test: enable Hail tests via session fixture and CI Java setup

.github/workflows/python_package.yml

@@ -25,6 +25,12 @@ jobs:
           enable-cache: 'true'
           cache-suffix: ${{ matrix.PYTHON_VERSION }}
 
+      - name: Set up Java
+        uses: actions/setup-java@be666c2fcd27ec809703dec50e508c2fdc7f6654  # v5.2.0
+        with:
+          distribution: temurin
+          java-version: '11'
+
       - name: Test the library
         run: |
           uv run --directory divref --locked poe check-all

divref/tests/conftest.py

@@ -0,0 +1,20 @@
+"""Shared pytest fixtures for the divref test suite."""
+
+from collections.abc import Generator
+
+import hail as hl
+import pytest
+
+
+@pytest.fixture(scope="session")
+def hail_context() -> Generator[None, None, None]:
+    """
+    Initialize a local Hail context for the test session.
+
+    Starts a local Spark/JVM context once per session and stops it on exit.
+    Tests that use Hail expressions must request this fixture explicitly.
+    Requires Java 11+ to be available in PATH (provided by pixi or setup-java).
+    """
+    hl.init(quiet=True)
+    yield
+    hl.stop()

divref/tests/tools/test_create_fasta_and_index.py

@@ -55,8 +55,7 @@ def mock_get_sequence(
     return mock_get_sequence
 
 
-@pytest.mark.skip(reason="Requires a running Hail/Spark JVM context")
-def test_get_haplo_sequence_edge_cases() -> None:
+def test_get_haplo_sequence_edge_cases(hail_context: None) -> None:  # noqa: ARG001
     """Test get_haplo_sequence with SNPs, insertions, and deletions."""
     reference = "01234567891"