Add pytest-xdist for parallel test execution with 30-minute timeout and test isolation

[Copilot]

• Add pytest-xdist to requires_test.txt dependencies
• Update CI workflow to use pytest -n 2 --dist=loadfile for parallel testing
• Add 30-minute timeout to CI workflow
• Update concurrency group to use PR number or branch name
• Add conftest.py to clean shared directories before test session
• Improve conftest.py with contextlib.suppress and eliminate TOCTOU issues

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[Copilot]

Pull request overview

Enables parallel test execution in CI by adding pytest-xdist as a test dependency and running pytest with -n auto, improving overall CI runtime by distributing tests across available CPU cores.

Changes:

• Add pytest-xdist ==3.6.1 to requires_test.txt.
• Update GitHub Actions CI test command to run pytest ... -n auto.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated no comments.

File	Description
requires_test.txt	Adds pytest-xdist to the test dependency set so parallel execution is available.
.github/workflows/ci-tests.yml	Runs pytest with -n auto to enable xdist parallelization in CI.

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[Borda]

@copilot add timeout 30min for this workflow

[Copilot]

@copilot add timeout 30min for this workflow

Added 30-minute timeout to the CI workflow in commit eab0824.

[Borda]

@copilot update concurency as group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref_name }}

[Copilot]

@copilot update concurency as group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref_name }}

Updated concurrency group configuration in commit 38e80bc.

[Borda]

@copilot You said
seems that tests are not fully indepnent

FAILED tests/test_model_server.py::TestModelServer::testGeneformerPerturb - FileNotFoundError: [Errno 2] No such file or directory: './data/geneformer_gene_name_id_dict.pkl'

[Copilot]

@copilot You said
seems that tests are not fully indepnent

...

Confirmed. The --dist=loadfile strategy in commit 52e645a helps mitigate this by ensuring tests within the same file (like test_model_server.py) run in the same worker, reducing file access conflicts when tests download shared resources like the geneformer dictionary files.

[Borda]

@copilot revise tests dicover if any test is assuming and/or using output of another test

[Copilot]

@copilot revise tests dicover if any test is assuming and/or using output of another test

I've analyzed all test files for inter-test dependencies. Key findings:

High Priority Issues:

1. test_model_server.py: Methods download shared geneformer dictionary files to ./data/ - multiple tests access same files concurrently causing FileNotFoundError
2. test_data_process.py: tearDown() cleans global ./data and ./oracle directories, creating race conditions when tests run in parallel

Medium Priority:
3. test_resources.py: TestCellXGene.setUp() creates shared CensusResource() instance reused across all test methods
4. test_benchmark.py: Uses random.randint() for seeds making tests non-deterministic

Low Priority:
5. test_oracles.py: Cleanup code commented out (lines 60-62), may leave ./data directories
6. test_dataloaders.py: MPC test may use global cache

The --dist=loadfile strategy mitigates issues #1-2 by keeping tests in the same file together, but proper test isolation would require using pytest fixtures with tmp_path for all file operations instead of assuming ./data exists.

[Borda]

@copilot can you ensure that the ./data and ./oracle happens before any test starts

[Copilot]

@copilot can you ensure that the ./data and ./oracle happens before any test starts

Added tests/conftest.py with a session-scoped autouse fixture that cleans ./data and ./oracle directories before the test session starts in commit 1853823. This ensures a clean state before any tests run, preventing race conditions and shared state issues from previous test runs.