        const Row& row = RA_opt::get_row(pos);
-        for (const auto& entry : row) {
-          std::cout << entry.get_column_index() << " ";
+        if (pos != static_cast<Index>(-1)){
+          const Row& row = RA_opt::get_row(pos);
+          for (const auto& entry : row) {
+            std::cout << entry.get_column_index() << " ";
+          }
+          std::cout << "(" << i << ", " << pos << ")\n";
         }
-        std::cout << "(" << i << ", " << pos << ")\n";
       }
     }
   } else {

diff --git a/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h b/src/Persistence_matrix/include/gudhi/Persistence_matrix/base_pairing.h
@@ -132,10 +132,11 @@ inline const typename Base_pairing<Master_matrix>::Barcode& Base_pairing<Master_
 template <class Master_matrix>
 inline void Base_pairing<Master_matrix>::_reduce() 
 {
-  std::unordered_map<ID_index, Index> pivotsToColumn(_matrix()->get_number_of_columns());
+  std::unordered_map<Index, Index> negativeColumns(_matrix()->get_number_of_columns());
 
   auto dim = _matrix()->get_max_dimension();
   std::vector<std::vector<Index> > columnsByDim(dim + 1);
+  for (auto& v : columnsByDim) v.reserve(_matrix()->get_number_of_columns());
   for (unsigned int i = 0; i < _matrix()->get_number_of_columns(); i++) {
     columnsByDim[dim - _matrix()->get_column_dimension(i)].push_back(i);
   }
@@ -144,17 +145,21 @@ inline void Base_pairing<Master_matrix>::_reduce()
     for (Index i : cols) {
       auto& curr = _matrix()->get_column(i);
       if (curr.is_empty()) {
-        if (pivotsToColumn.find(i) == pivotsToColumn.end()) {
+        if (negativeColumns.find(i) == negativeColumns.end()) {
           barcode_.emplace_back(i, -1, dim);
         }
       } else {
         ID_index pivot = curr.get_pivot();
+        auto it = idToPosition_.find(pivot);
+        Index pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
+        auto itNeg = negativeColumns.find(pivotColumnNumber);
+        Index pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
 
-        while (pivot != static_cast<ID_index>(-1) && pivotsToColumn.find(pivot) != pivotsToColumn.end()) {
+        while (pivot != static_cast<ID_index>(-1) && pivotKiller != static_cast<Index>(-1)) {
           if constexpr (Master_matrix::Option_list::is_z2) {
-            curr += _matrix()->get_column(pivotsToColumn.at(pivot));
+            curr += _matrix()->get_column(pivotKiller);
           } else {
-            auto& toadd = _matrix()->get_column(pivotsToColumn.at(pivot));
+            auto& toadd = _matrix()->get_column(pivotKiller);
             typename Master_matrix::Element coef = toadd.get_pivot_value();
             auto& operators = _matrix()->colSettings_->operators;
             coef = operators.get_inverse(coef);
@@ -163,12 +168,14 @@ inline void Base_pairing<Master_matrix>::_reduce()
           }
 
           pivot = curr.get_pivot();
+          it = idToPosition_.find(pivot);
+          pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
+          itNeg = negativeColumns.find(pivotColumnNumber);
+          pivotKiller = itNeg == negativeColumns.end() ? -1 : itNeg->second;
         }
 
         if (pivot != static_cast<ID_index>(-1)) {
-          pivotsToColumn.emplace(pivot, i);
-          auto it = idToPosition_.find(pivot);
-          auto pivotColumnNumber = it == idToPosition_.end() ? pivot : it->second;
+          negativeColumns.emplace(pivotColumnNumber, i);
           _matrix()->get_column(pivotColumnNumber).clear();
           barcode_.emplace_back(pivotColumnNumber, i, dim - 1);
         } else {