Add Cluster-based E2E tests for VCT

tests/conftest.py

@@ -1,21 +1,78 @@
+import shutil
+from datetime import datetime
+
 import pytest
 from _pytest.config import Config, argparsing
 from _pytest.python import Function
 
+SLOW_TEST_DAY = "Sunday"
+
 
 def pytest_addoption(parser: argparsing.Parser) -> None:
     parser.addoption("--runslow", action="store_true", default=False, help="run slow tests")
+    parser.addoption(
+        "--slurm-project",
+        type=str,
+        default="proj_simscience",
+        help="SLURM project for cluster tests (default: proj_simscience)",
+    )
 
 
 def pytest_configure(config: Config) -> None:
     config.addinivalue_line("markers", "slow: mark test as slow to run")
+    config.addinivalue_line(
+        "markers", "cluster: mark test as requiring a SLURM cluster environment"
+    )
 
 
 def pytest_collection_modifyitems(config: Config, items: list[Function]) -> None:
-    if config.getoption("--runslow"):
-        # --runslow given in cli: do not skip slow tests
-        return
-    skip_slow = pytest.mark.skip(reason="need --runslow option to run")
-    for item in items:
-        if "slow" in item.keywords:
-            item.add_marker(skip_slow)
+    if not config.getoption("--runslow"):
+        skip_slow = pytest.mark.skip(reason="need --runslow option to run")
+        for item in items:
+            if "slow" in item.keywords:
+                item.add_marker(skip_slow)
+
+    if not is_on_slurm():
+        skip_cluster = pytest.mark.skip(reason="not running on SLURM cluster")
+        for item in items:
+            if "cluster" in item.keywords:
+                item.add_marker(skip_cluster)
+
+    # E2E tests (cluster + slow) also require it to be the slow test day
+    if not is_slow_test_day():
+        skip_e2e = pytest.mark.skip(reason="not the designated slow test day for e2e tests")
+        for item in items:
+            if "weekly" in item.keywords:
+                item.add_marker(skip_e2e)
+
+
+def is_on_slurm() -> bool:
+    """Returns True if the current environment is a SLURM cluster."""
+    return shutil.which("sbatch") is not None
+
+
+def is_slow_test_day(slow_test_day: str = SLOW_TEST_DAY) -> bool:
+    """Determine if today is the day to run slow/weekly tests.
+
+    Parameters
+    ----------
+    slow_test_day
+        The day to run the weekly tests on. Acceptable values are "Monday",
+        "Tuesday", "Wednesday", "Thursday", "Friday", "Saturday", or "Sunday".
+        Default is "Sunday".
+
+    Notes
+    -----
+    There is some risk that a test will be inadvertently skipped if there is a
+    significant delay between when a pipeline is kicked off and when the test
+    itself is run.
+    """
+    return [
+        "Monday",
+        "Tuesday",
+        "Wednesday",
+        "Thursday",
+        "Friday",
+        "Saturday",
+        "Sunday",
+    ][datetime.today().weekday()] == slow_test_day

tests/psimulate/data/e2e_branches.yaml

@@ -0,0 +1,4 @@
+# Minimal branch configuration for E2E testing.
+# 2 draws x 2 seeds x 1 branch (empty) = 4 total jobs.
+input_draw_count: 2
+random_seed_count: 2

tests/psimulate/data/e2e_model_spec.yaml

@@ -0,0 +1,22 @@
+# Minimal vivarium model specification for E2E testing.
+# Runs 2 time steps with 10 simulants -- completes in seconds.
+# No components, no data artifact, no results observers.
+components:
+    vivarium.examples.disease_model:
+        population:
+            - BasePopulation()
+configuration:
+  time:
+    start:
+      year: 2025
+      month: 1
+      day: 1
+    end:
+      year: 2025
+      month: 1
+      day: 15
+    step_size: 7  # days
+  population:
+    population_size: 10
+  randomness:
+    key_columns: []