update last ones

docs/conf.py

@@ -8,7 +8,7 @@
 sys.path.append(str(Path(__file__).parent))
 from conf_extlinks import extlinks, intersphinx_mapping
 
-sys.path.insert(0, Path(__file__).resolve().parents[1])
+sys.path.insert(0, str(Path(__file__).resolve().parents[1]))
 
 project = "NWBInspector"
 copyright = "2022-2024, CatalystNeuro"

src/nwbinspector/_dandi_inspection.py

@@ -104,7 +104,7 @@ def inspect_dandi_file_path(
     dandi_file_path: str,
     dandiset_id: str,
     dandiset_version: Union[str, Literal["draft"], None] = None,
-    config: Union[str, pathlib.Path, dict, Literal["dandi"]] = "dandi",
+    config: Union[str, pathlib.Path, dict, Literal["dandi"], None] = "dandi",
     checks: Union[list, None] = None,
     ignore: Union[list[str], None] = None,
     select: Union[list[str], None] = None,
@@ -125,7 +125,7 @@ def inspect_dandi_file_path(
         The specific published version of the Dandiset to inspect.
         If None, the latest version is used.
         If there are no published versions, then 'draft' is used instead.
-    config : file path, dictionary, or "dandi", default: "dandi"
+    config : file path, dictionary, "dandi", or None, default: "dandi"
         If a file path, loads the dictionary configuration from the file.
         If a dictionary, it must be valid against the configuration schema.
         If "dandi", uses the requirements for DANDI validation.
@@ -178,7 +178,7 @@ def inspect_dandi_file_path(
 def inspect_url(
     *,
     url: str,
-    config: Union[str, pathlib.Path, dict, Literal["dandi"]] = "dandi",
+    config: Union[str, pathlib.Path, dict, Literal["dandi"], None] = "dandi",
     checks: Union[list, None] = None,
     ignore: Union[list[str], None] = None,
     select: Union[list[str], None] = None,
@@ -196,7 +196,7 @@ def inspect_url(
         https://dandiarchive.s3.amazonaws.com/blobs/636/57e/63657e32-ad33-4625-b664-31699b5bf664
 
         Note: this must be the `https` URL, not the 's3://' form.
-    config : file path, dictionary, or "dandi", default: "dandi"
+    config : file path, dictionary, "dandi", or None, default: "dandi"
         If a file path, loads the dictionary configuration from the file.
         If a dictionary, it must be valid against the configuration schema.
         If "dandi", uses the requirements for DANDI validation.
@@ -226,9 +226,10 @@ def inspect_url(
     filterwarnings(action="ignore", message="No cached namespaces found in .*")
     filterwarnings(action="ignore", message="Ignoring cached namespace .*")
 
-    if not isinstance(config, dict):
+    if isinstance(config, (str, pathlib.Path)):
         config = load_config(filepath_or_keyword=config)
-    validate_config(config=config)
+    if isinstance(config, dict):
+        validate_config(config=config)
 
     byte_stream = remfile.File(url=url)
     with (

src/nwbinspector/_formatting.py

@@ -76,14 +76,14 @@ class MessageFormatter:
 
     def __init__(
         self,
-        messages: list[InspectorMessage],
+        messages: list[Optional[InspectorMessage]],
         levels: list[str],
         reverse: Optional[list[bool]] = None,
         detailed: bool = False,
         formatter_options: Optional[FormatterOptions] = None,
     ) -> None:
         self.nmessages = len(messages)
-        self.nfiles = len(set(message.file_path for message in messages))
+        self.nfiles = len(set(message.file_path for message in messages))  # type: ignore
         self.message_count_by_importance = self._count_messages_by_importance(messages=messages)
         self.initial_organized_messages = organize_messages(messages=messages, levels=levels, reverse=reverse)
         self.detailed = detailed
@@ -108,10 +108,10 @@ def __init__(
         self.formatted_messages: list = []
 
     @staticmethod
-    def _count_messages_by_importance(messages: list[InspectorMessage]) -> dict[str, int]:
+    def _count_messages_by_importance(messages: list[Optional[InspectorMessage]]) -> dict[str, int]:
         message_count_by_importance = {importance_level.name: 0 for importance_level in Importance}
         for message in messages:
-            message_count_by_importance[message.importance.name] += 1
+            message_count_by_importance[message.importance.name] += 1  # type: ignore
         for key in [keys for keys, count in message_count_by_importance.items() if count == 0]:
             message_count_by_importance.pop(key)
         return message_count_by_importance
@@ -218,7 +218,7 @@ def format_messages(self) -> list[str]:
 
 
 def format_messages(
-    messages: list[InspectorMessage],
+    messages: list[Optional[InspectorMessage]],
     levels: Optional[list[str]] = None,
     reverse: Optional[list[bool]] = None,
     detailed: bool = False,

src/nwbinspector/_nwbinspector_cli.py

@@ -12,6 +12,7 @@
 from ._configuration import load_config
 from ._dandi_inspection import inspect_dandi_file_path, inspect_dandiset, inspect_url
 from ._formatting import (
+    InspectorOutputJSONEncoder,
     _get_report_header,
     format_messages,
     print_to_console,
@@ -89,9 +90,9 @@ def _nwbinspector_cli(
     path: str,
     stream: bool = False,
     version_id: Union[str, None] = None,
-    report_file_path: str = None,
+    report_file_path: Union[str, None] = None,
     config: Union[str, None] = None,
-    levels: str = None,
+    levels: Union[str, None] = None,
     reverse: Union[str, None] = None,
     overwrite: bool = False,
     ignore: Union[str, None] = None,
@@ -137,16 +138,17 @@ def _nwbinspector_cli(
     handled_select = select if select is None else select.split(",")
     handled_importance_threshold = Importance[threshold]
     show_progress_bar = True if progress_bar is None else strtobool(progress_bar)
-    modules = [] if modules is None else modules.split(",")
+    handled_modules = [] if modules is None else modules.split(",")
 
     # Trigger the import of custom checks that have been registered and exposed to their respective modules
-    for module in modules:
+    for module in handled_modules:
         importlib.import_module(name=module)
 
     # Scan entire Dandiset
     if stream and ":" not in path:
         dandiset_id = path
         dandiset_version = version_id
+
         messages_iterator = inspect_dandiset(
             dandiset_id=dandiset_id,
             dandiset_version=dandiset_version,
@@ -160,6 +162,8 @@ def _nwbinspector_cli(
     # Scan a single NWB file in a Dandiset
     elif stream and ":" in path:
         dandiset_id, dandi_file_path = path.split(":")
+        dandiset_version = version_id
+
         messages_iterator = inspect_dandi_file_path(
             dandi_file_path=dandi_file_path,
             dandiset_id=dandiset_id,
@@ -173,8 +177,9 @@ def _nwbinspector_cli(
     # Scan single NWB file at URL
     elif stream and path_is_url:
         dandi_s3_url = path
+
         messages_iterator = inspect_url(
-            dandi_s3_url=dandi_s3_url,
+            url=dandi_s3_url,
             config=handled_config,
             ignore=handled_ignore,
             select=handled_select,

src/nwbinspector/_organization.py

@@ -17,7 +17,7 @@ def _sort_unique_values(unique_values: list, reverse: bool = False) -> list:
 
 
 def organize_messages(
-    messages: list[InspectorMessage], levels: list[str], reverse: Optional[list[bool]] = None
+    messages: list[Optional[InspectorMessage]], levels: list[str], reverse: Optional[list[bool]] = None
 ) -> dict:
     """
     General function for organizing list of InspectorMessages.

src/nwbinspector/inspector_tools/__init__.py

@@ -9,5 +9,12 @@
 
 # Still keep imports functional with warning for soft deprecation cycle
 # TODO: remove after 9/15/2024
-from .._organization import organize_messages, _get_report_header
-from .._formatting import format_message, MessageFormatter, FormatterOptions, print_to_console, save_report
+from .._organization import organize_messages
+from .._formatting import (
+    format_messages,
+    MessageFormatter,
+    FormatterOptions,
+    print_to_console,
+    save_report,
+    _get_report_header,
+)

tests/test_inspector.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from shutil import rmtree
 from tempfile import mkdtemp
-from typing import Type
+from typing import Type, Union
 from unittest import TestCase
 
 import hdmf_zarr
@@ -118,7 +118,7 @@ class TestInspectorOnBackend(TestCase):
     skip_validate = False  # TODO: can be removed once NWBZarrIO validation issues are resolved
 
     @staticmethod
-    def assertFileExists(path: FilePathType):
+    def assertFileExists(path: Union[str, Path]):
         path = Path(path)
         assert path.exists()
 
@@ -882,7 +882,7 @@ def test_dandi_config_in_vitro_injection():
     assert messages == []
 
 
-def test_dandi_config_in_vitro_injection():
+def test_dandi_config_in_vitro_injection_safe():
     """Test the safe subject ID retrieval of the in vitro injection."""
     nwbfile = make_minimal_nwbfile()
     nwbfile.subject = Subject(subject_id=None, description="A detailed description about the in vitro setup.")