Merge master

8 files changed, 60 insertions, 67 deletions

diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md
index 812758e3..19ef168e 100644
--- a/.github/for_maintainers/new_gudhi_version_creation.md
+++ b/.github/for_maintainers/new_gudhi_version_creation.md
@@ -26,7 +26,7 @@ md5sum gudhi.@GUDHI_VERSION@.tar.gz > md5sum.txt
 sha256sum gudhi.@GUDHI_VERSION@.tar.gz > sha256sum.txt
 sha512sum gudhi.@GUDHI_VERSION@.tar.gz > sha512sum.txt
 
-make -j 4 all && ctest -j 4 --output-on-failure
+make && ctest --output-on-failure
 ```
 
 ***[Check there are no error]***
@@ -61,7 +61,7 @@ cd ../..
 tar -czvf gudhi.doc.@GUDHI_VERSION@.tar.gz gudhi.doc.@GUDHI_VERSION@
 
 cd gudhi.@GUDHI_VERSION@/build
-make -j 4 all && ctest -j 4 --output-on-failure
+make && ctest --output-on-failure
 ```
 
 ***[Check there are no error]***
diff --git a/.github/next_release.md b/.github/next_release.md
index dfe31855..1dc4529f 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -1,22 +1,20 @@
-We are pleased to announce the release 3.5.0 of the GUDHI library.
+We are pleased to announce the release 3.X.X of the GUDHI library.
 
 As a major new feature, the GUDHI library now offers ...
 
 We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
 
-Below is a list of changes made since GUDHI 3.4.0:
+Below is a list of changes made since GUDHI 3.5.0:
 
 - [Alpha complex](https://gudhi.inria.fr/python/latest/alpha_complex_user.html)
      - the python weighted version for alpha complex is now available in any dimension D.
      - `alpha_complex = gudhi.AlphaComplex(off_file='/data/points/tore3D_300.off')` is deprecated, please use [read_points_from_off_file](https://gudhi.inria.fr/python/latest/point_cloud.html#gudhi.read_points_from_off_file) instead.
-- [Coxeter triangulation](https://gudhi.inria.fr/doc/latest/group__coxeter__triangulation.html)
-     - constructs a piecewise-linear approximation of an m-dimensional smooth manifold embedded in R^d using an ambient triangulation. 
 
 - [Module](link)
      - ...
 
 - Miscellaneous
-     - The [list of bugs that were solved since GUDHI-3.4.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.5.0+is%3Aclosed) is available on GitHub.
+     - The [list of bugs that were solved since GUDHI-3.5.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.6.0+is%3Aclosed) is available on GitHub.
 
 All modules are distributed under the terms of the MIT license.
 However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details.
@@ -28,3 +26,4 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo
 Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks.
 
 For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/latest/installation.html) or [Python](https://gudhi.inria.fr/python/latest/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+
diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
index 12979a86..a2b4f085 100644
--- a/.github/workflows/pip-build-linux.yml
+++ b/.github/workflows/pip-build-linux.yml
@@ -12,15 +12,16 @@ jobs:
       - uses: actions/checkout@v1
         with:
           submodules: true
-      - name: Build wheel for Python 3.9
+      - name: Build wheel for Python 3.10
         run: |
-          mkdir build_39
-          cd build_39
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
+          mkdir build_310
+          cd build_310
+          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
           cd src/python
-          $PYTHON39/bin/python setup.py bdist_wheel
+          $PYTHON310/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Install and test wheel for Python 3.9
+      - name: Install and test wheel for Python 3.10
         run: |
-          $PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
-          $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
+          $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
+          $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
+          $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
index 1626bb77..99d515ff 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v1
@@ -35,4 +35,5 @@ jobs:
       - name: Install and test python wheel
         run: |
           python -m pip install --user pytest build/src/python/dist/*.whl
+          python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest src/python/test/test_alpha_complex.py
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index 0080f4d5..954b59d5 100644
--- a/.github/workflows/pip-build-windows.yml
+++ b/.github/workflows/pip-build-windows.yml
@@ -8,7 +8,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.9']
+        python-version: ['3.10']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v1
@@ -20,36 +20,30 @@ jobs:
           architecture: x64
       - name: Install dependencies
         run: |
-          cd c:/vcpkg
-          git fetch --all --tags
-          git checkout 2020.11-1
-          bootstrap-vcpkg.bat
           set VCPKG_BUILD_TYPE=release
-          vcpkg install eigen3 mpfr boost-accumulators boost-algorithm boost-bimap boost-callable-traits boost-concept-check boost-container boost-core boost-detail boost-filesystem boost-functional boost-fusion boost-geometry boost-graph boost-heap boost-intrusive boost-iostreams boost-iterator boost-lambda boost-logic boost-math boost-mpl boost-multi-index boost-multiprecision boost-numeric-conversion boost-optional boost-parameter boost-pool boost-preprocessor boost-property-map boost-property-tree boost-ptr-container boost-random boost-range boost-serialization boost-spirit boost-thread boost-tuple boost-type-traits boost-units boost-utility boost-variant --triplet x64-windows
+          vcpkg install eigen3 cgal --triplet x64-windows
           vcpkg version
-          ls C:/vcpkg/installed/x64-windows/bin
-          Invoke-WebRequest https://github.com/CGAL/cgal/releases/download/v5.2.1/CGAL-5.2.1.zip -OutFile CGAL-5.2.1.zip
-          Expand-Archive -Path CGAL-5.2.1.zip -DestinationPath .
-          cd CGAL-5.2.1
-          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll .
-          cd ${{ github.workspace }}
-          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+          ls "C:\vcpkg\installed\x64-windows\bin\"
+          python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
           python -m pip list
-      - name: Build python wheel
+      - name: Build python wheel and install it
         run: |
           mkdir build
-          cd build
-          cmake -DCGAL_DIR=c:/vcpkg/CGAL-5.2.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll ..
-          cd src/python
-          cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
-          cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
+          cd ".\build\"
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows ..
+          Get-Location
+          dir
+          cd ".\src\python\"
+          cp "C:\vcpkg\installed\x64-windows\bin\mpfr-6.dll" ".\gudhi\"
+          cp "C:\vcpkg\installed\x64-windows\bin\gmp.dll" ".\gudhi\"
           python setup.py bdist_wheel
           ls dist
-      - name: Install and test python wheel
-        run: |
-          cd ${{ github.workspace }}
-          cd build/src/python/dist/
+          cd ".\dist\"
           Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
-          cd ${{ github.workspace }}
+      - name: Test python wheel
+        run: |
+          Get-Location
+          dir
           python -m pip install --user pytest
-          python -m pytest src/python/test/test_alpha_complex.py
+          python -c "import gudhi; print(gudhi.__version__)"
+          python -m pytest ".\src\python\test\test_alpha_complex.py"
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 6ce0ba89..98173ed3 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -25,6 +25,7 @@ jobs:
       - name: Install and test wheel for Python 3.6
         run: |
           $PYTHON36/bin/python -m pip install --user pytest build_36/src/python/dist/*.whl
+          $PYTHON36/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON36/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Build wheel for Python 3.7
         run: |
@@ -37,6 +38,7 @@ jobs:
       - name: Install and test wheel for Python 3.7
         run: |
           $PYTHON37/bin/python -m pip install --user pytest build_37/src/python/dist/*.whl
+          $PYTHON37/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON37/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Build wheel for Python 3.8
         run: |
@@ -49,6 +51,7 @@ jobs:
       - name: Install and test wheel for Python 3.8
         run: |
           $PYTHON38/bin/python -m pip install --user pytest build_38/src/python/dist/*.whl
+          $PYTHON38/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON38/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Build wheel for Python 3.9
         run: |
@@ -61,6 +64,7 @@ jobs:
       - name: Install and test wheel for Python 3.9
         run: |
           $PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
+          $PYTHON39/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Build wheel for Python 3.10
         run: |
@@ -73,6 +77,7 @@ jobs:
       - name: Install and test wheel for Python 3.10
         run: |
           $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
+          $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
index 120c15b6..7417300a 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.7', '3.8', '3.9', '3.10']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v1
@@ -37,6 +37,7 @@ jobs:
       - name: Install and test python wheel
         run: |
           python -m pip install --user pytest build/src/python/dist/*.whl
+          python -c "import gudhi; print(gudhi.__version__)"
           python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index f387c5ff..962ae68a 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -10,7 +10,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+        python-version: ['3.6', '3.7', '3.8', '3.9', '3.10']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v1
@@ -22,40 +22,32 @@ jobs:
           architecture: x64
       - name: Install dependencies
         run: |
-          cd c:/vcpkg
-          git fetch --all --tags
-          git checkout 2020.11-1
-          bootstrap-vcpkg.bat
           set VCPKG_BUILD_TYPE=release
-          vcpkg install eigen3 mpfr boost-accumulators boost-algorithm boost-bimap boost-callable-traits boost-concept-check boost-container boost-core boost-detail boost-filesystem boost-functional boost-fusion boost-geometry boost-graph boost-heap boost-intrusive boost-iostreams boost-iterator boost-lambda boost-logic boost-math boost-mpl boost-multi-index boost-multiprecision boost-numeric-conversion boost-optional boost-parameter boost-pool boost-preprocessor boost-property-map boost-property-tree boost-ptr-container boost-random boost-range boost-serialization boost-spirit boost-thread boost-tuple boost-type-traits boost-units boost-utility boost-variant --triplet x64-windows
+          vcpkg install eigen3 cgal --triplet x64-windows
           vcpkg version
-          ls C:/vcpkg/installed/x64-windows/bin
-          Invoke-WebRequest https://github.com/CGAL/cgal/releases/download/v5.2.1/CGAL-5.2.1.zip -OutFile CGAL-5.2.1.zip
-          Expand-Archive -Path CGAL-5.2.1.zip -DestinationPath .
-          cd CGAL-5.2.1
-          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll .
-          cd ${{ github.workspace }}
-          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+          ls "C:\vcpkg\installed\x64-windows\bin\"
+          python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
           python -m pip install --user twine
           python -m pip list
-      - name: Build python wheel
+      - name: Build python wheel and install it
         run: |
           mkdir build
-          cd build
-          cmake -DCGAL_DIR=c:/vcpkg/CGAL-5.2.1 -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DGMP_INCLUDE_DIR=c:/vcpkg/installed/x64-windows/include -DGMP_LIBRARIES=c:/vcpkg/installed/x64-windows/bin/mpir.dll ..
-          cd src/python
-          cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
-          cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
+          cd ".\build\"
+          cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows ..
+          Get-Location
+          dir
+          cd ".\src\python\"
+          cp "C:\vcpkg\installed\x64-windows\bin\mpfr-6.dll" ".\gudhi\"
+          cp "C:\vcpkg\installed\x64-windows\bin\gmp.dll" ".\gudhi\"
           python setup.py bdist_wheel
           ls dist
-      - name: Install and test python wheel
-        run: |
-          cd ${{ github.workspace }}
-          cd build/src/python/dist/
+          cd ".\dist\"
           Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
-          cd ${{ github.workspace }}
+      - name: Test python wheel
+        run: |
           python -m pip install --user pytest
-          python -m pytest src/python/test/test_alpha_complex.py
+          python -c "import gudhi; print(gudhi.__version__)"
+          python -m pytest ".\src\python\test\test_alpha_complex.py"
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__