breaking: clarify obs handling + change output keys#115
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #115 +/- ##
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+ Coverage 92.41% 92.44% +0.02%
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Files 6 6
Lines 620 622 +2
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+ Hits 573 575 +2
Misses 47 47
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ilan-gold
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* chore: clarify obs handling * chore: clearer docs * fix: rename
selmanozleyen
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* chore: clarify obs handling * chore: clearer docs * fix: rename
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* chore: clarify obs handling * chore: clearer docs * fix: rename
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* resolve conflicts with main * load_obs thing was removed by auto formatting * update tests to resolve conflict * readthedocs merge * chore: clarify compatibility of `h5ad` + forward compat of old shuffled `zarr` (#114) * chore: clarify compatibility of `h5ad` + forward compat of old shuffled `zarr` * chore: version * fix: docs * clarify warning * fix: more * fix: `add_anndata` * fix: `h5ad` compat * breaking: clarify obs handling + change output keys (#115) * chore: clarify obs handling * chore: clearer docs * fix: rename * fix: header level (#116) * merge changes * apply suggestions * checkout readme from main * breaking: clarify obs handling + change output keys (#115) * chore: clarify obs handling * chore: clearer docs * fix: rename * parent 627eb08 author selmanozleyen <syozleyen@gmail.com> 1768761446 +0100 committer selmanozleyen <syozleyen@gmail.com> 1768846971 +0100 resolve conflicts with main update tests to resolve conflict readthedocs merge merge changes apply suggestions checkout readme from main * restore from main * fix: checking out: confused origin and upstream again... * continuation of the upstream origin confusion fix * breaking: clarify obs handling + change output keys (#115) * chore: clarify obs handling * chore: clearer docs * fix: rename * fix: header level (#116) * refactor _prepare_dataset_and_obs * update docstring for loadrequest * separate files for samplers * prepare_output is no longer needed * clarify docs * fix overlook: already sorted batch_indices no need to resort them * fix prepare_output refactor * add todo * rename from leftover to remainder for clarity. since there is no leftover * simplify validate_sampler * remove old generic params * add broad typing * clarify todos and add username * type and modify decorator * no need for lambdas in decorators * make decorator compatible in multiple cases * put ABC in abc folder * update test with the fix * qualname for fix. no sampler in public API * check coverage when shuffled otherwise also check order * fix to prev commit * clarify doc * update worker tests * new * location for ChunkSampler * add typing but can revert if too verbose * remove unused fields. (maybe linter check can be added) * remove old SO link * don't put generators into np.all !! * apply typing and docstring suggestion * change in folder structure * make batch sampler getter * remove empty line * apply docstring suggestions for Loader args * remove empty line * conf.py is same as main * change shuffle * remove todo * update to match old behaviour * put vstack inside accumulate chunks --------- Co-authored-by: Ilan Gold <ilanbassgold@gmail.com>
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