Merge branch 'dev' into remove_3_8

CHANGELOG.md

@@ -3,6 +3,9 @@
 ### Deprecation
 * Support for Python 3.8 has been removed. [#508](https://github.com/NeurodataWithoutBorders/nwbinspector/issues/508)
 
+### Deprecation (API)
+* The `inspect_nwb` method has been removed. Please use `inspect_nwbfile` or `inspect_nwbfile_object` instead. [#505](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/505)
+
 
 
 # v0.5.2

docs/user_guide/using_the_library.rst

@@ -22,7 +22,7 @@ Inspect a single NWBFile
 ------------------------
 
 The most basic function to use when inspecting a single NWB file is the
-:py:class:`~nwbinspector.nwbinspector.inspect_nwb` function.
+:py:class:`~nwbinspector.nwbinspector.inspect_nwbfile` function.
 
 .. code-block:: python
 
@@ -65,7 +65,7 @@ function.
 
     all_results = list(inspect_all(path=file_paths_or_folder, ...))
 
-This has the same return structure as :py:class:`~nwbinspector.nwbinspector.inspect_nwb`.
+This has the same return structure as :py:class:`~nwbinspector.nwbinspector.inspect_nwbfile`.
 
 
 .. note::

docs/user_guide/using_the_library_advanced.rst

@@ -7,18 +7,18 @@ This is a collection of tutorials illustrating some of the more advanced uses of
 Yielding and Iterating
 ----------------------
 
-Both the :py:class:`~nwbinspector.nwbinspector.inspect_all` and :py:class:`~nwbinspector.nwbinspector.inspect_nwb`
+Both the :py:class:`~nwbinspector.nwbinspector.inspect_all` and :py:class:`~nwbinspector.nwbinspector.inspect_nwbfile`
 functions return generators. That is, they do not actually run any checks on any NWBFile until the user
 performs an iteration command on them. The simplest way of doing this is to cast the generator as a ``list``,
-*i.e.*, ``list(inspect_nwb(...))`` which will automatically complete all checks.
+*i.e.*, ``list(inspect_nwbfile(...))`` which will automatically complete all checks.
 
 However, if a user chooses, they can harness these generators in more sophisticated ways. If you want to stop the
 checks early, the following will run the inspectors until the first
 :py:class:`~nwbinspector.register_checks.InspectorMessage` is returned:
 
 .. code-block:: python
 
-    results_generator = inspect_nwb(nwbfile_path="path_to_single_nwbfile")
+    results_generator = inspect_nwbfile(nwbfile_path="path_to_single_nwbfile")
 
     first_message = next(results_generator)
 
@@ -27,7 +27,7 @@ This will return either the first :py:class:`~nwbinspector.register_checks.Inspe
 
 .. code-block:: python
 
-    results_generator = inspect_nwb(nwbfile_path="path_to_single_nwbfile")
+    results_generator = inspect_nwbfile(nwbfile_path="path_to_single_nwbfile")
 
     try:
         first_message = next(results_generator)
@@ -38,7 +38,7 @@ Of course, the generator can be treated like any other iterable as well, such as
 
 .. code-block:: python
 
-    results_generator = inspect_nwb(nwbfile_path="path_to_single_nwbfile")
+    results_generator = inspect_nwbfile(nwbfile_path="path_to_single_nwbfile")
 
     for message in results_generator:
         print(message)

src/nwbinspector/__init__.py

@@ -8,7 +8,6 @@
     inspect_nwbfile_object,
     run_checks,
 )
-from ._nwb_inspection import inspect_nwb  # TODO: remove after 7/1/2023
 from ._formatting import (
     format_messages,
     print_to_console,
@@ -40,7 +39,6 @@
     "inspect_all",
     "inspect_nwbfile",
     "inspect_nwbfile_object",
-    "inspect_nwb",  # TODO: remove after 7/1/2023
     "run_checks",
     "format_messages",
     "print_to_console",

src/nwbinspector/_nwb_inspection.py

@@ -205,38 +205,6 @@ def _pickle_inspect_nwb(
     return list(inspect_nwbfile(nwbfile_path=nwbfile_path, checks=checks, skip_validate=skip_validate))
 
 
-# TODO: remove after 7/1/2023
-def inspect_nwb(
-    nwbfile_path: FilePathType,
-    checks: list = available_checks,
-    config: dict = None,
-    ignore: OptionalListOfStrings = None,
-    select: OptionalListOfStrings = None,
-    importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
-    driver: Optional[str] = None,
-    skip_validate: bool = False,
-    max_retries: int = 10,
-) -> Iterable[InspectorMessage]:
-    warn(
-        "The API function 'inspect_nwb' has been deprecated and will be removed in a future release! "
-        "To remove ambiguity, please call either "
-        "'inspect_nwbfile' giving a path to the unopened file on a system, or "
-        "'inspect_nwbfile_object' passing an already open pynwb.NWBFile object.",
-        category=DeprecationWarning,
-        stacklevel=2,
-    )
-    for inspector_message in inspect_nwbfile(
-        nwbfile_path=nwbfile_path,
-        checks=checks,
-        config=config,
-        ignore=ignore,
-        select=select,
-        importance_threshold=importance_threshold,
-        skip_validate=skip_validate,
-    ):
-        yield inspector_message
-
-
 def inspect_nwbfile(
     nwbfile_path: FilePathType,
     driver: Optional[str] = None,  # TODO: remove after 3/1/2025

src/nwbinspector/nwbinspector/__init__.py

@@ -18,7 +18,6 @@
 )
 from .._nwb_inspection import (
     inspect_all,
-    inspect_nwb,  # TODO: remove
     inspect_nwbfile,
     inspect_nwbfile_object,
     run_checks,