Merge pull request #19 from VisLab/main

Fussing with the imports to remove Ruff complaints

README.md

@@ -20,4 +20,4 @@ user guide explains in more detail how to use this extension for HED.
 pip install -U ndx-hed
 ```
 
-**Matlab:**  The Matlab extension is under development
+**Matlab:**  The Matlab extension is under development.

pyproject.toml

@@ -104,7 +104,7 @@ preview = true
 exclude = ".git|.mypy_cache|.tox|.venv|venv|.ipynb_checkpoints|_build/|dist/|__pypackages__|.ipynb|docs/"
 
 [tool.ruff]
-select = ["E", "F", "T100", "T201", "T203"]
+lint.select = ["E", "F", "T100", "T201", "T203"]
 exclude = [
   ".git",
   ".tox",
@@ -114,8 +114,8 @@ exclude = [
 ]
 line-length = 120
 
-[tool.ruff.per-file-ignores]
+[tool.ruff.lint.per-file-ignores]
 "src/spec/create_extension_spec.py" = ["T201"]
 
-[tool.ruff.mccabe]
+[tool.ruff.lint.mccabe]
 max-complexity = 17

setup.py

@@ -5,65 +5,3 @@
 if __name__ == "__main__":
     setup()
 
-# import os
-#
-# from setuptools import setup, find_packages
-# from shutil import copy2
-#
-# # load README.md/README.rst file
-# try:
-#     if os.path.exists('README.md'):
-#         with open('README.md', 'r') as fp:
-#             readme = fp.read()
-#             readme_type = 'text/markdown; charset=UTF-8'
-#     elif os.path.exists('README.rst'):
-#         with open('README.rst', 'r') as fp:
-#             readme = fp.read()
-#             readme_type = 'text/x-rst; charset=UTF-8'
-#     else:
-#         readme = ""
-# except Exception:
-#     readme = ""
-#
-# setup_args = {
-#     'name': 'ndx-hed',
-#     'version': '0.1.0',
-#     'description': 'NWB extension for storing HED annotations in VectorData format.',
-#     'long_description': readme,
-#     'long_description_content_type': readme_type,
-#     'author': 'Ryan Ly, Kay Robbins',
-#     'author_email': 'rly@lbl.gov, Kay.Robbins@utsa.edu',
-#     'url': 'https://github.com/hed-standard/ndx-hed',
-#     'license': 'BSD 3-Clause',
-#     'install_requires': [
-#         'pynwb>=1.1.2'
-#     ],
-#     'packages': find_packages('src/pynwb'),
-#     'package_dir': {'': 'src/pynwb'},
-#     'package_data': {'ndx_hed': [
-#         'spec/ndx-hed.namespace.yaml',
-#         'spec/ndx-hed.extensions.yaml',
-#     ]},
-#     'classifiers': [
-#         "Intended Audience :: Developers",
-#         "Intended Audience :: Science/Research",
-#     ],
-#     'zip_safe': False
-# }
-#
-#
-# def _copy_spec_files(project_dir):
-#     ns_path = os.path.join(project_dir, 'spec', 'ndx-hed.namespace.yaml')
-#     ext_path = os.path.join(project_dir, 'spec', 'ndx-hed.extensions.yaml')
-#
-#     dst_dir = os.path.join(project_dir, 'src', 'pynwb', 'ndx_hed', 'spec')
-#     if not os.path.exists(dst_dir):
-#         os.mkdir(dst_dir)
-#
-#     copy2(ns_path, dst_dir)
-#     copy2(ext_path, dst_dir)
-#
-#
-# if __name__ == '__main__':
-#     _copy_spec_files(os.path.dirname(__file__))
-#     setup(**setup_args)

src/pynwb/ndx_hed/__init__.py

@@ -2,14 +2,9 @@
 from pynwb import load_namespaces, get_class
 
 # Set path of the namespace.yaml file to the expected install location
-ndx_hed_specpath = os.path.join(
-    os.path.dirname(__file__),
-    'spec',
-    'ndx-hed.namespace.yaml'
-)
+ndx_hed_specpath = os.path.join(os.path.dirname(__file__), 'spec', 'ndx-hed.namespace.yaml')
 
-# If the extension has not been installed yet but we are running directly from
-# the git repo
+# If the extension has not been installed yet, but we are running directly from the git repo
 if not os.path.exists(ndx_hed_specpath):
     ndx_hed_specpath = os.path.abspath(os.path.join(
         os.path.dirname(__file__),
@@ -20,37 +15,7 @@
 
 # Load the namespace
 load_namespaces(ndx_hed_specpath)
-# 
-# from . import io as __io  # noqa: E402,F401
-# from .hed_models import NWBHedVersion
-# 
-# try:
-#     from importlib.resources import files
-# except ImportError:
-#     # TODO: Remove when python 3.9 becomes the new minimum
-#     from importlib_resources import files
-# 
-#     
-# 
-# # Get path to the namespace.yaml file with the expected location when installed not in editable mode
-# __location_of_this_file = files(__name__)
-# __spec_path = __location_of_this_file / "spec" / "ndx-hed.namespace.yaml"
-# 
-# # If that path does not exist, we are likely running in editable mode. Use the local path instead
-# if not os.path.exists(__spec_path):
-#     __spec_path = __location_of_this_file.parent.parent.parent / "spec" / "ndx-hed.namespace.yaml"
-# 
-# # Load the namespace
-# load_namespaces(str(__spec_path))
-# 
-# # TODO: Define your classes here to make them accessible at the package level.
-# # Either have PyNWB generate a class from the spec using `get_class` as shown
-# # below or write a custom class and register it using the class decorator
-# # `@register_class("TetrodeSeries", "ndx-hed")`
-# # HedAnnotations = get_class("HedAnnotations", "ndx-hed")
-# HedVersion = get_class("HedVersion", "ndx-hed")
-# 
-# # Remove these functions from the package
+
 del load_namespaces, get_class
 
-from .hed_tags import HedTags
+#from .hed_tags import HedTags as HedTags

src/pynwb/tests/test_hed_tags.py

@@ -8,7 +8,7 @@
 from pynwb import NWBHDF5IO, NWBFile
 from pynwb.testing.mock.file import mock_NWBFile
 from pynwb.testing import TestCase, remove_test_file
-from ndx_hed import HedTags
+from ndx_hed.hed_tags import HedTags
 
 
 class TestHedTagsConstructor(TestCase):
@@ -68,7 +68,7 @@ def test_get(self):
     def test_temp(self):
         tags = HedTags(hed_version='8.3.0', data=["Correct-action", "Incorrect-action"])
         tags.add_row("Sensory-event, Visual-presentation")
-        print(tags)
+
     def test_dynamic_table(self):
         """Add a HED column to a DynamicTable."""
         my_table = DynamicTable(

src/spec/create_extension_spec.py

@@ -1,10 +1,7 @@
 # -*- coding: utf-8 -*-
 import os.path
 
-from pynwb.spec import NWBNamespaceBuilder, export_spec, NWBDatasetSpec, NWBGroupSpec, NWBAttributeSpec
-
-# TODO: import other spec classes as needed
-# from pynwb.spec import , NWBLinkSpec, NWBDtypeSpec, NWBRefSpec
+from pynwb.spec import NWBNamespaceBuilder, export_spec, NWBDatasetSpec, NWBAttributeSpec
 
 
 def main():