Merge pull request #80 from catalystneuro/flatten

Modern reorgnizations
catalystneuro · Sep 24, 2024 · b83737b · b83737b
2 parents 053ef75 + 8d4194b
commit b83737b
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Showing 34 changed files with 44 additions and 30 deletions.
diff --git a/.github/workflows/deploy_tests_on_pull_request.yml b/.github/workflows/deploy_tests_on_pull_request.yml
@@ -9,4 +9,4 @@ concurrency:  # Cancel previous workflows on the same pull request
 
 jobs:
   TestInstallation:
-    uses: ./.github/workflows/installation.yml
+    uses: ./.github/workflows/test_installation.yml
diff --git a/.github/workflows/installation.yml → .github/workflows/test_installation.yml b/.github/workflows/installation.yml → .github/workflows/test_installation.yml
@@ -35,5 +35,8 @@ jobs:
       - name: Test import
         run: python -c "import ibl_to_nwb"
 
-      - name: Test import
-        run: python -c "import ibl_to_nwb.brainwide_map"
+      - name: Test data interface imports
+        run: python -c "import ibl_to_nwb.datainterfaces"
+
+      - name: Test converters imports
+        run: python -c "import ibl_to_nwb.converters"
diff --git a/pyproject.toml b/pyproject.toml
@@ -21,6 +21,8 @@ license = {file = "license.txt"}
 requires-python = ">=3.9"
 dependencies = [
     "neuroconv",
+    "spikeinterface",
+    "probeinterface",
     "ndx-pose>=0.1.1",
     "ndx-ibl==0.1.0",
     "ONE-api",

diff --git a/...de_map/initial_conversion_environment.txt → ...nments/initial_conversion_environment.txt b/...de_map/initial_conversion_environment.txt → ...nments/initial_conversion_environment.txt
diff --git a/src/__init__.py → src/ibl_to_nwb/_metadata/__init__.py b/src/__init__.py → src/ibl_to_nwb/_metadata/__init__.py
diff --git a/.../brainwide_map/brainwide_map_metadata.yml → ...o_nwb/_metadata/brainwide_map_general.yml b/.../brainwide_map/brainwide_map_metadata.yml → ...o_nwb/_metadata/brainwide_map_general.yml
diff --git a/src/ibl_to_nwb/metadata/ecephys.yml → src/ibl_to_nwb/_metadata/ecephys.yml b/src/ibl_to_nwb/metadata/ecephys.yml → src/ibl_to_nwb/_metadata/ecephys.yml
diff --git a/src/ibl_to_nwb/metadata/pupils.yml → src/ibl_to_nwb/_metadata/pupils.yml b/src/ibl_to_nwb/metadata/pupils.yml → src/ibl_to_nwb/_metadata/pupils.yml
diff --git a/..._to_nwb/brainwide_map/metadata/trials.yml → src/ibl_to_nwb/_metadata/trials.yml b/..._to_nwb/brainwide_map/metadata/trials.yml → src/ibl_to_nwb/_metadata/trials.yml
diff --git a/src/ibl_to_nwb/metadata/wheel.yml → src/ibl_to_nwb/_metadata/wheel.yml b/src/ibl_to_nwb/metadata/wheel.yml → src/ibl_to_nwb/_metadata/wheel.yml
diff --git a/...to_nwb/brainwide_map/metadata/__init__.py → src/ibl_to_nwb/_scripts/__init__.py b/...to_nwb/brainwide_map/metadata/__init__.py → src/ibl_to_nwb/_scripts/__init__.py
diff --git a/...wb/brainwide_map/convert_brainwide_map.py → ..._to_nwb/_scripts/convert_brainwide_map.py b/...wb/brainwide_map/convert_brainwide_map.py → ..._to_nwb/_scripts/convert_brainwide_map.py
diff --git a/...ide_map/convert_brainwide_map_parallel.py → ...scripts/convert_brainwide_map_parallel.py b/...ide_map/convert_brainwide_map_parallel.py → ...scripts/convert_brainwide_map_parallel.py
diff --git a/...p/convert_brainwide_map_processed_only.py → ...s/convert_brainwide_map_processed_only.py b/...p/convert_brainwide_map_processed_only.py → ...s/convert_brainwide_map_processed_only.py
diff --git a/...nwide_map_processed_only_local_testing.py → ...nwide_map_processed_only_local_testing.py b/...nwide_map_processed_only_local_testing.py → ...nwide_map_processed_only_local_testing.py
diff --git a/..._brainwide_map_processed_only_parallel.py → ..._brainwide_map_processed_only_parallel.py b/..._brainwide_map_processed_only_parallel.py → ..._brainwide_map_processed_only_parallel.py
diff --git a/...onvert_brainwide_map_raw_only_parallel.py → ...onvert_brainwide_map_raw_only_parallel.py b/...onvert_brainwide_map_raw_only_parallel.py → ...onvert_brainwide_map_raw_only_parallel.py
diff --git a/src/ibl_to_nwb/brainwide_map/__init__.py b/src/ibl_to_nwb/brainwide_map/__init__.py
diff --git a/src/ibl_to_nwb/brainwide_map/datainterfaces/__init__.py b/src/ibl_to_nwb/brainwide_map/datainterfaces/__init__.py
diff --git a/src/ibl_to_nwb/converters/__init__.py b/src/ibl_to_nwb/converters/__init__.py
@@ -0,0 +1,7 @@
+from ._brainwide_map_converter import BrainwideMapConverter
+from ._iblconverter import IblConverter
+
+__all__ = [
+    "BrainwideMapConverter",
+    "IblConverter",
+]
diff --git a/...wb/brainwide_map/brainwidemapconverter.py → ...wb/converters/_brainwide_map_converter.py b/...wb/brainwide_map/brainwidemapconverter.py → ...wb/converters/_brainwide_map_converter.py
@@ -2,14 +2,14 @@
 
 from neuroconv.utils import dict_deep_update, load_dict_from_file
 
-from ..iblconverter import IblConverter
+from src.ibl_to_nwb.converters._iblconverter import IblConverter
 
 
 class BrainwideMapConverter(IblConverter):
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
 
-        experiment_metadata = load_dict_from_file(file_path=Path(__file__).parent / "brainwide_map_metadata.yml")
+        experiment_metadata = load_dict_from_file(file_path=Path(__file__).parent / "brainwide_map_general.yml")
         metadata = dict_deep_update(metadata, experiment_metadata)
 
         return metadata
diff --git a/src/ibl_to_nwb/iblconverter.py → src/ibl_to_nwb/converters/_iblconverter.py b/src/ibl_to_nwb/iblconverter.py → src/ibl_to_nwb/converters/_iblconverter.py
diff --git a/src/ibl_to_nwb/datainterfaces/__init__.py b/src/ibl_to_nwb/datainterfaces/__init__.py
@@ -1,8 +1,20 @@
-from .iblposeestimationinterface import IblPoseEstimationInterface
-from .iblsortingextractor import IblSortingExtractor
-from .iblsortinginterface import IblSortingInterface
-from .iblstreaminginterface import IblStreamingApInterface, IblStreamingLfInterface
-from .lickinterface import LickInterface
-from .pupiltrackinginterface import PupilTrackingInterface
-from .roimotionenergyinterface import RoiMotionEnergyInterface
-from .wheelinterface import WheelInterface
+from ._pose_estimation import IblPoseEstimationInterface
+from ._ibl_sorting_extractor import IblSortingExtractor
+from ._ibl_sorting_interface import IblSortingInterface
+from ._ibl_streaming_interface import IblStreamingApInterface, IblStreamingLfInterface
+from ._lick_times import LickInterface
+from ._pupil_tracking import PupilTrackingInterface
+from ._roi_motion_energy import RoiMotionEnergyInterface
+from ._wheel_movement import WheelInterface
+
+__all__ = [
+    "IblPoseEstimationInterface",
+    "IblSortingExtractor",
+    "IblSortingInterface",
+    "IblStreamingApInterface",
+    "IblStreamingLfInterface",
+    "LickInterface",
+    "PupilTrackingInterface",
+    "RoiMotionEnergyInterface",
+    "WheelInterface",
+]
diff --git a/...interfaces/brainwidemaptrialsinterface.py → ...b/datainterfaces/_brainwide_map_trials.py b/...interfaces/brainwidemaptrialsinterface.py → ...b/datainterfaces/_brainwide_map_trials.py
@@ -15,7 +15,7 @@ def __init__(self, one: ONE, session: str):
 
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
-        trial_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "trials.yml")
+        trial_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "trials.yml")
         metadata.update(trial_metadata)
         return metadata
 

diff --git a/...nwb/datainterfaces/iblsortingextractor.py → .../datainterfaces/_ibl_sorting_extractor.py b/...nwb/datainterfaces/iblsortingextractor.py → .../datainterfaces/_ibl_sorting_extractor.py
diff --git a/...nwb/datainterfaces/iblsortinginterface.py → .../datainterfaces/_ibl_sorting_interface.py b/...nwb/datainterfaces/iblsortinginterface.py → .../datainterfaces/_ibl_sorting_interface.py
@@ -7,7 +7,7 @@
 )
 from neuroconv.utils import load_dict_from_file
 
-from .iblsortingextractor import IblSortingExtractor
+from ._ibl_sorting_extractor import IblSortingExtractor
 
 
 class IblSortingInterface(BaseSortingExtractorInterface):
@@ -16,7 +16,7 @@ class IblSortingInterface(BaseSortingExtractorInterface):
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
 
-        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "ecephys.yml")
+        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "ecephys.yml")
 
         metadata.update(Ecephys=dict())
         metadata["Ecephys"].update(UnitProperties=ecephys_metadata["Ecephys"]["UnitProperties"])

diff --git a/...b/datainterfaces/iblstreaminginterface.py → ...atainterfaces/_ibl_streaming_interface.py b/...b/datainterfaces/iblstreaminginterface.py → ...atainterfaces/_ibl_streaming_interface.py
@@ -104,7 +104,7 @@ def get_metadata_schema(self) -> dict:
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
 
-        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "ecephys.yml")
+        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "ecephys.yml")
 
         metadata["Ecephys"].update({self.es_key: ecephys_metadata["Ecephys"]["ElectricalSeriesAp"]})
         if len(self.available_streams) > 1:
@@ -176,7 +176,7 @@ def get_metadata(self) -> dict:
         metadata = super().get_metadata()
         metadata["Ecephys"].pop("ElectrodeGroup")
 
-        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "ecephys.yml")
+        ecephys_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "ecephys.yml")
 
         metadata["Ecephys"].update({self.es_key: ecephys_metadata["Ecephys"]["ElectricalSeriesLf"]})
         if len(self.available_streams) > 1:

diff --git a/...bl_to_nwb/datainterfaces/lickinterface.py → src/ibl_to_nwb/datainterfaces/_lick_times.py b/...bl_to_nwb/datainterfaces/lickinterface.py → src/ibl_to_nwb/datainterfaces/_lick_times.py
diff --git a/...ainterfaces/iblposeestimationinterface.py → ...to_nwb/datainterfaces/_pose_estimation.py b/...ainterfaces/iblposeestimationinterface.py → ...to_nwb/datainterfaces/_pose_estimation.py
diff --git a/.../datainterfaces/pupiltrackinginterface.py → ..._to_nwb/datainterfaces/_pupil_tracking.py b/.../datainterfaces/pupiltrackinginterface.py → ..._to_nwb/datainterfaces/_pupil_tracking.py
@@ -20,7 +20,7 @@ def __init__(self, one: ONE, session: str, camera_name: str):
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
 
-        pupils_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "pupils.yml")
+        pupils_metadata = load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "pupils.yml")
         metadata.update(pupils_metadata)
 
         return metadata

diff --git a/...atainterfaces/roimotionenergyinterface.py → ..._nwb/datainterfaces/_roi_motion_energy.py b/...atainterfaces/roimotionenergyinterface.py → ..._nwb/datainterfaces/_roi_motion_energy.py
diff --git a/...l_to_nwb/datainterfaces/wheelinterface.py → ..._to_nwb/datainterfaces/_wheel_movement.py b/...l_to_nwb/datainterfaces/wheelinterface.py → ..._to_nwb/datainterfaces/_wheel_movement.py
@@ -18,7 +18,7 @@ def __init__(self, one: ONE, session: str):
     def get_metadata(self) -> dict:
         metadata = super().get_metadata()
 
-        metadata.update(load_dict_from_file(file_path=Path(__file__).parent.parent / "metadata" / "wheel.yml"))
+        metadata.update(load_dict_from_file(file_path=Path(__file__).parent.parent / "_metadata" / "wheel.yml"))
 
         return metadata
 

diff --git a/src/ibl_to_nwb/metadata/__init__.py b/src/ibl_to_nwb/metadata/__init__.py
diff --git a/src/ibl_to_nwb/requirements.txt b/src/ibl_to_nwb/requirements.txt