update cicd config

.github/ISSUE_TEMPLATE/config.yml

@@ -1,5 +1,5 @@
 blank_issues_enabled: false
 contact_links:
-  - name: Discussions
-    url: https://github.com/AustralianCancerDataNetwork/hemonc-alchemy/discussions
-    about: Questions and general discussion about HemOnc Alchemy.
+  - name: Existing issues
+    url: https://github.com/AustralianCancerDataNetwork/hemonc-alchemy/issues
+    about: Search existing issues before opening a new report.

tests/test_enum_casting.py

@@ -138,6 +138,10 @@ def test_unknown_value_is_dropped_not_crashed(self, sqlite_session, tmp_path):
         assert set(rows) == {Canonicaltriples_Class_1Enum.PROCEDURE, Canonicaltriples_Class_1Enum.REGIMEN}
 
 
+@pytest.mark.skipif(
+    not _REAL_DATA_DIR.is_dir(),
+    reason=f"real HemOnc extracts not found at {_REAL_DATA_DIR} (set HEMONC_DATA_DIR)",
+)
 @pytest.mark.postgres
 class TestSurrogatePkEnumColumn:
     """`Drugs` is a surrogate-PK ("content") table with a nullable sa.Enum

tests/test_notebook_taxonomy.py

@@ -1,8 +1,11 @@
 """Tests for the notebooks' shared classification rules.
 
 `notebooks/_taxonomy.py` is not part of the installed package -- it is a
-helper the demonstration notebooks import. It is tested here because four
-notebooks depend on it and their published figures change if it drifts.
+helper the optional demonstration notebooks import. When the notebook bundle
+is present locally, it is tested here because several notebooks depend on it
+and their published figures change if it drifts. Package CI may not check out
+the ignored notebook bundle, so the module-level import is intentionally
+optional.
 """
 
 from __future__ import annotations
@@ -16,7 +19,10 @@
 if str(NOTEBOOKS) not in sys.path:
     sys.path.insert(0, str(NOTEBOOKS))
 
-import _taxonomy as taxonomy
+taxonomy = pytest.importorskip(
+    "_taxonomy",
+    reason="notebook helpers are optional and are not included in package CI",
+)
 
 
 @pytest.mark.parametrize(