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2017-09-29Rename a few functions in Kd_tree_searchcjamin
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2730 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f009977d25c76cc0f6116093a448fab258c8626b
2017-09-27Fix some cpplintsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2721 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76b127e54d9511b70294ab48336ca6dbd6fdb1d6
2017-09-27Merge last trunk modificationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2720 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 37cec1ea1e06c9e9656962614fcddc0fa022c5d0
2017-09-27Replace INFINITY with std::numeric_limits<Filtration_value>::infinity()vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2719 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: b24d3381da60cd634142e3024d5f5ed53294f8e8
2017-09-26Merge weighted alpha complex fix branchvrouvrea
Add some text to 3d alpha complexes in the usage function git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2716 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 6f2ee1897438a6bf75b484c2c625c43f2571ab41
2017-09-26Gudhi 2.0.1-rc2 versionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2715 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 76499766ca670017df0c963c3b5a49c343eb1a47
2017-09-25Do not advertise nor use the exact bottleneck distance versionvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2711 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e441b042d15bfbe727789803ca17b17711a48d9c
2017-09-25Fix weighted alpha complex 3dvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/weighted_alpha_complex_fix@2709 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3e7d1f73038d193b566e790a3095b6f802c48b48
2017-09-22Remove global filtration attribute of te simplex tree (including getter and ↵vrouvrea
setter) git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_remove_useless_global_filtration@2705 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a6c179ae47e61d1ca12d1f54c4ae1fc0e3c1fde2
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
2017-09-18Merge 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
2017-09-13radius 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
2017-09-12Fix 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
2017-08-22Version 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
2017-08-18Fix 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
2017-07-03Rename 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
2017-06-20Missing 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
2017-06-20Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Spatial_searching-Add_radius_search@2555 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3d0a3b2988bbbd0baa19fc09ba77e4e58e330a89
2017-06-16Fix auto lambda (requires C++14) compilation issuevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/read_persistence_from_file@2550 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: df64cfdde77500b06f00432a1d1532518cd4dd37
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