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2017-09-25Adding all that is needed for Rips complex construction from correlation ↵pdlotko
matrix. Moduo the fact that I cannot see the doc (althoug make doxygen do not create any errors), this is ready for review. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2712 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e8e7acceaf2be6f17baa3d77c85e207a74a4fb33
2017-09-25A new branch to develop rips complex from correlation matrixvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/rips_complex_from_correlation_matrix@2710 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f63fb2b61d0b729e343163782f94282072e39036
2017-09-19Merge branch python_memory_leak_fix for Rips complexvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2687 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7d19895af099fe6de6721401616bfabd3e67ea1a
2017-09-19Fix memory leakvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_memory_leak_fix@2686 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a8fd65accb5be293e9d3f5fe411225745cb76b0b
2017-09-19A branch to fix Python memory leakvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/python_memory_leak_fix@2684 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b13db90a338e1ecea3e0355c12a2019fd5bcf62e
2017-09-18Merge cythonization improvement branchvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2680 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 590be4537e3b1c79d3efa33efd2b420e14caa541
2017-09-18Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2679 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e4d0575f2279f2541329644c177c05c40614b761
2017-09-18Add a function to launch py.test as required for no cache files in sourcesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2678 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 92ca1aabcbe276198fa29ea75f763fb0aa3c504f
2017-09-18Add warning for developper version that sphinx is configured for user versionvrouvrea
Removes GudhUI ERROR mesages (just warnings git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2677 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0111272d9f6d6dc10e370360b2242eff4828611b
2017-09-14Radius search renamed near searchvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2670 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: cedddf14f68b31276c4e4935631ce4a3d24f32ae
2017-09-13radius search => near searchcjamin
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/call_it_near_search@2669 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e77c8b7de12df9cf5d0a6ef8d79e4b14a28237b3
2017-09-13git-svn-id: ↵cjamin
svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/call_it_near_search@2668 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7db5b52d49e75caa162e6087a407d40d26f92897
2017-09-12Fix sphinx build for python3 on Ubuntuvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2667 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c720b8be2919344e06f3d71cefdd7693439f63f0
2017-09-12Bottleneck does not require Eigen3 (C++ and Python)vrouvrea
Doc issue about examples requiring Eigen3 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2666 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5e127d4e8137a44ee3bd688c32653acfb4a55007
2017-09-12Modification rollbackvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2665 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2f977f8b93c6104d2b7c8f16c13da974b36f1535
2017-09-12Add debug tracesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2664 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e4c572d98f4628e7f9b36fd9925ba7ce68e3cf81
2017-09-12Fix in Python3 if sphinx is not installedvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2663 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0005d7fe2e7e8513a276543295c02351456595cc
2017-09-12Euclidean witness requires CGAL 4.6.0vrouvrea
Subsampling requires CGAL 4.8.1 All modules requiring CGAL requires also Eigen3 git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2662 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: df4c03882b8c5eb91f12939b460b3c9b85cbb870
2017-09-11remove debug tracesvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2656 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4ea039d0564268458ca64950113fbffdc86c10b3
2017-09-11Add comment for the dependencyvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2655 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ab03b16bc884fe3291e3308e4a975b7c6232a861
2017-09-07Fix doc for user_versionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2650 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 18aebd67968fd48ccfcfcfbff75c614496f4424e
2017-09-07Python documentation is now built from sources to the build directory.vrouvrea
Missing bibtex and images to be "as before" git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2649 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0deda91875e34ce534c88a601cfb167d9c7dfa01
2017-09-05Tests and compilation are now from sources (even if doc and examples are copied)vrouvrea
This modification does not fix it for the doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2645 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0fa4850747d3f18cd54e0622ef1831d5d5c5a0df
2017-08-25bug in Python SimplexTree (needs string)vrouvrea
Doc issue in alpha_complex user doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2629 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ab35f6f64af33414002d6899275170f781e9cfa8
2017-08-25A branch to improve cythonization.vrouvrea
For the moment, CMake copies everything, tis means dev need to CMake everytime a cyton modification is done. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cythonization_improvement@2626 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 02925aca6d22ac71b14038544047bd01131a0845
2017-08-22Version files modification for new releasevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2616 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8296050aef9e6658cd98080075f4047487e21b68
2017-08-21Merge persistence diagram improvement branchvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2614 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: eaccfe6c60c4a05bbec173a1042db7ad490a9f37
2017-08-18Fix sphinx bug when python3 is not in /usr/binvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2613 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 07f67d4cc1f3b558b191115e0979ce3ce0580206
2017-08-18Add display function in file format docvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2612 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b51ffdf8f7be07c6745ca2b6501c51a350deffd2
2017-08-17Add file formats for Python.vrouvrea
Binding for persistence write files Launch py.test with the command "python -m pytest" (shall work everywhere) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2611 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9443a7eb5b580ece7708ff57949ad08339c1c5c3
2017-08-10Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2609 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 7bd35b1a3515450f92efd4cb44d0b81d1e215dd3
2017-08-10Some modifications to file format documentation (utf8 test)vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2608 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2590184676603521a3ab175834670bb47a80c93b
2017-08-10Fix Python2 compatibilityvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2607 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b8744511b527f7117d3432c559dcb68b59253e53
2017-08-10utf8 file formatvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2606 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 0541d16e8818dfc9cd6ecd7960c0ec5638cd8277
2017-08-10Add Gudhi namespacevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2605 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6f004d1f7f8a741081181c1ead026fb952a21e6c
2017-08-09Merge last trunk modificationsvrouvrea
persistence file reader Python interface persistence_graphical_tools improvement (max_plots and max_barcodes, and from a persistence file) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2604 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: db80333d4f34151be0c32024af597d90d221a97f
2017-08-08Fix persistence files reader unitary testsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2603 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 1b3ab678420a63b6607d15f350697eccc42b56f7
2017-08-08Fix bug in read_persistence_intervals_in_dimension for only_this_dimvrouvrea
Add unitary tests for read_persistence Add .clang-format to clang format new files git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2601 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 28e870973f9ebd686d503246202fa6d6a549e9e3
2017-08-07Fix test reader utilsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2600 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 24bcf652d5374d158c6b4e90dd2233af7e153c49
2017-07-10simplex / complex confusionglisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2596 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 77c093029d3e2518260ce59705110df3fbfe11e3
2017-07-10Cubical: use +inf instead of UINT_MAX as filtration value for non-simplices.glisse
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2595 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c578be16d9559b6d271cdb63be3a58a015735ab7
2017-07-06Plot functions now returns a plot that can be modified before to be shownvrouvrea
Add confidence band in plot_persistence_diagram Cythonization of read_lower_triangular_matrix_from_csv_file and read_persistence_intervals functions Add Python tests of read functions git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2590 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 522ec31e9ad3a9a688875612d246114704b8c74e
2017-07-04Add Gudhi namespace for reader_utilsvrouvrea
Add confidence band in persistence_graphical_tools.py Persistence_diagram returns a plot that is no more showed. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2582 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4125f4f525057e89c8b0d5d164ea0b9d1df1bd72
2017-07-04A branch to improve persistence diagram python modulevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/persistence_diagram_improvement@2580 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fccd96ce458eddabcac3c722cae627b66e58ddbd
2017-07-03Rename cythonize_gudhi.py in setup.py to be conform with Python convention ↵vrouvrea
(for easy_install and pip) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2578 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: c514a7c5096293380254339e7e60782194040823
2017-06-28Add a commentvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2566 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 64cd59ca30ff82a1c116df20c4cee38a795dc518
2017-06-28Merge of branch boost_system_no_deprecated_test in order to :vrouvrea
- remove boost_system library dependency - repair conda package compilation issues found - Use Gudhi::Clock instead of boost::date_time library git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2565 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: d68764ab186bd44f2b2253ba21ad1c0e09584455
2017-06-28Merge of the branch read_persistence_from_filevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2564 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b534b8866e25cf86db1483d141ac217c82b36384
2017-06-20Merge Spatial searching-Add radius search branchvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2557 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ad29663d9f9ea8badcf70ebe48349af0b0cdb36d
2017-06-20Missing typedefcjamin
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Spatial_searching-Add_radius_search@2556 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3354bb63d0839ae8377e9c11ef2a1168cce7dd20
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