scatrans 0.9.8.dev5__tar.gz → 0.9.8.dev6__tar.gz

{scatrans-0.9.8.dev5 → scatrans-0.9.8.dev6}/CHANGELOG.md

@@ -8,6 +8,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ## [0.9.8 bugfix 2026-07-04]
 
 ### Fixed
+- **CI pytest failure on matrix legs without `pydeseq2`**: two new pseudobulk regression tests
+  (`test_strict_pydeseq2_counts_rejects_log_normalized_*`) now use the same
+  `@pytest.mark.skipif(importlib.util.find_spec("pydeseq2") is None, ...)` guard as
+  `tests/test_de_backends.py`, instead of relying on production-code check ordering.
+  Restored PyDESeq2 `ImportError` (missing dependency) ahead of data-validation `ValueError`
+  in `_run_de_wrapper`, so users without `pydeseq2` see the install hint first.
 - **Pseudobulk `strict_pydeseq2_counts` check ran on already-rounded data**: `_pseudobulk_with_layers`
   always rounds aggregated sums to integers, so the PyDESeq2 count-likeness check in
   `_run_de_wrapper` (which inspected the rounded pseudobulk `.X`) could never detect that the

{scatrans-0.9.8.dev5 → scatrans-0.9.8.dev6}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scatrans
-Version: 0.9.8.dev5
+Version: 0.9.8.dev6
 Summary: Single-cell Active Transcription Analysis
 Author: scATrans Developers
 License: Apache-2.0

{scatrans-0.9.8.dev5 → scatrans-0.9.8.dev6}/src/scatrans/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.9.8.dev5'
-__version_tuple__ = version_tuple = (0, 9, 8, 'dev5')
+__version__ = version = '0.9.8.dev6'
+__version_tuple__ = version_tuple = (0, 9, 8, 'dev6')
 
 __commit_id__ = commit_id = None

{scatrans-0.9.8.dev5 → scatrans-0.9.8.dev6}/tests/test_regression_bugs.py

@@ -2,6 +2,7 @@
 
 from __future__ import annotations
 
+import importlib.util
 import logging
 import sys
 from unittest.mock import patch
@@ -194,6 +195,10 @@ def test_diagnose_design_kb_python_layers(adata_mature_nascent):
     assert 0.0 <= diag["unspliced_global_fraction"] <= 1.0
 
 
+@pytest.mark.skipif(
+    importlib.util.find_spec("pydeseq2") is None,
+    reason="pydeseq2 not installed",
+)
 def test_strict_pydeseq2_counts_rejects_log_normalized_pseudobulk():
     """Rounding before integer check must not let log-normalized pb data through."""
     rng = np.random.default_rng(7)
@@ -238,6 +243,10 @@ def test_pseudobulk_with_layers_flags_non_count_source_before_rounding():
     assert pb.uns["pb_x_is_count_like"] is False
 
 
+@pytest.mark.skipif(
+    importlib.util.find_spec("pydeseq2") is None,
+    reason="pydeseq2 not installed",
+)
 def test_strict_pydeseq2_counts_rejects_log_normalized_layer_end_to_end():
     """End-to-end: use_pseudobulk=True + pb_x_layer pointing at log-normalized data must raise,
     not silently round the log-normalized sums into look-alike integers."""

{scatrans-0.9.8.dev5 → scatrans-0.9.8.dev6}/src/scatrans/_de.py

@@ -185,6 +185,18 @@ def _run_de_wrapper(
             _ann_log.setLevel(_prev_ann)
 
     if is_pseudobulk and pb_backend == "pydeseq2":
+        try:
+            from pydeseq2.dds import DeseqDataSet
+            from pydeseq2.ds import DeseqStats
+        except ImportError as e:
+            raise ImportError(
+                "PyDESeq2 backend requested but 'pydeseq2' is not installed.\n"
+                "Install with:\n"
+                '    pip install "scatrans[pseudobulk]"\n'
+                "or\n"
+                "    pip install pydeseq2"
+            ) from e
+
         n_t = (ad_temp.obs[use_groupby] == target_group).sum()
         n_r = (ad_temp.obs[use_groupby] == reference_group).sum()
         if n_t < 2 or n_r < 2:
@@ -256,18 +268,6 @@ def _run_de_wrapper(
                 f"No genes passed the DESeq2 count filter (sum(counts) >= {min_counts_per_gene})."
             )
 
-        try:
-            from pydeseq2.dds import DeseqDataSet
-            from pydeseq2.ds import DeseqStats
-        except ImportError as e:
-            raise ImportError(
-                "PyDESeq2 backend requested but 'pydeseq2' is not installed.\n"
-                "Install with:\n"
-                '    pip install "scatrans[pseudobulk]"\n'
-                "or\n"
-                "    pip install pydeseq2"
-            ) from e
-
         condition = ad_temp.obs[use_groupby].astype(str).values
         metadata = pd.DataFrame(
             {use_groupby: pd.Categorical(condition, categories=[reference_group, target_group])},