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2019-05-22Merge pull request #49 from mglisse/sparsev3Vincent Rouvreau
All seems good to me and the new interface (with min and max) will allow to benchmark it with Strong collapse.
2019-05-10Fix blocker formulaMarc Glisse
I had copied it straight from the paper, without adding the factor 2 we have everywhere.
2019-05-10max_dim=INT_MAX for sparse Rips by default.Marc Glisse
2019-04-26Merge branch 'master' into toplex_mapROUVREAU Vincent
2019-04-18Doc reformat.Marc Glisse
2019-04-18Merge remote-tracking branch 'origin/master' into sparsev3Marc Glisse
2019-04-16Add min and max filtration values for the sparse RipsMarc Glisse
2019-04-13Fix the documentation of what relation i and j satisfy in the lower ↵Marc Glisse
triangular part of a matrix.
2019-04-13Handle triangular matrixMarc Glisse
2019-04-11commentsMarc Glisse
2019-04-11sphinx-build seems to be here on sphinx 2.0.1ROUVREAU Vincent
2019-04-11Find sphinx module for documentation generationROUVREAU Vincent
2019-03-19FixesMarc Glisse
2019-03-19Filter during expansion. Completely untested.Marc Glisse
2019-03-19Start fixing the sparse rips to match the true definition (not a clique complex)Marc Glisse
2019-03-15Improve python installation documentationROUVREAU Vincent
2019-03-15Fix code reviewROUVREAU Vincent
2019-03-14Fix code reviewROUVREAU Vincent
2019-03-13Improve documentation for Tangential complex (Fix #16)ROUVREAU Vincent
2019-03-12Add some documentation for Fix #31ROUVREAU Vincent
Cythonization of Fix #31 Add some tests
2019-03-12Make 'safe' mode as default value for alpha complex 3d utilityROUVREAU Vincent
2019-03-11Fix README.md file name renamed for Doxygen generationROUVREAU Vincent
2019-02-18Add biblio and doc referencesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/toplex_map@4111 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 42a6e48271d333d604cb5cb0c9c9f1e56b8f1965
2019-02-14Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/28vrouvrea
[python - install] make install does not install properly Use 'python setup.py install' command instead of copying files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4108 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 652d3597897aa3e7d1df97083cc3e2e4ae14f090
2019-02-14Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/25 [python] A Cmake ↵vrouvrea
option to set/unset runtime_library_dirs cmake -DWITH_GUDHI_CYTHON_RUNTIME_LIBRARY_DIRS=OFF .. # to disable runtime_library_dirs set in setup.py cf. Debian disallows setting rpath, so I'm currently unsetting runtime_library_dirs for the Python extensions. Could this perhaps be made into a CMake option? https://git.nonempty.org/debian-gudhi/tree/debian/patches/0005-Don-t-set-runtime-library-dirs-for-Python-extensions.patch?h=debian/sid&id=fed62e52ab396f0d6ba9029f12d5ef35d7761989 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4105 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 75f19373b2f01c2757bf1b11c81beff64021ddd8
2019-02-12Fix doc for C++ and Python.vrouvrea
Fix some warnings on Nerve GIC sphinx doc generation git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4101 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 57eacb8c4108be212e61796c65e3b45bb9c13644
2019-02-12Add unitary test for inf value readvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4100 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5cdac452d9c79cf63c62ec1382de4140a719286f
2019-02-12Fix doc typovrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4099 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b9987650ddf369c58b46955de6af9cd2d94831b3
2019-02-04Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4088 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 422db01787f7c105092e7f12b023a7a8e1f7d316
2019-01-30Merge of last modifications in Nerve_GIC branch : remove input template type ↵vrouvrea
as the function code were restricting its type git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4082 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8cba0b33ef5c6fa4e5bead0a1332b920d89273e4
2019-01-24Fix persistence_from_file example when the file is not conform.vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4075 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9a1b15f6d0b02084babd70ce8001cd90b6c35c85
2019-01-18Add boost graph adjacency benchmarkvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/adjacency_list_direction_improvement@4068 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6970242e9449e0cab0c03819cd4373335a50c697
2019-01-18Add setS test for adjacency_list verticesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/adjacency_list_direction_improvement@4066 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 78e72b061f0e863617641384d7cca9291e107aac
2019-01-17Fix issue #5 : [Bitmap_cubical_complex] Perseus file reader rejects infinityvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4064 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 77ec6d5d1f69ba3e1b0a1027d902084bb25d08f3
2019-01-17Fix cpplintvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4063 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7186509b0d722fc7a4264eeaf504cef1c1be3a2a
2019-01-17Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4062 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 495752e4da032e54a1a88adbcd030f526bc80a43
2019-01-17adjacency lists can be directed, undirected or bidirectional for Simplex ↵vrouvrea
tree insert_graph method Use of directed adjacency lists to fasten computation and use less memory git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/adjacency_list_direction_improvement@4061 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 839fabc15398ce590d09806bd783cd656029f3c1
2018-12-17Merge tangential-miro branchvrouvrea
Add reference to cubical in persistence module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4038 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 832343cd6e2357c9e229d5b34f6de03e50d2da67
2018-11-27Fix cpplintvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4018 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e4b0a5d84504abc43c57511049a90f57d79deeec
2018-11-27Fix cpplintvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4017 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5c45240299ca8c373a0782e291da59c0e1375678
2018-11-27cpplint fixvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4016 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b27f48ffe04f04ca1320657ee4ef24df2ad1c673
2018-11-27Fix cpplintvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4015 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 706e843528c5f06a090215eaf2fc8c0e25cb5557
2018-11-23Code review : Use CGAL::to_double(it->exact()) for Exact version, and ↵vrouvrea
CGAL::to_double(*it) otherwise git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4013 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5ff40181e71c7df721df38fa90635cee8ab7e799
2018-11-23 // We could use Epick + CGAL::Tag_true for not weighted nor periodic, but ↵vrouvrea
during benchmark, we found a bug // https://github.com/CGAL/cgal/issues/3460 // This is the reason we only use Epick + CGAL::Tag_false, or Epeck // // FAST SAFE EXACT // Epick + CGAL::Tag_false Epeck Epeck git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4012 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 88e844333b5bae8fcfd1104e493cdada1e4a4a3b
2018-11-21Separate tests to parallelize compilationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4010 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 33bd17816b7258d16e20943e2f54b5379d174b84
2018-11-21Code review : Use # error instead of static_assert(false, ...) for CGAL ↵vrouvrea
version detection Doc review : Better document CGAL types (FT, Weighted_point_3, Point_3, ...) Weighted alpha complex 3d example simplification git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4009 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 187d7a08468c96192b3cb82c93a2df5b425290f9
2018-11-19Fix compilation issue in debug modevrouvrea
to_double(*it) is also available if *it is a double Bad comment in Value_from_iterator between Epeck and Epick git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4005 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cba42be09eeee39a12a6f0adf8ff72f9147f5d1a
2018-11-19Merge last trunk modifications and remove the note about create_complex ↵vrouvrea
max_alpha_square git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4004 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 64548e4d0674fb5dd07645eee5c63785b099a168
2018-11-19Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/alpha_complex_3d_module_vincent@4003 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 94bbb0a5588ceee1ecf73d0503892e2f6c78274f
2018-11-19Fix cpplint and no more need of incr_dim in propagate_alpha_filtrationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4002 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7e4a3924d93b8bbb235376bf074811ec827f4e9d
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