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Strong collapse vincent #48

Merged
merged 96 commits into from Apr 16, 2019
Merged

Strong collapse vincent #48

merged 96 commits into from Apr 16, 2019

Commits on Sep 20, 2018

  1. A new branch to fix a few issues on cubical complexes (namely, change… 

    … doumentation to avoid confusion with perseus format, add constructor from an array).

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@3898 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    pdlotko committed Sep 20, 2018
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  2. Fix to the documentation: to remove confusion with the perseus format. 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@3899 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    pdlotko committed Sep 20, 2018
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  3. The same comment in the file format description... 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@3900 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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Commits on Oct 31, 2018

  1. git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerv… 

    …e_GIC@3971 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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Commits on Nov 1, 2018

  1. changes example compilation in GUDHI_modules.cmake 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@3973 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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Commits on Jan 17, 2019

  1. Merge last trunk modifications 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4062 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Jan 17, 2019
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  2. Fix cpplint 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4063 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Jan 17, 2019
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  3. Fix issue GUDHI#5 : [Bitmap_cubical_complex] Perseus file reader reje… 

    …cts infinity

git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4064 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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Commits on Jan 24, 2019

  1. Fix persistence_from_file example when the file is not conform. 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4075 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Jan 24, 2019
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Commits on Jan 30, 2019

  1. Merge of last modifications in Nerve_GIC branch : remove input templa… 

    …te type 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

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Commits on Feb 4, 2019

  1. Merge last trunk modifications 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4088 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Feb 4, 2019
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Commits on Feb 12, 2019

  1. Fix doc typo 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4099 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Feb 12, 2019
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  2. Add unitary test for inf value read 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@4100 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Feb 12, 2019
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  3. Fix doc for C++ and Python. 

    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

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    vrouvrea committed Feb 12, 2019
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  4. merge cubical_small_fix to fix 

    https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/5 [Bitmap_cubical_complex] Perseus file reader rejects infinity


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4103 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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    vrouvrea committed Feb 12, 2019
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Commits on Feb 14, 2019

  1. Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/25 [python] A Cm… 

    …ake 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

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    vrouvrea committed Feb 14, 2019
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  2. Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/28 

    [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

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Commits on Mar 8, 2019

  1. Use Markdown for README and add some informations

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  2. Update README.md

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  3. Update README.md

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  4. Add Travis CI for examples tests and utils

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  5. more verbose

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  6. let's try tavis

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  7. add qtbase5-dev for CGAL

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  8. add all kind of stuff for CGAL

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  9. Try with Header Only version of CGAL

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  10. make install requires sudo

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  11. missing eigen3

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  12. Add travis build status

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  13. new target for doxygen

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  14. Merge branch 'master' of github.com:GUDHI/gudhi-devel

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  15. Some comments, split cmake commands and add specific make target

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  16. No utils on doxygen target

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  17. doxygen typo

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  18. Add Python and sphinx in the build matrix

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  19. Add Python pip and tests

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  20. Add setuptools and cache pip installation

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  21. upgrade pip installation

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  22. without setuptools

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  23. with apt setuptools

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  24. pip install --user

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  25. add scipy for sphinx documentation

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  26. Simplify to find the bug

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  27. Try to clean build directory

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  28. Try after clean

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  29. Try to cache CGAL dir

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  30. Remove branches

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  31. Download verbose

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  32. Travis could not parse the yaml

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  33. Travis could not parse the yaml

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  34. Try to cache CGAL

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  35. Missing then

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  36. Remove cache for CGAL and doxygen target that fails

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Commits on Mar 11, 2019

  1. Fix README.md file name renamed for Doxygen generation

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  2. Add .gitignore

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  3. Add osx support

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  4. Try with setting dist and osximages

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  5. Try to simplify build matrix

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  6. Try to simplify build matrix

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  7. Another way to matrix

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  8. No matrix in env

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  9. Try to install as much as possible with pip

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Commits on Mar 12, 2019

  1. Make 'safe' mode as default value for alpha complex 3d utility

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  2. Add some documentation for Fix GUDHI#31 

    Cythonization of Fix GUDHI#31
Add some tests
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Commits on Mar 13, 2019

  1. Improve documentation for Tangential complex (Fix GUDHI#16)

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Commits on Mar 14, 2019

  1. Fix code review

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Commits on Mar 15, 2019

  1. Fix code review

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  2. Improve python installation documentation

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Commits on Mar 26, 2019

  1. Fix typos

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  2. Rename Tower_assembler Flag_complex_tower_assembler. Fix Unitary tests

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Commits on Mar 27, 2019

  1. Rename Flag_complex_tower_assembler::build_tower_for_two_cmplxs as bu… 

    …ild_tower_for_two_complexes

New class Flag_complex_strong_collapse (not yet parallelized)
strong_collapse_distance_matrix utility that takes an OFF point cloud as input and outputs a csv distance matrix after collapse
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  2. Add sorted proximity graph construction for strong collapse example 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4019 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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  3. Rollback modifications 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4020 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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  4. Iterates and paralllel on alpha vector 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4021 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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  5. Add some comments 

    git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4023 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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  6. Move edge graph computation from compute_proximity_graph function in … 

    …a new function compute_edge_graph.

New data structure Filtered_edges_vector that can be used to compute_edge_graph.
Benchmark compute_edge_graph instead of compute_proximity_graph (Filtered_edges_vector is now benchmarked).


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4074 636b058d-ea47-450e-bf9e-a15bfbe3eedb

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  7. First version that makes the example compile. 

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  8. Clang format files 

    Remove unused using/typedefs
Remove useless pointers
constify get methods


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  9. Rename some variables and remove unused ones 

    Fix some warnings


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  10. A new version to strong collapse by indices on graph edge list 

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  11. Add flag_complex_sparse_matrix unitary tests 

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  12. Fix unitary tests compilation issue 

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  13. Rename types and attributes in Flag_complex_sparse_matrix.h 

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  14. Coding conventions 

    Unitary tests for sparse matrix and tower assembler
Sparse matrix redefine private/public access


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  15. Fix typos

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  16. Rename Tower_assembler Flag_complex_tower_assembler. Fix Unitary tests

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  17. Rename Flag_complex_tower_assembler::build_tower_for_two_cmplxs as bu… 

    …ild_tower_for_two_complexes

New class Flag_complex_strong_collapse (not yet parallelized)
strong_collapse_distance_matrix utility that takes an OFF point cloud as input and outputs a csv distance matrix after collapse
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  18. Resolve conflict after master rebase

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Commits on Apr 3, 2019

  1. Merge last modification from subversion branch 

    Fix bugs
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Commits on Apr 4, 2019

  1. Remove reduce map parameter from tower assembler build_tower_for_two_… 

    …complexes method

Fix unitary tests
Add strong_collapse_rips_persistence utility
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Commits on Apr 8, 2019

  1. reduction matrix is no more required for build_tower_for_two_complexe… 

    …s. Fix some issues.
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  2. std::tuple constructor is explicit

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  3. std::tuple constructor is explicit

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Commits on Apr 11, 2019

  1. Parallel version of strong collapse

    @VincentRouvreau
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  2. Move sparse matrix and tower in Strong_collapse folder

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    VincentRouvreau committed Apr 11, 2019
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Commits on Apr 16, 2019

  1. Add basics for Strong collapse documentation

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