Feature/hucira by Jenniliu12 · Pull Request #901 · scverse/pertpy

Jenniliu12 · 2026-01-11T21:33:32Z

PR Checklist

Referenced issue is linked
If you've fixed a bug or added code that should be tested, add tests!
Documentation in docs is updated

Description of changes
Removed hucira module; instead only implemented loading function.

Technical details
No technical changes. The analysis reuses methods from the existing enrichment module and scanpy. An example of use case is added to the enrichment tutorial.

Additional context
No tests added.
Tutorial not updated yet.

Zethson

Thank you very much already! Here's some first initial feedback:

Please ensure that you have a descriptive pull request title and the pull request description only has the necessary detail. This can also be done later but it's important.
Your implementation should not add any dependencies. Pertpy has to minimize dependencies because it's used by a loooot of people. Every dependency that we add has the potential to break users environment and increases complexity. Therefore, please remove bokeh, pycirclize, and tqdm. The plot should be implemented with seaborn and instead of using tqdm, you can use Rich directly. Not sure what to do about pycirclize - if necessary we can talk about it. That's one of the differences of implementing something for yourself vs implementing it for many.
Please ensure that all functions that have a bit more than trivial complexity have a proper docstring. Please adhere to our docstring style.
I didn't review everything yet because I think there's still a lot to do. Let's address these first.

Zethson · 2026-01-23T12:36:27Z

+        2. Creates ranking of query data genes contrasting condition1 vs condition2. A continuum from genes most associated with condition1 (top) to genes most associated with condition2 (bottom)
+        3. Computes enrichment of each cytokine by matching their associated gene set in the ranked list.
+
+        Parameters


Zethson · 2026-01-23T12:36:58Z

+        verbose: bool = False,
+        threads: int = 6,
+    ) -> pd.DataFrame:
+        """Function wrapper: Computes cytokine enrichment activity in one celltype using GSEA scoring. Loops through several threshold value to obtain more robust gene sets.


Suggested change

"""Function wrapper: Computes cytokine enrichment activity in one celltype using GSEA scoring. Loops through several threshold value to obtain more robust gene sets.

"""Computes cytokine enrichment activity in one celltype using GSEA scoring.

Loops through several threshold value to obtain more robust gene sets.

It's a rule that the first line is always just one sentence. No exceptions.

Zethson · 2026-01-23T12:37:06Z

+        weight: float = 1.0,
+        seed: int = 2025,
+        verbose: bool = False,
+        threads: int = 6,


This is a super random value

Zethson · 2026-01-23T12:38:04Z

+    ranked_stats, _num_cells = hucira._compute_ranking_statistic(dummy_adata, contrast_column, contrasts_combo)
+    assert isinstance(ranked_stats, pd.DataFrame)
+
+    # with pytest.raises(KeyError):


This shouldn't be commented out, right?

Zethson · 2026-01-23T12:38:31Z

+        ("B cell", "B_cell"),
+        ("CD8a", "CD8_T_cell"),
+        ("Mono", "CD14_Mono"),
+    ]  # can't be a list for "run_one_enrichment_test()"


Not sure what's meant with that.

Zethson · 2026-03-09T13:51:39Z

@Jenniliu12 are you going to follow up with this PR soon? Do you need some more comments?
Just want to ensure that I'm not blocking anything.

Zethson · 2026-05-19T10:14:19Z

@Jenniliu12 are you still going to work on this PR or should we close it?

codecov-commenter · 2026-05-20T11:44:18Z

Codecov Report

❌ Patch coverage is 15.38462% with 11 lines in your changes missing coverage. Please review.
✅ Project coverage is 77.26%. Comparing base (12897e1) to head (f253cc8).
⚠️ Report is 80 commits behind head on main.

Files with missing lines	Patch %	Lines
pertpy/data/_datasets.py	15.38%	11 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #901      +/-   ##
==========================================
+ Coverage   73.54%   77.26%   +3.72%     
==========================================
  Files          48       48              
  Lines        5613     6229     +616     
==========================================
+ Hits         4128     4813     +685     
+ Misses       1485     1416      -69

Files with missing lines	Coverage Δ
pertpy/data/__init__.py	`100.00% <ø> (ø)`
pertpy/data/_datasets.py	`42.10% <15.38%> (-57.90%)`	⬇️

... and 10 files with indirect coverage changes

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

Jenniliu12 · 2026-05-25T09:22:06Z

Tutorials PR: scverse/pertpy-tutorials#59 is ready for review. I think it needs to be merged into the scverse/pertpy-tutorials main branch first before I can update the submodule in here, is this correct?

Zethson · 2026-05-25T09:35:56Z

Tutorials PR: scverse/pertpy-tutorials#59 is ready for review. I think it needs to be merged into the scverse/pertpy-tutorials main branch first before I can update the submodule in here, is this correct?

Actually, no. You can update the submodule in this PR to point to your branch.

Jenniliu12 · 2026-05-25T16:20:10Z

Just updated the submodule. Does this build fail have anything to do with my changes? Claude says "it's a pre-existing pertpy docs config problem", but do I need to do anything else now or is it really ready for review now? :)

Zethson · 2026-05-25T17:47:04Z

 [submodule "docs/notebooks"]
 	path = docs/tutorials/notebooks
-	url = https://github.com/scverse/pertpy-tutorials/
+	url = https://github.com/Jenniliu12/pertpy-tutorials/


Do not change this, please! This is also not described in the contributing guide

Okay got it, sorry!

Can I please have some additional guidance on the correct steps? I could not find specific information about submodules in the contributing guide. Can you please point me to the specific section in the docs? (I followed steps recommended by claude, and I was misguided)

My current understanding:

I revert the .gitmodules url back to the original https://github.com/scverse/pertpy-tutorials/ ,

My only change is pointing the SHA in the submodule directory to the tutorial commit in my pertpy-tutorials branch (Is this all you meant with "update the submodule in this PR to point to your branch")

Zethson · 2026-05-26T07:43:06Z

Just updated the submodule. Does this build fail have anything to do with my changes? Claude says "it's a pre-existing pertpy docs config problem", but do I need to do anything else now or is it really ready for review now? :)

It's not ready for a review.

The PR has merge conflicts because the submodule pointer isn't right.
The pre-commit checks fail.
The ReadTheDocs build fails.

Please take some time to understand what's happening. I'm always happy to help. The contributing guide is your friend.

…xtension

Zethson · 2026-05-28T08:36:25Z

We're getting there 😄
However, the cytokine file is not a dataset. It belongs to the metadata module and should be there.

Concerning the tutorial:

try:
    import matplotlib.pyplot as plt
    import seaborn as sns
except ImportError as e:
    raise ImportError(
        f"Plotting requires matplotlib and seaborn ({e.name} not found). "
        "Install these separately."
    ) from e

Please remove this.

Please also ensure that sentences in markdown cells are on their own lines for easier reviews.

Thanks!

Jenniliu12 added 6 commits January 6, 2026 00:46

added hucira tool. Just run_one_enrichment

20ae692

added robustness_test.py from huCIRA package

768d0f9

Modified dict loading and added pl tools and sender receiver tl.

afafba3

added function wrapper run_all_enrichment_test()

3193fdd

removed import of gseapy

ea2fbfd

added dependencies and very generic tests

df4371c

Jenniliu12 marked this pull request as draft January 12, 2026 22:20

Zethson requested changes Jan 23, 2026

View reviewed changes

remove hucira module, keep only hcd loading function.

bbdae6a

Point tutorials submodule at fork branch for huCIRA enrichment tutorial

e423ccf

Jenniliu12 marked this pull request as ready for review May 25, 2026 16:16

Zethson reviewed May 25, 2026

View reviewed changes

Revert .gitmodules URL to scverse/pertpy-tutorials

38a3899

Jenniliu12 mentioned this pull request May 27, 2026

Added section for human cytokine dictionary in enrichment.py module scverse/pertpy-tutorials#59

Open

Jenniliu12 added 3 commits May 28, 2026 00:22

Merge remote-tracking branch 'upstream/main' into feature/hucira

3d4ea68

changed kernel to default and updated tutorial intro for the hucira e…

14e07c4

…xtension

Update tutorials submodule to latest enrichment notebook commit

f253cc8

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