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Feature/better io callbacks #413

Merged
merged 11 commits into from
Aug 17, 2023
Merged

Feature/better io callbacks #413

merged 11 commits into from
Aug 17, 2023

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michalk8
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closes #405

@michalk8 michalk8 added the enhancement New feature or request label Aug 17, 2023
@michalk8 michalk8 requested a review from marcocuturi August 17, 2023 12:36
@michalk8 michalk8 self-assigned this Aug 17, 2023
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@michalk8
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michalk8 commented Aug 17, 2023 •
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Seems like we will need to bump jax>=0.4 in order to make this work, which will break the GPU tests (the CUDA/cuDNN versions are too low).

marcocuturi
marcocuturi reviewed Aug 17, 2023
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Thanks Michal! This LGTM. Not sure how to deal with the GPU issues, maybe transfer them on another machine...

@michalk8
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Thanks Michal! This LGTM. Not sure how to deal with the GPU issues, maybe transfer them on another machine...

I will for now skip the progress_fn tests to require jax>=0.4, but we should soon use jax>=0.4 anyways.

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codecov bot commented Aug 17, 2023 •
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Codecov Report

Merging #413 (70f6148) into main (12e78a7) will decrease coverage by 0.01%.
The diff coverage is 90.90%.

❗ Current head 70f6148 differs from pull request most recent head 6a15e23. Consider uploading reports for the commit 6a15e23 to get more accurate results

Additional details and impacted files

Impacted file tree graph

@@            Coverage Diff             @@
##             main     #413      +/-   ##
==========================================
- Coverage   91.44%   91.44%   -0.01%     
==========================================
  Files          54       54              
  Lines        5902     5925      +23     
  Branches      860      861       +1     
==========================================
+ Hits         5397     5418      +21     
- Misses        370      372       +2     
  Partials      135      135
Files Changed Coverage Δ
src/ott/solvers/quadratic/gromov_wasserstein.py 87.50% <50.00%> (ø)
src/ott/utils.py 90.62% <92.59%> (+0.38%) ⬆️
src/ott/solvers/linear/sinkhorn.py 97.53% <100.00%> (ø)
src/ott/solvers/linear/sinkhorn_lr.py 98.37% <100.00%> (ø)

... and 2 files with indirect coverage changes

@michalk8 michalk8 merged commit d44fadc into ott-jax:main Aug 17, 2023
@michalk8 michalk8 deleted the feature/better-io-callbacks branch August 17, 2023 19:18
marcocuturi added a commit that referenced this pull request Aug 20, 2023
@marcocuturi @michalk8
merge (#414)
40f9063 
* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

---------

Co-authored-by: michalk8 <[email protected]>
marcocuturi added a commit that referenced this pull request Sep 8, 2023
@marcocuturi @michalk8
merge (#430)
0145c8f 
* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

* Update pre-commits (#416)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Feature/move solve (#418)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Move `ott.solvers.linear.sinkhorn.solve` to `linear`

* Fix typo

* Nicer docs for Sinkhorn output

* Fix math

* [ci skip] Update docs

* Feature/lineax ridge (#424)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Add `ridge` options to `lineax`

* Modify test for `lineax` ridge

* Fix linkchecker

---------

Co-authored-by: michalk8 <[email protected]>
marcocuturi added a commit that referenced this pull request Sep 11, 2023
@marcocuturi @michalk8
Re-run and refactoring of some docs/tutorials + minor changes (#431)
9efa5ff 
* docs

* mongegap

* mg

* mg

* more details in monge gap

* merge (#414)

* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

---------

Co-authored-by: michalk8 <[email protected]>

* precom

* merge (#430)

* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

* Update pre-commits (#416)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Feature/move solve (#418)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Move `ott.solvers.linear.sinkhorn.solve` to `linear`

* Fix typo

* Nicer docs for Sinkhorn output

* Fix math

* [ci skip] Update docs

* Feature/lineax ridge (#424)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Add `ridge` options to `lineax`

* Modify test for `lineax` ridge

* Fix linkchecker

---------

Co-authored-by: michalk8 <[email protected]>

* n_iters more precise

* clarify epsilon param in sinkhorn

* epsilon doc

* ott pot

* ott - pot

* add small comment

* fix check trees in test

* fitting / regularizer losses must return log

* spell

* improve coverage

* fix threshold of total mass

* again

---------

Co-authored-by: michalk8 <[email protected]>
michalk8 added a commit that referenced this pull request Jun 27, 2024
@michalk8
Feature/better io callbacks (#413)
2f453df 
* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test
michalk8 added a commit that referenced this pull request Jun 27, 2024
@marcocuturi @michalk8
Re-run and refactoring of some docs/tutorials + minor changes (#431)
c866b08 
* docs

* mongegap

* mg

* mg

* more details in monge gap

* merge (#414)

* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

---------

Co-authored-by: michalk8 <[email protected]>

* precom

* merge (#430)

* Feature/better io callbacks (#413)

* Add `tqdm` callback

* Polish docs, add examples

* Fix LRSink and GW

* Update notebook

* Update docstrings

* Update old tests

* More tests

* Add `tqdm` to testing requirements

* Skip progress fn tests on `jax<0.4`

* Fix last callback test

* Feature/optional dependencies (#412)

* Add `neural` extra requirements

* Add import wrappers for neural modules

* Update `tox`

* Fix linter

* Update docs

* Pin numpy from above, fix RTD

* Update pre-commits (#416)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Feature/move solve (#418)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Move `ott.solvers.linear.sinkhorn.solve` to `linear`

* Fix typo

* Nicer docs for Sinkhorn output

* Fix math

* [ci skip] Update docs

* Feature/lineax ridge (#424)

* Update pre-commits

* Dedent `tox` in `pyproject.toml`

* Temporarily indent again

* Run linters

* Update for `tox>=4.9.0`

* Add `ridge` options to `lineax`

* Modify test for `lineax` ridge

* Fix linkchecker

---------

Co-authored-by: michalk8 <[email protected]>

* n_iters more precise

* clarify epsilon param in sinkhorn

* epsilon doc

* ott pot

* ott - pot

* add small comment

* fix check trees in test

* fitting / regularizer losses must return log

* spell

* improve coverage

* fix threshold of total mass

* again

---------

Co-authored-by: michalk8 <[email protected]>
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Improve progress callbacks
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@michalk8 @marcocuturi