scatrans 0.9.6.dev0__tar.gz → 0.9.8.dev0__tar.gz

scatrans-0.9.8.dev0/.pre-commit-config.yaml

@@ -0,0 +1,34 @@
+# Pre-commit hooks for scATrans
+# Install: pip install pre-commit
+# Setup: pre-commit install
+# Run manually: pre-commit run --all-files
+
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.4.4
+    hooks:
+      - id: ruff
+        args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format
+
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.10.0
+    hooks:
+      - id: mypy
+        additional_dependencies: []
+        args: [--ignore-missing-imports, --no-error-summary]
+        # mypy on the src layout; relax for now to avoid blocking on third-party stubs
+        exclude: |
+          (?x)^(
+            tests/|
+            backup/|
+            src/scatrans/_version.py
+          )
+
+  # Optional pyright (static type checker, often stricter). Requires node + pyright.
+  # Uncomment if you have pyright in your env (npm i -g pyright or via pyright package).
+  # - repo: https://github.com/RobertCraigie/pyright-python
+  #   rev: v1.1.367
+  #   hooks:
+  #     - id: pyright
+  #       additional_dependencies: [".[dev]"]

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/CHANGELOG.md

@@ -5,6 +5,16 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.9.2 bugfix 2026-07-02]
+
+### Fixed
+- **filter_active_genes permissive mode**: default/permissive thresholds for `pval_cutoff`, `active_score_fdr_cutoff`, and `unspliced_excess_fdr_cutoff` now use `float("inf")` instead of `1.0`, so genes with adjusted p-value or permutation FDR exactly equal to 1.0 are no longer silently dropped (strict `<` vs `1.0` bug).
+- **CI lint**: removed unused `import scanpy as sc` from `tl.py` and `_permutation.py` (leftover from permutation refactor); fixed `test_enrich_api.py` formatting.
+- **CI tests**: `test_pp_bias_cli` GTF generator tests now `pytest.importorskip("gtfparse")` so base installs without `scatrans[gene_features]` skip instead of failing.
+
+### Added
+- Regression test `test_filter_active_genes_permissive_keeps_padj_one`.
+
 ## [Unreleased / Review 2026-06-27]
 ### Added / Improved
 - Clarified and documented the `gamma_method="empirical_bayes"` implementation as **hierarchical (分层) gamma estimation** for the reference U/S ratio (README keeps the CN term; source now English-only).

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scatrans
-Version: 0.9.6.dev0
+Version: 0.9.8.dev0
 Summary: Single-cell Active Transcription Analysis
 Author: scATrans Developers
 License: Apache-2.0

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/scatrans.egg-info/SOURCES.txt

@@ -1,4 +1,5 @@
 .gitignore
+.pre-commit-config.yaml
 CHANGELOG.md
 CITATION.cff
 LICENSE

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/src/scatrans/_permutation.py

@@ -12,7 +12,6 @@ import warnings
 from typing import Any
 
 import numpy as np
-import scanpy as sc
 from joblib import Parallel, delayed
 from statsmodels.stats.multitest import multipletests
 

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/src/scatrans/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '0.9.6.dev0'
-__version_tuple__ = version_tuple = (0, 9, 6, 'dev0')
+__version__ = version = '0.9.8.dev0'
+__version_tuple__ = version_tuple = (0, 9, 8, 'dev0')
 
-__commit_id__ = commit_id = 'g9392b05f0'
+__commit_id__ = commit_id = None

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/src/scatrans/tl.py

@@ -23,7 +23,6 @@ import anndata as ad
 import joblib
 import numpy as np
 import pandas as pd
-import scanpy as sc
 import scipy.sparse as sparse  # for type hints in signatures (e.g. spmatrix)
 
 # qc is imported lazily inside active_score to keep startup light, but exposed at package level
@@ -36,13 +35,13 @@ from ._utils import (
     UNSPLICED_EXCESS_FDR_COL,
     UNSPLICED_EXCESS_PVAL_COL,
     UNSPLICED_EXCESS_RESIDUAL_COL,
+    _apply_de_preprocess,
+    _clear_log_preprocess_metadata,
     _get_exponential_scale_lambda,
     _is_integer_counts_like,
     _normalize_group_label,
     _normalize_velocity_layers_by_size_factor,
     _pseudobulk_with_layers,
-    _apply_de_preprocess,
-    _clear_log_preprocess_metadata,
     _resolve_aligned_raw_counts,
     _soft_scale,
     _validate_group_contrast,
@@ -2104,12 +2103,12 @@ def filter_active_genes(
         elif p in ("permissive", "none", "all", "no_filter"):
             preset_vals = {
                 "active_score_cutoff": 0.0,
-                "pval_cutoff": 1.0,
+                "pval_cutoff": float("inf"),
                 "velocity_residual_cutoff": float("-inf"),
                 "unspliced_excess_residual_cutoff": float("-inf"),
                 "logfc_cutoff": float("inf"),
-                "active_score_fdr_cutoff": 1.0,
-                "unspliced_excess_fdr_cutoff": 1.0,
+                "active_score_fdr_cutoff": float("inf"),
+                "unspliced_excess_fdr_cutoff": float("inf"),
                 "effective_gamma_min": float("-inf"),
                 "effective_gamma_max": None,
                 "delta_variance_min": None,
@@ -2143,10 +2142,10 @@ def filter_active_genes(
         "active_score_cutoff",
     )
     pval_cutoff = _coerce_numeric_cutoff(
-        _resolve("pval_cutoff", pval_cutoff, 1.0), 1.0, "pval_cutoff"
+        _resolve("pval_cutoff", pval_cutoff, float("inf")), float("inf"), "pval_cutoff"
     )
-    if not math.isfinite(pval_cutoff) or pval_cutoff < 0:
-        raise ValueError("pval_cutoff must be a finite non-negative number.")
+    if pval_cutoff < 0 or (not math.isfinite(pval_cutoff) and not math.isinf(pval_cutoff)):
+        raise ValueError("pval_cutoff must be non-negative, finite, or +inf (permissive).")
     if (
         velocity_residual_cutoff is not _NOT_PROVIDED
         and unspliced_excess_residual_cutoff is _NOT_PROVIDED
@@ -2175,9 +2174,11 @@ def filter_active_genes(
         raise ValueError(
             f'logfc_direction={logfc_direction!r} not recognized. Use one of: "up", "down", "both".'
         )
-    active_score_fdr_cutoff = _resolve("active_score_fdr_cutoff", active_score_fdr_cutoff, 1.0)
+    active_score_fdr_cutoff = _resolve(
+        "active_score_fdr_cutoff", active_score_fdr_cutoff, float("inf")
+    )
     unspliced_excess_fdr_cutoff = _resolve(
-        "unspliced_excess_fdr_cutoff", unspliced_excess_fdr_cutoff, 1.0
+        "unspliced_excess_fdr_cutoff", unspliced_excess_fdr_cutoff, float("inf")
     )
     effective_gamma_min = _resolve("effective_gamma_min", effective_gamma_min, float("-inf"))
     effective_gamma_max = _resolve("effective_gamma_max", effective_gamma_max, None)

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/tests/test_basic.py

@@ -161,6 +161,25 @@ def test_filter_active_genes_permissive_inf_logfc(adata_basic):
     assert len(out) == len(allr)
 
 
+def test_filter_active_genes_permissive_keeps_padj_one():
+    """Default/permissive mode must not drop genes with p_adj or FDR exactly 1.0."""
+    df = pd.DataFrame(
+        {
+            "logFC": [0.1, -0.2, 0.5, -0.9, 0.0],
+            "p_val": [1.0, 0.9, 0.5, 0.2, 1.0],
+            "p_adj": [1.0, 1.0, 0.8, 0.3, 1.0],
+            "active_score_fdr": [1.0, 0.9, 0.5, 0.2, 1.0],
+            "unspliced_excess_fdr": [1.0, 1.0, 0.8, 0.3, 1.0],
+        },
+        index=[f"g{i}" for i in range(5)],
+    )
+    out_default = scat.filter_active_genes(df)
+    out_permissive = scat.filter_active_genes(df, preset="permissive")
+    assert len(out_default) == 5
+    assert len(out_permissive) == 5
+    assert set(out_default.index) == set(df.index)
+
+
 def test_add_gene_features_and_list(adata_basic):
     # Should not crash even if features are incomplete
     adata_basic.var.columns.tolist()

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/tests/test_enrich_api.py

@@ -53,7 +53,11 @@ def test_extract_gene_lists_single_df():
 def test_extract_gene_lists_prefers_gene_column_over_range_index():
     """Scanpy-style DE tables use a 'gene'/'names' column with a default RangeIndex."""
     df = pd.DataFrame(
-        {"gene": ["G_up", "G_down", "G_ns"], "logFC": [1.2, -0.9, 0.1], "p_adj": [0.01, 0.02, 0.5]},
+        {
+            "gene": ["G_up", "G_down", "G_ns"],
+            "logFC": [1.2, -0.9, 0.1],
+            "p_adj": [0.01, 0.02, 0.5],
+        },
     )
     out = scat.extract_gene_lists(df, logfc_cutoff=0.5, pval_cutoff=0.05, logfc_direction="up")
     assert out["contrast"] == ["G_up"]
@@ -67,9 +71,7 @@ def test_extract_gene_lists_separate_directions_single_df_matches_dict():
     single = scat.extract_gene_lists(
         df, logfc_direction="up", separate_directions=True, name_prefix="X"
     )
-    multi = scat.extract_gene_lists(
-        {"X": df}, logfc_direction="up", separate_directions=True
-    )
+    multi = scat.extract_gene_lists({"X": df}, logfc_direction="up", separate_directions=True)
     assert single == multi
     assert single == {"X_up": ["G1", "G3"], "X_down": ["G2", "G4"]}
 

{scatrans-0.9.6.dev0 → scatrans-0.9.8.dev0}/tests/test_pp_bias_cli.py

@@ -8,6 +8,7 @@ import scatrans as scat
 
 
 def test_generate_gene_features_no_exon_rows(tmp_path):
+    pytest.importorskip("gtfparse")
     from scatrans.pp_bias import generate_gene_features_from_gtf
 
     gtf = tmp_path / "no_exon.gtf"
@@ -22,6 +23,7 @@ def test_generate_gene_features_no_exon_rows(tmp_path):
 
 
 def test_generate_gene_features_dedup_gene_names(tmp_path):
+    pytest.importorskip("gtfparse")
     from scatrans.pp_bias import generate_gene_features_from_gtf
 
     gtf = tmp_path / "dup.gtf"