scib-metrics 0.5.7__tar.gz → 0.5.8__tar.gz

{scib_metrics-0.5.7 → scib_metrics-0.5.8}/.pre-commit-config.yaml

@@ -11,7 +11,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.12
+    rev: v0.14.14
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]
@@ -41,6 +41,6 @@ repos:
         language: fail
         files: '.*\.rej$'
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.1
+    rev: 0.9.0
     hooks:
       - id: nbstripout

{scib_metrics-0.5.7 → scib_metrics-0.5.8}/CHANGELOG.md

@@ -10,6 +10,27 @@ and this project adheres to [Semantic Versioning][].
 
 ## 0.6.0 (unreleased)
 
+## 0.5.8 (2025-XX-XX)
+
+### Added
+
+- Add set seed if using Leiden, {pr}`240`.
+
+### Changed
+
+### Fixed
+
+## 0.5.7 (2025-09-14)
+
+### Added
+
+- Add added solver selection to benchmarker for arpack stability issues {pr}`229`.
+- Add support for Python 3.13 and removed support for 3.10 {pr}`229`.
+
+### Changed
+
+### Fixed
+
 ## 0.5.6 (2025-07-08)
 
 ### Added

{scib_metrics-0.5.7 → scib_metrics-0.5.8}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: scib-metrics
-Version: 0.5.7
+Version: 0.5.8
 Summary: Accelerated and Python-only scIB metrics
 Project-URL: Documentation, https://scib-metrics.readthedocs.io/
 Project-URL: Source, https://github.com/yoseflab/scib-metrics
@@ -62,11 +62,12 @@ Requires-Dist: ipykernel; extra == 'doc'
 Requires-Dist: ipython; extra == 'doc'
 Requires-Dist: myst-nb; extra == 'doc'
 Requires-Dist: numba>=0.57.1; extra == 'doc'
+Requires-Dist: pybtex-docutils>=1.0.0; extra == 'doc'
 Requires-Dist: scanpydoc[typehints]>=0.7.4; extra == 'doc'
 Requires-Dist: sphinx-book-theme>=1.0; extra == 'doc'
 Requires-Dist: sphinx-copybutton; extra == 'doc'
 Requires-Dist: sphinx>=4; extra == 'doc'
-Requires-Dist: sphinxcontrib-bibtex>=1.0.0; extra == 'doc'
+Requires-Dist: sphinxcontrib-bibtex>=2.6; extra == 'doc'
 Requires-Dist: sphinxext-opengraph; extra == 'doc'
 Provides-Extra: parallel
 Requires-Dist: joblib; extra == 'parallel'

{scib_metrics-0.5.7 → scib_metrics-0.5.8}/pyproject.toml

@@ -5,7 +5,7 @@ requires = ["hatchling"]
 
 [project]
 name = "scib-metrics"
-version = "0.5.7"
+version = "0.5.8"
 description = "Accelerated and Python-only scIB metrics"
 readme = "README.md"
 requires-python = ">=3.11"
@@ -40,7 +40,8 @@ doc = [
     "sphinx>=4",
     "sphinx-book-theme>=1.0",
     "myst-nb",
-    "sphinxcontrib-bibtex>=1.0.0",
+    "sphinxcontrib-bibtex>=2.6",
+    "pybtex-docutils>=1.0.0",
     "scanpydoc[typehints]>=0.7.4",
     "sphinxext-opengraph",
     # For notebooks

{scib_metrics-0.5.7 → scib_metrics-0.5.8}/src/scib_metrics/metrics/_nmi_ari.py

@@ -120,7 +120,7 @@ def nmi_ari_cluster_labels_leiden(
             from joblib import Parallel, delayed
 
             out = Parallel(n_jobs=n_jobs)(
-                delayed(_compute_nmi_ari_cluster_labels)(conn_graph, labels, r) for r in resolutions
+                delayed(_compute_nmi_ari_cluster_labels)(conn_graph, labels, r, seed=seed) for r in resolutions
             )
         except ImportError:
             warnings.warn("Using for loop over clustering resolutions. `pip install joblib` for parallelization.")
@@ -130,6 +130,6 @@ def nmi_ari_cluster_labels_leiden(
         nmi, ari = nmi_ari[nmi_ind, :]
         return {"nmi": nmi, "ari": ari}
     else:
-        nmi, ari = _compute_nmi_ari_cluster_labels(conn_graph, labels, resolution)
+        nmi, ari = _compute_nmi_ari_cluster_labels(conn_graph, labels, resolution, seed=seed)
 
     return {"nmi": nmi, "ari": ari}