memento #918
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memento #918
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- Migrated code from https://github.com/mincheoly/memento-cxg/blob/atol/codify-and-compare-notebooks/ - Reorganized code to fit this repo, splitting api and builder into api/ and tools/ dirs, repsectively - Added type hints - Updated docs
- add all Census obs metadata attributes as cube dimensions - remove unused estimator columns - add test fixture code to extract a small subset of a Census Experiment for local testing of the memento estimators cube
- use TileDB categorical types
- fix TileDB handling of Pandas categoricals - fix approx_size_factors filtering - add assertion sanity checks for debugging - add cube validator
- add validation for "all obs dims present" - cleanup debug assertions
- add missing suspension_type dim - compute for all features
…/877-cube-schema-updates--simplify-joins
- add regression test for cube builder, testing against a previously built and committed cube - add parameterized build() method - add CLI entrypoint for cube builder
- Ensure the size_factors for obs group is created correctly, with one row per obs row - add validation check for n_obs
too noisy as warnings, and not useful during production runs
- use single concat() call instead of a join - factor out code into sub-methods for better profiling insight
If starting with a new cube, do not bother to check whether obs group needs to be computed; assume it does
This avoids having to return result to parent process
Obs groups (i.e., cube rows) are now represented by an obs_group_joinid that can be used to join the estimators to the original obs dimension columns. This saves considerable space, as the obs dimension values do not need to be repeated for each feature (gene). Also, Group By operations should be more efficient now that grouping can occur on a single value.
…pr-profiler-polars
not faster
also, uncomment step 2 and 3
- fix dummies matrix - pass reduced obs_groups_df columns to child processes - fix mypy typing errors - disable profiling decorators (not mypy-friendly, as is)
add static test fixtures
…ne-census into atol/memento/epic
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## main #918 +/- ##
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- Coverage 81.32% 80.59% -0.74%
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Files 73 75 +2
Lines 5553 5715 +162
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+ Hits 4516 4606 +90
- Misses 1037 1109 +72
Flags with carried forward coverage won't be shown. Click here to find out more. ☔ View full report in Codecov by Sentry. |
* Defer python package version pinning for memento cube builder * Add unit test for memento differential expression * Fix markdown lint complaints * Regenerate test fixtures * Update unit test * Use a different default covariate list --------- Co-authored-by: atarashansky <[email protected]>
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For #847