diff --git a/nomad/app/dcat/mapping.py b/nomad/app/dcat/mapping.py
index 26c47495853e7237176759dbb0dcb6b0dd13a70b..d22399a7628fba69adf3d0309b1b1cf1f63072dc 100644
--- a/nomad/app/dcat/mapping.py
+++ b/nomad/app/dcat/mapping.py
@@ -118,8 +118,9 @@ class Mapping:
dataset,
DCAT.landingPage,
URIRef(
- '%s/entry/id/%s/%s'
- % (config.gui_url(), entry['upload_id'], entry['entry_id'])
+ '{}/entry/id/{}/{}'.format(
+ config.gui_url(), entry['upload_id'], entry['entry_id']
+ )
),
)
)
@@ -175,7 +176,7 @@ class Mapping:
self.g.add((person, FOAF.givenName, Literal(user.first_name)))
self.g.add((person, FOAF.familyName, Literal(user.last_name)))
self.g.add((person, FOAF.nick, Literal(user.username)))
- self.g.add((person, FOAF.mbox, URIRef('mailto:%s' % (user.email))))
+ self.g.add((person, FOAF.mbox, URIRef(f'mailto:{user.email}')))
self.persons[user.user_id] = person
diff --git a/nomad/app/optimade/__init__.py b/nomad/app/optimade/__init__.py
index c10f5c65ca70489080833e924e65d579edf26078..c9e5f0ad5c5efc340629c4f6e0a09149da81a57e 100644
--- a/nomad/app/optimade/__init__.py
+++ b/nomad/app/optimade/__init__.py
@@ -104,7 +104,7 @@ from nomad import utils # nopep8
from nomad.config import config
from optimade.server.config import CONFIG # nopep8
-CONFIG.root_path = '%s/optimade' % config.services.api_base_path
+CONFIG.root_path = f'{config.services.api_base_path}/optimade'
CONFIG.base_url = '{}://{}'.format(
'https' if config.services.https else 'http',
config.services.api_host.strip('/'),
diff --git a/nomad/app/optimade/elasticsearch.py b/nomad/app/optimade/elasticsearch.py
index 6c8836638faacb847ab7a83f7c0cabfcc3baca12..910306b4199e4808c0f3d4268f8ab3deb4721c42 100644
--- a/nomad/app/optimade/elasticsearch.py
+++ b/nomad/app/optimade/elasticsearch.py
@@ -247,10 +247,10 @@ class StructureCollection(EntryCollection):
sort, order = criteria.get('sort', (('chemical_formula_reduced', 1),))[0]
sort_quantity = datamodel.OptimadeEntry.m_def.all_quantities.get(sort, None)
if sort_quantity is None:
- raise BadRequest(detail='Unable to sort on field %s' % sort)
+ raise BadRequest(detail=f'Unable to sort on field {sort}')
sort_quantity_a_optimade = sort_quantity.m_get_annotations('optimade')
if not sort_quantity_a_optimade.sortable:
- raise BadRequest(detail='Unable to sort on field %s' % sort)
+ raise BadRequest(detail=f'Unable to sort on field {sort}')
search_query = self._base_search_query()
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 75cec2fd210ebd7665df4007a270362419ca8e84..c24b6c540071f11b06f95e60e5aa484a0e5807c5 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -45,7 +45,7 @@ def _get_transformer(without_prefix, **kwargs):
quantities: dict[str, Quantity] = {
q.name: Quantity(
q.name,
- backend_field='optimade.%s' % q.name,
+ backend_field=f'optimade.{q.name}',
elastic_mapping_type=q.a_elasticsearch.mapping['type'],
)
for q in OptimadeEntry.m_def.all_quantities.values()
@@ -101,12 +101,12 @@ def parse_filter(filter_str: str, without_prefix=False) -> Q:
try:
parse_tree = _parser.parse(filter_str)
except Exception as e:
- raise FilterException('Syntax error: %s' % str(e))
+ raise FilterException(f'Syntax error: {str(e)}')
try:
query = transformer.transform(parse_tree)
except Exception as e:
- raise FilterException('Semantic error: %s' % str(e))
+ raise FilterException(f'Semantic error: {str(e)}')
return query
@@ -155,7 +155,7 @@ class ElasticTransformer(OPTElasticTransformer):
quantity = quantities[0]
if quantity.length_quantity is None:
- raise Exception('HAS ONLY is not supported by %s' % quantity.name)
+ raise Exception(f'HAS ONLY is not supported by {quantity.name}')
has_all = super()._has_query_op(quantities, 'HAS ALL', predicate_zip_list)
has_length = Q(
diff --git a/nomad/app/v1/models/graph/utils.py b/nomad/app/v1/models/graph/utils.py
index f7d59b63dab1452064ffb718be455eb8ce7189fd..6d420a6e1002c51bca54bd55ccbb815ddac4c34d 100644
--- a/nomad/app/v1/models/graph/utils.py
+++ b/nomad/app/v1/models/graph/utils.py
@@ -223,7 +223,7 @@ def _get_response_type(type_hint: Any, ns: ModelNamespace) -> Any:
raise NotImplementedError(type_hint)
-ModelNamespace = dict[str, Union[type[BaseModel], ForwardRef]]
+ModelNamespace = dict[str, type[BaseModel] | ForwardRef]
def _generate_model(
@@ -297,7 +297,7 @@ def _generate_model(
if field_name == 'm_errors':
if suffix == response_suffix:
- fields[field_name] = (Optional[Union[type_hint]], None) # type: ignore
+ fields[field_name] = (Optional[type_hint], None) # type: ignore
continue
if field_name.startswith('m_') and field_name not in ['m_def', 'm_def_id']:
diff --git a/nomad/app/v1/models/models.py b/nomad/app/v1/models/models.py
index 8921dfe90b2e28e0cac42be4eaca444e102b43bb..4513d7b03e1f3d136364f408db12446779825e7e 100644
--- a/nomad/app/v1/models/models.py
+++ b/nomad/app/v1/models/models.py
@@ -20,7 +20,7 @@ import enum
import fnmatch
import json
import re
-from typing import Any, Dict, List, Optional, Union
+from typing import Any
from collections.abc import Mapping
import pydantic
@@ -56,8 +56,8 @@ from typing import Annotated
User: Any = datamodel.User.m_def.a_pydantic.model
# It is important that datetime.datetime comes last. Otherwise, number valued strings
# are interpreted as epoch dates by pydantic
-Value = Union[StrictInt, StrictFloat, StrictBool, str, datetime.datetime]
-ComparableValue = Union[StrictInt, StrictFloat, str, datetime.datetime]
+Value = StrictInt | StrictFloat | StrictBool | str | datetime.datetime
+ComparableValue = StrictInt | StrictFloat | str | datetime.datetime
owner_documentation = strip(
@@ -188,7 +188,7 @@ ops = {
'any': Any_,
}
-CriteriaValue = Union[Value, list[Value], Range, Any_, All, None_, dict[str, Any]]
+CriteriaValue = Value | list[Value] | Range | Any_ | All | None_ | dict[str, Any]
class LogicalOperator(NoneEmptyBaseModel):
@@ -267,7 +267,7 @@ class Empty(BaseModel):
pass
-Query = Union[And, Or, Not, Nested, Criteria, Empty, Mapping[str, CriteriaValue]]
+Query = And | Or | Not | Nested | Criteria | Empty | Mapping[str, CriteriaValue]
And.model_rebuild()
@@ -557,8 +557,7 @@ class QueryParameters:
detail=[
{
'loc': ['query', key],
- 'msg': 'operator %s does not support multiple values'
- % op,
+ 'msg': f'operator {op} does not support multiple values',
}
],
)
@@ -567,7 +566,7 @@ class QueryParameters:
raise HTTPException(
422,
detail=[
- {'loc': ['query', key], 'msg': 'operator %s is unknown' % op}
+ {'loc': ['query', key], 'msg': f'operator {op} is unknown'}
],
)
@@ -1230,13 +1229,13 @@ for quantity in datamodel.EditableUserMetadata.m_def.definitions:
quantity.type if quantity.type in (str, int, float, bool) else str
)
else:
- pydantic_type = Union[str, list[str], MetadataEditListAction]
+ pydantic_type = str | list[str] | MetadataEditListAction
if getattr(quantity, 'a_auth_level', None) == datamodel.AuthLevel.admin:
description = '**NOTE:** Only editable by admin user'
else:
description = None
_metadata_edit_actions_fields[quantity.name] = (
- Optional[pydantic_type],
+ pydantic_type | None,
Field(None, description=description),
)
@@ -1346,7 +1345,7 @@ class Files(BaseModel):
return re.compile(re_pattern)
except re.error as e:
raise PydanticCustomError(
- 'invalid_pattern', 'could not parse the re pattern: %s' % e
+ 'invalid_pattern', f'could not parse the re pattern: {e}'
)
@model_validator(mode='after')
diff --git a/nomad/app/v1/routers/auth.py b/nomad/app/v1/routers/auth.py
index 318aa5682fdb23d6b0f7ed513f51b453eead8a01..8cf79a9df7e5f22536959550c6dca67ff4a011f5 100644
--- a/nomad/app/v1/routers/auth.py
+++ b/nomad/app/v1/routers/auth.py
@@ -463,7 +463,4 @@ def generate_upload_token(user):
bytes(config.services.api_secret, 'utf-8'), msg=payload, digestmod=hashlib.sha1
)
- return '{}.{}'.format(
- utils.base64_encode(payload),
- utils.base64_encode(signature.digest()),
- )
+ return f'{utils.base64_encode(payload)}.{utils.base64_encode(signature.digest())}'
diff --git a/nomad/app/v1/routers/datasets.py b/nomad/app/v1/routers/datasets.py
index 6cecffb685f91c813fdf57e6ca4b4223186f9ef8..c4850b0d29b59b4b23576a740281691fe63e7488 100644
--- a/nomad/app/v1/routers/datasets.py
+++ b/nomad/app/v1/routers/datasets.py
@@ -300,7 +300,7 @@ async def get_datasets(
doi=doi,
)
if prefix is not None and prefix != '':
- query_params.update(dataset_name=re.compile('^%s.*' % prefix, re.IGNORECASE)) # type: ignore
+ query_params.update(dataset_name=re.compile(f'^{prefix}.*', re.IGNORECASE)) # type: ignore
query_params = {k: v for k, v in query_params.items() if v is not None}
mongodb_query = pagination.order_result(mongodb_objects(**query_params))
@@ -554,7 +554,7 @@ async def assign_doi(
detail=_dataset_has_unpublished_contents[1]['description'],
)
- doi = DOI.create(title='NOMAD dataset: %s' % dataset.dataset_name, user=user)
+ doi = DOI.create(title=f'NOMAD dataset: {dataset.dataset_name}', user=user)
try:
doi.create_draft()
diff --git a/nomad/app/v1/routers/entries.py b/nomad/app/v1/routers/entries.py
index 0f7abd0f340e1a1bf517708f159f6fc5d2fab679..5e1836894cffe5c628a433c56d36bb0f15c172df 100644
--- a/nomad/app/v1/routers/entries.py
+++ b/nomad/app/v1/routers/entries.py
@@ -18,7 +18,7 @@
from datetime import datetime
from enum import Enum
-from typing import Annotated, Optional, Set, Union, Dict, Any, List, Type
+from typing import Any
from collections.abc import Iterator
from fastapi import (
APIRouter,
@@ -197,7 +197,7 @@ replace the references:
)
-ArchiveRequired = Union[str, dict[str, Any]]
+ArchiveRequired = str | dict[str, Any]
_archive_required_field = Body(
'*',
@@ -291,9 +291,9 @@ EntryMetadataEditActions = create_model(
'EntryMetadataEditActions',
**{ # type: ignore
quantity.name: (
- Optional[EntryMetadataEditActionField]
+ EntryMetadataEditActionField | None
if quantity.is_scalar
- else Optional[list[EntryMetadataEditActionField]],
+ else list[EntryMetadataEditActionField] | None,
None,
)
for quantity in EditableUserMetadata.m_def.definitions
@@ -705,8 +705,10 @@ def _answer_entries_raw_request(owner: Owner, query: Query, files: Files, user:
if response.pagination.total > config.services.max_entry_download:
raise HTTPException(
status.HTTP_400_BAD_REQUEST,
- detail='The limit of maximum number of entries in a single download (%d) has been exeeded (%d).'
- % (config.services.max_entry_download, response.pagination.total),
+ detail=(
+ f'The limit of maximum number of entries in a single download '
+ f'({config.services.max_entry_download}) has been exceeded ({response.pagination.total}).'
+ ),
)
files_params = Files() if files is None else files
@@ -1741,7 +1743,7 @@ async def post_entry_metadata_edit(
if quantity is None:
raise HTTPException(
status.HTTP_400_BAD_REQUEST,
- detail='Unknown quantity %s' % action_quantity_name,
+ detail=f'Unknown quantity {action_quantity_name}',
)
# TODO this does not work. Because the quantities are not in EditableUserMetadata
@@ -1751,13 +1753,13 @@ async def post_entry_metadata_edit(
if not user.is_admin():
raise HTTPException(
status.HTTP_400_BAD_REQUEST,
- detail='Only the admin user can set %s' % quantity.name,
+ detail=f'Only the admin user can set {quantity.name}',
)
if isinstance(quantity_actions, list) == quantity.is_scalar:
raise HTTPException(
status.HTTP_400_BAD_REQUEST,
- detail='Wrong shape for quantity %s' % action_quantity_name,
+ detail=f'Wrong shape for quantity {action_quantity_name}',
)
if not isinstance(quantity_actions, list):
@@ -1866,8 +1868,7 @@ async def post_entry_metadata_edit(
if doi_ds is not None and not user.is_admin:
data.success = False
data.message = (data.message if data.message else '') + (
- 'Edit would remove entries from a dataset with DOI (%s) '
- % doi_ds.dataset_name
+ f'Edit would remove entries from a dataset with DOI ({doi_ds.dataset_name}) '
)
has_error = True
diff --git a/nomad/app/v1/routers/materials.py b/nomad/app/v1/routers/materials.py
index 05793772d1a5263098063063149cf1e28923d5ba..579342c5fb1e8e0ec7a6fd89f6642fc8c562300c 100644
--- a/nomad/app/v1/routers/materials.py
+++ b/nomad/app/v1/routers/materials.py
@@ -95,7 +95,7 @@ def perform_search(*args, **kwargs) -> MetadataResponse:
except SearchError as e:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
- detail='Elasticsearch could not process your query: %s' % str(e),
+ detail=f'Elasticsearch could not process your query: {str(e)}',
)
diff --git a/nomad/app/v1/routers/users.py b/nomad/app/v1/routers/users.py
index e5f92534f4312dd824ceb7b489a62e172f43f5a8..3b47845604a862381f4434284b4f7d06a485b952 100644
--- a/nomad/app/v1/routers/users.py
+++ b/nomad/app/v1/routers/users.py
@@ -198,7 +198,7 @@ async def invite_user(
except Exception as e:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
- detail='Invalid user data: %s' % str(e),
+ detail=f'Invalid user data: {str(e)}',
)
if user.email is None:
@@ -212,13 +212,13 @@ async def invite_user(
except KeyError as e:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
- detail='Invalid user data: %s' % str(e),
+ detail=f'Invalid user data: {str(e)}',
)
if error is not None:
raise HTTPException(
status_code=status.HTTP_400_BAD_REQUEST,
- detail='Could not invite user: %s' % str(error),
+ detail=f'Could not invite user: {str(error)}',
)
return datamodel.User.get(username=user.username)
diff --git a/nomad/app/v1/utils.py b/nomad/app/v1/utils.py
index 319958b76750f4ce4e5398b4e1986551a5495dad..e889fba0858ff8bd17cc88005a2758e13ef16ba5 100644
--- a/nomad/app/v1/utils.py
+++ b/nomad/app/v1/utils.py
@@ -62,17 +62,16 @@ def parameter_dependency_from_model(
code = inspect.cleandoc(
"""
- def %s(%s):
+ def {}({}):
try:
- return %s(%s)
+ return {}({})
except ValidationError as e:
errors = e.errors()
for error in errors:
error['loc'] = ['query'] + list(error['loc'])
raise HTTPException(422, detail=errors)
- """
- % (
+ """.format(
name,
', '.join(names),
model_cls.__name__, # type: ignore
diff --git a/nomad/archive/converter.py b/nomad/archive/converter.py
index 2f581b032bde61db701ec18dd621fc9688ffae02..b72233f3ffdf3053471751b669d3cd11ca181780 100644
--- a/nomad/archive/converter.py
+++ b/nomad/archive/converter.py
@@ -274,7 +274,7 @@ def convert_upload(
force_repack (bool, optional): Force repacking the existing archive (in new format). Defaults to False.
size_limit (int, optional): Size limit in GB for the archive. Defaults to -1 (no limit).
"""
- if isinstance(uploads, (str, Upload)):
+ if isinstance(uploads, str | Upload):
uploads = [uploads]
if not uploads:
diff --git a/nomad/archive/query.py b/nomad/archive/query.py
index 822392656dbb0ca330da8a34ad6b3f52ff774e61..05bbc2700eade759945cfa1312fc3c1917332784 100644
--- a/nomad/archive/query.py
+++ b/nomad/archive/query.py
@@ -64,7 +64,7 @@ def _extract_child(archive_item, prop, index) -> dict | list:
archive_child = archive_item[prop]
from .storage_v2 import ArchiveList as ArchiveListNew
- is_list = isinstance(archive_child, (ArchiveListNew, ArchiveList, list))
+ is_list = isinstance(archive_child, ArchiveListNew | ArchiveList | list)
if index is None and is_list:
index = (0, None)
@@ -132,7 +132,7 @@ def query_archive(
if isinstance(f_or_archive_reader, ArchiveReader):
return _load_data(query_dict, f_or_archive_reader)
- elif isinstance(f_or_archive_reader, (BytesIO, str)):
+ elif isinstance(f_or_archive_reader, BytesIO | str):
with read_archive(f_or_archive_reader, **kwargs) as archive:
return _load_data(query_dict, archive)
@@ -198,14 +198,14 @@ def filter_archive(
# TODO
raise ArchiveQueryError('key wildcards not yet implemented')
else:
- raise ArchiveQueryError('invalid key format: %s' % key)
+ raise ArchiveQueryError(f'invalid key format: {key}')
try:
archive_child = _extract_child(archive_item, key, index)
from .storage_v2 import ArchiveList as ArchiveListNew
- if isinstance(archive_child, (ArchiveListNew, ArchiveList, list)):
+ if isinstance(archive_child, ArchiveListNew | ArchiveList | list):
result[key] = [
filter_archive(val, item, transform=transform)
for item in archive_child
diff --git a/nomad/archive/required.py b/nomad/archive/required.py
index f3ef389c4549f54879ca4a05bcc098164b1a9efe..6a08652900df662c92b9eb958cf3c29d149e938b 100644
--- a/nomad/archive/required.py
+++ b/nomad/archive/required.py
@@ -329,7 +329,7 @@ class RequiredReader:
try:
result[prop] = (
[handle_item(item) for item in value]
- if isinstance(value, (list, ArchiveList, ArchiveListNew))
+ if isinstance(value, list | ArchiveList | ArchiveListNew)
else handle_item(value)
)
except ArchiveError as e:
@@ -552,7 +552,7 @@ class RequiredReader:
if isinstance(archive_item, ArchiveDict):
archive_item = to_json(archive_item)
- if isinstance(archive_item, (dict, NewArchiveDict)) and 'm_def' in archive_item:
+ if isinstance(archive_item, dict | NewArchiveDict) and 'm_def' in archive_item:
dataset = dataset.replace(
definition=self._resolve_definition(
dataset.upload_id,
@@ -606,7 +606,7 @@ class RequiredReader:
from .storage_v2 import ArchiveList as ArchiveListNew
- if isinstance(archive_child, (ArchiveListNew, ArchiveList, list)):
+ if isinstance(archive_child, ArchiveListNew | ArchiveList | list):
result[prop] = [
self._apply_required(
val, item, dataset.replace(definition=prop_def)
diff --git a/nomad/archive/storage.py b/nomad/archive/storage.py
index c0baeb75c87900e9f73fa249ada9802d52022aaf..6d33ecfdd378ec709decfa3d6d476bbe26f5b7ed 100644
--- a/nomad/archive/storage.py
+++ b/nomad/archive/storage.py
@@ -151,7 +151,7 @@ class ArchiveReader(ArchiveDict):
self._file_or_path, 'rb', buffering=config.archive.read_buffer_size
),
)
- elif isinstance(self._file_or_path, (BytesIO, BufferedReader)):
+ elif isinstance(self._file_or_path, BytesIO | BufferedReader):
f = cast(BytesIO, self._file_or_path)
else:
raise ValueError('not a file or path')
diff --git a/nomad/archive/storage_v2.py b/nomad/archive/storage_v2.py
index 6d525e2ef6eeb5dbab7a7a0e0276c39b71a96f5a..6a5d1e59af5aa7ad6dd82a3b87d647c44927df1c 100644
--- a/nomad/archive/storage_v2.py
+++ b/nomad/archive/storage_v2.py
@@ -123,7 +123,7 @@ class TOCPacker:
"""
_pack_direct(Utility.packb(_obj))
- if self._depth >= self._toc_depth or not isinstance(obj, (dict, list)):
+ if self._depth >= self._toc_depth or not isinstance(obj, dict | list):
start_pos = self._pos
_pack_raw(obj)
return {'pos': [start_pos, self._pos]}
diff --git a/nomad/atomutils.py b/nomad/atomutils.py
index b6c089282cdb753994a1c5b71bc291da265937e9..0e142213d4d1c50728d9e681366be3102764b97d 100644
--- a/nomad/atomutils.py
+++ b/nomad/atomutils.py
@@ -684,7 +684,7 @@ def get_formula_string(symbols: Iterable[str], counts: Iterable[int]) -> str:
formula = ''
for symbol, count in zip(symbols, counts):
if count > 1:
- formula += '%s%d' % (symbol, count)
+ formula += f'{symbol}{count}'
else:
formula += symbol
return formula
@@ -744,7 +744,7 @@ def get_normalized_wyckoff(
sorted_species.sort(key=functools.cmp_to_key(compare_atomic_number))
standard_atom_names = {}
for i, at in enumerate(sorted_species):
- standard_atom_names[at] = 'X_%d' % i
+ standard_atom_names[at] = f'X_{i}'
# Rename with anonymized species labels
standard_wyc: dict = {}
diff --git a/nomad/cli/admin/admin.py b/nomad/cli/admin/admin.py
index 5871edd593e1d16707e443e069a4353207586b4f..7c02a16cdd51457e9b241def679e6d26b8a492ba 100644
--- a/nomad/cli/admin/admin.py
+++ b/nomad/cli/admin/admin.py
@@ -77,8 +77,7 @@ def reset_processing(zero_complete_time):
process_status__in=proc.ProcessStatus.STATUSES_PROCESSING
)
print(
- '%d %s processes need to be reset due to incomplete process'
- % (in_processing.count(), cls.__name__)
+ f'{in_processing.count()} {cls.__name__} processes need to be reset due to incomplete process'
)
in_processing.update(
process_status=proc.ProcessStatus.READY,
@@ -126,10 +125,8 @@ def lift_embargo(dry, parallel):
if upload.publish_time + relativedelta(months=embargo_length) < datetime.now():
print(
- 'need to lift the embargo of %s (publish_time=%s, embargo=%d)'
- % (upload.upload_id, upload.publish_time, embargo_length)
+ f'need to lift the embargo of {upload.upload_id} (publish_time={upload.publish_time}, embargo={embargo_length})'
)
-
if not dry:
upload.edit_upload_metadata(
edit_request_json=dict(metadata={'embargo_length': 0}),
@@ -154,9 +151,7 @@ def dump(restore: bool):
date_str = datetime.utcnow().strftime('%Y_%m_%d')
print(
- 'mongodump --host {} --port {} --db {} -o /backup/fairdi/mongo/{}'.format(
- config.mongo.host, config.mongo.port, config.mongo.db_name, date_str
- )
+ f'mongodump --host {config.mongo.host} --port {config.mongo.port} --db {config.mongo.db_name} -o /backup/fairdi/mongo/{date_str}'
)
@@ -164,9 +159,7 @@ def dump(restore: bool):
@click.argument('PATH_TO_DUMP', type=str, nargs=1)
def restore(path_to_dump):
print(
- 'mongorestore --host {} --port {} --db {} {}'.format(
- config.mongo.host, config.mongo.port, config.mongo.db_name, path_to_dump
- )
+ f'mongorestore --host {config.mongo.host} --port {config.mongo.port} --db {config.mongo.db_name} {path_to_dump}'
)
@@ -199,7 +192,7 @@ def restore(path_to_dump):
)
def nginx_conf(prefix, host, port, server):
prefix = prefix.rstrip('/')
- prefix = '/%s' % prefix.lstrip('/')
+ prefix = '/{}'.format(prefix.lstrip('/'))
if server:
print(
@@ -211,24 +204,24 @@ def nginx_conf(prefix, host, port, server):
)
print(
- """
+ f"""
location / {{
- proxy_pass http://{1}:{2};
+ proxy_pass http://{host}:{port};
}}
- location ~ {0}\\/?(gui)?$ {{
- rewrite ^ {0}/gui/ permanent;
+ location ~ {prefix}\\/?(gui)?$ {{
+ rewrite ^ {prefix}/gui/ permanent;
}}
- location {0}/gui/ {{
+ location {prefix}/gui/ {{
proxy_intercept_errors on;
error_page 404 = @redirect_to_index;
- proxy_pass http://{1}:{2};
+ proxy_pass http://{host}:{port};
}}
location @redirect_to_index {{
- rewrite ^ {0}/gui/index.html break;
- proxy_pass http://{1}:{2};
+ rewrite ^ {prefix}/gui/index.html break;
+ proxy_pass http://{host}:{port};
}}
location ~ \\/gui\\/(service-worker\\.js|meta\\.json)$ {{
@@ -237,20 +230,20 @@ def nginx_conf(prefix, host, port, server):
if_modified_since off;
expires off;
etag off;
- proxy_pass http://{1}:{2};
+ proxy_pass http://{host}:{port};
}}
location ~ /api/v1/uploads(/?$|.*/raw|.*/bundle?$) {{
client_max_body_size 35g;
proxy_request_buffering off;
- proxy_pass http://{1}:{2};
+ proxy_pass http://{host}:{port};
}}
location ~ /api/v1/.*/download {{
proxy_buffering off;
- proxy_pass http://{1}:{2};
+ proxy_pass http://{host}:{port};
}}
-""".format(prefix, host, port)
+"""
)
if server:
print('}')
diff --git a/nomad/cli/admin/clean.py b/nomad/cli/admin/clean.py
index 74964478356a2be7c3002cb8649dbc0c26463943..6ca3d6c7ca5773b59bf79b7a716508f890d9be98 100644
--- a/nomad/cli/admin/clean.py
+++ b/nomad/cli/admin/clean.py
@@ -68,8 +68,7 @@ def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
if not dry and len(missing_uploads) > 0:
if not force:
input(
- 'Will delete entries (mongo + es) for %d missing uploads. Press any key to continue ...'
- % len(missing_uploads)
+ f'Will delete entries (mongo + es) for {len(missing_uploads)} missing uploads. Press any key to continue ...'
)
for upload in missing_uploads:
@@ -81,8 +80,7 @@ def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
).query('term', upload_id=upload).delete()
else:
print(
- 'Found %s uploads that have entries in mongo, but there is no upload entry.'
- % len(missing_uploads)
+ f'Found {len(missing_uploads)} uploads that have entries in mongo, but there is no upload entry.'
)
print('List first 10:')
for upload in missing_uploads[:10]:
@@ -109,16 +107,13 @@ def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
if not dry and len(to_delete) > 0:
if not force:
input(
- 'Will delete %d upload directories. Press any key to continue ...'
- % len(to_delete)
+ f'Will delete {len(to_delete)} upload directories. Press any key to continue ...'
)
for path in to_delete:
shutil.rmtree(path)
else:
- print(
- 'Found %d upload directories with no upload in mongo.' % len(to_delete)
- )
+ print(f'Found {len(to_delete)} upload directories with no upload in mongo.')
print('List first 10:')
for path in to_delete[:10]:
print(path)
@@ -131,16 +126,14 @@ def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
if not dry and len(to_delete) > 0:
if not force:
input(
- 'Will delete %d staging upload directories. Press any key to continue ...'
- % len(to_delete)
+ f'Will delete {len(to_delete)} staging upload directories. Press any key to continue ...'
)
for path in to_delete:
shutil.rmtree(path)
else:
print(
- 'Found %d staging upload directories with upload directory in public.'
- % len(to_delete)
+ f'Found {len(to_delete)} staging upload directories with upload directory in public.'
)
print('List first 10:')
for path in to_delete[:10]:
@@ -164,15 +157,13 @@ def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
if not dry and len(to_delete) > 0:
if not force:
input(
- 'Will delete %d entries in %d uploads from ES. Press any key to continue ...'
- % (entries, len(to_delete))
+ f'Will delete {entries} entries in {len(to_delete)} uploads from ES. Press any key to continue ...'
)
for upload_id, _ in to_delete:
delete_by_query(owner='all', query=dict(upload_id=upload_id))
else:
print(
- 'Found %d entries in %d uploads from ES with no upload in mongo.'
- % (entries, len(to_delete))
+ f'Found {entries} entries in {len(to_delete)} uploads from ES with no upload in mongo.'
)
print('List first 10:')
tabulate.tabulate(to_delete, headers=['id', '#entries'])
diff --git a/nomad/cli/admin/entries.py b/nomad/cli/admin/entries.py
index 77b3f5bbcdcc64157b03f593d53c43d0576d09fb..54ac693eed7dcd6510287497f0733e912432729a 100644
--- a/nomad/cli/admin/entries.py
+++ b/nomad/cli/admin/entries.py
@@ -38,7 +38,7 @@ def rm(entries, skip_es, skip_mongo):
infrastructure.setup_mongo()
infrastructure.setup_elastic()
- print('%d entries selected, deleting ...' % len(entries))
+ print(f'{len(entries)} entries selected, deleting ...')
if not skip_es:
for entry in entries:
diff --git a/nomad/cli/admin/springer.py b/nomad/cli/admin/springer.py
index 74dde0e7350ba1b56a4806f8736156e80f4d2540..7c468d179682ee84ea3c5c333073a538a40b2444 100644
--- a/nomad/cli/admin/springer.py
+++ b/nomad/cli/admin/springer.py
@@ -86,8 +86,7 @@ def normalize_formula(formula_str: str) -> str:
symbol_normamount = {e: round(a / total * 100.0) for e, a in symbol_amount.items()}
formula_sorted = [
- '%s%d' % (s, symbol_normamount[s])
- for s in sorted(list(symbol_normamount.keys()))
+ f'{s}{symbol_normamount[s]}' for s in sorted(list(symbol_normamount.keys()))
]
return ''.join(formula_sorted)
@@ -198,10 +197,7 @@ def update_springer(max_n_query: int = 10, retry_time: int = 120):
page = 1
while True:
# check springer database for new entries by comparing with local database
- root = (
- 'http://materials.springer.com/search?searchTerm=&pageNumber=%d&datasourceFacet=sm_isp&substanceId='
- % page
- )
+ root = f'http://materials.springer.com/search?searchTerm=&pageNumber={page}&datasourceFacet=sm_isp&substanceId='
req_text = _download(root, max_n_query, retry_time)
if 'Sorry,' in req_text:
break
@@ -216,7 +212,7 @@ def update_springer(max_n_query: int = 10, retry_time: int = 120):
if sp_id in sp_ids:
continue
- path = 'http://materials.springer.com%s' % path
+ path = f'http://materials.springer.com{path}'
req_text = _download(path, max_n_query, retry_time)
try:
data = parse(req_text)
diff --git a/nomad/cli/admin/uploads.py b/nomad/cli/admin/uploads.py
index 55d35f783e400a01d6d915893a9981e7a62b534d..258e8affdbe03cb23a239b250ac28f59d5de3921 100644
--- a/nomad/cli/admin/uploads.py
+++ b/nomad/cli/admin/uploads.py
@@ -37,7 +37,7 @@ def _run_parallel(
from nomad import utils, processing as proc
- if isinstance(uploads, (tuple, list)):
+ if isinstance(uploads, tuple | list):
uploads_count = len(uploads)
else:
@@ -53,10 +53,10 @@ def _run_parallel(
logger = utils.get_logger(__name__)
- print('%d uploads selected, %s ...' % (uploads_count, label))
+ print(f'{uploads_count} uploads selected, {label} ...')
def process_upload(upload: proc.Upload):
- logger.info('%s started' % label, upload_id=upload.upload_id)
+ logger.info(f'{label} started', upload_id=upload.upload_id)
completed = False
try:
@@ -64,7 +64,7 @@ def _run_parallel(
completed = True
except Exception as e:
completed = True
- logger.error('%s failed' % label, upload_id=upload.upload_id, exc_info=e)
+ logger.error(f'{label} failed', upload_id=upload.upload_id, exc_info=e)
with cv:
state['completed_count'] += 1 if completed else 0
@@ -72,8 +72,7 @@ def _run_parallel(
state['available_threads_count'] += 1
print(
- ' %s %s and skipped %s of %s uploads'
- % (
+ ' {} {} and skipped {} of {} uploads'.format(
label,
state['completed_count'],
state['skipped_count'],
@@ -85,7 +84,7 @@ def _run_parallel(
for upload in uploads:
logger.info(
- 'cli schedules parallel %s processing for upload' % label,
+ f'cli schedules parallel {label} processing for upload',
current_process=upload.current_process,
last_status_message=upload.last_status_message,
upload_id=upload.upload_id,
@@ -125,15 +124,14 @@ def _run_processing(
def run_process(upload, logger):
logger.info(
- 'cli calls %s processing' % label,
+ f'cli calls {label} processing',
current_process=upload.current_process,
last_status_message=upload.last_status_message,
upload_id=upload.upload_id,
)
if upload.process_running and not process_running:
logger.warn(
- 'cannot trigger %s, since the upload is already/still processing'
- % label,
+ f'cannot trigger {label}, since the upload is already/still processing',
current_process=upload.current_process,
last_status_message=upload.last_status_message,
upload_id=upload.upload_id,
@@ -152,9 +150,9 @@ def _run_processing(
upload.block_until_complete_or_waiting_for_result(interval=0.5)
if upload.process_status == proc.ProcessStatus.FAILURE:
- logger.info('%s with failure' % label, upload_id=upload.upload_id)
+ logger.info(f'{label} with failure', upload_id=upload.upload_id)
- logger.info('%s complete' % label, upload_id=upload.upload_id)
+ logger.info(f'{label} complete', upload_id=upload.upload_id)
return True
_run_parallel(
@@ -514,7 +512,7 @@ def chown(ctx, username, uploads):
_, uploads = _query_uploads(uploads, **ctx.obj.uploads_kwargs)
- print('%d uploads selected, changing owner ...' % uploads.count())
+ print(f'{uploads.count()} uploads selected, changing owner ...')
user = datamodel.User.get(username=username)
for upload in uploads:
@@ -544,7 +542,7 @@ def reset(ctx, uploads, with_entries, success, failure):
_, uploads = _query_uploads(uploads, **ctx.obj.uploads_kwargs)
uploads_count = uploads.count()
- print('%d uploads selected, resetting their processing ...' % uploads_count)
+ print(f'{uploads_count} uploads selected, resetting their processing ...')
i = 0
for upload in uploads:
@@ -566,7 +564,7 @@ def reset(ctx, uploads, with_entries, success, failure):
upload.process_status = proc.ProcessStatus.FAILURE
upload.save()
i += 1
- print('resetted %d of %d uploads' % (i, uploads_count))
+ print(f'resetted {i} of {uploads_count} uploads')
@uploads.command(help='(Re-)index all entries of the given uploads.')
@@ -671,7 +669,7 @@ def delete_upload(
def rm(ctx, uploads, skip_es, skip_mongo, skip_files):
_, uploads = _query_uploads(uploads, **ctx.obj.uploads_kwargs)
- print('%d uploads selected, deleting ...' % uploads.count())
+ print(f'{uploads.count()} uploads selected, deleting ...')
for upload in uploads:
delete_upload(
diff --git a/nomad/cli/admin/users.py b/nomad/cli/admin/users.py
index 49a54132d73b9ebcebc7fe38783ca6a47e683af0..21253fb313395efbbc99604d35c864f22b40e3ed 100644
--- a/nomad/cli/admin/users.py
+++ b/nomad/cli/admin/users.py
@@ -49,6 +49,6 @@ def import_command(path_to_users_file):
infrastructure.user_management.add_user(
user, bcrypt_password=password, invite=False
)
- print('Imported %s' % user.name)
+ print(f'Imported {user.name}')
except Exception as e:
logger.error('could not import user', exc_info=e)
diff --git a/nomad/cli/aflow.py b/nomad/cli/aflow.py
index 0548025e18bc522a880de218459857a4e7cf7c06..6912ec39dde56d95bd5106ead7305b83d0efadcf 100644
--- a/nomad/cli/aflow.py
+++ b/nomad/cli/aflow.py
@@ -76,7 +76,7 @@ class DbUpdater:
if hasattr(self, key):
setattr(self, key, val)
else:
- raise KeyError('Invalid key %s' % key)
+ raise KeyError(f'Invalid key {key}')
# create directory to save data
subdir = ''
@@ -99,7 +99,7 @@ class DbUpdater:
else 'OUTCAR.static.xz'
)
else:
- raise NotImplementedError('%s not yet supported.' % self.db_name)
+ raise NotImplementedError(f'{self.db_name} not yet supported.')
self._session = requests.Session()
@@ -126,7 +126,7 @@ class DbUpdater:
return re.sub(r'[^\w\d-]', '_', path)
def _read_from_file(self, filename):
- print('Reading from file %s' % filename)
+ print(f'Reading from file {filename}')
data = []
with open(filename) as f:
line = f.readline()
@@ -147,7 +147,7 @@ class DbUpdater:
with open(filename, 'w') as f:
for i in range(len(data)):
if isinstance(data[i], str):
- f.write('%s\n' % data[i])
+ f.write(f'{data[i]}\n')
else:
f.write(f'{data[i][0]} {data[i][1]} \n')
@@ -155,7 +155,7 @@ class DbUpdater:
if self.dbfile is not None and os.path.isfile(self.dbfile):
self.db_files = self._read_from_file(self.dbfile)
else:
- print('Generating list from %s' % self.root_url)
+ print(f'Generating list from {self.root_url}')
self.db_files = []
todo = self._get_paths(self.root_url)
while len(todo) > 0:
@@ -189,7 +189,7 @@ class DbUpdater:
else:
print('Generating NOMAD list')
if self.db_name.lower() == 'aflowlib':
- servers = ['LIB%d_LIB' % n for n in range(1, 10)] + ['ICSD_WEB']
+ servers = [f'LIB{n}_LIB' for n in range(1, 10)] + ['ICSD_WEB']
paths = [s for s in servers if s in self.root_url]
paths = paths if paths else servers
# main_author: Stefano Curtarolo
@@ -258,7 +258,7 @@ class DbUpdater:
if len(in_nomad) > 0:
fn = 'in_nomad.txt'
print('Warning: Some NOMAD entries not found in db.')
- print('See %s for list.' % fn)
+ print(f'See {fn} for list.')
self._write_to_file(in_nomad, fn)
# add the root back
@@ -267,7 +267,7 @@ class DbUpdater:
root = f'{u.scheme}://{u.netloc}/{up}'
self.update_list = [os.path.join(root, e) for e in self.update_list]
self.is_updated_list = [False] * len(self.update_list)
- print('Found %d entries to be added in NOMAD' % len(self.update_list))
+ print(f'Found {len(self.update_list)} entries to be added in NOMAD')
if self.outfile is not None:
data = [self.update_list[i] for i in range(len(self.update_list))]
@@ -345,7 +345,7 @@ class DbUpdater:
tarname = f'{d1}-{d2}'
uploadname = f'{self.db_name.upper()}_{tarname}'
- tarname = os.path.join(self._local_path, '%s.tar' % tarname)
+ tarname = os.path.join(self._local_path, f'{tarname}.tar')
return tarname, uploadname
@@ -477,7 +477,7 @@ class DbUpdater:
"""
Download files from database.
"""
- print('Downloading from %s' % self.root_url)
+ print(f'Downloading from {self.root_url}')
s = time.time()
plist = [[] for i in range(self.parallel)]
cur = 0
@@ -669,9 +669,7 @@ def update_prototypes(ctx, filepath, matches_only):
atoms = ase.io.read(poscar_file, format='vasp')
except Exception:
print(
- 'Error in getting prototype structure from POSCAR: {}'.format(
- poscarurl
- )
+ f'Error in getting prototype structure from POSCAR: {poscarurl}'
)
print(
'Could not read prototype structure from CIF or POSCAR file for prototype: {}, {}, '.format(
@@ -705,9 +703,7 @@ def update_prototypes(ctx, filepath, matches_only):
aflow_prototypes = {'prototypes_by_spacegroup': structure_types_by_spacegroup}
print(
'Extracted latest AFLOW prototypes online. Total number of '
- 'successfully fetched prototypes: {}, missing: {}'.format(
- n_prototypes, n_missing
- )
+ f'successfully fetched prototypes: {n_prototypes}, missing: {n_missing}'
)
# Update matches
@@ -748,9 +744,7 @@ def update_prototypes(ctx, filepath, matches_only):
n_unmatched += 1
print(
'Updated matches in AFLOW prototype library. Total number of '
- 'prototypes: {}, unmatched: {}, failed: {}'.format(
- n_prototypes, n_unmatched, n_failed
- )
+ f'prototypes: {n_prototypes}, unmatched: {n_unmatched}, failed: {n_failed}'
)
# Write data file to the specified path
diff --git a/nomad/cli/client/__init__.py b/nomad/cli/client/__init__.py
index 5a7cd1edce8c055c9903c679d2bae6e35fcfe4be..8b1ca40a86ff6fc48c9c6d8b2abac27b481ab5b9 100644
--- a/nomad/cli/client/__init__.py
+++ b/nomad/cli/client/__init__.py
@@ -28,7 +28,7 @@ from nomad.config import config
'-n',
'--url',
default=config.client.url,
- help='The URL where nomad is running, default is "%s".' % config.client.url,
+ help=f'The URL where nomad is running, default is "{config.client.url}".',
)
@click.option(
'-u', '--user', default=None, help='the user name to login, default is no login.'
@@ -235,7 +235,7 @@ def local(
from nomad.client import LocalEntryProcessing
- print('Using %s' % config.client.url)
+ print(f'Using {config.client.url}')
auth = _create_auth(ctx)
with LocalEntryProcessing(entry_id, auth=auth, **kwargs) as local:
diff --git a/nomad/cli/dev.py b/nomad/cli/dev.py
index 074c88bd1093d68b0d23d459c51164efe2bdd926..e7ff602405fd1c7f177d26d301180a72ba10afdc 100644
--- a/nomad/cli/dev.py
+++ b/nomad/cli/dev.py
@@ -98,7 +98,7 @@ def api_model(model):
if isinstance(data, dict):
processed_dict = {}
for key, value in data.items():
- if isinstance(value, (dict, list)):
+ if isinstance(value, dict | list):
processed_value = remove_null_types(value)
# Only add the key if the processed value is not a "type": "null" dictionary
diff --git a/nomad/client/processing.py b/nomad/client/processing.py
index 97af552bb41fc83642d9a884ffad4c4bb1cc7cce..3445fc88711a48284f432cd15507ac0c93955adb 100644
--- a/nomad/client/processing.py
+++ b/nomad/client/processing.py
@@ -59,7 +59,7 @@ def parse(
else:
parser_name = parser.__class__.__name__
- assert parser is not None, 'there is no parser matching %s' % mainfile
+ assert parser is not None, f'there is no parser matching {mainfile}'
logger = logger.bind(parser=parser.name) # type: ignore
logger.info('identified parser')
if hasattr(parser, 'backend_factory'):
@@ -86,7 +86,7 @@ def normalize(normalizer: str | typing.Callable, entry_archive, logger=None):
if normalizer_instance.__class__.__name__ == normalizer
)
- assert normalizer is not None, 'there is no normalizer %s' % str(normalizer)
+ assert normalizer is not None, f'there is no normalizer {str(normalizer)}'
normalizer_instance = typing.cast(typing.Callable, normalizer)(entry_archive)
logger = logger.bind(normalizer=normalizer_instance.__class__.__name__)
logger.info('identified normalizer')
diff --git a/nomad/client/upload.py b/nomad/client/upload.py
index 7594196df7c5ac2af07197ba805f013da6b07687..e800b8da04781ad004150d26b8cc47042d5917e6 100644
--- a/nomad/client/upload.py
+++ b/nomad/client/upload.py
@@ -51,7 +51,7 @@ def upload_file(
headers={'Accept': 'application/json'},
auth=auth,
)
- print('process offline: %s' % file_path)
+ print(f'process offline: {file_path}')
else:
with open(file_path, 'rb') as f:
response = api.post(
@@ -62,7 +62,7 @@ def upload_file(
auth=auth,
)
if response.status_code != 200:
- print('Could not create upload: %s' % response.text)
+ print(f'Could not create upload: {response.text}')
return None
upload = response.json()['data']
@@ -86,15 +86,8 @@ def upload_file(
)
print(
- 'status: %s; process: %s; parsing: %d/%d/%d %s'
- % (
- upload['process_status'],
- upload['current_process'],
- successes,
- failures,
- total,
- ret,
- ),
+ f'status: {upload["process_status"]}; process: {upload["current_process"]}; '
+ f'parsing: {successes}/{failures}/{total} {ret}',
end='',
)
@@ -103,11 +96,11 @@ def upload_file(
if upload['process_status'] == ProcessStatus.FAILURE:
print('There have been errors:')
for error in upload['errors']:
- print(' %s' % error)
+ print(f' {error}')
elif publish:
response = api.post(f'uploads/{upload["upload_id"]}/action/publish', auth=auth)
if response.status_code != 200:
- print('Could not publish upload: %s' % response.text)
+ print(f'Could not publish upload: {response.text}')
return None
return upload['upload_id']
diff --git a/nomad/config/models/config.py b/nomad/config/models/config.py
index 12c424e4ec985913e6dd26e846ef79a2bfd23e49..2ec981ae5b53d69f9af968692f5499e2e23b53f3 100644
--- a/nomad/config/models/config.py
+++ b/nomad/config/models/config.py
@@ -598,7 +598,7 @@ class Normalize(ConfigBaseModel):
""",
)
angle_rounding: float = Field(
- float(10.0),
+ 10.0,
description="""
Defines the "bin size" for rounding cell angles for the material hash in degree.
""",
@@ -966,14 +966,10 @@ class Config(ConfigBaseModel):
if page is not None:
return f'{base}/gui/{page}'
- return '%s/gui' % base
+ return f'{base}/gui'
def rabbitmq_url(self):
- return 'pyamqp://{}:{}@{}//'.format(
- self.rabbitmq.user,
- self.rabbitmq.password,
- self.rabbitmq.host,
- )
+ return f'pyamqp://{self.rabbitmq.user}:{self.rabbitmq.password}@{self.rabbitmq.host}//'
def north_url(self, ssl: bool = True):
return self.api_url(
diff --git a/nomad/config/models/plugins.py b/nomad/config/models/plugins.py
index 9657130e6cc68f1bb1e3ff5fa1ce5c69c033d211..eeade496bca2cea5bfd59018510aa28a2d85d805 100644
--- a/nomad/config/models/plugins.py
+++ b/nomad/config/models/plugins.py
@@ -681,7 +681,7 @@ class Parser(PythonPluginBase):
return MatchingParserInterface(**data)
-EntryPointType = Union[
+EntryPointType = Union[ # noqa
Schema,
Normalizer,
Parser,
diff --git a/nomad/config/models/ui.py b/nomad/config/models/ui.py
index a0ad71defd404aa4e8ed64e079e2802a4bbe0e84..88845aba8eaff855fdb7e5af268f9532a0637597 100644
--- a/nomad/config/models/ui.py
+++ b/nomad/config/models/ui.py
@@ -853,15 +853,13 @@ class MenuItemCustomQuantities(MenuItem):
# The 'discriminated union' feature of Pydantic is used here:
# https://docs.pydantic.dev/usage/types/#discriminated-unions-aka-tagged-unions
MenuItemTypeNested = Annotated[
- Union[
- MenuItemTerms,
- MenuItemHistogram,
- MenuItemPeriodicTable,
- MenuItemVisibility,
- MenuItemDefinitions,
- MenuItemOptimade,
- MenuItemCustomQuantities,
- ],
+ MenuItemTerms
+ | MenuItemHistogram
+ | MenuItemPeriodicTable
+ | MenuItemVisibility
+ | MenuItemDefinitions
+ | MenuItemOptimade
+ | MenuItemCustomQuantities,
Field(discriminator='type'),
]
@@ -1199,14 +1197,12 @@ class WidgetScatterPlotDeprecated(WidgetScatterPlot):
# The 'discriminated union' feature of Pydantic is used here:
# https://docs.pydantic.dev/usage/types/#discriminated-unions-aka-tagged-unions
WidgetAnnotated = Annotated[
- Union[
- WidgetTerms,
- WidgetHistogram,
- WidgetScatterPlot,
- WidgetScatterPlotDeprecated,
- WidgetPeriodicTable,
- WidgetPeriodicTableDeprecated,
- ],
+ WidgetTerms
+ | WidgetHistogram
+ | WidgetScatterPlot
+ | WidgetScatterPlotDeprecated
+ | WidgetPeriodicTable
+ | WidgetPeriodicTableDeprecated,
Field(discriminator='type'),
]
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index a90eecef2abe75a849fcfa55749e220d917e3568..2bf32ebd83c6091725c8048090d19d636020f335 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -1094,7 +1094,7 @@ class EntryMetadata(MSection):
if section_path.startswith('data') and isinstance(property_def, Quantity):
# From each string dtype, we get a truncated sample to put into
# the keywords field, unless we are already storing too many unique values.
- if (isinstance(property_def.type, (MEnum, m_str))) and len(
+ if (isinstance(property_def.type, MEnum | m_str)) and len(
keywords_set
) < 10000:
keyword = section.m_get(property_def)
diff --git a/nomad/datamodel/hdf5.py b/nomad/datamodel/hdf5.py
index bcb89e36f55ef278c31c51f5c4aa47200201354e..5bfa5c2e8452196ff65ec6b2f9d432a22e974f72 100644
--- a/nomad/datamodel/hdf5.py
+++ b/nomad/datamodel/hdf5.py
@@ -216,7 +216,7 @@ class HDF5Dataset(NonPrimitive):
raise ValueError('Cannot normalize HDF5 value without context.')
if not isinstance(
- value, (str, np.ndarray, h5py.Dataset, pint.Quantity, HDF5Wrapper)
+ value, str | np.ndarray | h5py.Dataset | pint.Quantity | HDF5Wrapper
):
raise ValueError(f'Invalid HDF5 dataset value: {value}.')
diff --git a/nomad/datamodel/optimade.py b/nomad/datamodel/optimade.py
index 101bb5a0497038b897ee18af852d0d2c25b38a77..f72fa69cbf3a836fc54d7b3ab0af320716d91868 100644
--- a/nomad/datamodel/optimade.py
+++ b/nomad/datamodel/optimade.py
@@ -33,8 +33,7 @@ from nomad.metainfo.elasticsearch_extension import Elasticsearch
def optimade_links(section: str):
return [
- 'https://github.com/Materials-Consortia/OPTiMaDe/blob/develop/optimade.md#%s'
- % section
+ f'https://github.com/Materials-Consortia/OPTiMaDe/blob/develop/optimade.md#{section}'
]
diff --git a/nomad/datamodel/util.py b/nomad/datamodel/util.py
index ce8b7580cbe13ae45c052fb82297489796edca69..63ab9e0c481a61278f3dbee0373d5beb7626780e 100644
--- a/nomad/datamodel/util.py
+++ b/nomad/datamodel/util.py
@@ -151,7 +151,7 @@ def create_custom_mapping(
if isinstance(value, float) and math.isnan(value):
value = None
- if isinstance(value, (int, float, str)):
+ if isinstance(value, int | float | str):
value = np.array([value])
if value is not None:
diff --git a/nomad/doi.py b/nomad/doi.py
index 994a840896793da98985af5dd003af1aea74963a..a755e19c31e6059503dbef60b6d59340b954bbda 100644
--- a/nomad/doi.py
+++ b/nomad/doi.py
@@ -87,8 +87,7 @@ def edit_doi_url(doi: str, url: str = None):
if response.status_code >= 300:
raise Exception(
- 'Unexpected datacite response (status code %d): %s'
- % (response.status_code, response.text)
+ f'Unexpected datacite response (status code {response.status_code}): {response.text}'
)
@@ -127,12 +126,7 @@ class DOI(Document):
create_time = datetime.datetime.utcnow()
while True:
- doi_str = '%s/NOMAD/%s-%d' % (
- config.datacite.prefix,
- create_time.strftime('%Y.%m.%d'),
- counter,
- )
-
+ doi_str = f'{config.datacite.prefix}/NOMAD/{create_time.strftime("%Y.%m.%d")}-{counter}'
try:
doi = DOI(doi=doi_str)
doi.save(force_insert=True)
@@ -188,7 +182,7 @@ class DOI(Document):
def __handle_datacite_errors(self, response, msg: str):
if response is None or response.status_code >= 300:
utils.get_logger(__name__).error(
- 'could not %s' % msg,
+ f'could not {msg}',
status_code=response.status_code,
body=response.content,
doi=self.doi,
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 9370c4bf2dd9df4416c508c57aadb59e73baf8a9..63473f36cda60f050161a2ea53e53649ca6e10b1 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -112,8 +112,8 @@ logger = utils.get_logger(__name__)
# bug when used in isinstance() with mypy
# see https://github.com/python/mypy/issues/11673
-GenericList = Union[list, ArchiveList, ArchiveListNew]
-GenericDict = Union[dict, ArchiveDict, ArchiveDictNew]
+GenericList = list | ArchiveList | ArchiveListNew
+GenericDict = dict | ArchiveDict | ArchiveDictNew
@dataclasses.dataclass(frozen=True)
@@ -187,7 +187,7 @@ class ConfigError(Exception):
async def goto_child(container, key: str | int | list):
if not isinstance(key, list):
- if isinstance(container, (list, dict)):
+ if isinstance(container, list | dict):
return container[key] # type: ignore
return await asyncio.to_thread(container.__getitem__, key)
@@ -2510,7 +2510,7 @@ def _is_quantity_reference(definition) -> bool:
isinstance(definition, Quantity)
and isinstance(definition.type, Reference)
and not isinstance(
- definition.type, (UserReference, AuthorReference, DatasetReference)
+ definition.type, UserReference | AuthorReference | DatasetReference
)
)
@@ -2801,7 +2801,7 @@ class ArchiveReader(ArchiveLikeReader):
)
if isinstance(node.definition, Quantity) or isinstance(
- getattr(node.definition, 'type', None), (JSON, AnyType)
+ getattr(node.definition, 'type', None), JSON | AnyType
):
# the container size limit does not recursively apply to JSON
result_to_write = (
@@ -3065,7 +3065,7 @@ class DefinitionReader(ArchiveLikeReader):
# for derived quantities like 'all_properties', 'all_quantities', etc.
# normalise them to maps
is_plain_container: bool = (
- False if is_list else isinstance(child_def, (list, set, dict))
+ False if is_list else isinstance(child_def, list | set | dict)
)
child_path: list = node.current_path + [name]
@@ -3090,7 +3090,7 @@ class DefinitionReader(ArchiveLikeReader):
await _populate_result(
node.result_root, child_path + [k], __convert(v)
)
- elif isinstance(child_def, (set, list)):
+ elif isinstance(child_def, set | list):
await _populate_result(node.result_root, child_path, [])
for i, v in enumerate(child_def):
await _populate_result(
@@ -3109,7 +3109,7 @@ class DefinitionReader(ArchiveLikeReader):
if isinstance(child_def, dict):
for _k, _v in child_def.items():
await __func(child_path + [_k], _v)
- elif isinstance(child_def, (set, list)):
+ elif isinstance(child_def, set | list):
for _i, _v in enumerate(child_def):
await __func(child_path + [str(_i)], _v)
else:
@@ -3264,7 +3264,7 @@ class DefinitionReader(ArchiveLikeReader):
_unwrap_subsection(v)
for v in (
target
- if isinstance(target, (list, set))
+ if isinstance(target, list | set)
else target.values()
)
)
diff --git a/nomad/infrastructure.py b/nomad/infrastructure.py
index ae53636d9657050d72d3396e91cb6dd49c942f58..02b35346c1dbdbd49b84b29080babad8d17f5c51 100644
--- a/nomad/infrastructure.py
+++ b/nomad/infrastructure.py
@@ -106,7 +106,7 @@ def setup_elastic():
http_auth = (config.elastic.username, config.elastic.password)
global elastic_client
elastic_client = connections.create_connection(
- hosts=['%s:%d' % (config.elastic.host, config.elastic.port)],
+ hosts=[f'{config.elastic.host}:{config.elastic.port}'],
timeout=config.elastic.timeout,
max_retries=10,
retry_on_timeout=True,
@@ -348,7 +348,7 @@ class KeycloakUserManagement(UserManagement):
index = 1
try:
while self.get_user(username=user.username):
- user.username += '%d' % index
+ user.username += f'{index}'
index += 1
except KeyError:
pass
@@ -415,12 +415,12 @@ class KeycloakUserManagement(UserManagement):
if user.user_id != 'not_set':
try:
self._admin_client.get_user(user.user_id)
- return 'User %s with given id already exists' % user.email
+ return f'User {user.email} with given id already exists'
except KeycloakGetError:
pass
if self._admin_client.get_user_id(user.email) is not None:
- return 'User with email %s already exists' % user.email
+ return f'User with email {user.email} already exists'
try:
self._admin_client.create_user(keycloak_user)
@@ -484,7 +484,7 @@ class KeycloakUserManagement(UserManagement):
user_id = self._admin_client.get_user_id(username)
if user_id is None:
- raise KeyError('User with username %s does not exist' % username)
+ raise KeyError(f'User with username {username} does not exist')
if email is not None and user_id is None:
with utils.lnr(logger, 'Could not use keycloak admin client'):
@@ -494,7 +494,7 @@ class KeycloakUserManagement(UserManagement):
user_id = users[0]['id']
if user_id is None:
- raise KeyError('User with email %s does not exist' % email)
+ raise KeyError(f'User with email {email} does not exist')
assert user_id is not None, 'Could not determine user from given kwargs'
@@ -625,7 +625,7 @@ def send_mail(name: str, email: str, message: str, subject: str):
to_addrs = [email]
if config.mail.cc_address is not None:
- msg['Cc'] = 'The nomad team <%s>' % config.mail.cc_address
+ msg['Cc'] = f'The nomad team <{config.mail.cc_address}>'
to_addrs.append(config.mail.cc_address)
try:
diff --git a/nomad/metainfo/data_type.py b/nomad/metainfo/data_type.py
index 992cced7ef98d275244ceed79f705b38cd97d9b3..04b4c724651ac2a2307d9d3c55b8aba26799605b 100644
--- a/nomad/metainfo/data_type.py
+++ b/nomad/metainfo/data_type.py
@@ -25,7 +25,7 @@ from base64 import b64decode, b64encode
from datetime import datetime, date
from functools import reduce
from inspect import isclass
-from typing import Any as TypingAny, Optional
+from typing import Any as TypingAny
from urllib.parse import urlparse, urlunparse
import numpy as np
@@ -230,7 +230,7 @@ class Primitive(Datatype):
return value
if self.is_scalar:
- if isinstance(value, (list, np.ndarray)):
+ if isinstance(value, list | np.ndarray):
raise ValueError(f'Shape mismatch for {value}.')
else:
if not self.support_array:
@@ -261,7 +261,7 @@ class Primitive(Datatype):
'type_data': self._dtype.__name__,
} | self.flags
- if issubclass(self._dtype, (np.number, np.str_, np.bool_)):
+ if issubclass(self._dtype, np.number | np.str_ | np.bool_):
return {
'type_kind': 'numpy',
'type_data': self._dtype.__name__,
@@ -274,7 +274,7 @@ class Primitive(Datatype):
return value
def extract_magnitude(v):
- if isinstance(v, (list, tuple)):
+ if isinstance(v, list | tuple):
return [extract_magnitude(x) for x in v]
if not isinstance(v, pint.Quantity):
@@ -333,9 +333,9 @@ class Primitive(Datatype):
if isinstance(value, np.ndarray):
array = value
- elif isinstance(value, (pd.DataFrame, pd.Series)):
+ elif isinstance(value, pd.DataFrame | pd.Series):
array = value.to_numpy()
- elif isinstance(value, (list, tuple)):
+ elif isinstance(value, list | tuple):
array = np.array(value)
else:
raise ValueError(f'Cannot identify type for {value}.')
@@ -363,7 +363,7 @@ class Primitive(Datatype):
array = array.astype(self._dtype, casting='safe')
except TypeError:
new_array = array.astype(self._dtype).astype(original_dtype)
- if isinstance(self, (m_str, m_bool)):
+ if isinstance(self, m_str | m_bool):
if not np.all(array == new_array):
raise ValueError(
f'Cannot convert {array} to {self._dtype}.'
@@ -535,7 +535,7 @@ class InexactNumber(Number):
"""
def _preprocess(v):
- if isinstance(v, (list, tuple)):
+ if isinstance(v, list | tuple):
return [_preprocess(x) for x in v]
return float('nan') if v is None else v
@@ -658,7 +658,7 @@ class m_complex128(m_complex):
return {'re': value.real, 'im': value.imag}
# 1D
- if isinstance(value, (list, tuple)):
+ if isinstance(value, list | tuple):
return {'re': [v.real for v in value], 'im': [v.imag for v in value]}
# ND
@@ -993,7 +993,7 @@ class Datetime(NonPrimitive):
datetime_obj = datetime(value.year, value.month, value.day)
elif isinstance(value, str):
datetime_obj = parse(value)
- elif isinstance(value, (int, float)):
+ elif isinstance(value, int | float):
datetime_obj = datetime.fromtimestamp(value)
elif isinstance(value, pd.Timestamp):
datetime_obj = value.to_pydatetime()
@@ -1278,20 +1278,19 @@ def to_pydantic_type(in_type: Datatype):
standard_type = in_type.standard_type()
if standard_type.startswith('int'):
- return Optional[int]
+ return int | None
if standard_type.startswith('float'):
- return Optional[float]
+ return float | None
if standard_type.startswith('complex'):
- return Optional[complex]
+ return complex | None
if standard_type == 'bool':
- return Optional[bool]
+ return bool | None
if standard_type in ('str', 'enum'):
- return Optional[str]
+ return str | None
if standard_type == 'datetime':
- return Optional[datetime]
+ return datetime | None
if standard_type == 'dict':
- return Optional[dict]
-
+ return dict | None
raise NotImplementedError(f'Unsupported pydantic data type {in_type}.')
@@ -1399,7 +1398,7 @@ def _normalize_complex(value, complex_type, to_unit: str | ureg.Unit | None):
)
# complex or real part only
- if isinstance(value, (int, float, complex, np.number)):
+ if isinstance(value, int | float | complex | np.number):
__check_precision(type(value))
return complex_type(value)
diff --git a/nomad/metainfo/elasticsearch_extension.py b/nomad/metainfo/elasticsearch_extension.py
index 6c44725683a1c9a07188259b3845fa767f7101cc..605b0bb779cc0f2f453ac3f2d63557ea42912b49 100644
--- a/nomad/metainfo/elasticsearch_extension.py
+++ b/nomad/metainfo/elasticsearch_extension.py
@@ -245,7 +245,7 @@ class DocumentType:
"""
Creates an indexable document from the given archive.
"""
- suggestions: DefaultDict = defaultdict(list)
+ suggestions: defaultdict = defaultdict(list)
def transform(quantity, section, value, path):
"""
@@ -498,7 +498,7 @@ class DocumentType:
package_names = set()
packages_from_plugins = {}
for plugin in config.plugins.entry_points.filtered_values():
- if isinstance(plugin, (Schema, Parser)):
+ if isinstance(plugin, Schema | Parser):
package_name = plugin.python_package
if package_name in package_names:
raise ValueError(
@@ -608,15 +608,13 @@ class DocumentType:
assert (
name not in self.quantities or self.quantities[name] == search_quantity
- ), 'Search quantity names must be unique: %s' % name
+ ), f'Search quantity names must be unique: {name}'
self.quantities[name] = search_quantity
if annotation.metrics is not None:
for name, metric in annotation.metrics.items():
- assert name not in self.metrics, (
- 'Metric names must be unique: %s' % name
- )
+ assert name not in self.metrics, f'Metric names must be unique: {name}'
self.metrics[name] = (metric, search_quantity)
if self == entry_type:
@@ -939,8 +937,7 @@ class Elasticsearch(DefinitionAnnotation):
if self.dynamic:
raise NotImplementedError(
- 'Quantity type %s for dynamic quantity %s is not supported.'
- % (quantity.type, quantity)
+ f'Quantity type {quantity.type} for dynamic quantity {quantity} is not supported.'
)
if isinstance(quantity.type, QuantityReference):
return compute_mapping(quantity.type.target_quantity_def)
@@ -950,8 +947,7 @@ class Elasticsearch(DefinitionAnnotation):
)
else:
raise NotImplementedError(
- 'Quantity type %s for quantity %s is not supported.'
- % (quantity.type, quantity)
+ f'Quantity type {quantity.type} for quantity {quantity} is not supported.'
)
if self.suggestion:
diff --git a/nomad/metainfo/example.py b/nomad/metainfo/example.py
index 3f18e1b52ca0446bf8408a4d96fe65a9f58bff5b..3e7f7443b41013722c1058de5bf70e0491629b7d 100644
--- a/nomad/metainfo/example.py
+++ b/nomad/metainfo/example.py
@@ -182,7 +182,7 @@ if __name__ == '__main__':
print(system.n_atoms)
# To validate dimensions and custom constraints
- print('errors: %s' % run.m_all_validate())
+ print(f'errors: {run.m_all_validate()}')
# To serialize the data:
serializable = run.m_to_dict()
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index d047228ea513561cbbff80d4c795ed7e1b1318fd..c5e99bac8c8f4c16709beda576e15beb8a7b1c43 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -507,7 +507,7 @@ class Reference:
}
def _normalize_impl(self, section, value):
- if isinstance(value, (str, int, dict)):
+ if isinstance(value, str | int | dict):
if isinstance(value, str):
context = section.m_root().m_context if section else None
value = (
@@ -984,7 +984,7 @@ class MSection(metaclass=MObjectMeta):
event_handlers: set[TypingCallable] = set(m_def.event_handlers)
for name, attr in cls.__dict__.items():
# transfer names and descriptions for properties, init properties
- if isinstance(attr, (Attribute, Property)):
+ if isinstance(attr, Attribute | Property):
attr.name = name
if attr.description is not None:
attr.description = re.sub(
@@ -1110,7 +1110,7 @@ class MSection(metaclass=MObjectMeta):
return default_name
quantity_def = self.m_def.all_quantities.get(key_quantity)
- if not isinstance(quantity_def.type, (m_str, Enum)):
+ if not isinstance(quantity_def.type, m_str | Enum):
raise TypeError(f'Key quantity {key_quantity} must be of type str.')
if self.m_is_set(quantity_def):
@@ -1332,7 +1332,7 @@ class MSection(metaclass=MObjectMeta):
target = definition.__get__(self)
if isinstance(target, list) and index is not None:
- assert isinstance(index, (int, slice))
+ assert isinstance(index, int | slice)
try:
sliced = target[index]
except IndexError:
@@ -2505,7 +2505,7 @@ class MSection(metaclass=MObjectMeta):
"""
if isinstance(key, str):
value = self.m_annotations.get(key, default)
- if as_list and not isinstance(value, (list, tuple)):
+ if as_list and not isinstance(value, list | tuple):
return [value]
else:
return value
@@ -2513,7 +2513,7 @@ class MSection(metaclass=MObjectMeta):
elif isinstance(key, type):
result_list = []
for values in self.m_annotations.values():
- if isinstance(values, (tuple, list)):
+ if isinstance(values, tuple | list):
for value in values:
if isinstance(value, key):
result_list.append(value)
@@ -3207,7 +3207,7 @@ class Quantity(Property):
except Exception as e:
raise DeriveError(f'Could not derive value for {self}: {str(e)}')
- if isinstance(self.default, (dict, list)):
+ if isinstance(self.default, dict | list):
value = self.default.copy()
else:
value = self.default
@@ -3487,13 +3487,13 @@ class SubSection(Property):
"""
existing: MSection | MSubSectionList | None = self.__get__(obj)
if self.repeats:
- if value is not None and not isinstance(value, (list, set)):
+ if value is not None and not isinstance(value, list | set):
raise TypeError(
'Cannot set a repeating subsection directly, modify the list, e.a. via append.'
)
existing = cast(MSubSectionList, existing)
existing.clear()
- if isinstance(value, (list, set)):
+ if isinstance(value, list | set):
existing.extend(value)
else:
if existing is value:
diff --git a/nomad/metainfo/util.py b/nomad/metainfo/util.py
index f542325e24cc13fc0f1a51a9fda358c7936cf501..53e59e2e3fb8bebecde44edc416a05e12a5821d6 100644
--- a/nomad/metainfo/util.py
+++ b/nomad/metainfo/util.py
@@ -406,7 +406,7 @@ def validate_allowable_unit(
except KeyError:
return False
- if isinstance(allowable_list, (pint.Unit, pint.Quantity)):
+ if isinstance(allowable_list, pint.Unit | pint.Quantity):
if dimensionality in ('1', 'dimensionless'):
return allowable_list.dimensionless
diff --git a/nomad/mkdocs.py b/nomad/mkdocs.py
index 25efa82810ed9dcc27304ed57fde48178ae40dbb..281046c19a2e41ecd2fd36d9dd9fe398ad4c72f4 100644
--- a/nomad/mkdocs.py
+++ b/nomad/mkdocs.py
@@ -158,7 +158,7 @@ def get_field_default(field) -> str | None:
"""
default_value = field.default
if default_value is not None:
- if isinstance(default_value, (dict, BaseModel)):
+ if isinstance(default_value, dict | BaseModel):
default_value = 'Complex object, default value not displayed.'
elif default_value == '':
default_value = '""'
diff --git a/nomad/normalizing/method.py b/nomad/normalizing/method.py
index c4423ec72d3f398c46ccea59451f3b8eab808f71..0fc961ec59be8499fe209547351a58d40abe2f8b 100644
--- a/nomad/normalizing/method.py
+++ b/nomad/normalizing/method.py
@@ -20,7 +20,6 @@ from ase.dft.kpoints import monkhorst_pack, get_monkhorst_pack_size_and_offset
from collections import OrderedDict
import re
import numpy as np
-from typing import List, Tuple, Union, Optional
from nomad.datamodel import EntryArchive, ArchiveSection
from nomad.metainfo import MSection
@@ -718,7 +717,7 @@ class DFTMethod(ElectronicMethod):
method_dict['smearing_kind'] = smearing_kind
smearing_width = self._repr_method.electronic.smearing.width
if smearing_width is not None:
- smearing_width = '%.4f' % (smearing_width)
+ smearing_width = f'{smearing_width:.4f}'
method_dict['smearing_width'] = smearing_width
except Exception:
pass
@@ -737,7 +736,7 @@ class DFTMethod(ElectronicMethod):
try:
conv_thr = self._repr_method.scf.threshold_energy_change
if conv_thr is not None:
- conv_thr = '%.13f' % (conv_thr.to(ureg.rydberg).magnitude)
+ conv_thr = f'{conv_thr.to(ureg.rydberg).magnitude:.13f}'
method_dict['scf_threshold_energy_change'] = conv_thr
except Exception:
pass
@@ -789,12 +788,12 @@ class DFTMethod(ElectronicMethod):
atom_positions = atoms['positions']
geom_dict['atom_positions'] = np.array2string(
atom_positions.to(ureg.angstrom).magnitude, # convert to Angstrom
- formatter={'float_kind': lambda x: '%.6f' % x}, # type: ignore
+ formatter={'float_kind': lambda x: f'{x:.6f}'}, # type: ignore
).replace('\n', '')
cell = atoms['lattice_vectors']
geom_dict['simulation_cell'] = np.array2string(
cell.to(ureg.angstrom).magnitude, # convert to Angstrom
- formatter={'float_kind': lambda x: '%.6f' % x}, # type: ignore
+ formatter={'float_kind': lambda x: f'{x:.6f}'}, # type: ignore
).replace('\n', '')
except Exception:
pass
@@ -813,7 +812,7 @@ class DFTMethod(ElectronicMethod):
else None
)
if conv_thr is not None:
- conv_thr = '%.13f' % (conv_thr.to(ureg.rydberg).magnitude)
+ conv_thr = f'{conv_thr.to(ureg.rydberg).magnitude:.13f}'
param_dict['scf_threshold_energy_change'] = conv_thr
# Pseudopotentials are kept constant, if applicable
@@ -1109,10 +1108,10 @@ class BasisSetFHIAims(MethodNormalizerBasisSet):
result = None
if data is None:
return None
- elif isinstance(data, (Section, dict)):
+ elif isinstance(data, Section | dict):
result = OrderedDict()
for k in sorted(cls._filtered_section_keys(data)):
- v = data.get(k, None)
+ v = data.get(k, None) # type: ignore
result[k] = cls._values_to_dict(v, level=level + 1)
elif isinstance(data, (list)):
result = []
@@ -1170,14 +1169,14 @@ class BasisSetExciting(MethodNormalizerBasisSet):
for group in groups:
label = group.x_exciting_geometry_atom_labels
try:
- muffin_tin_settings[f'{label}_muffin_tin_radius'] = '%.6f' % (
- group.x_exciting_muffin_tin_radius.to(ureg.angstrom).magnitude
+ muffin_tin_settings[f'{label}_muffin_tin_radius'] = (
+ f'{group.x_exciting_muffin_tin_radius.to(ureg.angstrom).magnitude:.6f}'
)
except Exception:
muffin_tin_settings[f'{label}_muffin_tin_radius'] = None
try:
muffin_tin_settings[f'{label}_muffin_tin_points'] = (
- '%d' % group.x_exciting_muffin_tin_points
+ f'{group.x_exciting_muffin_tin_points}'
)
except Exception:
muffin_tin_settings[f'{label}_muffin_tin_points'] = None
@@ -1188,7 +1187,7 @@ class BasisSetExciting(MethodNormalizerBasisSet):
# Other important method settings
system = self._repr_system
try:
- self.settings['rgkmax'] = '%.6f' % (system.x_exciting_rgkmax.magnitude)
+ self.settings['rgkmax'] = f'{system.x_exciting_rgkmax.magnitude:.6f}'
except Exception:
pass
try:
@@ -1198,11 +1197,11 @@ class BasisSetExciting(MethodNormalizerBasisSet):
except Exception:
pass
try:
- self.settings['lo'] = '%d' % (system.x_exciting_lo)
+ self.settings['lo'] = f'{system.x_exciting_lo}'
except Exception:
pass
try:
- self.settings['lmaxapw'] = '%d' % (system.x_exciting_lmaxapw)
+ self.settings['lmaxapw'] = f'{system.x_exciting_lmaxapw}'
except Exception:
pass
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index 3e734e6f26049715ad910ec2ed7fba2041e3be61..6f5f4ebde1e15ef57b0668b85d49efb63c332d82 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -1097,7 +1097,7 @@ class ResultsNormalizer(Normalizer):
msd.diffusion_constant_errors = (
diffusion_constant.errors
if isinstance(
- diffusion_constant.errors, (list, np.ndarray)
+ diffusion_constant.errors, list | np.ndarray
)
else [diffusion_constant.errors]
)
diff --git a/nomad/parsing/artificial.py b/nomad/parsing/artificial.py
index 484f97ae15268f3feae2cd449a3ac47b0b0b650e..6302b72dde31231c95de7924a889b9d38d20423e 100644
--- a/nomad/parsing/artificial.py
+++ b/nomad/parsing/artificial.py
@@ -140,7 +140,7 @@ class ChaosParser(Parser):
while True:
data.append('a' * 10**6)
i += 1
- logger.info('ate %d mb' % i)
+ logger.info(f'ate {i} mb')
elif chaos == 'exception':
raise Exception('Some chaos happened, muhuha...')
elif chaos == 'segfault':
diff --git a/nomad/parsing/file_parser/file_parser.py b/nomad/parsing/file_parser/file_parser.py
index 488fb026565f2a62887969b29fd7994ce8a6f6e8..79b4f9086a8fc43858b11dbd5fe5ee17c26c72af 100644
--- a/nomad/parsing/file_parser/file_parser.py
+++ b/nomad/parsing/file_parser/file_parser.py
@@ -184,7 +184,7 @@ class FileParser(ABC):
return
if unit is not None:
- if isinstance(unit, (pint.Quantity, pint.Unit)):
+ if isinstance(unit, pint.Quantity | pint.Unit):
val = val * unit
elif isinstance(val, pint.Quantity):
diff --git a/nomad/parsing/file_parser/text_parser.py b/nomad/parsing/file_parser/text_parser.py
index 6b8804c507a0198e3bb4391b020af63e27232afb..10802db4aa74c8fee7928a14df1aaedac06f97eb 100644
--- a/nomad/parsing/file_parser/text_parser.py
+++ b/nomad/parsing/file_parser/text_parser.py
@@ -41,7 +41,7 @@ class ParsePattern:
token += r'\w'
if 'array' in value:
token += r' '
- value = r'[%s]+' % token
+ value = rf'[{token}]+'
self._value = value
self._tail = kwargs.get('tail', '\n')
self._re_pattern = None
@@ -49,14 +49,9 @@ class ParsePattern:
@property
def re_pattern(self):
if self._re_pattern is None:
- head = r'%s[\s\S]*?' % self._head if self._head else ''
- key = r'%s\s*\:*\=*\s*' % self._key if self._key else ''
- self._re_pattern = r'{}{}\s*\:*\=*\s*({}){}'.format(
- head,
- key,
- self._value,
- self._tail,
- )
+ head = rf'{self._head}[\s\S]*?' if self._head else ''
+ key = rf'{self._key}\s*\:*\=*\s*' if self._key else ''
+ self._re_pattern = rf'{head}{key}\s*\:*\=*\s*({self._value}){self._tail}'
return self._re_pattern
def __call__(self, text, repeats=True):
@@ -163,7 +158,7 @@ class Quantity:
Returns a compiled re pattern.
"""
if isinstance(self._re_pattern, str):
- re_pattern = self._re_pattern.replace('__unit', '__unit_%s' % self.name)
+ re_pattern = self._re_pattern.replace('__unit', f'__unit_{self.name}')
self._re_pattern = re.compile(re_pattern.encode())
return self._re_pattern
@@ -194,7 +189,7 @@ class Quantity:
return val
- elif isinstance(val, (list, np.ndarray)):
+ elif isinstance(val, list | np.ndarray):
try:
dtype = float if self.dtype is None else self.dtype
val_test = np.array(val, dtype=dtype)
@@ -429,7 +424,7 @@ class TextParser(FileParser):
re_findall = '|'.join([q.re_pattern.pattern.decode() for q in quantities])
if len(quantities) == 1:
# necessary to add a dummy variable to make multiple matches
- re_findall = '%s|(__dummy__)' % re_findall
+ re_findall = f'{re_findall}|(__dummy__)'
re_findall_b = re.compile(re_findall.encode())
if self._re_findall is None:
self._re_findall = re_findall_b
@@ -451,7 +446,7 @@ class TextParser(FileParser):
continue
non_empty_matches.append(non_empty_match)
index_unit = quantity.re_pattern.groupindex.get(
- '__unit_%s' % quantity.name, None
+ f'__unit_{quantity.name}', None
)
for non_empty_match in non_empty_matches:
try:
@@ -498,7 +493,7 @@ class TextParser(FileParser):
else:
try:
- unit = res.groupdict().get('__unit_%s' % quantity.name, None)
+ unit = res.groupdict().get(f'__unit_{quantity.name}', None)
units.append(unit.decode() if unit is not None else None)
value.append(
' '.join(
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index 73ec9a4e2ef346dd50dfd43d5b3c05c551e05351..cc74a0297f8c294050b16edce966fc45ad600fe4 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -577,4 +577,4 @@ class MissingParser(MatchingParser):
def parse(
self, mainfile: str, archive: EntryArchive, logger=None, child_archives=None
):
- raise Exception('The code %s is not yet supported.' % self.code_name)
+ raise Exception(f'The code {self.code_name} is not yet supported.')
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index 3cd806d4b20645dd63308ac0af61709b167cfcc6..3375e235c7803ac90e53969a9a02a685f62d4c4d 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -114,7 +114,7 @@ def match_parser(
else:
parsers_to_check = parsers
for parser in parsers_to_check:
- if strict and isinstance(parser, (MissingParser, EmptyParser)):
+ if strict and isinstance(parser, MissingParser | EmptyParser):
continue
match_result = parser.is_mainfile(
diff --git a/nomad/parsing/tabular.py b/nomad/parsing/tabular.py
index 55c6364902853ff362b335701ae3db1bbba7ea01..dcd4eb25946187e48f13fa36f57ccc7955b5f56a 100644
--- a/nomad/parsing/tabular.py
+++ b/nomad/parsing/tabular.py
@@ -657,7 +657,7 @@ def _create_column_to_quantity_mapping(section_def: Section):
if isinstance(value, float) and math.isnan(value):
value = None
- if isinstance(value, (int, float, str, pd.Timestamp)):
+ if isinstance(value, int | float | str | pd.Timestamp):
value = np.array([value])
if value is not None:
diff --git a/nomad/processing/base.py b/nomad/processing/base.py
index 8207337e762194ec80884338bdc4038729dabc5c..c9a3a52c7197f1a45e0c37fdb481b8acbf1d9f39 100644
--- a/nomad/processing/base.py
+++ b/nomad/processing/base.py
@@ -77,7 +77,7 @@ def setup(**kwargs):
infrastructure.setup()
utils.get_logger(__name__).info(
- 'celery configured with acks_late=%s' % str(config.celery.acks_late)
+ f'celery configured with acks_late={str(config.celery.acks_late)}'
)
@@ -398,7 +398,7 @@ class Proc(Document):
try:
obj = cls.objects(**{id_field: id}).first()
except ValidationError:
- raise InvalidId('%s is not a valid id' % id)
+ raise InvalidId(f'{id} is not a valid id')
except ConnectionFailure as e:
raise e
@@ -559,10 +559,7 @@ class Proc(Document):
)
def __str__(self):
- return 'proc celery_task_id={} worker_hostname={}'.format(
- self.celery_task_id,
- self.worker_hostname,
- )
+ return f'proc celery_task_id={self.celery_task_id} worker_hostname={self.worker_hostname}'
def parent(self) -> 'Proc':
"""
@@ -884,7 +881,7 @@ class NomadCeleryRequest(Request):
'detected WorkerLostError', exc_info=exc_info.exception
)
self._fail(
- 'process failed due to worker lost: %s' % str(exc_info.exception),
+ f'process failed due to worker lost: {str(exc_info.exception)}',
exc_info=exc_info,
)
@@ -913,7 +910,7 @@ def unwarp_task(task, cls_name, self_id, *args, **kwargs):
if cls is None:
logger.critical('document not a subclass of Proc')
- raise ProcNotRegistered('document %s not a subclass of Proc' % cls_name)
+ raise ProcNotRegistered(f'document {cls_name} not a subclass of Proc')
# get the process instance
try:
@@ -962,8 +959,7 @@ def proc_task(task, cls_name, self_id, func_name, args, kwargs):
if func is None: # "Should not happen"
logger.error('called function not a function of proc class')
proc.fail(
- 'called function %s is not a function of proc class %s'
- % (func_name, cls_name)
+ f'called function {func_name} is not a function of proc class {cls_name}'
)
return
@@ -971,7 +967,7 @@ def proc_task(task, cls_name, self_id, func_name, args, kwargs):
unwrapped_func = getattr(func, '__process_unwrapped', None)
if unwrapped_func is None: # "Should not happen"
logger.error('called function was not decorated with @process')
- proc.fail('called function %s was not decorated with @process' % func_name)
+ proc.fail(f'called function {func_name} was not decorated with @process')
return
# call the process function
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index b1298479f752560b900d314f2de1a3066bc38d88..bc91723d7cb4a88885298b247d430e2a05425135 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -309,7 +309,7 @@ class MetadataEditRequestHandler:
):
# Initialization
assert user, 'Must specify `user`'
- assert isinstance(edit_request, (StagingUploadFiles, dict)), (
+ assert isinstance(edit_request, StagingUploadFiles | dict), (
'`edit_request` must be either a json dictionary or a :class:`StagingUploadfiles` object'
)
self.logger = logger
@@ -344,7 +344,7 @@ class MetadataEditRequestHandler:
self.verified_entries: dict[
str, dict[str, Any]
] = {} # Metadata specified for individual entries
- self.affected_uploads: list['Upload'] = (
+ self.affected_uploads: list[Upload] = (
None # A MetadataEditRequest may involve multiple uploads
)
@@ -969,7 +969,7 @@ class Entry(Proc):
self._upload: Upload = None
self._upload_files: StagingUploadFiles = None
self._proc_logs: list[Any] = []
- self._child_entries: list['Entry'] = []
+ self._child_entries: list[Entry] = []
self._entry_metadata: EntryMetadata = None
self._perform_index = True
@@ -1661,11 +1661,7 @@ class Entry(Proc):
return self._proc_logs
def __str__(self):
- return 'entry {} entry_id={} upload_id{}'.format(
- super().__str__(),
- self.entry_id,
- self.upload_id,
- )
+ return f'entry {super().__str__()} entry_id={self.entry_id} upload_id{self.upload_id}'
class Upload(Proc):
@@ -1781,10 +1777,7 @@ class Upload(Proc):
def get_logger(self, **kwargs):
logger = super().get_logger()
main_author_user = self.main_author_user
- main_author_name = '{} {}'.format(
- main_author_user.first_name,
- main_author_user.last_name,
- )
+ main_author_name = f'{main_author_user.first_name} {main_author_user.last_name}'
# We are not using 'main_author' because logstash (?) will filter these entries ?!
logger = logger.bind(
upload_id=self.upload_id,
@@ -2306,21 +2299,16 @@ class Upload(Proc):
self.staging_upload_files.raw_file_object(stripped_path).os_path, 'w'
) as stripped_f:
stripped_f.write(
- 'Stripped POTCAR file. Checksum of original file (sha224): %s\n'
- % checksum
+ f'Stripped POTCAR file. Checksum of original file (sha224): {checksum}\n'
)
os.system(
+ f"""
+ awk < '{self.staging_upload_files.raw_file_object(path).os_path}' >> '{self.staging_upload_files.raw_file_object(stripped_path).os_path}' '
+ BEGIN {{ dump=1 }}
+ /End of Dataset/ {{ dump=1 }}
+ dump==1 {{ print }}
+ /END of PSCTR/ {{ dump=0 }}'
"""
- awk < '%s' >> '%s' '
- BEGIN { dump=1 }
- /End of Dataset/ { dump=1 }
- dump==1 { print }
- /END of PSCTR/ { dump=0 }'
- """
- % (
- self.staging_upload_files.raw_file_object(path).os_path,
- self.staging_upload_files.raw_file_object(stripped_path).os_path,
- )
)
def match_mainfiles(
diff --git a/nomad/search.py b/nomad/search.py
index eb34d65764cb191151e238c877fd89c4539be33c..1dc31f8abd05cd74a95393253f7fc35b75d2d15d 100644
--- a/nomad/search.py
+++ b/nomad/search.py
@@ -362,7 +362,7 @@ _entry_metadata_defaults = {
_all_author_quantities = [
quantity.name
for quantity in EntryMetadata.m_def.all_quantities.values()
- if isinstance(quantity.type, (UserReference, AuthorReference))
+ if isinstance(quantity.type, UserReference | AuthorReference)
]
@@ -825,7 +825,7 @@ def normalize_api_query(
query=normalize_api_query(query, doc_type=doc_type, prefix=query.prefix),
)
- if isinstance(query, (models.Empty, models.Criteria)):
+ if isinstance(query, models.Empty | models.Criteria):
return query
raise NotImplementedError(f'Query type {query.__class__} is not supported')
@@ -952,7 +952,7 @@ def _api_to_es_query(
quantity = validate_quantity(name, doc_type=doc_type)
return quantity.get_range_query(value)
- elif isinstance(value, (models.And, models.Or, models.Not)):
+ elif isinstance(value, models.And | models.Or | models.Not):
return validate_query(value)
# list of values is treated as an "all" over the items
@@ -1029,7 +1029,7 @@ def validate_pagination(
and pagination.order_by != doc_type.id_field
and ':' not in page_after_value
):
- pagination.page_after_value = '%s:' % page_after_value
+ pagination.page_after_value = f'{page_after_value}:'
return order_quantity, page_after_value
@@ -1117,7 +1117,7 @@ def _api_to_es_aggregation(
)
metric_aggregation, metric_quantity = metrics[metric_name]
es_aggs.metric(
- 'statistics:%s' % metric_name,
+ f'statistics:{metric_name}',
A(metric_aggregation, field=metric_quantity.qualified_field),
)
@@ -1134,7 +1134,7 @@ def _api_to_es_aggregation(
is_nested = False
for nested_key in doc_type.nested_object_keys:
if agg.quantity.startswith(nested_key):
- es_aggs = es_aggs.bucket('nested_agg:%s' % name, 'nested', path=nested_key)
+ es_aggs = es_aggs.bucket(f'nested_agg:{name}', 'nested', path=nested_key)
longest_nested_key = nested_key
is_nested = True
@@ -1143,7 +1143,7 @@ def _api_to_es_aggregation(
# quantity.
if quantity.dynamic:
es_aggs = es_aggs.bucket(
- 'nested_agg:%s' % name, 'nested', path='search_quantities'
+ f'nested_agg:{name}', 'nested', path='search_quantities'
)
is_nested = True
longest_nested_key = 'search_quantities'
@@ -1227,7 +1227,7 @@ def _api_to_es_aggregation(
# additional cardinality to get total
es_aggs.metric(
- 'agg:%s:total' % name, 'cardinality', field=quantity.search_field
+ f'agg:{name}:total', 'cardinality', field=quantity.search_field
)
else:
if agg.size is None:
@@ -1360,7 +1360,7 @@ def _api_to_es_aggregation(
)
metric_aggregation, metric_quantity = metrics[metric_name]
es_agg.metric(
- 'metric:%s' % metric_name,
+ f'metric:{metric_name}',
A(metric_aggregation, field=metric_quantity.qualified_field),
)
@@ -1498,7 +1498,7 @@ def _es_to_api_aggregation(
data.append(Bucket(value=value, count=0, metrics=metrics))
else:
- total = es_aggs['agg:%s:total' % name]['value']
+ total = es_aggs[f'agg:{name}:total']['value']
pagination = PaginationResponse(
total=total, **aggregation_dict['pagination']
)
@@ -1544,8 +1544,8 @@ def _es_to_api_aggregation(
raise NotImplementedError()
if isinstance(agg, MinMaxAggregation):
- min_value = es_aggs['agg:%s:min' % name]['value']
- max_value = es_aggs['agg:%s:max' % name]['value']
+ min_value = es_aggs[f'agg:{name}:min']['value']
+ max_value = es_aggs[f'agg:{name}:max']['value']
return AggregationResponse(
min_max=MinMaxAggregationResponse(
diff --git a/nomad/utils/__init__.py b/nomad/utils/__init__.py
index a580d088f98d59cb7e34c246cb29de1f56f13131..3400910cfb9218c8f0e03ee201b07177556b5543 100644
--- a/nomad/utils/__init__.py
+++ b/nomad/utils/__init__.py
@@ -147,10 +147,7 @@ def set_console_log_level(level):
for handler in root.handlers:
if not isinstance(
handler,
- (
- LogstashHandler,
- LogtransferHandler,
- ),
+ LogstashHandler | LogtransferHandler,
):
handler.setLevel(level)
@@ -317,7 +314,7 @@ def timer(
if logger_method is not None:
logger_method(event, exec_time=stop - start, **kwargs)
else:
- logger.error('Unknown logger method %s.' % method)
+ logger.error(f'Unknown logger method {method}.')
class archive:
@@ -454,7 +451,7 @@ class RestrictedDict(OrderedDict):
"""
super().__init__()
- if isinstance(mandatory_keys, (list, tuple, set)):
+ if isinstance(mandatory_keys, list | tuple | set):
self._mandatory_keys = set(mandatory_keys)
elif mandatory_keys is None:
self._mandatory_keys = set()
@@ -463,7 +460,7 @@ class RestrictedDict(OrderedDict):
'Please provide the mandatory_keys as a list, tuple or set.'
)
- if isinstance(optional_keys, (list, tuple, set)):
+ if isinstance(optional_keys, list | tuple | set):
self._optional_keys = set(optional_keys)
elif optional_keys is None:
self._optional_keys = set()
@@ -472,7 +469,7 @@ class RestrictedDict(OrderedDict):
'Please provide the optional_keys as a list, tuple or set.'
)
- if isinstance(forbidden_values, (list, tuple, set)):
+ if isinstance(forbidden_values, list | tuple | set):
self._forbidden_values = set(forbidden_values)
elif forbidden_values is None:
self._forbidden_values = set()
@@ -521,9 +518,7 @@ class RestrictedDict(OrderedDict):
else:
if match:
raise ValueError(
- "The value '{}' is not allowed but was set for key '{}'.".format(
- value, key
- )
+ f"The value '{value}' is not allowed but was set for key '{key}'."
)
# Check recursively
@@ -1060,7 +1055,7 @@ def dict_to_dataframe(
elif isinstance(nested_dict, dict):
for key, value in nested_dict.items():
new_key = f'{parent_key}{sep}{key}' if parent_key else key
- if isinstance(value, (dict, list)):
+ if isinstance(value, dict | list):
items.update(
flatten_dict(value, new_key, current_depth + 1, df, col_name)
)
diff --git a/nomad/utils/exampledata.py b/nomad/utils/exampledata.py
index 31ac1586733439f0093ebabc1505cf4b08898cb9..6fec3a33a862a355d12967ccdf3b98d339b43a09 100644
--- a/nomad/utils/exampledata.py
+++ b/nomad/utils/exampledata.py
@@ -166,7 +166,7 @@ class ExampleData:
else:
parser_name = parser.__class__.__name__
- assert parser is not None, 'there is no parser matching %s' % mainfile
+ assert parser is not None, f'there is no parser matching {mainfile}'
parser.parse(mainfile=mainfile, archive=entry_archive)
entry_metadata = entry_archive.metadata
@@ -406,7 +406,7 @@ class ExampleData:
self.create_entry(
entry_archive=archive,
upload_id=upload_id,
- entry_id='test_entry_id_%d' % id,
+ entry_id=f'test_entry_id_{id}',
domain='dft',
**kwargs,
)
diff --git a/nomad/utils/structlogging.py b/nomad/utils/structlogging.py
index 879f4a208a39f6b07a4abe59fc719085efb0ed8e..0a97f0a9546af4c65106a12d06abcc3c20a6e4a0 100644
--- a/nomad/utils/structlogging.py
+++ b/nomad/utils/structlogging.py
@@ -145,7 +145,7 @@ class LogstashFormatter(logstash.formatter.LogstashFormatterBase):
'user_id',
'mainfile',
]:
- key = 'nomad.%s' % key
+ key = f'nomad.{key}'
else:
key = f'{record.name}.{key}'
@@ -229,11 +229,12 @@ class ConsoleFormatter(LogstashFormatter):
out = StringIO()
out.write(
- '%s %s %s %s'
- % (level.ljust(8), logger.ljust(20)[:20], time.ljust(19)[:19], event)
+ f'{level.ljust(8)} {logger.ljust(20)[:20]} {time.ljust(19)[:19]} {event}'
)
if exception is not None:
- out.write('\n - exception: %s' % str(exception).replace('\n', '\n '))
+ out.write(
+ '\n - exception: {}'.format(str(exception).replace('\n', '\n '))
+ )
for key in keys:
if cls.short_format and key.startswith('nomad.'):
@@ -340,10 +341,7 @@ def configure_logging(console_log_level=config.services.console_log_level):
for handler in root.handlers:
if not isinstance(
handler,
- (
- LogstashHandler,
- LogtransferHandler,
- ),
+ LogstashHandler | LogtransferHandler,
):
handler.setLevel(console_log_level)
handler.setFormatter(ConsoleFormatter())
diff --git a/pyproject.toml b/pyproject.toml
index 2ec3f67eb796cfa5da9700100d4927529f543bc2..54045953a4e3080aaa004eda935e615c0947f1f6 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -11,7 +11,7 @@ authors = [
]
dynamic = ["version"]
license = { text = "Apache-2.0" }
-requires-python = ">=3.10" # remember to update scripts/pyupgrade.sh
+requires-python = ">=3.10"
dependencies = [
'aniso8601>=7.0.0',
@@ -153,6 +153,7 @@ select = [
"E", # pycodestyle
"W", # pycodestyle
"PL", # pylint
+ "UP", # pyupgrade
]
ignore = [
"E501", # Line too long ({width} > {limit} characters)
@@ -168,9 +169,15 @@ ignore = [
"PLW2901", # redefined-loop-name
"PLR1714", # consider-using-in
"PLR5501", # else-if-used
+ "UP035", # deprecated-import
]
fixable = ["ALL"]
+[tool.ruff.lint.extend-per-file-ignores]
+"nomad/app/v1/models/graph/utils.py" = [
+ "UP007",
+] # causes pydantic model building errors
+
[tool.ruff.format]
# use single quotes for strings.
quote-style = "single"
diff --git a/scripts/pyupgrade.sh b/scripts/pyupgrade.sh
deleted file mode 100644
index f60515a860e24595820277ebcf0386e392612453..0000000000000000000000000000000000000000
--- a/scripts/pyupgrade.sh
+++ /dev/null
@@ -1,20 +0,0 @@
-#!/bin/bash
-
-# Upgrade syntax of all python files under nomad/ folder using pyupgrade
-# pyupgrade is not installed by default
-# install it using `pip install pyupgrade` or `uv pip install pyupgrade`
-# using modern syntax to maximise maintainability and readability
-# it is also possible to use pyupgrade as a commit hook
-
-if ! command -v pyupgrade &> /dev/null; then
- echo "Error: pyupgrade is not installed. Please install it using 'pip install pyupgrade'."
- exit 1
-fi
-
-# Navigate to the parent folder based on script location
-cd "$(dirname "$0")/.." || exit 1
-
-# Find all Python files in the "nomad" folder and apply pyupgrade
-find nomad -type f -name "*.py" | while read -r file; do
- pyupgrade --py310-plus "$file"
-done
diff --git a/tests/app/test_dcat.py b/tests/app/test_dcat.py
index 8e5b4b68291cd6e30faf8a9ae4b8b49fea7b4172..4f08b698f2a66cf80bed6f094aaaa07989a98cb2 100644
--- a/tests/app/test_dcat.py
+++ b/tests/app/test_dcat.py
@@ -79,7 +79,7 @@ def data(user1, user2, elastic_infra, mongo_module):
for i in range(1, 11):
example_attrs.update(
- entry_id='test-id-%d' % i, last_processing_time=datetime(2020, 1, i)
+ entry_id=f'test-id-{i}', last_processing_time=datetime(2020, 1, i)
)
data.create_entry(**example_attrs)
@@ -101,7 +101,7 @@ def test_mapping(example_entry):
def test_get_dataset(api, example_entry):
entry_id = 'test-id'
- rv = api.get('/datasets/%s' % entry_id)
+ rv = api.get(f'/datasets/{entry_id}')
assert rv.status_code == 200
diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index 468ca15fc71851cf4d59eebac174e64913eacedc..a7841ff89a7a45e7ca0c8977f932047c5dab4623 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -184,9 +184,7 @@ def assert_eq_attrib(data, key, ref, item=None):
@pytest.mark.parametrize('limit, offset, results', [(1, 1, 1), (3, 2, 2), (5, 0, 4)])
def test_list_endpoint_pagination(client, example_structures, limit, offset, results):
- rv = client.get(
- '/optimade/structures?page_limit=%d&page_offset=%d' % (limit, offset)
- )
+ rv = client.get(f'/optimade/structures?page_limit={limit}&page_offset={offset}')
assert rv.status_code == 200
data = rv.json()
assert len(data['data']) == results
@@ -194,7 +192,7 @@ def test_list_endpoint_pagination(client, example_structures, limit, offset, res
@pytest.mark.parametrize('sort, order', [('nelements', 1), ('-nelements', -1)])
def test_list_endpoint_sort(client, example_structures, sort, order):
- rv = client.get('/optimade/structures?sort=%s' % sort)
+ rv = client.get(f'/optimade/structures?sort={sort}')
assert rv.status_code == 200
data = rv.json()['data']
@@ -228,7 +226,9 @@ def test_list_endpoint_response_fields(client, example_structures):
def test_single_endpoint_response_fields(client, example_structures):
rv = client.get(
- '/optimade/structures/%s?response_fields=nelements,elements' % 'test_entry_id_1'
+ '/optimade/structures/{}?response_fields=nelements,elements'.format(
+ 'test_entry_id_1'
+ )
)
assert rv.status_code == 200, json.dumps(rv.json(), indent=2)
data = rv.json()
@@ -240,7 +240,7 @@ def test_single_endpoint_response_fields(client, example_structures):
def test_single_endpoint(client, example_structures):
- rv = client.get('/optimade/structures/%s' % 'test_entry_id_1')
+ rv = client.get('/optimade/structures/{}'.format('test_entry_id_1'))
assert rv.status_code == 200
data = rv.json()
for key in ['type', 'id', 'attributes']:
@@ -323,7 +323,7 @@ def test_structures_endpoint(client, example_structures):
def test_structure_endpoint(client, example_structures):
- rv = client.get('/optimade/structures/%s' % 'test_entry_id_1')
+ rv = client.get('/optimade/structures/{}'.format('test_entry_id_1'))
assert rv.status_code == 200
data = rv.json()
assert data.get('data') is not None
@@ -347,8 +347,9 @@ def test_nmd_properties_info(client, example_structures):
def test_nmd_properties(client, example_structures):
rv = client.get(
- '/optimade/structures/%s'
- % 'test_entry_id_1?response_fields=_nmd_results_material_elements,_nmd_results_material_structural_type,_nmd_doesnotexist,_nmd_archive_url'
+ '/optimade/structures/{}'.format(
+ 'test_entry_id_1?response_fields=_nmd_results_material_elements,_nmd_results_material_structural_type,_nmd_doesnotexist,_nmd_archive_url'
+ )
)
assert rv.status_code == 200
data = rv.json()
diff --git a/tests/app/v1/routers/common.py b/tests/app/v1/routers/common.py
index 81192fd430f817f34335a96f8e78695e072a4a14..19acc77e630f4f28250149dcc648a772472b60e9 100644
--- a/tests/app/v1/routers/common.py
+++ b/tests/app/v1/routers/common.py
@@ -139,7 +139,7 @@ def post_query_test_parameters(
def get_query_test_parameters(
str: dict, int: dict, date: dict, subsection: dict, total: int
-) -> List[Any]:
+) -> list[Any]:
"""Convenience function for constructing GET query test parameters.
Args:
@@ -439,14 +439,14 @@ def aggregation_test_parameters(
bool: dict,
int: dict,
pagination: dict,
- pagination_order_by: Optional[dict],
+ pagination_order_by: dict | None,
histogram_int: dict,
histogram_date: dict,
include: dict,
metrics: dict,
empty: dict,
- fixed: Optional[dict],
-) -> List[Any]:
+ fixed: dict | None,
+) -> list[Any]:
"""Convenience function for constructing aggregation tests.
Args:
@@ -1222,7 +1222,7 @@ def assert_metadata_response(response, status_code=None):
def assert_required(data, required, default_key: str):
# We flat out all keys in data and then make sure that the full qualified keys in the
# data are consistent with the keys given in the required include and exclude.
- keys: Set[str] = set()
+ keys: set[str] = set()
def collect_keys(data, prefix=None):
if isinstance(data, list):
@@ -1294,13 +1294,13 @@ def assert_aggregations(
if agg_type == 'min_max':
assert len(data) == 2
- assert isinstance(data[0], (float, int))
- assert isinstance(data[1], (float, int))
+ assert isinstance(data[0], float | int)
+ assert isinstance(data[1], float | int)
elif agg_type == 'statistics':
assert 'metrics' in agg_response
for metric in agg.get('metrics', []):
assert metric in data
- assert isinstance(data[metric], (float, int))
+ assert isinstance(data[metric], float | int)
else:
assert total == -1 or total >= n_data
assert size == -1 or size == n_data
@@ -1317,11 +1317,11 @@ def assert_aggregations(
if agg_type == 'date_histogram':
assert re.match(r'\d{4}\-\d{2}\-\d{2}', value)
elif agg_type == 'histogram':
- assert isinstance(value, (float, int))
+ assert isinstance(value, float | int)
for metric in agg.get('metrics', []):
assert metric in bucket['metrics']
- assert isinstance(bucket['metrics'][metric], (float, int))
+ assert isinstance(bucket['metrics'][metric], float | int)
if 'entries' in agg:
for bucket in data:
@@ -1346,7 +1346,7 @@ def assert_query_response(client, test_method, query, total, status_code):
if 'pagination' not in response_json:
return
- response = client.get('entries?%s' % urlencode(query, doseq=True))
+ response = client.get(f'entries?{urlencode(query, doseq=True)}')
response_json = assert_metadata_response(response, status_code=status_code)
@@ -1547,7 +1547,7 @@ def perform_quantity_search_test(
assert api_result == result
-def build_headers(accept: Optional[str] = None, user_auth: Optional[dict] = None):
+def build_headers(accept: str | None = None, user_auth: dict | None = None):
headers = {}
if accept:
headers['Accept'] = accept
diff --git a/tests/app/v1/routers/test_auth.py b/tests/app/v1/routers/test_auth.py
index 904c80e7028dc10e67a1828863396b4efd84a2f5..c814260a3c4b502c8c841b09a2cb1fd2eb1302fe 100644
--- a/tests/app/v1/routers/test_auth.py
+++ b/tests/app/v1/routers/test_auth.py
@@ -27,7 +27,7 @@ def perform_get_token_test(client, http_method, status_code, username, password)
)
else:
response = client.get(
- 'auth/token?%s' % urlencode(dict(username=username, password=password))
+ f'auth/token?{urlencode(dict(username=username, password=password))}'
)
assert response.status_code == status_code
diff --git a/tests/app/v1/routers/test_datasets.py b/tests/app/v1/routers/test_datasets.py
index a83c4d4f2806e048a5b4acbfe91d64ea3802fd0a..eecbdf50251be6853bbadb898d844a11726bf255 100644
--- a/tests/app/v1/routers/test_datasets.py
+++ b/tests/app/v1/routers/test_datasets.py
@@ -100,8 +100,8 @@ def data(elastic_function, raw_files_function, mongo_function, user1, user2):
for i in range(1, 4):
data.create_entry(
upload_id='other_data',
- entry_id='id_%02d' % i,
- mainfile='test_content/%02d/mainfile.json' % i,
+ entry_id=f'id_{i:02d}',
+ mainfile=f'test_content/{i:02d}/mainfile.json',
)
data.save(with_files=False)
@@ -127,7 +127,7 @@ def assert_pagination(pagination):
def assert_dataset(
dataset,
query: Query = None,
- entries: List[str] = None,
+ entries: list[str] = None,
n_entries: int = -1,
**kwargs,
):
@@ -223,7 +223,7 @@ def test_datasets(client, data, query, size, status_code):
],
)
def test_dataset(client, data, dataset_id, result, status_code):
- response = client.get('datasets/%s' % dataset_id)
+ response = client.get(f'datasets/{dataset_id}')
assert_response(response, status_code=status_code)
if status_code != 200:
@@ -354,7 +354,7 @@ def test_post_datasets(
],
)
def test_delete_dataset(auth_headers, client, data, dataset_id, user, status_code):
- response = client.delete('datasets/%s' % dataset_id, headers=auth_headers[user])
+ response = client.delete(f'datasets/{dataset_id}', headers=auth_headers[user])
assert_response(response, status_code=status_code)
if status_code != 200:
@@ -410,7 +410,7 @@ def test_assign_doi_dataset(
more_data.save(with_files=False)
headers = auth_headers[user]
- response = client.post('datasets/%s/action/doi' % dataset_id, headers=headers)
+ response = client.post(f'datasets/{dataset_id}/action/doi', headers=headers)
assert_response(response, status_code=status_code)
if status_code != 200:
diff --git a/tests/app/v1/routers/test_entries.py b/tests/app/v1/routers/test_entries.py
index 87cd767e34c84d65af7be017bc216d322ffb7b2e..8ec76fef0bfa476fb44668b678ee03be7fa34bc2 100644
--- a/tests/app/v1/routers/test_entries.py
+++ b/tests/app/v1/routers/test_entries.py
@@ -92,7 +92,7 @@ def perform_entries_raw_test(
if owner is not None:
params['owner'] = owner
response = client.get(
- 'entries/raw?%s' % urlencode(params, doseq=True), headers=headers
+ f'entries/raw?{urlencode(params, doseq=True)}', headers=headers
)
else:
@@ -129,7 +129,7 @@ def perform_entries_rawdir_test(
for value in kwargs.values():
params.update(**value)
response = client.get(
- 'entries/rawdir?%s' % urlencode(params, doseq=True), headers=headers
+ f'entries/rawdir?{urlencode(params, doseq=True)}', headers=headers
)
elif http_method == 'post':
@@ -188,7 +188,7 @@ def perform_entries_archive_download_test(
if owner is not None:
params['owner'] = owner
response = client.get(
- 'entries/archive/download?%s' % urlencode(params, doseq=True),
+ f'entries/archive/download?{urlencode(params, doseq=True)}',
headers=headers,
)
@@ -219,7 +219,7 @@ def perform_entries_archive_test(
if 'pagination' in kwargs:
params.update(**kwargs['pagination'])
response = client.get(
- 'entries/archive?%s' % urlencode(params, doseq=True), headers=headers
+ f'entries/archive?{urlencode(params, doseq=True)}', headers=headers
)
else:
@@ -590,7 +590,7 @@ def test_entry_metadata(
auth_headers, client, example_data, user, entry_id, required, status_code
):
response = client.get(
- 'entries/%s?%s' % (entry_id, urlencode(required, doseq=True)),
+ f'entries/{entry_id}?{urlencode(required, doseq=True)}',
headers=auth_headers[user],
)
response_json = assert_metadata_response(response, status_code=status_code)
@@ -773,7 +773,7 @@ def test_entries_download_max(
def test_entry_rawdir(
auth_headers, client, example_data, user, entry_id, files_per_entry, status_code
):
- response = client.get('entries/%s/rawdir' % entry_id, headers=auth_headers[user])
+ response = client.get(f'entries/{entry_id}/rawdir', headers=auth_headers[user])
assert_response(response, status_code)
if status_code == 200:
assert_entry_rawdir_response(response.json(), files_per_entry=files_per_entry)
@@ -806,7 +806,7 @@ def test_entry_raw(
status_code,
):
response = client.get(
- 'entries/%s/raw?%s' % (entry_id, urlencode(files, doseq=True)),
+ f'entries/{entry_id}/raw?{urlencode(files, doseq=True)}',
headers=auth_headers[user],
)
assert_response(response, status_code)
@@ -1074,7 +1074,7 @@ def test_entries_archive(client, example_data, required, status_code):
],
)
def test_entry_archive(auth_headers, client, example_data, user, entry_id, status_code):
- response = client.get('entries/%s/archive' % entry_id, headers=auth_headers[user])
+ response = client.get(f'entries/{entry_id}/archive', headers=auth_headers[user])
assert_response(response, status_code)
if status_code == 200:
assert_archive_response(response.json())
diff --git a/tests/app/v1/routers/test_entries_edit.py b/tests/app/v1/routers/test_entries_edit.py
index 07cd132275b4032bc51114459eedd21abfed156f..cd793d3fb4c43a5696bf9dc7800296de9b254b88 100644
--- a/tests/app/v1/routers/test_entries_edit.py
+++ b/tests/app/v1/routers/test_entries_edit.py
@@ -128,7 +128,7 @@ class TestEditRepo:
def mongo(self, *args, edited: bool = True, **kwargs):
for entry_id in args:
- entry = proc.Entry.objects(entry_id='test_entry_id_%d' % entry_id).first()
+ entry = proc.Entry.objects(entry_id=f'test_entry_id_{entry_id}').first()
assert entry is not None
if edited:
assert entry.last_edit_time is not None
@@ -141,7 +141,7 @@ class TestEditRepo:
def assert_elastic(self, *args, invert: bool = False, **kwargs):
def assert_entry(get_entries):
for arg in args:
- entry_id = 'test_entry_id_%d' % arg
+ entry_id = f'test_entry_id_{arg}'
entries = list(get_entries(entry_id))
assert len(entries) > 0, entry_id
for entry in entries:
@@ -285,7 +285,7 @@ class TestEditRepo:
assert rv.status_code == 200
rv = self.api.post(
- 'datasets/%s/action/doi' % self.example_dataset.dataset_name,
+ f'datasets/{self.example_dataset.dataset_name}/action/doi',
headers=self.user_auth,
)
assert rv.status_code == 200
diff --git a/tests/app/v1/routers/test_materials.py b/tests/app/v1/routers/test_materials.py
index eacdc7e376d1443d4ad800e96400a2ee05a90f09..3adbb143e28db88adf816bda0b6fb246d073b7c3 100644
--- a/tests/app/v1/routers/test_materials.py
+++ b/tests/app/v1/routers/test_materials.py
@@ -161,9 +161,7 @@ def test_materials_required(client, example_data, required, status_code, http_me
],
)
def test_material_metadata(client, example_data, material_id, required, status_code):
- response = client.get(
- 'materials/%s?%s' % (material_id, urlencode(required, doseq=True))
- )
+ response = client.get(f'materials/{material_id}?{urlencode(required, doseq=True)}')
response_json = assert_metadata_response(response, status_code=status_code)
if response_json is None:
@@ -302,7 +300,7 @@ def test_materials_get_query(client, example_data, query, status_code, total):
if 'pagination' not in response_json:
return
- response = client.get('materials?%s' % urlencode(query, doseq=True))
+ response = client.get(f'materials?{urlencode(query, doseq=True)}')
response_json = assert_metadata_response(response, status_code=status_code)
diff --git a/tests/app/v1/routers/uploads/test_basic_uploads.py b/tests/app/v1/routers/uploads/test_basic_uploads.py
index f539acf485acd26ebd73cf53aae0f9e1499a4965..f1e6d9bbed79041c3260d0a6d0be12c43bf38f88 100644
--- a/tests/app/v1/routers/uploads/test_basic_uploads.py
+++ b/tests/app/v1/routers/uploads/test_basic_uploads.py
@@ -22,7 +22,8 @@ import time
import zipfile
from datetime import datetime
import tempfile
-from typing import Any, Dict, Iterable, List
+from typing import Any, Dict, List
+from collections.abc import Iterable
import pytest
import requests
@@ -401,7 +402,7 @@ def block_until_completed(client, upload_id: str, user_auth):
start_time = time.time()
while time.time() - start_time < config.tests.default_timeout:
time.sleep(0.1)
- response = client.get('uploads/%s' % upload_id, headers=user_auth)
+ response = client.get(f'uploads/{upload_id}', headers=user_auth)
if response.status_code == 200:
response_json = response.json()
assert_upload(response_json)
@@ -412,14 +413,13 @@ def block_until_completed(client, upload_id: str, user_auth):
return None
else:
raise Exception(
- 'unexpected status code while blocking for upload processing: %s'
- % str(response.status_code)
+ f'unexpected status code while blocking for upload processing: {str(response.status_code)}'
)
raise Exception('Timed out while waiting for upload processing to finish')
def get_upload_entries_metadata(
- entries: List[Dict[str, Any]],
+ entries: list[dict[str, Any]],
) -> Iterable[EntryMetadata]:
"""
Create a iterable of :class:`EntryMetadata` from a API upload json record, plus a
diff --git a/tests/app/v1/test_models.py b/tests/app/v1/test_models.py
index 130483bbc0e8b89711b07c7b5cbd4bf564f10c29..821fea8dc341e26b531b3b046b979c4492159faa 100644
--- a/tests/app/v1/test_models.py
+++ b/tests/app/v1/test_models.py
@@ -167,7 +167,7 @@ def test_module():
),
],
)
-def test_validation(request_yaml: str, paths: List[str], error_path: str):
+def test_validation(request_yaml: str, paths: list[str], error_path: str):
try:
request = GraphRequest.model_validate(yaml.safe_load(strip(request_yaml)))
except ValidationError as error:
diff --git a/tests/archive/test_archive.py b/tests/archive/test_archive.py
index 36e604641c2a9197f4581f6e61872a43a01671a4..0d972d4ff9a887c25045db690f50a68cb3a92a47 100644
--- a/tests/archive/test_archive.py
+++ b/tests/archive/test_archive.py
@@ -56,7 +56,7 @@ from nomad.utils.exampledata import ExampleData
def create_example_uuid(index: int = 0):
- return ('{:%dd}' % utils.default_hash_len).format(index)
+ return f'{index:{utils.default_hash_len}d}'
@pytest.fixture(scope='session')
@@ -221,7 +221,7 @@ def test_read_archive_multi(monkeypatch, example_uuid, example_entry, use_blocke
assert float(i) == entry['large_list'][i]
-test_query_example: Dict[Any, Any] = {
+test_query_example: dict[Any, Any] = {
'c1': {
's1': {'ss1': [{'p1': 1.0, 'p2': 'x'}, {'p1': 1.5, 'p2': 'y'}]},
's2': [{'p1': ['a', 'b'], 'p2': True}],
@@ -1117,8 +1117,8 @@ def assert_required_results(
results: dict,
required: dict,
archive: MSection,
- current_results: Union[dict, str] = None,
- current_archive_serialized: Union[str, dict] = None,
+ current_results: dict | str = None,
+ current_archive_serialized: str | dict = None,
):
"""
Asserts if the resulting dict from a :class:`RequiredReader` contains everything that
diff --git a/tests/archive/test_storage.py b/tests/archive/test_storage.py
index 72d9f241664c2647b581f3591f5394e79ac2c562..4a2de3dbf6bce3c2e3b9ab8bfd8553060b55f3f7 100644
--- a/tests/archive/test_storage.py
+++ b/tests/archive/test_storage.py
@@ -49,11 +49,11 @@ def find_all_paths(json_obj, path=None, paths_list=None):
if paths_list is None:
paths_list = []
- if isinstance(json_obj, (dict, ArchiveDict)):
+ if isinstance(json_obj, dict | ArchiveDict):
for key, value in json_obj.items():
new_path = [key] if not path else path + [key]
find_all_paths(value, new_path, paths_list)
- elif isinstance(json_obj, (list, ArchiveList)):
+ elif isinstance(json_obj, list | ArchiveList):
for index, value in enumerate(json_obj):
new_path = [index] if not path else path + [index]
find_all_paths(value, new_path, paths_list)
diff --git a/tests/conftest.py b/tests/conftest.py
index 9cc503438128a6feb9f50f2ca239b94894c71ef5..bea0af18be93252b6f5715d635e09546e75e1e83 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -291,7 +291,7 @@ def central_logstash_mock(monkeypatch):
try:
line = self.rfile.readline()
# print(f'received {line=}')
- except socket.timeout:
+ except TimeoutError:
# print(f'server timed out')
line = b'' # if time out, close connection
@@ -365,7 +365,7 @@ class MockFileManager:
def read(self, name):
name = os.path.abspath(name)
if name not in self.files:
- raise IOError(2, "No such file or directory: '%s'" % name)
+ raise OSError(2, f"No such file or directory: '{name}'")
return self.files[name].getvalue()
diff --git a/tests/data/schemas/nomadschemaexample/schema.py b/tests/data/schemas/nomadschemaexample/schema.py
index 6d93b8d258549b38265c622ede60334f594baa69..2bf501f0067643332f9dd9d0f98312a11d090b1e 100644
--- a/tests/data/schemas/nomadschemaexample/schema.py
+++ b/tests/data/schemas/nomadschemaexample/schema.py
@@ -96,7 +96,7 @@ class MySchema(EntryData):
child_recursive = SubSection(section_def=MySectionRecursiveA)
def normalize(self, archive, logger):
- super(MySchema, self).normalize(archive, logger)
+ super().normalize(archive, logger)
m_package.__init_metainfo__()
diff --git a/tests/datamodel/metainfo/test_substance.py b/tests/datamodel/metainfo/test_substance.py
index c30135d817e1b39d5a4865f490058084d5233e1c..78c63e39a54c7ba8257f95167652b4698bb1b8a3 100644
--- a/tests/datamodel/metainfo/test_substance.py
+++ b/tests/datamodel/metainfo/test_substance.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
-from typing import Iterable
+from collections.abc import Iterable
import pytest
import json
@@ -39,9 +39,7 @@ class MockResponse:
@pytest.fixture(scope='function')
def external_api_fixture(monkeypatch):
- with open(
- 'tests/data/datamodel/metainfo/external_api_mock_response.json', 'r'
- ) as fp:
+ with open('tests/data/datamodel/metainfo/external_api_mock_response.json') as fp:
mock_responses = json.load(fp)
def pub_chem_api_get_properties(cid: int, properties: Iterable[str]):
diff --git a/tests/datamodel/test_context.py b/tests/datamodel/test_context.py
index 267e71aed435818a9c2d5628660b6cffffb6e417..410c385b5d0fea5d2679321c74e5dafaaf2556d4 100644
--- a/tests/datamodel/test_context.py
+++ b/tests/datamodel/test_context.py
@@ -439,7 +439,7 @@ def test_server_external_schema(upload1_contents, upload2_contents, raw_files_fu
for index, (file_name, content) in enumerate(upload1_contents.items()):
if not re.match(r'.*.archive.json', file_name):
continue
- entry_id = 'upload1_entry{}'.format(index)
+ entry_id = f'upload1_entry{index}'
archive = EntryArchive(
m_context=context1,
metadata=EntryMetadata(
@@ -462,7 +462,7 @@ def test_server_external_schema(upload1_contents, upload2_contents, raw_files_fu
parser = ArchiveParser()
for index, (file_name, content) in enumerate(upload2_contents.items()):
- entry_id = 'upload2_entry{}'.format(index)
+ entry_id = f'upload2_entry{index}'
archive = EntryArchive(
m_context=context2,
metadata=EntryMetadata(
@@ -491,7 +491,7 @@ def test_client_custom_schema(api_v1, published_wo_user_metadata):
published_wo_user_metadata.upload_id, f'examples_template/template.json'
)
- with open(full_path, 'r') as f:
+ with open(full_path) as f:
text = f.read().replace(
'/run/0',
f'{url}/uploads/{published_wo_user_metadata.upload_id}/archive/{entry_id}#/run/0',
@@ -572,7 +572,7 @@ def test_client_external_schema(
parser = ArchiveParser()
for index, (file_name, content) in enumerate(referencing_upload_contents.items()):
- entry_id = 'upload2_entry{}'.format(index)
+ entry_id = f'upload2_entry{index}'
archive = EntryArchive(
m_context=context2,
metadata=EntryMetadata(
diff --git a/tests/examples/test_docs.py b/tests/examples/test_docs.py
index 46c43ed8ed9eed3c273294472191dfc6030bef1b..e8b737a9fbc0a21a85cd8e5d7893d0b0a5080697 100644
--- a/tests/examples/test_docs.py
+++ b/tests/examples/test_docs.py
@@ -14,7 +14,7 @@ def _file(path):
def _load_yaml(path):
- with open(_file(path), 'rt') as f:
+ with open(_file(path)) as f:
return yaml.safe_load(f)
diff --git a/tests/fixtures/data.py b/tests/fixtures/data.py
index 190bdde29598d2cef300e154d7dba0377d61ef96..d974026e243d981642b9701349b7d5257dda528a 100644
--- a/tests/fixtures/data.py
+++ b/tests/fixtures/data.py
@@ -31,7 +31,7 @@ from tests.utils import (
@pytest.fixture(scope='session')
-def example_mainfile() -> Tuple[str, str]:
+def example_mainfile() -> tuple[str, str]:
return ('parsers/template', 'tests/data/templates/template.json')
@@ -82,7 +82,7 @@ def internal_example_user_metadata(example_user_metadata) -> dict:
@pytest.fixture(scope='session')
-def parsed(example_mainfile: Tuple[str, str]) -> EntryArchive:
+def parsed(example_mainfile: tuple[str, str]) -> EntryArchive:
"""Provides a parsed entry in the form of an EntryArchive."""
parser, mainfile = example_mainfile
return test_parsing.run_singular_parser(parser, mainfile)
@@ -103,7 +103,7 @@ def normalized(parsed: EntryArchive) -> EntryArchive:
@pytest.fixture(scope='function')
-def uploaded(example_upload: str, raw_files_function) -> Tuple[str, str]:
+def uploaded(example_upload: str, raw_files_function) -> tuple[str, str]:
"""
Provides a uploaded with uploaded example file and gives the upload_id.
Clears files after test.
@@ -115,7 +115,7 @@ def uploaded(example_upload: str, raw_files_function) -> Tuple[str, str]:
@pytest.fixture(scope='function')
def non_empty_uploaded(
non_empty_example_upload: str, raw_files_function
-) -> Tuple[str, str]:
+) -> tuple[str, str]:
example_upload_id = os.path.basename(non_empty_example_upload).replace('.zip', '')
return example_upload_id, non_empty_example_upload
@@ -212,7 +212,7 @@ def oasis_publishable_upload(
@pytest.mark.timeout(config.tests.default_timeout)
@pytest.fixture(scope='function')
def processed(
- uploaded: Tuple[str, str], user1: User, proc_infra, mails
+ uploaded: tuple[str, str], user1: User, proc_infra, mails
) -> processing.Upload:
"""
Provides a processed upload. Upload was uploaded with user1.
@@ -224,12 +224,11 @@ def processed(
@pytest.fixture(scope='function')
def processeds(
non_empty_example_upload: str, user1: User, proc_infra
-) -> List[processing.Upload]:
- result: List[processing.Upload] = []
+) -> list[processing.Upload]:
+ result: list[processing.Upload] = []
for i in range(2):
- upload_id = '%s_%d' % (
- os.path.basename(non_empty_example_upload).replace('.zip', ''),
- i,
+ upload_id = (
+ f'{os.path.basename(non_empty_example_upload).replace(".zip", "")}_{i}'
)
result.append(
test_processing.run_processing((upload_id, non_empty_example_upload), user1)
@@ -241,7 +240,7 @@ def processeds(
@pytest.mark.timeout(config.tests.default_timeout)
@pytest.fixture(scope='function')
def non_empty_processed(
- non_empty_uploaded: Tuple[str, str], user1: User, proc_infra
+ non_empty_uploaded: tuple[str, str], user1: User, proc_infra
) -> processing.Upload:
"""
Provides a processed upload. Upload was uploaded with user1.
@@ -358,9 +357,9 @@ def example_data(
upload_id='id_published', upload_name='name_published', published=True
)
for i in range(1, 24):
- entry_id = 'id_%02d' % i
- material_id = 'id_%02d' % (int(math.floor(i / 4)) + 1)
- mainfile = 'test_content/subdir/test_entry_%02d/mainfile.json' % i
+ entry_id = f'id_{i:02d}'
+ material_id = f'id_{int(math.floor(i / 4)) + 1:02d}'
+ mainfile = f'test_content/subdir/test_entry_{i:02d}/mainfile.json'
kwargs = dict(
optimade=OptimadeEntry(nelements=2, elements=['H', 'O']),
)
diff --git a/tests/fixtures/group_uploads.py b/tests/fixtures/group_uploads.py
index 9b03ae9e69db4eab8df5d639c96cb4cd848a252c..b0d8109c89dfc6a64e179ae0e36233d505ff6331 100644
--- a/tests/fixtures/group_uploads.py
+++ b/tests/fixtures/group_uploads.py
@@ -10,7 +10,7 @@ Values:
- XgKLgMN: field X with groupKL and groupMN
"""
-from typing import Sequence
+from collections.abc import Sequence
import pytest
from nomad.utils.exampledata import ExampleData
diff --git a/tests/fixtures/infrastructure.py b/tests/fixtures/infrastructure.py
index 29d53ca8a7067d3eba653de3a2d0ddd3356c2566..d2840f2fd39afe12321cdcf26424d62f94438057 100644
--- a/tests/fixtures/infrastructure.py
+++ b/tests/fixtures/infrastructure.py
@@ -160,7 +160,7 @@ def clear_elastic_infra():
from elasticsearch_dsl import connections
connection = connections.create_connection(
- hosts=['%s:%d' % (config.elastic.host, config.elastic.port)]
+ hosts=[f'{config.elastic.host}:{config.elastic.port}']
)
for index in indices:
diff --git a/tests/metainfo/test_elasticsearch_extension.py b/tests/metainfo/test_elasticsearch_extension.py
index 0dd64730b87d688b761ca2beb02ab5ac2d8a03cb..d1e4b04da5ada696fbd9a5a10531dfa417c21b65 100644
--- a/tests/metainfo/test_elasticsearch_extension.py
+++ b/tests/metainfo/test_elasticsearch_extension.py
@@ -270,7 +270,7 @@ def assert_entry_indexed(entry: Entry):
)
-def assert_entries_indexed(entries: List[Entry]):
+def assert_entries_indexed(entries: list[Entry]):
"""
Assert that the given entries and only the given entries and their materials are
indexed.
diff --git a/tests/metainfo/test_quantities.py b/tests/metainfo/test_quantities.py
index feed120d44403ba91164ef537ccdcc832f3bd000..ad39b0e06313fce8e2dfffb4b6845d420cd79adb 100644
--- a/tests/metainfo/test_quantities.py
+++ b/tests/metainfo/test_quantities.py
@@ -233,7 +233,7 @@ def test_complex_number(unit, quantity_type, value, shape):
def assert_complex_equal():
result = section.quantity.m if unit else section.quantity
- if isinstance(value, (list, np.ndarray)):
+ if isinstance(value, list | np.ndarray):
for a, b in zip(result, value):
assert a == quantity_type(b)
elif not isinstance(value, pint.Quantity):
diff --git a/tests/metainfo/test_to_dict.py b/tests/metainfo/test_to_dict.py
index dc698f47ec90ecfa93bc09cdfd158b87f78f3034..1069001b29f14a2d5395dcd80cc2a4b2a559f687 100644
--- a/tests/metainfo/test_to_dict.py
+++ b/tests/metainfo/test_to_dict.py
@@ -347,7 +347,7 @@ def test_schema_definition_id(schema_yaml):
pkg.init_metainfo()
def check_dict(value):
- if not isinstance(value, (dict, list)):
+ if not isinstance(value, dict | list):
return value
if isinstance(value, list):
return [check_dict(v) for v in value]
diff --git a/tests/normalizing/conftest.py b/tests/normalizing/conftest.py
index 7a5596fa7bd662b1a0c84f0068b8277059325982..2ac967401754e234cab41f6c1d59001ad845bbb7 100644
--- a/tests/normalizing/conftest.py
+++ b/tests/normalizing/conftest.py
@@ -17,7 +17,8 @@
#
from collections import defaultdict
import numpy as np
-from typing import Any, Iterable, List, Union
+from typing import Any, List, Union
+from collections.abc import Iterable
import pytest
from ase import Atoms
import ase.build
@@ -277,8 +278,8 @@ def robust_compare(a: Any, b: Any) -> bool:
elif isinstance(a, np.ndarray) and isinstance(b, np.ndarray):
return np.array_equal(a, b)
# Check if both are non-iterables (e.g., int, float)
- elif not isinstance(a, (np.ndarray, list, tuple)) and not isinstance(
- b, (np.ndarray, list, tuple)
+ elif not isinstance(a, np.ndarray | list | tuple) and not isinstance(
+ b, np.ndarray | list | tuple
):
return a == b
# Fallback case if one is an iterable and the other is not
@@ -308,11 +309,11 @@ def check_template_active_orbitals(template: EntryArchive, **kwargs) -> dict[str
continue # skip quantities that were unasked for
# Assuming quantity_value is either a list or a single data object
if not isinstance(
- quantity_value, (list, np.ndarray)
+ quantity_value, list | np.ndarray
): # for multiple core holes
quantity_value = [quantity_value]
extracted_values = getattr(top.active_orbitals, quantity_name, [])
- if not isinstance(extracted_values, (list, np.ndarray)):
+ if not isinstance(extracted_values, list | np.ndarray):
extracted_values = [extracted_values]
# run over all reference values
if len(extracted_values) != len(quantity_value):
@@ -445,10 +446,10 @@ def get_section_system(atoms: Atoms):
def add_template_dos(
template: EntryArchive,
- fill: List = [[[0, 1], [2, 3]]],
- energy_reference_fermi: Union[float, None] = None,
- energy_reference_highest_occupied: Union[float, None] = None,
- energy_reference_lowest_unoccupied: Union[float, None] = None,
+ fill: list = [[[0, 1], [2, 3]]],
+ energy_reference_fermi: float | None = None,
+ energy_reference_highest_occupied: float | None = None,
+ energy_reference_lowest_unoccupied: float | None = None,
n_values: int = 101,
type: str = 'electronic',
) -> EntryArchive:
@@ -498,10 +499,10 @@ def add_template_dos(
def get_template_dos(
- fill: List = [[[0, 1], [2, 3]]],
- energy_reference_fermi: Union[float, None] = None,
- energy_reference_highest_occupied: Union[float, None] = None,
- energy_reference_lowest_unoccupied: Union[float, None] = None,
+ fill: list = [[[0, 1], [2, 3]]],
+ energy_reference_fermi: float | None = None,
+ energy_reference_highest_occupied: float | None = None,
+ energy_reference_lowest_unoccupied: float | None = None,
n_values: int = 101,
type: str = 'electronic',
normalize: bool = True,
@@ -523,7 +524,7 @@ def get_template_dos(
def add_template_band_structure(
template: EntryArchive,
- band_gaps: List = None,
+ band_gaps: list = None,
type: str = 'electronic',
has_references: bool = True,
has_reciprocal_cell: bool = True,
@@ -548,9 +549,9 @@ def add_template_band_structure(
bs = runschema.calculation.BandStructure()
scc.band_structure_electronic.append(bs)
n_spin_channels = len(band_gaps)
- fermi: List[float] = []
- highest: List[float] = []
- lowest: List[float] = []
+ fermi: list[float] = []
+ highest: list[float] = []
+ lowest: list[float] = []
for gap in band_gaps:
if gap is None:
highest.append(0)
@@ -573,10 +574,8 @@ def add_template_band_structure(
full_space = np.linspace(0, 2 * np.pi, 200)
k, m = divmod(len(full_space), n_segments)
space = list(
- (
- full_space[i * k + min(i, m) : (i + 1) * k + min(i + 1, m)]
- for i in range(n_segments)
- )
+ full_space[i * k + min(i, m) : (i + 1) * k + min(i + 1, m)]
+ for i in range(n_segments)
)
for i_seg in range(n_segments):
krange = space[i_seg]
@@ -610,7 +609,7 @@ def add_template_band_structure(
def get_template_band_structure(
- band_gaps: List = None,
+ band_gaps: list = None,
type: str = 'electronic',
has_references: bool = True,
has_reciprocal_cell: bool = True,
@@ -1675,12 +1674,12 @@ def create_system(
structural_type: str,
dimensionality: str,
building_block: str,
- elements: List[str],
+ elements: list[str],
formula_hill: str,
formula_reduced: str,
formula_anonymous: str,
system_relation: Relation,
- indices: List[List[int]] = None,
+ indices: list[list[int]] = None,
material_id: str = None,
atoms: ArchiveSection = None,
cell: Cell = None,
@@ -1766,7 +1765,7 @@ def rattle(atoms):
return atoms
-def single_cu_surface_topology() -> List[ResultSystem]:
+def single_cu_surface_topology() -> list[ResultSystem]:
"""Copper surface topology"""
conv_cell = conv_fcc('Cu')
surface = surf(conv_cell, (1, 0, 0))
@@ -1815,7 +1814,7 @@ def single_cu_surface_topology() -> List[ResultSystem]:
return [subsystem, convsystem]
-def single_cr_surface_topology() -> List[ResultSystem]:
+def single_cr_surface_topology() -> list[ResultSystem]:
"""Cr surface topology"""
conv_cell = conv_bcc('Cr')
surface = surf(conv_cell, (1, 0, 0))
@@ -1863,7 +1862,7 @@ def single_cr_surface_topology() -> List[ResultSystem]:
return [subsystem, convsystem]
-def single_ni_surface_topology() -> List[ResultSystem]:
+def single_ni_surface_topology() -> list[ResultSystem]:
"""Ni surface topology"""
conv_cell = conv_fcc('Ni')
surface = surf(conv_cell, (1, 0, 0))
@@ -1911,7 +1910,7 @@ def single_ni_surface_topology() -> List[ResultSystem]:
return [subsystem, convsystem]
-def stacked_cu_ni_surface_topology() -> List[ResultSystem]:
+def stacked_cu_ni_surface_topology() -> list[ResultSystem]:
topologies_cu = single_cu_surface_topology()
topologies_ni = single_ni_surface_topology()
@@ -1942,7 +1941,7 @@ def graphene() -> Atoms:
return system_c
-def graphene_topology() -> List[ResultSystem]:
+def graphene_topology() -> list[ResultSystem]:
"""Graphene topology"""
subsystem = create_system(
label='subsystem',
@@ -2020,7 +2019,7 @@ def boron_nitride() -> Atoms:
return bn_16
-def boron_nitride_topology() -> List[ResultSystem]:
+def boron_nitride_topology() -> list[ResultSystem]:
"""Boron nitride topology"""
subsystem = create_system(
label='subsystem',
@@ -2099,7 +2098,7 @@ def mos2() -> Atoms:
return stacked_2d_mos2_2
-def mos2_topology() -> List[ResultSystem]:
+def mos2_topology() -> list[ResultSystem]:
subsystem = create_system(
label='subsystem',
structural_type='2D',
diff --git a/tests/normalizing/test_topology.py b/tests/normalizing/test_topology.py
index 3d3983e7399cd91a33ae6e3248dbdf0de7a67df2..7dc058c0834204f2ffc892647a13aacf3c91596f 100644
--- a/tests/normalizing/test_topology.py
+++ b/tests/normalizing/test_topology.py
@@ -315,7 +315,7 @@ def test_topology_2d(surface, ref_topologies):
assert real_value.magnitude == pytest.approx(
ref_value.magnitude, rel=0.01, abs=0
)
- elif isinstance(ref_value, (np.ndarray, list)):
+ elif isinstance(ref_value, np.ndarray | list):
real_array = np.array(real_value)
ref_array = np.array(ref_value)
if ref_array.dtype == bool:
diff --git a/tests/parsing/test_archive_parser.py b/tests/parsing/test_archive_parser.py
index 1ac3b157431bbf02ef0bc4ea01ce2f36b7b982a3..b9666aa564265de69aeb7d5bb64f9dcada4f8245 100644
--- a/tests/parsing/test_archive_parser.py
+++ b/tests/parsing/test_archive_parser.py
@@ -44,7 +44,7 @@ def test_archive_parser(raw_files_function):
}
mainfile = os.path.join(config.fs.tmp, 'test_mainfile.archive.json')
- with open(mainfile, 'wt') as f:
+ with open(mainfile, 'w') as f:
json.dump(archive_data, f)
archive = EntryArchive()
diff --git a/tests/parsing/test_parsing.py b/tests/parsing/test_parsing.py
index 9a2047ac8f79ebf933763f82181cad5acb3af29c..adfbece7378ccc90039d204d6b9a42ca1e502ba5 100644
--- a/tests/parsing/test_parsing.py
+++ b/tests/parsing/test_parsing.py
@@ -160,7 +160,7 @@ def parse_file(parser_name_and_mainfile) -> EntryArchive:
return run_singular_parser(parser_name, mainfile)
-@pytest.fixture(params=parser_examples, ids=lambda spec: '%s-%s' % spec)
+@pytest.fixture(params=parser_examples, ids=lambda spec: '{}-{}'.format(*spec))
def parsed_example(request) -> EntryArchive:
parser_name, mainfile = request.param
result = run_singular_parser(parser_name, mainfile)
@@ -290,10 +290,7 @@ def test_match(
matched_mainfiles[mainfile] = parser
assert len(matched_mainfiles) >= num_output_files, ', '.join(
- [
- '%s: %s' % (parser.name, mainfile)
- for mainfile, parser in matched_mainfiles.items()
- ]
+ [f'{parser.name}: {mainfile}' for mainfile, parser in matched_mainfiles.items()]
)
diff --git a/tests/parsing/test_tabular.py b/tests/parsing/test_tabular.py
index 04af3aa4922ac146af0753c95f5620a80d240a48..c1554851b48f49e518c3955794a164ecaca2fe12 100644
--- a/tests/parsing/test_tabular.py
+++ b/tests/parsing/test_tabular.py
@@ -907,13 +907,13 @@ def get_files(schema=None, content=None):
"""
if schema:
schema_file = os.path.join(config.fs.tmp, 'my_schema.archive.yaml')
- with open(schema_file, 'wt') as f:
+ with open(schema_file, 'w') as f:
f.write(schema)
else:
schema_file = None
if content:
mainfile = os.path.join(config.fs.tmp, 'test.my_schema.archive.csv')
- with open(mainfile, 'wt') as f:
+ with open(mainfile, 'w') as f:
f.write(content)
else:
mainfile = None
diff --git a/tests/processing/test_base.py b/tests/processing/test_base.py
index d2704e91fbb8b33f1eff240e9b99faed575788ea..3a3384ddc1f2c450ac1f5664c89f1ff566febc34 100644
--- a/tests/processing/test_base.py
+++ b/tests/processing/test_base.py
@@ -36,7 +36,7 @@ random.seed(0)
fail = 'FAIL'
-events: List[str] = []
+events: list[str] = []
@pytest.fixture(scope='function')
@@ -54,7 +54,7 @@ def assert_proc(
assert not proc.process_running
-def assert_events(expected_events: List[Union[str, List[str]]]):
+def assert_events(expected_events: list[str | list[str]]):
ind = 0
for expected in expected_events:
if isinstance(expected, str):
@@ -205,8 +205,8 @@ class ParentProc(Proc):
fail_spawn: bool = False,
suffix: str = '',
delay=0.1,
- child_args: List[Any] = [],
- join_args: List[Any] = [],
+ child_args: list[Any] = [],
+ join_args: list[Any] = [],
):
"""
Arguments:
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index 105f56b92e6f25f29de2e807428583b017232efa..121dc06fbfd1613b5cc187bd56a258617973d009 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -16,7 +16,8 @@
# limitations under the License.
#
-from typing import Generator, Tuple, Dict
+from typing import Tuple, Dict
+from collections.abc import Generator
import pytest
import os.path
import re
@@ -79,7 +80,7 @@ class TestBatch(EntryData):
)
def normalize(self, archive, logger):
- super(TestBatch, self).normalize(archive, logger)
+ super().normalize(archive, logger)
if not self.n_samples:
return
sample_refs = []
@@ -139,14 +140,14 @@ def mongo_forall(mongo_function):
@pytest.fixture
def uploaded_id_with_warning(
raw_files_function,
-) -> Generator[Tuple[str, str], None, None]:
+) -> Generator[tuple[str, str], None, None]:
example_file = 'tests/data/proc/examples_with_warning_template.zip'
example_upload_id = os.path.basename(example_file).replace('.zip', '')
yield example_upload_id, example_file
-def run_processing(uploaded: Tuple[str, str], main_author, **kwargs) -> Upload:
+def run_processing(uploaded: tuple[str, str], main_author, **kwargs) -> Upload:
uploaded_id, uploaded_path = uploaded
upload = Upload.create(upload_id=uploaded_id, main_author=main_author, **kwargs)
assert upload.process_status == ProcessStatus.READY
@@ -349,7 +350,7 @@ def test_republish(
@pytest.mark.timeout(config.tests.default_timeout)
def test_publish_failed(
- non_empty_uploaded: Tuple[str, str],
+ non_empty_uploaded: tuple[str, str],
internal_example_user_metadata,
user1,
monkeypatch,
@@ -869,9 +870,7 @@ def mock_failure(cls, function_name, monkeypatch):
mock.__name__ = function_name
- monkeypatch.setattr(
- 'nomad.processing.data.%s.%s' % (cls.__name__, function_name), mock
- )
+ monkeypatch.setattr(f'nomad.processing.data.{cls.__name__}.{function_name}', mock)
@pytest.mark.parametrize(
@@ -974,7 +973,7 @@ def test_parent_child_parser(proc_infra, user1, tmp):
mainfile: str,
archive: EntryArchive,
logger=None,
- child_archives: Dict[str, EntryArchive] = None,
+ child_archives: dict[str, EntryArchive] = None,
):
archive.metadata.comment = 'parent'
for mainfile_key, child_archive in child_archives.items():
diff --git a/tests/test_client.py b/tests/test_client.py
index 18e07809c0ed77a2d157fbf727f96704ba96f609..75956e8a604f67efc7dbdb7fdb0e54e2725a3037 100644
--- a/tests/test_client.py
+++ b/tests/test_client.py
@@ -42,7 +42,7 @@ from tests.processing import test_data as test_processing
def assert_results(
- results: List[MSection], sub_section_defs: List[SubSection] = None, total=1
+ results: list[MSection], sub_section_defs: list[SubSection] = None, total=1
):
assert len(results) == total
for result in results:
@@ -62,11 +62,11 @@ def assert_results(
@pytest.fixture(scope='function')
-def many_uploads(non_empty_uploaded: Tuple[str, str], user1: User, proc_infra):
+def many_uploads(non_empty_uploaded: tuple[str, str], user1: User, proc_infra):
_, upload_file = non_empty_uploaded
for index in range(0, 4):
upload = test_processing.run_processing(
- ('test_upload_%d' % index, upload_file), user1
+ (f'test_upload_{index}', upload_file), user1
)
upload.publish_upload() # pylint: disable=no-member
try:
@@ -166,9 +166,9 @@ def load_example(path: str):
expected_path = os.path.join(
current_dir, 'examples', 'data', 'json_transformer', 'expected.json'
)
- with open(rules_path, 'r') as file:
+ with open(rules_path) as file:
rules_data = json.load(file)
- with open(expected_path, 'r') as f:
+ with open(expected_path) as f:
expected = json.load(f)
transformation_dict = {}
diff --git a/tests/test_config.py b/tests/test_config.py
index b76767d798928bf0a31fd61f8abdc8cf528c8d20..7cc0f5070576d2c59b4fed4bd1acf8cebadb24e2 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -332,7 +332,7 @@ def test_parser_plugins():
parsers = [
entry_point
for entry_point in config.plugins.entry_points.options.values()
- if isinstance(entry_point, (Parser, ParserEntryPoint))
+ if isinstance(entry_point, Parser | ParserEntryPoint)
]
assert len(parsers) == 72
diff --git a/tests/test_files.py b/tests/test_files.py
index 07c9ecdc3322e5156a8d63dbc19b86cf3d6cf70b..77fc88fcf47e91ed4585cc9cc6df94a769059e7f 100644
--- a/tests/test_files.py
+++ b/tests/test_files.py
@@ -16,7 +16,8 @@
# limitations under the License.
#
-from typing import Generator, Any, Dict, Tuple, Iterable, List, Union
+from typing import Any, Dict, Tuple, List, Union
+from collections.abc import Generator, Iterable
from datetime import datetime
import os
import os.path
@@ -40,10 +41,10 @@ from nomad.files import StagingUploadFiles, PublicUploadFiles, UploadFiles
from nomad.processing import Upload
-EntryWithFiles = Tuple[datamodel.EntryMetadata, str]
-UploadWithFiles = Tuple[str, List[datamodel.EntryMetadata], UploadFiles]
-StagingUploadWithFiles = Tuple[str, List[datamodel.EntryMetadata], StagingUploadFiles]
-PublicUploadWithFiles = Tuple[str, List[datamodel.EntryMetadata], PublicUploadFiles]
+EntryWithFiles = tuple[datamodel.EntryMetadata, str]
+UploadWithFiles = tuple[str, list[datamodel.EntryMetadata], UploadFiles]
+StagingUploadWithFiles = tuple[str, list[datamodel.EntryMetadata], StagingUploadFiles]
+PublicUploadWithFiles = tuple[str, list[datamodel.EntryMetadata], PublicUploadFiles]
# example_file uses an artificial parser for faster test execution, can also be
# changed to examples_vasp.zip for using vasp parser
@@ -129,7 +130,7 @@ class TestObjects:
assert os.path.exists(os.path.dirname(file.os_path)) == create
-example_entry: Dict[str, Any] = {
+example_entry: dict[str, Any] = {
'entry_id': '0',
'mainfile': 'examples_template/template.json',
'data': 'value',
@@ -145,7 +146,7 @@ def generate_example_entry(
example_entry = datamodel.EntryMetadata(domain='dft', entry_id=str(entry_id))
if with_mainfile_prefix:
- mainfile = '%d.template.json' % entry_id
+ mainfile = f'{entry_id}.template.json'
else:
mainfile = 'template.json'
@@ -162,7 +163,7 @@ def generate_example_entry(
filename = os.path.basename(filepath)
arcname = filename
if arcname == 'template.json' and with_mainfile_prefix:
- arcname = '%d.template.json' % entry_id
+ arcname = f'{entry_id}.template.json'
if subdirectory is not None:
arcname = os.path.join(subdirectory, arcname)
@@ -685,8 +686,8 @@ def assert_upload_files(
def create_test_upload_files(
- upload_id: Union[str, None],
- archives: Union[List[datamodel.EntryArchive], None] = None,
+ upload_id: str | None,
+ archives: list[datamodel.EntryArchive] | None = None,
published: bool = True,
embargo_length: int = 0,
raw_files: str = None,
@@ -790,8 +791,8 @@ def test_test_upload_files(raw_files_infra):
for index in range(0, 3):
archive = datamodel.EntryArchive()
metadata = archive.m_create(datamodel.EntryMetadata)
- metadata.entry_id = 'example_entry_id_%d' % index
- metadata.mainfile = 'test/test/entry_%d/mainfile_%d.json' % (index, index)
+ metadata.entry_id = f'example_entry_id_{index}'
+ metadata.mainfile = f'test/test/entry_{index}/mainfile_{index}.json'
archives.append(archive)
upload_files = create_test_upload_files(upload_id, archives, embargo_length=0)
diff --git a/tests/test_logtransfer.py b/tests/test_logtransfer.py
index 1cb171b058722fd1c12a64e5f9582fd393222461..b67262fbeedf50b7db7a447f8e0e58da2374c5fb 100644
--- a/tests/test_logtransfer.py
+++ b/tests/test_logtransfer.py
@@ -31,7 +31,7 @@ def test_logtransfer_handler(log_handler):
test_logger.info('test event', data='test data')
assert os.path.exists(log_handler.baseFilename)
- with open(log_handler.baseFilename, 'r') as f:
+ with open(log_handler.baseFilename) as f:
logs = f.readlines()
assert len(logs) == 1
@@ -68,7 +68,7 @@ def test_transfer_logs(log_handler, monkeypatch, api_v1, central_logstash_mock,
test_logger.info('test event', data='test data')
assert os.path.exists(log_handler.baseFilename)
- with open(log_handler.baseFilename, 'r') as f:
+ with open(log_handler.baseFilename) as f:
logs = f.readlines()
assert len(logs) == size
diff --git a/tests/test_mkdocs.py b/tests/test_mkdocs.py
index 6b6ca47a1c3538a4d65c47ecb5bdf0e1dc98eba6..713c087b6e73458628e1a5105f6a2ef5778e716d 100644
--- a/tests/test_mkdocs.py
+++ b/tests/test_mkdocs.py
@@ -19,7 +19,7 @@
from enum import Enum
import pytest
from typing import Union, List, Dict, Optional
-from typing_extensions import Literal, Annotated # type: ignore
+from typing import Literal, Annotated # type: ignore
from pydantic import BaseModel, Field
from nomad.config.models.ui import WidgetHistogram, WidgetTerms
from nomad.mkdocs import (
@@ -54,26 +54,26 @@ class MyIntEnum(int, Enum):
),
pytest.param(Enum, 'Enum', {Enum}, id='class'),
pytest.param(
- Optional[WidgetHistogram],
+ Optional[WidgetHistogram], # noqa
'Optional[WidgetHistogram, NoneType]',
{WidgetHistogram, Union, type(None)},
id='optional-ignored',
),
pytest.param(
- Union[str, WidgetHistogram],
+ Union[str, WidgetHistogram], # noqa
'Union[str, WidgetHistogram]',
{Union, str, WidgetHistogram},
id='union',
),
pytest.param(
- List[Union[str, WidgetHistogram]],
- 'List[Union[str, WidgetHistogram]]',
+ list[Union[str, WidgetHistogram]], # noqa
+ 'list[Union[str, WidgetHistogram]]',
{list, Union, str, WidgetHistogram},
id='list-with-union',
),
pytest.param(
- Dict[str, WidgetHistogram],
- 'Dict[str, WidgetHistogram]',
+ dict[str, WidgetHistogram],
+ 'dict[str, WidgetHistogram]',
{dict, str, WidgetHistogram},
id='dict',
),
@@ -82,12 +82,12 @@ class MyIntEnum(int, Enum):
pytest.param(MyStrEnum, 'str', {MyStrEnum}, id='enum-string'),
pytest.param(MyIntEnum, 'int', {MyIntEnum}, id='enum-int'),
pytest.param(
- List[
+ list[
Annotated[
- Union[WidgetTerms, WidgetHistogram], Field(discriminator='type')
+ Union[WidgetTerms, WidgetHistogram], Field(discriminator='type') # noqa
]
], # type: ignore
- 'List[Union[WidgetTerms, WidgetHistogram]]',
+ 'list[Union[WidgetTerms, WidgetHistogram]]',
{list, Union, WidgetTerms, WidgetHistogram},
id='annotated-ignored',
),
diff --git a/tests/test_search.py b/tests/test_search.py
index 6f033aff28b7548b2a5045431197e30bb2d1640e..06dd47db9e4621ff0bb0354be80d0c38ad692607 100644
--- a/tests/test_search.py
+++ b/tests/test_search.py
@@ -18,7 +18,8 @@
import json
from datetime import datetime
-from typing import Any, Dict, Iterable, List, Sequence, Union
+from typing import Any, Dict, List, Union
+from collections.abc import Iterable, Sequence
import pytest
@@ -59,8 +60,8 @@ def split(path):
def assert_search_upload(
- entries: Union[int, Iterable] = -1,
- additional_keys: List[str] = [],
+ entries: int | Iterable = -1,
+ additional_keys: list[str] = [],
upload_id: str = None,
**kwargs,
):
@@ -73,7 +74,7 @@ def assert_search_upload(
keys = ['entry_id', 'upload_id', 'mainfile']
refresh()
- body: Dict[str, Any] = {}
+ body: dict[str, Any] = {}
body.update(size=10)
if upload_id is not None:
body['query'] = dict(match=dict(upload_id=upload_id))
diff --git a/tests/utils.py b/tests/utils.py
index 4ae5c223df4abd17cb377c0825046a1012656c49..cfd95f936b141015af038242dcb117dbab630fd3 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -66,18 +66,14 @@ def assert_at_least(source, target):
the same information in target. Additional information in target is ignored.
"""
for key, value in source.items():
- assert key in target, '%s with value %s in %s is not in %s' % (
- key,
- source[key],
- source,
- target,
+ assert key in target, (
+ f'{key} with value {source[key]} in {source} is not in {target}'
)
if isinstance(value, dict):
assert_at_least(value, target[key])
else:
assert value == target[key], (
- '%s with value %s in %s is not equal the target value %s in %s'
- % (key, source[key], source, target[key], target)
+ f'{key} with value {source[key]} in {source} is not equal the target value {target[key]} in {target}'
)
@@ -94,7 +90,7 @@ def assert_url_query_args(url: str, **kwargs):
assert query_dict[k][0] == str(v)
-def build_url(base_url: str, query_args: Dict[str, Any]) -> str:
+def build_url(base_url: str, query_args: dict[str, Any]) -> str:
"""
Takes a base_url and a dictionary, and combines to a url with query arguments.
Arguments with value None are ignored.
@@ -106,7 +102,7 @@ def build_url(base_url: str, query_args: Dict[str, Any]) -> str:
return base_url + '?' + urllib.parse.urlencode(query_args_clean, doseq=True)
-def set_upload_entry_metadata(upload, metadata: Dict[str, Any]):
+def set_upload_entry_metadata(upload, metadata: dict[str, Any]):
"""
Sets the provided metadata values on all entries of the given upload.
"""
@@ -119,11 +115,11 @@ def set_upload_entry_metadata(upload, metadata: Dict[str, Any]):
def create_template_upload_file(
tmp,
- mainfiles: Union[str, List[str]] = None,
+ mainfiles: str | list[str] = None,
auxfiles: int = 4,
directory: str = 'examples_template',
name: str = 'examples_template.zip',
- more_files: Union[str, List[str]] = None,
+ more_files: str | list[str] = None,
):
"""
Creates a temporary upload.zip file based on template.json (for the artificial test