test: add pytest markers (@unit / @integration) to all legacy test files

hera/tests/test_datalayer.py

@@ -103,6 +103,7 @@ def clean_proj():
 # 1. Project CRUD — all three collections
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestMeasurementsCRUD:
     """Add, get, get-as-dict, delete for Measurements collection."""
@@ -154,6 +155,7 @@ def test_delete(self, proj):
         assert len(remaining) == 0
 
 
+@pytest.mark.integration
 @requires_mongo
 class TestSimulationsCRUD:
     """Add, get, get-as-dict, delete for Simulations collection."""
@@ -193,6 +195,7 @@ def test_delete(self, proj):
         assert len(remaining) == 0
 
 
+@pytest.mark.integration
 @requires_mongo
 class TestCacheCRUD:
     """Add, get, get-as-dict, delete for Cache collection."""
@@ -236,6 +239,7 @@ def test_delete(self, proj):
 # 2. Nested queries (dictToMongoQuery)
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestNestedQueries:
     """Test querying with nested desc fields."""
@@ -273,6 +277,7 @@ def test_multi_level_nested_query(self, clean_proj):
 # 3. getAllDocuments — cross-collection query
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestGetAllDocuments:
     """Test getAllDocuments aggregates across collections."""
@@ -295,6 +300,7 @@ def test_returns_from_all_collections(self, clean_proj):
 # 4. getDocumentByID
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestGetDocumentByID:
     """Test retrieving a document by its MongoDB ID."""
@@ -313,6 +319,7 @@ def test_round_trip(self, clean_proj):
 # 5. getMetadata
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestGetMetadata:
     """Test getMetadata returns DataFrame of document descriptions."""
@@ -335,6 +342,7 @@ def test_returns_dataframe(self, clean_proj):
 # 6. addDocumentFromDict
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestAddDocumentFromDict:
     """Test adding documents from a dictionary representation."""
@@ -358,6 +366,7 @@ def test_add_measurements_from_dict(self, clean_proj):
 # 7. Counters
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestCounters:
     """Test counter operations: define, set, get, getAndAdd."""
@@ -401,6 +410,7 @@ def test_set_counter_overwrites(self, clean_proj):
 # 8. Configuration
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestConfiguration:
     """Test initConfig, setConfig, getConfig."""
@@ -439,6 +449,7 @@ def test_init_config_does_not_overwrite(self, clean_proj):
 # 9. Project properties
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestProjectProperties:
     """Test Project properties."""
@@ -468,6 +479,7 @@ def test_files_directory(self, proj):
 # 10. saveData family — round-trip with real files
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestSaveData:
     """Test saveMeasurementData, saveCacheData, saveSimulationData with real data."""
@@ -575,6 +587,7 @@ def test_save_pickle(self, clean_proj, tmp_dir):
 # 11. DataHandler round-trips (unit tests, no DB needed)
 # ===========================================================================
 
+@pytest.mark.unit
 class TestDataHandlers:
     """Test DataHandler saveData/getData round-trips for key formats."""
 
@@ -639,6 +652,7 @@ def test_handler_pickle(self, tmp_dir):
 # 12. datatypes class methods
 # ===========================================================================
 
+@pytest.mark.unit
 class TestDatatypes:
     """Test datatypes introspection methods."""
 
@@ -684,6 +698,7 @@ def test_get_data_format_extension(self):
 # 13. Collection direct access
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestCollectionDirect:
     """Test AbstractCollection and subclasses directly."""
@@ -809,6 +824,7 @@ def test_get_project_list(self):
 # 14. MetadataFrame
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestMetadataFrame:
     """Test MetadataFrame.asDict and MetadataFrame.getData."""
@@ -851,6 +867,7 @@ def test_get_data_string(self, clean_proj):
 # 15. nonDBMetadataFrame
 # ===========================================================================
 
+@pytest.mark.unit
 class TestNonDBMetadataFrame:
     """Test nonDBMetadataFrame wrapping."""
 
@@ -889,6 +906,7 @@ def test_get_data_with_numpy(self):
 # 16. autocache — @cacheFunction decorator
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestAutoCache:
     """Test cacheFunction decorator with real MongoDB caching."""
@@ -952,6 +970,7 @@ def func_b():
 # 17. Export / Import round-trip
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestExportImport:
     """Test Project export and load round-trip."""
@@ -1004,6 +1023,7 @@ def test_export_and_load(self, tmp_dir):
 # 18. Module-level functions
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestModuleFunctionsDB:
     """Test module-level functions that require MongoDB."""
@@ -1018,6 +1038,7 @@ def test_get_project_list(self, proj):
         assert PROJECT_NAME in projects
 
 
+@pytest.mark.unit
 class TestModuleFunctionsLocal:
     """Test module-level functions that do NOT require MongoDB."""
 
@@ -1037,6 +1058,7 @@ def test_create_project_directory(self, tmp_dir):
 # 19. parseConnectionString (no DB, no config file)
 # ===========================================================================
 
+@pytest.mark.unit
 class TestParseConnectionString:
     """Test connection string parsing — pure function, no side effects."""
 
@@ -1068,6 +1090,7 @@ def test_special_chars_in_password_raises(self):
 # 20. Config file management (mocked — no real config file touched)
 # ===========================================================================
 
+@pytest.mark.unit
 class TestConfigFileManagement:
     """Test getMongoJSON, addOrUpdateDatabase, removeConnection, getDBNamesFromJSON.
 
@@ -1190,6 +1213,7 @@ def test_addOrUpdateDatabase_no_config_raises(self, tmp_dir, monkeypatch):
 # 21. saveData with auto-format detection (requires MongoDB)
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestSaveDataAutoDetect:
     """Test that saveData auto-detects the format when dataFormat is not specified."""
@@ -1239,6 +1263,7 @@ def test_auto_detect_numpy(self, clean_proj, tmp_dir):
 # 22. Simulations/Cache getDocumentsAsDict (requires MongoDB)
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestSimulationsCacheAsDict:
     """Test getDocumentsAsDict for Simulations and Cache (Measurements already tested)."""
@@ -1266,6 +1291,7 @@ def test_cache_as_dict(self, clean_proj):
 # 23. Empty project edge cases (requires MongoDB)
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 class TestEmptyProjectEdgeCases:
     """Test queries against a project with no documents."""
@@ -1296,6 +1322,7 @@ def test_get_metadata_empty(self, clean_proj):
 # 24. guessHandler (no DB)
 # ===========================================================================
 
+@pytest.mark.unit
 class TestGuessHandler:
     """Test guessHandler with various Python objects."""
 

hera/tests/test_demography.py

@@ -131,6 +131,7 @@ def population_gdf(demo_toolkit):
 # 1. Toolkit initialization and properties
 # ===========================================================================
 
+@pytest.mark.integration
 class TestDemographyToolkitInit:
     """Test toolkit construction and properties (requires DB)."""
 
@@ -155,6 +156,7 @@ def test_population_types(self, demo_toolkit):
 # 2. setDefaultDirectory
 # ===========================================================================
 
+@pytest.mark.integration
 class TestSetDefaultDirectory:
     def test_creates_and_sets_path(self, demo_toolkit):
         with tempfile.TemporaryDirectory() as tmpdir:
@@ -172,6 +174,7 @@ def test_raises_if_not_found_and_create_false(self, demo_toolkit):
 # 3. analysis.calculatePopulationInPolygon
 # ===========================================================================
 
+@pytest.mark.integration
 class TestCalculatePopulationInPolygon:
     def test_basic(self, demo_toolkit, population_gdf):
         """Polygon enclosing a census area returns non-empty result."""
@@ -294,6 +297,7 @@ def test_full_coverage_sums_to_total(self, demo_toolkit, synthetic_gdf, large_po
 # 4. analysis.createNewArea
 # ===========================================================================
 
+@pytest.mark.integration
 class TestCreateNewArea:
     def test_simple(self, demo_toolkit, population_gdf):
         """Create area covering all population data."""
@@ -369,6 +373,7 @@ def test_with_specific_population_types(self, demo_toolkit, synthetic_gdf, large
 # 5. presentation.plotPopulationDensity
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotPopulationDensity:
     """Test plotPopulationDensity with synthetic data (no DB needed)."""
 
@@ -459,6 +464,7 @@ def test_wgs84_input_with_reprojection(self, demo_toolkit, synthetic_gdf_wgs84):
 # 6. presentation.plotPopulation
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotPopulation:
     """Test plotPopulation (absolute counts)."""
 
@@ -503,6 +509,7 @@ def test_with_existing_axes(self, demo_toolkit, synthetic_gdf):
 # 7. presentation.plotPopulationByType
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotPopulationByType:
     """Test plotPopulationByType (subplot grid)."""
 
@@ -545,6 +552,7 @@ def test_custom_figsize_and_cmap(self, demo_toolkit, synthetic_gdf):
 # 8. presentation.plotPopulationInPolygon
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotPopulationInPolygon:
     """Test plotPopulationInPolygon (intersection visualization)."""
 
@@ -593,6 +601,7 @@ def test_with_all_options(self, demo_toolkit, intersection_result,
 # 9. presentation.plotArea
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotArea:
     """Test plotArea (custom area with population annotation)."""
 
@@ -651,6 +660,7 @@ def test_custom_styling(self, demo_toolkit, area_result, synthetic_gdf):
 # 10. presentation.plotPopulationOnMap (mocked TilesToolkit)
 # ===========================================================================
 
+@pytest.mark.integration
 class TestPlotPopulationOnMap:
     """Test plotPopulationOnMap with a mocked TilesToolkit."""
 
@@ -716,6 +726,7 @@ def test_custom_zoom_and_styling(self, demo_toolkit, synthetic_gdf):
 # 11. Edge cases
 # ===========================================================================
 
+@pytest.mark.integration
 class TestEdgeCases:
     """Edge cases and error handling."""
 

hera/tests/test_experiment.py

@@ -358,6 +358,7 @@ def experiment(exp_home):
 # 1. experimentHome
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestExperimentHome:
@@ -393,6 +394,7 @@ def test_nonexistent_experiment(self, exp_home):
 # 2. experimentSetupWithData — properties
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestExperimentSetup:
@@ -426,6 +428,7 @@ def test_get_experiment_data(self, experiment):
 # 3. TrialSetWithData and TrialWithdata
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestTrialAccess:
@@ -469,6 +472,7 @@ def test_trial_get_data_trh(self, experiment):
 # 4. EntityTypeWithData
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestEntityType:
@@ -501,6 +505,7 @@ def test_get_data_trial(self, experiment):
 # 5. EntityWithData
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestEntity:
@@ -522,6 +527,7 @@ def test_entity_get_data(self, experiment):
 # 6. getDataFromDateRange
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestGetDataFromDateRange:
@@ -542,6 +548,7 @@ def test_basic(self, experiment):
 # 7. dataEngineFactory
 # ===========================================================================
 
+@pytest.mark.unit
 @pytest.mark.skipif(not _ENGINE_AVAILABLE, reason="dataEngine not importable")
 class TestDataEngineFactory:
     """Test engine type constants (no DB needed)."""
@@ -561,6 +568,7 @@ def test_constants_are_strings(self):
 # 8. experimentAnalysis — synthetic (no DB)
 # ===========================================================================
 
+@pytest.mark.unit
 @pytest.mark.skipif(not _ANALYSIS_AVAILABLE, reason="experimentAnalysis not importable")
 class TestAnalysisSynthetic:
     """Test analysis methods with synthetic DataFrames."""
@@ -608,6 +616,7 @@ def __init__(self):
 # 9. experimentPresentation — smoke test (no DB)
 # ===========================================================================
 
+@pytest.mark.unit
 @pytest.mark.skipif(not _PRESENTATION_AVAILABLE, reason="experimentPresentation not importable")
 class TestPresentationInit:
     """Test presentation can be instantiated."""
@@ -632,6 +641,7 @@ class MockAnalysis:
 # 10. Parsers — synthetic (no DB)
 # ===========================================================================
 
+@pytest.mark.unit
 class TestParsers:
     """Test parsers with synthetic data."""
 
@@ -648,6 +658,7 @@ def test_campbell_binary_parser_import(self):
 # 11. Argos zip parsing (no DB)
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_experiment
 class TestArgosZipParsing:
     """Test that Argos zip files are parsed correctly."""
@@ -717,6 +728,7 @@ def test_trial_entities_table(self, experiment_dir):
 # 12. Full integration: load → navigate → get data
 # ===========================================================================
 
+@pytest.mark.integration
 @requires_mongo
 @requires_experiment
 class TestFullIntegration: