fix conflicts

.github/workflows/dailies.yml

@@ -26,8 +26,8 @@ jobs:
 
   notify:
     runs-on: ubuntu-latest
-    needs: [run-daily-tests, run-daily-doc-link-checks]
-    if: ${{ always() && contains(needs.*.result, 'failure') }}
+    needs: [run-daily-tests, run-daily-doc-link-checks, test-dandi-latest, test-dandi-dev, test-dandi-dev-live]
+    if: failure()
     steps:
     - uses: dawidd6/action-send-mail@v3
       with:
@@ -36,6 +36,6 @@ jobs:
         username: ${{ secrets.MAIL_USERNAME }}
         password: ${{ secrets.MAIL_PASSWORD }}
         subject: NWB Inspector Daily Failure
-        to: ${{ secrets.DAILY_FAILURE_EMAIL_LIST }}  # add more with commas, no separation
+        to: [email protected],[email protected]
         from: NWB Inspector
         body: "The daily workflow for the NWB Inspector failed: please check status at https://github.com/NeurodataWithoutBorders/nwbinspector/actions/workflows/dailies.yml"

.pre-commit-config.yaml

@@ -10,6 +10,12 @@ repos:
     hooks:
     -   id: black
 
+- repo: https://github.com/astral-sh/ruff-pre-commit
+  rev: v0.6.2
+  hooks:
+  - id: ruff
+    args: [ --fix ]
+
 - repo: https://github.com/codespell-project/codespell
   rev: v2.3.0
   hooks:

CHANGELOG.md

@@ -8,9 +8,13 @@
 ### Pending Deprecation (API)
 * The `stream` and `version_id` arguments have been removed from `nwbinspector.inspect_all`. Please use `nwbinspector.inspect_dandiset` instead. [#490](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/490)
 
-## New Features
+### New Features
 * Introduced the `inspect_dandiset` and `inspect_dandi_file_path` API functions to replace the functionality in `nwbinspector --stream`. The new feature uses `remfile` instead of `ros3`. [#490](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/490)
 
+### Fixes
+* Fixed import error when using the CLI with `--config dandi`. [#494](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/494)
+* Removed unused imports throughout package. [#496](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/496)
+
 
 
 # v0.5.0

pyproject.toml

@@ -21,6 +21,27 @@ extend-exclude = '''
 )/
 '''
 
+
+
+[tool.ruff]
+exclude = ["docs/*"]
+
+[tool.ruff.lint]
+select = ["F401", "I002"] # TODO: eventually, expand to other 'I', 'D', and other 'F' linting
+fixable = ["ALL"]
+
+[tool.ruff.lint.per-file-ignores]
+"src/nwbinspector/__init__.py" = ["I"]  # Must maintain explicit order for imports for check registration
+"src/nwbinspector/utils/__init__.py" = ["F401", "I"]  # Several items planned for long-term deprecation
+
+# Temporarily keeping all exposure below for back-compatibility
+# Deprecation scheduled for 9/15/2024
+"src/nwbinspector/nwbinspector/__init__.py" = ["F401", "I"]
+"src/nwbinspector/inspector_tools/__init__.py" = ["F401", "I"]
+"src/nwbinspector/version/__init__.py" = ["F401", "I"]
+"src/nwbinspector/register_checks/__init__.py" = ["F401", "I"]
+
+
 [tool.codespell]
 skip = '.git*,*.pdf,*.css'
 check-hidden = true

src/nwbinspector/__init__.py

@@ -30,6 +30,7 @@
     "Importance",
     "Severity",
     "InspectorMessage",
+    "validate_config",
     "load_config",
     "configure_checks",
     "InspectorOutputJSONEncoder",

src/nwbinspector/_configuration.py

@@ -3,15 +3,13 @@
 import json
 import jsonschema
 from pathlib import Path
-from enum import Enum
 from typing import Optional, List
 from types import FunctionType
-from packaging.version import Version
 
 import yaml
 
 from . import available_checks
-from ._registration import InspectorMessage, Importance
+from ._registration import Importance
 from nwbinspector.utils._utils import (
     PathType,
 )

src/nwbinspector/_inspection_cli.py

@@ -0,0 +1,147 @@
+"""Primary functions for inspecting NWBFiles."""
+
+import os
+import re
+import json
+from pathlib import Path
+from typing import Optional
+from warnings import warn
+
+import click
+
+from ._formatting import _get_report_header, InspectorOutputJSONEncoder
+from ._types import Importance
+from ._nwb_inspection import inspect_all
+from ._formatting import format_messages, print_to_console, save_report, InspectorOutputJSONEncoder
+from ._version import __version__
+from ._configuration import load_config
+from .utils import strtobool
+
+
+@click.command()
+@click.argument("path")
+@click.option("--modules", help="Modules to import prior to reading the file(s).")
+@click.option(
+    "--report-file-path",
+    default=None,
+    help="Save path for the report file.",
+    type=click.Path(writable=True),
+)
+@click.option("--levels", help="Comma-separated names of InspectorMessage attributes to organize by.")
+@click.option(
+    "--reverse", help="Comma-separated booleans corresponding to reversing the order for each value of 'levels'."
+)
+@click.option("--overwrite", help="Overwrite an existing report file at the location.", is_flag=True)
+@click.option("--ignore", help="Comma-separated names of checks to skip.")
+@click.option("--select", help="Comma-separated names of checks to run.")
+@click.option(
+    "--threshold",
+    default="BEST_PRACTICE_SUGGESTION",
+    type=click.Choice(["CRITICAL", "BEST_PRACTICE_VIOLATION", "BEST_PRACTICE_SUGGESTION"]),
+    help="Ignores tests with an assigned importance below this threshold.",
+)
+@click.option("--config", help="Name of config or path of config .yaml file that overwrites importance of checks.")
+@click.option("--json-file-path", help="Write json output to this location.")
+@click.option("--n-jobs", help="Number of jobs to use in parallel.", default=1)
+@click.option("--skip-validate", help="Skip the PyNWB validation step.", is_flag=True)
+@click.option(
+    "--detailed",
+    help=(
+        "If file_path is the last of 'levels' (the default), identical checks will be aggregated in the display. "
+        "Use '--detailed' to see the complete report."
+    ),
+    is_flag=True,
+)
+@click.option("--progress-bar", help="Set this flag to False to disable display of the progress bar.")
+@click.option(
+    "--stream",
+    help=(
+        "Stream data from the DANDI archive. If the 'path' is a local copy of the target DANDISet, specifying this "
+        "flag will still force the data to be streamed instead of using the local copy. To use the local copy, simply "
+        "remove this flag. Requires the Read Only S3 (ros3) driver to be installed with h5py."
+    ),
+    is_flag=True,
+)
+@click.option(
+    "--version-id",
+    help=(
+        "When 'path' is a six-digit DANDISet ID, this further specifies which version of " "the DANDISet to inspect."
+    ),
+)
+@click.version_option(__version__)
+def _inspect_all_cli(
+    path: str,
+    modules: Optional[str] = None,
+    report_file_path: str = None,
+    levels: str = None,
+    reverse: Optional[str] = None,
+    overwrite: bool = False,
+    ignore: Optional[str] = None,
+    select: Optional[str] = None,
+    threshold: str = "BEST_PRACTICE_SUGGESTION",
+    config: Optional[str] = None,
+    json_file_path: Optional[str] = None,
+    n_jobs: int = 1,
+    skip_validate: bool = False,
+    detailed: bool = False,
+    progress_bar: Optional[str] = None,
+    stream: bool = False,
+    version_id: Optional[str] = None,
+):
+    """
+    Run the NWBInspector via the command line.
+
+    path :
+    Path to either a local NWBFile, a local folder containing NWBFiles, a link to a dataset on
+    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:
+        config = load_config(filepath_or_keyword=config)
+    if stream:
+        url_path = path if path.startswith("https://") else None
+        if url_path:
+            dandiset_id, version_id = url_path.split("/")[-2:]
+            path = dandiset_id
+        assert url_path or re.fullmatch(
+            pattern="^[0-9]{6}$", string=path
+        ), "'--stream' flag was enabled, but 'path' is neither a full link to the DANDI archive nor a DANDISet ID."
+        if Path(path).is_dir():
+            warn(
+                f"The local DANDISet '{path}' exists, but the '--stream' flag was used. "
+                "NWBInspector will use S3 streaming from DANDI. To use local data, remove the '--stream' flag."
+            )
+    messages = list(
+        inspect_all(
+            path=path,
+            modules=modules,
+            ignore=ignore if ignore is None else ignore.split(","),
+            select=select if select is None else select.split(","),
+            importance_threshold=Importance[threshold],
+            config=config,
+            n_jobs=n_jobs,
+            skip_validate=skip_validate,
+            progress_bar=progress_bar,
+            stream=stream,
+            version_id=version_id,
+        )
+    )
+    if json_file_path is not None:
+        if Path(json_file_path).exists() and not overwrite:
+            raise FileExistsError(f"The file {json_file_path} already exists! Specify the '-o' flag to overwrite.")
+        with open(file=json_file_path, mode="w") as fp:
+            json_report = dict(header=_get_report_header(), messages=messages)
+            json.dump(obj=json_report, fp=fp, cls=InspectorOutputJSONEncoder)
+            print(f"{os.linesep*2}Report saved to {str(Path(json_file_path).absolute())}!{os.linesep}")
+    formatted_messages = format_messages(messages=messages, levels=levels, reverse=reverse, detailed=detailed)
+    print_to_console(formatted_messages=formatted_messages)
+    if report_file_path is not None:
+        save_report(report_file_path=report_file_path, formatted_messages=formatted_messages, overwrite=overwrite)
+        print(f"{os.linesep*2}Report saved to {str(Path(report_file_path).absolute())}!{os.linesep}")
+
+
+if __name__ == "__main__":
+    _inspect_all_cli()

src/nwbinspector/_registration.py

@@ -1,9 +1,6 @@
 """Primary decorator used on a check function to add it to the registry and automatically parse its output."""
 
-from collections.abc import Iterable
 from functools import wraps
-from enum import Enum
-from dataclasses import dataclass
 from typing import Optional
 
 import h5py

src/nwbinspector/_types.py

@@ -1,16 +1,9 @@
 """Primary decorator used on a check function to add it to the registry and automatically parse its output."""
 
-from collections.abc import Iterable
-from functools import wraps
 from enum import Enum
 from dataclasses import dataclass
 from typing import Optional
 
-import h5py
-from pynwb import NWBFile
-from pynwb.file import Subject
-from pynwb.ecephys import Device, ElectrodeGroup
-
 
 class Importance(Enum):
     """A definition of the valid importance levels for a given check function."""