Re-organize gin test by modality (#1049)

catalystneuro · Sep 2, 2024 · 925f183 · 925f183
1 parent 905dc73
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,7 @@
 
 ### Improvements
 * Using ruff to enforce existence of public classes' docstrings [PR #1034](https://github.com/catalystneuro/neuroconv/pull/1034)
+* Separated tests that use external data by modality [PR #1049](https://github.com/catalystneuro/neuroconv/pull/1049)
 
 ## v0.6.1 (August 30, 2024)
 

diff --git a/docs/conversion_examples_gallery/fiberphotometry/tdt_fp.rst b/docs/conversion_examples_gallery/fiberphotometry/tdt_fp.rst
@@ -205,7 +205,7 @@ Convert TDT Fiber Photometry data to NWB using
 
     >>> folder_path = OPHYS_DATA_PATH / "fiber_photometry_datasets" / "TDT" / "Photo_249_391-200721-120136_stubbed"
     >>> LOCAL_PATH = Path(".") # Path to neuroconv
-    >>> editable_metadata_path = LOCAL_PATH / "tests" / "test_on_data" / "fiber_photometry_metadata.yaml"
+    >>> editable_metadata_path = LOCAL_PATH / "tests" / "test_on_data" / "ophys" / "fiber_photometry_metadata.yaml"
 
     >>> interface = TDTFiberPhotometryInterface(folder_path=folder_path, verbose=True)
     >>> metadata = interface.get_metadata()

diff --git a/tests/test_internals/test_schemas.py → tests/test_minimal/test_schemas.py b/tests/test_internals/test_schemas.py → tests/test_minimal/test_schemas.py
diff --git a/tests/test_internals/__init__.py → tests/test_on_data/behavior/__init__.py b/tests/test_internals/__init__.py → tests/test_on_data/behavior/__init__.py
diff --git a/.../test_on_data/test_behavior_interfaces.py → ...data/behavior/test_behavior_interfaces.py b/.../test_on_data/test_behavior_interfaces.py → ...data/behavior/test_behavior_interfaces.py
@@ -37,7 +37,7 @@
 from neuroconv.utils import DeepDict
 
 try:
-    from .setup_paths import BEHAVIOR_DATA_PATH, OPHYS_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import BEHAVIOR_DATA_PATH, OPHYS_DATA_PATH, OUTPUT_PATH
 except ImportError:
     from setup_paths import BEHAVIOR_DATA_PATH, OUTPUT_PATH
 

diff --git a/...onverters/test_lightningpose_converter.py → .../behavior/test_lightningpose_converter.py b/...onverters/test_lightningpose_converter.py → .../behavior/test_lightningpose_converter.py
diff --git a/...n_data/test_format_converters/__init__.py → tests/test_on_data/ecephys/__init__.py b/...n_data/test_format_converters/__init__.py → tests/test_on_data/ecephys/__init__.py
diff --git a/...erters/spikeglx_multi_probe_metadata.json → ...cephys/spikeglx_multi_probe_metadata.json b/...erters/spikeglx_multi_probe_metadata.json → ...cephys/spikeglx_multi_probe_metadata.json
diff --git a/...rters/spikeglx_single_probe_metadata.json → ...ephys/spikeglx_single_probe_metadata.json b/...rters/spikeglx_single_probe_metadata.json → ...ephys/spikeglx_single_probe_metadata.json
diff --git a/...a/test_gin_ecephys/test_aux_interfaces.py → ...st_on_data/ecephys/test_aux_interfaces.py b/...a/test_gin_ecephys/test_aux_interfaces.py → ...st_on_data/ecephys/test_aux_interfaces.py
diff --git a/...test_on_data/test_gin_ecephys/test_lfp.py → tests/test_on_data/ecephys/test_lfp.py b/...test_on_data/test_gin_ecephys/test_lfp.py → tests/test_on_data/ecephys/test_lfp.py
diff --git a/.../test_gin_ecephys/test_openephyslegacy.py → ...t_on_data/ecephys/test_openephyslegacy.py b/.../test_gin_ecephys/test_openephyslegacy.py → ...t_on_data/ecephys/test_openephyslegacy.py
diff --git a/...ata/test_metadata/test_plexon_metadata.py → ...t_on_data/ecephys/test_plexon_metadata.py b/...ata/test_metadata/test_plexon_metadata.py → ...t_on_data/ecephys/test_plexon_metadata.py
diff --git a/...a/test_gin_ecephys/test_raw_recordings.py → ...st_on_data/ecephys/test_raw_recordings.py b/...a/test_gin_ecephys/test_raw_recordings.py → ...st_on_data/ecephys/test_raw_recordings.py
@@ -19,8 +19,8 @@
     from ..setup_paths import ECEPHY_DATA_PATH as DATA_PATH
     from ..setup_paths import OUTPUT_PATH
 except ImportError:
-    from setup_paths import ECEPHY_DATA_PATH as DATA_PATH
-    from setup_paths import OUTPUT_PATH
+    from ..setup_paths import ECEPHY_DATA_PATH as DATA_PATH
+    from ..setup_paths import OUTPUT_PATH
 
 if not DATA_PATH.exists():
     pytest.fail(f"No folder found in location: {DATA_PATH}!")

diff --git a/...test_on_data/test_recording_interfaces.py → ...data/ecephys/test_recording_interfaces.py b/...test_on_data/test_recording_interfaces.py → ...data/ecephys/test_recording_interfaces.py
@@ -37,9 +37,9 @@
 )
 
 try:
-    from .setup_paths import ECEPHY_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import ECEPHY_DATA_PATH, OUTPUT_PATH
 except ImportError:
-    from setup_paths import ECEPHY_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import ECEPHY_DATA_PATH, OUTPUT_PATH
 
 
 this_python_version = version.parse(python_version())

diff --git a/...s/test_on_data/test_sorting_interfaces.py → ...n_data/ecephys/test_sorting_interfaces.py b/...s/test_on_data/test_sorting_interfaces.py → ...n_data/ecephys/test_sorting_interfaces.py
@@ -17,8 +17,8 @@
 )
 
 try:
-    from .setup_paths import ECEPHY_DATA_PATH as DATA_PATH
-    from .setup_paths import OUTPUT_PATH
+    from ..setup_paths import ECEPHY_DATA_PATH as DATA_PATH
+    from ..setup_paths import OUTPUT_PATH
 except ImportError:
     from setup_paths import ECEPHY_DATA_PATH as DATA_PATH
     from setup_paths import OUTPUT_PATH

diff --git a/...mat_converters/test_spikeglx_converter.py → ...n_data/ecephys/test_spikeglx_converter.py b/...mat_converters/test_spikeglx_converter.py → ...n_data/ecephys/test_spikeglx_converter.py
diff --git a/...a/test_metadata/test_spikeglx_metadata.py → ...on_data/ecephys/test_spikeglx_metadata.py b/...a/test_metadata/test_spikeglx_metadata.py → ...on_data/ecephys/test_spikeglx_metadata.py
diff --git a/tests/test_on_data/test_gin_icephys.py → .../test_on_data/icephys/test_gin_icephys.py b/tests/test_on_data/test_gin_icephys.py → .../test_on_data/icephys/test_gin_icephys.py
@@ -20,7 +20,7 @@
 except ImportError:
     HAVE_PARAMETERIZED = False
 # Load the configuration for the data tests
-test_config_dict = load_dict_from_file(Path(__file__).parent / "gin_test_config.json")
+test_config_dict = load_dict_from_file(Path(__file__).parent.parent / "gin_test_config.json")
 
 # GIN dataset: https://gin.g-node.org/NeuralEnsemble/ephy_testing_data
 if os.getenv("CI"):

diff --git a/...test_on_data/test_gin_ecephys/__init__.py → tests/test_on_data/ophys/__init__.py b/...test_on_data/test_gin_ecephys/__init__.py → tests/test_on_data/ophys/__init__.py
diff --git a/...st_on_data/fiber_photometry_metadata.yaml → ...data/ophys/fiber_photometry_metadata.yaml b/...st_on_data/fiber_photometry_metadata.yaml → ...data/ophys/fiber_photometry_metadata.yaml
diff --git a/...t_converters/test_brukertiff_converter.py → ...n_data/ophys/test_brukertiff_converter.py b/...t_converters/test_brukertiff_converter.py → ...n_data/ophys/test_brukertiff_converter.py
diff --git a/..._data/test_fiber_photometry_interfaces.py → ...ophys/test_fiber_photometry_interfaces.py b/..._data/test_fiber_photometry_interfaces.py → ...ophys/test_fiber_photometry_interfaces.py
@@ -14,7 +14,7 @@
 from neuroconv.utils import dict_deep_update, load_dict_from_file
 
 try:
-    from .setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 except ImportError:
     from setup_paths import OUTPUT_PATH
 

diff --git a/...s/test_on_data/test_imaging_interfaces.py → ..._on_data/ophys/test_imaging_interfaces.py b/...s/test_on_data/test_imaging_interfaces.py → ..._on_data/ophys/test_imaging_interfaces.py
@@ -36,7 +36,7 @@
 )
 
 try:
-    from .setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 except ImportError:
     from setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 

diff --git a/...est_on_data/test_metadata_combinations.py → ..._data/ophys/test_metadata_combinations.py b/...est_on_data/test_metadata_combinations.py → ..._data/ophys/test_metadata_combinations.py
@@ -6,7 +6,7 @@
 from neuroconv import NWBConverter
 from neuroconv.datainterfaces import Suite2pSegmentationInterface, TiffImagingInterface
 
-from .setup_paths import OPHYS_DATA_PATH
+from ..setup_paths import OPHYS_DATA_PATH
 
 TiffImagingInterface_source_data = dict(
     file_path=str(OPHYS_DATA_PATH / "imaging_datasets" / "Tif" / "demoMovie.tif"), sampling_frequency=15.0

diff --git a/...at_converters/test_miniscope_converter.py → ...on_data/ophys/test_miniscope_converter.py b/...at_converters/test_miniscope_converter.py → ...on_data/ophys/test_miniscope_converter.py
diff --git a/...t_metadata/test_neuralynx_nvt_metadata.py → ...data/ophys/test_neuralynx_nvt_metadata.py b/...t_metadata/test_neuralynx_nvt_metadata.py → ...data/ophys/test_neuralynx_nvt_metadata.py
diff --git a/...t_on_data/test_segmentation_interfaces.py → ...ata/ophys/test_segmentation_interfaces.py b/...t_on_data/test_segmentation_interfaces.py → ...ata/ophys/test_segmentation_interfaces.py
@@ -11,9 +11,9 @@
 )
 
 try:
-    from .setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 except ImportError:
-    from setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
+    from ..setup_paths import OPHYS_DATA_PATH, OUTPUT_PATH
 
 
 class TestCaimanSegmentationInterface(SegmentationExtractorInterfaceTestMixin):

diff --git a/tests/test_on_data/test_metadata/test_maxwell_metadata.py b/tests/test_on_data/test_metadata/test_maxwell_metadata.py
diff --git a/tests/test_on_data/test_metadata/test_neuroscope.py b/tests/test_on_data/test_metadata/test_neuroscope.py
diff --git a/tests/test_on_data/test_metadata/__init__.py → tests/test_on_data/test_yaml/__init__.py b/tests/test_on_data/test_metadata/__init__.py → tests/test_on_data/test_yaml/__init__.py
diff --git a/...ications/GIN_conversion_specification.yml → ...ications/GIN_conversion_specification.yml b/...ications/GIN_conversion_specification.yml → ...ications/GIN_conversion_specification.yml
diff --git a/...n_specification_missing_nwbfile_names.yml → ...n_specification_missing_nwbfile_names.yml b/...n_specification_missing_nwbfile_names.yml → ...n_specification_missing_nwbfile_names.yml
diff --git a/...ion_no_nwbfile_name_or_other_metadata.yml → ...ion_no_nwbfile_name_or_other_metadata.yml b/...ion_no_nwbfile_name_or_other_metadata.yml → ...ion_no_nwbfile_name_or_other_metadata.yml
diff --git a/...s/GIN_conversion_specification_videos.yml → ...s/GIN_conversion_specification_videos.yml b/...s/GIN_conversion_specification_videos.yml → ...s/GIN_conversion_specification_videos.yml
diff --git a/...ata/test_yaml_conversion_specification.py → ...aml/test_yaml_conversion_specification.py b/...ata/test_yaml_conversion_specification.py → ...aml/test_yaml_conversion_specification.py
@@ -11,8 +11,8 @@
 from neuroconv import run_conversion_from_yaml
 from neuroconv.utils import load_dict_from_file
 
-from .setup_paths import BEHAVIOR_DATA_PATH, OUTPUT_PATH
-from .setup_paths import ECEPHY_DATA_PATH as DATA_PATH
+from ..setup_paths import BEHAVIOR_DATA_PATH, OUTPUT_PATH
+from ..setup_paths import ECEPHY_DATA_PATH as DATA_PATH
 
 
 @pytest.mark.parametrize(
@@ -26,7 +26,7 @@
 )
 def test_validate_example_specifications(fname):
     path_to_test_yml_files = Path(__file__).parent / "conversion_specifications"
-    schema_folder = path_to_test_yml_files.parent.parent.parent / "src" / "neuroconv" / "schemas"
+    schema_folder = path_to_test_yml_files.parent.parent.parent.parent / "src" / "neuroconv" / "schemas"
     specification_schema = load_dict_from_file(file_path=schema_folder / "yaml_conversion_specification_schema.json")
     sys_uri_base = "file://"
     if sys.platform.startswith("win32"):

diff --git a/...test_yaml_conversion_specification_cli.py → ...test_yaml_conversion_specification_cli.py b/...test_yaml_conversion_specification_cli.py → ...test_yaml_conversion_specification_cli.py
@@ -7,8 +7,8 @@
 
 from neuroconv.tools import deploy_process
 
-from .setup_paths import ECEPHY_DATA_PATH as DATA_PATH
-from .setup_paths import OUTPUT_PATH
+from ..setup_paths import ECEPHY_DATA_PATH as DATA_PATH
+from ..setup_paths import OUTPUT_PATH
 
 
 class TestYAMLConversionSpecification(TestCase):