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Misc/project structure #176

Merged
merged 35 commits into from
Nov 22, 2022
Merged

Misc/project structure #176

merged 35 commits into from
Nov 22, 2022

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michalk8
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@michalk8 michalk8 commented Nov 16, 2022 •
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TODOs:

  • deal with examples/
  • update docstrings to reflect the new structure
  • update notebook imports
  • update links in notebooks
  • update docs
  • update README.rst
  • update CONTRIBUTING.rst
  • fix UnbalancedBures

closes #168

@michalk8 michalk8 self-assigned this Nov 16, 2022
marcocuturi
marcocuturi reviewed Nov 16, 2022
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ott/geometry/costs.py

c(x,y) = norm(x) + norm(y) + pairwise(x,y)
c(x,y) = norm(x) + norm(y) + pairwise(x,y)
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I think this won't look good with maths

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Think it renders ok-ish, maybe we can just replace norm(x) with ||x||

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codecov-commenter commented Nov 21, 2022 •
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Codecov Report

Merging #176 (aea8912) into main (c9ff6fb) will decrease coverage by 2.08%.
The diff coverage is 84.89%.

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #176      +/-   ##
==========================================
- Coverage   84.21%   82.12%   -2.09%     
==========================================
  Files          51       51              
  Lines        5118     5187      +69     
  Branches      521      527       +6     
==========================================
- Hits         4310     4260      -50     
- Misses        657      781     +124     
+ Partials      151      146       -5
Impacted Files Coverage Δ
ott/math/unbalanced_functions.py 100.00% <ø> (ø)
ott/tools/gaussian_mixture/fit_gmm.py 74.07% <50.00%> (-0.32%) ⬇️
ott/tools/segment_sinkhorn.py 43.75% <60.00%> (ø)
ott/tools/sinkhorn_divergence.py 62.50% <60.00%> (+0.68%) ⬆️
ott/solvers/was_solver.py 90.90% <66.66%> (ø)
ott/tools/transport.py 83.11% <68.57%> (-12.72%) ⬇️
ott/problems/quadratic/gw_barycenter.py 28.82% <70.00%> (ø)
ott/types.py 70.00% <70.00%> (ø)
ott/problems/quadratic/quadratic_costs.py 70.83% <70.83%> (ø)
ott/problems/linear/potentials.py 81.00% <75.00%> (ø)
... and 40 more

@michalk8 michalk8 requested a review from marcocuturi November 22, 2022 14:14
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marcocuturi approved these changes Nov 22, 2022
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Thanks a lot for this macro PR Michal. I think we're ready for v.0.3.0!

@michalk8 michalk8 added documentation Improvements or additions to documentation enhancement New feature or request bugfix labels Nov 22, 2022
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Thanks a lot for this macro PR Michal. I think we're ready for v.0.3.0!

Thanks, will let the tests pass and merge. For v0.3.0, would still consider closing more issues, will create a milestone.

@michalk8 michalk8 merged commit 156ef2b into ott-jax:main Nov 22, 2022
@michalk8 michalk8 deleted the misc/project-structure branch November 22, 2022 17:38
michalk8 added a commit that referenced this pull request Jun 27, 2024
@michalk8
Misc/project structure (#176)
32962a1 
* Reorganize repo structure

* Update PC docs

* Update imports, fix some types

* Fix more types, pet-peeves

* Fix tests

* Update cost funcs and potentials

* Fix LR initializer

* Fix k-means initializer

* Move `utils`

* Update imports in notebooks

* Update geometry docs

* Update initializers

* Update math docs

* Update problem docstrings

* Update `solvers` docstrings

* Update `tools` docstrings

* Remove remaining `core` mentions from docstrings

* Start updating documentation

* Fix typing

* Update solvers docs

* Add initializers

* Update docs

* Fix MetaOT links

* Fix bibliography links

* Fix more links in the notebooks

* Follow line length in README.md

* Update `tests` structure

* Update badges

* Add TODOs, fix citation in `index.rst`, move `implicit_diff`

* Fix implicit_diff, TODOs in costs

* Use `jax.lax.cond` in `UnbalancedBures`

* Fix `UnbalancedBures`

* Update CI versions

* Fix UnbalancedBures's norm
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@marcocuturi marcocuturi marcocuturi approved these changes

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Restructuring the codebase
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