Age | Commit message (Collapse) | Author |
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* avoid overflow on openmp version of emd solver
* monothread version updated
* Fixed typo in readme
* added PR in releases
* typo in releases.md
* added a precision to releases.md
* added a precision to releases.md
* correct readme
* forgot to cast
* lower error
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* Correct test_mm_convergence for cupy
* Fix bug where number of iterations is limited to 2^31
* Update RELEASES.md
* Replace size_t with long long
* Use uint64_t instead of long long
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typo in releases
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* fix transpose in sinkhorn barycenters
* add test for assymetric cost barycenters
* fix pep8
Co-authored-by: Hicham Janati <hicham.janati@inria.fr>
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* Solve bug
* Update release file
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* GWB first solver version
* tests + example for gwb (untested) + free_bar doc fix
* improved doc, fixed minor bugs, better example visu
* minor doc + visu fixes
* plot GWB pep8 fix
* fixed partial gromov test reproductibility
* added an animation for the GWB visu
* added PR num
* minor doc fixes + better gwb logo
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* release text and number
* add examples in release fil build wheels
* switch gallery to release
* add much needed contributors file
* debug circleci
* une line of logos
* working logo
* back to stable sphinx galery
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* center gradients for mass of emd2 and gw2
* debug fgw gradient
* debug fgw
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* bugfix
* update refs partial OT
* fixes small typos in plot_partial_wass_and_gromov
* fix small bugs in partial.py
* update README
* pep8 bugfix
* modif doctest
* fix bugtests
* update on test_partial and test on the numerical precision on ot/partial
* resolve merge pb
* Delete partial.py
* update unbalanced: mm algo+plot
* update unbalanced: mm algo+plot
* update unbalanced: mm algo+plot
* update unbalanced: mm algo+plot
* update unbalanced: mm algo+plot
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* add test mm algo unbalanced OT
* update unbalanced: mm algo+plot
* update unbalanced: mm algo+plot
* update releases.md with new MM UOT algorithms
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* remove all cpu submodule and tests
* speedup tests gromov
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or regularized OT (#360)
* add losses and plan computations and exmaple for dual oiptimization
* pep8
* add nice exmaple
* update awesome example stochasti dual
* add all tests
* pep8 + speedup exmaple
* add release info
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* add gfactored ot
* pep8 and add doc
* add exmaple for factotred OT
* final number of PR
* correct test on backends
* remove useless loss
* better tests
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* First draft
* Add matrix inverse and square root to backend
* Eigen decomposition for older versions of pytorch (1.8.1 and older)
* Corrected eigen decomposition for pytorch 1.8.1 and older
* Spectral theorem is a thing
* Optimization
* small optimization
* More functions converted
* pep8
* remove a warning and prepare torch meshgrid for future torch release (which will change default indexing)
* dots and pep8
* Meshgrid corrected for older version and prepared for future versions changes
* New backend functions
* Base transport
* LinearTransport
* All transport classes + pep8
* PR added to release file
* Jcpot barycenter test
* unbalanced with backend
* pep8
* bug solve
* test of domain adaptation with backends
* solve bug for tic toc & macos
* solving scipy deprecation warning
* solving scipy deprecation warning attempt2
* solving scipy deprecation warning attempt3
* A warning is triggered when a float->int conversion is detected
* bug solve
* docs
* release file updated
* Better handling of float->int conversion in EMD
* Corrected test for is_floating_point
* docs
* release file updated
* cupy does not allow implicit cast
* fromnumpy
* added test
* test da tf jax
* test unbalanced with no provided histogram
* using type_as argument in unif function correctly
* pep8
* transport plan cast in emd changed behaviour, now trying to cast as histogram's dtype, defaulting to cost matrix
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Resolves gromov wasserstein backward bug
* release file updated
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* add fgw dictionary learning feature
* add fgw dictionary learning feature
* plot gromov wasserstein dictionary learning
* Update __init__.py
* fix pep8 errors exact E501 line too long
* fix last pep8 issues
* add unitary tests for (F)GW dictionary learning without using autodifferentiable functions
* correct tests for (F)GW dictionary learning without using autodiff
* correct tests for (F)GW dictionary learning without using autodiff
* fix docs and notations
* answer to review: improve tests, docs, examples + make node weights optional
* fix pep8 and examples
* improve docs + tests + thumbnail
* make example faster
* improve ex
* update README.md
* make GDL tests faster
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* add info in release file
* update tests
* pep8
* add weak OT example
* update plot in doc
* correction ewample with empirical sinkhorn
* better thumbnail
* comment from review
* update documenation
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* backend version barycenter
* new tests
* cleanup release file and doc
* f*ing pep8
* remove unused variable
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* [MRG] Implement Sinkhorn in log-domain for WDA
* for small values of the regularization parameter (reg) the current implementation runs into numerical issues (nans and infs)
* this can be resolved by using log-domain implementation of the sinkhorn algorithm
* Add feature to RELEASES and contributor name
* Add 'sinkhorn_method' parameter to WDA
* use the standard Sinkhorn solver by default (faster)
* use log-domain Sinkhorn if asked by the user
Co-authored-by: Jakub Zadrożny <jz@qed.ai>
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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PyTorch) (#338)
* Not instantiating `ValFunction`
`ValFunction` should not be instantiated since `autograd` functions are
supposed to only ever use static methods. This solves a warning message
raised by PyTorch.
* Updated release information
* Fixed PR number
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* change version and add minigallery in quickstart guide
* remove ot.gpu from documentation because it is deprecated and bacckends should be used
* start 0.8.2dev and description in releases.md
* typo for gallery sinkhorn2
* test better doc update for files in .githib folder
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* update ersion and change doc build
* update release file
* debug release of doc
* set version number to 0.8.1.0
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* update delease file and add it to doc ith mystè_parser
* typos in release file
* update PR template
* test debug doc build
* test debug doc build
* wrog circleci
* set proper version number
* add numpy 1.20 constraint
* remove python 3.6 deprecated in december
* add python 3.10
* debug pip on windows
* proper yml
* remoe 3.10 becauqe of troch
* next try
* try distutils
* back
* try something
* new stuf
* debug yaml
* test back to old vriso f numpy
* try something
* windows is worksing?
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* update delease file and add it to doc ith mystè_parser
* typos in release file
* update PR template
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* First batch of tf methods (to be continued)
* Second batch of method (yet to debug)
* tensorflow for cpu
* add tf requirement
* pep8 + bug
* small changes
* attempt to solve pymanopt bug with tf2
* attempt #2
* attempt #3
* attempt 4
* docstring
* correct pep8 violation introduced in merge conflicts resolution
* attempt 5
* attempt 6
* just a random try
* Revert "just a random try"
This reverts commit 8223e768bfe33635549fb66cca2267514a60ebbf.
* GPU tests for tensorflow
* pep8
* attempt to solve issue with m2r2
* Remove transpose backend method
* first draft of benchmarker (need to correct time measurement)
* prettier bench table
* Bitsize and prettier device methods
* prettified table bench
* Bug corrected (results were mixed up in the final table)
* Better perf counter (for GPU support)
* pep8
* EMD bench
* solve bug if no GPU available
* pep8
* warning about tensorflow numpy api being required in the backend.py docstring
* Bug solve in backend docstring
* not covering code which requires a GPU
* Tensorflow gradients manipulation tested
* Number of warmup runs is now customizable
* typo
* Remove some warnings while building docs
* Change prettier_device to device_type in backend
* Correct JAX mistakes preventing to see the CPU if a GPU is present
* Attempt to solve JAX bug in case no GPU is found
* Reworked benchmarks order and results storage & clear GPU after usage by benchmark
* Add bench to backend docstring
* better benchs
* remove useless stuff
* Better device_type
* Now using MYST_PARSER and solving links issue in the README.md / online docs
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* Fix issue 317
* Update with docs and tests
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Cupy backend
* pep8 + bug
* working even if cupy not installed
* attempt to force codecov to ignore cupy because no gpu can be used for testing on github
* docstring
* readme
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* Now limiting alpha to a minimum value as well as a max value
* Docs
* typo
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* solve bug
* Linesearch no longer return None as alpha, only 0
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* orrect gradient bug in emd2
* small comment in test
* deploy properly on tag release
* subplot fail
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* solve bug
* Weights & docs
* tests for dist
* test dist
* pep8
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* working on release
* test circleci
* try again
* cleanup circle ci run
* add all PR and releant Issues
* update doc
* thanks idris
* update version + add pyproject.toml
* test pyproject.toml
* revert tests
* build wheels
* use windows-latest for tests
* add tests python 3.10
* build all whels
* all versions
* build all wheels
* build all wheels
* cleanup pep8 and minimal acions
* forst shot text release
* bettr text
* stuff
* release text updated
* update manifest to allow build from source
* update doc again
* update release
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* First draft : making pytest use gpu for torch testing
* bug solve
* Revert "bug solve"
This reverts commit 29b013abd162f8693128f26d8129186b79923609.
* Revert "First draft : making pytest use gpu for torch testing"
This reverts commit 2778175bcc338016c704efa4187d132fe5162e3a.
* sliced
* sliced
* ot 1dsolver
* bregman
* better print
* jax works with sinkhorn, sinkhorn_log and sinkhornn_stabilized, no need to skip them
* gromov & entropic gromov
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wasserstein1d (#304)
* new test gpu
* pep 8 of couse
* debug torch
* jax with gpu
* device put
* device put
* it works
* emd1d and emd2_1d working
* emd_1d and emd2_1d done
* cleanup
* of course
* should work on gpu now
* tests done+ pep8
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* grmov differentable
* new stuff
* test gromov gradients
* fgwdifferentiable
* fgw tested
* correc name test
* add awesome example with gromov optimizatrion
* pep8+ typos
* damn pep8
* thunbnail
* remove prints
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* bregman docs
* sliced docs
* docs partial
* unbalanced docs
* stochastic docs
* plot docs
* datasets docs
* utils docs
* dr docs
* dr docs corrected
* smooth docs
* docs da
* pep8
* docs gromov
* more space after min and argmin
* docs lp
* bregman docs
* bregman docs mistake corrected
* pep8
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* add debiased sinkhorn barycenter + make loops pythonic
* add debiased arg in tests
* add 1d and 2d examples of debiased barycenters
* fix doctest
* fix flake8
* pep8 + make func private + add convergence warnings
* remove rel paths + add rng + pylab to pyplot
* fix stopping criterion debiased
* pass alex
* change params with new API
* add logdomain barycenters + separate debiased API
* test new API
* fix jax read-only ?
* raise error for jax
* test catch jax error
* fix pytest catch error
* fix relative path
* fix flake8
* add warn arg everywhere
* fix ref number
* catch warnings in tests
* add contrib to readme + change ref number
* fix convolution example + gallery thumbnails
* increase coverage
* fix flake
Co-authored-by: Hicham Janati <hicham.janati@inria.fr>
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
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* add numpy and torch backends
* stat sets on functions
* proper import
* install recent torch on windows
* install recent torch on windows
* now testing all functions in backedn
* add jax backedn
* clenaup windowds
* proper convert for jax backedn
* pep8
* try again windows tests
* test jax conversion
* try proper widows tests
* emd fuction ses backedn
* better test partial OT
* proper tests to_numpy and teplate Backend
* pep8
* pep8 x2
* feaking sinkhorn works with torch
* sinkhorn2 compatible
* working ot.emd2
* important detach
* it should work
* jax autodiff emd
* pep8
* no tast same for jax
* new independat tests per backedn
* freaking pep8
* add tests for gradients
* deprecate ot.gpu
* worging dist function
* working dist
* dist done in backedn
* not in
* remove indexing
* change accuacy for jax
* first pull backend
* projection simplex
* projection simplex
* projection simplex
* projection simplex no ci
* projection simplex no ci
* projection simplex no ci
* pep8
* add backedn discusion to quickstart guide
* projection simplex no ci
* projection simplex no ci
* projection simplex no ci
* pep8 + better doc
* proper links
* corect doctest
* big debug documentation
* doctest again
* doctest again bis
* doctest again ter (last one or i kill myself)
* backend test + doc proj simplex
* correction test_utils
* correction test_utils
* correction cumsum
* correction flip
* correction flip v2
* more debug
* more debug
* more debug + pep8
* pep8
* argh
* proj_simplex
* backedn works for sort
* proj simplex
* jax sucks
* update doc
* Update test/test_utils.py
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update docs/source/quickstart.rst
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update docs/source/quickstart.rst
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update docs/source/quickstart.rst
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update docs/source/readme.rst
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update test/test_utils.py
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update ot/utils.py
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update docs/source/readme.rst
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* Update ot/lp/__init__.py
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
* begin comment alex
* comment alex part 2
* optimize test gromov
* proj_simplex on vectors
* add awesome gradient decsnt example on the weights
* pep98 of course
* proof read example by alex
* pep8 again
* encoding oos in translation
* correct legend
* new backend functions for sliced
* small indent pb
* Optimized backendversion of sliced W
* error in sliced W
* after master merge
* error sliced
* error sliced
* pep8
* test_sliced pep8
* doctest + precision for sliced
* doctest
* type win test_backend gather
* type win test_backend gather
* Update sliced.py
change argument of padding pad_width
* Update backend.py
update redefinition
* Update backend.py
pep8
* Update backend.py
pep 8 again....
* pep8
* build docs
* emd2_1D example
* refectoring emd_1d and variants
* remove unused previous wasserstein_1d
* pep8
* upate example
* move stuff
* tesys should work + implemù random backend
* test random generayor functions
* correction
* better random generation
* update sliced
* update sliced
* proper tests sliced
* max sliced
* chae file nam
* add stuff
* example sliced flow and barycenter
* correct typo + update readme
* exemple sliced flow done
* pep8
* solver1d works
* pep8
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
Co-authored-by: Alexandre Gramfort <alexandre.gramfort@m4x.org>
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* bregman: small correction
* gromov backend first draft
* Removing decorators
* Reworked casting method
* Bug solve
* Removing casting
* Bug solve
* toarray renamed todense ; expand_dims removed
* Warning (jax not supporting sparse matrix) moved
* Mistake corrected
* test backend
* Sparsity test for older versions of pytorch
* Trying pytorch/1.10
* Attempt to correct torch sparse bug
* Backend version of gromov tests
* Random state introduced for remaining gromov functions
* review changes
* code coverage
* Docs (first draft, to be continued)
* Gromov docs
* Prettified docs
* mistake corrected in the docs
* little change
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* edit dr.py
* Correct normalization + optional parameter
* pep8?
* final!
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* adda sinkhorn log and working sinkhorn2 function
* more tests pass
* more tests pass
* it works but not by default yet
* remove warningd
* update circleci doc
* update circleci doc
* new sinkhorn implemeted but not by default
* better
* doctest pass
* test doctest
* new test utils
* remove pep8 errors
* remove pep8 errors
* doc new implementtaion with log
* test sinkhorn 2
* doc for log implementation
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* Backend for optim
* Bug solve
* Doc update
* backend tests now with fixture
* Unused imports removed
* Docs
* Docs
* Docs
* Outer product backend docs
* Prettier docs
* Pep8
* Mistakes corrected
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Bregman
* Resolve conflicts
* Bug solve
* Bregman updated for JAX compatibility
* Tests coherence between backend improved
* No longer enforcing 64 bits operations on Jax except for tests
* Now using mixtures, to make backend dependent tests with less code
* Better test skipping code
* Pep8 + test optimizations
* redundancy removed
* Docs
* Typo corrected
* Typo
* Typo
* Docs
* Docs
* pep8
* Backend docs
* Prettier docs
* Mistake corrected
* small changes
* Better wording
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* add reg path
* debug examples and verify pep8
* pep8 and move the reg path examples in unbalanced folder
Co-authored-by: haoran010 <haoran.wu@insa-rennes.fr>
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* gpus tests now passing
* pep8 compliance
* GPU tests succeeding even if b has rank higher than 1
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Added : OpenMP support
Restored : Epsilon and Debug mode
Replaced : parmap => multiprocessing is now replace by multithreading
* Commit clean up
* Number of CPUs correctly calculated on SLURM clusters
* Corrected number of processes for cluster slurm
* Mistake corrected
* parmap is now deprecated
* Now a different solver is used depending on the requested number of threads
* Tiny mistake corrected
* Folders are now in the ot library instead of at the root
* Helpers is now correctly placed
* Attempt to make compilation work smoothly
* OS compatible path
* NumThreads now defaults to 1
* Better flags
* Mistake corrected in case of OpenMP unavailability
* Revert OpenMP flags modification, which do not compile on Windows
* Test helper functions
* Helpers comments
* Documentation update
* File title corrected
* Warning no longer using print
* Last attempt for macos compilation
* pls work
* atempt
* solving a type error
* TypeError OpenMP
* Compilation finally working on Windows
* Bug solve, number of threads now correctly selected
* 64 bits solver to avoid overflows for bigger problems
* 64 bits EMD corrected
Co-authored-by: kguerda-idris <ssos023@jean-zay3.idris.fr>
Co-authored-by: ncassereau-idris <84033440+ncassereau-idris@users.noreply.github.com>
Co-authored-by: ncassereau <nathan.cassereau@idris.fr>
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* Line search stops when derphi is 0 instead of bugging out like in some instances
* pep8 compliance
* Tests
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* Add two new algorithms to solve Gromov Wasserstein: Sampled Gromov Wasserstein and Pointwise Gromov Wasserstein.
* Correct some lines in SaGroW and PoGroW to follow pep8 guide.
* Change nb_samples name. Use rdm state. Change symmetric check.
* Change names of len(p) and len(q) in SaGroW and PoGroW.
* Re-add some deleted lines in the comments of gromov.py
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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* ot.dr: PRW code; text.text_dr: PRW test code.
* ot.dr: PRW code; test.test_dr: PRW test code.
* fix errors: pep8(3.8)
* fix errors: pep8(3.8)
* modified readme; prw code review
* fix pep error
* edit comment
* modified math comment
Co-authored-by: Rémi Flamary <remi.flamary@gmail.com>
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