Merge branch 'guide_progress_bars_1' into parallel_nwbinspector_bars_…

…for_guide

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [dev]
+  pull_request:
+    branches: [dev]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

.pre-commit-config.yaml

@@ -1,11 +1,19 @@
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: v4.6.0
     hooks:
     -   id: check-yaml
     -   id: end-of-file-fixer
     -   id: trailing-whitespace
 -   repo: https://github.com/psf/black
-    rev: 24.3.0
+    rev: 24.4.0
     hooks:
     -   id: black
+
+- repo: https://github.com/codespell-project/codespell
+  # Configuration for codespell is in pyproject.toml
+  rev: v2.2.6
+  hooks:
+  - id: codespell
+    additional_dependencies:
+    - tomli

CHANGELOG.md

@@ -1,5 +1,11 @@
 # Upcoming
 
+# v0.4.34
+
+### Fixes
+
+* Fixed `--modules` flag in `nwbinspector` command line interface to allow for import of additional modules in the command line. This was necessary to be able to register new customized checks to the NWB Inspector. [#446](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/446)
+
 # v0.4.33
 
 ### Fixes
@@ -185,7 +191,7 @@
 # v0.4.14
 
 ### Fixes
-* Fixed an error with attribute retrieval specific to the `cell_id` of the `IntracellularElectrode` neurodata type that occured with respect to older versions of PyNWB. [PR #264](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/264)
+* Fixed an error with attribute retrieval specific to the `cell_id` of the `IntracellularElectrode` neurodata type that occurred with respect to older versions of PyNWB. [PR #264](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/264)
 
 
 

docs/best_practices/best_practices_index.rst

@@ -7,7 +7,7 @@ and its ecosystem of software tools.
 
 To enable NWB to accommodate the needs of the diverse neuroscience community, NWB provides a great degree of flexibility.
 In particular, the number of instances of a particular neurodata_type and corresponding names are often not fixed, to enable,
-e.g., storage of data from arbitrary numbers of devices withing the same file. While this flexibility is essential to enable
+e.g., storage of data from arbitrary numbers of devices within the same file. While this flexibility is essential to enable
 coverage of a broad range of use-cases, it can also lead to ambiguity. At the same time, we ultimately have the desire to have
 the schema as strict-as-possible to provide users and tool builders with a consistent organization of data. As such, we need to
 strike a fine balance between flexibility to enable support for varying experiments and use-cases and strictness in the schema

docs/best_practices/ecephys.rst

@@ -58,6 +58,12 @@ For relative position of an electrode on a probe, use ``rel_x``, ``rel_y``, and
 that are close enough to share a neuron.
 
 
+Avoid Duplication of Metadata
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+The ``ElectrodeTable`` should not contain redundant information that is present somewhere else within the :ref:`nwb-schema:sec-NWBFile` . Avoid adding columns to the `ElectrodeTable` that correspond to properties of the :ref:`nwb-schema:sec-ElectricalSeries` such as ``unit``, ``offsets`` or ``channel gains`` These properties should be stored in the corresponding attributes of the :ref:`nwb-schema:sec-ElectricalSeries` object.
+
+As a concrete example, the package objects from the `SpikeInterface <https://spikeinterface.readthedocs.io/en/latest/>`__ package contain two properties named ``gain_to_uv`` and ``offset_to_uv`` that are used to convert the raw data to microvolts. These properties should not be stored in the `ElectrodeTable` but rather in the ``ElectricalSeries`` object as ``channel_conversion`` and ``offset`` respectively.
 
 Units Table
 -----------

docs/best_practices/extensions.rst

@@ -5,7 +5,7 @@ Extend the core NWB schema only when necessary. Extensions are an essential mech
 data with NWB that is otherwise not supported. However, we here need to consider that there are certain costs associated
 with extensions, *e.g.*, cost of creating, supporting, documenting, and maintaining new extensions and effort for users
 to use and learn already-created extensions. As such, users should attempt to use core ``neurodata_types`` or
-pre-existing extentions before creating new ones. :ref:`hdmf-schema:sec-dynamictable`, which are used throughout the
+pre-existing extensions before creating new ones. :ref:`hdmf-schema:sec-dynamictable`, which are used throughout the
 NWB schema to store information about time intervals, electrodes, or spiking output, provide the ability to
 dynamically add columns without the need for extensions, and can help avoid the need for custom extensions in many
 cases.

docs/best_practices/general.rst

@@ -68,3 +68,9 @@ Empty Strings
 Required free-text fields for neurodata types should not use placeholders such as empty strings (`""`), ``"no description"``, or ``"PLACEHOLDER"``. For example, the :py:attr:`description` field should always richly describe that particular neurodata type and its interpretation within the experiment.
 
 Many attributes of neurodata types in NWB are optional details to include. It is not necessary, therefore, to use placeholders for these attributes. Instead, they should not be specified at all.
+
+
+Avoid Duplication of Metadata
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Avoid duplication of metadata across different objects. If a piece of metadata is shared between multiple objects, consider creating a separate object to store that metadata and linking to it from the other objects. This will help to keep the metadata consistent and reduce the risk of errors when updating the metadata.

docs/user_guide/using_the_command_line_interface.rst

@@ -25,7 +25,7 @@ the most useful of these options.
 Streaming
 ---------
 
-If the NWB file(s) you wish to inspect are already on the :dandi-archive:`DANDI archive <>`, you can run the NWB Inspector directly on that DANDI set instead of having to download it. All that is needed is to specfy the DANDI set ID (six-digit identifier) as the path and add the ``--stream`` flag.
+If the NWB file(s) you wish to inspect are already on the :dandi-archive:`DANDI archive <>`, you can run the NWB Inspector directly on that DANDI set instead of having to download it. All that is needed is to specify the DANDI set ID (six-digit identifier) as the path and add the ``--stream`` flag.
 
 ::
 
@@ -75,7 +75,7 @@ For example,
     numbers like ``"0, 1"``.
 
 
-The defalt report also aggregates identical outputs into a summary over multiple files; running
+The default report also aggregates identical outputs into a summary over multiple files; running
 
 ::
 

pyproject.toml

@@ -20,3 +20,10 @@ extend-exclude = '''
   |dist
 )/
 '''
+
+[tool.codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = '.git*,*.pdf,*.css'
+check-hidden = true
+# ignore-regex = ''
+# ignore-words-list = ''

src/nwbinspector/nwbinspector.py

@@ -252,6 +252,7 @@ def inspect_all_cli(
     DANDI archive (i.e., https://dandiarchive.org/dandiset/{dandiset_id}/{version_id}), or a six-digit Dandiset ID.
     """
     levels = ["importance", "file_path"] if levels is None else levels.split(",")
+    modules = [] if modules is None else modules.split(",")
     reverse = [False] * len(levels) if reverse is None else [strtobool(x) for x in reverse.split(",")]
     progress_bar = strtobool(progress_bar) if progress_bar is not None else True
     if config is not None:

src/nwbinspector/version.py

@@ -1 +1 @@
-__version__ = "0.4.34"
+__version__ = "0.4.35"

tests/test_inspector.py

@@ -390,7 +390,8 @@ def test_command_line_runs_cli_only(self):
         console_output_file = self.tempdir / "test_console_output.txt"
         os.system(
             f"nwbinspector {str(self.tempdir)} --overwrite --select check_timestamps_match_first_dimension,"
-            "check_data_orientation,check_regular_timestamps,check_small_dataset_compression"
+            "check_data_orientation,check_regular_timestamps,check_small_dataset_compression "
+            "--modules random,math,datetime"
             f"> {console_output_file}"
         )
         self.assertLogFileContentsEqual(