add slurm and pytest configuration options to plugin

src/vivarium_testing_utils/pytest_plugin.py

@@ -4,10 +4,89 @@
 via the pytest11 entry point defined in setup.py.
 """
 
+import shutil
+from datetime import datetime
+
 import pytest
+from _pytest.config import Config, argparsing
+from _pytest.python import Function
 from layered_config_tree import LayeredConfigTree
 from pytest_mock import MockerFixture
 
+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 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)
+
+    # Weekly tests also require it to be the slow test day
+    if not is_slow_test_day():
+        skip_weekly = pytest.mark.skip(
+            reason="not the designated slow test day for weekly tests"
+        )
+        for item in items:
+            if "weekly" in item.keywords:
+                item.add_marker(skip_weekly)
+
+
+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
+
 
 @pytest.fixture
 def no_gbd_cache(mocker: MockerFixture) -> None:

tests/automated_validation/conftest.py

@@ -616,14 +616,6 @@ def reference_weights() -> pd.DataFrame:
     )
 
 
-def is_on_slurm() -> bool:
-    """Returns True if the current environment is a SLURM cluster."""
-    return shutil.which("sbatch") is not None
-
-
-IS_ON_SLURM = is_on_slurm()
-
-
 @pytest.fixture
 def gbd_pop() -> pd.DataFrame:
     """Sample GBD population structure data."""

tests/automated_validation/test_comparison.py

@@ -10,7 +10,6 @@
 from pytest_mock import MockFixture
 from vivarium_inputs import interface
 
-from tests.automated_validation.conftest import IS_ON_SLURM
 from vivarium_testing_utils.automated_validation.bundle import RatioMeasureDataBundle
 from vivarium_testing_utils.automated_validation.comparison import FuzzyComparison
 from vivarium_testing_utils.automated_validation.constants import (
@@ -315,10 +314,8 @@ def test_fuzzy_comparison_align_datasets_calculation(
 
 
 @pytest.mark.slow
+@pytest.mark.cluster
 def test_comparison_with_gbd_init(sim_result_dir: Path) -> None:
-    if not IS_ON_SLURM:
-        pytest.skip("No cluster access to use GBD data.")
-
     age_bins = interface.get_age_bins()
     age_bins.index.rename({"age_group_name": INPUT_DATA_INDEX_NAMES.AGE_GROUP}, inplace=True)
 

tests/automated_validation/test_data_bundle.py

@@ -8,7 +8,6 @@
 from pytest_mock import MockFixture
 from vivarium_inputs import interface
 
-from tests.automated_validation.conftest import IS_ON_SLURM
 from vivarium_testing_utils.automated_validation.bundle import RatioMeasureDataBundle
 from vivarium_testing_utils.automated_validation.constants import (
     DRAW_INDEX,
@@ -222,10 +221,9 @@ def test_aggregate_reference_stratifications(
 
 
 @pytest.mark.slow
+@pytest.mark.cluster
 def test_data_bundle_gbd_source(sim_result_dir: Path) -> None:
     """Test that GBD data source is handled correctly in RatioMeasureDataBundle."""
-    if not IS_ON_SLURM:
-        pytest.skip("GBD access not available for this test.")
 
     age_bins = interface.get_age_bins()
     age_bins.index.rename({"age_group_name": INPUT_DATA_INDEX_NAMES.AGE_GROUP}, inplace=True)

tests/automated_validation/test_data_loader.py

@@ -4,7 +4,6 @@
 import pandas as pd
 import pytest
 
-from tests.automated_validation.conftest import IS_ON_SLURM
 from vivarium_testing_utils.automated_validation.constants import (
     DRAW_INDEX,
     POPULATION_STRUCTURE_ARTIFACT_KEY,
@@ -222,6 +221,7 @@ def test___get_raw_data_from_source(
 
 
 @pytest.mark.slow
+@pytest.mark.cluster
 @pytest.mark.parametrize(
     "key",
     [
@@ -232,8 +232,6 @@ def test___get_raw_data_from_source(
 )
 def test__load_gbd_data(key: str, sim_result_dir: Path) -> None:
     """Ensure that we can load standard GBD data"""
-    if not IS_ON_SLURM:
-        pytest.skip("No access to IHME cluster to extract GBD data.")
 
     data_loader = DataLoader(sim_result_dir)
     gbd_data = data_loader._load_from_gbd(key)

tests/automated_validation/test_interface.py

@@ -11,11 +11,7 @@
 from vivarium.framework.artifact.artifact import ArtifactException
 from vivarium_inputs import interface
 
-from tests.automated_validation.conftest import (
-    IS_ON_SLURM,
-    get_model_spec,
-    load_exposure_categories,
-)
+from tests.automated_validation.conftest import get_model_spec, load_exposure_categories
 from vivarium_testing_utils.automated_validation.constants import (
     DRAW_INDEX,
     INPUT_DATA_INDEX_NAMES,
@@ -328,6 +324,7 @@ def test_get_frame_different_test_source(test_source: str, sim_result_dir: Path)
     assert set(data.columns) == {"test_rate", "reference_rate", "percent_error"}
 
 
+@pytest.mark.cluster
 @pytest.mark.parametrize(
     "data_key",
     [
@@ -344,8 +341,6 @@ def test_get_frame_different_test_source(test_source: str, sim_result_dir: Path)
 def test_cache_gbd_data(sim_result_dir: Path, data_key: str) -> None:
     """Tests that we can cache custom GBD and retreive it. More importantly, tests that
     GBD data is properly mapped from id columns to value columns upon caching."""
-    if not IS_ON_SLURM:
-        pytest.skip("No access to slurm shared filesystem available for testing.")
 
     context = ValidationContext(sim_result_dir)
     # NOTE: Some of these CSVs are reused but have the same schema. Users will be expected to
@@ -557,14 +552,12 @@ def test_get_frame_filters(mocker: MockFixture, sim_result_dir: Path) -> None:
     ],
 )
 @pytest.mark.slow
+@pytest.mark.cluster
 def test_compare_artifact_and_gbd(
     integration_artifact_data_mapper: dict[str, pd.DataFrame | str],
     tmp_path_factory: TempPathFactory,
     data_key: str,
 ) -> None:
-    if not IS_ON_SLURM:
-        pytest.skip("No cluster access to use GBD data.")
-
     # Create sim output directory
     tmp_path = tmp_path_factory.mktemp("model_run_output")
     # Create the directory structure

tests/conftest.py

@@ -1,30 +1,10 @@
 from typing import Generator
 
 import pytest
-from _pytest.config import Config, argparsing
 from _pytest.logging import LogCaptureFixture
-from _pytest.python import Function
 from loguru import logger
 
 
-def pytest_addoption(parser: argparsing.Parser) -> None:
-    parser.addoption("--runslow", action="store_true", default=False, help="run slow tests")
-
-
-def pytest_configure(config: Config) -> None:
-    config.addinivalue_line("markers", "slow: mark test as slow to run")
-
-
-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)
-
-
 @pytest.fixture
 def caplog(caplog: LogCaptureFixture) -> Generator[LogCaptureFixture, None, None]:
     handler_id = logger.add(