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

.github/workflows/ci-tests.yml

@@ -12,12 +12,13 @@ on:
   workflow_dispatch:
 
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref_name }}
   cancel-in-progress: ${{ github.event_name == 'pull_request' }}
 
 jobs:
   pytester:
     runs-on: ${{ matrix.os }}
+    timeout-minutes: 30
     strategy:
         fail-fast: false
         matrix:
@@ -50,4 +51,4 @@ jobs:
           uv pip list
 
       - name: Run tests
-        run: pytest tests/ -v --disable-warnings --color=yes
+        run: pytest tests/ -v --color=yes -n 2 --dist=loadfile

requires_test.txt

@@ -1,4 +1,5 @@
 pytest ==8.3.2
+pytest-xdist ==3.6.1
 
 mygene ==3.2.2
 scvi-tools >=1.1.0, <1.3.0

tests/conftest.py

@@ -0,0 +1,46 @@
+# -*- coding: utf-8 -*-
+"""
+Pytest configuration and fixtures for TDC tests.
+
+This conftest.py ensures shared directories are cleaned before test execution
+to prevent race conditions and shared state issues in parallel testing.
+"""
+
+import os
+import shutil
+from contextlib import suppress
+
+import pytest
+
+
+@pytest.fixture(scope="session", autouse=True)
+def cleanup_shared_directories():
+    """
+    Clean up shared ./data and ./oracle directories before test session starts.
+
+    This fixture runs automatically before any tests to ensure a clean state,
+    preventing race conditions when tests run in parallel with pytest-xdist.
+
+    With pytest-xdist, session-scoped fixtures run once per worker process,
+    but since all workers share the same working directory, we need to be
+    careful about race conditions. The --dist=loadfile strategy helps by
+    grouping tests by file to the same worker.
+    """
+    # Get the root directory where tests are run from
+    root_dir = os.getcwd()
+
+    # Clean up before tests start
+    for directory in ["data", "oracle"]:
+        dir_path = os.path.join(root_dir, directory)
+        with suppress(FileNotFoundError):
+            shutil.rmtree(dir_path)
+
+    # Let tests run
+    yield
+
+    # Optional: Clean up after tests complete
+    # Commented out to allow inspection of test artifacts
+    # for directory in ["data", "oracle"]:
+    #     dir_path = os.path.join(root_dir, directory)
+    #     with suppress(FileNotFoundError):
+    #         shutil.rmtree(dir_path)