Feature/tmap kernel connectivities #828
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Codecov Report
@@ Coverage Diff @@
## dev #828 +/- ##
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- Coverage 82.43% 81.00% -1.43%
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Files 67 70 +3
Lines 9136 9280 +144
Branches 1850 1876 +26
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- Hits 7531 7517 -14
- Misses 1030 1189 +159
+ Partials 575 574 -1
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What's missing to merge this? |
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It just adds functionality but doesn't take anything away, right? You can still add global connectivities by adding a connectivity kernel. |
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* Fix/wot pickle (#748) * Fix WOTKernel saving OTModel * [ci skip] Polish docs * [auto][ci skip] Generate news fragment (#748) * Fix term/macro states dtype mixture (#750) * Fix states association having mixture dtypes * Fix stat dist * Install Cython in CI * Add numpy to tox.ini 3.9 * Do not install WOT on 3.9 * Install Cython external * Fix importorskip * Don't install statOT on 3.9 CI * [auto][ci skip] Generate news fragment (#750) * Feature/update tmat kernel (#764) * First TmatKernel update * Add QoL changes to TransportMapKernel * Refactor transport map kernel * [auto][ci skip] Generate news fragment (#764) * Update CytoTRACE calcultation (#761) * Update CytoTRACE calcultation * [ci skip] Remove NaN check * Check whether top correlated genes have NaNs * [ci skip] Update docstring * [auto][ci skip] Generate news fragment (#761) * CI cron on dev (#769) * Add Edit on GitHub (#775) * Add Edit on GitHub * [ci skip] Fix README.rst GPCCA link * Expose ascending when plotting gene correlations (#779) * [auto][ci skip] Generate news fragment (#779) * Fix exp. time kernel colors (#784) * Fix exp. time kernel colors * Update news workflow * [auto][ci skip] Generate news fragment (#784) * [auto][ci skip] Update dev release notes (#784) * Fix pyGAM deprecation warnings (#798) * [auto][ci skip] Generate news fragment (#798) * [auto][ci skip] Update dev release notes (#798) * Update PAGA message in cluster_fates (#799) * Update PAGA message in cluster_fates * Fix wrong import * [auto][ci skip] Update dev release notes (#799) * Fix bad pandas version * Add order option in GPCCA.plot_coarse_T (#804) * Add order option in GPCCA.plot_coarse_T * Remove outgoing order for coarse T * Add test * [auto][ci skip] Update dev release notes (#804) * Feature/refactor kernels (#791) * Add tmap_as_tmat ctx manager * Add Edit on GitHub * [ci skip] Fix README.rst GPCCA link * Decouple CTPT from __init__ * Add negative corr to CytoTRACE * Alpha version of kernel refactorings * Add ConnectivityKernel * Start refactoring VelocityKernel * Fix typos * Finish DisplacementKernel * Switch to new impl. * Dont copy expression when combining them * Remove old impl. * Fix typo in deterministic model * Fix VK backward case * Refactor RW plotting * Refactor compute_projection -> plot_projection * Start clean-up * Fix transport kernel TODOs * Fix pseudotime kernel TODOs * Refactor precomputed kernel * Add _copy_ignore * Update external kernels * Update str/repr * Fix combining * Change cache handler * Fix getitem, update tmat setter * Update precomputed kernel, add tmat decorator * Fix superfluous dedent * First round of test fixes * Second round of test fixing * Fix projection tests * Fix VelocityKernel tests * Fix TransportMapKernel * Fix minor tests * Update PrecomputedKernel, fix more tests * Fix a few more tests * Fix WOT + thresholding again * Fix GPCCA tests * Fix absorption probabilities when array is dense * Clean the function a bit * Fix tools tests * Fix estimator precomputed kernel * Fix RandomWalk tests * Fix rest of the tests * Update manuscript links, bump pyGPCCA>=1.0.3 * Update bibtex * [auto][ci skip] Generate v1.5.1 release notes * [auto][ci skip] Release v1.5.1 * Change verbosity level * Remove neg. correlated genes in CytoTRACE * [ci skip] Add unnormalized transition matrix in VK * [ci skip] Update PrecomputedKernel docs * [ci skip] Finish updating docstrings * [ci skip] Fix transport maps not being set * [ci skip] Add missing docstrings, fix a few typos * Fix PrecomputedKernel and add tests * Fix external, add more tests * Add copy_ignore test * Fix PrecomputedKernel behavior, update estim docs * [ci skip] Fix typo * Fix docs * Fix n_cells in fit, examples and update docstring * Fix typo in kernel tests * Regenerate figures Co-authored-by: michalk8 <michalk8@users.noreply.github.com> * [auto][ci skip] Generate news fragment (#791) * [auto][ci skip] Update dev release notes (#791) * Fix/correlation qval nan (#835) * Fix qvalue calculation resulting in all NaN values * Add test, set to NaN if any corr not in [-1, 1] * [auto][ci skip] Generate news fragment (#835) * [auto][ci skip] Update dev release notes (#835) * Fix None subset in VelocityKernel * Change order to ascending when plotting macros (#839) * Change order to ascending when plotting macros * Add outgoing order of plotting coarse T * [auto][ci skip] Update dev release notes (#839) * Feature/tmap kernel connectivities (#828) * Add initial diag conn implementation * Expose conn_weight * Update docs, fix minor issues * Fix typo in import, add test, update docs * Fix type * Threshold before added diagonal connectivities * Fix minor dtype bug and typo, fix tests * [auto][ci skip] Generate news fragment (#828) * [auto][ci skip] Update dev release notes (#828) * Do not save Enums in AnnData (#842) * [auto][ci skip] Generate news fragment (#842) * [auto][ci skip] Update dev release notes (#842) * Misc/nested anndata (#841) * Don't save nested AnnData * Fix reading from AnnData * Misc/remove dev (#843) * Remove references to dev * Update pre-commit * Fix badges * Temporarily pin AnnData from above
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Description
Allow local block-diagonal connectivities in :class:
cellrank.tl.kernels.TransportMapKernel. Renamelast_time_pointargument toself_transitionsand addconn_weight.self_transitionscan also be applied to specific diagonal blocks only.How has this been tested?
Add new test for this.
Closes
closes #827