Custom dataloader registry support #2932
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…try' into ori-2907-custom-dataloader-registry
…module / registry big change
for more information, see https://pre-commit.ci
…un, we will later adjust this file
Codecov ReportAttention: Patch coverage is
❌ Your project check has failed because the head coverage (81.96%) is below the target coverage (83.00%). You can increase the head coverage or adjust the target coverage.
Additional details and impacted files@@ Coverage Diff @@
## main #2932 +/- ##
==========================================
- Coverage 89.43% 81.96% -7.48%
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Files 185 186 +1
Lines 16182 16439 +257
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- Hits 14473 13474 -999
- Misses 1709 2965 +1256
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and fix the test for custom dataloaders
for more information, see https://pre-commit.ci
…oader-registry # Conflicts: # docs/tutorials/notebooks
…com/scverse/scvi-tools into ori-2907-custom-dataloader-registry
for more information, see https://pre-commit.ci
…com/scverse/scvi-tools into ori-2907-custom-dataloader-registry
for more information, see https://pre-commit.ci
…oader-registry # Conflicts: # docs/tutorials/notebooks
…oader-registry # Conflicts: # docs/tutorials/notebooks
canergen
reviewed
Feb 18, 2025
| import scvi | ||
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| if TYPE_CHECKING: | ||
| import lamindb as ln |
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does this create a requirement for lamindb? Can we make MappedCollectionDataModule a lazy load?
canergen
reviewed
Feb 18, 2025
| "state_registry": { | ||
| "categorical_mapping": self.label_keys, | ||
| "original_key": self._label_key, | ||
| "unlabeled_category": "unlabeled", |
canergen
reviewed
Feb 18, 2025
| **datasplitter_kwargs, | ||
| ) | ||
| else: | ||
| # TODO fix in external dataloader? |
canergen
reviewed
Feb 18, 2025
| @@ -134,6 +148,7 @@ def __init__( | |||
| f"dropout_rate: {dropout_rate}, dispersion: {dispersion}, " | |||
| f"gene_likelihood: {gene_likelihood}, latent_distribution: {latent_distribution}." | |||
| ) | |||
| self._module_init_on_train = False | |||
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| if self._module_init_on_train: | |||
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remove module_init_on_train. This is deprecated code with the new dataloader implementation.
canergen
reviewed
Feb 18, 2025
| ) | ||
| else: | ||
| # custom datamodule | ||
| n_cats_per_cov = self.summary_stats[f"n_{REGISTRY_KEYS.CAT_COVS_KEY}"] |
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does this work for AnnData? Can we remove the if statement here?
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