fix

setup.py

@@ -34,7 +34,13 @@
     install_requires=install_requires,
     # zarr<2.18.0 because of https://github.com/NeurodataWithoutBorders/nwbinspector/pull/460
     extras_require=dict(dandi=["dandi>=0.39.2", "zarr<2.18.0", "remfile"], zarr=["hdmf_zarr>=0.3.0", "zarr<2.18.0"]),
-    entry_points={"console_scripts": ["nwbinspector=nwbinspector._inspection_cli:_inspect_all_cli"]},
+    entry_points={
+        "console_scripts": [
+            "nwbinspector=nwbinspector._nwb_inspection_cli:_inspect_all_cli",
+            "inspect_dandiset=nwbinspector._inspect_dandiset_cli:_inspect_dandiset_cli",
+            "inspect_dandi_file_path=nwbinspector._inspect_dandi_file_path_cli:_inspect_dandi_file_path_cli",
+        ],
+    },
     license="BSD-3-Clause",
     classifiers=[
         "Development Status :: 4 - Beta",

src/nwbinspector/_dandi_inspection_cli.py → src/nwbinspector/_inspect_dandi_file_path_cli.py

@@ -10,7 +10,7 @@
 import click
 
 from ._formatting import _get_report_header
-from . import Importance, inspect_all, format_messages, print_to_console, save_report, __version__
+from . import Importance, inspect_all, format_messages, print_to_console, save_report
 from .utils import strtobool
 from ._dandi_inspection import inspect_dandiset, inspect_dandi_file_path
 
@@ -22,7 +22,6 @@
     required=True,
     type=str,
 )
-@click.option("--modules", help="Modules to import prior to reading the file(s).")
 @click.option(
     "--report-file-path",
     default=None,
@@ -37,43 +36,45 @@
 @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"]),
+    "--importance_threshold",
     help="Ignores tests with an assigned importance below this threshold.",
+    type=click.Choice(["CRITICAL", "BEST_PRACTICE_VIOLATION", "BEST_PRACTICE_SUGGESTION"]),
+    default="BEST_PRACTICE_SUGGESTION",
 )
 @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("--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(
+    "--skip-validate",
+    help="Skip the PyNWB validation step.",
+    is_flag=True,
+    required=False,
+    default=False,
+)
 @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."
+        "Use `--detailed` to see the complete report."
     ),
     is_flag=True,
+    required=False,
+    default=False,
 )
-@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,
+    "--progress-bar",
+    help="Set this flag to False to disable display of the progress bar.",
+    type=str,
+    required=False,
 )
 @click.option(
-    "--version-id",
-    help=(
-        "When 'path' is a six-digit DANDISet ID, this further specifies which version of " "the DANDISet to inspect."
-    ),
+    "--modules",
+    help="Modules to import prior to reading the file(s). Necessary for registration of custom checks functions.",
+    type=str,
+    required=False,
 )
-@click.version_option(__version__)
 def _inspect_dandiset_cli(
-    path: str,
-    modules: Optional[str] = None,
+    dandiset_id: str,
     report_file_path: str = None,
     levels: str = None,
     reverse: Optional[str] = None,
@@ -87,38 +88,20 @@ def _inspect_dandiset_cli(
     skip_validate: bool = False,
     detailed: bool = False,
     progress_bar: Optional[str] = None,
-    stream: bool = False,
-    version_id: Optional[str] = None,
+    modules: 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.
-    """
+    """Run the NWBInspector via the command line."""
     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
+    modules = [] if modules is None else modules.split(",")
+
     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,
+        inspect_dandiset(
+            dandiset_id=dandiset_id,
             modules=modules,
             ignore=ignore if ignore is None else ignore.split(","),
             select=select if select is None else select.split(","),
@@ -131,13 +114,15 @@ def _inspect_dandiset_cli(
             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:
@@ -146,7 +131,12 @@ def _inspect_dandiset_cli(
 
 
 @click.command("--inspect_dandi_file_path")
-@click.argument("path")
+@click.option(
+    "--dandi_file_path",
+    help="The path to the Dandifile as seen on the archive; e.g., 'sub-123_ses-456+ecephys.nwb'.",
+    required=True,
+    type=str,
+)
 @click.option("--modules", help="Modules to import prior to reading the file(s).")
 @click.option(
     "--report-file-path",
@@ -195,8 +185,7 @@ def _inspect_dandiset_cli(
         "When 'path' is a six-digit DANDISet ID, this further specifies which version of " "the DANDISet to inspect."
     ),
 )
-@click.version_option(__version__)
-def _inspect_dandiset_cli(
+def _inspect_dandi_file_path_cli(
     path: str,
     modules: Optional[str] = None,
     report_file_path: str = None,