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ENH: Add lightning.Trainer config, fix #691 #687 #742 #745 #752

Merged
merged 47 commits into from
May 5, 2024
Merged

ENH: Add lightning.Trainer config, fix #691 #687 #742 #745 #752

merged 47 commits into from
May 5, 2024

Commits on May 5, 2024

  1. WIP: Add config/trainer.py with TrainerConfig

    @NickleDave
    NickleDave committed May 5, 2024
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  2. Rename common.device -> common.accelerator, return 'gpu' not 'cuda' i… 

    …f torch.cuda.is_available
    @NickleDave
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  3. Fix config section in doc/api/index.rst

    @NickleDave
    NickleDave committed May 5, 2024
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  4. Import trainer and TrainerConfig in src/vak/config/__init__.py, add t… 

    …o __all__
    @NickleDave
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  5. Add pytorch-lightning to intersphinx in doc/conf.py

    @NickleDave
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  6. Fix cross-ref in docstring in src/vak/prep/frame_classification/make_… 

    …splits.py: :constant: -> :const:
    @NickleDave
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  7. Make lightning a dependency, instead of pytorch_lightning; import lig… 

    …htning.pytorch everywhere instead of pytorch_lightning as lightning -- trying to make it so we can resolve API correctly in docstrings
    @NickleDave
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  8. Fix in doc/api/index.rst: common.device -> common.accelerator

    @NickleDave
    NickleDave committed May 5, 2024
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  9. Finish writing TrainerConfig class

    @NickleDave
    NickleDave committed May 5, 2024
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  10. Add tests for TrainerConfig class

    @NickleDave
    NickleDave committed May 5, 2024
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  11. Add trainer sub-table to all configs in tests/data_for_tests/configs

    @NickleDave
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  12. Add trainer sub-table to all configs in doc/toml

    @NickleDave
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  13. Add trainer sub-table in config/valid-version-1.0.toml, rename -> val… 

    …id-version-1.1.toml
    @NickleDave
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  14. Remove device key from top-level tables in config/valid-version-1.1.toml

    @NickleDave
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  15. Remove device key from top-level tables in tests/data_for_tests/configs

    @NickleDave
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  16. Remove 'device' key from configs in doc/toml

    @NickleDave
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  17. Add 'trainer' attribute to EvalConfig, an instance of TrainerConfig; … 

    …remove 'device' attribute
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  18. Add 'trainer' attribute to PredictConfig, an instance of TrainerConfi… 

    …g; remove 'device' attribute
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  19. Add 'trainer' attribute to TrainConfig, an instance of TrainerConfig;… 

    … remove 'device' attribute
    @NickleDave
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  20. Fix typo in docstring in src/vak/config/train.py

    @NickleDave
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  21. Add 'trainer' attribute to LearncurveConfig, an instance of TrainerCo… 

    …nfig; remove 'device' attribute. Also clean up docstring, removing attributes that no longer exist
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  22. Remove device attribute from TrainConfig docstring

    @NickleDave
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  23. Fix VALID_TOML_PATH in config/validators.py -> 'valid-version-1.1.toml'

    @NickleDave
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  24. Fix how we instantiate TrainerConfig classes in from_config_dict meth… 

    …od of EvalConfig/LearncurveConfig/PredictConfig/TrainConfig
    @NickleDave
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  25. Fix typo in src/vak/config/valid-version-1.1.toml: predictor -> predict

    @NickleDave
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  26. Fix unit tests after adding trainer attribute that is instance of Tra… 

    …inerConfig
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  27. Change src/vak/train/frame_classification.py to take trainer_config a… 

    …rgument
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  28. Change src/vak/train/parametric_umap.py to take trainer_config argument

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  29. Change src/vak/train/train_.py to take trainer_config argument

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  30. Fix src/vak/cli/train.py to pass trainer_config.asdict() into vak.tra… 

    …in.train_.train
    @NickleDave
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  31. Replace 'device' with 'trainer_config' in vak/eval

    @NickleDave
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  32. Fix cli.eval to pass trainer_config into eval.eval_.eval

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  33. Replace 'device' with 'trainer_config' in vak/predict

    @NickleDave
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  34. Fix cli.predict to pass trainer_config into predict.predict_.predict

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  35. Replace 'device' with 'trainer_config' in vak/learncurve

    @NickleDave
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  36. Fix cli.learncurve to pass trainer_config into learncurve.learncurve.… 

    …learning_curve
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  37. Rename/replace 'device' fixture with 'trainer' fixture in tests/

    @NickleDave
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  38. Use config.table.trainer attribute throughout tests, remove config.ta… 

    …ble.device attribute that no longer exists
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  39. Fix value for devices in fixtures/trainer.py: when device is 'cpu' tr… 

    …ainer must be > 0
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  40. Fix default devices value for when accelerator is cpu in TrainerConfig

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  41. Fix unit tests for TrainerConfig after fixing default devices for acc… 

    …elerator=cpu
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  42. Fix default value for 'devices' set to -1 in some unit tests where we… 

    … over-ride config in toml file
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  43. fixup use config.table.trainer attribute throughout tests -- missed o… 

    …ne place in tests/test_eval/
    @NickleDave
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  44. Add back 'device' fixture so we can use it to test Model class

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  45. Fix unit tests in test_models/test_base.by that literally used device… 

    … to put tensors on device, not to change a config
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  46. Fix assertion in tests/test_models/test_tweetynet.py, from where we s… 

    …witched to using lightning as the dependency
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  47. Fix test for DiceLoss, change trainer_type fixture back to device fix… 

    …ture
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