Misc/nested anndata #841
Merged
Misc/nested anndata #841
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
michalk8
added
misc
Codecov Report
@@ Coverage Diff @@
## dev #841 +/- ##
==========================================
- Coverage 80.95% 80.95% -0.01%
==========================================
Files 70 70
Lines 9285 9284 -1
Branches 1878 1878
==========================================
- Hits 7517 7516 -1
Misses 1192 1192
Partials 576 576
|
Closed
michalk8
added a commit
that referenced
this pull request
Mar 21, 2022
* 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
michalk8
added a commit
that referenced
this pull request
Apr 21, 2022
* Add IOspec for Lineage class * Revert #841 * Fix IOSpec version to 0.2.0, remove reader
michalk8
added a commit
that referenced
this pull request
Apr 28, 2022
* Add IOspec for Lineage class * Revert #841 * Fix IOSpec version to 0.2.0, remove reader * Remove LIN enum * Remove " or " joining in Lineage * Fix typo: ... or True * Reorder methods, add few comments * Add `copy=False` to `Lineage.from_adata` * Update circular projection * Update cluster_fates * Fix typo * Update cluster_lineage * Update gene_trends * Update heatmap * Update log_odds * Update BaseModel.prepare * Fix heatmap * Fix heatmap v2 * [ci skip] Add test
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
IMPORTANT: Please search among the Pull requests before creating one.
Description
Do not save nested :class:
anndata.AnnData.How has this been tested?
N/A
Closes
closes #797