Refactor: Handling Unrecognized Arguments for Prepare

[selmanozleyen]

These are the things I want to do first. related: #596

From reading through ottjax only the __call__ functions on solvers absorb kwargs that aren't recognized. And they are because either they are given to create_geometry methods or create_initializer methods:

• https://github.com/ott-jax/ott/blob/458e265a1282d417f87bc0e07a5b6b77ffe9ae50/src/ott/initializers/quadratic/initializers.py#L134-L155
• https://github.com/ott-jax/ott/blob/458e265a1282d417f87bc0e07a5b6b77ffe9ae50/src/ott/initializers/linear/initializers_lr.py#L232-L243

So this is kind of good news because from what I read from moscot, call_fn arguments are filtered before here: https://github.com/theislab/moscot/blob/e21677e6fbf1e5484b1c69a8ba55587dbf40f009/src/moscot/base/solver.py#L145-L164

Overall this means:

• We can fix theprepare methods absorbing kwargs ourselves in moscot, by simply removing the usage of kwargs in concrete classes, so I will dedicate this PR to it
• But for solve we will need to refactor things from ottjax. It won't be too hard and I already spotted where they are being ignored. If we refactor ottjax we might not need any changes in moscot since the error will be thrown from there.

Related issues (will be closed after merge):

• https://github.com/theislab/moscot/issues/698
• https://github.com/theislab/moscot/issues/699
• https://github.com/theislab/moscot/issues/700
• https://github.com/theislab/moscot/issues/701

I separated some issues from this PR so that we can work on them later:

• https://github.com/theislab/moscot/issues/716 : I did this one because when inheriting docstring GW removed the arguments for linear, and this lead to duplicate docstrings
• https://github.com/theislab/moscot/issues/715 : Because although in terms of software, current PR makes sense, there might be some cases where a parent classes argument is ignored/fixed but is not yet discovered. I am not confident about this as I am not completely familiar with the Biology use cases of all classes.
• https://github.com/theislab/moscot/issues/721

Now that the tests pass these are the things to do:

• [x] clean up code (most likely requires refactoring of handle_joint_attr)
• [x] update docstrings
• [x] clean the TODO's and ensure that everyone agrees on the new docs and docstrings
• [x] write tests to ensure it fails (not sure if tests are necessary at this point since the checks are static now, will probably figure out cases to test when working on https://github.com/theislab/moscot/issues/715)

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 85.81560% with 20 lines in your changes missing coverage. Please review.

Project coverage is 78.13%. Comparing base (3151da7) to head (7535065). Report is 46 commits behind head on main.

:exclamation: Current head 7535065 differs from pull request most recent head b11efac

Please upload reports for the commit b11efac to get more accurate results.

Additional details and impacted files

[](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) ```diff @@ Coverage Diff @@ ## main #696 +/- ## ========================================== - Coverage 78.19% 78.13% -0.06% ========================================== Files 36 36 Lines 3806 3865 +59 Branches 706 727 +21 ========================================== + Hits 2976 3020 +44 - Misses 524 530 +6 - Partials 306 315 +9 ``` | [Files](https://app.codecov.io/gh/theislab/moscot/pull/696?dropdown=coverage&src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab) | Coverage Δ | | |---|---|---| | [src/moscot/base/problems/birth\_death.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fbase%2Fproblems%2Fbirth_death.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9iYXNlL3Byb2JsZW1zL2JpcnRoX2RlYXRoLnB5) | `90.76% <100.00%> (+0.93%)` | :arrow_up: | | [src/moscot/base/problems/compound\_problem.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fbase%2Fproblems%2Fcompound_problem.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9iYXNlL3Byb2JsZW1zL2NvbXBvdW5kX3Byb2JsZW0ucHk=) | `75.67% <100.00%> (ø)` | | | [src/moscot/problems/cross\_modality/\_translation.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Fcross_modality%2F_translation.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9jcm9zc19tb2RhbGl0eS9fdHJhbnNsYXRpb24ucHk=) | `96.07% <100.00%> (-0.08%)` | :arrow_down: | | [src/moscot/problems/generic/\_generic.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Fgeneric%2F_generic.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9nZW5lcmljL19nZW5lcmljLnB5) | `93.44% <100.00%> (-3.17%)` | :arrow_down: | | [...moscot/problems/spatiotemporal/\_spatio\_temporal.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Fspatiotemporal%2F_spatio_temporal.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9zcGF0aW90ZW1wb3JhbC9fc3BhdGlvX3RlbXBvcmFsLnB5) | `100.00% <100.00%> (ø)` | | | [src/moscot/problems/time/\_lineage.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Ftime%2F_lineage.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy90aW1lL19saW5lYWdlLnB5) | `96.15% <100.00%> (+0.32%)` | :arrow_up: | | [src/moscot/base/problems/problem.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fbase%2Fproblems%2Fproblem.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9iYXNlL3Byb2JsZW1zL3Byb2JsZW0ucHk=) | `77.80% <90.00%> (+0.30%)` | :arrow_up: | | [src/moscot/problems/space/\_mapping.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Fspace%2F_mapping.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9zcGFjZS9fbWFwcGluZy5weQ==) | `98.33% <87.50%> (-1.67%)` | :arrow_down: | | [src/moscot/problems/space/\_alignment.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2Fspace%2F_alignment.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9zcGFjZS9fYWxpZ25tZW50LnB5) | `83.33% <61.11%> (-16.67%)` | :arrow_down: | | [src/moscot/problems/\_utils.py](https://app.codecov.io/gh/theislab/moscot/pull/696?src=pr&el=tree&filepath=src%2Fmoscot%2Fproblems%2F_utils.py&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab#diff-c3JjL21vc2NvdC9wcm9ibGVtcy9fdXRpbHMucHk=) | `75.75% <80.35%> (+2.07%)` | :arrow_up: | ... and [1 file with indirect coverage changes](https://app.codecov.io/gh/theislab/moscot/pull/696/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=theislab)

[selmanozleyen]

@MUCDK the problem is even though 3.10 passes 3.9 now fails. The results change between these versions

[MUCDK]

Ok can we skip the test for python 3.9?

[selmanozleyen]

Sure will update the tests in a new PR then