pre-commit nox

Author: strasserle

.github/workflows/run_tests.yml

@@ -13,42 +13,42 @@ jobs:
             matrix:
                 include:
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "pre-commit",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "safety",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "mypy",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: windows-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: macos-latest,
                           session: "tests",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "typeguard",
                       }
                     - {
-                          python-version: 3.9,
+                          python-version: 3.13,
                           os: ubuntu-latest,
                           session: "xdoctest",
                       }

docs/_tutorials/spapros_tutorial_advanced_evaluation.ipynb

@@ -19,13 +19,14 @@
       ~spapros.ev.ProbesetEvaluator.compute_or_load_shared_results
       ~spapros.ev.ProbesetEvaluator.evaluate_probeset
       ~spapros.ev.ProbesetEvaluator.evaluate_probeset_pipeline
+      ~spapros.ev.ProbesetEvaluator.load_results
       ~spapros.ev.ProbesetEvaluator.pipeline_summary_statistics
       ~spapros.ev.ProbesetEvaluator.plot_cluster_similarity
+      ~spapros.ev.ProbesetEvaluator.plot_coexpression
       ~spapros.ev.ProbesetEvaluator.plot_confusion_matrix
-      ~spapros.ev.ProbesetEvaluator.plot_correlation_matrix
       ~spapros.ev.ProbesetEvaluator.plot_evaluations
       ~spapros.ev.ProbesetEvaluator.plot_knn_overlap
-      ~spapros.ev.ProbesetEvaluator.plot_marker_correlation
+      ~spapros.ev.ProbesetEvaluator.plot_marker_corr
       ~spapros.ev.ProbesetEvaluator.plot_summary
       ~spapros.ev.ProbesetEvaluator.summary_statistics
 

docs/ev/spapros.ev.ProbesetEvaluator.rst

@@ -17,9 +17,8 @@
       :toctree: .
 
       ~spapros.se.ProbesetSelector.info
-      ~spapros.se.ProbesetSelector.plot_classification_rule_umaps
+      ~spapros.se.ProbesetSelector.plot_clf_genes
       ~spapros.se.ProbesetSelector.plot_coexpression
-      ~spapros.se.ProbesetSelector.plot_decision_genes
       ~spapros.se.ProbesetSelector.plot_gene_overlap
       ~spapros.se.ProbesetSelector.plot_histogram
       ~spapros.se.ProbesetSelector.plot_masked_dotplot

docs/se/spapros.se.ProbesetSelector.rst

@@ -18,14 +18,15 @@
     sys.exit(1)
 
 package = "spapros"
-python_versions = ["3.9", "3.10", "3.13"]
+python_versions = ["3.13"]
 nox.options.sessions = (
     "pre-commit",
     "safety",
     "mypy",
     "tests",
-    # "xdoctest",
-    # "docs-build",
+    "xdoctest",
+    "docs-build",
+    "typeguard",
 )