Merge pull request #78 from catalystneuro/remove_top_level_imports

Remove top level imports of big modules

.github/workflows/testing.yml

@@ -37,6 +37,11 @@ jobs:
 
       - name: Install neuroconv with minimal requirements
         run: pip install .[test]
+      - name: Run import tests
+        run: |
+          pytest tests/imports.py::TestImportStructure::test_top_level
+          pytest tests/imports.py::TestImportStructure::test_tools
+          pytest tests/imports.py::TestImportStructure::test_datainterfaces
       - name: Run minimal tests
         run: pytest tests/test_minimal -n auto --dist loadscope
 
@@ -49,6 +54,7 @@ jobs:
 
       - name: Install with icephys requirements
         run: pip install .[icephys]
+
       #- name: Run icephys tests  # There are no icephys specific tests without data
       #  run: pytest tests/test_icephys -n auto --dist loadscope
 

src/neuroconv/__init__.py

@@ -1,6 +1,2 @@
 from .nwbconverter import NWBConverter
-
-# TODO: temporarily disabled until decision to remove in other PR
-# from .tools import spikeinterface, roiextractors, neo
-
 from .tools.yaml_conversion_specification import run_conversion_from_yaml

src/neuroconv/tools/__init__.py

@@ -1,8 +1 @@
-# To be treated as sub-modules or plugins
-# TODO: temporarily disabled until decision to remove in other PR
-# from .spikeinterface import spikeinterface
-# from .roiextractors import roiextractors
-# from .neo import neo
-
-# Basically utils but rely on external dependencies
 from .importing import get_package

tests/test_minimal/test_import_structure.py → tests/imports.py

@@ -1,10 +1,11 @@
-from unittest import TestCase
+# This module is meant for the tests to be run as stand-alone so as to emulate a fresh import
+# Run them by using:
+# pytest tests/import_structure.py::TestImportStructure::test_name
 
-import neuroconv
-from neuroconv import datainterfaces
+from unittest import TestCase
 
 
-def _strip_magic_module_attributes(dictionary: dict) -> dict:
+def _strip_magic_module_attributes(ls: list) -> list:
     exclude_keys = [
         "__name__",
         "__doc__",
@@ -16,31 +17,46 @@ def _strip_magic_module_attributes(dictionary: dict) -> dict:
         "__cached__",
         "__builtins__",
     ]
-    return {k: v for k, v in dictionary.items() if k not in exclude_keys}
+    return list(filter(lambda key: key not in exclude_keys, ls))
 
 
 class TestImportStructure(TestCase):
-    def test_outer_import_structure(self):
-        current_structure = _strip_magic_module_attributes(dictionary=neuroconv.__dict__)
+    def test_top_level(self):
+        import neuroconv
+
+        current_structure = _strip_magic_module_attributes(ls=neuroconv.__dict__)
         expected_structure = [
             # Sub-modules
             "nwbconverter",
-            "basedatainterface",
-            "baseextractorinterface",
-            "datainterfaces",
-            "tools",
-            "utils",
+            "tools",  # Attached to namespace by NWBConverter import
+            "utils",  # Attached to namesapce by NWBconverter import
             # Exposed attributes
             "NWBConverter",
-            # "spikeinterface",  # TODO: decide what to do here
-            # "roiextractors",
-            # "neo",
             "run_conversion_from_yaml",
         ]
         self.assertCountEqual(first=current_structure, second=expected_structure)
 
-    def test_datainterfaces_import_structure(self):
-        current_structure = _strip_magic_module_attributes(dictionary=datainterfaces.__dict__)
+    def test_tools(self):
+        """Python dir() calls (and __dict__ as well) update dynamically based on global imports."""
+
+        from neuroconv import tools
+
+        current_structure = _strip_magic_module_attributes(ls=tools.__dict__)
+        expected_structure = [
+            # Sub-Packages
+            "yaml_conversion_specification",  # Attached to namespace  by top __init__ call of NWBConverter
+            # Sub-modules
+            "importing",  # Attached to namespace by importing get_package
+            "nwb_helpers",  # Attached to namespace by top __init__ call of NWBConverter
+            # Functions imported on the __init__
+            "get_package",
+        ]
+        self.assertCountEqual(first=current_structure, second=expected_structure)
+
+    def test_datainterfaces(self):
+        from neuroconv import datainterfaces
+
+        current_structure = _strip_magic_module_attributes(ls=datainterfaces.__dict__)
         expected_structure = [
             # Sub-modules
             "behavior",

tests/test_ecephys/test_tools_spikeextractors.py

@@ -17,7 +17,7 @@
     get_default_nwbfile_metadata,
 )
 
-# from neuroconv import spikeinterface  # TODO: testing aliased import; possibly remove
+from neuroconv.tools import spikeinterface  # testing aliased import
 from neuroconv.tools.spikeinterface import (
     get_nwb_metadata,
     write_recording,
@@ -135,12 +135,12 @@ def check_si_roundtrip(self, path: FilePathType):
     def test_write_recording(self):
         path = self.test_dir + "/test.nwb"
 
-        # spikeinterface.write_recording(self.RX, path, metadata=self.placeholder_metadata)  # testing aliased import
-        # RX_nwb = se.NwbRecordingExtractor(path)
-        # check_recording_return_types(RX_nwb)
-        # check_recordings_equal(self.RX, RX_nwb)
-        # check_dumping(RX_nwb)
-        # del RX_nwb
+        spikeinterface.write_recording(self.RX, path, metadata=self.placeholder_metadata)  # testing aliased import
+        RX_nwb = se.NwbRecordingExtractor(path)
+        check_recording_return_types(RX_nwb)
+        check_recordings_equal(self.RX, RX_nwb)
+        check_dumping(RX_nwb)
+        del RX_nwb
 
         write_recording(recording=self.RX, nwbfile_path=path, overwrite=True, metadata=self.placeholder_metadata)
         RX_nwb = se.NwbRecordingExtractor(path)
@@ -288,12 +288,12 @@ def test_write_sorting(self):
         path = self.test_dir + "/test.nwb"
         sf = self.RX.get_sampling_frequency()
 
-        # # Append sorting to existing file
-        # write_recording(recording=self.RX, nwbfile_path=path, overwrite=True, metadata=self.placeholder_metadata)
-        # spikeinterface.write_sorting(sorting=self.SX, nwbfile_path=path, overwrite=False)  # testing aliased import
-        # SX_nwb = se.NwbSortingExtractor(path)
-        # check_sortings_equal(self.SX, SX_nwb)
-        # check_dumping(SX_nwb)
+        # Append sorting to existing file
+        write_recording(recording=self.RX, nwbfile_path=path, overwrite=True, metadata=self.placeholder_metadata)
+        spikeinterface.write_sorting(sorting=self.SX, nwbfile_path=path, overwrite=False)  # testing aliased import
+        SX_nwb = se.NwbSortingExtractor(path)
+        check_sortings_equal(self.SX, SX_nwb)
+        check_dumping(SX_nwb)
 
         # Test for handling unit property descriptions argument
         property_descriptions = dict(stability="This is a description of stability.")