reformat code

Author: GuyTeichman

packaging/generate_changelog.py

@@ -1,10 +1,9 @@
 import re
 import warnings
 from pathlib import Path
-from typing import Union
+from typing import Literal, Union
 
 import rst_to_myst
-from typing import Literal
 
 
 def get_change_log_for(version: Union[str, Literal['latest']] = 'latest'):

rnalysis/utils/enrichment_runner.py

@@ -923,11 +923,10 @@ def format_results(self, unformatted_results_list: list):
 
         # filter non-significant results
         if not self.return_nonsignificant:
-            self.results = self.results.filter(pl.col('significant') is True)
-
+            self.results = self.results.filter(pl.col('significant'))
     def _correct_multiple_comparisons(self):
-        results_nulls = self.results.filter(pl.col('pval').is_nan())
-        self.results = self.results.filter(pl.col('pval').is_not_nan())
+        results_nulls = self.results.filter(pl.col('pval').is_null())
+        self.results = self.results.filter(pl.col('pval').is_not_null())
 
         significant, padj = multitest.fdrcorrection(self.results['pval'].to_list(), alpha=self.alpha)
         self.results = pl.concat([self.results.with_columns(padj=padj, significant=significant), results_nulls],
@@ -1390,6 +1389,7 @@ def _go_classic_on_batch(self, go_term_batch: Iterable[str], annotation_idx: int
         """
         gene_set = self.ranked_genes if self.single_set else self.gene_set
         annotations = self.mutable_annotations[annotation_idx]
+        print(annotations)
         return {go_id: self.stats_test.run(go_id, annotations[go_id], gene_set, self.background_set) for go_id in
                 go_term_batch}
 

setup.py

@@ -3,7 +3,7 @@
 
 """The setup script."""
 
-from setuptools import setup, find_packages
+from setuptools import find_packages, setup
 
 
 def get_extra_requires(path, add_all=True):

tests/test_enrichment_runner.py

@@ -3,6 +3,7 @@
 
 import matplotlib
 import pytest
+from polars.testing import assert_frame_equal
 
 from rnalysis import filtering
 from rnalysis.utils import enrichment_runner
@@ -17,7 +18,7 @@ def _df_to_dict(df, null_mode: bool = True):
     if null_mode:
         return {attr: set(df.filter(pl.col(attr).is_not_null()).select(pl.first()).to_series()) for attr in
                 df.columns[1:]}
-    return {attr: set(df.filter(pl.col(attr) is True).select(pl.first()).to_series()) for attr in df.columns[1:]}
+    return {attr: set(df.filter(pl.col(attr)).select(pl.first()).to_series()) for attr in df.columns[1:]}
 
 
 def test_enrichment_runner_from_results():
@@ -182,7 +183,7 @@ def test_results_to_csv():
 def _compare_go_result_dfs(res, truth):
     res = res.sort(pl.first())
     truth = truth.sort(pl.first())
-    assert res.select(pl.col('GO ID', 'n', 'obs')).equals(truth.select(pl.col('GO ID', 'n', 'obs')))
+    assert_frame_equal(res.select(pl.col('GO ID', 'n', 'obs')),truth.select(pl.col('GO ID', 'n', 'obs')))
     assert np.allclose(res.select(pl.col('exp', 'log2fc', 'pval')), res.select(pl.col('exp', 'log2fc', 'pval')), atol=0)
 
 
@@ -207,7 +208,6 @@ def __getitem__(self, item):
     e.annotations = annotations
     e.mutable_annotations = annotations,
     e.attributes = list(annotations.keys())
-
     res = pl.DataFrame([i for i in e._go_classic_on_batch(tuple(annotations.keys()), 0).values()],
                        schema=['GO ID', 'n', 'obs', 'exp', 'log2fc', 'pval'])
     _compare_go_result_dfs(res, truth)
@@ -354,7 +354,6 @@ def alt_calc_pval(self, log2fc: float, reps: int, obs_frac: float, bg_size: int,
 
     attr = truth[0]
     res = stats_test.run(attr, annotations[attr], gene_set, background_set)
-    print(res)
     assert res == truth
 
 
@@ -732,8 +731,6 @@ def test_noncategorical_enrichment_runner_format_results(monkeypatch):
     truth = io.load_table('tests/test_files/non_categorical_enrichment_runner_format_results_truth.csv')
     runner.return_nonsignificant = True
     runner.format_results(results_list)
-    print(truth)
-    print(runner.results)
     assert truth.equals(runner.results)
 
 
@@ -1040,9 +1037,8 @@ def add_sig(self):
     runner.en_score_col = 'colName'
     runner.single_set = False
     runner.return_nonsignificant = return_nonsignificant
-
     runner.format_results(results_dict)
-    assert truth.equals(runner.results)
+    assert_frame_equal(truth, runner.results)
 
 
 @pytest.mark.parametrize("propagate_annotations,truth",
@@ -1200,7 +1196,6 @@ def _get_annotation_iter_zero(self):
         runner.organism = "organism"
         runner.taxon_id = "taxon id"
         runner._process_annotations()
-    print(e)
 
 
 def test_go_enrichment_runner_process_annotations(monkeypatch):