remove 3.8; update typing

.github/workflows/read-nwbfile-tests.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "windows-latest"]  # TODO: update mac and streaming methods
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: s-weigand/setup-conda@v1
         with:

.github/workflows/streaming-tests.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "windows-latest"]  # TODO: update mac and streaming methods
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: s-weigand/setup-conda@v1
         with:

.github/workflows/testing.yml

@@ -13,7 +13,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-13", "windows-latest"]
-        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
     steps:
       - uses: conda-incubator/setup-miniconda@v3
         with:

setup.py

@@ -40,7 +40,6 @@
     classifiers=[
         "Development Status :: 4 - Beta",
         "Programming Language :: Python :: 3",
-        "Programming Language :: Python :: 3.8",
         "Programming Language :: Python :: 3.9",
         "Programming Language :: Python :: 3.10",
         "Programming Language :: Python :: 3.11",

src/nwbinspector/_configuration.py

@@ -3,7 +3,7 @@
 import json
 from pathlib import Path
 from types import FunctionType
-from typing import List, Optional
+from typing import Optional
 
 import jsonschema
 import yaml
@@ -65,8 +65,8 @@ def load_config(filepath_or_keyword: PathType) -> dict:
 def configure_checks(
     checks: list = available_checks,
     config: Optional[dict] = None,
-    ignore: Optional[List[str]] = None,
-    select: Optional[List[str]] = None,
+    ignore: Optional[list[str]] = None,
+    select: Optional[list[str]] = None,
     importance_threshold: Importance = Importance.BEST_PRACTICE_SUGGESTION,
 ) -> list:
     """

src/nwbinspector/_dandi_inspection.py

@@ -1,5 +1,5 @@
 import pathlib
-from typing import Iterable, List, Literal, Union
+from typing import Iterable, Literal, Union
 from warnings import filterwarnings
 
 import h5py
@@ -16,8 +16,8 @@ def inspect_dandiset(
     dandiset_version: Union[str, Literal["draft"], None] = None,
     config: Union[str, pathlib.Path, dict, Literal["dandi"], None] = None,
     checks: Union[list, None] = None,
-    ignore: Union[List[str], None] = None,
-    select: Union[List[str], None] = None,
+    ignore: Union[list[str], None] = None,
+    select: Union[list[str], None] = None,
     importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
     skip_validate: bool = False,
     show_progress_bar: bool = True,
@@ -112,8 +112,8 @@ def inspect_dandi_file_path(
     dandiset_version: Union[str, Literal["draft"], None] = None,
     config: Union[str, pathlib.Path, dict, Literal["dandi"]] = "dandi",
     checks: Union[list, None] = None,
-    ignore: Union[List[str], None] = None,
-    select: Union[List[str], None] = None,
+    ignore: Union[list[str], None] = None,
+    select: Union[list[str], None] = None,
     importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
     skip_validate: bool = False,
     client: Union["dandi.dandiapi.DandiAPIClient", None] = None,

src/nwbinspector/_formatting.py

@@ -8,7 +8,7 @@
 from enum import Enum
 from pathlib import Path
 from platform import platform
-from typing import Dict, List, Optional, Union
+from typing import Optional, Union
 
 import numpy as np
 
@@ -75,9 +75,9 @@ class MessageFormatter:
 
     def __init__(
         self,
-        messages: List[InspectorMessage],
-        levels: List[str],
-        reverse: Optional[List[bool]] = None,
+        messages: list[InspectorMessage],
+        levels: list[str],
+        reverse: Optional[list[bool]] = None,
         detailed: bool = False,
         formatter_options: Optional[FormatterOptions] = None,
     ):
@@ -107,7 +107,7 @@ def __init__(
         self.formatted_messages = []
 
     @staticmethod
-    def _count_messages_by_importance(messages: List[InspectorMessage]) -> Dict[str, int]:
+    def _count_messages_by_importance(messages: list[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
@@ -138,16 +138,16 @@ def _get_message_header(self, message: InspectorMessage):
             message_header += f"with name '{message.object_name}'"
         return message_header
 
-    def _get_message_increment(self, level_counter: List[int]):
+    def _get_message_increment(self, level_counter: list[int]):
         return (
             f"{'.'.join(np.array(level_counter, dtype=str))}.{self.message_counter}" f"{self.formatter_options.indent}"
         )
 
     def _add_subsection(
         self,
-        organized_messages: Dict[str, Union[dict, List[InspectorMessage]]],
-        levels: List[str],
-        level_counter: List[int],
+        organized_messages: dict[str, Union[dict, list[InspectorMessage]]],
+        levels: list[str],
+        level_counter: list[int],
     ):
         """Recursive helper for display_messages."""
         this_level_counter = list(level_counter)  # local copy passed from previous recursion level
@@ -193,7 +193,7 @@ def _add_subsection(
                         self.formatted_messages.extend([f"{' ' * len(increment)}  Message: {message.message}", ""])
                         self.message_counter += 1
 
-    def format_messages(self) -> List[str]:
+    def format_messages(self) -> list[str]:
         """Deploy recursive addition of sections, terminating with message display."""
         report_header = _get_report_header()
         self.formatted_messages.extend(
@@ -217,9 +217,9 @@ def format_messages(self) -> List[str]:
 
 
 def format_messages(
-    messages: List[InspectorMessage],
-    levels: List[str] = None,
-    reverse: Optional[List[bool]] = None,
+    messages: list[InspectorMessage],
+    levels: list[str] = None,
+    reverse: Optional[list[bool]] = None,
     detailed: bool = False,
 ) -> List[str]:
     """Print InspectorMessages in order specified by the organization structure."""

src/nwbinspector/_nwb_inspection.py

@@ -5,7 +5,7 @@
 from collections import defaultdict
 from concurrent.futures import ProcessPoolExecutor, as_completed
 from pathlib import Path
-from typing import Iterable, List, Optional, Type, Union
+from typing import Iterable, Optional, Type, Union
 from warnings import filterwarnings, warn
 
 import pynwb
@@ -375,8 +375,8 @@ def inspect_nwbfile_object(
     nwbfile_object: pynwb.NWBFile,
     checks: Optional[list] = None,
     config: Optional[dict] = None,
-    ignore: Optional[List[str]] = None,
-    select: Optional[List[str]] = None,
+    ignore: Optional[list[str]] = None,
+    select: Optional[list[str]] = None,
     importance_threshold: Union[str, Importance] = Importance.BEST_PRACTICE_SUGGESTION,
 ) -> Iterable[InspectorMessage]:
     """

src/nwbinspector/_organization.py

@@ -1,7 +1,7 @@
 """Internally used tools specifically for rendering more human-readable output from collected check results."""
 
 from enum import Enum
-from typing import List, Optional
+from typing import Optional
 
 from natsort import natsorted
 
@@ -16,7 +16,7 @@ def _sort_unique_values(unique_values: list, reverse: bool = False):
         return natsorted(unique_values, reverse=reverse)
 
 
-def organize_messages(messages: List[InspectorMessage], levels: List[str], reverse: Optional[List[bool]] = None):
+def organize_messages(messages: list[InspectorMessage], levels: list[str], reverse: Optional[list[bool]] = None):
     """
     General function for organizing list of InspectorMessages.
 

src/nwbinspector/testing/_testing.py

@@ -4,7 +4,7 @@
 import os
 from datetime import datetime
 from pathlib import Path
-from typing import Optional, Tuple
+from typing import Optional
 from urllib import request
 from uuid import uuid4
 
@@ -20,7 +20,7 @@
 TESTING_CONFIG_FILE_PATH = Path.cwd() / "tests" / "testing_config.json"
 
 
-def check_streaming_tests_enabled() -> Tuple[bool, Optional[str]]:
+def check_streaming_tests_enabled() -> tuple[bool, Optional[str]]:
     """
     General purpose helper for determining if the testing environment can support S3 DANDI streaming.
 

src/nwbinspector/tools/_dandi.py

@@ -2,12 +2,12 @@
 
 import re
 from concurrent.futures import ProcessPoolExecutor, as_completed
-from typing import Dict, Optional
+from typing import Optional
 
 from ..utils import calculate_number_of_cpu, is_module_installed
 
 
-def get_s3_urls_and_dandi_paths(dandiset_id: str, version_id: Optional[str] = None, n_jobs: int = 1) -> Dict[str, str]:
+def get_s3_urls_and_dandi_paths(dandiset_id: str, version_id: Optional[str] = None, n_jobs: int = 1) -> dict[str, str]:
     """
     Collect S3 URLS from a DANDISet ID.
 
@@ -46,7 +46,7 @@ def get_s3_urls_and_dandi_paths(dandiset_id: str, version_id: Optional[str] = No
     return s3_urls_to_dandi_paths
 
 
-def _get_content_url_and_path(asset, follow_redirects: int = 1, strip_query: bool = True) -> Dict[str, str]:
+def _get_content_url_and_path(asset, follow_redirects: int = 1, strip_query: bool = True) -> dict[str, str]:
     """
     Private helper function for parallelization in 'get_s3_urls_and_dandi_paths'.
 

src/nwbinspector/utils/_utils.py

@@ -7,33 +7,33 @@
 from importlib import import_module
 from pathlib import Path
 from time import sleep
-from typing import Callable, Dict, List, Optional, Tuple, TypeVar, Union
+from typing import Callable, Optional, TypeVar, Union
 
 import h5py
 import numpy as np
 from hdmf.backends.hdf5.h5_utils import H5Dataset
 from numpy.typing import ArrayLike
 from packaging import version
 
-# TODO: deprecated these in favor of explicit typing
+# TODO: deprecat these in favor of explicit typing
 PathType = TypeVar("PathType", str, Path)  # For types that can be either files or folders
 FilePathType = TypeVar("FilePathType", str, Path)
-OptionalListOfStrings = Optional[List[str]]
+OptionalListOfStrings = Optional[list[str]]
 
 dict_regex = r"({.+:.+})"  # TODO: remove this from global scope
 MAX_CACHE_ITEMS = 1000  # lru_cache default is 128 calls of matching input/output, but might need more to get use here
 
 
 @lru_cache(maxsize=MAX_CACHE_ITEMS)
 def _cache_data_retrieval_command(
-    data: h5py.Dataset, reduced_selection: Tuple[Tuple[Optional[int], Optional[int], Optional[int]]]
+    data: h5py.Dataset, reduced_selection: tuple[tuple[Optional[int], Optional[int], Optional[int]]]
 ) -> np.ndarray:
     """LRU caching for _cache_data_selection cannot be applied to list inputs; this expects the tuple or Dataset."""
     selection = tuple([slice(*reduced_slice) for reduced_slice in reduced_selection])  # reconstitute the slices
     return data[selection]
 
 
-def cache_data_selection(data: Union[h5py.Dataset, ArrayLike], selection: Union[slice, Tuple[slice]]) -> np.ndarray:
+def cache_data_selection(data: Union[h5py.Dataset, ArrayLike], selection: Union[slice, tuple[slice]]) -> np.ndarray:
     """Extract the selection lazily from the data object for efficient caching (most beneficial during streaming)."""
     if isinstance(data, np.memmap):  # np.memmap objects are not hashable - simply return the selection lazily
         return data[selection]
@@ -166,7 +166,7 @@ def get_package_version(name: str) -> version.Version:
 
 
 def robust_s3_read(
-    command: Callable, max_retries: int = 10, command_args: Optional[list] = None, command_kwargs: Optional[Dict] = None
+    command: Callable, max_retries: int = 10, command_args: Optional[list] = None, command_kwargs: Optional[dict] = None
 ):
     """Attempt the command (usually acting on an S3 IO) up to the number of max_retries using exponential backoff."""
     command_args = command_args or []