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2017-10-01Euclidean Witness examples requires CGAL >= 4.8.1 because it is using ↵vrouvrea
subsampling (CMake and install doc) Bad link to Gudhi bibtex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@2741 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8c1b84a4030029ec7d1470c49662e15836cf02de
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
2017-09-12Fix 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
2017-09-12Euclidean 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
2017-09-07Python 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
2017-08-18Fix 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
2017-08-17Add 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
2017-07-06Plot 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
2017-07-03Rename 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
2017-06-16Fix CUSTOMBUILD : error : don't know how to set runtime library search path ↵vrouvrea
for MSVC git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2549 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 94c7625b3bc8e943e3856e0e65dc65bb5d8cd0f7
2017-06-16Add warning about boost_thread link for the Mac GUDHI python modulevrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2548 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4a9f6c43f4868bd4f303579c22fdc7a54728e68c
2017-06-14Fix try vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2543 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: da6eb0ef7b79c0d21d8e98d17d78459d1768a5db
2017-06-14Add traces for debugvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2542 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a9e8098443114a4fe6e9c19e6410169580c134c6
2017-06-13Try to fix Windows compilation for Condavrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2541 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: afa1b10e300aafbc92a85b3519f4b39add2ae6e4
2017-06-09No more need of find_the_lib cmake macro to find Windows boost lib namevrouvrea
Fix cmake warning on if with quotes git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2527 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a352820ab0a596961b9851d4a30c40196a70ff98
2017-06-02Try to remove boost systemvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/boost_system_no_deprecated_test@2504 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: fd12c45af5ebeb72c4b49142abab91b46ce1a9da
2017-05-30Add a warningvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2465 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a873c9c6fff031968747c3dec197aec06738c32a
2017-05-19Move src/common/utilities/hypergenerator.cpp in src/common/utilitiesvrouvrea
Management of Python distribution packages make install is now installing utilities and GUDHI python module git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cmake_modules_for_gudhi@2453 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a85576c7ae062718900f0db2bfb0dd3f26e87177
2017-04-14Try of a fix for Windows cython find mechanismvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2347 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4c93e7042d79bfea7c758e726f6393b97334c798
2017-04-10mac osx version is 10.12 and not 10.9 (cf. mail Bertrand Michel)vrouvrea
Add text for Windows Python 3.X installation and forinstallation with several Python installed on the system. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2324 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 939d5d4a94c2430de11b3dcbc29a65aad4bfd885
2017-03-31Fix examples testsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2289 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9d386b82c89601da233f7c61254a023ddffc9abc
2017-03-30Move example tests in a new CMakeLists.txtvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2288 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8b2bce4c8be8a34b8fba9c664d2f0b3b60a50c20
2017-03-29Small modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2286 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 34dc48a00ed8270967952b8763006b17f96a13e7
2017-03-29Small modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2285 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4bf077b4d3b729c4d133e242d57d08ed9a04ae76
2017-03-28Missing a testvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2274 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 30330428b0071967367d1708338de0c7d40d8a67
2017-03-28Missing a test for cythonvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2272 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 223961ca5575e07d0db2c93ee0326864166980d8
2017-03-28Make Python interface compile, test and doc for Python2 and Python3vrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2267 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: f7397ecc5aba27ad4ecc794f4fbf5ca857847113
2017-03-28Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2263 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 9b430e79ecc94bee975d748eb3e2106c7dbab3ce
2017-03-24Workaround for CGAL version 4.8 compilation issuevrouvrea
New target CGAL_WITH_EIGEN3_VERSION set with CGAL_VERSION when CGAL and Eigen3 found to ease CMakeLists.txt git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cgal_4.8_issue@2241 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2fbf1f9397aa1549ba05aa26ac6852b882dce147
2017-03-17Euclidean strong witness complex cytonizationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2195 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: de15e40b8f0efcc59b2f07ffb5f5d59ccab8d51c
2017-03-14Add Windows and CGAL_HEADER_ONLY cythonization supportvrouvrea
Add OFF reader interfaces (required by Euclidean witness complex) Add Euclidean_witness_complex git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2186 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 4d780f05c3409bea47a81e4377dbaf509b9e718c
2017-03-08New revision of witness and its documentationvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2181 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 5f002c1a58b2daff6c6826a2552d1c101f6810e1
2017-03-03Merge last trunk modificatinosvrouvrea
make sphinx depends on cython target git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2155 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: ebb1709872963ffd30a6d31ab596f2715ca14436
2017-02-27Add TBB compilation support and documentationvrouvrea
Add Matplotlib results in GUDHI persistence graphical tools git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2112 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: e9fe1111d3a7d82c004a390cee77197221f117ec
2017-02-27Alpha complex requires CGAL 4.7 (not 4.8)vrouvrea
Add CMake configuration to cythonize with TBB when found git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2110 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 8341a46af52d74f17e5b1fcbb609f5a2d1da52af
2017-02-24Modifications for MacOSX compilationvrouvrea
Add GUDHI web site eader and nice colors for the python doc git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2109 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 20923bc3f304cfe96aec58030920c043400c3dd4
2017-02-16Remove pandas examples and use of OFF files interfaces to be more consistent ↵vrouvrea
(pandas interface is not that hard to be done) Add of distance matrix in Rips git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2081 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 3a3b24f0824eed2710edb5bf17d120039973bf62
2017-02-03Automatic examples documentation page generationvrouvrea
alpha_rips_persistence_bottleneck_distance example for python Add intervals_in_dim function for simplex tree git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2055 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 460fbe5db9f0c08776952106e729a21460bec36f
2017-02-02Change doc html theme.vrouvrea
Change tables git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2047 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: aaa29b8f610d506efc3762ad17c4fd768e74d399
2017-01-26Merge last trunk modificationsvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@2013 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 28547c36fb65eea6cf30091678e132763c3d0507
2016-12-01Merge last trunk modificationsvrouvrea
add Py test for subsampling Add choose_n_furthest from off file git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1810 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: a23746a3dd427edc958b375f9f0ac4b4d2901fcb
2016-12-01Add Subsampling cpp interface and cythonvrouvrea
Remove deref cyton import git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1809 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 2dc0469d2401e0c99e879c064a0f608c8ba78ed6
2016-11-29Fix interface for Alpha complex and Tangential complexvrouvrea
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/ST_cythonize@1801 636b058d-ea47-450e-bf9e-a15bfbe3eedb Former-commit-id: 995b53c7f65057ec155988b90f17299665eab4ae
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