Update pre-commit repo versions and configure isort to properly handl…

…e "from . import" lines

.pre-commit-config.yaml

@@ -2,19 +2,19 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.0.1
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 21.5b2
     hooks:
     -   id: black
         exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py)$
 -   repo: https://github.com/PyCQA/isort
-    rev: 5.7.0
+    rev: 5.8.0
     hooks:
     -   id: isort
         exclude: ^(dandi/_version\.py|dandi/due\.py|versioneer\.py)$

dandi/cli/base.py

@@ -3,8 +3,8 @@
 
 import click
 
-from ..consts import known_instances
 from .. import get_logger, set_logger_level  # noqa: F401
+from ..consts import known_instances
 
 lgr = get_logger()
 

dandi/cli/cmd_digest.py

@@ -18,7 +18,7 @@
 @click.argument("paths", nargs=-1, type=click.Path(exists=True, dir_okay=False))
 @map_to_click_exceptions
 def digest(paths, digest_alg):
-    """ Calculate file digests """
+    """Calculate file digests"""
     from ..support.digests import get_digest
 
     for p in paths:

dandi/cli/cmd_ls.py

@@ -63,7 +63,7 @@
 @click.argument("paths", nargs=-1, type=click.Path(exists=False, dir_okay=True))
 @map_to_click_exceptions
 def ls(paths, schema, metadata, fields=None, format="auto", recursive=False, jobs=6):
-    """ List .nwb files and dandisets metadata. """
+    """List .nwb files and dandisets metadata."""
 
     # TODO: more logical ordering in case of fields = None
     from .formatter import (

dandi/dandiapi.py

@@ -10,8 +10,8 @@
 import requests
 import tenacity
 
-from .consts import MAX_CHUNK_SIZE, known_instances_rev
 from . import get_logger
+from .consts import MAX_CHUNK_SIZE, known_instances_rev
 from .keyring import keyring_lookup
 from .utils import USER_AGENT, is_interactive, try_multiple
 
@@ -334,7 +334,7 @@ def delete_dandiset(self, dandiset_id):
     def get_dandiset_assets(
         self, dandiset_id, version, page_size=None, path=None, include_metadata=False
     ):
-        """ A generator to provide asset records """
+        """A generator to provide asset records"""
         resp = self.get(
             f"/dandisets/{dandiset_id}/versions/{version}/assets/",
             parameters={"page_size": page_size, "path": path},

dandi/dandiarchive.py

@@ -7,10 +7,10 @@
 from pydantic import AnyHttpUrl, BaseModel, parse_obj_as, validator
 import requests
 
+from . import get_logger
 from .consts import known_instances
 from .dandiapi import DandiAPIClient
 from .exceptions import FailedToConnectError, NotFoundError, UnknownURLError
-from . import get_logger
 from .utils import get_instance
 
 lgr = get_logger()
@@ -41,7 +41,7 @@ def _validate_api_url(cls, v: AnyHttpUrl) -> AnyHttpUrl:
         return parse_obj_as(AnyHttpUrl, v.rstrip("/"))
 
     def get_client(self) -> DandiAPIClient:
-        """ Returns an unauthenticated `DandiAPIClient` for `api_url` """
+        """Returns an unauthenticated `DandiAPIClient` for `api_url`"""
         return DandiAPIClient(self.api_url)
 
     def get_dandiset(self, client: DandiAPIClient) -> dict:
@@ -119,7 +119,7 @@ class DandisetURL(ParsedDandiURL):
     def get_assets(
         self, client: DandiAPIClient, include_metadata: bool = False
     ) -> Iterator[dict]:
-        """ Returns all assets in the Dandiset """
+        """Returns all assets in the Dandiset"""
         return client.get_dandiset_assets(
             self.dandiset_id,
             self.get_version_id(client),
@@ -128,19 +128,19 @@ def get_assets(
 
 
 class SingleAssetURL(ParsedDandiURL):
-    """ Superclass for parsed URLs that refer to a single asset """
+    """Superclass for parsed URLs that refer to a single asset"""
 
     pass
 
 
 class MultiAssetURL(ParsedDandiURL):
-    """ Superclass for parsed URLs that refer to multiple assets """
+    """Superclass for parsed URLs that refer to multiple assets"""
 
     path: str
 
 
 class AssetIDURL(SingleAssetURL):
-    """ Parsed from a URL that refers to an asset by ID """
+    """Parsed from a URL that refers to an asset by ID"""
 
     asset_id: str
 
@@ -172,7 +172,7 @@ def get_assets(
         }
 
     def get_asset_ids(self, client: DandiAPIClient) -> Iterator[str]:
-        """ Yields the ID of the asset (regardless of whether it exists) """
+        """Yields the ID of the asset (regardless of whether it exists)"""
         yield self.asset_id
 
 
@@ -184,7 +184,7 @@ class AssetPathPrefixURL(MultiAssetURL):
     def get_assets(
         self, client: DandiAPIClient, include_metadata: bool = False
     ) -> Iterator[dict]:
-        """ Returns the assets whose paths start with `path` """
+        """Returns the assets whose paths start with `path`"""
         return client.get_dandiset_assets(
             self.dandiset_id,
             self.get_version_id(client),
@@ -194,7 +194,7 @@ def get_assets(
 
 
 class AssetItemURL(SingleAssetURL):
-    """ Parsed from a URL that refers to a specific asset by path """
+    """Parsed from a URL that refers to a specific asset by path"""
 
     path: str
 

dandi/dandiset.py

@@ -3,8 +3,8 @@
 
 from dandischema.models import get_schema_version
 
-from .consts import dandiset_metadata_file
 from . import get_logger
+from .consts import dandiset_metadata_file
 from .utils import find_parent_directory_containing, yaml_dump, yaml_load
 
 lgr = get_logger()

dandi/download.py

@@ -11,10 +11,10 @@
 import humanize
 import requests
 
+from . import get_logger
 from .consts import dandiset_metadata_file
 from .dandiarchive import DandisetURL, MultiAssetURL, SingleAssetURL, parse_dandi_url
 from .dandiset import Dandiset
-from . import get_logger
 from .support.digests import get_digest
 from .support.pyout import naturalsize
 from .utils import (

dandi/exceptions.py

@@ -32,7 +32,7 @@ class LockingError(RuntimeError):
 
 
 class CliVersionError(RuntimeError):
-    """ Base class for `CliVersionTooOldError` and `BadCliVersionError` """
+    """Base class for `CliVersionTooOldError` and `BadCliVersionError`"""
 
     def __init__(self, our_version, minversion, bad_versions):
         self.our_version = our_version

dandi/metadata.py

@@ -6,8 +6,8 @@
 
 from dandischema import models
 
-from .dandiset import Dandiset
 from . import __version__, get_logger
+from .dandiset import Dandiset
 from .pynwb_utils import (
     _get_pynwb_metadata,
     get_neurodata_types,

dandi/organize.py

@@ -12,8 +12,8 @@
 
 import numpy as np
 
-from .exceptions import OrganizeImpossibleError
 from . import get_logger
+from .exceptions import OrganizeImpossibleError
 from .pynwb_utils import get_neurodata_types_to_modalities_map, get_object_id
 from .utils import ensure_datetime, flattened, yaml_load
 
@@ -230,7 +230,7 @@ def _get_hashable(v):
 
 
 def _get_unique_values_among_non_unique(metadata, non_unique_paths, field):
-    """Per each non-unique path return values """
+    """Per each non-unique path return values"""
     return {
         _get_hashable(r.get(field))
         for r in metadata

dandi/pynwb_utils.py

@@ -13,12 +13,12 @@
 from pynwb import NWBHDF5IO
 import semantic_version
 
+from . import __version__, get_logger
 from .consts import (
     metadata_nwb_computed_fields,
     metadata_nwb_file_fields,
     metadata_nwb_subject_fields,
 )
-from . import __version__, get_logger
 from .utils import get_module_version
 
 lgr = get_logger()

dandi/support/pyout.py

@@ -9,8 +9,8 @@
 import humanize
 import pyout
 
-from ..consts import metadata_dandiset_fields, metadata_nwb_fields
 from .. import get_logger
+from ..consts import metadata_dandiset_fields, metadata_nwb_fields
 
 lgr = get_logger()
 

dandi/tests/fixtures.py

@@ -15,10 +15,10 @@
 import requests
 
 from .skip import skipif
+from .. import get_logger
 from ..cli.command import organize
 from ..consts import dandiset_metadata_file, known_instances
 from ..dandiapi import DandiAPIClient
-from .. import get_logger
 from ..pynwb_utils import make_nwb_file, metadata_nwb_file_fields
 from ..upload import upload
 

dandi/tests/test_dandiapi.py

@@ -6,10 +6,10 @@
 
 import click
 
+from .. import dandiapi
 from ..consts import dandiset_metadata_file
 from ..dandiapi import DandiAPIClient
 from ..download import download
-from .. import dandiapi
 from ..upload import upload
 from ..utils import find_files
 

dandi/tests/test_utils.py

@@ -8,9 +8,9 @@
 import responses
 from semantic_version import Version
 
+from .. import __version__
 from ..consts import dandi_instance, known_instances
 from ..exceptions import BadCliVersionError, CliVersionTooOldError
-from .. import __version__
 from ..utils import (
     ensure_datetime,
     ensure_strtime,

dandi/upload.py

@@ -6,8 +6,8 @@
 
 import click
 
-from .consts import dandiset_identifier_regex, dandiset_metadata_file
 from . import lgr
+from .consts import dandiset_identifier_regex, dandiset_metadata_file
 from .utils import ensure_datetime, get_instance, pluralize
 
 

dandi/utils.py

@@ -5,6 +5,7 @@
 except ImportError:
     # TODO - remove whenever python >= 3.8
     from importlib_metadata import version as importlib_version
+
 import inspect
 import io
 import itertools
@@ -26,13 +27,12 @@
 from semantic_version import Version
 import tenacity
 
-from .consts import dandi_instance, known_instances, known_instances_rev
-from .exceptions import BadCliVersionError, CliVersionTooOldError
-
 #
 # Additional handlers
 #
 from . import __version__, get_logger
+from .consts import dandi_instance, known_instances, known_instances_rev
+from .exceptions import BadCliVersionError, CliVersionTooOldError
 
 lgr = get_logger()
 
@@ -362,7 +362,7 @@ def good_file(path):
 
 
 def copy_file(src, dst):
-    """ Copy file from src to dst """
+    """Copy file from src to dst"""
     global _cp_supports_reflink
     if _cp_supports_reflink is None:
         r = subprocess.run(

dandi/validate.py

@@ -1,7 +1,7 @@
 import os.path as op
 
-from .consts import dandiset_metadata_file
 from . import get_logger
+from .consts import dandiset_metadata_file
 from .metadata import get_metadata
 from .pynwb_utils import validate as pynwb_validate
 from .pynwb_utils import validate_cache

pyproject.toml

@@ -10,4 +10,5 @@ exclude='\.eggs|\.git|\.mypy_cache|\.tox|\.venv|_build|buck-out|build|dist|_vers
 profile = "black"
 force_sort_within_sections = true
 reverse_relative = true
+sort_relative_in_force_sorted_sections = true
 known_first_party = ["dandi"]