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docs: compare gene selection among model configurations #596

Merged
merged 133 commits into from
Aug 8, 2024
Merged

docs: compare gene selection among model configurations #596

merged 133 commits into from
Aug 8, 2024

Commits on Jul 30, 2024

  1. deps(pyproject): reenable expression 

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

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  3. chore(requirements): sync 

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  4. chore(conda): sync 

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  5. fix(nbs): use subdirectory for pancreas tutorial 

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  6. chore(nbs): add gitignore 

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  7. feat(nbs): initialize downsampled pancreas tutorial 

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  8. chore(nbs): sync freeze 

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Commits on Jul 31, 2024

  1. fix(io): allow specification of a download filename prefix 

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  2. feat(io): add cluster module 

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  3. feat(nbs): add support for model comparison to pancreas notebook 

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  4. chore(nbs): sync freeze 

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  5. test(io): add test for cluster module 

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  6. fix(io): add doctest for get_remote_task_results 

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Commits on Aug 1, 2024

  1. fix(nix): add workflows to check groups 

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  2. chore(src): lint 

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  3. fix(nbs): separate references to preprocessing and results 

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  4. fix(nbs): add stub for preprocessing notebook 

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  5. refactor(nbs): migrate results notebook to subdir 

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Commits on Aug 2, 2024

  1. refactor(tests): mirror package folder structure 

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  2. chore(bazel): update test module paths 

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  3. chore(nbs): sync freeze 

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  4. fix(make): run slow tests with test-cov-xml target 

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  5. fix(tasks): download_dataset accepts Path type 

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  6. test(tasks): add package fixtures 

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  7. fix(tasks): declare skip preprocess doctest once 

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  8. test(tasks): add slow call to preprocess function 

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  9. tests(analysis): init 

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  10. tests(io): init 

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  11. tests(metrics): init 

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  12. tests(models): init 

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  13. tests(plots): init 

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  14. tests(tasks): init 

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  15. fix(io): use tmp dir fixture for compressedpickle doctests 

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  16. fix(tasks): skip postprocess dataset xdoctest 

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  17. test(tasks): add preprocess and training fixtures to subpackage tests 

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  18. fix(tasks): enable nested mlflow runs 

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  19. fix(tasks): enable Path objects where applicable 

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  20. test(tasks): return train dataset fixture 

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  21. test(tasks): return preprocess data set fixture 

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Commits on Aug 3, 2024

  1. nit(tasks): use kwargs in doctest 

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  2. test(tasks): add postprocess fixture 

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  3. test(tasks): return postprocess data set fixture 

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  4. fix(tasks): update args and examples for summarize dataset 

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  5. test(tasks): add summarize dataset fixture 

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  6. test(tasks): return summarize dataset output 

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  7. test(tasks): addr train, postprocess, and summarize fixtures for mode… 

    …l 1 configuration

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  8. test(tasks): return model 1 training outputs 

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  9. test(tasks): return model 1 postprocess outputs 

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  10. test(tasks): return model 1 summarize outputs 

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  11. refactor(test): migrate tasks fixtures to top-level 

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  12. test(plots): add vector fields module 

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  13. fix(bazel): add marker to args 

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  14. chore(bazel): add test modules to build file 

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  15. fix(bazel): remove small/large duplicate test module 

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  16. fix(bazel): migrate tests <5 min to size medium 

    - https://bazel.build/reference/be/common-definitions#common-attributes-tests

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  17. chore(pyproject): matplotlib 3.9.1 

    - need matplotlib PR #28498 to avoid calling undeclared system dependencies from bazel/nix sandboxes during test execution

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  18. chore(bazel): sync lock 

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  19. chore(requirements): sync 

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  20. test(plots): run shared time uncertainty 

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  21. chore(bazel): add test time module 

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  22. fix(plots): ensure path for posterior predictive phase portraits 

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  23. fix(tests): add in-memory fixtures used by plotting modules 

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  24. test(plots): use in-memory fixtures for vector field plots 

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  25. test(plots): use in-memory fixtures for shared time plots 

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  26. test(plots): run posterior predictive plots 

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  27. chore(bazel): add posterior predictive plots test module 

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  28. fix(plots): add option to save gene ranking plot 

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  29. fix(tasks): remove manual figure write 

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  30. test(plots): run plot gene ranking 

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  31. chore(bazel): add test genes module 

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Commits on Aug 4, 2024

  1. refactor(tests): set session-level scope on integration fixtures 

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  2. test(plots): use session-level reports path for vector field plots 

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  3. test(plots): use session-level reports path for shared time plot 

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  4. test(plots): use session-level reports path for predictive plots 

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  5. test(plots): use session-level reports path for gene selection plots 

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  6. test(plots): add test for summary plots 

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  7. test(pyproject): add slow and integration pytest markers to pytest ini 

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  8. test(plots): add test for parameter posteriors plots 

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  9. refactor(tests): add integration marker to integration tests 

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  10. chore(bazel): add posteriors and summary test modules 

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  11. fix(plots): add option to save rainbow plot 

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  12. fix(tasks): remove redundant logic to save rainbow plot in summarize … 

    …task

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  13. test(plots): add rainbow plot test 

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  14. chore(bazel): add rainbow plot test module 

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Commits on Aug 5, 2024

  1. fix(analysis): remove cell marker comments 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(models): remove unused branching in generate_posterior_samples me… 

    …thod

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  3. feat(utils): add function to save parameter posterior means to dataframe 

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  4. feat(tasks): save parameter posterior means to dataframe 

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  5. config(workflows): toggle testing flags off 

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  6. chore(workflows): set cache version 2024.8.5 

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  7. fix(workflows): toggle data subset flag on 

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  8. fix(cid): set sha-specific concurrency groups for workflow execution 

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  9. fix(pyproject): temporarily pin yanked matplotlib 3.9.1 

    - only relevant for pip installs
- see https://www.github.com/matplotlib/matplotlib/issues/28551

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  10. fix(workflows): disable flyte decks causing type error 

    `TypeError: __str__ returned non-string (type PosixPath)`

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  11. feat(summarize): save gene ranking table to csv 

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  12. fix(io): include csv files in default model summary archive 

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  13. fix(workflows): explicitly include csv in model summary archive 

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  14. docs(nbs): write data tables to files 

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  15. chore(nbs): sync freeze 

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  16. docs(nbs): generate phase portraits from custom gene list 

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  17. chore(nbs): sync freeze 

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  18. fix(workflows): disable upload summary cache 

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Commits on Aug 6, 2024

  1. test(analysis): add tests for pareto frontier genes function 

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  2. test(analyze): add tests for top_mae_genes function 

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  3. feat(analyze): add function to extract top mae genes 

    - sorted by descending shared time correlation

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  4. fix(summarize): pareto_frontier_genes -> top_mae_genes 

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  5. test(conftest): use top_mae_genes in marker gene fixtures 

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  6. chore(workflows): bump summarize cache to 2024.8.5.1 

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  7. fix(pyproject): note intention to exclude markers associated with slo… 

    …w tests

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Commits on Aug 7, 2024

  1. fix(analysis): get top mae genes by correlation bin 

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  2. test(analysis): account for correlation bins in top mae genes 

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  3. fix(tests): remove gene number specification 

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  4. fix(summarize): use mae percentiles and min genes per bin in marker g… 

    …ene selection

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  5. feat(plots): add normalized data to rainbow plot 

    Signed-off-by: Cameron Smith <[email protected]>
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  6. fix(plots): disable normalized data on summary plot 

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  7. chore(workflows): bump summarize cache to 2024.8.5.2 

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  8. fix(plots): ensure data is a dense array before flattening 

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  9. docs(tutorials): add more detailed gene selection data 

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  10. chore(nbs): sync freeze 

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  11. feat(plots): add option to plot log spliced data to rainbow plot 

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  12. fix(plots): default to highest and lowest shared time correlation gen… 

    …es in summary plot

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  13. fix(plots): use cividis in plot posterior time 

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  14. chore(workflows): bump summarize cache to 2024.8.5.3 

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  15. fix(nbs): add parameter posterior estimates to pancreas results 

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  16. chore(nbs): sync freeze 

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  17. fix(plots): enable offset parameters in posterior distribution plots 

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  18. fix(tasks): remove unused t0 from model1 posterior samples 

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  19. chore(workflows): bump summarize cache to 2024.8.5.4 

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Commits on Aug 8, 2024

  1. fix(plots): make parameter names an argument of posterior plot function 

    Signed-off-by: Cameron Smith <[email protected]>
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  2. fix(tasks): remove ad hoc modification of posterior samples 

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  3. chore(nbs): sync freeze 

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  4. chore(version): 0.3.0b2 

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