Merge branch 'master' of https://github.com/GUDHI/gudhi-devel into perslay

9 files changed, 108 insertions, 18 deletions

diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
index 11b6271d..bc4f999e 100644
--- a/.github/workflows/pip-build-linux.yml
+++ b/.github/workflows/pip-build-linux.yml
@@ -12,16 +12,16 @@ jobs:
       - uses: actions/checkout@v3
         with:
           submodules: true
-      - name: Build wheel for Python 3.10
+      - name: Build wheel for Python 3.11
         run: |
-          mkdir build_310
-          cd build_310
-          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
+          mkdir build_311
+          cd build_311
+          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
           cd src/python
-          $PYTHON310/bin/python setup.py bdist_wheel
+          $PYTHON311/bin/python setup.py bdist_wheel
           auditwheel repair dist/*.whl
-      - name: Install and test wheel for Python 3.10
+      - name: Install and test wheel for Python 3.11
         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
+          $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/dist/*.whl
+          $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
+          $PYTHON311/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 59e94ca5..a438124a 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -2,13 +2,18 @@ name: pip build osx
 
 on: [push, pull_request]
 
+env:
+  MACOSX_DEPLOYMENT_TARGET: 10.14
+  _PYTHON_HOST_PLATFORM: macosx-10.14-universal2
+  ARCHFLAGS: "-arch arm64 -arch x86_64"
+
 jobs:
   build:
     runs-on: macos-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.10']
+        python-version: ['3.11']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -24,14 +29,21 @@ jobs:
           brew install boost eigen gmp mpfr cgal || true
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine delocate
+          ./scripts/build_osx_universal_gmpfr.sh
+          # Now the universal libraries are in $PWD/deps-uni/lib
       - name: Build python wheel
         run: |
+          export   GMP_LIB_DIR=$PWD/deps-uni/lib
+          export GMPXX_LIB_DIR=$PWD/deps-uni/lib
+          export  MPFR_LIB_DIR=$PWD/deps-uni/lib
           python --version
           mkdir build
           cd build
           cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
           cd src/python
           python setup.py bdist_wheel
+          export PATH="$PATH:`python -m site --user-base`/bin"
+          delocate-wheel --require-archs universal2 -v dist/*.whl
       - name: Install and test python wheel
         run: |
           python -m pip install --user pytest build/src/python/dist/*.whl
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index b3d75706..50bdfe2c 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: ['3.10']
+        python-version: ['3.11']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 285cfa00..14b1cf7a 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -79,6 +79,19 @@ jobs:
           $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
           $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
           $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
+      - name: Build wheel for Python 3.11
+        run: |
+          mkdir build_311
+          cd build_311
+          cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
+          cd src/python
+          $PYTHON311/bin/python setup.py bdist_wheel
+          auditwheel repair dist/*.whl
+      - name: Install and test wheel for Python 3.11
+        run: |
+          $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/dist/*.whl
+          $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
+          $PYTHON311/bin/python -m pytest src/python/test/test_alpha_complex.py
       - name: Publish on PyPi
         env:
           TWINE_USERNAME: __token__
@@ -89,3 +102,4 @@ jobs:
           $PYTHON36/bin/python -m twine upload build_38/src/python/wheelhouse/*
           $PYTHON36/bin/python -m twine upload build_39/src/python/wheelhouse/*
           $PYTHON36/bin/python -m twine upload build_310/src/python/wheelhouse/*
+          $PYTHON36/bin/python -m twine upload build_311/src/python/wheelhouse/*
diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
index 3ae840c6..9ddbcfce 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -4,13 +4,18 @@ on:
   release:
     types: [published]
 
+env:
+  MACOSX_DEPLOYMENT_TARGET: 10.15
+  _PYTHON_HOST_PLATFORM: macosx-10.15-universal2
+  ARCHFLAGS: "-arch arm64 -arch x86_64"
+
 jobs:
   build:
     runs-on: macos-latest
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
@@ -26,8 +31,13 @@ jobs:
           brew install boost eigen gmp mpfr cgal || true
           python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine delocate
+          ./scripts/build_osx_universal_gmpfr.sh
+          # Now the universal libs are in $PWD/deps-uni/lib
       - name: Build python wheel
         run: |
+          export   GMP_LIB_DIR=$PWD/deps-uni/lib
+          export GMPXX_LIB_DIR=$PWD/deps-uni/lib
+          export  MPFR_LIB_DIR=$PWD/deps-uni/lib
           python --version
           mkdir build
           cd build
@@ -45,6 +55,7 @@ jobs:
           TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
         run: |
           mkdir wheelhouse
-          /Users/runner/.local/bin/delocate-listdeps build/src/python/dist/*
-          /Users/runner/.local/bin/delocate-wheel --require-archs x86_64 -w wheelhouse build/src/python/dist/*
-          python -m twine upload wheelhouse/*
\ No newline at end of file
+          export PATH="$PATH:`python -m site --user-base`/bin"
+          delocate-listdeps build/src/python/dist/*
+          delocate-wheel --require-archs universal2 -w wheelhouse build/src/python/dist/*
+          python -m twine upload wheelhouse/*
diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index 6f544499..df0db9a5 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: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
     name: Build wheels for Python ${{ matrix.python-version }}
     steps:
       - uses: actions/checkout@v3
diff --git a/scripts/build_osx_universal_gmpfr.sh b/scripts/build_osx_universal_gmpfr.sh
new file mode 100755
index 00000000..3dafa3ce
--- /dev/null
+++ b/scripts/build_osx_universal_gmpfr.sh
@@ -0,0 +1,47 @@
+#!/bin/bash
+set -e
+
+# In the working directory, creates deps-uni/lib/*
+# Assumes that the user has enough rights to run brew fetch
+
+# Downloading
+mkdir deps-amd64
+cd deps-amd64
+tar xf "`brew fetch --bottle-tag=big_sur gmp        | sed -ne 's/^Downloaded to: //p'`"
+tar xf "`brew fetch --bottle-tag=big_sur mpfr       | sed -ne 's/^Downloaded to: //p'`"
+cd ..
+mkdir deps-arm64
+cd deps-arm64
+tar xf "`brew fetch --bottle-tag=arm64_big_sur gmp  | sed -ne 's/^Downloaded to: //p'`"
+tar xf "`brew fetch --bottle-tag=arm64_big_sur mpfr | sed -ne 's/^Downloaded to: //p'`"
+cd ..
+
+# Merging
+mkdir -p deps-uni/lib
+GMP1=deps-amd64/gmp/*/lib/libgmp.*.dylib
+GMP=`basename $GMP1`
+GMPXX1=deps-amd64/gmp/*/lib/libgmpxx.*.dylib
+GMPXX=`basename $GMPXX1`
+MPFR1=deps-amd64/mpfr/*/lib/libmpfr.*.dylib
+MPFR=`basename $MPFR1`
+lipo -create $GMP1 deps-arm64/gmp/*/lib/$GMP -output deps-uni/lib/$GMP
+lipo -create $GMPXX1 deps-arm64/gmp/*/lib/$GMPXX -output deps-uni/lib/$GMPXX
+lipo -create $MPFR1 deps-arm64/mpfr/*/lib/$MPFR -output deps-uni/lib/$MPFR
+
+# Necessary even for libs created by lipo
+install_name_tool -id $PWD/deps-uni/lib/$GMP deps-uni/lib/$GMP
+install_name_tool -id $PWD/deps-uni/lib/$GMPXX deps-uni/lib/$GMPXX
+install_name_tool -id $PWD/deps-uni/lib/$MPFR deps-uni/lib/$MPFR
+# Also fix dependencies
+BADGMP=`otool -L deps-uni/lib/$MPFR|sed -ne 's/[[:space:]]*\(.*libgmp\..*dylib\).*/\1/p'`
+install_name_tool -change $BADGMP $PWD/deps-uni/lib/$GMP deps-uni/lib/$MPFR
+BADGMP=`otool -L deps-uni/lib/$GMPXX|sed -ne 's/[[:space:]]*\(.*libgmp\..*dylib\).*/\1/p'`
+install_name_tool -change $BADGMP $PWD/deps-uni/lib/$GMP deps-uni/lib/$GMPXX
+
+ln -s $GMP deps-uni/lib/libgmp.dylib
+ln -s $GMPXX deps-uni/lib/libgmpxx.dylib
+ln -s $MPFR deps-uni/lib/libmpfr.dylib
+
+# Debug
+ls -l deps-uni/lib
+otool -L deps-uni/lib/*.*.dylib
diff --git a/src/Cech_complex/utilities/cechcomplex.md b/src/Cech_complex/utilities/cechcomplex.md
index 0e82674d..54c4e88d 100644
--- a/src/Cech_complex/utilities/cechcomplex.md
+++ b/src/Cech_complex/utilities/cechcomplex.md
@@ -36,14 +36,14 @@ where
 
 * `-h [ --help ]` Produce help message
 * `-o [ --output-file ]` Name of file in which the persistence diagram is written. Default print in standard output.
-* `-r [ --max-edge-length ]` (default = inf) Maximal length of an edge for the Čech complex construction.
+* `-r [ --max-radius ]` (default = inf) Maximal radius for the Čech complex construction.
 * `-d [ --cpx-dimension ]` (default = 1) Maximal dimension of the Čech complex we want to compute.
 * `-p [ --field-charac ]` (default = 11) Characteristic p of the coefficient field Z/pZ for computing homology.
 * `-m [ --min-persistence ]` (default = 0) Minimal lifetime of homology feature to be recorded. Enter a negative value to see zero length intervals.
 * `-e [ --exact ]` for the exact computation version.
 * `-f [ --fast ]` for the fast computation version.
 
-Beware: this program may use a lot of RAM and take a lot of time if `max-edge-length` is set to a large value.
+Beware: this program may use a lot of RAM and take a lot of time if `max-radius` is set to a large value.
 
 **Example 1 with Z/2Z coefficients**
 
diff --git a/src/Tangential_complex/include/gudhi/Tangential_complex.h b/src/Tangential_complex/include/gudhi/Tangential_complex.h
index b448db2d..ab203ca5 100644
--- a/src/Tangential_complex/include/gudhi/Tangential_complex.h
+++ b/src/Tangential_complex/include/gudhi/Tangential_complex.h
@@ -56,6 +56,7 @@
 #include <string>
 #include <cstddef>  // for std::size_t
 #include <optional>
+#include <numeric>  // for std::iota
 
 #ifdef GUDHI_USE_TBB
 #include <tbb/parallel_for.h>
@@ -624,6 +625,11 @@ class Tangential_complex {
 
     int max_dim = -1;
 
+    // Ordered vertices to be inserted first by the create_complex method to avoid quadratic complexity.
+    std::vector<typename Simplex_tree_::Vertex_handle> vertices(m_points.size());
+    std::iota(vertices.begin(), vertices.end(), 0);
+    tree.insert_batch_vertices(vertices);
+
     // For each triangulation
     for (std::size_t idx = 0; idx < m_points.size(); ++idx) {
       // For each cell of the star