adapt callbacks and rename tag cost to cost_matrix
#426
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Additional details and impacted files@@ Coverage Diff @@
## main #426 +/- ##
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- Coverage 78.08% 77.76% -0.33%
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Files 39 39
Lines 3382 3413 +31
Branches 547 557 +10
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+ Hits 2641 2654 +13
- Misses 506 523 +17
- Partials 235 236 +1
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MUCDK
changed the title
cost to cost_matrixcost to cost_matrix
michalk8
requested changes
Dec 8, 2022
michalk8
requested changes
Dec 9, 2022
MUCDK
added a commit
that referenced
this pull request
Jun 22, 2023
* rename tag cost to cost_matrix * fix renaming * [CI skip], adapt callback * incorporate requested changes * add test for quad custom callback * adapt kwargs for callback * fix handle_joint_attr * incorporate requested changes
MUCDK
added a commit
that referenced
this pull request
Aug 21, 2024
* fix jaxsampler * fix jaxsampler * fix jaxsampler * fix tests * add plot_convergence * remove jit from _compute_unbalanced marginals * fix sinkhorn_divergence * adapt tox.ini file * shape mismatch fixed without precommit * remove print statement * finish merge * adapt callbacks and rename tag `cost` to `cost_matrix` (#426) * rename tag cost to cost_matrix * fix renaming * [CI skip], adapt callback * incorporate requested changes * add test for quad custom callback * adapt kwargs for callback * fix handle_joint_attr * incorporate requested changes * Feature/correlation test (#423) * fix test in FGWProblem * add correlation test * add first test for correlation computation * add more tests * fix tests * add tfs to compute_feature_correlation * add testing for no nans in compute_feature_correlation * incorporate requested changes * fix docstring * fix sankey return statement (#428) * fix sankey return statement * adapt test * adapt return_fig * Bump version: 0.1.0 → 0.1.1 * fix return statements * add save tests * fix return type in mpl (#432) * fix return type in mpl * change import acronyms * fix tests * Simplify linear operator (#431) * Simplify linear operator * Simplify `align`, fix test * Explicitly jit the solvers (#433) * Feature/interpolate colors sankey (#434) * fix return type in mpl * change import acronyms * fix tests * add interpolation option to sankey * add test to interpolate color * define colors for pull/push` * adapt tests * introduce axes in mpl.push/pull * incorporate requested changes * change default color * adapt plotting * introduce scaling * fix scale * make start/end categorical in plot * regenerate images * Remove `FGWSolver` (#437) * Remove `FGWSolver` * Fix `tox.ini` * Fix wrong shape check * Use pure GW in generic solver * Update tests * fix bug in SinkhornProblem (#442) * fix bug in SinkhornProblem * fix tox.ini * fix pre commits * make push/pull always use source/target (#443) * make push/pull always use source/target * fix bug in StarPolicy _apply * adapt plotting to source/target * fix strip plotting in sankey (#445) * fix strip plotting in sankey * simplify code * Feature/spearman correlation (#444) * add spearman correlation * add tests * adapt tests * Delete logo.png * Feature/plot order (#453) * make push/pull plot in good order * [CI skip], try setting adata.uns color explicitly * [CI skip], fix copying of adata * fix pre commits * fix bug * Expose marginal kwargs for `moscot.temporal` and check for numeric type of `temporal_key` (#449) * make marginal_kwargs explicit in temporal problems * introduce check for numeric dtype in temporal mixin * add alternative way for marginal prior * adapt tolerances in tests * correct docs * fix bug * Fix math rendering * fix test Co-authored-by: Michal Klein <46717574+michalk8@users.noreply.github.com> * adapt plot_convergence (#454) * Bug/docs generic analysis mixin (#455) * adapt plot_convergence * remove temporal-alluding docs in generic analysis mixin * Docs/improvements (#456) * adapt plot_convergence * remove temporal-alluding docs in generic analysis mixin * docs suggestions * remove uns_key from set_plotting_vars (#458) * resolve `fig referenced before assignment` (#460) * move generic mixins tests to problems` (#461) * Tests/spatiotemporalproblem (#464) * add more tests for spatiotemporalProblem * move some functions from TemporalProblem to TemporalMixin * add tests LineageProblem * fix tests * Feature/move taggedarray (#457) * adapt plot_convergence * remove temporal-alluding docs in generic analysis mixin * docs suggestions * move tagged array * move taggedarray back to solvers * add marginal_kwargs to prepare method of TemporalNeuralProblem * fix to scaling in * Revert "fix to scaling in" This reverts commit 0a6f7db. * fix to scaling argument in marginal_kwargs * updated conditional not pipeline * merge into condot branch * incoporated comments * incoporated comments * incoporated comments * removed new_adata for push/pull * [ci skip] start docs * added temporal neural test * [ci skip] continue docs * continue docs * continue docs * change validation epsilon * fixed error when not computing wasserstein baseline * fixed error when not computing wasserstein baseline * correct typo * fix bug * added neural tests * [ci skip] draft CondNeuralOutput * include CondDualPotentials and CondDualSolver * fixes to main merge * fix test_cell_transition_subset_pipeline * fix tests * update conditionalDualPotentials * update conditionalDualPotentials * fix most pre-commit hooks and fix tests * fix pandas version to <2.0 * fix tests for non-conditional solvers * continue * fix * continue fixing * fix ICNN setup * fix tests * swap role of f and g, such that push/pull is correct again * [ci skip] restructure to include more general neural solvers * [ci skip] restructure ICNNs to allow passing instances of ICNN * adapt tests * Filled in Monge Gap structure * Added Monge Gap paper to documentation * Ammend PointCloud Import * Update _utils.py Ammend PointCloud import * Solve compatibility issue with ProblemKind * Solve missing Import * Fix call to deprecated function * Fix style and comment issues * add callback, swap f & g * add callback, swap f & g * add callback, swap f & g * intermediate save * intermediate save * intermediate save * [ci skip] fix merge conflicts * resolve conflict * remove pairwise policy * add neural dependencies * add neural dependencies * add flax * fix _call_kwargs * fix marginal kwargs * remove monge gap solver * clean condneuralsolver * [ci skip] introduce new data container for joint neural problems * add conditions in distirbutioncontainer * resolve unfreeze/freeze * enable pretraining and weight clipping * make dicts compatible with older python versions * resolve precommit errors partially * resolve precommit errors partially * adapt tests * [ci skip] draft unbalancedNeuralMixin * [ci skip] fix naming of posterior marginals * [ci skip] add MLP_marginals * adapt neural output to incorporate learnt rescaling functions * fix _solve in neuraldualsolver * incorporate feedback * fix distributioncollection class * unify _split_data * fix tests * fix some precommit hooks * make neural dependencies optional * make neural dependencies optional * delete old files * adapt pyproject.toml * adapt pyproject.toml * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [ci skip] adjust _format_params * adapt neuraldualsolver to be more similar to ott-jax * adapt neuraldualsolver * TODO: make JaxSampler return conditions * add basic neural test * [ci skip] intermediate save * adapt neuraldualsolver and finish tests for neural backend * [ci skip] TODO: re-iterate on initialisation of neural solver * adapt distributioncontainer * fix dict bug * resolve passing of arguments in solver call methods * [ci skip] adapt `solve` in `CondOTProblem` * adapt tests and valid loader conditions * adapt neural backend tests * fix mypy errors * make basesolveroutput to basediscretesolveroutput * move `to` to BaseSolverOutput` " * adapt transport_matrix docs * adapt transport_matrix docs * adapt tests * adapt tests * update unbalancedness mixin * use implementation from moscot * uncomment unused code * before passing states to loss-fn * intermediate save * adapt neuraldualsolver * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * resolve some / not all pre commit errors * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * (wip): tests run, code swapped out for now * (wip): `NeuralSolver`s implemented minus quad/linear * (wip): begin more generic problem * (wip): more refactoring to pass arguments to GENOT * (chore): remove more kantorovich * (chore): update branch to moscot neural + first test moving to solving * (fix): split data remains in numpy * (fix): push/pull api * (fix): make push test work * (feat): allow for custom optimziers * (chore): remove unclear test * (refactor): change to composition API * (refactor): start towards model-specific problems * (chore): clean up all unnecessary classes * (chore): updating to moscot latest * Merge branch 'main' into ig/neural_solvers * (chore): remove (hopefully) final ICNN vestiges * (chore): more cleanup * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * (fix): pass pre-commit hooks * (chore): remove duplicatec docs * (chore): add torch for testing * (fix): add ott jax branch as dep * (fix): repo name * (chore): remove unbalanced, update api, fix tests + drive by typing fix * (feat): first pass at neural mixin * (chore): add my name to todos * (fix): conditions left out if not necessary * (feat): logs and fix conditional attr * (fix): add `seed` to call_kwargs so reproducibility works * (chore): remove `is_conditional` business * (fix): create hidden dims arg for velocity field * (chore): raise not implemented error for `pull` * (fix): default args * (fix): add explicit policy * (fix): allow iteration to continue * (chore): add star policy to GENOT * (chore): notebooks * (chore): remove deps * (chore): remove unnecessary spaces * (chore): simplify quad handling * (fix): need to require `optax`/`flax` * (fix): use `ott-jax[neural]` * (chore): fix docs * (fix): small test fixes * (chore): small notebook changes * (fix): broken link in citation * (chore): make notebook dependent on ci * (fix): small todos just to push something * (fix): variable is a string * (fix): pass environment variable to tox * (fix): actually pass through * (fix): hidden dims ci * (fix): re-add notebook * (chore): make`recall_target` and `aggregate_to_topk` * (chore): fix default arguments * (chore): `project_transport_matrix` -> `project_to_transport_matrix` * (fix): remove dead `NeuralAnalysisMixin` code * (feat): allow custom `data_match_fn` * (fix): inherit from `MutableMapping` instead of `dict` * (Fix): docs * (fix): notebooks * (fix): docs reference * (fix): remove `attr` * (fix): erroneous change * (fix): remove empty * (fix): notebooks again? * (chore): ok? --------- Co-authored-by: Dominik Klein <dominik.klein@helmholtz-munich.de> Co-authored-by: Dominik Klein <domin.klein@gmail.com> Co-authored-by: AlejandroTL <alejandrotejada10@gmail.com> Co-authored-by: michalk8 <46717574+michalk8@users.noreply.github.com> Co-authored-by: lucaeyring <luca.eyring@googlemail.com> Co-authored-by: gocato <104785310+gocato@users.noreply.github.com> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
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