Vary rank for CP and RISE

[Nathaniel-github]

No description provided.

[Copilot]

Pull Request Overview

This PR enables specifying a separate CP decomposition rank (cp_rank) in the CC-PF2 workflow, refactors plotting and utility functions accordingly, and adds end-to-end figure generation tests.

• Introduce and propagate the cp_rank parameter through cc_pf2, run_cc_pf2_workflow, and plotting scripts.
• Add utility functions resample and calculateFMS for bootstrapping and factor match scoring.
• Add tests to automatically run all figure scripts and update existing CC-PF2 tests to match the new output structure.

Reviewed Changes

Copilot reviewed 11 out of 14 changed files in this pull request and generated no comments.

Show a summary per file

File	Description
pyproject.toml	Add tensorly-viz dependency for CP visualization
cellcommunicationpf2/utils.py	Add resample and calculateFMS helper functions
cellcommunicationpf2/tests/test_figures.py	New test to auto-run all figures (dynamic import logic)
cellcommunicationpf2/tests/test_ccpf2.py	Update unpacking of cc_pf2 results to use the new cp_rank output
cellcommunicationpf2/figures/figure1.py	Refactor Figure 1 generation with run_cc_pf2_workflow and new plotting helpers
cellcommunicationpf2/figures/figure2.py	Update stability analysis to use resample and calculateFMS
cellcommunicationpf2/figures/figure3.py	Add Figure 3 showing CP component weight vs. sample size
cellcommunicationpf2/figures/commonFuncs/plotFactors.py	Improve row-color legend placement and fix hierarchical clustering
cellcommunicationpf2/figures/common.py	Add run_cc_pf2_workflow, correct_conditions, and integrate CP rank logic
cellcommunicationpf2/ccc.py	Simplify loops using _ and use inline conditionals
cellcommunicationpf2/cc_pf2.py	Introduce cp_rank parameter, update return signature and CP logic

Comments suppressed due to low confidence (3)

cellcommunicationpf2/utils.py:31

• [nitpick] Function name calculateFMS does not follow PEP8 snake_case conventions. Consider renaming it to calculate_fms for consistency.

def calculateFMS(A: anndata.AnnData, B: anndata.AnnData) -> float:

cellcommunicationpf2/utils.py:6

• The new utility functions resample and calculateFMS are not covered by any unit tests. Consider adding dedicated tests to verify correct stratified resampling and factor match score calculation.

def resample(data: anndata.AnnData, random_seed: int = None) -> anndata.AnnData:

cellcommunicationpf2/tests/test_figures.py:23

• The import_module call assumes the figures live under the cellcommunicationpf2.tests.figures package, but they are located in cellcommunicationpf2/figures. Update the import path to cellcommunicationpf2.figures.{module_name} or adjust the package argument accordingly.

            module = importlib.import_module(f"..figures.{module_name}", package="cellcommunicationpf2.tests")

[andrewram4287]

@Nathaniel-github I'll review this once we get your other PRs merged

[codecov]

Codecov Report

Attention: Patch coverage is 97.83394% with 6 lines in your changes missing coverage. Please review.

Project coverage is 78.14%. Comparing base (3be1ac3) to head (2c0b8a8).
Report is 32 commits behind head on main.

Files with missing lines	Patch %	Lines
cellcommunicationpf2/cc_pf2.py	89.65%	3 Missing ⚠️
cellcommunicationpf2/ccc.py	66.66%	2 Missing ⚠️
...ommunicationpf2/figures/commonFuncs/plotFactors.py	94.73%	1 Missing ⚠️

Additional details and impacted files

@@             Coverage Diff             @@
##             main      #30       +/-   ##
===========================================
+ Coverage   46.81%   78.14%   +31.32%     
===========================================
  Files           6       11        +5     
  Lines         361      668      +307     
===========================================
+ Hits          169      522      +353     
+ Misses        192      146       -46     

Flag	Coverage Δ
unittests	78.14% <97.83%> (+31.32%)	⬆️

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