From 1e5ed0c724f7df5ca06045100d75caaef2a6e409 Mon Sep 17 00:00:00 2001
From: Alexander Schlemmer <a.schlemmer@indiscale.com>
Date: Mon, 11 Nov 2024 09:43:37 +0100
Subject: [PATCH] MAINT: removed unused imports and sorted imports
---
src/caoscrawler/authorize.py | 4 +--
src/caoscrawler/converters/__init__.py | 5 ++--
src/caoscrawler/converters/hdf5_converter.py | 10 +++----
src/caoscrawler/converters/rocrate.py | 1 -
src/caoscrawler/converters/spss.py | 7 ++---
src/caoscrawler/converters/xml_converter.py | 10 +++----
src/caoscrawler/crawl.py | 8 ++---
src/caoscrawler/debug_tree.py | 29 +++++--------------
src/caoscrawler/identifiable_adapters.py | 8 ++---
src/caoscrawler/logging.py | 4 +--
src/caoscrawler/macros/macro_yaml_object.py | 5 ++--
src/caoscrawler/scanner.py | 2 +-
src/caoscrawler/scripts/generators.py | 1 -
.../rocrate_structure_elements.py | 1 +
.../structure_elements/structure_elements.py | 1 +
src/caoscrawler/sync_graph.py | 7 ++---
src/caoscrawler/sync_node.py | 4 +--
src/caoscrawler/utils.py | 1 -
src/caoscrawler/version.py | 3 +-
src/doc/conf.py | 2 +-
20 files changed, 43 insertions(+), 70 deletions(-)
diff --git a/src/caoscrawler/authorize.py b/src/caoscrawler/authorize.py
index 6f1011b2..f3deed4f 100644
--- a/src/caoscrawler/authorize.py
+++ b/src/caoscrawler/authorize.py
@@ -19,10 +19,10 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
-from caosadvancedtools.crawler import Crawler as OldCrawler
-
import argparse
+from caosadvancedtools.crawler import Crawler as OldCrawler
+
def parse_args():
parser = argparse.ArgumentParser()
diff --git a/src/caoscrawler/converters/__init__.py b/src/caoscrawler/converters/__init__.py
index 70fca6c4..670d4e96 100644
--- a/src/caoscrawler/converters/__init__.py
+++ b/src/caoscrawler/converters/__init__.py
@@ -32,9 +32,8 @@ except ImportError as err:
err=err)
try:
- from .rocrate import ROCrateEntityConverter
- from .rocrate import ROCrateConverter
- from .rocrate import ELNFileConverter
+ from .rocrate import (ELNFileConverter, ROCrateConverter,
+ ROCrateEntityConverter)
except ImportError as err:
ROCrateEntityConverter: type = utils.MissingImport(
name="ROCrateEntityConverter", hint="Try installing with the `rocrate` extra option.",
diff --git a/src/caoscrawler/converters/hdf5_converter.py b/src/caoscrawler/converters/hdf5_converter.py
index a4d974bd..97dac53d 100644
--- a/src/caoscrawler/converters/hdf5_converter.py
+++ b/src/caoscrawler/converters/hdf5_converter.py
@@ -28,16 +28,16 @@ except ModuleNotFoundError:
"its optional `h5-crawler` dependency?"
)
-import numpy as np
-
from typing import Union
import linkahead as db
+import numpy as np
-from .converters import (convert_basic_element, Converter, DictElementConverter,
- match_name_and_value, SimpleFileConverter)
from ..stores import GeneralStore, RecordStore
-from ..structure_elements import DictElement, File, FloatElement, IntegerElement, StructureElement
+from ..structure_elements import (DictElement, File, FloatElement,
+ IntegerElement, StructureElement)
+from .converters import (Converter, DictElementConverter, SimpleFileConverter,
+ convert_basic_element, match_name_and_value)
def convert_attributes(elt: Union[h5py.File, h5py.Group, h5py.Dataset]):
diff --git a/src/caoscrawler/converters/rocrate.py b/src/caoscrawler/converters/rocrate.py
index 189d936c..b84462ac 100644
--- a/src/caoscrawler/converters/rocrate.py
+++ b/src/caoscrawler/converters/rocrate.py
@@ -33,7 +33,6 @@ from typing import Optional
from zipfile import ZipFile
import linkahead as db
-
import rocrate
from rocrate.rocrate import ROCrate
diff --git a/src/caoscrawler/converters/spss.py b/src/caoscrawler/converters/spss.py
index b4f03aea..00742e91 100644
--- a/src/caoscrawler/converters/spss.py
+++ b/src/caoscrawler/converters/spss.py
@@ -22,17 +22,16 @@ from __future__ import annotations # Can be removed with 3.10.
import argparse
from collections import OrderedDict
+from typing import Any, Optional
import numpy as np
import pandas as pd
import pyreadstat
import yaml
-from . import converters
from ..stores import GeneralStore
-from ..structure_elements import (File, StructureElement)
-from typing import Optional, Any
-
+from ..structure_elements import File, StructureElement
+from . import converters
READSTAT_TYPES = {
"double": "DOUBLE",
diff --git a/src/caoscrawler/converters/xml_converter.py b/src/caoscrawler/converters/xml_converter.py
index bd3f6cf0..b9f7487e 100644
--- a/src/caoscrawler/converters/xml_converter.py
+++ b/src/caoscrawler/converters/xml_converter.py
@@ -22,17 +22,17 @@
from __future__ import annotations
-import lxml.etree
import re
-
from typing import Optional
import linkahead as db
+import lxml.etree
-from .converters import SimpleFileConverter, ConverterValidationError, Converter
from ..stores import GeneralStore, RecordStore
-from ..structure_elements import (File, StructureElement,
- XMLTagElement, XMLTextNode, XMLAttributeNode)
+from ..structure_elements import (File, StructureElement, XMLAttributeNode,
+ XMLTagElement, XMLTextNode)
+from .converters import (Converter, ConverterValidationError,
+ SimpleFileConverter)
class XMLFileConverter(SimpleFileConverter):
diff --git a/src/caoscrawler/crawl.py b/src/caoscrawler/crawl.py
index 9e4e2a80..a79e4434 100644
--- a/src/caoscrawler/crawl.py
+++ b/src/caoscrawler/crawl.py
@@ -39,7 +39,6 @@ import sys
import traceback
import uuid
import warnings
-
from argparse import RawTextHelpFormatter
from copy import deepcopy
from datetime import datetime
@@ -52,13 +51,10 @@ from caosadvancedtools.cache import UpdateCache
from caosadvancedtools.crawler import Crawler as OldCrawler
from caosadvancedtools.serverside.helper import send_mail
from caosadvancedtools.utils import create_entity_link
-from linkahead.apiutils import (compare_entities,
- merge_entities)
+from linkahead.apiutils import compare_entities, merge_entities
from linkahead.cached import cache_clear, cached_get_entity_by
from linkahead.common.datatype import get_list_datatype, is_reference
-from linkahead.exceptions import (
- TransactionError,
-)
+from linkahead.exceptions import TransactionError
from linkahead.utils.escape import escape_squoted_text
from .config import get_config_setting
diff --git a/src/caoscrawler/debug_tree.py b/src/caoscrawler/debug_tree.py
index 0d57040f..c154f5b9 100644
--- a/src/caoscrawler/debug_tree.py
+++ b/src/caoscrawler/debug_tree.py
@@ -29,35 +29,20 @@ A structure containing debug tree information.
from __future__ import annotations
-import argparse
-import importlib
-import logging
-import os
-import sys
-import warnings
-import yaml
-
-from argparse import RawTextHelpFormatter
from collections import defaultdict
-from copy import deepcopy
-from enum import Enum
-from importlib_resources import files
-from jsonschema import validate
-from typing import Any, Optional, Type, Union
import linkahead as db
-
-from caosadvancedtools.cache import UpdateCache, Cache
-from caosadvancedtools.crawler import Crawler as OldCrawler
-from linkahead.apiutils import (compare_entities, EntityMergeConflictError,
+import yaml
+from importlib_resources import files
+from jsonschema import validate
+from linkahead.apiutils import (EntityMergeConflictError, compare_entities,
merge_entities)
from linkahead.common.datatype import is_reference
-from .converters import Converter, DirectoryConverter, ConverterValidationError
-
+from .converters import Converter, ConverterValidationError, DirectoryConverter
from .macros import defmacro_constructor, macro_constructor
-from .stores import Store, GeneralStore, RecordStore
-from .structure_elements import StructureElement, Directory, NoneElement
+from .stores import GeneralStore, RecordStore, Store
+from .structure_elements import Directory, NoneElement, StructureElement
from .version import check_cfood_version
diff --git a/src/caoscrawler/identifiable_adapters.py b/src/caoscrawler/identifiable_adapters.py
index 854ee614..592f603b 100644
--- a/src/caoscrawler/identifiable_adapters.py
+++ b/src/caoscrawler/identifiable_adapters.py
@@ -36,12 +36,8 @@ import yaml
from linkahead.cached import cached_get_entity_by, cached_query
from linkahead.utils.escape import escape_squoted_text
-from .exceptions import (
- InvalidIdentifiableYAML,
- MissingIdentifyingProperty,
- MissingRecordType,
- MissingReferencingEntityError,
-)
+from .exceptions import (InvalidIdentifiableYAML, MissingIdentifyingProperty,
+ MissingRecordType, MissingReferencingEntityError)
from .identifiable import Identifiable
from .sync_node import SyncNode
from .utils import has_parent
diff --git a/src/caoscrawler/logging.py b/src/caoscrawler/logging.py
index f22f9678..b57a067d 100644
--- a/src/caoscrawler/logging.py
+++ b/src/caoscrawler/logging.py
@@ -20,10 +20,10 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
import logging
+import sys
-from caosadvancedtools.webui_formatter import WebUI_Formatter
from caosadvancedtools.serverside.helper import get_shared_filename
-import sys
+from caosadvancedtools.webui_formatter import WebUI_Formatter
def configure_server_side_logging(max_log_level: int = logging.INFO):
diff --git a/src/caoscrawler/macros/macro_yaml_object.py b/src/caoscrawler/macros/macro_yaml_object.py
index d8588301..5d2bc1fe 100644
--- a/src/caoscrawler/macros/macro_yaml_object.py
+++ b/src/caoscrawler/macros/macro_yaml_object.py
@@ -26,11 +26,10 @@
# A. Schlemmer, 05/2022
import re
-from dataclasses import dataclass
-from typing import Any, Dict
from copy import deepcopy
+from dataclasses import dataclass
from string import Template
-
+from typing import Any, Dict
_SAFE_SUBST_PAT = re.compile(r"^\$(?P<key>\w+)$")
_SAFE_SUBST_PAT_BRACES = re.compile(r"^\$\{(?P<key>\w+)}$")
diff --git a/src/caoscrawler/scanner.py b/src/caoscrawler/scanner.py
index 27711e6a..89bd1c04 100644
--- a/src/caoscrawler/scanner.py
+++ b/src/caoscrawler/scanner.py
@@ -39,7 +39,7 @@ import logging
import os
import warnings
from collections.abc import Callable
-from typing import Any, Optional, Type, Union
+from typing import Any, Optional, Union
import linkahead as db
import yaml
diff --git a/src/caoscrawler/scripts/generators.py b/src/caoscrawler/scripts/generators.py
index ba8e6e39..2bf8a90f 100644
--- a/src/caoscrawler/scripts/generators.py
+++ b/src/caoscrawler/scripts/generators.py
@@ -30,7 +30,6 @@ from typing import Optional
import pandas as pd
import yaml
-
DM_TEMPLATE = """# auto-generated data model from file "[]{infile}".
# To insert a datamodel into LinkAhead, run:
#
diff --git a/src/caoscrawler/structure_elements/rocrate_structure_elements.py b/src/caoscrawler/structure_elements/rocrate_structure_elements.py
index d3961743..66768ad8 100644
--- a/src/caoscrawler/structure_elements/rocrate_structure_elements.py
+++ b/src/caoscrawler/structure_elements/rocrate_structure_elements.py
@@ -23,6 +23,7 @@
#
from rocrate.model.entity import Entity
+
from .structure_elements import StructureElement
diff --git a/src/caoscrawler/structure_elements/structure_elements.py b/src/caoscrawler/structure_elements/structure_elements.py
index 67cd1056..3b4c6e9b 100644
--- a/src/caoscrawler/structure_elements/structure_elements.py
+++ b/src/caoscrawler/structure_elements/structure_elements.py
@@ -24,6 +24,7 @@
#
import warnings
+
import lxml.etree
diff --git a/src/caoscrawler/sync_graph.py b/src/caoscrawler/sync_graph.py
index 9c021a10..a05e6320 100644
--- a/src/caoscrawler/sync_graph.py
+++ b/src/caoscrawler/sync_graph.py
@@ -27,18 +27,17 @@ crawler.
from __future__ import annotations
import logging
-from typing import Any, Optional, Union, Callable
+import re
+from typing import Any, Callable, Optional, Union
import linkahead as db
from linkahead.cached import cached_get_entity_by
from linkahead.exceptions import EmptyUniqueQueryError
-from .identifiable_adapters import IdentifiableAdapter
from .identifiable import Identifiable
+from .identifiable_adapters import IdentifiableAdapter
from .sync_node import SyncNode, TempID
-import re
-
logger = logging.getLogger(__name__)
diff --git a/src/caoscrawler/sync_node.py b/src/caoscrawler/sync_node.py
index ad0feb98..d912d646 100644
--- a/src/caoscrawler/sync_node.py
+++ b/src/caoscrawler/sync_node.py
@@ -22,12 +22,12 @@
from __future__ import annotations
-from typing import TYPE_CHECKING, Any, Optional, Union
+from typing import TYPE_CHECKING, Any, Optional
+from warnings import warn
import linkahead as db
import yaml
from linkahead.common.models import Parent, ParentList, PropertyList
-from warnings import warn
from .exceptions import ImpossibleMergeError
diff --git a/src/caoscrawler/utils.py b/src/caoscrawler/utils.py
index d9a5af83..5f736d5a 100644
--- a/src/caoscrawler/utils.py
+++ b/src/caoscrawler/utils.py
@@ -26,7 +26,6 @@
# Some utility functions, e.g. for extending pylib.
import sys
-
from posixpath import join as posixjoin
from typing import Optional
from urllib.parse import urljoin
diff --git a/src/caoscrawler/version.py b/src/caoscrawler/version.py
index 0b72dd65..4cd43548 100644
--- a/src/caoscrawler/version.py
+++ b/src/caoscrawler/version.py
@@ -18,9 +18,10 @@
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
from importlib import metadata as importlib_metadata
-from packaging.version import parse as parse_version
from warnings import warn
+from packaging.version import parse as parse_version
+
def get_caoscrawler_version():
""" Read in version of locally installed caoscrawler package"""
diff --git a/src/doc/conf.py b/src/doc/conf.py
index c52442aa..54b2bed2 100644
--- a/src/doc/conf.py
+++ b/src/doc/conf.py
@@ -21,11 +21,11 @@
#
import os
import sys
+
sys.path.insert(0, os.path.abspath('..'))
import sphinx_rtd_theme # noqa: E402
-
# -- Project information -----------------------------------------------------
project = 'caosdb-caoscrawler'
--
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