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feat(workflows): create model training tasks #513

Merged
merged 117 commits into from
Feb 3, 2024
Merged

feat(workflows): create model training tasks #513

merged 117 commits into from
Feb 3, 2024

Commits on Jan 26, 2024

  1. chore(changelog): lint 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Jan 27, 2024

  1. chore(cspell): update dictionary 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. feat(api): typecheck train_model and allow path inputs 

    Signed-off-by: Cameron Smith <[email protected]>
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  3. feat(train): add training script for workflow usage 

    Signed-off-by: Cameron Smith <[email protected]>
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  4. fix(gitignore): models directory 

    Signed-off-by: Cameron Smith <[email protected]>
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  5. feat(main_workflow): add model training task 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. test(main_workflow): comment extra data sets 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. fix(main_workflow): use NamedTuple class 

    Signed-off-by: Cameron Smith <[email protected]>
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  8. fix(api): discard returned adata in doctest 

    Signed-off-by: Cameron Smith <[email protected]>
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    cameronraysmith committed Jan 27, 2024
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Commits on Jan 28, 2024

  1. fix(execution_utils): construct dataclasses given defaults 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(velocity_model): set u0/s0 types to RNAInputType 

    Signed-off-by: Cameron Smith <[email protected]>
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  3. feat(data): add load_anndata_from_path 

    Signed-off-by: Cameron Smith <[email protected]>
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  4. refactor(api): use load_anndata_from_path 

    Signed-off-by: Cameron Smith <[email protected]>
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  5. feat(data): support subsetting during data download 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. fix(utils): update AnnData type import 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. refactor(train): move interface type to dedicated module 

    remove model save which is done in postprocessing
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  8. feat(preprocess): refactor for compatibility with dataclass interface 

    Signed-off-by: Cameron Smith <[email protected]>
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  9. feat(interfaces): collect dataclass interfaces 

    Signed-off-by: Cameron Smith <[email protected]>
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  10. feat(main_workflow): use dataclass interfaces 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Jan 29, 2024

  1. feat(make): add cluster-shell target 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. feat(pyproject): upgrade stable dependencies 

    Signed-off-by: Cameron Smith <[email protected]>
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  3. chore(pypi): sync pyproject 

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  4. chore(pypi): sync cpu with pyproject 

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  5. chore(conda): sync pyproject 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. feat(flake): update torch >2 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. fix(workflows): set preprocess data path 

    Signed-off-by: Cameron Smith <[email protected]>
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  8. fix(cid): increase swap size 

    actions/runner-images#7188 (comment)
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  9. fix(vscode): disable coverage to respect debugging breakpoints 

    microsoft/vscode-python#693 (comment)
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  10. fix(make): move pod ID extraction inside cluster-shell target 

    Signed-off-by: Cameron Smith <[email protected]>
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  11. fix(velocity): cast categorical/integers as floats for log-transforma… 

    …tion

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  12. fix(trainer): cast categorical/integers as floats for log-transformation 

    Signed-off-by: Cameron Smith <[email protected]>
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  13. fix(data): make var names unique 

    Signed-off-by: Cameron Smith <[email protected]>
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  14. fix(preprocess): remove completed TODOs 

    Signed-off-by: Cameron Smith <[email protected]>
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  15. feat(workflows): add pbmc68k, pons, and larry data sets 

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  16. test(cid): toggle workflow dev mode 

    Signed-off-by: Cameron Smith <[email protected]>
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  17. fix(workflows): increase resources for preprocessing and training tasks 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Jan 30, 2024

  1. fix(workflows): set task resource limits 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. chore(cspell): update dictionary 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Jan 31, 2024

  1. refactor(train): migrate train_model from api module to train 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(interfaces): use train_dataset from train module 

    Signed-off-by: Cameron Smith <[email protected]>
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  3. refactor(workflows): move configuration to separate module 

    Signed-off-by: Cameron Smith <[email protected]>
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  4. refactor(main_workflow): move configuration to separate module 

    Signed-off-by: Cameron Smith <[email protected]>
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  5. fix(workflows): enable cache for training tasks 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. fix(dev): add example security context overrides 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. refactor(conftest): move sample_data fixture to shared scope 

    Signed-off-by: Cameron Smith <[email protected]>
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  8. refactor(test_utils): use shared sample data 

    Signed-off-by: Cameron Smith <[email protected]>
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  9. fix(main_workflow): update docstrings 

    Signed-off-by: Cameron Smith <[email protected]>
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  10. feat(conftest): provide global fixture to file for sample data 

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  11. feat(test_data): add tests for data module methods 

    Signed-off-by: Cameron Smith <[email protected]>
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  12. fix(requirements-cpu): remove outdated hashed version 

    not required
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  13. feat(pyproject): add requests-mock for testing 

    Signed-off-by: Cameron Smith <[email protected]>
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  14. chore(requirements): sync with pyproject 

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  15. fix(cspell): update dictionary 

    add pyproject
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  16. chore(conda): sync with pyproject 

    Signed-off-by: Cameron Smith <[email protected]>
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  17. test(cid): build images before workflow execution 

    Signed-off-by: Cameron Smith <[email protected]>
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  18. chore(cspell): update dictionary 

    add bazel
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  19. chore(bazel): update lock 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Feb 1, 2024

  1. ci(pre-commit): add commitizen 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. ci(pre-commit): upgrade repo revs 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Feb 2, 2024

  1. chore(cid): update dep version pins 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(make): exclude additional modules from dep graph 

    Signed-off-by: Cameron Smith <[email protected]>
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  3. ci(pre-commit): remove commitizen 

    Signed-off-by: Cameron Smith <[email protected]>
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  4. chore(flake): lint lock 

    Signed-off-by: Cameron Smith <[email protected]>
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  5. refactor(velocity): move deprecated modules to archive 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. refactor(api): move deprecated modules to archive 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. refactor(config): move deprecated modules to archive 

    Signed-off-by: Cameron Smith <[email protected]>
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  8. fix(train): update import path in doctest 

    Signed-off-by: Cameron Smith <[email protected]>
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  9. chore(make): remove unused exclusions from pydeps 

    Signed-off-by: Cameron Smith <[email protected]>
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  10. fix(setup_environment): update setup-pandoc pin 

    latest v2 release upgrades to dependencies that use node 20
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  11. fix(pyproject): pytest ignore reproducibility folder 

    Signed-off-by: Cameron Smith <[email protected]>
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  12. fix(bazel): remove unused test modules 

    Signed-off-by: Cameron Smith <[email protected]>
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  13. refactor(transcription_dynamics): separate from utils 

    Signed-off-by: Cameron Smith <[email protected]>
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  14. refactor(utils): move transcription dynamics functions to separate mo… 

    …dule

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  15. fix(velocity_model): update imports 

    Signed-off-by: Cameron Smith <[email protected]>
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  16. fix(transcription_dynamics): enable type-checking 

    remove unused comments
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  17. test(transcription_dynamics): add test module 

    Signed-off-by: Cameron Smith <[email protected]>
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  18. test(transcription_dynamics): update tests 

    - numerical output
- typechecking is enabled
- gamma==beta
- small values return results
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  19. chore(bazel): enable transcription dynamics test module 

    Signed-off-by: Cameron Smith <[email protected]>
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  20. fix(velocity_model): handle likelihood not implemented 

    Signed-off-by: Cameron Smith <[email protected]>
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  21. test(velocity_model): update tests 

    - init
- plates
- likelihood +/- valid
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  22. fix(velocity_model): remove optional type defaults for observations 

    Signed-off-by: Cameron Smith <[email protected]>
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  23. test(velocity_model): update tests 

    - VelocityModelAuto class
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  24. refactor(workflows): remove unused 

    Signed-off-by: Cameron Smith <[email protected]>
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  25. fix(make): remove unused pydeps exclusion 

    Signed-off-by: Cameron Smith <[email protected]>
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  26. fix(magic-nix-cache): revert v3 update 

    Signed-off-by: Cameron Smith <[email protected]>
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  27. fix(cid): update nix-installer to main 

    Signed-off-by: Cameron Smith <[email protected]>
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  28. test(cid): enable debugging 

    Signed-off-by: Cameron Smith <[email protected]>
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  29. test(cid): disable nix cache 

    Signed-off-by: Cameron Smith <[email protected]>
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  30. fix(cid): enable cachix cache for build-nix-images job 

    Signed-off-by: Cameron Smith <[email protected]>
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  31. chore(cid): update magic-nix-cache action 

    Signed-off-by: Cameron Smith <[email protected]>
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  32. fix(cid): enable cachix for release images 

    Signed-off-by: Cameron Smith <[email protected]>
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  33. fix(cid): enable cachix for test-nix job 

    Signed-off-by: Cameron Smith <[email protected]>
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  34. fix(cid): update codecov-action to v4 

    Signed-off-by: Cameron Smith <[email protected]>
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  35. fix(make): set cachix in gh vars/secrets 

    Signed-off-by: Cameron Smith <[email protected]>
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  36. fix(cid): remove debug 

    Signed-off-by: Cameron Smith <[email protected]>
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  37. fix(cid): reduce swap 

    Signed-off-by: Cameron Smith <[email protected]>
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  38. fix(make): filter io and configuration from pydeps 

    Signed-off-by: Cameron Smith <[email protected]>
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  39. test(preprocess): init test module 

    Signed-off-by: Cameron Smith <[email protected]>
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Commits on Feb 3, 2024

  1. fix(utils): comment unused functions 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. refactor(analyze): receive functions from plot module 

    - compute_mean_vector_field
- compute_volcano_data
- vector_field_uncertainty
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  3. refactor(plot): move _velocity functions to analyze module 

    Signed-off-by: Cameron Smith <[email protected]>
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  4. refactor(velocity): import from analyze <- plot 

    Signed-off-by: Cameron Smith <[email protected]>
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  5. test(pyproject): update coverage ommissions 

    - all init
- workflows
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  6. refactor(models): move model code to models package 

    Signed-off-by: Cameron Smith <[email protected]>
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  7. fix(gitignore): only ignore top-level models directory 

    Signed-off-by: Cameron Smith <[email protected]>
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  8. refactor(transcription_dynamics): rename mRNA -> mrna_dynamics 

    export from models package
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  9. refactor(pyrovelocity): remove unused top-level module 

    Signed-off-by: Cameron Smith <[email protected]>
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  10. test(workflows): define parameter configurations for testing 

    Signed-off-by: Cameron Smith <[email protected]>
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  11. docs: update api 

    Signed-off-by: Cameron Smith <[email protected]>
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  12. refactor(utils): move mse_loss_sum to plot 

    Signed-off-by: Cameron Smith <[email protected]>
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  13. chore(lint): archive 

    Signed-off-by: Cameron Smith <[email protected]>
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  14. chore(workflows): set 0.2.0b9 cache version 

    Signed-off-by: Cameron Smith <[email protected]>
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  15. fix(cid): increase root reserve and swap 

    Signed-off-by: Cameron Smith <[email protected]>
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  16. chore(flake): update lock 

    Signed-off-by: Cameron Smith <[email protected]>
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  17. chore(conda): sync lock 

    Signed-off-by: Cameron Smith <[email protected]>
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  18. test(cid): update build space removal 

    Signed-off-by: Cameron Smith <[email protected]>
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  19. chore(version): 0.2.0b9 (#513) 

    Signed-off-by: Cameron Smith <[email protected]>
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