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

[ameynert]

Summary

• Adds divref/tests/conftest.py with a session-scoped hail_context fixture that calls hl.init(quiet=True) once per test session and hl.stop() on exit
• Removes @pytest.mark.skip from test_get_haplo_sequence_edge_cases — the test already mocked hl.get_sequence correctly and only needed an active Hail context to call hl.eval()
• Adds a setup-java step (Temurin JDK 11) to python_package.yml so hl.init() can find a JVM on the GitHub Actions runner

How it works

Tests that require Hail add hail_context: None as a parameter; pytest injects the session fixture, ensuring hl.init() has been called before any Hail expressions are evaluated. The fixture is not autouse, so non-Hail tests incur no startup overhead.

Test plan

• pixi run check-all passes locally (Java provided by pixi hail feature)
• Python toolkit checks CI passes with Java available (JDK 11 via setup-java)
• test_get_haplo_sequence_edge_cases passes (not skipped)

🤖 Generated with Claude Code

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on base/target branches other than the default branch.

Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 982e47f8-68c4-49dd-991f-b0574b30d764

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch am_13_enable_hail_tests

---

_{Comment @coderabbitai help to get the list of available commands and usage tips.}