Remove 3.8; updating annotation typing (#508)

* remove 3.8; update typing

* changelog

* fix

* more fixes

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* forgot about this one

* remove 3.8 from template, workflow, docs

---------

Co-authored-by: CodyCBakerPhD <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Co-authored-by: Steph Prince <[email protected]>

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -36,7 +36,6 @@ body:
       label: Python Version
       options:
         - earlier
-        - 3.8
         - 3.9
         - "3.10"
         - "3.11"

.github/workflows/auto-publish.yml

@@ -15,7 +15,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v2
         with:
-          python-version: "3.8"
+          python-version: "3.9"
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip

.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:

CHANGELOG.md

@@ -1,13 +1,15 @@
 # Upcoming
 
+### 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)
 
 ### Improvements
 * Removed the `robust_ros3_read` utility helper. [#506](https://github.com/NeurodataWithoutBorders/nwbinspector/pull/506)
 
 
-
 # v0.5.2
 
 ### Deprecation (API)

docs/user_guide/installation.rst

@@ -6,7 +6,7 @@ If you haven't checked it out already, please read the :nwb-overview:`NWB Overvi
 
 The NWBInspector tool offers convenient command-line usage via any standard Conda or Python terminal.
 
-To install the package in any generic Python v3.8-v3.12 environment, simply type
+To install the package in any generic Python v3.9-v3.12 environment, simply type
 
 ::
 

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,
@@ -186,8 +186,8 @@ def inspect_url(
     url: str,
     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,
 ) -> Iterable[Union[InspectorMessage, None]]:
@@ -237,34 +237,31 @@ def inspect_url(
     validate_config(config=config)
 
     byte_stream = remfile.File(url=url)
-    # TODO: when 3.8 support is removed, uncomment to replace block and de-indent
-    # with (
-    #    h5py.File(name=byte_stream) as file,
-    #    pynwb.NWBHDF5IO(file=file) as io,
-    # )
-    with h5py.File(name=byte_stream) as file:
-        with pynwb.NWBHDF5IO(file=file) as io:
-            if skip_validate is False:
-                validation_errors = pynwb.validate(io=io)
-
-                for validation_error in validation_errors:
-                    yield InspectorMessage(
-                        message=validation_error.reason,
-                        importance=Importance.PYNWB_VALIDATION,
-                        check_function_name=validation_error.name,
-                        location=validation_error.location,
-                        file_path=nwbfile_path,
-                    )
-
-            nwbfile = io.read()
-
-            for message in inspect_nwbfile_object(
-                nwbfile_object=nwbfile,
-                config=config,
-                checks=checks,
-                ignore=ignore,
-                select=select,
-                importance_threshold=importance_threshold,
-            ):
-                message.file_path = url
-                yield message
+    with (
+        h5py.File(name=byte_stream) as file,
+        pynwb.NWBHDF5IO(file=file) as io,
+    ):
+        if not skip_validate:
+            validation_errors = pynwb.validate(io=io)
+
+            for validation_error in validation_errors:
+                yield InspectorMessage(
+                    message=validation_error.reason,
+                    importance=Importance.PYNWB_VALIDATION,
+                    check_function_name=validation_error.name,
+                    location=validation_error.location,
+                    file_path=nwbfile_path,
+                )
+
+        nwbfile = io.read()
+
+        for message in inspect_nwbfile_object(
+            nwbfile_object=nwbfile,
+            config=config,
+            checks=checks,
+            ignore=ignore,
+            select=select,
+            importance_threshold=importance_threshold,
+        ):
+            message.file_path = url
+            yield message

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
 
@@ -44,7 +44,7 @@ class FormatterOptions:
     """Class structure for defining all free attributes for the design of a report format."""
 
     def __init__(
-        self, indent_size: int = 2, indent: Optional[str] = None, section_headers: List[str] = ["=", "-", "~"]
+        self, indent_size: int = 2, indent: Optional[str] = None, section_headers: list[str] = ["=", "-", "~"]
     ):
         """
         Class that defines all the format parameters used by the generic MessageFormatter.
@@ -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(
@@ -217,11 +217,11 @@ 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]:
+) -> list[str]:
     """Print InspectorMessages in order specified by the organization structure."""
     if levels is None:
         levels = ["file_path", "importance"]
@@ -230,14 +230,14 @@ def format_messages(
     return formatted_messages
 
 
-def print_to_console(formatted_messages: List[str]):
+def print_to_console(formatted_messages: list[str]):
     """Print report file contents to console."""
     sys.stdout.write(os.linesep * 2)
     for line in formatted_messages:
         sys.stdout.write(line + "\n")
 
 
-def save_report(report_file_path: FilePathType, formatted_messages: List[str], overwrite=False):
+def save_report(report_file_path: FilePathType, formatted_messages: list[str], overwrite=False):
     """Write the list of organized check results to a nicely formatted text file."""
     report_file_path = Path(report_file_path)
     if report_file_path.exists() and not overwrite:

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
@@ -316,7 +316,7 @@ def inspect_nwbfile(
 
 
 # TODO: deprecate once subject types and dandi schemas have been extended
-def _intercept_in_vitro_protein(nwbfile_object: pynwb.NWBFile, checks: Optional[list] = None) -> List[callable]:
+def _intercept_in_vitro_protein(nwbfile_object: pynwb.NWBFile, checks: Optional[list] = None) -> list[callable]:
     """
     If the special 'protein' subject_id is specified, return a truncated list of checks to run.
 
@@ -351,8 +351,8 @@ 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.
 
@@ -136,7 +136,7 @@ def make_minimal_nwbfile():
     return NWBFile(session_description="", identifier=str(uuid4()), session_start_time=datetime.now().astimezone())
 
 
-def check_streaming_enabled() -> Tuple[bool, Optional[str]]:
+def check_streaming_enabled() -> tuple[bool, Optional[str]]:
     """
     General purpose helper for determining if the environment can support S3 DANDI streaming.