Update gudhi bindings to latest changes on August 2020 (#468)

* Pull latest changes on Gudhi-devel:giotto * Add Eigen as a submodule Eigen is now required for latest Gudhi version * Add Eigen for gudhi modules that require it * Update get_filtration and get_skeleton with the new Gudhi API * Update ccache in CI * Fix type issue for get_persistence in simplex_tree * Fix persistence in periodic cubical complex * Fix simplex tree * Fix cubical complex * Beautify setup.py * Move towards fixing #307 in azure_pipelines.yml (still not addressing docker_scripts.sh) Signed-off-by: julian <julian.burellaperez@heig-vd.ch> Co-authored-by: Umberto Lupo <umberto.lupo@gmail.com>
giotto-ai · Aug 28, 2020 · bc2bc29 · bc2bc29
1 parent 9d7ce62
commit bc2bc29
Show file tree

Hide file tree

Showing 15 changed files with 200 additions and 175 deletions.
diff --git a/.azure-ci/docker_scripts.sh b/.azure-ci/docker_scripts.sh
@@ -25,7 +25,7 @@ tar -zxvf /boost_1_69_0.tar.gz
 mkdir boost
 cd /boost_1_69_0
 ./bootstrap.sh --prefix=/boost
-./b2 install -j3 || echo "Parts of boost failed to build. Continuing.."
+./b2 install -j3 || echo "Parts of boost failed to build. Continuing..."
 cd ..
 
 ccache -s
@@ -36,6 +36,7 @@ export Boost_INCLUDE_DIR=/boost/include
 
 # Install dev environment
 cd /io
+pip install wheel
 pip install -e ".[dev]"
 
 # Test dev install with pytest
@@ -46,10 +47,10 @@ pip uninstall -y giotto-tda
 pip uninstall -y giotto-tda-nightly
 
 # Build wheels
-pip install wheel==0.34.1 auditwheel==3.1.0
 python setup.py bdist_wheel
 
 # Repair wheels with auditwheel
+pip install auditwheel
 auditwheel repair dist/*whl -w dist/
 # remove wheels that are not manylinux2010
 rm -rf dist/*-linux*.whl
diff --git a/.gitmodules b/.gitmodules
@@ -8,3 +8,6 @@
 [submodule "gtda/externals/hera"]
 	path = gtda/externals/hera
 	url = https://github.com/grey-narn/hera
+[submodule "gtda/externals/eigen"]
+	path = gtda/externals/eigen
+	url = https://gitlab.com/libeigen/eigen
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -12,6 +12,7 @@ find_package(OpenMP)
 set(RIPSER_SRC_DIR "gtda/externals/ripser")
 set(GUDHI_SRC_DIR "gtda/externals/gudhi-devel/src")
 set(HERA_DIR "gtda/externals/hera")
+set(EIGEN_DIR "gtda/externals/eigen")
 
 #######################################################################
 #                               Ripser                                #
@@ -171,6 +172,8 @@ target_include_directories(gtda_simplex_tree PRIVATE "${GUDHI_SRC_DIR}/Cech_comp
 target_include_directories(gtda_simplex_tree PRIVATE "${GUDHI_SRC_DIR}/Persistent_cohomology/include")
 target_include_directories(gtda_simplex_tree PRIVATE "${GUDHI_SRC_DIR}/Subsampling/include")
 target_include_directories(gtda_simplex_tree PRIVATE "${GUDHI_SRC_DIR}/python/include")
+target_include_directories(gtda_simplex_tree PRIVATE "${GUDHI_SRC_DIR}/Collapse/include")
+target_include_directories(gtda_simplex_tree PRIVATE "${EIGEN_DIR}")
 
 if(MSVC)
     target_compile_options(gtda_simplex_tree PUBLIC $<$<CONFIG:RELEASE>: /O2 /Wall /fp:strict>)
@@ -227,6 +230,8 @@ target_include_directories(gtda_witness_complex PRIVATE "${GUDHI_SRC_DIR}/Cech_c
 target_include_directories(gtda_witness_complex PRIVATE "${GUDHI_SRC_DIR}/Persistent_cohomology/include")
 target_include_directories(gtda_witness_complex PRIVATE "${GUDHI_SRC_DIR}/python/include")
 target_include_directories(gtda_witness_complex PRIVATE "${GUDHI_SRC_DIR}/common/include")
+target_include_directories(gtda_witness_complex PRIVATE "${GUDHI_SRC_DIR}/Collapse/include")
+target_include_directories(gtda_witness_complex PRIVATE "${EIGEN_DIR}")
 
 if(MSVC)
     target_compile_options(gtda_witness_complex PUBLIC $<$<CONFIG:RELEASE>: /O2 /Wall /fp:strict>)
@@ -256,6 +261,8 @@ target_include_directories(gtda_strong_witness_complex PRIVATE "${GUDHI_SRC_DIR}
 target_include_directories(gtda_strong_witness_complex PRIVATE "${GUDHI_SRC_DIR}/Persistent_cohomology/include")
 target_include_directories(gtda_strong_witness_complex PRIVATE "${GUDHI_SRC_DIR}/python/include")
 target_include_directories(gtda_strong_witness_complex PRIVATE "${GUDHI_SRC_DIR}/common/include")
+target_include_directories(gtda_strong_witness_complex PRIVATE "${GUDHI_SRC_DIR}/Collapse/include")
+target_include_directories(gtda_strong_witness_complex PRIVATE "${EIGEN_DIR}")
 
 if(MSVC)
     target_compile_options(gtda_strong_witness_complex PUBLIC $<$<CONFIG:RELEASE>: /O2 /Wall /fp:strict>)
@@ -286,6 +293,8 @@ target_include_directories(gtda_sparse_rips_complex PRIVATE "${GUDHI_SRC_DIR}/Pe
 target_include_directories(gtda_sparse_rips_complex PRIVATE "${GUDHI_SRC_DIR}/Rips_complex/include")
 target_include_directories(gtda_sparse_rips_complex PRIVATE "${GUDHI_SRC_DIR}/Subsampling/include")
 target_include_directories(gtda_sparse_rips_complex PRIVATE "${GUDHI_SRC_DIR}/python/include")
+target_include_directories(gtda_sparse_rips_complex PRIVATE "${GUDHI_SRC_DIR}/Collapse/include")
+target_include_directories(gtda_sparse_rips_complex PRIVATE "${EIGEN_DIR}")
 
 if(MSVC)
     target_compile_options(gtda_sparse_rips_complex PUBLIC $<$<CONFIG:RELEASE>: /O2 /Wall /fp:strict>)
@@ -314,6 +323,8 @@ target_include_directories(gtda_cech_complex PRIVATE "${GUDHI_SRC_DIR}/Cech_comp
 target_include_directories(gtda_cech_complex PRIVATE "${GUDHI_SRC_DIR}/Persistent_cohomology/include")
 target_include_directories(gtda_cech_complex PRIVATE "${GUDHI_SRC_DIR}/python/include")
 target_include_directories(gtda_cech_complex PRIVATE "${GUDHI_SRC_DIR}/common/include")
+target_include_directories(gtda_cech_complex PRIVATE "${GUDHI_SRC_DIR}/Collapse/include")
+target_include_directories(gtda_cech_complex PRIVATE "${EIGEN_DIR}")
 
 if(MSVC)
     target_compile_options(gtda_cech_complex PUBLIC $<$<CONFIG:RELEASE>: /O2 /Wall /fp:strict>)

diff --git a/azure-pipelines.yml b/azure-pipelines.yml
@@ -41,7 +41,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-wheels-v2020.08.08" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-wheels-v2020.08.28" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 
@@ -63,21 +63,21 @@ jobs:
   - script: |
       set -e
       python -m pip install --upgrade pip
-      pip install dist/*manylinux2010*.whl
+      python -m pip install dist/*manylinux2010*.whl
     displayName: 'Install the wheels'
 
   - script: |
       set -e
-      pip install pytest pytest-cov pytest-azurepipelines pytest-benchmark hypothesis
+      python -m pip install pytest pytest-cov pytest-azurepipelines pytest-benchmark hypothesis
       mkdir tmp_test_cov
       cd tmp_test_cov
       pytest --pyargs gtda --ignore-glob='*externals*' --no-cov --no-coverage-upload
     displayName: 'Test the wheels with pytest'
 
   - script: |
       set -e
-      pip install pandas openml matplotlib
-      pip install "papermill==1.2.1"
+      python -m pip install pandas openml matplotlib
+      python -m pip install "papermill==1.2.1"
       cd examples
       for n in *.ipynb
       do
@@ -100,7 +100,7 @@ jobs:
 
   - bash: |
       set -e
-      pip install twine
+      python -m pip install twine
       twine upload -u giotto-learn -p $(pypi_psw) --skip-existing dist/*manylinux2010*.whl
     condition: eq(variables.nightlyRelease, true)
     displayName: 'Upload nightly wheels to PyPI'
@@ -136,7 +136,7 @@ jobs:
 
   - task: Cache@2
     inputs:
-      key: '"ccache-v2020.08.08" | $(Agent.OS) | "$(python.version)"'
+      key: '"ccache-v2020.08.28" | $(Agent.OS) | "$(python.version)"'
       path: $(CCACHE_DIR)
     displayName: ccache
 
@@ -149,6 +149,7 @@ jobs:
   - script: |
       set -e
       python -m pip install --upgrade pip setuptools
+      python -m pip install wheel
       source .azure-ci/setup_ccache.sh
       python -m pip install -e ".[dev]"
       ccache -s
@@ -172,11 +173,10 @@ jobs:
 
   - script: |
       set -e
-      pip install wheel
       python setup.py bdist_wheel
     displayName: 'Build the wheels'
 
-  - script: pip install dist/*.whl
+  - script: python -m pip install dist/*.whl
     displayName: 'Install the wheels'
 
   - script: |
@@ -189,7 +189,7 @@ jobs:
   - script: |
       set -e
       python -m pip install -e ".[examples]"
-      pip install "papermill==1.2.1"
+      python -m pip install "papermill==1.2.1"
       cd examples
       for n in *.ipynb
       do
@@ -205,7 +205,7 @@ jobs:
 
   - script: |
       set -e
-      pip install twine
+      python -m pip install twine
       twine check dist/*
     displayName: 'Check distribution with twine'
 
@@ -257,6 +257,7 @@ jobs:
 
   - script: |
       python -m pip install --upgrade pip setuptools
+      python -m pip install wheel
       python -m pip install -e ".[dev]"
     displayName: 'Install dev environment'
 
@@ -265,18 +266,17 @@ jobs:
     displayName: 'Test dev install with pytest'
 
   - script: |
-      pip uninstall -y giotto-tda
-      pip uninstall -y giotto-tda-nightly
+      python -m pip uninstall -y giotto-tda
+      python -m pip uninstall -y giotto-tda-nightly
     displayName: 'Uninstall giotto-tda/giotto-tda-nightly dev'
 
   - bash: |
       set -e
       sed -i $'s/\r$//' README.rst
-      pip install wheel
       python setup.py bdist_wheel
     displayName: 'Build the wheels'
 
-  - bash: pip install dist/*.whl
+  - bash: python -m pip install dist/*.whl
     displayName: 'Install the wheels'
 
   - script: |
@@ -287,7 +287,7 @@ jobs:
 
   - script: |
       python -m pip install -e ".[examples]"
-      pip install "papermill==1.2.1"
+      python -m pip install "papermill==1.2.1"
       cd examples
       FOR %%n in (*.ipynb) DO (papermill --start_timeout 2000 %%n - || exit /b)
     condition: eq(variables['notebooks_check'], 'true')
@@ -307,7 +307,8 @@ jobs:
 
   - bash: |
       set -e
-      pip install twine
+      python -m pip install twine
       twine upload -u giotto-learn -p $(pypi_psw) --skip-existing dist/*
     condition: eq(variables.nightlyRelease, true)
     displayName: 'Upload nightly wheels to PyPI'
+
diff --git a/cmake/HelperBoost.cmake b/cmake/HelperBoost.cmake
@@ -1,6 +1,5 @@
-
 # Add to BOOST_ROOT variable a custom path to 
-# ease installation of giotto-tda on Windows platform
+# ease installation of giotto-tda on Windows platforms
 # The custom path will be at `C:\\local\`
 if(WIN32)
     list(APPEND BOOST_ROOT "C:/local")

diff --git a/gtda/externals/bindings/periodic_cubical_complex_bindings.cpp b/gtda/externals/bindings/periodic_cubical_complex_bindings.cpp
@@ -48,6 +48,8 @@ PYBIND11_MODULE(gtda_periodic_cubical_complex, m) {
                    Bitmap_cubical_complex_periodic_boundary_conditions_base<
                        double>>*,
            bool>())
+      .def("compute_persistence",
+           &Persistent_cohomology_interface_inst::compute_persistence)
       .def("get_persistence",
            &Persistent_cohomology_interface_inst::get_persistence)
       .def("betti_numbers",
@@ -58,4 +60,3 @@ PYBIND11_MODULE(gtda_periodic_cubical_complex, m) {
            &Persistent_cohomology_interface_inst::intervals_in_dimension);
   m.doc() = "GUDHI periocal cubical complex function interfacing";
 }
-
diff --git a/gtda/externals/bindings/persistent_cohomology_bindings.cpp b/gtda/externals/bindings/persistent_cohomology_bindings.cpp
@@ -20,6 +20,8 @@ PYBIND11_MODULE(gtda_persistent_cohomology, m) {
       .def(py::init<Gudhi::cubical_complex::Cubical_complex_interface<>*>())
       .def(py::init<Gudhi::cubical_complex::Cubical_complex_interface<>*,
                     bool>())
+      .def("compute_persistence",
+           &Persistent_cohomology_interface_inst::compute_persistence)
       .def("get_persistence",
            &Persistent_cohomology_interface_inst::get_persistence)
       .def("betti_numbers",
@@ -28,5 +30,5 @@ PYBIND11_MODULE(gtda_persistent_cohomology, m) {
            &Persistent_cohomology_interface_inst::persistent_betti_numbers)
       .def("intervals_in_dimension",
            &Persistent_cohomology_interface_inst::intervals_in_dimension);
-  m.doc() = "GUDHI persistant homology interfacing";
+  m.doc() = "GUDHI persistent homology interfacing";
 }
diff --git a/gtda/externals/bindings/ripser_bindings.cpp b/gtda/externals/bindings/ripser_bindings.cpp
@@ -52,4 +52,3 @@ PYBIND11_MODULE(gtda_ripser, m) {
         "I"_a, "J"_a, "V"_a, "NEdges"_a, "N"_a, "modulus"_a, "dim_max"_a,
         "threshold"_a, "do_cocycles"_a, "ripser sparse distance matrix");
 }
-
diff --git a/gtda/externals/bindings/simplex_tree_bindings.cpp b/gtda/externals/bindings/simplex_tree_bindings.cpp
@@ -3,8 +3,8 @@
  * License:          Apache 2.0
  *****************************************************************************/
 
-
 #include <iostream>
+
 #include <Persistent_cohomology_interface.h>
 #include <Simplex_tree_interface.h>
 
@@ -41,8 +41,26 @@ PYBIND11_MODULE(gtda_simplex_tree, m) {
                const std::vector<simplex_tree_interface_inst::Vertex_handle>&,
                double>(
                &simplex_tree_interface_inst::insert_simplex_and_subfaces))
-      .def("get_filtration", &simplex_tree_interface_inst::get_filtration)
-      .def("get_skeleton", &simplex_tree_interface_inst::get_skeleton)
+      .def("get_filtration",
+           [](simplex_tree_interface_inst& self)
+               -> std::vector<simplex_tree_interface_inst::Simplex_and_filtration> {
+             std::vector<simplex_tree_interface_inst::Simplex_and_filtration> tmp;
+             for (auto elem = self.get_filtration_iterator_begin();
+                  elem != self.get_filtration_iterator_end(); elem++)
+               tmp.push_back(self.get_simplex_and_filtration(*elem));
+             return tmp;
+           })
+      .def("get_skeleton",
+           [](simplex_tree_interface_inst& self, size_t dim)
+               -> std::vector<
+                   simplex_tree_interface_inst::Simplex_and_filtration> {
+             std::vector<simplex_tree_interface_inst::Simplex_and_filtration>
+                 tmp;
+             for (auto elem = self.get_skeleton_iterator_begin(dim);
+                  elem != self.get_skeleton_iterator_end(dim); elem++)
+               tmp.push_back(self.get_simplex_and_filtration(*elem));
+             return tmp;
+           })
       .def("get_star", &simplex_tree_interface_inst::get_star)
       .def("get_cofaces", &simplex_tree_interface_inst::get_cofaces)
       .def("expansion", &simplex_tree_interface_inst::expansion)
@@ -59,6 +77,8 @@ PYBIND11_MODULE(gtda_simplex_tree, m) {
   py::class_<Persistent_cohomology_interface_inst>(
       m, "Simplex_tree_persistence_interface")
       .def(py::init<simplex_tree_interface_inst*, bool>())
+      .def("compute_persistence",
+           &Persistent_cohomology_interface_inst::compute_persistence)
       .def("get_persistence",
            &Persistent_cohomology_interface_inst::get_persistence)
       .def("betti_numbers",

diff --git a/gtda/externals/eigen b/gtda/externals/eigen
diff --git a/gtda/externals/gudhi-devel b/gtda/externals/gudhi-devel
diff --git a/gtda/externals/python/cubical_complex_interface.py b/gtda/externals/python/cubical_complex_interface.py
@@ -100,9 +100,9 @@ def persistence(self, homology_coeff_field=11, min_persistence=0):
                                                                  True)
         persistence_result = []
         if self.pcohptr is not None:
-            persistence_result = self.pcohptr.get_persistence(
-                homology_coeff_field, min_persistence)
-
+            self.pcohptr.compute_persistence(homology_coeff_field,
+                                             min_persistence)
+            persistence_result = self.pcohptr.get_persistence()
         return persistence_result
 
     def betti_numbers(self):

diff --git a/gtda/externals/python/periodic_cubical_complex_interface.py b/gtda/externals/python/periodic_cubical_complex_interface.py
@@ -100,9 +100,9 @@ def persistence(self, homology_coeff_field=11, min_persistence=0):
                                                                True)
         persistence_result = []
         if self.pcohptr is not None:
-            persistence_result = \
-                self.pcohptr.get_persistence(homology_coeff_field,
+            self.pcohptr.compute_persistence(homology_coeff_field,
                                              min_persistence)
+            persistence_result = self.pcohptr.get_persistence()
         return persistence_result
 
     def betti_numbers(self):
Original file line number	Diff line number	Diff line change
Expand Up		@@ -52,4 +52,3 @@ PYBIND11_MODULE(gtda_ripser, m) {
		"I"_a, "J"_a, "V"_a, "NEdges"_a, "N"_a, "modulus"_a, "dim_max"_a,
		"threshold"_a, "do_cocycles"_a, "ripser sparse distance matrix");
		}