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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

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VincentRouvreau
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  • Parallel version
  • Basics for doxygen documentation
  • Use code conventions

pdlotko and others added 30 commits September 20, 2018 08:54
A new branch to fix a few issues on cubical complexes (namely, change…
7961566 
… 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

Former-commit-id: e0cb89bbb2429e737d5d2d6e8e59d0848b176231
Fix to the documentation: to remove confusion with the perseus format.
3ae2a05 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@3899 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 6d600838396236ca95346719058bd8b834541814
The same comment in the file format description...
a3b3e52 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/cubical_complex_small_fix@3900 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 656bfe12681707838a564d886b803b6b8f3f90de
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerv…
26781f8 
…e_GIC@3971 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 55e1647f8361d2fb59ea672091d30d6697b887dc
changes example compilation in GUDHI_modules.cmake
2ad604e 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/Nerve_GIC@3973 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5e0b803f01774750a9b63f9d691d30b3c625ccd1
Merge last trunk modifications
6b70186 
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
Fix cpplint
e1b61dc 
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
Fix issue GUDHI#5 : [Bitmap_cubical_complex] Perseus file reader reje…
644076d 
…cts infinity

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
Fix persistence_from_file example when the file is not conform.
32bde4c 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/trunk@4075 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9a1b15f6d0b02084babd70ce8001cd90b6c35c85
Merge of last modifications in Nerve_GIC branch : remove input templa…
2905296 
…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

Former-commit-id: 8cba0b33ef5c6fa4e5bead0a1332b920d89273e4
Merge last trunk modifications
ea43738 
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
Fix doc typo
7eda621 
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
Add unitary test for inf value read
b184350 
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
Fix doc for C++ and Python.
f29a6e9 
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
merge cubical_small_fix to fix
36e6544 
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

Former-commit-id: b036b89564e31e4c385cb0b782db22a3ca445a9f
Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/25 [python] A Cm…
68c4ffe 
…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

Former-commit-id: 75f19373b2f01c2757bf1b11c81beff64021ddd8
Fix https://gitlab.inria.fr/GUDHI/gudhi-devel/issues/28
d7216ff 
[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
@VincentRouvreau
Use Markdown for README and add some informations
85f2f9b
@VincentRouvreau
Update README.md
0566202
@VincentRouvreau
Update README.md
e49133e
@VincentRouvreau
Add Travis CI for examples tests and utils
1b08181
@VincentRouvreau
more verbose
86cbdc0
@VincentRouvreau
let's try tavis
dc10a4d
@VincentRouvreau
add qtbase5-dev for CGAL
47f4df1
@VincentRouvreau
add all kind of stuff for CGAL
70bc9d0
@VincentRouvreau
Try with Header Only version of CGAL
38857f7
@VincentRouvreau
make install requires sudo
d69ad44
@VincentRouvreau
missing eigen3
676e0a0
@VincentRouvreau
Add travis build status
a763d05
@VincentRouvreau
new target for doxygen
bdd9ef4
VincentRouvreau and others added 29 commits March 15, 2019 16:36
@VincentRouvreau
Improve python installation documentation
b2675aa
@VincentRouvreau
Fix typos
65eca98
@VincentRouvreau
Rename Tower_assembler Flag_complex_tower_assembler. Fix Unitary tests
e6e9309
@VincentRouvreau
Rename Flag_complex_tower_assembler::build_tower_for_two_cmplxs as bu…
afd1e27 
…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
@VincentRouvreau
Add sorted proximity graph construction for strong collapse example
6607be4 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4019 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 7a0f47c4ce7a64ee9b4b224aff6d27b65676af0d
@VincentRouvreau
Rollback modifications
022953c 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4020 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 04e02f65ce8a43926a598a2b8313138521347bd7
@VincentRouvreau
Iterates and paralllel on alpha vector
dce11b6 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4021 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 703c0ec2035fa3ab3201eb744f44594556a8d0a4
@VincentRouvreau
Add some comments
8a309c9 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4023 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: f0ecece47c411400c5628b89fccd243f6d1758cd
@VincentRouvreau
Move edge graph computation from compute_proximity_graph function in …
b9176df 
…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

Former-commit-id: 57cc4c61d9ed9fd3673f8a5751986eccf3b8c4bc
@VincentRouvreau
First version that makes the example compile.
4ec2c67 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4076 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: de2deb65a751d8b28c04f427ffdc7b36245a6b99
@VincentRouvreau
Clang format files
2f93c17 
Remove unused using/typedefs
Remove useless pointers
constify get methods


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4077 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 2405e57601dcef3b1fc44f5fce94dc66e26c40c2
@VincentRouvreau
Rename some variables and remove unused ones
e0c0363 
Fix some warnings


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4078 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: ae328a4737705e123b6ec355462a36c5d0354cb5
@VincentRouvreau
A new version to strong collapse by indices on graph edge list
a64b245 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4080 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 9eb247b8fd155319d30d1e4a77963b7413c954e0
@VincentRouvreau
Add flag_complex_sparse_matrix unitary tests
4cdd10b 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4084 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 5981983a5d69c08260d6f97f4b9fb3e8b8b3ee9f
@VincentRouvreau
Fix unitary tests compilation issue
97c75aa 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4085 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 80446da31870ea18f6f7adad6595baca7c403683
@VincentRouvreau
Rename types and attributes in Flag_complex_sparse_matrix.h
42b86df 
git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4086 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 03ee49d196643f8879d29d0f2fb7861435830a87
@VincentRouvreau
Coding conventions
ae65f26 
Unitary tests for sparse matrix and tower assembler
Sparse matrix redefine private/public access


git-svn-id: svn+ssh://scm.gforge.inria.fr/svnroot/gudhi/branches/strong_collapse_vincent@4094 636b058d-ea47-450e-bf9e-a15bfbe3eedb

Former-commit-id: 426652ef84cfd0c701c06b00e277c5abce1da9e6
@VincentRouvreau
Fix typos
c4d80cb
@VincentRouvreau
Rename Tower_assembler Flag_complex_tower_assembler. Fix Unitary tests
2f118e6
@VincentRouvreau
Rename Flag_complex_tower_assembler::build_tower_for_two_cmplxs as bu…
3929d40 
…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
@VincentRouvreau
Resolve conflict after master rebase
7d48572
@VincentRouvreau
Merge last modification from subversion branch
8d02e39 
Fix bugs
@VincentRouvreau
Remove reduce map parameter from tower assembler build_tower_for_two_…
f301e2b 
…complexes method

Fix unitary tests
Add strong_collapse_rips_persistence utility
@VincentRouvreau
reduction matrix is no more required for build_tower_for_two_complexe…
71de25f 
…s. Fix some issues.
@VincentRouvreau
std::tuple constructor is explicit
d69e4c1
@VincentRouvreau
std::tuple constructor is explicit
df5b61b
@VincentRouvreau
Parallel version of strong collapse
d907a2a
@VincentRouvreau
Move sparse matrix and tower in Strong_collapse folder
39a027f
@VincentRouvreau
Add basics for Strong collapse documentation
0aff4d1
@VincentRouvreau VincentRouvreau merged commit 323b84a into GUDHI:strong_collapse_vincent Apr 16, 2019
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