Refactor

.pre-commit-config.yaml

@@ -14,11 +14,15 @@ repos:
       - id: poetry-check
       - id: poetry-lock
   - repo: https://github.com/psf/black
-    rev: 23.9.0
+    rev: 24.3.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
       - id: isort
         args: ["--profile", "black"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.9.0
+    hooks:
+      - id: mypy

data/hrdetect_labels_training.csv

@@ -0,0 +1,312 @@
+,hrdetect_score,hrd_label
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mypy.ini

@@ -0,0 +1,35 @@
+[mypy]
+allow_redefinition = True
+warn_unused_configs = True
+python_version = 3.11
+
+files =
+    src
+
+#
+# Third party dependencies that don't have types.
+#
+
+[mypy-adjustText.*]
+ignore_missing_imports = True
+
+[mypy-anndata.*]
+ignore_missing_imports = True
+
+[mypy-fastcluster.*]
+ignore_missing_imports = True
+
+[mypy-mudata.*]
+ignore_missing_imports = True
+
+[mypy-numba.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-sklearn.*]
+ignore_missing_imports = True
+
+[mypy-umap.*]
+ignore_missing_imports = True