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Custom dataloader registry support#2932

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ori-kron-wis wants to merge 96 commits intomainscverse/scvi-tools:mainfrom ori-2907-custom-dataloader-registryscverse/scvi-tools:ori-2907-custom-dataloader-registryCopy head branch name to clipboard

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Commits

Commits on Jul 28, 2024

• copying CZI custom dataloader into our repo

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Commits on Jul 30, 2024

• added some fixes to the custom dataloader stuff

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  cc72b05

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• Some suggestions

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Commits on Jul 31, 2024

• Changes to datamodule pipeline

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• Fixed attr_dict

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Commits on Aug 1, 2024

• added some fixes based on custom data loader test

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Commits on Aug 6, 2024

• Changes to dataloader

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  69abc47

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Commits on Aug 7, 2024

• copying CZI custom dataloader into our repo

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  dc21a3d

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• added some fixes to the custom dataloader stuff

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  a1098b3

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• Some suggestions

  

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• Changes to datamodule pipeline

  

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  a578af1

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• Fixed attr_dict

  

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  42434ec

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• added some fixes based on custom data loader test

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  3d0c890

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• Changes to dataloader

  

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• Merge remote-tracking branch 'origin/ori-2907-custom-dataloader-registry' into ori-2907-custom-dataloader-registry

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• add changes to tests and some merging with main following custom datamodule / registry big change

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• just put the cutom dataloder2 test under remarks so hook tests will run, we will later adjust this file

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• fixes

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• additional external models fixes once there is a registry

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Commits on Aug 11, 2024

• fixed a few failed tests

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• fix archesmixin init and added new custom dataloader test and github action

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• fix again for from __future__ import annotations

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• fix for run custom dataloader in github action

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• rollback

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• added label to the new githubaction for custom dataloader

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  6ec5d4d

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Commits on Aug 12, 2024

• fix for github action for custom dataloaders

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• another fix to custom dataloder test and github action

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• another fix to custom dataloder test and github action

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• another fix to custom dataloder test and github action

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• another fix to custom dataloder test and github action

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• another fix to custom dataloder test and github action

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  48627d9

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• another fix to custom dataloder test and github action

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  609094d

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• another fix to custom dataloder test and github action

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  8cf3517

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• another fix to custom dataloder test and github action

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  ba5a028

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• another fix to custom dataloder test and github action

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  a7dc3fe

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• another fix to custom dataloder test and github action

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Commits on Sep 9, 2024

• Merge branch 'main' into ori-2907-custom-dataloader-registry

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Commits on Sep 15, 2024

• Merge branch 'main' into ori-2907-custom-dataloader-registry

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Commits on Sep 16, 2024

• Merge branch 'main' into ori-2907-custom-dataloader-registry

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• Returned REGISTRY_KEYS for import, after was drop in recent merges

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• It is ok to drop it after scarches categorial covariates fix

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Commits on Sep 17, 2024

• Merge branch 'main' into ori-2907-custom-dataloader-registry

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• Merge branch 'main' into ori-2907-custom-dataloader-registry

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• moved to type checking blocks beucase of ruff updates

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Commits on Sep 26, 2024

• Merge branch 'main' into ori-2907-custom-dataloader-registry

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Commits on Oct 7, 2024

• Merge remote-tracking branch 'origin/main' into ori-2907-custom-dataloader-registry

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  bf4d3bf

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Commits on Oct 9, 2024

• updated for CZI custom dataloader test and backend

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• Merge branch 'main' into ori-2907-custom-dataloader-registry

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• added cellxgene-census folder as well for debug (will not be merged)

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• added cellxgene-census packge to run test

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• added torchdata packge to run test

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  dd3649c

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• fixed the test workwflow

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Commits on Oct 10, 2024

• adding the lamindb as well

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  b35c6eb

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• fix the c.dataloders test

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• fix the c.dataloders test

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• fix the c.dataloders test

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• fix the c.dataloders test

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• fix the c.dataloders test

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Commits on Oct 13, 2024

• removed redundat functions in code base

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Commits on Oct 15, 2024

• Added scanvi support, including CZI datamodule fix for it

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Commits on Oct 20, 2024

• Merge remote-tracking branch 'origin/main' into ori-2907-custom-dataloader-registry

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Commits on Dec 25, 2024

• updates from main

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• more updates from main

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• Merge branch 'main' into ori-2907-custom-dataloader-registry

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• Merge remote-tracking branch 'origin/ori-2907-custom-dataloader-registry' into ori-2907-custom-dataloader-registry

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  6d4f368

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• updated related to tests

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• updated related to tests

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Commits on Dec 30, 2024

• Running DataLoader MappedCollection

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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Commits on Dec 31, 2024

• Fixed LaminDB dataloader

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• Merge branch 'ori-2907-custom-dataloader-registry' of https://github.com/scverse/scvi-tools into ori-2907-custom-dataloader-registry

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• LaminDB dataloader test.

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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• Merge branch 'main' into ori-2907-custom-dataloader-registry

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Commits on Jan 8, 2025

• Merge remote-tracking branch 'origin/main' into ori-2907-custom-dataloader-registry

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• Changes for MappedCollection.

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• Merge branch 'ori-2907-custom-dataloader-registry' of https://github.com/scverse/scvi-tools into ori-2907-custom-dataloader-registry

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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Commits on Jan 9, 2025

• Add other notebook for testing new dataloader

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• Merge branch 'ori-2907-custom-dataloader-registry' of https://github.com/scverse/scvi-tools into ori-2907-custom-dataloader-registry

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• [pre-commit.ci] auto fixes from pre-commit.com hooks

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Commits on Jan 16, 2025

• Merge remote-tracking branch 'origin/main' into ori-2907-custom-dataloader-registry

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• updates to test script

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• remove old test nb

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• update test

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• update test

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• updated czi cdl

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• updated czi cdl

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Commits on Jan 20, 2025

• Merge remote-tracking branch 'origin/main' into ori-2907-custom-dataloader-registry

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Commits on Feb 9, 2025

• merge with main + updates

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• more updates

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• more updates

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• more updates

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Commits on Feb 10, 2025

• pyproject update

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