Merge pull request #1343 from dandi/better-types

Modernize type annotations and improve mypy config

dandi/cli/__init__.py

@@ -12,7 +12,7 @@
     # A trick found on https://github.com/h5py/h5py/issues/1079#issuecomment-567081386
     # to avoid some weird behavior on Yarik's laptop where MPI fails to initialize
     # and that takes h5py additional 5 seconds to import
-    import mpi4py
+    import mpi4py  # type: ignore[import-not-found]
 
     mpi4py.rc(initialize=False)
 except Exception:

dandi/cli/cmd_move.py

@@ -1,7 +1,5 @@
 from __future__ import annotations
 
-from typing import Optional
-
 import click
 
 from .base import devel_debug_option, instance_option, map_to_click_exceptions
@@ -47,10 +45,10 @@
 @map_to_click_exceptions
 def move(
     paths: tuple[str],
-    dandiset: Optional[str],
+    dandiset: str | None,
     dry_run: bool,
     existing: str,
-    jobs: Optional[int],
+    jobs: int | None,
     regex: bool,
     work_on: str,
     dandi_instance: str,

dandi/cli/cmd_validate.py

@@ -4,7 +4,7 @@
 import logging
 import os
 import re
-from typing import List, Optional, cast
+from typing import cast
 import warnings
 
 import click
@@ -90,10 +90,10 @@ def validate_bids(
 @map_to_click_exceptions
 def validate(
     paths: tuple[str, ...],
-    ignore: Optional[str],
+    ignore: str | None,
     grouping: str,
     min_severity: str,
-    schema: Optional[str] = None,
+    schema: str | None = None,
     devel_debug: bool = False,
     allow_any_path: bool = False,
 ) -> None:
@@ -139,7 +139,7 @@ def validate(
 def _process_issues(
     validator_result: Iterable[ValidationResult],
     grouping: str,
-    ignore: Optional[str] = None,
+    ignore: str | None = None,
 ) -> None:
     issues = [i for i in validator_result if i.severity is not None]
     if ignore is not None:
@@ -149,7 +149,7 @@ def _process_issues(
         display_errors(
             purviews,
             [i.id for i in issues],
-            cast(List[Severity], [i.severity for i in issues]),
+            cast("list[Severity]", [i.severity for i in issues]),
             [i.message for i in issues],
         )
     elif grouping == "path":
@@ -161,7 +161,7 @@ def _process_issues(
             display_errors(
                 [purview],
                 [i.id for i in applies_to],
-                cast(List[Severity], [i.severity for i in applies_to]),
+                cast("list[Severity]", [i.severity for i in applies_to]),
                 [i.message for i in applies_to],
             )
     else:
@@ -185,10 +185,10 @@ def _get_severity_color(severities: list[Severity]) -> str:
 
 
 def display_errors(
-    purviews: list[Optional[str]],
+    purviews: list[str | None],
     errors: list[str],
     severities: list[Severity],
-    messages: list[Optional[str]],
+    messages: list[str | None],
 ) -> None:
     """
     Unified error display for validation CLI, which auto-resolves grouping

dandi/cli/tests/test_cmd_ls.py

@@ -11,7 +11,7 @@
 
 from dandi.tests.skip import mark
 
-from ..command import ls
+from ..cmd_ls import ls
 from ...utils import yaml_load
 
 

dandi/cli/tests/test_command.py

@@ -6,7 +6,9 @@
 from click.testing import CliRunner
 import pytest
 
-from ..command import __all_commands__, ls, validate
+from ..cmd_ls import ls
+from ..cmd_validate import validate
+from ..command import __all_commands__
 
 
 @pytest.mark.parametrize("command", (ls, validate))

dandi/cli/tests/test_download.py

@@ -5,7 +5,7 @@
 from click.testing import CliRunner
 import pytest
 
-from ..command import download
+from ..cmd_download import download
 from ...consts import dandiset_metadata_file, known_instances
 
 

dandi/cli/tests/test_instances.py

@@ -2,7 +2,7 @@
 
 from click.testing import CliRunner
 
-from ..command import instances
+from ..cmd_instances import instances
 
 
 def test_cmd_instances(monkeypatch):

dandi/cli/tests/test_move.py

@@ -7,7 +7,7 @@
 import pytest
 from pytest_mock import MockerFixture
 
-from ..command import move
+from ..cmd_move import move
 
 
 @pytest.mark.parametrize(

dandi/cli/tests/test_service_scripts.py

@@ -16,7 +16,7 @@
 from dandi import __version__
 from dandi.tests.fixtures import SampleDandiset
 
-from ..command import service_scripts
+from ..cmd_service_scripts import service_scripts
 
 DATA_DIR = Path(__file__).with_name("data")
 

dandi/conftest.py

@@ -1,4 +1,4 @@
-from typing import List
+from __future__ import annotations
 
 from _pytest.config import Config
 from _pytest.config.argparsing import Parser
@@ -16,7 +16,7 @@ def pytest_addoption(parser: Parser) -> None:
     )
 
 
-def pytest_collection_modifyitems(items: List[Item], config: Config) -> None:
+def pytest_collection_modifyitems(items: list[Item], config: Config) -> None:
     # Based on <https://pythontesting.net/framework/pytest/pytest-run-tests
     # -using-particular-fixture/>
     if config.getoption("--dandi-api"):

dandi/consts.py

@@ -4,7 +4,7 @@
 from dataclasses import dataclass
 from enum import Enum
 import os
-from typing import Optional
+from typing import Union
 
 #: A list of metadata fields which dandi extracts from .nwb files.
 #: Additional fields (such as ``number_of_*``) might be added by
@@ -99,7 +99,9 @@ class EmbargoStatus(Enum):
 @dataclass(frozen=True)
 class DandiInstance:
     name: str
-    gui: Optional[str]
+    # This class is used as an attribute of ParsedDandiURL, a Pydantic class,
+    # and thus we need non-future annotations:
+    gui: Union[str, None]
     api: str
 
     @property