Merge branch 'GUDHI:master' into Multiparameter-Simplextree-C++-part

DavidLapous · web-flow · commit bf9ecf69f976 · 2024-11-21T17:05:23.000+01:00
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
