Release/v1.9.301 #131
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Release/v1.9.301 #131
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* Use mito as bool not changing to category * Trials scanpy 1.9.1 for the mnn - numba issue. * Fix 1.9.1 hgv not finding base on log1p * Please black * Try log fix regardless of option * Check direct installation * Set base explicitly to avoid it being dropped * Please black * Add igrahp and reinstate leidenalg * Also louvain is needed * Pin back h5py * Passing all tests locally * Keep todo * Try github actions with mamba * Black formatting * Python versions, better mamba * Avoid treating versions as numbers * Actions changes * Black with no options * Black fixes * Check co structure * Why do we get extra files? * Black manually * Make sure env is activated * pytest fix * Try with original extra dir for pytest * Type * missing extra dir * Use importlib.metadata instead * pip install before tests * impose pin on scipy for mnnpy * Avoid python 3.10 * Allow single group in one to one marker comp * Rerun automatic tests * Try pinning bknn below 1.6.0 * Pin sklearn for bbknn * Fix package name * Pin numba for mnnpy * Downgrade numba even more for mnnpy * Pin numpy for mmnpy * Further pin numpy * Further pin numpy * More stringent pinning based on 2022 scanpy-scripts latest container * More pinning for mnnpy * More mnnpy pinning * Commented `mnn_batch_correction` test as it fails with scanpy 1.9.1 * adds warning message for `mnn_correct` * Reformat _mnn.py * Reformat _mnn.py --------- Co-authored-by: Iris Diana Yu <[email protected]> Co-authored-by: Anil Thanki <[email protected]>
* HVG genes setting through files * Always avoid the unexpected arguments
Co-authored-by: Pedro Madrigal <[email protected]>
Co-authored-by: Pedro Madrigal <[email protected]>
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This PR represents the merge to master for the release. To be done directly on sourcetree, do not merge here please.