From b27c771155b12bde4b14dbb713029e0d25b3eab2 Mon Sep 17 00:00:00 2001 From: Georgie Kennedy Date: Sun, 6 Sep 2026 15:39:30 +1000 Subject: [PATCH 1/3] update cicd config --- .github/ISSUE_TEMPLATE/config.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 63fa676..b61727b 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.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. From 39fab27eea801084d3d9092ee534e133e182d0f0 Mon Sep 17 00:00:00 2001 From: Georgie Kennedy Date: Sun, 6 Sep 2026 15:49:18 +1000 Subject: [PATCH 2/3] modified tests --- tests/test_notebook_taxonomy.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/tests/test_notebook_taxonomy.py b/tests/test_notebook_taxonomy.py index d40e8b7..da5de60 100644 --- a/tests/test_notebook_taxonomy.py +++ b/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( From 3e1776097f98f034cbf4a8cbca995825814b445e Mon Sep 17 00:00:00 2001 From: Georgie Kennedy Date: Sun, 6 Sep 2026 15:55:56 +1000 Subject: [PATCH 3/3] fixing data-specific tests --- tests/test_enum_casting.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/test_enum_casting.py b/tests/test_enum_casting.py index d4c3a9f..b08fb6e 100644 --- a/tests/test_enum_casting.py +++ b/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