diff --git a/nomad/app/dcat/common.py b/nomad/app/dcat/common.py
index 90e6fc4876220a103f264a83c77806d0d34e9391..3d782dad8884a344cad2a4dbe6e66af47bc68e4b 100644
--- a/nomad/app/dcat/common.py
+++ b/nomad/app/dcat/common.py
@@ -16,14 +16,14 @@
# limitations under the License.
#
+from fastapi import Response, Query, Header
import urllib.parse
-from enum import Enum
-
-from fastapi import Header, Query, Response
from rdflib import Graph
+from enum import Enum
from nomad.config import config
+
root_path = f'{config.services.api_base_path}/dcat'
base_url = config.api_url(api='dcat')
diff --git a/nomad/app/dcat/main.py b/nomad/app/dcat/main.py
index 0fbfa0d4f6d193a255273a904c3afdca47f25769..49d4d68d50fcfb197fb6d2afb15718fcf9414ce4 100644
--- a/nomad/app/dcat/main.py
+++ b/nomad/app/dcat/main.py
@@ -16,11 +16,10 @@
# limitations under the License.
#
-import traceback
-
-from fastapi import FastAPI, Request, status
+from fastapi import FastAPI, status, Request
from fastapi.middleware.cors import CORSMiddleware
from fastapi.responses import JSONResponse, RedirectResponse
+import traceback
from nomad import utils
from nomad.config import config
@@ -28,6 +27,7 @@ from nomad.config import config
from .common import root_path
from .routers import dcat
+
logger = utils.get_logger(__name__)
diff --git a/nomad/app/dcat/mapping.py b/nomad/app/dcat/mapping.py
index c15ec0a87693b66ae4be9c291f64ff839517dc42..d22399a7628fba69adf3d0309b1b1cf1f63072dc 100644
--- a/nomad/app/dcat/mapping.py
+++ b/nomad/app/dcat/mapping.py
@@ -16,15 +16,15 @@
# limitations under the License.
#
-from rdflib import RDF, BNode, Graph, Literal, URIRef
-from rdflib.namespace import DCAT, FOAF, RDF, Namespace
-from rdflib.namespace import DCTERMS as DCT
+from rdflib import Graph, Literal, RDF, URIRef, BNode
+from rdflib.namespace import Namespace, DCAT, DCTERMS as DCT, FOAF, RDF
from nomad.config import config
from nomad.datamodel import User
from .common import url
+
VCARD = Namespace('http://www.w3.org/2006/vcard/ns#')
HYDRA = Namespace('http://www.w3.org/ns/hydra/core#')
diff --git a/nomad/app/dcat/routers/dcat.py b/nomad/app/dcat/routers/dcat.py
index 0aa5b6b6ece36af188994b1a6ac63f91d0b5ffb6..99a2f0256a77339adb8efbef6ef2fcaafbdf2196 100644
--- a/nomad/app/dcat/routers/dcat.py
+++ b/nomad/app/dcat/routers/dcat.py
@@ -16,17 +16,17 @@
# limitations under the License.
#
-from datetime import date, datetime
from enum import Enum
+from fastapi import APIRouter, Query, Path, HTTPException, status, Depends
+from datetime import datetime, date
from elasticsearch_dsl import Q
-from fastapi import APIRouter, Depends, HTTPException, Path, Query, status
from nomad import utils
-from nomad.app.v1.models import HTTPExceptionModel, MetadataPagination
-from nomad.app.v1.utils import create_responses
-from nomad.search import search
from nomad.utils import strip
+from nomad.search import search
+from nomad.app.v1.models import MetadataPagination, HTTPExceptionModel
+from nomad.app.v1.utils import create_responses
from ..common import rdf_response
from ..mapping import Mapping
diff --git a/nomad/app/h5grove_app.py b/nomad/app/h5grove_app.py
index 8e01225ff41914e31848e83f5e3d250ef4300f13..d409e01ee9ff2493a02a777427773bcc33a81d38 100644
--- a/nomad/app/h5grove_app.py
+++ b/nomad/app/h5grove_app.py
@@ -17,24 +17,23 @@
#
from __future__ import annotations
-import re
+from fastapi import FastAPI, status, Request, Depends
+from fastapi.middleware.cors import CORSMiddleware
+from fastapi.responses import JSONResponse
import traceback
+import re
import urllib.parse
+import h5py
+from typing import Any, IO
from collections.abc import Callable
-from typing import IO, Any
-import h5py
-from fastapi import Depends, FastAPI, Request, status
-from fastapi.middleware.cors import CORSMiddleware
-from fastapi.responses import JSONResponse
-from h5grove import fastapi_utils as h5grove_router
-from h5grove import utils as h5grove_utils
+from h5grove import fastapi_utils as h5grove_router, utils as h5grove_utils
from nomad import utils
+from nomad.files import UploadFiles, PublicUploadFiles
from nomad.app.v1.models import User
from nomad.app.v1.routers.auth import create_user_dependency
from nomad.app.v1.routers.uploads import get_upload_with_read_access
-from nomad.files import PublicUploadFiles, UploadFiles
logger = utils.get_logger(__name__)
@@ -44,9 +43,8 @@ def open_zipped_h5_file(
create_error: Callable[[int, str], Exception],
h5py_options: dict[str, Any] = {},
) -> h5py.File:
- import io
import re
-
+ import io
from nomad import files
"""
diff --git a/nomad/app/main.py b/nomad/app/main.py
index 29829f997ace12d293728e89518a0cb1c668850b..2168e5fd965f7e7bd939d5779e7f707dd2cf7c6f 100644
--- a/nomad/app/main.py
+++ b/nomad/app/main.py
@@ -23,17 +23,16 @@ from fastapi import FastAPI, Response, status
from fastapi.exception_handlers import (
http_exception_handler as default_http_exception_handler,
)
-from fastapi.responses import HTMLResponse, JSONResponse
from starlette.exceptions import HTTPException as StarletteHTTPException
+from fastapi.responses import HTMLResponse, JSONResponse
from starlette.middleware.base import BaseHTTPMiddleware
from nomad import infrastructure
from nomad.config import config
from nomad.config.models.plugins import APIEntryPoint
-from .static import GuiFiles
-from .static import app as static_files_app
from .v1.main import app as v1_app
+from .static import app as static_files_app, GuiFiles
class OasisAuthenticationMiddleware(BaseHTTPMiddleware):
@@ -165,10 +164,11 @@ async def http_exception_handler(request, exc):
@app.on_event('startup')
async def startup_event():
+ from nomad.cli.dev import get_gui_artifacts_js
+ from nomad.cli.dev import get_gui_config
+ from nomad.parsing.parsers import import_all_parsers
from nomad import infrastructure
- from nomad.cli.dev import get_gui_artifacts_js, get_gui_config
from nomad.metainfo.elasticsearch_extension import entry_type
- from nomad.parsing.parsers import import_all_parsers
import_all_parsers()
diff --git a/nomad/app/optimade/common.py b/nomad/app/optimade/common.py
index 45824ef06bce9789286da9887d30f52151adbc1d..fb0df1cc8513dbda9fea34702348aac99e47d50a 100644
--- a/nomad/app/optimade/common.py
+++ b/nomad/app/optimade/common.py
@@ -19,8 +19,9 @@
from typing import cast
from nomad.metainfo.data_type import Datatype, to_optimade_type
-from nomad.metainfo.elasticsearch_extension import SearchQuantity, entry_type
from nomad.metainfo.metainfo import Quantity, Reference
+from nomad.metainfo.elasticsearch_extension import SearchQuantity, entry_type
+
_provider_specific_fields: dict[str, SearchQuantity] = None
diff --git a/nomad/app/optimade/elasticsearch.py b/nomad/app/optimade/elasticsearch.py
index d966f7d7ccbba75f9e8c7b8c47d14695b43494a0..d90607b3398c06e38654d7fd207da9c8c4c3a292 100644
--- a/nomad/app/optimade/elasticsearch.py
+++ b/nomad/app/optimade/elasticsearch.py
@@ -1,23 +1,23 @@
from typing import Any
-
from elasticsearch_dsl import Q
+
from optimade.filterparser import LarkParser
-from optimade.models import StructureResource
from optimade.server.entry_collections import EntryCollection
from optimade.server.exceptions import BadRequest
from optimade.server.mappers import StructureMapper
from optimade.server.mappers.entries import classproperty
+from optimade.models import StructureResource
-from nomad import datamodel, files, utils
-from nomad.app.v1.models import MetadataPagination, MetadataRequired
+from nomad.units import ureg
from nomad.atomutils import Formula
-from nomad.config import config
from nomad.search import search
-from nomad.units import ureg
+from nomad.app.v1.models import MetadataPagination, MetadataRequired
+from nomad.config import config
+from nomad import datamodel, files, utils
-from ...archive import to_json
-from .common import provider_specific_fields
from .filterparser import _get_transformer as get_transformer
+from .common import provider_specific_fields
+from ...archive import to_json
logger = utils.get_logger(__name__)
diff --git a/nomad/app/optimade/filterparser.py b/nomad/app/optimade/filterparser.py
index 11caebaf9e9625d820b365292fc1b8ddaeb1a448..6ff5b0e26abc54535c0acc9d4ba58625be5ce587 100644
--- a/nomad/app/optimade/filterparser.py
+++ b/nomad/app/optimade/filterparser.py
@@ -16,16 +16,18 @@
# limitations under the License.
#
-from cachetools import cached
from elasticsearch_dsl import Q
+from cachetools import cached
+
from optimade.filterparser import LarkParser
-from optimade.filtertransformers.elasticsearch import ElasticsearchQuantity as Quantity
from optimade.filtertransformers.elasticsearch import (
+ ElasticsearchQuantity as Quantity,
ElasticTransformer as OPTElasticTransformer,
)
from .common import provider_specific_fields
+
_parser = LarkParser(version=(1, 0, 1))
diff --git a/nomad/app/resources/common.py b/nomad/app/resources/common.py
index 96a0e9c977d4e6b25fb515c2b45d029f5563b760..f0cedfb72be356e1a06565929ef2d59554392ec2 100644
--- a/nomad/app/resources/common.py
+++ b/nomad/app/resources/common.py
@@ -18,5 +18,6 @@
from nomad.config import config
+
root_path = f'{config.services.api_base_path}/resources'
base_url = config.api_url(api='resources')
diff --git a/nomad/app/resources/main.py b/nomad/app/resources/main.py
index ab6e17d11d972638ef073fb55525c9156328d475..e5c4b6992de2ffdd2ea96610a917f511023567f9 100644
--- a/nomad/app/resources/main.py
+++ b/nomad/app/resources/main.py
@@ -16,18 +16,18 @@
# limitations under the License.
#
-import traceback
-
-from celery.signals import worker_process_init
-from fastapi import FastAPI, Request, status
+from fastapi import FastAPI, status, Request
from fastapi.middleware.cors import CORSMiddleware
from fastapi.responses import JSONResponse
+import traceback
+from celery.signals import worker_process_init
from nomad import utils
from nomad.config import config
from .routers import resources
+
logger = utils.get_logger(__name__)
mongo_client_resources = None
diff --git a/nomad/app/resources/routers/resources.py b/nomad/app/resources/routers/resources.py
index 45f4f9559bd3e8a20bc373aca798d13b4d6eb6d4..242e82950d2af0bfe5507004d665ce1f1e8e093e 100644
--- a/nomad/app/resources/routers/resources.py
+++ b/nomad/app/resources/routers/resources.py
@@ -16,36 +16,35 @@
# limitations under the License.
#
-import asyncio
-import io
-import os
import re
-from datetime import datetime
+import os
+import io
+import bs4
+import asyncio
+import httpx
from enum import Enum
+from fastapi import APIRouter, Query as FastApiQuery
+from pydantic import BaseModel, Field
from typing import Any
-
+from datetime import datetime
import ase.io
-import bs4
-import httpx
-from asgiref.sync import async_to_sync
-from fastapi import APIRouter
-from fastapi import Query as FastApiQuery
from mongoengine import (
- BooleanField,
- DateTimeField,
Document,
+ StringField,
+ DateTimeField,
IntField,
ListField,
- StringField,
+ BooleanField,
)
from mongoengine.queryset.visitor import Q
-from pydantic import BaseModel, Field
+from asgiref.sync import async_to_sync
from nomad import utils
-from nomad.atomutils import Formula
from nomad.config import config
+from nomad.atomutils import Formula
from nomad.processing.base import app
+
logger = utils.get_logger(__name__)
router = APIRouter()
diff --git a/nomad/app/v1/main.py b/nomad/app/v1/main.py
index af4def92478e5e50ecd01f38c3e3fc652838063c..2c3e7b66062d037e8f0d3f26283ec3515d423317 100644
--- a/nomad/app/v1/main.py
+++ b/nomad/app/v1/main.py
@@ -18,9 +18,9 @@
import traceback
-from fastapi import FastAPI, Request, status
+from fastapi import FastAPI, status, Request
from fastapi.middleware.cors import CORSMiddleware
-from fastapi.responses import JSONResponse, ORJSONResponse, RedirectResponse
+from fastapi.responses import JSONResponse, RedirectResponse, ORJSONResponse
from pyinstrument import Profiler
from starlette.middleware import Middleware
from starlette.middleware.base import BaseHTTPMiddleware
@@ -29,23 +29,22 @@ from starlette.types import ASGIApp, Receive, Scope, Send
from nomad import utils
from nomad.config import config
-
from .common import root_path
from .routers import (
- auth,
- datasets,
+ users,
entries,
- federation,
- graph,
- groups,
- info,
materials,
+ auth,
+ info,
+ datasets,
+ uploads,
+ suggestions,
metainfo,
north,
- suggestions,
systems,
- uploads,
- users,
+ federation,
+ graph,
+ groups,
)
logger = utils.get_logger(__name__)
diff --git a/nomad/app/v1/models/graph/graph_models.py b/nomad/app/v1/models/graph/graph_models.py
index dff9d7d42bdf3fc109d4d23e1a32c92613bccf00..480221c93f4a6393027888b2a89eafc47925717c 100644
--- a/nomad/app/v1/models/graph/graph_models.py
+++ b/nomad/app/v1/models/graph/graph_models.py
@@ -17,37 +17,35 @@
#
from __future__ import annotations
-
from typing import Any, Literal
+from pydantic import BaseModel, ConfigDict, Field, Extra
-from pydantic import BaseModel, ConfigDict, Extra, Field
+from ..groups import UserGroup, UserGroupPagination, UserGroupQuery
-from nomad.app.v1.models.graph.utils import (
- generate_request_model,
- generate_response_model,
- mapped,
+from nomad.graph.model import (
+ RequestConfig,
+ DatasetQuery,
+ MetainfoQuery,
+ MetainfoPagination,
)
+from nomad.metainfo.pydantic_extension import PydanticModel
+from nomad.datamodel.data import User as UserModel
from nomad.app.v1.models.models import Metadata, MetadataResponse
-from nomad.app.v1.routers.datasets import Dataset as DatasetV1
-from nomad.app.v1.routers.datasets import DatasetPagination
+from nomad.app.v1.routers.datasets import Dataset as DatasetV1, DatasetPagination
from nomad.app.v1.routers.uploads import (
- EntryProcData,
- EntryProcDataPagination,
- PaginationResponse,
UploadProcData,
UploadProcDataPagination,
UploadProcDataQuery,
+ PaginationResponse,
+ EntryProcData,
+ EntryProcDataPagination,
)
-from nomad.datamodel.data import User as UserModel
-from nomad.graph.model import (
- DatasetQuery,
- MetainfoPagination,
- MetainfoQuery,
- RequestConfig,
-)
-from nomad.metainfo.pydantic_extension import PydanticModel
-from ..groups import UserGroup, UserGroupPagination, UserGroupQuery
+from nomad.app.v1.models.graph.utils import (
+ generate_request_model,
+ generate_response_model,
+ mapped,
+)
class Error(BaseModel):
diff --git a/nomad/app/v1/models/graph/utils.py b/nomad/app/v1/models/graph/utils.py
index 6c871c55478ef09754f5998ac8aa97686b1e645f..6d420a6e1002c51bca54bd55ccbb815ddac4c34d 100644
--- a/nomad/app/v1/models/graph/utils.py
+++ b/nomad/app/v1/models/graph/utils.py
@@ -17,33 +17,32 @@
#
from __future__ import annotations
-
-import sys
-from collections.abc import Callable
-from datetime import datetime
-from types import UnionType
from typing import (
- Any,
- ForwardRef,
- Literal,
Optional,
+ Literal,
Union,
- cast,
- get_args,
- get_origin,
+ Any,
+ ForwardRef,
get_type_hints,
+ get_origin,
+ get_args,
+ cast,
)
-
+from collections.abc import Callable
+from types import UnionType
+from datetime import datetime
from pydantic import (
BaseModel,
ConfigDict,
- Field,
TypeAdapter,
- ValidationError,
create_model,
+ Field,
model_validator,
+ ValidationError,
)
from pydantic.config import ConfigDict as BaseConfigDict
+import sys
+
ref_prefix = '#/components/schemas'
request_suffix = 'Request'
diff --git a/nomad/app/v1/models/groups.py b/nomad/app/v1/models/groups.py
index dbdae164fba850f19314e7cb855e8312bf9d10d3..3a83a81818de492b89788d5c500a011d2895981d 100644
--- a/nomad/app/v1/models/groups.py
+++ b/nomad/app/v1/models/groups.py
@@ -1,4 +1,9 @@
-from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic import (
+ BaseModel,
+ ConfigDict,
+ Field,
+ field_validator,
+)
from pydantic_core import PydanticCustomError
from .pagination import Direction, Pagination, PaginationResponse
diff --git a/nomad/app/v1/models/models.py b/nomad/app/v1/models/models.py
index 7dab17d0f8e71bbe934b4646085151a71b885b2e..32841a883274651dca779aae60bfe2c262b7e397 100644
--- a/nomad/app/v1/models/models.py
+++ b/nomad/app/v1/models/models.py
@@ -16,25 +16,25 @@
# limitations under the License.
#
import datetime
+from enum import Enum
import fnmatch
import json
import re
+from typing import Any
from collections.abc import Mapping
-from enum import Enum
-from typing import Annotated, Any
from fastapi import Body, HTTPException, Request
from fastapi import Query as FastApiQuery
from pydantic import ( # noqa: F401
- BaseModel,
+ field_validator,
+ model_validator,
+ StringConstraints,
ConfigDict,
+ BaseModel,
Field,
StrictBool,
StrictFloat,
StrictInt,
- StringConstraints,
- field_validator,
- model_validator,
)
from pydantic.main import create_model
from pydantic_core import PydanticCustomError
@@ -49,6 +49,8 @@ from nomad.metainfo.elasticsearch_extension import (
from nomad.utils import strip
from .pagination import Pagination, PaginationResponse
+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
diff --git a/nomad/app/v1/models/pagination.py b/nomad/app/v1/models/pagination.py
index c3fba17369172950363d5af640d5c8390cadb97c..6cb92b5c54ba81f45d720f5afffe2914fe2d18cb 100644
--- a/nomad/app/v1/models/pagination.py
+++ b/nomad/app/v1/models/pagination.py
@@ -1,7 +1,12 @@
from enum import Enum
-
from fastapi import HTTPException, Request
-from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
+from pydantic import (
+ BaseModel,
+ ConfigDict,
+ Field,
+ field_validator,
+ model_validator,
+)
from pydantic_core import PydanticCustomError
from nomad.app.v1.utils import update_url_query_arguments
diff --git a/nomad/app/v1/routers/auth.py b/nomad/app/v1/routers/auth.py
index 01740cda39d9ec2026a2d50fd7694631716c9052..d64981f471a270e93d84e243b94e695cc198ae68 100644
--- a/nomad/app/v1/routers/auth.py
+++ b/nomad/app/v1/routers/auth.py
@@ -16,29 +16,34 @@
# limitations under the License.
#
-import datetime
-import hashlib
import hmac
+import hashlib
import uuid
-from collections.abc import Callable
+import requests
from enum import Enum
-from functools import wraps
-from inspect import Parameter, signature
from typing import cast
-
-import jwt
-import requests
-from fastapi import APIRouter, Depends, HTTPException, Request, status
-from fastapi import Query as FastApiQuery
+from collections.abc import Callable
+from inspect import Parameter, signature
+from functools import wraps
+from fastapi import (
+ APIRouter,
+ Depends,
+ Query as FastApiQuery,
+ Request,
+ HTTPException,
+ status,
+)
from fastapi.security import OAuth2PasswordBearer, OAuth2PasswordRequestForm
from pydantic import BaseModel
+import jwt
+import datetime
-from nomad import datamodel, infrastructure, utils
+from nomad import utils, infrastructure, datamodel
from nomad.config import config
from nomad.utils import get_logger, strip
from ..common import root_path
-from ..models import HTTPExceptionModel, User
+from ..models import User, HTTPExceptionModel
from ..utils import create_responses
logger = get_logger(__name__)
diff --git a/nomad/app/v1/routers/datasets.py b/nomad/app/v1/routers/datasets.py
index 6038f44f98ccd1af3a4174e7022a3161e0b72d2c..34eec597479dcf5f8d1a2cdd3eafe137f43f03db 100644
--- a/nomad/app/v1/routers/datasets.py
+++ b/nomad/app/v1/routers/datasets.py
@@ -17,37 +17,44 @@
#
import re
-from datetime import datetime
from enum import Enum
from typing import cast
+from fastapi import (
+ APIRouter,
+ Request,
+ Depends,
+ Query as FastApiQuery,
+ Path,
+ HTTPException,
+ status,
+)
+from pydantic import field_validator, BaseModel, Field
+from datetime import datetime
-from fastapi import APIRouter, Depends, HTTPException, Path, Request, status
-from fastapi import Query as FastApiQuery
-from pydantic import BaseModel, Field, field_validator
-
-from nomad import datamodel, processing, utils
+from nomad import utils, datamodel, processing
from nomad.config import config
+from nomad.metainfo.elasticsearch_extension import entry_type
+from nomad.utils import strip, create_uuid
from nomad.datamodel import Dataset as DatasetDefinitionCls
from nomad.doi import DOI, DOIException
-from nomad.metainfo.elasticsearch_extension import entry_type
from nomad.search import search, update_by_query
-from nomad.utils import create_uuid, strip
+from .auth import create_user_dependency
+from .entries import _do_exhaustive_search
+from ..utils import create_responses, parameter_dependency_from_model
from ..models import (
- Any_,
- Direction,
- HTTPExceptionModel,
- MetadataPagination,
- MetadataRequired,
- Owner,
Pagination,
PaginationResponse,
+ MetadataPagination,
Query,
+ HTTPExceptionModel,
User,
+ Direction,
+ Owner,
+ Any_,
+ MetadataRequired,
)
-from ..utils import create_responses, parameter_dependency_from_model
-from .auth import create_user_dependency
-from .entries import _do_exhaustive_search
+
router = APIRouter()
diff --git a/nomad/app/v1/routers/entries.py b/nomad/app/v1/routers/entries.py
index f974e154214bba6607ac9a7d8f79ff0a7267ab12..7f25c97581bc3b2e33bf94f4c50e2f230a3906c1 100644
--- a/nomad/app/v1/routers/entries.py
+++ b/nomad/app/v1/routers/entries.py
@@ -15,75 +15,89 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import io
-import json
-import os.path
-from collections.abc import Iterator
from datetime import datetime
+
from enum import Enum
from typing import Any
-
-import orjson
-import yaml
-from fastapi import APIRouter, Body, Depends, HTTPException, Path, Request, status
-from fastapi import Query as QueryParameter
+from collections.abc import Iterator
+from fastapi import (
+ APIRouter,
+ Depends,
+ Path,
+ status,
+ HTTPException,
+ Request,
+ Query as QueryParameter,
+ Body,
+)
+from fastapi.responses import StreamingResponse, ORJSONResponse
from fastapi.exceptions import RequestValidationError
-from fastapi.responses import ORJSONResponse, StreamingResponse
-from pydantic import BaseModel, ConfigDict, Field, field_validator
+from pydantic import (
+ ConfigDict,
+ field_validator,
+ BaseModel,
+ Field,
+)
+import os.path
+import io
+import json
+import orjson
from pydantic.main import create_model
from starlette.responses import Response
+import yaml
-from nomad import datamodel, files, metainfo, utils
-from nomad import processing as proc
-from nomad.archive import ArchiveQueryError, RequiredReader, RequiredValidationError
+from nomad import files, utils, metainfo, processing as proc
+from nomad import datamodel
from nomad.config import config
from nomad.config.models.config import Reprocess
from nomad.datamodel import EditableUserMetadata
from nomad.datamodel.context import ServerContext
from nomad.files import StreamedFile, create_zipstream_async
-from nomad.groups import get_group_ids
-from nomad.metainfo.elasticsearch_extension import entry_type
from nomad.processing.data import Upload
+from nomad.utils import strip
+from nomad.archive import RequiredReader, RequiredValidationError, ArchiveQueryError
+from nomad.groups import get_group_ids
from nomad.search import (
AuthenticationRequiredError,
QueryValidationError,
SearchError,
search,
+ update_metadata as es_update_metadata,
)
-from nomad.search import update_metadata as es_update_metadata
-from nomad.utils import strip
+from nomad.metainfo.elasticsearch_extension import entry_type
+from .auth import create_user_dependency
+from ..utils import (
+ create_download_stream_zipped,
+ create_download_stream_raw_file,
+ browser_download_headers,
+ DownloadItem,
+ create_responses,
+ log_query,
+)
from ..models import (
Aggregation,
- Files,
- HTTPExceptionModel,
- Metadata,
- MetadataEditRequest,
- MetadataPagination,
- MetadataRequired,
- MetadataResponse,
- Owner,
Pagination,
PaginationResponse,
- Query,
- QueryParameters,
+ MetadataPagination,
TermsAggregation,
- User,
WithQuery,
WithQueryAndPagination,
+ MetadataRequired,
+ MetadataResponse,
+ Metadata,
+ MetadataEditRequest,
+ Files,
+ Query,
+ User,
+ Owner,
+ QueryParameters,
+ metadata_required_parameters,
files_parameters,
metadata_pagination_parameters,
- metadata_required_parameters,
-)
-from ..utils import (
- DownloadItem,
- browser_download_headers,
- create_download_stream_raw_file,
- create_download_stream_zipped,
- create_responses,
- log_query,
+ HTTPExceptionModel,
)
-from .auth import create_user_dependency
+
router = APIRouter()
diff --git a/nomad/app/v1/routers/federation.py b/nomad/app/v1/routers/federation.py
index c554228d0bffcc7b92666bed3a3f82dbcc7a4329..11c7ff4eb5c570e0067209df0cc37967ff896a8f 100644
--- a/nomad/app/v1/routers/federation.py
+++ b/nomad/app/v1/routers/federation.py
@@ -24,7 +24,7 @@ import socket
import zlib
from enum import Enum
-from fastapi import HTTPException, Request
+from fastapi import Request, HTTPException
from fastapi.routing import APIRouter
from nomad import utils
diff --git a/nomad/app/v1/routers/graph.py b/nomad/app/v1/routers/graph.py
index 1d1006c53c11f2f8198d23cda71807b6c1003ee8..c3715787c69d2c448f8acca55777eefc5eff2a50 100644
--- a/nomad/app/v1/routers/graph.py
+++ b/nomad/app/v1/routers/graph.py
@@ -18,22 +18,21 @@
from enum import Enum
-from fastapi import APIRouter, Body, Depends, HTTPException
+from fastapi import Depends, APIRouter, Body, HTTPException
from fastapi.responses import ORJSONResponse
-from nomad.app.v1.models.graph import GraphRequest, GraphResponse
from nomad.graph.graph_reader import (
+ MongoReader,
ConfigError,
GeneralReader,
- MongoReader,
- Token,
UserReader,
+ Token,
)
from nomad.graph.lazy_wrapper import LazyWrapper
-
-from ..models import User
from .auth import create_user_dependency
from .entries import EntriesArchive
+from ..models import User
+from nomad.app.v1.models.graph import GraphRequest, GraphResponse
router = APIRouter()
diff --git a/nomad/app/v1/routers/groups.py b/nomad/app/v1/routers/groups.py
index 945b95f75706b66025c04ac8970047ae2b48e5bd..a41342eb461808d5de715b06b921271fa0d231e2 100644
--- a/nomad/app/v1/routers/groups.py
+++ b/nomad/app/v1/routers/groups.py
@@ -29,6 +29,9 @@ from nomad.app.v1.models.groups import (
)
from nomad.app.v1.models.pagination import PaginationResponse
from nomad.app.v1.utils import parameter_dependency_from_model
+
+from fastapi import APIRouter, Depends, HTTPException, status
+
from nomad.datamodel import User as UserDataModel
from nomad.groups import MongoUserGroup
from nomad.groups import create_user_group as create_mongo_user_group
diff --git a/nomad/app/v1/routers/info.py b/nomad/app/v1/routers/info.py
index 0e63c5778822a8f4cca30a14645ac58435b09d2a..1efa9a15fcbd3100f58a80725d97c49079bc7b1b 100644
--- a/nomad/app/v1/routers/info.py
+++ b/nomad/app/v1/routers/info.py
@@ -20,22 +20,22 @@
API endpoint that deliver backend configuration details.
"""
-from datetime import datetime
from enum import Enum
from typing import Any
-
+from datetime import datetime
from fastapi.routing import APIRouter
from pydantic.fields import Field
from pydantic.main import BaseModel
from nomad import normalizing
-from nomad.app.v1.models import Aggregation, StatisticsAggregation
from nomad.config import config
-from nomad.metainfo.elasticsearch_extension import entry_type
+from nomad.utils import strip
+from nomad.search import search
from nomad.parsing import parsers
from nomad.parsing.parsers import code_metadata
-from nomad.search import search
-from nomad.utils import strip
+from nomad.app.v1.models import Aggregation, StatisticsAggregation
+from nomad.metainfo.elasticsearch_extension import entry_type
+
router = APIRouter()
diff --git a/nomad/app/v1/routers/materials.py b/nomad/app/v1/routers/materials.py
index 70c6ef56b6b52531df4ac31d5a9090e82abcfeb3..579342c5fb1e8e0ec7a6fd89f6642fc8c562300c 100644
--- a/nomad/app/v1/routers/materials.py
+++ b/nomad/app/v1/routers/materials.py
@@ -17,36 +17,32 @@
#
from typing import Any
-
-from fastapi import APIRouter, Depends, HTTPException, Path, Request, status
+from fastapi import APIRouter, Depends, Path, status, HTTPException, Request
from fastapi.exception_handlers import RequestValidationError
from pydantic import BaseModel, Field
from nomad import utils
-from nomad.metainfo.elasticsearch_extension import material_index, material_type
-from nomad.search import (
- AuthenticationRequiredError,
- QueryValidationError,
- SearchError,
- search,
-)
from nomad.utils import strip
+from nomad.search import AuthenticationRequiredError, SearchError
+from nomad.search import search, QueryValidationError
+from nomad.metainfo.elasticsearch_extension import material_type, material_index
+from .auth import create_user_dependency
+from ..utils import create_responses
from ..models import (
- HTTPExceptionModel,
+ User,
+ Owner,
+ WithQuery,
+ MetadataResponse,
Metadata,
MetadataPagination,
MetadataRequired,
- MetadataResponse,
- Owner,
- QueryParameters,
- User,
- WithQuery,
metadata_pagination_parameters,
metadata_required_parameters,
+ QueryParameters,
+ HTTPExceptionModel,
)
-from ..utils import create_responses
-from .auth import create_user_dependency
+
router = APIRouter()
diff --git a/nomad/app/v1/routers/metainfo.py b/nomad/app/v1/routers/metainfo.py
index a92fccbb529875004a86ca8dc889a7ab047dea92..882e21b6d283ad168ff593079f6ef5a57e84af98 100644
--- a/nomad/app/v1/routers/metainfo.py
+++ b/nomad/app/v1/routers/metainfo.py
@@ -19,16 +19,16 @@ import copy
import datetime
from typing import Any
-from fastapi import APIRouter, HTTPException, Path, status
+from fastapi import APIRouter, Path, status, HTTPException
from pydantic import BaseModel, Field
from nomad.app.v1.models import HTTPExceptionModel
from nomad.app.v1.utils import create_responses
-from nomad.config import config
from nomad.metainfo import Package
-from nomad.metainfo.metainfo import JSON, Datetime, MSection, Quantity, Section
-from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
-from nomad.utils import get_logger, strip
+from nomad.metainfo.metainfo import MSection, Section, Quantity, Datetime, JSON
+from nomad.metainfo.mongoengine_extension import MongoDocument, Mongo
+from nomad.utils import strip, get_logger
+from nomad.config import config
logger = get_logger(__name__)
diff --git a/nomad/app/v1/routers/north.py b/nomad/app/v1/routers/north.py
index 73c795bcf98baf1a2e78a37a02c94c2ccfe14312..c026348e6ed29d9f52a71beb52d5badb37b00fe1 100644
--- a/nomad/app/v1/routers/north.py
+++ b/nomad/app/v1/routers/north.py
@@ -17,23 +17,23 @@
#
import os
-from enum import Enum
-
import requests
-from fastapi import APIRouter, Depends, HTTPException, status
-from mongoengine.queryset.visitor import Q
+
+from enum import Enum
+from nomad.groups import get_group_ids
from pydantic import BaseModel
+from fastapi import APIRouter, Depends, status, HTTPException
+from mongoengine.queryset.visitor import Q
-from nomad.app.v1.routers.auth import generate_simple_token
from nomad.config import config
from nomad.config.models.north import NORTHTool
-from nomad.groups import get_group_ids
+from nomad.utils import strip, get_logger, slugify
from nomad.processing import Upload
-from nomad.utils import get_logger, slugify, strip
-
-from ..models import HTTPExceptionModel, User
-from ..utils import create_responses
+from nomad.app.v1.routers.auth import generate_simple_token
from .auth import create_user_dependency
+from ..models import User, HTTPExceptionModel
+from ..utils import create_responses
+
TOOLS = {k: v for k, v in config.north.tools.filtered_items()}
diff --git a/nomad/app/v1/routers/suggestions.py b/nomad/app/v1/routers/suggestions.py
index 2bd6e515e3a2d446c29cde595e9bd5bb126f8195..0d0b68229f4edbc30b66376152d07338580257ed 100644
--- a/nomad/app/v1/routers/suggestions.py
+++ b/nomad/app/v1/routers/suggestions.py
@@ -17,17 +17,17 @@
#
from collections import defaultdict
-
-from elasticsearch.exceptions import RequestError
+from pydantic import BaseModel, Field
+from fastapi import APIRouter, Depends, Request, HTTPException, status
from elasticsearch_dsl import Search
from elasticsearch_dsl.utils import AttrList
-from fastapi import APIRouter, Depends, HTTPException, Request, status
-from pydantic import BaseModel, Field
+from elasticsearch.exceptions import RequestError
from nomad.metainfo.elasticsearch_extension import entry_index, entry_type
-from ..models import User
from .auth import create_user_dependency
+from ..models import User
+
router = APIRouter()
diff --git a/nomad/app/v1/routers/systems.py b/nomad/app/v1/routers/systems.py
index c92e1c44f4520b1198a395817a214afec987ccc9..6d56d61d2c1b3763c1eaf51cd93b8b35ef5227fc 100644
--- a/nomad/app/v1/routers/systems.py
+++ b/nomad/app/v1/routers/systems.py
@@ -15,27 +15,29 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+from io import StringIO, BytesIO
import sys
from collections import OrderedDict
from enum import Enum
-from io import BytesIO, StringIO
-import ase.build
-import ase.io
import numpy as np
-from fastapi import APIRouter, Depends, HTTPException, Path, Query, status
+from fastapi import APIRouter, Depends, Path, Query, status, HTTPException
from fastapi.responses import Response
+import ase.io
+import ase.build
-from nomad.atomutils import Formula, unwrap_positions, wrap_positions
-from nomad.datamodel.metainfo.system import Atoms as NOMADAtoms
-from nomad.normalizing.common import ase_atoms_from_nomad_atoms
from nomad.units import ureg
-from nomad.utils import deep_get, query_list_to_dict, strip
+from nomad.utils import strip, deep_get, query_list_to_dict
+from nomad.atomutils import Formula, wrap_positions, unwrap_positions
+from nomad.normalizing.common import (
+ ase_atoms_from_nomad_atoms,
+)
+from nomad.datamodel.metainfo.system import Atoms as NOMADAtoms
+from .entries import answer_entry_archive_request
-from ..models import HTTPExceptionModel, User
-from ..utils import create_responses
from .auth import create_user_dependency
-from .entries import answer_entry_archive_request
+from ..utils import create_responses
+from ..models import User, HTTPExceptionModel
router = APIRouter()
diff --git a/nomad/app/v1/routers/uploads.py b/nomad/app/v1/routers/uploads.py
index fa6ff235ca0c7454634a8c64fe93f062507048f1..5c5400701493cfdc1cea8e4e40e67a1b7f5d4d8b 100644
--- a/nomad/app/v1/routers/uploads.py
+++ b/nomad/app/v1/routers/uploads.py
@@ -15,79 +15,92 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import io
import os
+import io
import shutil
-import tarfile
import zipfile
-from datetime import datetime
+import tarfile
from enum import Enum
+from datetime import datetime
from typing import Any, cast
+from pydantic import (
+ field_validator,
+ ConfigDict,
+ BaseModel,
+ Field,
+ model_validator,
+)
+from mongoengine.queryset.visitor import Q
from urllib.parse import unquote
-
from fastapi import (
APIRouter,
- Body,
- Depends,
- File,
- HTTPException,
- Path,
Request,
+ File,
UploadFile,
status,
+ Depends,
+ Body,
+ Path,
+ Query as FastApiQuery,
+ HTTPException,
)
-from fastapi import Query as FastApiQuery
+from fastapi.responses import StreamingResponse, FileResponse
from fastapi.exceptions import RequestValidationError
-from fastapi.responses import FileResponse, StreamingResponse
-from mongoengine.queryset.visitor import Q
-from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
from pydantic_core import PydanticCustomError
-from nomad import files, utils
-from nomad.bundles import BundleExporter, BundleImporter
-from nomad.common import get_compression_format, is_safe_basename, is_safe_relative_path
+from nomad import utils, files
+from nomad.common import is_safe_relative_path, is_safe_basename
from nomad.config import config
-from nomad.config.models.config import Reprocess
from nomad.config.models.plugins import ExampleUploadEntryPoint
-from nomad.files import PublicUploadFiles, StagingUploadFiles
+from nomad.files import (
+ StagingUploadFiles,
+ PublicUploadFiles,
+)
+from nomad.bundles import BundleExporter, BundleImporter
+from nomad.config.models.config import Reprocess
from nomad.groups import get_group_ids
from nomad.processing import (
+ Upload,
Entry,
- MetadataEditRequestHandler,
ProcessAlreadyRunning,
ProcessStatus,
- Upload,
+ MetadataEditRequestHandler,
)
-from nomad.search import QueryValidationError, search, search_iterator
-from nomad.search import refresh as search_refresh
+from nomad.common import get_compression_format
from nomad.utils import strip
+from nomad.search import (
+ search,
+ search_iterator,
+ refresh as search_refresh,
+ QueryValidationError,
+)
+from .auth import create_user_dependency, generate_upload_token
from ..models import (
- Direction,
- Files,
- HTTPExceptionModel,
- MetadataEditRequest,
MetadataPagination,
- MetadataRequired,
- Owner,
+ User,
+ Direction,
Pagination,
PaginationResponse,
- User,
- WithQuery,
+ HTTPExceptionModel,
+ Files,
files_parameters,
+ Owner,
+ WithQuery,
+ MetadataRequired,
+ MetadataEditRequest,
restrict_query_to_upload,
)
+from .entries import EntryArchiveResponse, answer_entry_archive_request
from ..utils import (
+ parameter_dependency_from_model,
+ create_responses,
DownloadItem,
browser_download_headers,
- create_download_stream_raw_file,
create_download_stream_zipped,
- create_responses,
+ create_download_stream_raw_file,
create_stream_from_string,
- parameter_dependency_from_model,
)
-from .auth import create_user_dependency, generate_upload_token
-from .entries import EntryArchiveResponse, answer_entry_archive_request
router = APIRouter()
diff --git a/nomad/app/v1/routers/users.py b/nomad/app/v1/routers/users.py
index 3e48ee899559efa081d41d6c16481e6ea2200028..50c003e8068b22f3b1cdb1b045e07bce7096396b 100644
--- a/nomad/app/v1/routers/users.py
+++ b/nomad/app/v1/routers/users.py
@@ -18,16 +18,16 @@
from enum import Enum
-from fastapi import APIRouter, Depends, HTTPException, Query, status
+from fastapi import Depends, APIRouter, status, HTTPException, Query
from pydantic.main import BaseModel
-from nomad import datamodel, infrastructure
+from nomad import infrastructure, datamodel
from nomad.config import config
from nomad.utils import strip
-from ..models import HTTPExceptionModel, User
-from ..utils import create_responses
from .auth import create_user_dependency
+from ..models import User, HTTPExceptionModel
+from ..utils import create_responses
router = APIRouter()
diff --git a/nomad/app/v1/utils.py b/nomad/app/v1/utils.py
index c62316fe4e8a02263d5a69014c25d6ea913939d7..1a6b04574c8270b3d826be958f6fe98d15569ba7 100644
--- a/nomad/app/v1/utils.py
+++ b/nomad/app/v1/utils.py
@@ -16,21 +16,19 @@
# limitations under the License.
#
-import gzip
-import inspect
+from typing import Any
+from collections.abc import Iterator
+from types import FunctionType
+import urllib
import io
import json
-import lzma
import os
-import urllib
-from collections.abc import Iterator
-from types import FunctionType
-from typing import Any
-
-from fastapi import HTTPException, Query, Request, status # noqa: F401
-from pydantic import BaseModel, ValidationError # noqa: F401
-
-from nomad.files import StreamedFile, UploadFiles, create_zipstream
+import inspect
+from fastapi import Request, Query, HTTPException, status # noqa: F401
+from pydantic import ValidationError, BaseModel # noqa: F401
+import gzip
+import lzma
+from nomad.files import UploadFiles, StreamedFile, create_zipstream
def parameter_dependency_from_model(
diff --git a/nomad/archive/converter.py b/nomad/archive/converter.py
index 96b6e494fd78e1b69613958571f556b81c4273ef..b72233f3ffdf3053471751b669d3cd11ca181780 100644
--- a/nomad/archive/converter.py
+++ b/nomad/archive/converter.py
@@ -21,14 +21,15 @@ import functools
import hashlib
import os.path
import signal
-from collections.abc import Callable, Iterable
from concurrent.futures import ProcessPoolExecutor
from multiprocessing import Manager
+from collections.abc import Callable
+from collections.abc import Iterable
-from nomad.archive import read_archive, to_json
-from nomad.archive.storage_v2 import ArchiveWriter as ArchiveWriterNew
from nomad.config import config
-from nomad.files import PublicUploadFiles, StagingUploadFiles
+from nomad.archive import to_json, read_archive
+from nomad.archive.storage_v2 import ArchiveWriter as ArchiveWriterNew
+from nomad.files import StagingUploadFiles, PublicUploadFiles
from nomad.infrastructure import setup
from nomad.processing import Upload
diff --git a/nomad/archive/partial.py b/nomad/archive/partial.py
index 6d0f4012f0096975be51eb4ab53d6596a5b4436b..0f503dbd06d426b106c1f3e67c26531e2aabb138 100644
--- a/nomad/archive/partial.py
+++ b/nomad/archive/partial.py
@@ -20,16 +20,16 @@ from typing import Any
from nomad import infrastructure
from nomad.config import config
-from nomad.datamodel import EntryArchive
-from nomad.datamodel.metainfo.common import FastAccess
from nomad.metainfo import (
- Definition,
MSection,
+ Definition,
Quantity,
Reference,
- Section,
SubSection,
+ Section,
)
+from nomad.datamodel import EntryArchive
+from nomad.datamodel.metainfo.common import FastAccess
def create_partial_archive(archive: EntryArchive) -> dict:
diff --git a/nomad/archive/query.py b/nomad/archive/query.py
index 09696fcdbcb95ce81219b57fe8511f4e984ce78a..2097a2f7ba8a4381e6a42c1ad00c2ff5bcb428eb 100644
--- a/nomad/archive/query.py
+++ b/nomad/archive/query.py
@@ -18,13 +18,13 @@
import functools
import re
+from typing import Any
from collections.abc import Callable
from io import BytesIO
-from typing import Any
from nomad import utils
-from .storage import ArchiveDict, ArchiveList, ArchiveReader, read_archive, to_json
+from .storage import ArchiveReader, ArchiveList, ArchiveDict, to_json, read_archive
_query_archive_key_pattern = re.compile(r'^([\s\w\-]+)(\[([-?0-9]*)(:([-?0-9]*))?])?$')
diff --git a/nomad/archive/required.py b/nomad/archive/required.py
index 402e116ad6fdaea53b8cfb08ae25137145984c31..df5fa96f51311e0f25c34be7dfb6b355842689cf 100644
--- a/nomad/archive/required.py
+++ b/nomad/archive/required.py
@@ -28,25 +28,24 @@ from fastapi import HTTPException
from nomad import utils
from nomad.metainfo import (
Definition,
- Package,
+ Section,
Quantity,
- QuantityReference,
+ SubSection,
Reference,
- Section,
+ QuantityReference,
SectionReference,
- SubSection,
+ Package,
)
-
-from ..datamodel.context import ServerContext, parse_path
from .query import (
ArchiveQueryError,
- _extract_child,
- _extract_key_and_index,
- _query_archive_key_pattern,
to_json,
+ _query_archive_key_pattern,
+ _extract_key_and_index,
+ _extract_child,
)
-from .storage import ArchiveDict, ArchiveError, ArchiveList, ArchiveReader
+from .storage import ArchiveReader, ArchiveList, ArchiveError, ArchiveDict
from .storage_v2 import ArchiveDict as NewArchiveDict
+from ..datamodel.context import parse_path, ServerContext
class RequiredValidationError(Exception):
diff --git a/nomad/archive/storage.py b/nomad/archive/storage.py
index 29102e1eae6ddd68cf10542a797954c4804d41f2..fa90306564d748f958e1c5d6695a6f650909a50c 100644
--- a/nomad/archive/storage.py
+++ b/nomad/archive/storage.py
@@ -17,10 +17,12 @@
#
from __future__ import annotations
-import struct
-from collections.abc import Generator, Mapping, Sequence
-from io import BufferedReader, BytesIO
from typing import Any, cast
+from collections.abc import Generator
+from io import BytesIO, BufferedReader
+from collections.abc import Mapping, Sequence
+
+import struct
import msgspec
@@ -326,8 +328,10 @@ def read_archive(file_or_path: str | BytesIO, **kwargs) -> ArchiveReader:
will lazily load data as it is used. The mapping needs to be closed or used within
a 'with' statement to free the underlying file resource after use.
"""
- from .storage_v2 import ArchiveReader as ArchiveReaderNew
- from .storage_v2 import ArchiveWriter as ArchiveWriterNew
+ from .storage_v2 import (
+ ArchiveWriter as ArchiveWriterNew,
+ ArchiveReader as ArchiveReaderNew,
+ )
# todo: replace implementation to enable automatic conversion
# if isinstance(file_or_path, str):
diff --git a/nomad/archive/storage_v2.py b/nomad/archive/storage_v2.py
index ffb8fdaf6fdfdc0eca76797f591756a71ea0934a..6a5d1e59af5aa7ad6dd82a3b87d647c44927df1c 100644
--- a/nomad/archive/storage_v2.py
+++ b/nomad/archive/storage_v2.py
@@ -27,8 +27,8 @@ from bitarray import bitarray
from msgpack import Unpacker
from nomad import utils
-from nomad.archive import ArchiveError
from nomad.config import config
+from nomad.archive import ArchiveError
_packer = msgpack.Packer(autoreset=True, use_bin_type=True)
diff --git a/nomad/atomutils.py b/nomad/atomutils.py
index d0deb7ded1bd8e66ea46a6b4bb693d7ad44391b1..3b7a6f5cc14e4cf499fc04f6e30b74362297ad6b 100644
--- a/nomad/atomutils.py
+++ b/nomad/atomutils.py
@@ -23,10 +23,14 @@ import itertools
import logging
import math
import re
-from collections.abc import Iterable
from functools import reduce
from string import ascii_uppercase
-from typing import TYPE_CHECKING, Any, cast
+from typing import (
+ TYPE_CHECKING,
+ Any,
+ cast,
+)
+from collections.abc import Iterable
import ase.data
import ase.geometry
diff --git a/nomad/bundles.py b/nomad/bundles.py
index 93c45612e1fa0d47e75ed604e9ae4406517a5794..9ed5ef631607eee8d0b02f2fb0180c3edc2e92b0 100644
--- a/nomad/bundles.py
+++ b/nomad/bundles.py
@@ -8,36 +8,35 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import json
-import os
+from typing import cast, Any
from collections.abc import Iterable
+import os
+import json
from datetime import datetime, timedelta
-from typing import Any, cast
-
-from fastapi import HTTPException, status
from packaging import version
-from nomad import datamodel, search, utils
+from nomad import utils, datamodel, search
from nomad.config import config
-from nomad.config.models.config import BundleExportSettings, BundleImportSettings
+from nomad.config.models.config import BundleImportSettings, BundleExportSettings
from nomad.files import (
- BrowsableFileSource,
- CombinedFileSource,
- DiskFileSource,
- FileSource,
+ zipfile,
PathObject,
+ UploadFiles,
PublicUploadFiles,
StagingUploadFiles,
- StandardJSONDecoder,
+ FileSource,
+ BrowsableFileSource,
+ CombinedFileSource,
StreamedFileSource,
- UploadFiles,
+ DiskFileSource,
ZipFileSource,
- bundle_info_filename,
json_to_streamed_file,
- zipfile,
+ bundle_info_filename,
+ StandardJSONDecoder,
)
from nomad.processing.base import ProcessStatus
-from nomad.processing.data import Entry, Upload, mongo_entry_metadata
+from nomad.processing.data import Upload, Entry, mongo_entry_metadata
+from fastapi import HTTPException, status
class BundleExporter:
diff --git a/nomad/cli/admin/admin.py b/nomad/cli/admin/admin.py
index 75f5cc88179cf5d44b972ddc2b668d05fa898419..7c02a16cdd51457e9b241def679e6d26b8a492ba 100644
--- a/nomad/cli/admin/admin.py
+++ b/nomad/cli/admin/admin.py
@@ -18,8 +18,8 @@
import click
-from nomad.cli.cli import cli
from nomad.config import config
+from nomad.cli.cli import cli
@cli.group(
@@ -68,8 +68,7 @@ def reset(remove, i_am_really_sure):
def reset_processing(zero_complete_time):
from datetime import datetime
- from nomad import infrastructure
- from nomad import processing as proc
+ from nomad import infrastructure, processing as proc
infrastructure.setup_mongo()
@@ -110,11 +109,9 @@ def reset_processing(zero_complete_time):
)
def lift_embargo(dry, parallel):
from datetime import datetime
-
from dateutil.relativedelta import relativedelta
- from nomad import infrastructure
- from nomad import processing as proc
+ from nomad import infrastructure, processing as proc
from nomad.search import quantity_values
infrastructure.setup_mongo()
@@ -418,7 +415,6 @@ def migrate_mongo(
import sys
from pymongo.database import Database
-
from nomad import infrastructure
from nomad.cli.admin import migrate
@@ -494,10 +490,9 @@ def migrate_mongo(
)
def rewrite_doi_urls(dois, dry, save_existing_records):
import json
-
import requests
- from nomad.doi import _create_dataset_url, edit_doi_url
+ from nomad.doi import edit_doi_url, _create_dataset_url
existing_records = []
diff --git a/nomad/cli/admin/clean.py b/nomad/cli/admin/clean.py
index 2522466c06d18e88161157447efe52e7d6264092..6ca3d6c7ca5773b59bf79b7a716508f890d9be98 100644
--- a/nomad/cli/admin/clean.py
+++ b/nomad/cli/admin/clean.py
@@ -39,13 +39,13 @@ from .admin import admin
def clean(dry, skip_entries, skip_fs, skip_es, staging_too, force):
import os
import shutil
-
- import elasticsearch_dsl
import tabulate
+ import elasticsearch_dsl
from nomad import infrastructure, processing
from nomad.config import config as nomad_config
- from nomad.search import delete_by_query, quantity_values
+ from nomad.search import delete_by_query
+ from nomad.search import quantity_values
mongo_client = infrastructure.setup_mongo()
infrastructure.setup_elastic()
diff --git a/nomad/cli/admin/entries.py b/nomad/cli/admin/entries.py
index 91728ae86d3c413947cacffb9e98d7d3782efe7c..54ac693eed7dcd6510287497f0733e912432729a 100644
--- a/nomad/cli/admin/entries.py
+++ b/nomad/cli/admin/entries.py
@@ -33,8 +33,7 @@ def entries():
)
@click.option('--skip-mongo', help='Keep uploads and entries in mongo.', is_flag=True)
def rm(entries, skip_es, skip_mongo):
- from nomad import infrastructure, search
- from nomad import processing as proc
+ from nomad import processing as proc, infrastructure, search
infrastructure.setup_mongo()
infrastructure.setup_elastic()
diff --git a/nomad/cli/admin/migrate.py b/nomad/cli/admin/migrate.py
index 5f28df89b19ae28ec8b7378d3a8545489e355b8c..495423de7c8cc9c65c10b674bbd793e65f834aa8 100644
--- a/nomad/cli/admin/migrate.py
+++ b/nomad/cli/admin/migrate.py
@@ -19,15 +19,15 @@
import time
from datetime import datetime
from typing import Any
-
from pydantic import BaseModel
-from pymongo import ReplaceOne
-from pymongo.database import Collection, Database
+from pymongo import ReplaceOne
+from pymongo.database import Database, Collection
from nomad import utils
+from nomad.processing import ProcessStatus, Upload, Entry
from nomad.datamodel import Dataset
from nomad.parsing.parsers import parser_dict
-from nomad.processing import Entry, ProcessStatus, Upload
+
_upload_keys_to_remove_v0 = (
'published',
diff --git a/nomad/cli/admin/run.py b/nomad/cli/admin/run.py
index 1739b89c1e2dc22d887f9172f5dec9c5e68002ed..ab846f3e0e203bbe039094be8d0393eac403915d 100644
--- a/nomad/cli/admin/run.py
+++ b/nomad/cli/admin/run.py
@@ -75,9 +75,9 @@ def run_app(
# port = port or config.services.api_port
if with_gui:
- import glob
import os
import os.path
+ import glob
import shutil
gui_folder = os.path.abspath(
@@ -122,9 +122,8 @@ def run_app(
from nomad.utils import get_logger
if gunicorn:
- import logging.config
-
from gunicorn.app.wsgiapp import WSGIApplication
+ import logging.config
if log_config:
logging.config.fileConfig(log_config)
@@ -153,7 +152,7 @@ def run_app(
get_logger(__name__).info('created gunicorn server', data=str(gunicorn_app.cfg))
gunicorn_app.run()
else:
- from uvicorn import Config, Server
+ from uvicorn import Server, Config
kwargs['log_config'] = log_config
@@ -183,11 +182,10 @@ def run_worker(*, workers=None):
def run_hub():
+ from jupyterhub.app import main
+ import sys
import os
import subprocess
- import sys
-
- from jupyterhub.app import main
if 'JUPYTERHUB_CRYPT_KEY' not in os.environ:
crypt_key = config.north.jupyterhub_crypt_key
diff --git a/nomad/cli/admin/springer.py b/nomad/cli/admin/springer.py
index dec3b88fdc0c4f71670124933d6757971dceebcc..23b3c59e336be4b5f1745d4cb052309b875c0eb9 100644
--- a/nomad/cli/admin/springer.py
+++ b/nomad/cli/admin/springer.py
@@ -23,18 +23,17 @@ http://materials.springer.com. The database is stuctured as
space_group_number : normalized_formula : springer_id : entry
"""
-import os.path
-import re
-import time
from typing import Any
-
-import bs4
import requests
+import re
+import bs4
+import time
+import os.path
import nomad.archive.storage_v2
from nomad import archive
-from nomad.archive import read_archive
from nomad.config import config
+from nomad.archive import read_archive
required_items = {
'Alphabetic Formula:': 'alphabetic_formula',
diff --git a/nomad/cli/admin/uploads.py b/nomad/cli/admin/uploads.py
index c55c64948f43df3568160bffa7438f1f9bc04783..cd1cd9eb7a31698a0d147005de771d94b2502fd7 100644
--- a/nomad/cli/admin/uploads.py
+++ b/nomad/cli/admin/uploads.py
@@ -25,7 +25,6 @@ import click
from orjson import dumps
from nomad.config import config
-
from .admin import admin
@@ -35,8 +34,7 @@ def _run_parallel(
import threading
import time
- from nomad import processing as proc
- from nomad import utils
+ from nomad import utils, processing as proc
if isinstance(uploads, tuple | list):
uploads_count = len(uploads)
@@ -239,13 +237,11 @@ def _query_uploads(
list of upoad ids and further filter parameters.
"""
- import json
from typing import cast
-
+ import json
from mongoengine import Q
- from nomad import infrastructure, search
- from nomad import processing as proc
+ from nomad import infrastructure, processing as proc, search
from nomad.app.v1 import models
infrastructure.setup_mongo()
@@ -355,13 +351,12 @@ def _query_uploads(
@click.pass_context
def export(ctx, uploads, required, output: str):
import sys
- import time
- import zipfile
-
- from nomad.archive import ArchiveQueryError, RequiredReader
- from nomad.files import UploadFiles
from nomad.processing import Entry
from nomad.utils import get_logger
+ from nomad.files import UploadFiles
+ from nomad.archive import ArchiveQueryError, RequiredReader
+ import time
+ import zipfile
logger = get_logger(__name__)
@@ -634,8 +629,7 @@ def index(ctx, uploads, parallel, transformer, skip_materials, print_progress):
def delete_upload(
upload, skip_es: bool = False, skip_files: bool = False, skip_mongo: bool = False
):
- from nomad import files, search, utils
- from nomad import processing as proc
+ from nomad import search, files, utils, processing as proc
# delete elastic
if not skip_es:
@@ -788,8 +782,7 @@ def re_pack(ctx, uploads):
def stop(ctx, uploads, entries: bool, kill: bool, no_celery: bool):
import mongoengine
- from nomad import processing as proc
- from nomad import utils
+ from nomad import utils, processing as proc
query, _ = _query_uploads(uploads, **ctx.obj.uploads_kwargs)
@@ -918,8 +911,9 @@ def integrity(
):
from nomad.app.v1.models import MetadataPagination, MetadataRequired
from nomad.archive.storage_v2 import ArchiveWriter
- from nomad.files import PublicUploadFiles, StagingUploadFiles
- from nomad.processing import Entry, Upload
+ from nomad.files import StagingUploadFiles, PublicUploadFiles
+ from nomad.processing import Entry
+ from nomad.processing import Upload
from nomad.search import search
def search_params(upload_id: str):
@@ -1306,8 +1300,8 @@ def export_bundle(
def import_bundle(
ctx, input_path, multi, settings, embargo_length, use_celery, ignore_errors
):
- from nomad import infrastructure
from nomad.bundles import BundleImporter
+ from nomad import infrastructure
for key, value in ctx.obj.uploads_kwargs.items():
if value:
diff --git a/nomad/cli/admin/users.py b/nomad/cli/admin/users.py
index 7752903f2977a4f8dc0431260abfd215c72aa258..21253fb313395efbbc99604d35c864f22b40e3ed 100644
--- a/nomad/cli/admin/users.py
+++ b/nomad/cli/admin/users.py
@@ -29,10 +29,10 @@ def users():
@users.command(help='Import users to keycloak from a JSON file.', name='import')
@click.argument('PATH_TO_USERS_FILE', type=str, nargs=1)
def import_command(path_to_users_file):
- import datetime
import json
+ import datetime
- from nomad import datamodel, infrastructure, utils
+ from nomad import infrastructure, datamodel, utils
with open(path_to_users_file) as f:
users = json.load(f)
diff --git a/nomad/cli/aflow.py b/nomad/cli/aflow.py
index eec1729ad7319cf9e3cce68591a3270b9ee55de3..501b5f3764e2323bdc22bccefdf686cc1750ba4a 100644
--- a/nomad/cli/aflow.py
+++ b/nomad/cli/aflow.py
@@ -20,27 +20,26 @@
# code will fail.
# TODO The metadata should not be set via API, but added to the uploads as nomad.json.
-import io
-import json
-import os
+import requests
import re
import subprocess
+from urllib import parse as urllib_parse
+import os
import tarfile
import threading
import time
+import io
+import re
import uuid
-from urllib import parse as urllib_parse
-
+import json
+import numpy as np
import ase
import bs4
import matid # pylint: disable=import-error
-import numpy as np
-import requests
-from nomad import atomutils, client
-from nomad import processing as proc
-from nomad.client import api, upload_file
+from nomad import atomutils, client, processing as proc
from nomad.config import config
+from nomad.client import api, upload_file
class DbUpdater:
diff --git a/nomad/cli/cli.py b/nomad/cli/cli.py
index 316293d1cbfc0fe6fd86009c60130b078289a95a..4120b883cc02d3b73789554071ff3c2fa4af150d 100644
--- a/nomad/cli/cli.py
+++ b/nomad/cli/cli.py
@@ -16,11 +16,10 @@
# limitations under the License.
#
+import click
import logging
import os
-import click
-
from nomad import utils
from nomad.config import config
diff --git a/nomad/cli/client/integrationtests.py b/nomad/cli/client/integrationtests.py
index 0f99ca2327b36d8faf2d049f1de3a4e23eed4393..744cba59c894a99e755cf379fc887877e2ba088d 100644
--- a/nomad/cli/client/integrationtests.py
+++ b/nomad/cli/client/integrationtests.py
@@ -21,9 +21,9 @@ A command that runs some example operations on a working nomad@FAIRDI installati
as a final integration test.
"""
-import json
-import os
import time
+import os
+import json
from nomad.client import api
diff --git a/nomad/cli/dev.py b/nomad/cli/dev.py
index 4491c228e9c25be42b5474982c0e95a14e4f861c..7a3b4a11adf3b01dc093296bd3c36bb08c426977 100644
--- a/nomad/cli/dev.py
+++ b/nomad/cli/dev.py
@@ -15,18 +15,17 @@
# limitations under the License.
#
+from typing import Any
+import sys
import json
import os
-import sys
-from typing import Any
-
import click
+
from pint import Unit
from pint.errors import UndefinedUnitError
from nomad.config import config
from nomad.metainfo.elasticsearch_extension import schema_separator
-
from .cli import cli
@@ -81,8 +80,8 @@ def gui_qa(skip_tests: bool):
@dev.command(help='Export an API model in JSON schema.')
@click.argument('model')
def api_model(model):
- import importlib
import json
+ import importlib
def remove_null_types(data):
"""
@@ -124,11 +123,11 @@ def api_model(model):
'nomad.app.v1.models.graph.GraphRequest',
'nomad.app.v1.models.graph.GraphResponse',
]:
- from nomad.app.v1.models.graph.graph_models import Graph
from nomad.app.v1.models.graph.utils import (
generate_request_model,
generate_response_model,
)
+ from nomad.app.v1.models.graph.graph_models import Graph
sys.modules['nomad.app.v1.models.graph.utils'].ref_prefix = '#/definitions'
sys.modules['nomad.app.v1.models.graph.utils'].graph_model_export = True
@@ -189,8 +188,8 @@ def metainfo():
def _generate_search_quantities():
# Currently only quantities with "entry_type" are included.
+ from nomad.metainfo.elasticsearch_extension import entry_type, Elasticsearch
from nomad.datamodel import EntryArchive
- from nomad.metainfo.elasticsearch_extension import Elasticsearch, entry_type
def to_dict(search_quantity, section=False, repeats=False):
if section:
@@ -350,9 +349,8 @@ def gui_config():
'--parser', help='Only updated the README of the given parsers subdirctory.'
)
def update_parser_readmes(parser):
- import re
from glob import glob
-
+ import re
import yaml
os.chdir(os.path.join(os.path.dirname(__file__), '../..'))
@@ -491,10 +489,8 @@ def example_data(username: str):
def _generate_units_json() -> tuple[Any, Any]:
- from collections import defaultdict
-
from pint.converters import ScaleConverter
-
+ from collections import defaultdict
from nomad.units import ureg
# TODO: Check that all units are unambiguously defined, and that there are
diff --git a/nomad/cli/parse.py b/nomad/cli/parse.py
index 275cdf80ce8c1dbd42f50c8589b2545148d48212..723796dfbac151b3372d61ca5592c47c59dcde89 100644
--- a/nomad/cli/parse.py
+++ b/nomad/cli/parse.py
@@ -84,12 +84,12 @@ def _parse(
save_plot_dir,
):
import json
- import os
import sys
+ import os
- from nomad import utils
from nomad.client import normalize_all, parse
from nomad.datamodel.metainfo.plot import resolve_plot_references
+ from nomad import utils
kwargs = dict(
strict=not not_strict,
diff --git a/nomad/client/api.py b/nomad/client/api.py
index fe85171217a799fc0f6a4d52e5959e0262580a26..414eb02a03ad0eb6c0cdf0aed8843cf3519d9c9c 100644
--- a/nomad/client/api.py
+++ b/nomad/client/api.py
@@ -16,10 +16,9 @@
# limitations under the License.
#
-import time
-
import requests
from keycloak import KeycloakOpenID
+import time
from nomad.config import config
diff --git a/nomad/client/archive.py b/nomad/client/archive.py
index 1c0f496e09df39b92e5ba41ec22620eda40df145..971d87ef06408ce26484bec268894f08a93ec53c 100644
--- a/nomad/client/archive.py
+++ b/nomad/client/archive.py
@@ -18,19 +18,19 @@
from __future__ import annotations
import asyncio
-import threading
from asyncio import Semaphore
from itertools import islice
-from time import monotonic
from typing import Any
+from time import monotonic
+import threading
from click import progressbar
-from httpx import AsyncClient, Timeout
+from httpx import Timeout, AsyncClient
from keycloak import KeycloakOpenID
from nomad import metainfo as mi
from nomad.config import config
-from nomad.datamodel import ClientContext, EntryArchive
+from nomad.datamodel import EntryArchive, ClientContext
from nomad.utils import dict_to_dataframe
diff --git a/nomad/client/processing.py b/nomad/client/processing.py
index 03d54ba78cd8bd8ec47892cd42d83a7ea02c711c..3445fc88711a48284f432cd15507ac0c93955adb 100644
--- a/nomad/client/processing.py
+++ b/nomad/client/processing.py
@@ -16,14 +16,15 @@
# limitations under the License.
#
-import io
import os
-import sys
+import io
import typing
+import sys
-from nomad import datamodel, utils
+from nomad import utils, datamodel
from nomad.config import config
+
from .api import Auth
diff --git a/nomad/client/upload.py b/nomad/client/upload.py
index 8b2c6f4c38d1e974cd1b72637338df1c1854cf6f..e800b8da04781ad004150d26b8cc47042d5917e6 100644
--- a/nomad/client/upload.py
+++ b/nomad/client/upload.py
@@ -41,8 +41,8 @@ def upload_file(
Returns: The upload_id if successful or None if not.
"""
- from nomad.client import api
from nomad.processing import ProcessStatus
+ from nomad.client import api
if local_path:
response = api.post(
diff --git a/nomad/common.py b/nomad/common.py
index 181c232cbe600ea4f0914ace29c5a710f7cb4825..e3f7bc67a3ea072f581100f0bf74d6e94c6a7185 100644
--- a/nomad/common.py
+++ b/nomad/common.py
@@ -24,11 +24,10 @@ source code without circular imports.
import os
import pkgutil
import shutil
-import tarfile
import zipfile
-from tempfile import TemporaryDirectory
+import tarfile
from typing import Literal
-
+from tempfile import TemporaryDirectory
import httpx
diff --git a/nomad/config/models/common.py b/nomad/config/models/common.py
index 02f68c3814f991baaaf0f26089e97ef342817919..576c4aa03d0852346485a6922f877f5f86d98900 100644
--- a/nomad/config/models/common.py
+++ b/nomad/config/models/common.py
@@ -16,9 +16,8 @@
# limitations under the License.
#
-from typing import Any, TypeVar, cast
-
-from pydantic import BaseModel, ConfigDict, Field, model_validator # noqa: F401
+from typing import Any, cast, TypeVar
+from pydantic import ConfigDict, model_validator, BaseModel, Field # noqa: F401
ConfigBaseModelBound = TypeVar('ConfigBaseModelBound', bound='ConfigBaseModel')
diff --git a/nomad/config/models/config.py b/nomad/config/models/config.py
index 385f0d8ba62b059589d96448b1e237d1b804b0c7..ffba90ddc9af27b13d51d36c04854eb913e716ae 100644
--- a/nomad/config/models/config.py
+++ b/nomad/config/models/config.py
@@ -23,7 +23,13 @@ from importlib.metadata import version
from typing import Any
import yaml
-from pydantic import BaseModel, ConfigDict, Field, field_validator, model_validator
+from pydantic import (
+ BaseModel,
+ field_validator,
+ model_validator,
+ Field,
+ ConfigDict,
+)
try:
__version__ = version('nomad-lab')
@@ -33,12 +39,15 @@ except Exception: # noqa
from importlib.metadata import entry_points
-from nomad.common import get_package_path
-from .common import ConfigBaseModel, Options
+from .common import (
+ ConfigBaseModel,
+ Options,
+)
from .north import NORTH
from .plugins import EntryPointType, PluginPackage, Plugins
from .ui import UI
+from nomad.common import get_package_path
warnings.filterwarnings('ignore', message='numpy.dtype size changed')
warnings.filterwarnings('ignore', message='numpy.ufunc size changed')
diff --git a/nomad/config/models/plugins.py b/nomad/config/models/plugins.py
index 6ab41803294bc867da0327930d7c622ef6859fa4..d0fe2af9f0073fe64639af4b343f2252c8c563b1 100644
--- a/nomad/config/models/plugins.py
+++ b/nomad/config/models/plugins.py
@@ -16,16 +16,15 @@
# limitations under the License.
#
-import importlib
import os
-import shutil
import sys
+import shutil
from abc import ABCMeta, abstractmethod
-from typing import TYPE_CHECKING, Literal, Union, cast
-
-from pydantic import BaseModel, Field, model_validator
+import importlib
+from typing import Union, Literal, cast, TYPE_CHECKING
+from pydantic import model_validator, BaseModel, Field
-from nomad.common import download_file, get_package_path, is_safe_relative_path, is_url
+from nomad.common import get_package_path, download_file, is_url, is_safe_relative_path
from .common import Options
from .ui import App
@@ -33,11 +32,10 @@ from .ui import App
example_prefix = '__examples__'
if TYPE_CHECKING:
- from fastapi import FastAPI
-
from nomad.metainfo import SchemaPackage
from nomad.normalizing import Normalizer as NormalizerBaseClass
from nomad.parsing import Parser as ParserBaseClass
+ from fastapi import FastAPI
class EntryPoint(BaseModel):
@@ -764,8 +762,8 @@ def add_plugin(plugin: Schema) -> None:
def remove_plugin(plugin) -> None:
"""Function for removing a plugin."""
from nomad.config import config
- from nomad.metainfo import Package
from nomad.metainfo.elasticsearch_extension import entry_type
+ from nomad.metainfo import Package
# Remove from path
try:
diff --git a/nomad/config/models/ui.py b/nomad/config/models/ui.py
index ed171ebd81925128e2e02dcf960a5d2483f900f3..3e42990c93a731be07e070eb451349c01641405e 100644
--- a/nomad/config/models/ui.py
+++ b/nomad/config/models/ui.py
@@ -17,17 +17,18 @@
#
from enum import Enum
-from typing import Annotated, Literal, Union
-
-from pydantic import BaseModel, ConfigDict, Field, model_validator
+from typing import Union
+from typing import Literal
+from typing import Annotated
+from pydantic import BaseModel, ConfigDict, model_validator, Field
from .common import (
ConfigBaseModel,
Options,
- OptionsBase,
- OptionsGlob,
- OptionsMulti,
OptionsSingle,
+ OptionsMulti,
+ OptionsGlob,
+ OptionsBase,
)
@@ -115,9 +116,8 @@ class UnitSystem(ConfigBaseModel):
values = values.model_dump(exclude_none=True)
"""Adds SI defaults for dimensions that are missing a unit."""
units = values.get('units', {})
- from pint import UndefinedUnitError
-
from nomad.units import ureg
+ from pint import UndefinedUnitError
# Check that only supported dimensions and units are used
for key in units.keys():
diff --git a/nomad/datamodel/context.py b/nomad/datamodel/context.py
index 3c4529c903c1b6107159863d0976416c76390676..e9ca61a9ee0868cc046367e9553b37a71d420e1e 100644
--- a/nomad/datamodel/context.py
+++ b/nomad/datamodel/context.py
@@ -16,19 +16,24 @@
# limitations under the License.
#
-import os.path
-import re
from urllib.parse import urlsplit, urlunsplit
+import re
+import os.path
import requests
from nomad import utils
from nomad.config import config
-from nomad.datamodel import EntryArchive
-from nomad.datamodel.datamodel import EntryMetadata
from nomad.datamodel.util import parse_path
-from nomad.metainfo import Context as MetainfoContext
-from nomad.metainfo import MetainfoReferenceError, MSection, Package, Quantity
+from nomad.datamodel.datamodel import EntryMetadata
+from nomad.metainfo import (
+ Context as MetainfoContext,
+ MSection,
+ Quantity,
+ MetainfoReferenceError,
+ Package,
+)
+from nomad.datamodel import EntryArchive
class Context(MetainfoContext):
diff --git a/nomad/datamodel/data.py b/nomad/datamodel/data.py
index ca029f896327fc8748978d8c9380f74d5ab4a41e..595156644c733089da5dc12f9359004bb63f9dd0 100644
--- a/nomad/datamodel/data.py
+++ b/nomad/datamodel/data.py
@@ -17,23 +17,24 @@
#
import os.path
-from typing import Any
from cachetools import TTLCache, cached
+
+from typing import Any
from pydantic import Field
from nomad.config import config
from nomad.metainfo.elasticsearch_extension import Elasticsearch, material_entry_type
from nomad.metainfo.metainfo import (
- JSON,
- Capitalized,
Category,
- Datetime,
MCategory,
MSection,
Quantity,
- Reference,
+ Capitalized,
Section,
+ Datetime,
+ Reference,
+ JSON,
)
from nomad.metainfo.pydantic_extension import PydanticModel
@@ -95,8 +96,8 @@ class EntryData(ArchiveSection):
def normalize(self, archive, logger):
super().normalize(archive, logger)
- from nomad.datamodel import EntryArchive
from nomad.datamodel.results import Results
+ from nomad.datamodel import EntryArchive
# TODO entry_type should only be assigned if not already defined (done to pass eln test)
if archive.metadata:
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index 3b048eec5182b6980d3b40a9dabe92e5194a4d80..f32012bc14297a83dec7bcbcf9338c5caf4b1789 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -18,40 +18,39 @@
"""All generic entry metadata and related classes."""
-import os.path
-from enum import Enum
from typing import Any
+from enum import Enum
+import os.path
import rfc3161ng
from elasticsearch_dsl import analyzer, tokenizer
from nomad import utils
from nomad.datamodel.metainfo.common import FastAccess
+from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
+from nomad.metainfo.pydantic_extension import PydanticModel
from nomad.metainfo.elasticsearch_extension import (
Elasticsearch,
- create_searchable_quantity,
material_entry_type,
+ entry_type as es_entry_type,
+ create_searchable_quantity,
)
-from nomad.metainfo.elasticsearch_extension import entry_type as es_entry_type
-from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
-from nomad.metainfo.pydantic_extension import PydanticModel
-
+from .util import parse_path
from ..metainfo import (
- JSON,
Bytes,
- Datetime,
+ Package,
Definition,
- MCategory,
- MEnum,
MSection,
- Package,
- Quantity,
+ MCategory,
Section,
SubSection,
+ Quantity,
+ MEnum,
+ Datetime,
+ JSON,
)
from ..metainfo.data_type import m_str
from ..metainfo.metainfo import Reference
-from .util import parse_path
# This is usually defined automatically when the first metainfo definition is evaluated, but
# due to the next imports requiring the m_package already, this would be too late.
diff --git a/nomad/datamodel/hdf5.py b/nomad/datamodel/hdf5.py
index daf56c68ad8fdd8de9750f7de76a07d8abff82f5..fa04a76f9465b26cfa6eb6f0271cd40e7f0cd396 100644
--- a/nomad/datamodel/hdf5.py
+++ b/nomad/datamodel/hdf5.py
@@ -17,16 +17,16 @@
#
from __future__ import annotations
-import re
from typing import Any
-
import h5py
+import re
+
import numpy as np
import pint
from h5py import File
-from nomad.datamodel.metainfo.annotations import H5WebAnnotation
from nomad.metainfo.data_type import NonPrimitive
+from nomad.datamodel.metainfo.annotations import H5WebAnnotation
from nomad.utils import get_logger
LOGGER = get_logger(__name__)
diff --git a/nomad/datamodel/metainfo/action.py b/nomad/datamodel/metainfo/action.py
index 8f219878de54194a6c1eb9040efbd3a7a4f8e184..a4c73d3de524f16e174415d663477c1bbde37261 100644
--- a/nomad/datamodel/metainfo/action.py
+++ b/nomad/datamodel/metainfo/action.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
from nomad.datamodel.data import ArchiveSection
-from nomad.metainfo import Package, Quantity
+from nomad.metainfo import Quantity, Package
m_package = Package()
diff --git a/nomad/datamodel/metainfo/annotations.py b/nomad/datamodel/metainfo/annotations.py
index ed177b2541d635769a755fa10fc544f220765c29..fb9fc113241354a6f1c61d62a15a4ce9f795d048 100644
--- a/nomad/datamodel/metainfo/annotations.py
+++ b/nomad/datamodel/metainfo/annotations.py
@@ -16,19 +16,18 @@
# limitations under the License.
#
-import re
-from enum import Enum
from typing import Any
+from enum import Enum
+from pydantic import field_validator, ConfigDict, Field, model_validator
+import re
-from pydantic import ConfigDict, Field, field_validator, model_validator
from pydantic.main import BaseModel
-from nomad.metainfo import AnnotationModel, Datetime, MEnum, Quantity, Reference
from nomad.utils import strip
-
-from ...metainfo.data_type import Datatype
-from ..data import Query
+from nomad.metainfo import AnnotationModel, MEnum, Datetime, Reference, Quantity
from .plot import PlotlyError
+from ..data import Query
+from ...metainfo.data_type import Datatype
class ELNComponentEnum(str, Enum):
diff --git a/nomad/datamodel/metainfo/basesections/v1.py b/nomad/datamodel/metainfo/basesections/v1.py
index eacde4ab5eab8fb1ba55d743ad57606d1ef5b009..69cebd02de08bdcd4b554099203208030662b3f0 100644
--- a/nomad/datamodel/metainfo/basesections/v1.py
+++ b/nomad/datamodel/metainfo/basesections/v1.py
@@ -20,8 +20,8 @@ import os
import random
import re
import time
-from collections.abc import Iterable
from typing import TYPE_CHECKING
+from collections.abc import Iterable
import h5py
import numpy as np
@@ -29,17 +29,22 @@ import requests
from ase.data import atomic_masses, atomic_numbers, chemical_symbols
from unidecode import unidecode
-from nomad.datamodel.metainfo.workflow import Link, Task, TaskReference, Workflow
from nomad.metainfo import SchemaPackage
+from nomad.datamodel.metainfo.workflow import Link, Task, TaskReference, Workflow
from nomad.metainfo.data_type import m_str
if TYPE_CHECKING:
- from structlog.stdlib import BoundLogger
+ from structlog.stdlib import (
+ BoundLogger,
+ )
from nomad import utils
from nomad.atomutils import Formula
from nomad.datamodel.data import ArchiveSection, EntryData
-from nomad.datamodel.metainfo.annotations import ELNAnnotation, HDF5Annotation
+from nomad.datamodel.metainfo.annotations import (
+ ELNAnnotation,
+ HDF5Annotation,
+)
from nomad.datamodel.results import ELN, Material, Results
from nomad.datamodel.results import ElementalComposition as ResultsElementalComposition
from nomad.datamodel.util import create_custom_mapping
@@ -2034,7 +2039,6 @@ class PublicationReference(ArchiveSection):
super().normalize(archive, logger)
import dateutil.parser
import requests
-
from nomad.datamodel.datamodel import EntryMetadata
# Parse journal name, lead author and publication date from crossref
diff --git a/nomad/datamodel/metainfo/basesections/v2.py b/nomad/datamodel/metainfo/basesections/v2.py
index 1ad7e401f79d68d49a8ba972424a624f9e427b15..01aad791e139f31922c58306c6d2cb353daa03a3 100644
--- a/nomad/datamodel/metainfo/basesections/v2.py
+++ b/nomad/datamodel/metainfo/basesections/v2.py
@@ -15,39 +15,62 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import datetime
import os
+from typing import TYPE_CHECKING
+from collections.abc import Iterable
import random
-import re
import time
-from collections.abc import Iterable
-from typing import TYPE_CHECKING
+import datetime
+import re
-import h5py
+from unidecode import unidecode
import numpy as np
+import h5py
+from ase.data import (
+ chemical_symbols,
+ atomic_numbers,
+ atomic_masses,
+)
import requests
-from ase.data import atomic_masses, atomic_numbers, chemical_symbols
-from unidecode import unidecode
from nomad.datamodel.metainfo.workflow import Link, Task, Workflow
from nomad.metainfo.data_type import m_str
if TYPE_CHECKING:
- from structlog.stdlib import BoundLogger
-from nomad import utils
-from nomad.datamodel.data import ArchiveSection
+ from structlog.stdlib import (
+ BoundLogger,
+ )
+from nomad import (
+ utils,
+)
+from nomad.units import (
+ ureg,
+)
+from nomad.metainfo import (
+ Quantity,
+ Datetime,
+ Section,
+ SectionProxy,
+ SubSection,
+)
+from nomad.metainfo.util import MEnum
+from nomad.datamodel.util import create_custom_mapping
+from nomad.datamodel.data import (
+ ArchiveSection,
+)
+from nomad.datamodel.results import (
+ Results,
+ ELN,
+ ElementalComposition as ResultsElementalComposition,
+ Material,
+)
from nomad.datamodel.metainfo.annotations import (
ELNAnnotation,
Filter,
- HDF5Annotation,
SectionProperties,
+ HDF5Annotation,
)
-from nomad.datamodel.results import ELN, Material, Results
-from nomad.datamodel.results import ElementalComposition as ResultsElementalComposition
-from nomad.datamodel.util import create_custom_mapping
-from nomad.metainfo import Datetime, Quantity, Section, SectionProxy, SubSection
-from nomad.metainfo.util import MEnum
-from nomad.units import ureg
+
PUB_CHEM_PUG_PATH = 'https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound'
CAS_API_PATH = 'https://commonchemistry.cas.org/api'
@@ -385,7 +408,7 @@ class EntityReference(SectionReference):
"""
super().normalize(archive, logger)
if self.reference is None and self.lab_id is not None:
- from nomad.search import MetadataPagination, search
+ from nomad.search import search, MetadataPagination
query = {'results.eln.lab_ids': self.lab_id}
search_result = search(
@@ -1572,11 +1595,10 @@ class PublicationReference(ArchiveSection):
logger ('BoundLogger'): A structlog logger.
"""
super().normalize(archive, logger)
+ from nomad.datamodel.datamodel import EntryMetadata
import dateutil.parser
import requests
- from nomad.datamodel.datamodel import EntryMetadata
-
# Parse journal name, lead author and publication date from crossref
if self.DOI_number:
try:
diff --git a/nomad/datamodel/metainfo/common.py b/nomad/datamodel/metainfo/common.py
index beeb755d6d910afe3250dbe525b763c6ed54a4b2..14bc1024ec90ec024b8bb863729254b268c6dbfa 100644
--- a/nomad/datamodel/metainfo/common.py
+++ b/nomad/datamodel/metainfo/common.py
@@ -16,7 +16,8 @@
# limitations under the License.
#
-from nomad.metainfo import Category, MCategory, MSection, Quantity, Section, SubSection
+from nomad.metainfo import MCategory, Category
+from nomad.metainfo import MSection, Section, SubSection, Quantity
from nomad.metainfo.elasticsearch_extension import Elasticsearch, material_entry_type
diff --git a/nomad/datamodel/metainfo/downloads.py b/nomad/datamodel/metainfo/downloads.py
index 8ada69e13bc3735549b3955517b4a5ccd762af1e..9ff64389d79966909ddf158a38a2cc249d61f781 100644
--- a/nomad/datamodel/metainfo/downloads.py
+++ b/nomad/datamodel/metainfo/downloads.py
@@ -18,9 +18,11 @@
import os.path
-from nomad.datamodel.data import ArchiveSection
from nomad.metainfo import MSection, Package, Quantity, SubSection
+from nomad.datamodel.data import ArchiveSection
+
+
m_package = Package(name='downloads')
@@ -135,8 +137,7 @@ class Downloads(ArchiveSection):
import pathlib
import urllib.request
-
- from nomad.common import extract_file, get_compression_format
+ from nomad.common import get_compression_format, extract_file
# download and extract files
skip_download = True
diff --git a/nomad/datamodel/metainfo/measurements.py b/nomad/datamodel/metainfo/measurements.py
index a6bb1fca5cf666c4c9699d8b15d3ec1228248011..c10787470caf5c12a1fde04e29fd44a6daa80698 100644
--- a/nomad/datamodel/metainfo/measurements.py
+++ b/nomad/datamodel/metainfo/measurements.py
@@ -18,9 +18,10 @@
import numpy as np
-from nomad.datamodel import Author
-from nomad.metainfo import Datetime, MSection, Package, Quantity, SubSection
+from nomad.metainfo import MSection, Package, Quantity, SubSection, Datetime
from nomad.metainfo.metainfo import Reference, SectionProxy
+from nomad.datamodel import Author
+
m_package = Package(name='measurements')
diff --git a/nomad/datamodel/metainfo/plot.py b/nomad/datamodel/metainfo/plot.py
index caaf30037f341d1d9038009d2d75094d12a85b2a..3618263f8e78b5f19f434f6af17791de836de6a4 100644
--- a/nomad/datamodel/metainfo/plot.py
+++ b/nomad/datamodel/metainfo/plot.py
@@ -15,16 +15,14 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from copy import deepcopy
-from datetime import datetime
-
-import numpy as np
+from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Quantity, SubSection, Package, MSection, JSON, Section
import plotly.express as px
import plotly.graph_objs as go
from plotly.subplots import make_subplots
-
-from nomad.datamodel.data import ArchiveSection
-from nomad.metainfo import JSON, MSection, Package, Quantity, Section, SubSection
+import numpy as np
+from copy import deepcopy
+from datetime import datetime
class PlotlyError(Exception):
diff --git a/nomad/datamodel/metainfo/simulation/calculation.py b/nomad/datamodel/metainfo/simulation/calculation.py
index a4ecc9095459db3682c480b3cfcd6b9693620f14..1dc907a8eefc03bc6bb1a42692179f29e2234103 100644
--- a/nomad/datamodel/metainfo/simulation/calculation.py
+++ b/nomad/datamodel/metainfo/simulation/calculation.py
@@ -21,27 +21,27 @@
# https://github.com/nomad-coe/nomad-schema-plugin-run.git
import numpy as np # noqa: F401
-
-from nomad.datamodel.data import ArchiveSection
-from nomad.datamodel.metainfo.common import PropertySection, ProvenanceTracker
-from nomad.datamodel.metainfo.simulation.method import HoppingMatrix, Method
-from nomad.datamodel.metainfo.simulation.system import AtomsGroup, System
from nomad.metainfo import ( # noqa: F401
- Category,
- MCategory,
- MEnum,
MSection,
+ MCategory,
+ Category,
Package,
Quantity,
- Reference,
Section,
- SectionProxy,
SubSection,
+ SectionProxy,
+ Reference,
+ MEnum,
derived,
)
+from nomad.datamodel.metainfo.common import ProvenanceTracker, PropertySection
+from nomad.datamodel.metainfo.simulation.system import System, AtomsGroup
+from nomad.datamodel.metainfo.simulation.method import Method, HoppingMatrix
+from nomad.datamodel.data import ArchiveSection
from ..common import FastAccess
+
m_package = Package()
diff --git a/nomad/datamodel/metainfo/simulation/legacy_workflows.py b/nomad/datamodel/metainfo/simulation/legacy_workflows.py
index 7a4eef3e5d887f275b911570155e4d03d2b81b4c..52a62e4a1f4833c630a4ef2202e7a739863088ac 100644
--- a/nomad/datamodel/metainfo/simulation/legacy_workflows.py
+++ b/nomad/datamodel/metainfo/simulation/legacy_workflows.py
@@ -22,26 +22,26 @@
import numpy as np
from nptyping import NDArray
-
-from nomad.datamodel.metainfo.common import FastAccess
-from nomad.datamodel.metainfo.simulation.calculation import (
- BandStructure,
- Calculation,
- Dos,
-)
-from nomad.datamodel.metainfo.simulation.run import Run
-from nomad.datamodel.metainfo.simulation.system import Atoms, AtomsGroup, System
from nomad.metainfo import (
- MEnum,
MSection,
- Package,
+ MEnum,
Quantity,
- Reference,
Section,
- SectionProxy,
SubSection,
+ SectionProxy,
+ Reference,
+ Package,
derived,
)
+from nomad.datamodel.metainfo.simulation.calculation import (
+ Calculation,
+ Dos,
+ BandStructure,
+)
+from nomad.datamodel.metainfo.simulation.run import Run
+from nomad.datamodel.metainfo.simulation.system import System, Atoms, AtomsGroup
+from nomad.datamodel.metainfo.common import FastAccess
+
m_package = Package()
diff --git a/nomad/datamodel/metainfo/simulation/method.py b/nomad/datamodel/metainfo/simulation/method.py
index 0d88668563fd6c5dcbd90c76a15f92d0e65381d9..165fdfa0ae05dcab3ac0fd245e7dcd730cfda1e0 100644
--- a/nomad/datamodel/metainfo/simulation/method.py
+++ b/nomad/datamodel/metainfo/simulation/method.py
@@ -20,29 +20,28 @@
# Only for purpose of compatibility. Use run schema plugin.
# https://github.com/nomad-coe/nomad-schema-plugin-run.git
-import typing
from logging import Logger
-
import numpy as np # noqa: F401
-from pint.util import SharedRegistryObject # noqa: F401
+import typing
+from pint.util import SharedRegistryObject # noqa: F401
from nomad.datamodel.data import ArchiveSection
from nomad.metainfo import ( # noqa: F401
- Category,
- MCategory,
- MEnum,
MSection,
+ MCategory,
+ Category,
Package,
Quantity,
- Reference,
Section,
- SectionProxy,
SubSection,
+ SectionProxy,
+ Reference,
+ MEnum,
)
from nomad.quantum_states import RussellSaundersState
-
from ..common import FastAccess
+
m_package = Package()
diff --git a/nomad/datamodel/metainfo/simulation/run.py b/nomad/datamodel/metainfo/simulation/run.py
index 2dd64bf26696ef6d4b7450071f435851a39a8eed..93cca85f6a29e593ccd2de76e606b459818a1c33 100644
--- a/nomad/datamodel/metainfo/simulation/run.py
+++ b/nomad/datamodel/metainfo/simulation/run.py
@@ -22,22 +22,22 @@
import numpy as np # noqa: F401
-from nomad.datamodel.data import ArchiveSection
-from nomad.datamodel.metainfo.common import FastAccess
-from nomad.datamodel.metainfo.simulation.calculation import Calculation
-from nomad.datamodel.metainfo.simulation.method import Method
-from nomad.datamodel.metainfo.simulation.system import System
from nomad.metainfo import ( # noqa: F401
- Category,
- MCategory,
MSection,
+ MCategory,
+ Category,
Package,
Quantity,
- Reference,
Section,
- SectionProxy,
SubSection,
+ SectionProxy,
+ Reference,
)
+from nomad.datamodel.metainfo.simulation.method import Method
+from nomad.datamodel.metainfo.simulation.system import System
+from nomad.datamodel.metainfo.simulation.calculation import Calculation
+from nomad.datamodel.metainfo.common import FastAccess
+from nomad.datamodel.data import ArchiveSection
m_package = Package()
diff --git a/nomad/datamodel/metainfo/simulation/system.py b/nomad/datamodel/metainfo/simulation/system.py
index c5645aebbf0f6aa5dd19826b6213f13a52f88019..fe4a73deab62e75a8de3a205f123976c6f73284d 100644
--- a/nomad/datamodel/metainfo/simulation/system.py
+++ b/nomad/datamodel/metainfo/simulation/system.py
@@ -20,28 +20,26 @@
# Only for purpose of compatibility. Use run schema plugin.
# https://github.com/nomad-coe/nomad-schema-plugin-run.git
-import typing # noqa: F401
-
import numpy as np # noqa: F401
-
-from nomad.datamodel.data import ArchiveSection
+import typing # noqa: F401
from nomad.metainfo import ( # noqa: F401
- Category,
- MCategory,
- MEnum,
MSection,
+ MCategory,
+ Category,
Package,
Quantity,
- Reference,
Section,
- SectionProxy,
SubSection,
+ SectionProxy,
+ Reference,
+ MEnum,
derived,
)
+from nomad.datamodel.data import ArchiveSection
from nomad.metainfo.data_type import m_float64
-from nomad.units import ureg
from ..common import FastAccess
+from nomad.units import ureg
m_package = Package()
diff --git a/nomad/datamodel/metainfo/simulation/workflow.py b/nomad/datamodel/metainfo/simulation/workflow.py
index aa77ddb2d01bccb48645324e4d9986c897058ba3..ae5dde4f1b2eef7c68a5c61fef655413506721f8 100644
--- a/nomad/datamodel/metainfo/simulation/workflow.py
+++ b/nomad/datamodel/metainfo/simulation/workflow.py
@@ -27,48 +27,45 @@ from nptyping import NDArray
from nomad.atomutils import get_volume
from nomad.datamodel.data import ArchiveSection
+from nomad.units import ureg
+from nomad.metainfo import (
+ MSection,
+ SubSection,
+ Section,
+ Quantity,
+ MEnum,
+ Reference,
+ Package,
+ derived,
+)
from nomad.datamodel.metainfo.common import FastAccess
+from nomad.datamodel.metainfo.workflow import Workflow, Link, Task
+from nomad.datamodel.metainfo.simulation.system import System, AtomsGroup
+from nomad.datamodel.metainfo.simulation.method import (
+ Method,
+ XCFunctional,
+ BasisSetContainer,
+ GW as GWMethodology,
+ TB as TBMethodology,
+ DMFT as DMFTMethodology,
+ BSE as BSEMethodology,
+)
from nomad.datamodel.metainfo.simulation.calculation import (
- BandEnergies,
+ Calculation,
BandGap,
+ Dos,
BandStructure,
- Calculation,
+ BandEnergies,
Density,
- Dos,
- ElectronicStructureProvenance,
- EnergyEntry,
- GreensFunctions,
Potential,
Spectra,
-)
-from nomad.datamodel.metainfo.simulation.calculation import (
+ ElectronicStructureProvenance,
+ GreensFunctions,
RadiusOfGyration as RadiusOfGyrationCalculation,
-)
-from nomad.datamodel.metainfo.simulation.calculation import (
RadiusOfGyrationValues as RadiusOfGyrationValuesCalculation,
+ EnergyEntry,
)
-from nomad.datamodel.metainfo.simulation.method import BSE as BSEMethodology
-from nomad.datamodel.metainfo.simulation.method import DMFT as DMFTMethodology
-from nomad.datamodel.metainfo.simulation.method import GW as GWMethodology
-from nomad.datamodel.metainfo.simulation.method import TB as TBMethodology
-from nomad.datamodel.metainfo.simulation.method import (
- BasisSetContainer,
- Method,
- XCFunctional,
-)
-from nomad.datamodel.metainfo.simulation.system import AtomsGroup, System
-from nomad.datamodel.metainfo.workflow import Link, Task, Workflow
-from nomad.metainfo import (
- MEnum,
- MSection,
- Package,
- Quantity,
- Reference,
- Section,
- SubSection,
- derived,
-)
-from nomad.units import ureg
+
# TODO remove this after reprocessing with the new schema defined in
# simulationworkflowschema plug in https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git
@@ -2205,11 +2202,11 @@ class MolecularDynamicsResults(ThermodynamicsResults):
super().normalize(archive, logger)
try:
+ from simulationworkflowschema.molecular_dynamics import archive_to_universe
from simulationworkflowschema.molecular_dynamics import (
- archive_to_universe,
+ calc_molecular_rdf,
calc_molecular_mean_squared_displacements,
calc_molecular_radius_of_gyration,
- calc_molecular_rdf,
)
universe = archive_to_universe(archive)
diff --git a/nomad/datamodel/metainfo/system.py b/nomad/datamodel/metainfo/system.py
index 05fce8c21c63a8dc2c831dde8a8647fef4c31ca0..bcff5a8172b802abbdf02991f982c954c32b47b2 100644
--- a/nomad/datamodel/metainfo/system.py
+++ b/nomad/datamodel/metainfo/system.py
@@ -15,11 +15,11 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import ase
import numpy as np
+import ase
+from nomad.metainfo import Package, Quantity, Section, SubSection, SectionProxy
from nomad.datamodel.data import ArchiveSection
-from nomad.metainfo import Package, Quantity, Section, SectionProxy, SubSection
from nomad.units import ureg
# TODO System should be redefined from base section
diff --git a/nomad/datamodel/metainfo/tabulartree.py b/nomad/datamodel/metainfo/tabulartree.py
index 496090623503842216ee0543243152407caa7f84..806be1c2c6651d346cf82af29a3006dd3b66984f 100644
--- a/nomad/datamodel/metainfo/tabulartree.py
+++ b/nomad/datamodel/metainfo/tabulartree.py
@@ -20,6 +20,7 @@ import typing
from nomad.metainfo import MSection, Package, Quantity, SubSection
+
m_package = Package(name='tabulartree')
diff --git a/nomad/datamodel/metainfo/workflow.py b/nomad/datamodel/metainfo/workflow.py
index a1c3fe137a10327b3ec04aeb1ad514d736e9c8b1..2f446ebaeec2da83ff31e47e2809bf03d0dc5971 100644
--- a/nomad/datamodel/metainfo/workflow.py
+++ b/nomad/datamodel/metainfo/workflow.py
@@ -16,8 +16,9 @@
# limitations under the License.
#
+from nomad.metainfo import Quantity, SubSection, Section
+
from nomad.datamodel.data import ArchiveSection, EntryData, WorkflowsElnCategory
-from nomad.metainfo import Quantity, Section, SubSection
class Link(ArchiveSection):
diff --git a/nomad/datamodel/optimade.py b/nomad/datamodel/optimade.py
index 5dfea496884e1083320992269c16d073e97cdb3e..f72fa69cbf3a836fc54d7b3ab0af320716d91868 100644
--- a/nomad/datamodel/optimade.py
+++ b/nomad/datamodel/optimade.py
@@ -16,19 +16,19 @@
# limitations under the License.
#
-import numpy as np
from ase.data import chemical_symbols
+import numpy as np
+from nomad.units import ureg
from nomad.metainfo import (
- DefinitionAnnotation,
- MEnum,
MSection,
- Quantity,
Section,
+ Quantity,
SubSection,
+ MEnum,
+ DefinitionAnnotation,
)
from nomad.metainfo.elasticsearch_extension import Elasticsearch
-from nomad.units import ureg
def optimade_links(section: str):
diff --git a/nomad/datamodel/results.py b/nomad/datamodel/results.py
index 2942b4bd44cfe49ccaeae5cae4dfd147b145d576..f4f090d2ba4e7b46c5d5cedfc30a17257a4ba676 100644
--- a/nomad/datamodel/results.py
+++ b/nomad/datamodel/results.py
@@ -18,40 +18,43 @@
from logging import Logger
from typing import TYPE_CHECKING
-
import numpy as np
-from ase.data import chemical_symbols
from elasticsearch_dsl import Text
+from ase.data import chemical_symbols
+
from nomad.config import config
-from nomad.datamodel.metainfo.annotations import H5WebAnnotation
-from nomad.datamodel.metainfo.common import PropertySection, ProvenanceTracker
+from nomad.datamodel.metainfo.common import ProvenanceTracker, PropertySection
from nomad.datamodel.metainfo.simulation.method import CoreHole as CoreHoleRun
-from nomad.datamodel.optimade import Species as OptimadeSpecies # noqa
+from nomad.metainfo.elasticsearch_extension import (
+ Elasticsearch,
+ material_type,
+ material_entry_type,
+ get_tokenizer,
+)
+
from nomad.metainfo import (
- Datetime,
- MEnum,
MSection,
- Package,
- Quantity,
- Reference,
Section,
SubSection,
+ Quantity,
+ MEnum,
+ Package,
+ Datetime,
+ Reference,
)
-from nomad.metainfo.elasticsearch_extension import (
- Elasticsearch,
- get_tokenizer,
- material_entry_type,
- material_type,
-)
+from nomad.datamodel.metainfo.common import ProvenanceTracker, PropertySection
+from nomad.datamodel.optimade import Species as OptimadeSpecies # noqa
+from nomad.datamodel.metainfo.annotations import H5WebAnnotation
try:
import runschema
runschema.run_schema_entry_point.load()
- import runschema.calculation
import runschema.method
+ import runschema.calculation
import runschema.system
+
import simulationworkflowschema
simulationworkflowschema.simulationworkflow_schema_entry_point.load()
diff --git a/nomad/datamodel/util.py b/nomad/datamodel/util.py
index 60780338245abd42e1bfc44f3715804742c4a8f9..63ab9e0c481a61278f3dbee0373d5beb7626780e 100644
--- a/nomad/datamodel/util.py
+++ b/nomad/datamodel/util.py
@@ -17,19 +17,19 @@
#
import math
import re
-from collections.abc import Callable
from typing import Any
+from collections.abc import Callable
import numpy as np
from nomad import utils
from nomad.metainfo import (
+ Section,
AnnotationModel,
- MetainfoError,
MSection,
- Property,
- Section,
SubSection,
+ Property,
+ MetainfoError,
)
from nomad.units import ureg
diff --git a/nomad/doi.py b/nomad/doi.py
index fe1df5f0492c2500fee31111c48572c19ab58f76..a755e19c31e6059503dbef60b6d59340b954bbda 100644
--- a/nomad/doi.py
+++ b/nomad/doi.py
@@ -21,18 +21,17 @@ This module contains all functions necessary to manage DOI via datacite.org and
MDS API (https://support.datacite.org/docs/mds-api-guide).
"""
-import datetime
import xml.etree.ElementTree as ET
-
+import datetime
import requests
-from fastapi import HTTPException
-from mongoengine import DateTimeField, Document, StringField
-from mongoengine.errors import NotUniqueError
from requests.auth import HTTPBasicAuth
+from mongoengine import Document, StringField, DateTimeField
+from mongoengine.errors import NotUniqueError
-from nomad import utils
-from nomad.config import config
from nomad.datamodel import User
+from nomad.config import config
+from nomad import utils
+from fastapi import HTTPException
class DOIException(Exception):
diff --git a/nomad/files.py b/nomad/files.py
index d40bf0e1024af97eaaf1339d03d6c8021c39d542..fdf0f0b8ee144a08c552cf4717b79ed77e58bfab 100644
--- a/nomad/files.py
+++ b/nomad/files.py
@@ -45,35 +45,40 @@ original mainfile, and vice versa.
from __future__ import annotations
+from abc import ABCMeta
+from typing import (
+ IO,
+ Any,
+ NamedTuple,
+)
+from collections.abc import Callable
+from collections.abc import Iterable, Iterator
+from pydantic import BaseModel
+from datetime import datetime
+import os.path
+import os
+import shutil
+import zipstream
import hashlib
import io
import json
-import os
-import os.path
-import shutil
+import yaml
+import magic
import tarfile # noqa: F401
import zipfile
-from abc import ABCMeta
-from collections.abc import Callable, Iterable, Iterator
-from datetime import datetime
-from typing import IO, Any, NamedTuple
-import magic
-import yaml
-import zipstream
-from pydantic import BaseModel
-from nomad import datamodel, utils
-from nomad.archive import ArchiveReader, read_archive, to_json, write_archive
-from nomad.archive.storage_v2 import combine_archive
+from nomad import utils, datamodel
from nomad.common import (
- extract_file,
get_compression_format,
+ extract_file,
is_safe_basename,
is_safe_relative_path,
)
from nomad.config import config
-from nomad.config.models.config import BundleExportSettings, BundleImportSettings
+from nomad.archive.storage_v2 import combine_archive
+from nomad.config.models.config import BundleImportSettings, BundleExportSettings
+from nomad.archive import write_archive, read_archive, ArchiveReader, to_json
bundle_info_filename = 'bundle_info.json'
diff --git a/nomad/graph/graph_reader.py b/nomad/graph/graph_reader.py
index 24139f771409b93ca2c6d3ee3cd064f12790534d..d813a8f3755159a98aa44e1533793f4f0645ea43 100644
--- a/nomad/graph/graph_reader.py
+++ b/nomad/graph/graph_reader.py
@@ -24,10 +24,11 @@ import functools
import itertools
import os
import re
-from collections.abc import AsyncIterator, Callable, Iterator
+from collections.abc import AsyncIterator, Iterator
from contextlib import contextmanager
from threading import Lock
from typing import Any
+from collections.abc import Callable
import orjson
from cachetools import TTLCache
@@ -54,10 +55,23 @@ from nomad.app.v1.routers.uploads import (
get_upload_with_read_access,
upload_to_pydantic,
)
-from nomad.archive import ArchiveDict, ArchiveList, to_json
-from nomad.archive.storage_v2 import ArchiveDict as ArchiveDictNew
-from nomad.archive.storage_v2 import ArchiveList as ArchiveListNew
-from nomad.datamodel import Dataset, EntryArchive, ServerContext, User
+from nomad.archive import (
+ ArchiveDict,
+ ArchiveList,
+ to_json,
+)
+from nomad.archive.storage_v2 import (
+ ArchiveDict as ArchiveDictNew,
+)
+from nomad.archive.storage_v2 import (
+ ArchiveList as ArchiveListNew,
+)
+from nomad.datamodel import (
+ Dataset,
+ EntryArchive,
+ ServerContext,
+ User,
+)
from nomad.datamodel.util import parse_path
from nomad.files import RawPathInfo, UploadFiles
from nomad.graph.lazy_wrapper import (
@@ -88,8 +102,8 @@ from nomad.metainfo import (
SectionReference,
SubSection,
)
-from nomad.metainfo.data_type import JSON, Datatype
from nomad.metainfo.data_type import Any as AnyType
+from nomad.metainfo.data_type import JSON, Datatype
from nomad.metainfo.util import MSubSectionList, split_python_definition
from nomad.processing import Entry, ProcessStatus, Upload
from nomad.utils import timer
diff --git a/nomad/graph/lazy_wrapper.py b/nomad/graph/lazy_wrapper.py
index 148a6c079de5944615cf1edbfd162360050392d4..87b777b4833de13f0c7344454a94a0315cb25fa9 100644
--- a/nomad/graph/lazy_wrapper.py
+++ b/nomad/graph/lazy_wrapper.py
@@ -26,7 +26,6 @@ Different wrappers are catered for different types of objects/operations.
"""
from __future__ import annotations
-
from functools import cached_property
from nomad.datamodel import User
diff --git a/nomad/graph/model.py b/nomad/graph/model.py
index 669d7f1276e4a8386e1aadea61583917473cc7ed..f8bf6f1c38f1150f2c4d8284d1fbeb455efd0e0f 100644
--- a/nomad/graph/model.py
+++ b/nomad/graph/model.py
@@ -25,15 +25,14 @@ from typing import Annotated, Union
from pydantic import (
AfterValidator,
- BaseModel,
+ field_validator,
ConfigDict,
+ BaseModel,
Field,
ValidationError,
- field_validator,
)
from nomad.app.v1.models import Direction, Metadata, MetadataPagination, Pagination
-from nomad.app.v1.models.groups import UserGroupPagination, UserGroupQuery
from nomad.app.v1.routers.datasets import DatasetPagination
from nomad.app.v1.routers.uploads import (
EntryProcDataPagination,
@@ -41,6 +40,7 @@ from nomad.app.v1.routers.uploads import (
UploadProcDataPagination,
UploadProcDataQuery,
)
+from nomad.app.v1.models.groups import UserGroupQuery, UserGroupPagination
class DatasetQuery(BaseModel):
diff --git a/nomad/infrastructure.py b/nomad/infrastructure.py
index 0d98646a160f725c7ce489d61a6d16ce8187ac95..5adbf9f90beef51ff0602410e00d50785f95812b 100644
--- a/nomad/infrastructure.py
+++ b/nomad/infrastructure.py
@@ -23,34 +23,33 @@ is run once for each *api* and *worker* process. Individual functions for partia
exist to facilitate testing, aspects of :py:mod:`nomad.cli`, etc.
"""
-import json
-import os
import os.path
-import re
+import os
import shutil
+from elasticsearch_dsl import connections
+from mongoengine import connect, disconnect
+from mongoengine.connection import ConnectionFailure
import smtplib
-
-# TODO put somemore thought into warnings
-import warnings
-from datetime import datetime
from email.mime.text import MIMEText
-
+from keycloak import KeycloakOpenID, KeycloakAdmin
+from keycloak.exceptions import KeycloakAuthenticationError, KeycloakGetError
+import json
import jwt
+from datetime import datetime
+import re
import unidecode
-from elasticsearch_dsl import connections
-from keycloak import KeycloakAdmin, KeycloakOpenID
-from keycloak.exceptions import KeycloakAuthenticationError, KeycloakGetError
-from mongoengine import connect, disconnect
-from mongoengine.connection import ConnectionFailure
from nomad import utils
from nomad.config import config
+from nomad.utils.structlogging import get_logger
# The metainfo is defined and used during imports. This is problematic.
# We import all parsers very early in the infrastructure setup. This will populate
# the metainfo with parser specific definitions, before the metainfo might be used.
from nomad.parsing import parsers # noqa: F401
-from nomad.utils.structlogging import get_logger
+
+# TODO put somemore thought into warnings
+import warnings
warnings.filterwarnings('ignore')
diff --git a/nomad/logtransfer.py b/nomad/logtransfer.py
index f85170d8bd3d43d93212bc83b3c9e6609bf7937b..6c884540c21a379be6f8eb4bbf005ef5ec207a7b 100644
--- a/nomad/logtransfer.py
+++ b/nomad/logtransfer.py
@@ -16,15 +16,15 @@
# limitations under the License.
#
-import os
+import requests
+import zlib
import os.path
+import os
import time
-import zlib
-import requests
-from nomad import utils
from nomad.config import config
+from nomad import utils
logger = utils.get_logger(__name__)
diff --git a/nomad/metainfo/annotation.py b/nomad/metainfo/annotation.py
index 6ee540abe928d152d28b324e2ca686c93f708f75..b3bec23d57457dcf2a420fc8a68e83574ae4088c 100644
--- a/nomad/metainfo/annotation.py
+++ b/nomad/metainfo/annotation.py
@@ -20,7 +20,7 @@ from __future__ import annotations
from typing import Any, ClassVar, ForwardRef
-from pydantic import BaseModel, ConfigDict, Field
+from pydantic import ConfigDict, BaseModel, Field
class Annotation:
diff --git a/nomad/metainfo/data_frames.py b/nomad/metainfo/data_frames.py
index 4f2f1fc7d1079f32328e601cc83a30c5d7138d14..94f510e9b6952e8e940f55814702ef3ed0e745ea 100644
--- a/nomad/metainfo/data_frames.py
+++ b/nomad/metainfo/data_frames.py
@@ -1,13 +1,19 @@
-import inspect
import types
-from collections.abc import Iterable
from typing import Union, cast
-
+from collections.abc import Iterable
import numpy as np
-import xarray as xr
+import inspect
from pydantic import BaseModel
+import xarray as xr
-from nomad.metainfo import MSection, Package, Quantity, Section, SubSection, constraint
+from nomad.metainfo import (
+ MSection,
+ Section,
+ Quantity,
+ SubSection,
+ Package,
+ constraint,
+)
from nomad.metainfo.metainfo import _placeholder_quantity
from nomad.units import ureg
diff --git a/nomad/metainfo/data_type.py b/nomad/metainfo/data_type.py
index 6f9b89f798ae35a02ff7bcb57afcb6cb714d36dd..04b4c724651ac2a2307d9d3c55b8aba26799605b 100644
--- a/nomad/metainfo/data_type.py
+++ b/nomad/metainfo/data_type.py
@@ -22,7 +22,7 @@ import importlib
import re
import typing
from base64 import b64decode, b64encode
-from datetime import date, datetime
+from datetime import datetime, date
from functools import reduce
from inspect import isclass
from typing import Any as TypingAny
@@ -1248,12 +1248,12 @@ def to_optimade_type(in_type: Datatype):
def to_mongo_type(in_type: Datatype):
from mongoengine import (
+ IntField,
+ FloatField,
BooleanField,
+ StringField,
DateTimeField,
DictField,
- FloatField,
- IntField,
- StringField,
)
standard_type = in_type.standard_type()
diff --git a/nomad/metainfo/elasticsearch_extension.py b/nomad/metainfo/elasticsearch_extension.py
index 9d386d432962409b16d2d4f8cc34019d87cf0eb3..f45f5ece73bd9d80b49030b437087563d5afef13 100644
--- a/nomad/metainfo/elasticsearch_extension.py
+++ b/nomad/metainfo/elasticsearch_extension.py
@@ -159,15 +159,19 @@ sub-sections as if they were direct sub-sections.
import math
import re
from collections import defaultdict
+from typing import (
+ TYPE_CHECKING,
+ Any,
+ Optional,
+ cast,
+)
from collections.abc import Callable
-from typing import TYPE_CHECKING, Any, Optional, cast
from elasticsearch_dsl import Q
-from pint import Quantity as PintQuantity
-
from nomad import utils
from nomad.config import config
from nomad.config.models.plugins import Parser, Schema, SchemaPackageEntryPoint
+from pint import Quantity as PintQuantity
from . import DefinitionAnnotation
from .data_type import Datatype, to_elastic_type
diff --git a/nomad/metainfo/example.py b/nomad/metainfo/example.py
index d7acce8ee9bae8c5514cce7113692b3e3663a5de..3e7f7443b41013722c1058de5bf70e0491629b7d 100644
--- a/nomad/metainfo/example.py
+++ b/nomad/metainfo/example.py
@@ -18,22 +18,21 @@
"""An example metainfo package."""
-from datetime import datetime
-
import numpy as np
+from datetime import datetime
+from nomad.units import ureg
from nomad.metainfo import (
- Datetime,
- MCategory,
- MEnum,
MSection,
- Package,
- Quantity,
+ MCategory,
Section,
+ Quantity,
+ Package,
SubSection,
+ MEnum,
+ Datetime,
constraint,
)
-from nomad.units import ureg
m_package = Package(links=['https://nomad-lab.eu/prod/rae/docs/metainfo.html'])
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index 67072e835dee58c21f0007d82df38f6dc6ae3e1f..1532e571e369188ec09b1742dd25dd3f61d8a67d 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -34,7 +34,7 @@ from urllib.parse import urlsplit, urlunsplit
import docstring_parser
import jmespath
import pint
-from pydantic import BaseModel, TypeAdapter, ValidationError
+from pydantic import TypeAdapter, ValidationError, BaseModel
from nomad.config import config
from nomad.metainfo.data_type import JSON as JSONType
@@ -43,20 +43,14 @@ from nomad.metainfo.data_type import Any as AnyType
from nomad.metainfo.data_type import Bytes as BytesType
from nomad.metainfo.data_type import Callable as CallableType
from nomad.metainfo.data_type import Capitalized as CapitalizedType
-from nomad.metainfo.data_type import (
- Datatype,
- Enum,
- ExactNumber,
- InexactNumber,
- Number,
- check_dimensionality,
- m_str,
- normalize_type,
-)
+from nomad.metainfo.data_type import Datatype
from nomad.metainfo.data_type import Datetime as DatetimeType
from nomad.metainfo.data_type import Dimension as DimensionType
+from nomad.metainfo.data_type import Enum, ExactNumber
from nomad.metainfo.data_type import File as FileType
+from nomad.metainfo.data_type import InexactNumber, Number
from nomad.metainfo.data_type import Unit as UnitType
+from nomad.metainfo.data_type import check_dimensionality, m_str, normalize_type
from nomad.metainfo.util import (
MQuantity,
MSubSectionList,
@@ -68,6 +62,7 @@ from nomad.metainfo.util import (
to_dict,
)
from nomad.units import ureg as units
+from pydantic import TypeAdapter, ValidationError
from .annotation import (
Annotation,
diff --git a/nomad/metainfo/mongoengine_extension.py b/nomad/metainfo/mongoengine_extension.py
index c7dd4baa97feed7ab5921ed8e3f926708c902558..34c43289bf804231bc7a8e7a7bb0b87419de133d 100644
--- a/nomad/metainfo/mongoengine_extension.py
+++ b/nomad/metainfo/mongoengine_extension.py
@@ -35,9 +35,12 @@ sections from mongoengine. The annotation key is 'mongo'.
from typing import Any
-from . import Annotation, DefinitionAnnotation, SectionAnnotation
from .data_type import Datatype, to_mongo_type
-from .metainfo import MSection, Quantity
+from .metainfo import (
+ MSection,
+ Quantity,
+)
+from . import Annotation, DefinitionAnnotation, SectionAnnotation
class Mongo(DefinitionAnnotation):
diff --git a/nomad/metainfo/pydantic_extension.py b/nomad/metainfo/pydantic_extension.py
index 155140406df838c76120e987d18527833f04861f..f556768aef564c43f38d0ffe5df79537cfd15af4 100644
--- a/nomad/metainfo/pydantic_extension.py
+++ b/nomad/metainfo/pydantic_extension.py
@@ -33,12 +33,15 @@ Allows to create pydantic models from section definitions.
"""
from typing import cast
+from pydantic import create_model, Field, BaseModel
-from pydantic import BaseModel, Field, create_model
-
-from . import DefinitionAnnotation
from .data_type import to_pydantic_type
-from .metainfo import Definition, Quantity, Section
+from .metainfo import (
+ Definition,
+ Section,
+ Quantity,
+)
+from . import DefinitionAnnotation
class PydanticModel(DefinitionAnnotation):
diff --git a/nomad/metainfo/util.py b/nomad/metainfo/util.py
index a46e70d43c38bbb9eda3fb6807a3bd37af570357..cbaf0eb3c6f32d11bb444842afd71ff7a41e41df 100644
--- a/nomad/metainfo/util.py
+++ b/nomad/metainfo/util.py
@@ -22,7 +22,6 @@ import re
from typing import Any
import pint
-
from nomad.metainfo.data_type import Enum
from nomad.units import ureg
diff --git a/nomad/mkdocs/metainfo.py b/nomad/mkdocs/metainfo.py
index 710a6383dc7cb8ab8ae30b4a667077a7a45e49b3..52c4ea2e3bf1f16aea0ef99a4e3b4af620a51b1a 100644
--- a/nomad/mkdocs/metainfo.py
+++ b/nomad/mkdocs/metainfo.py
@@ -15,8 +15,8 @@
#
from nomad import utils
+from nomad.metainfo import Property, Quantity, Datatype, Reference, SubSection
from nomad.datamodel.data import ArchiveSection
-from nomad.metainfo import Datatype, Property, Quantity, Reference, SubSection
def get_reference(section_def, pkg) -> str:
diff --git a/nomad/mkdocs/pydantic.py b/nomad/mkdocs/pydantic.py
index 774843aa3d48ee149cdda56f32517b3e9543fd54..eb55aa89b76ebc3c16cfa55e1545b34be41c70ac 100644
--- a/nomad/mkdocs/pydantic.py
+++ b/nomad/mkdocs/pydantic.py
@@ -20,16 +20,19 @@
Definitions that are used in the documentation via mkdocs-macro-plugin.
"""
-from enum import Enum
-from inspect import isclass
from types import UnionType
-from typing import Annotated, Any, Literal, Union, get_args, get_origin
+from pydantic.fields import FieldInfo
+from enum import Enum
from pydantic import BaseModel
-from pydantic.fields import FieldInfo
+
+from typing import Annotated, Any, Union, get_args, get_origin
+from typing import Literal
+from inspect import isclass
from nomad import utils
+
exported_config_models = set() # type: ignore
diff --git a/nomad/normalizing/common.py b/nomad/normalizing/common.py
index f03185579dc8dbdbec5a0075841fa9f115be9ade..9075f97a704174bfaacb5662aa1ef225ae23a2ba 100644
--- a/nomad/normalizing/common.py
+++ b/nomad/normalizing/common.py
@@ -15,24 +15,26 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from typing import Any
-
-import matid.geometry # pylint: disable=import-error
import numpy as np
from ase import Atoms
-from matid import SymmetryAnalyzer # pylint: disable=import-error
-from matid.symmetry.wyckoffset import (
- WyckoffSet as WyckoffSetMatID, # pylint: disable=import-error
-)
+from typing import Any
from nptyping import NDArray
+from matid import SymmetryAnalyzer # pylint: disable=import-error
+from matid.symmetry.wyckoffset import WyckoffSet as WyckoffSetMatID # pylint: disable=import-error
+import matid.geometry # pylint: disable=import-error
from nomad import atomutils
from nomad.config import config
+from nomad.utils import hash
+from nomad.units import ureg
from nomad.datamodel.metainfo.system import Atoms as NOMADAtoms
from nomad.datamodel.optimade import Species
-from nomad.datamodel.results import Cell, LatticeParameters, Structure, WyckoffSet
-from nomad.units import ureg
-from nomad.utils import hash
+from nomad.datamodel.results import (
+ Cell,
+ Structure,
+ LatticeParameters,
+ WyckoffSet,
+)
def wyckoff_sets_from_matid(wyckoff_sets: list[WyckoffSetMatID]) -> list[WyckoffSet]:
diff --git a/nomad/normalizing/material.py b/nomad/normalizing/material.py
index 9192162c68cabba23ff671779e183f158afb39b6..f5eed863aa88ba8ed2c8790dfd673e74de7e6de0 100644
--- a/nomad/normalizing/material.py
+++ b/nomad/normalizing/material.py
@@ -16,24 +16,24 @@
#
import re
+from nptyping import NDArray
import ase.data
from matid.classification.classifications import (
- Atom,
Class0D,
+ Atom,
Class1D,
Class2D,
- Class3D,
Material2D,
Surface,
+ Class3D,
)
-from nptyping import NDArray
from nomad import atomutils
from nomad.atomutils import Formula
-from nomad.datamodel.results import Material, Symmetry, structure_name_map
-from nomad.normalizing.common import material_id_1d, material_id_2d, material_id_bulk
+from nomad.normalizing.common import material_id_bulk, material_id_2d, material_id_1d
from nomad.normalizing.topology import TopologyNormalizer
+from nomad.datamodel.results import Symmetry, Material, structure_name_map
class MaterialNormalizer:
diff --git a/nomad/normalizing/metainfo.py b/nomad/normalizing/metainfo.py
index 73e3ddd01829687edab628a8065c73107b60fe26..11238e9224a839a1d4e538c90343ae695bfa18d9 100644
--- a/nomad/normalizing/metainfo.py
+++ b/nomad/normalizing/metainfo.py
@@ -18,7 +18,7 @@
from nomad.datamodel import EntryArchive
from nomad.datamodel.data import ArchiveSection
-
+from nomad.datamodel import EntryArchive
from . import Normalizer
diff --git a/nomad/normalizing/method.py b/nomad/normalizing/method.py
index 2a3355f8b13bf6b9c87d5be54b4f0c5aa54011e1..0fc961ec59be8499fe209547351a58d40abe2f8b 100644
--- a/nomad/normalizing/method.py
+++ b/nomad/normalizing/method.py
@@ -15,33 +15,33 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import re
from abc import ABC, abstractmethod
+from ase.dft.kpoints import monkhorst_pack, get_monkhorst_pack_size_and_offset
from collections import OrderedDict
-
+import re
import numpy as np
-from ase.dft.kpoints import get_monkhorst_pack_size_and_offset, monkhorst_pack
+from nomad.datamodel import EntryArchive, ArchiveSection
+from nomad.metainfo import MSection
+from nomad.metainfo.data_type import Number
+from nomad.units import ureg
+from nomad.metainfo import Section
+from nomad.utils import RestrictedDict
from nomad.config import config
-from nomad.datamodel import ArchiveSection, EntryArchive
from nomad.datamodel.results import (
- BSE,
+ Method,
+ Simulation,
+ HubbardKanamoriModel,
DFT,
- DMFT,
- GW,
TB,
- HubbardKanamoriModel,
- Material,
- Method,
+ GW,
+ BSE,
+ DMFT,
Precision,
- Simulation,
+ Material,
xc_treatments,
xc_treatments_extended,
)
-from nomad.metainfo import MSection, Section
-from nomad.metainfo.data_type import Number
-from nomad.units import ureg
-from nomad.utils import RestrictedDict
class MethodNormalizer: # TODO: add normalizer for atom_parameters.label
diff --git a/nomad/normalizing/normalizer.py b/nomad/normalizing/normalizer.py
index 0c3976f29788071f990c8c94349cacf36134cc81..320571ccbae420d69c1ccbd3a23aedf4c28bf3d2 100644
--- a/nomad/normalizing/normalizer.py
+++ b/nomad/normalizing/normalizer.py
@@ -18,9 +18,9 @@
from abc import ABCMeta, abstractmethod
-from nomad.datamodel import EntryArchive
-from nomad.metainfo import MSection
from nomad.utils import get_logger
+from nomad.metainfo import MSection
+from nomad.datamodel import EntryArchive
class Normalizer(metaclass=ABCMeta):
diff --git a/nomad/normalizing/optimade.py b/nomad/normalizing/optimade.py
index 3c78ab4ca58561576318bd6507cce93685270a8e..f6e1913e46d6d7afef2d40d5e9c16272d5172065 100644
--- a/nomad/normalizing/optimade.py
+++ b/nomad/normalizing/optimade.py
@@ -16,18 +16,19 @@
# limitations under the License.
#
-import re
from typing import Any
-
+import numpy as np
+import re
import ase.data
import ase.formula
-import numpy as np
import pint.quantity
+from nomad.datamodel import EntryArchive
from nomad.atomutils import Formula
-from nomad.datamodel import EntryArchive, EntryMetadata, OptimadeEntry, Species
from nomad.normalizing.normalizer import SystemBasedNormalizer
from nomad.units import ureg
+from nomad.datamodel import OptimadeEntry, Species, EntryMetadata
+
species_re = re.compile(r'^([A-Z][a-z]?)(\d*)$')
atom_label_re = re.compile(
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index 2316cb4510002da124d5deb5408224a3354218ea..85657aa40696c203ea4f667020b439e34ac6bb99 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -17,78 +17,77 @@
#
import re
+import numpy as np
from typing import Any
-
import ase.data
-import matid.geometry # pylint: disable=import-error
-import numpy as np
from matid import SymmetryAnalyzer # pylint: disable=import-error
+import matid.geometry # pylint: disable=import-error
from nomad import atomutils
-from nomad.atomutils import Formula
from nomad.config import config
+from nomad.utils import traverse_reversed, extract_section
+from nomad.atomutils import Formula
+from nomad.normalizing.normalizer import Normalizer
+from nomad.normalizing.method import MethodNormalizer
+from nomad.normalizing.material import MaterialNormalizer
from nomad.datamodel import EntryArchive
-from nomad.datamodel.data import ArchiveSection
from nomad.datamodel.metainfo.workflow import Workflow
+from nomad.datamodel.data import ArchiveSection
+from nomad.normalizing.common import structures_2d
from nomad.datamodel.results import (
BandGap,
BandGapDeprecated,
+ RadialDistributionFunction,
+ RadiusOfGyration,
+ MeanSquaredDisplacement,
+ Results,
+ Material,
+ Method,
+ GeometryOptimization,
+ Trajectory,
+ MolecularDynamics,
+ MDProvenance,
+ TemperatureDynamic,
+ VolumeDynamic,
+ PressureDynamic,
+ EnergyDynamic,
+ Properties,
+ StructuralProperties,
+ DynamicalProperties,
+ EnergyVolumeCurve,
+ BulkModulus,
+ ShearModulus,
+ MechanicalProperties,
+ ElectronicProperties,
+ VibrationalProperties,
+ ThermodynamicProperties,
BandStructureElectronic,
BandStructurePhonon,
- BulkModulus,
- DensityCharge,
DOSElectronic,
- DOSElectronicNew,
DOSNew,
+ DOSElectronicNew,
DOSPhonon,
- DynamicalProperties,
- EELSMethodology,
- ElectricFieldGradient,
- ElectronicProperties,
- EnergyDynamic,
- EnergyFreeHelmholtz,
- EnergyVolumeCurve,
- GeometryOptimization,
GreensFunctionsElectronic,
+ EnergyFreeHelmholtz,
HeatCapacityConstantVolume,
+ SpectroscopicProperties,
+ EELSMethodology,
+ SpectraProvenance,
+ Spectra,
MagneticProperties,
MagneticShielding,
MagneticSusceptibility,
- Material,
- MDProvenance,
- MeanSquaredDisplacement,
- MechanicalProperties,
- Method,
- MolecularDynamics,
- PressureDynamic,
- Properties,
- RadialDistributionFunction,
- RadiusOfGyration,
- Results,
- ShearModulus,
- Spectra,
- SpectraProvenance,
- SpectroscopicProperties,
+ ElectricFieldGradient,
SpinSpinCoupling,
- StructuralProperties,
- TemperatureDynamic,
- ThermodynamicProperties,
- Trajectory,
- VibrationalProperties,
- VolumeDynamic,
+ DensityCharge,
)
-from nomad.normalizing.common import structures_2d
-from nomad.normalizing.material import MaterialNormalizer
-from nomad.normalizing.method import MethodNormalizer
-from nomad.normalizing.normalizer import Normalizer
-from nomad.utils import extract_section, traverse_reversed
try:
import runschema
runschema.run_schema_entry_point.load()
- import runschema.calculation
import runschema.method
+ import runschema.calculation
import runschema.system
except Exception as e:
runschema, simulationworkflowschema = None, None
diff --git a/nomad/normalizing/topology.py b/nomad/normalizing/topology.py
index 2477f91ad67dbb7dd591002a481001838c511919..3a6f4a22e4ee5e84d051b5f7f89485ffdd5c71dc 100644
--- a/nomad/normalizing/topology.py
+++ b/nomad/normalizing/topology.py
@@ -16,45 +16,46 @@
# limitations under the License.
#
-import json
-import pathlib
from collections import defaultdict
+import pathlib
+import json
-import numpy as np
from ase import Atoms
from ase.data import chemical_symbols
+import numpy as np
+from matid.clustering import SBC, Cluster
+from matid.symmetry.symmetryanalyzer import SymmetryAnalyzer
from matid.classification.classifications import (
- Atom,
Class0D,
+ Atom,
Class1D,
Class2D,
- Class3D,
Material2D,
Surface,
+ Class3D,
)
-from matid.clustering import SBC, Cluster
-from matid.symmetry.symmetryanalyzer import SymmetryAnalyzer
-from nomad import atomutils, utils
+from nomad import utils
from nomad.config import config
-from nomad.datamodel.datamodel import EntryArchive
+from nomad import atomutils
from nomad.datamodel.results import (
CoreHole,
+ SymmetryNew as Symmetry,
Material,
- Relation,
System,
+ Relation,
structure_name_map,
)
-from nomad.datamodel.results import SymmetryNew as Symmetry
+from nomad.datamodel.datamodel import EntryArchive
from nomad.normalizing.common import (
- ase_atoms_from_nomad_atoms,
cell_from_ase_atoms,
- material_id_1d,
- material_id_2d,
- material_id_bulk,
+ ase_atoms_from_nomad_atoms,
nomad_atoms_from_ase_atoms,
- structures_2d,
wyckoff_sets_from_matid,
+ structures_2d,
+ material_id_bulk,
+ material_id_2d,
+ material_id_1d,
)
conventional_description = 'The conventional cell of the material from which the subsystem is constructed from.'
diff --git a/nomad/parsing/artificial.py b/nomad/parsing/artificial.py
index ae4f1b74b182c8bda27412689866722071b53fbd..6302b72dde31231c95de7924a889b9d38d20423e 100644
--- a/nomad/parsing/artificial.py
+++ b/nomad/parsing/artificial.py
@@ -21,20 +21,19 @@ Parser for creating artificial test, brenchmark, and demonstration data.
"""
import json
-import os
import os.path
import random
-import signal
+from ase.data import chemical_symbols
+import numpy
import sys
import time
-
-import numpy
-from ase.data import chemical_symbols
+import os
+import signal
from nomad.datamodel import EntryArchive
from nomad.datamodel.metainfo import runschema
-from .parser import MatchingParser, Parser
+from .parser import Parser, MatchingParser
class EmptyParser(MatchingParser):
diff --git a/nomad/parsing/file_parser/file_parser.py b/nomad/parsing/file_parser/file_parser.py
index b9bef402991694ccb5fa5b64d5d25f5eedecbeb4..f66274b69b1c638d585f26926ec4f2a2979183f6 100644
--- a/nomad/parsing/file_parser/file_parser.py
+++ b/nomad/parsing/file_parser/file_parser.py
@@ -12,21 +12,20 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-import bz2
+from abc import ABC, abstractmethod
+import os
+import pint
+from typing import Any, IO
+from collections.abc import Callable
import gzip
+import bz2
import lzma
-import os
import tarfile
-from abc import ABC, abstractmethod
-from collections.abc import Callable
from contextlib import contextmanager
-from typing import IO, Any
-
-import pint
-from nomad.datamodel import EntryArchive
from nomad.metainfo import MSection, SubSection
from nomad.utils import get_logger
+from nomad.datamodel import EntryArchive
class FileParser(ABC):
diff --git a/nomad/parsing/file_parser/mapping_parser.py b/nomad/parsing/file_parser/mapping_parser.py
index 5d0be33bcab33d614518f8d1528a47c37a635750..d443d93fc0207ee0e6968f0091c3ee3cf1b6bc9a 100644
--- a/nomad/parsing/file_parser/mapping_parser.py
+++ b/nomad/parsing/file_parser/mapping_parser.py
@@ -11,8 +11,6 @@ import jmespath.visitor
import numpy as np
from jsonpath_ng.parser import JsonPathParser
from lxml import etree
-from pydantic import BaseModel, Field, model_validator
-
from nomad.datamodel import EntryArchive
from nomad.datamodel.metainfo.annotations import Mapper as MapperAnnotation
from nomad.metainfo import MSection, SubSection
@@ -20,6 +18,7 @@ from nomad.parsing.file_parser import TextParser as TextFileParser
from nomad.parsing.parser import ArchiveParser
from nomad.units import ureg
from nomad.utils import get_logger
+from pydantic import BaseModel, Field, model_validator
MAPPING_ANNOTATION_KEY = 'mapping'
diff --git a/nomad/parsing/file_parser/text_parser.py b/nomad/parsing/file_parser/text_parser.py
index a742e171ebae728ad626fd92ec69f010acd41f39..5010ee16736025e94a6d5e8f4abce69bcf2856c1 100644
--- a/nomad/parsing/file_parser/text_parser.py
+++ b/nomad/parsing/file_parser/text_parser.py
@@ -13,17 +13,16 @@
# limitations under the License.
-import io
import mmap
+import io
import re
-from collections.abc import Callable
-from typing import Any
-
import numpy as np
import pint
+from typing import Any
+from collections.abc import Callable
-from nomad.metainfo import Quantity as mQuantity
from nomad.parsing.file_parser import FileParser
+from nomad.metainfo import Quantity as mQuantity
from nomad.utils import get_logger
diff --git a/nomad/parsing/file_parser/xml_parser.py b/nomad/parsing/file_parser/xml_parser.py
index 5739ec9bf394c42c376a4a2fcd82de38437494dc..e1fecc6b3f32a359ad4c3ca96806cd56731ab4d8 100644
--- a/nomad/parsing/file_parser/xml_parser.py
+++ b/nomad/parsing/file_parser/xml_parser.py
@@ -15,9 +15,8 @@
import os
import re
-from xml.etree import ElementTree
-
import numpy as np
+from xml.etree import ElementTree
from lxml import etree
from nomad.parsing.file_parser import FileParser
diff --git a/nomad/parsing/parser.py b/nomad/parsing/parser.py
index 9dd04e06fd0d6f699571370befde56b6fecb26dd..b8882362997506f89dbe900330f22e7805afc6c5 100644
--- a/nomad/parsing/parser.py
+++ b/nomad/parsing/parser.py
@@ -16,20 +16,19 @@
# limitations under the License.
#
-import importlib
-import json
+from typing import Any, IO
+from collections.abc import Iterable
+from abc import ABCMeta, abstractmethod
+import re
import os
import os.path
-import re
-from abc import ABCMeta, abstractmethod
-from collections.abc import Iterable
from functools import lru_cache
-from typing import IO, Any
-
+import importlib
+from pydantic import BaseModel, Extra # noqa: F401
+import yaml
import h5py
import numpy as np
-import yaml
-from pydantic import BaseModel, Extra # noqa: F401
+import json
from nomad import utils
from nomad.config import config
diff --git a/nomad/parsing/parsers.py b/nomad/parsing/parsers.py
index 47b3653da34dc7836ffe9823189a033f536d71ce..f6b5acdd5494617f9482aaa94015c6b97b93e114 100644
--- a/nomad/parsing/parsers.py
+++ b/nomad/parsing/parsers.py
@@ -20,30 +20,28 @@ import os.path
from collections.abc import Iterable
from nomad.config import config
-from nomad.config.models.plugins import Parser as ParserPlugin
-from nomad.config.models.plugins import ParserEntryPoint
+from nomad.config.models.plugins import Parser as ParserPlugin, ParserEntryPoint
from nomad.datamodel import EntryArchive, EntryMetadata, results
-from nomad.datamodel.context import ClientContext, Context
+from nomad.datamodel.context import Context, ClientContext
-from .artificial import ChaosParser, EmptyParser, GenerateRandomParser, TemplateParser
from .parser import (
- ArchiveParser,
- BrokenParser,
- MatchingParserInterface,
MissingParser,
+ BrokenParser,
Parser,
+ ArchiveParser,
+ MatchingParserInterface,
)
+from .artificial import EmptyParser, GenerateRandomParser, TemplateParser, ChaosParser
from .tabular import TabularDataParser
try:
# these packages are not available without parsing extra, which is ok, if the
# parsers are only initialized to load their metainfo definitions
- import bz2
+ import magic
import gzip
+ import bz2
import lzma
- import magic
-
_compressions = {
b'\x1f\x8b\x08': ('gz', gzip.open),
b'\x42\x5a\x68': ('bz2', bz2.open),
diff --git a/nomad/parsing/tabular.py b/nomad/parsing/tabular.py
index 38082a6d814ba919501bdb945d90823910d586a1..ebfd2a873d158662a91f69429d0852fcf45e7d0e 100644
--- a/nomad/parsing/tabular.py
+++ b/nomad/parsing/tabular.py
@@ -15,31 +15,32 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import json
-import math
import os
-import re
-from collections.abc import Callable, Iterable, Iterator
from typing import Any
+from collections.abc import Callable
+from collections.abc import Iterator, Iterable
-import numpy as np
import pandas as pd
+import re
+import math
+import numpy as np
+import json
import yaml
-from cachetools import LRUCache, cached
+from cachetools import cached, LRUCache
from nomad import utils
+from nomad.parsing import MatchingParser
+from nomad.units import ureg
from nomad.datamodel.data import ArchiveSection
+from nomad.metainfo import Section, Quantity, Package, Reference, MSection, Property
+from nomad.metainfo.metainfo import MetainfoError, SubSection, MProxy
from nomad.datamodel.metainfo.annotations import (
TabularAnnotation,
+ TabularParserAnnotation,
TabularFileModeEnum,
TabularMode,
- TabularParserAnnotation,
)
-from nomad.metainfo import MSection, Package, Property, Quantity, Reference, Section
-from nomad.metainfo.metainfo import MetainfoError, MProxy, SubSection
from nomad.metainfo.util import MSubSectionList
-from nomad.parsing import MatchingParser
-from nomad.units import ureg
from nomad.utils import generate_entry_id
# We define a simple base schema for tabular data. The parser will then generate more
diff --git a/nomad/processing/base.py b/nomad/processing/base.py
index 40a93ce18ee9eae21f113746ca5307e6322684db..17a6d7d6821e2d534c282331241057d68b937d2c 100644
--- a/nomad/processing/base.py
+++ b/nomad/processing/base.py
@@ -16,42 +16,42 @@
# limitations under the License.
#
-import functools
+from typing import Any, NamedTuple
import logging
-import os
import time
+import os
from collections import defaultdict
-from datetime import datetime
-from typing import Any, NamedTuple
-
-import billiard
-from billiard.exceptions import WorkerLostError
from celery import Celery, Task
-from celery.exceptions import SoftTimeLimitExceeded
+from celery.worker.request import Request
from celery.signals import (
- after_setup_logger,
after_setup_task_logger,
- celeryd_after_setup,
+ after_setup_logger,
worker_process_init,
+ celeryd_after_setup,
worker_process_shutdown,
)
from celery.utils import worker_direct
-from celery.worker.request import Request
+from celery.exceptions import SoftTimeLimitExceeded
+import billiard
+from billiard.exceptions import WorkerLostError
from mongoengine import (
- DateTimeField,
Document,
- IntField,
- ListField,
StringField,
+ ListField,
+ DateTimeField,
+ IntField,
ValidationError,
)
from mongoengine.connection import ConnectionFailure
+from datetime import datetime
+import functools
-import nomad.patch # noqa: F401
-from nomad import infrastructure, utils
-from nomad.app.v1.routers.info import statistics
+from nomad import utils, infrastructure
from nomad.config import config
from nomad.config.models.config import CELERY_WORKER_ROUTING
+from nomad.app.v1.routers.info import statistics
+import nomad.patch # noqa: F401
+
if config.logstash.enabled:
from nomad.utils import structlogging
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 706ebd80ebe3c3ff45b89cce651efac314d19bb0..b75902e2c3391da3d8d6700205ab1ec25bdb377a 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -29,84 +29,96 @@ entries, and files
"""
import base64
-import copy
-import hashlib
-import os.path
-from collections.abc import Iterable, Iterator, Sequence
-from contextlib import contextmanager
-from datetime import datetime
-from typing import Any, Union, cast
-
-import requests
+from typing import (
+ cast,
+ Any,
+ Union,
+)
+from collections.abc import Iterator, Iterable, Sequence
import rfc3161ng
-import validators
-from fastapi.exceptions import RequestValidationError
from mongoengine import (
- BooleanField,
+ StringField,
DateTimeField,
+ BooleanField,
+ IntField,
+ ListField,
DictField,
EmbeddedDocument,
EmbeddedDocumentField,
- IntField,
- ListField,
- StringField,
)
from pymongo import UpdateOne
from structlog import wrap_logger
-from structlog.processors import StackInfoRenderer, TimeStamper, format_exc_info
+from contextlib import contextmanager
+import copy
+import os.path
+from datetime import datetime
+import hashlib
+from structlog.processors import StackInfoRenderer, format_exc_info, TimeStamper
+import requests
+from fastapi.exceptions import RequestValidationError
+import validators
-from nomad import client, datamodel, infrastructure, metainfo, parsing, search, utils
-from nomad.app.v1.models import (
- Aggregation,
- MetadataEditRequest,
- MetadataPagination,
- MetadataRequired,
- TermsAggregation,
- restrict_query_to_upload,
+from nomad import (
+ utils,
+ infrastructure,
+ search,
+ datamodel,
+ metainfo,
+ parsing,
+ client,
)
-from nomad.app.v1.routers.metainfo import store_package_definition
-from nomad.archive import (
- delete_partial_archives_from_mongo,
- to_json,
- write_partial_archive_to_mongo,
-)
-from nomad.common import is_safe_relative_path
from nomad.config import config
-from nomad.config.models.config import Reprocess
+from nomad.common import is_safe_relative_path
from nomad.config.models.plugins import ExampleUploadEntryPoint
-from nomad.datamodel import (
- AuthLevel,
- EditableUserMetadata,
- EntryArchive,
- EntryMetadata,
- MongoEntryMetadata,
- MongoSystemMetadata,
- MongoUploadMetadata,
- ServerContext,
-)
+
from nomad.datamodel.datamodel import RFC3161Timestamp
from nomad.files import (
+ RawPathInfo,
PathObject,
+ UploadFiles,
PublicUploadFiles,
- RawPathInfo,
StagingUploadFiles,
- UploadFiles,
create_tmp_dir,
)
-from nomad.groups import get_group_ids, user_group_exists
+from nomad.groups import user_group_exists, get_group_ids
from nomad.metainfo.data_type import Datatype, Datetime
-from nomad.normalizing import normalizers
-from nomad.parsing import Parser
-from nomad.parsing.parsers import match_parser, parser_dict
from nomad.processing.base import (
Proc,
- ProcessAlreadyRunning,
- ProcessFailure,
- ProcessStatus,
process,
process_local,
+ ProcessStatus,
+ ProcessFailure,
+ ProcessAlreadyRunning,
+)
+from nomad.parsing import Parser
+from nomad.parsing.parsers import parser_dict, match_parser
+from nomad.normalizing import normalizers
+from nomad.datamodel import (
+ EntryArchive,
+ EntryMetadata,
+ MongoUploadMetadata,
+ MongoEntryMetadata,
+ MongoSystemMetadata,
+ EditableUserMetadata,
+ AuthLevel,
+ ServerContext,
)
+from nomad.archive import (
+ write_partial_archive_to_mongo,
+ delete_partial_archives_from_mongo,
+ to_json,
+)
+from nomad.app.v1.models import (
+ MetadataEditRequest,
+ Aggregation,
+ TermsAggregation,
+ MetadataPagination,
+ MetadataRequired,
+ restrict_query_to_upload,
+)
+from nomad.app.v1.routers.metainfo import store_package_definition
from nomad.search import update_metadata as es_update_metadata
+from nomad.config.models.config import Reprocess
from nomad.utils.pydantic import CustomErrorWrapper
section_metadata = datamodel.EntryArchive.metadata.name
diff --git a/nomad/search.py b/nomad/search.py
index 0a3785622d88504bdd5733db27ae3134972d54ae..52b8a21d85b65d513a4bcad67c2c568a1f81d5f4 100644
--- a/nomad/search.py
+++ b/nomad/search.py
@@ -34,9 +34,13 @@ partially implemented.
import json
import math
-from collections.abc import Callable, Generator, Iterable, Iterator
from enum import Enum
-from typing import Any, cast
+from typing import (
+ Any,
+ cast,
+)
+from collections.abc import Callable
+from collections.abc import Generator, Iterable, Iterator
import elasticsearch.helpers
from elasticsearch.exceptions import RequestError, TransportError
@@ -76,7 +80,12 @@ from nomad.app.v1.models.models import (
Value,
)
from nomad.config import config
-from nomad.datamodel import AuthorReference, EntryArchive, EntryMetadata, UserReference
+from nomad.datamodel import (
+ EntryArchive,
+ EntryMetadata,
+ AuthorReference,
+ UserReference,
+)
from nomad.groups import MongoUserGroup
from nomad.metainfo import Datetime, Package, Quantity
from nomad.metainfo.elasticsearch_extension import (
diff --git a/nomad/utils/exampledata.py b/nomad/utils/exampledata.py
index 4603a39b65b32d6c9e5afa016c34e1ed1275981d..7846e8f9fe99aef0a3064ede2d5fbd3bf5b2db3e 100644
--- a/nomad/utils/exampledata.py
+++ b/nomad/utils/exampledata.py
@@ -16,16 +16,16 @@
# limitations under the License.
#
-import os
-from datetime import datetime, timedelta
from typing import Any
+from datetime import datetime, timedelta
+import os
-from nomad import files, search
-from nomad.datamodel import EntryArchive, EntryMetadata, Results
-from nomad.datamodel.metainfo import runschema
+from nomad import search, files
+from nomad.datamodel import EntryMetadata, EntryArchive, Results
from nomad.datamodel.metainfo.workflow import Workflow
-from nomad.normalizing import normalizers
from nomad.processing.data import mongo_upload_metadata
+from nomad.normalizing import normalizers
+from nomad.datamodel.metainfo import runschema
class ExampleData:
@@ -61,8 +61,8 @@ class ExampleData:
es_nomad_version: str = None,
archive_nomad_version: str = None,
):
- from nomad import processing as proc
from tests.test_files import create_test_upload_files
+ from nomad import processing as proc
errors = None
@@ -145,8 +145,8 @@ class ExampleData:
parser_name: str | None = None,
):
"""Creates an entry from a mainfile which then gets parsed and normalized."""
- from nomad import parsing
from nomad.parsing import parsers
+ from nomad import parsing
assert upload_id in self.uploads, 'Must create the upload first'
diff --git a/nomad/utils/json_transformer.py b/nomad/utils/json_transformer.py
index 1a59ace7925db142aa3ab2849de82dd2272890b4..4d07d685371147fc33757916abc611e8afc42254 100644
--- a/nomad/utils/json_transformer.py
+++ b/nomad/utils/json_transformer.py
@@ -20,7 +20,7 @@ from typing import Any
import jmespath
-from nomad.datamodel.metainfo.annotations import Condition, Rule, Rules
+from nomad.datamodel.metainfo.annotations import Rules, Rule, Condition
class Transformer:
diff --git a/nomad/utils/structlogging.py b/nomad/utils/structlogging.py
index 3cd4d85ba4e90b837d2be650e1cb8c6d9420d017..f0303ee1b55cdc05211bdfdb52809a4fd8d8e427 100644
--- a/nomad/utils/structlogging.py
+++ b/nomad/utils/structlogging.py
@@ -25,22 +25,21 @@ take keyword arguments for structured data. Otherwise `get_logger` can
be used similar to the standard `logging.getLogger`.
"""
-import json
+from typing import cast, Any
import logging
-import os.path
-import re
from logging.handlers import WatchedFileHandler
-from typing import Any, cast
-
-import logstash
import structlog
from structlog.processors import (
- JSONRenderer,
StackInfoRenderer,
- TimeStamper,
format_exc_info,
+ TimeStamper,
+ JSONRenderer,
)
from structlog.stdlib import LoggerFactory
+import logstash
+import json
+import re
+import os.path
from nomad import utils
from nomad.config import config
diff --git a/pyproject.toml b/pyproject.toml
index a51ecf825cdcd9d828d9370f63acb2b6b405bd38..698b09fa88a9a80f465903ccda0607ac6755d448 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -154,7 +154,6 @@ indent-width = 4
select = [
"E", # pycodestyle
"F401", # remove unused import
- "I001", # sort imports
"PL", # pylint
"UP", # pyupgrade
"W", # pycodestyle
@@ -175,10 +174,9 @@ ignore = [
"PLR5501", # else-if-used
]
fixable = ["ALL"]
-isort.split-on-trailing-comma = false
[tool.ruff.lint.extend-per-file-ignores]
-"__init__.py" = ["F401", "I001"]
+"__init__.py" = ["F401"]
"nomad/app/v1/models/graph/utils.py" = [
"UP007",
] # causes pydantic model building errors
diff --git a/tests/app/test_app.py b/tests/app/test_app.py
index 6140f085b980fbecd8dbbd1f1ce20ebff0759611..12a36607c0894240027972d8c5fabd4664d73e00 100644
--- a/tests/app/test_app.py
+++ b/tests/app/test_app.py
@@ -16,9 +16,8 @@
# limitations under the License.
#
-import os
-
import pytest
+import os
from nomad.config import config
diff --git a/tests/app/test_dcat.py b/tests/app/test_dcat.py
index 1f0ecd711152a3b32edbf0e60731fe4e04016f3e..4f08b698f2a66cf80bed6f094aaaa07989a98cb2 100644
--- a/tests/app/test_dcat.py
+++ b/tests/app/test_dcat.py
@@ -16,15 +16,14 @@
# limitations under the License.
#
-from datetime import datetime
-
import pytest
+from datetime import datetime
from fastapi.testclient import TestClient
from nomad.app.dcat.main import app
from nomad.app.dcat.mapping import Mapping
-from nomad.datamodel import Dataset
from nomad.datamodel.results import Material, Results
+from nomad.datamodel import Dataset
from nomad.utils.exampledata import ExampleData
diff --git a/tests/app/test_h5grove.py b/tests/app/test_h5grove.py
index a5b7446b381109205ee1799ba17acbb10e3aaf30..592cb623ec0faca0212bb4fe56f70f17a8620f2c 100644
--- a/tests/app/test_h5grove.py
+++ b/tests/app/test_h5grove.py
@@ -15,16 +15,15 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import pytest
import os
-
import h5py
-import pytest
from fastapi.testclient import TestClient
from nomad.app import h5grove_app
-from nomad.config import config
-from nomad.files import StagingUploadFiles
from nomad.utils.exampledata import ExampleData
+from nomad.files import StagingUploadFiles
+from nomad.config import config
@pytest.fixture
diff --git a/tests/app/test_optimade.py b/tests/app/test_optimade.py
index 3b95f9173ba0f0cfad64ecda1cad549457118c8e..a7841ff89a7a45e7ca0c8977f932047c5dab4623 100644
--- a/tests/app/test_optimade.py
+++ b/tests/app/test_optimade.py
@@ -17,15 +17,15 @@
#
import json
-
import pytest
+from nomad.processing import Upload
from nomad import utils
+from nomad.search import search
from nomad.app.optimade import parse_filter
from nomad.app.optimade.common import provider_specific_fields
-from nomad.processing import Upload
-from nomad.search import search
from nomad.utils.exampledata import ExampleData
+
from tests.fixtures.infrastructure import clear_elastic, clear_raw_files
diff --git a/tests/app/test_resources.py b/tests/app/test_resources.py
index 4f1b3929fa0e0bcd263241dd16877d77cc56cfcc..e76d787079aabe24883b2fa234e448f52ee16363 100644
--- a/tests/app/test_resources.py
+++ b/tests/app/test_resources.py
@@ -15,22 +15,21 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import pytest
import json
-import time
+from fastapi.testclient import TestClient
+import httpx
from urllib.parse import urlencode
-
+import time
import dateutil.parser
-import httpx
-import pytest
-from fastapi.testclient import TestClient
+from nomad.config import config
from nomad.app.resources.main import app, remove_mongo
from nomad.app.resources.routers.resources import (
aflow_prototypes_db,
- optimade_providers,
springer_materials_db,
+ optimade_providers,
)
-from nomad.config import config
def _to_datetime(datetime_str):
diff --git a/tests/app/v1/routers/common.py b/tests/app/v1/routers/common.py
index 20f17289ddb49fa9e1b8a23161ce85ada5f1fafe..55a522a635e37c435cfb0fcc0eafec66a80fce26 100644
--- a/tests/app/v1/routers/common.py
+++ b/tests/app/v1/routers/common.py
@@ -16,16 +16,17 @@
# limitations under the License.
#
+import pytest
+from typing import Literal, Any
import json
import re
-from typing import Any, Literal
+from devtools import debug
from urllib.parse import urlencode
-import pytest
-from devtools import debug
+from nomad.utils import deep_get
from nomad.datamodel import results
-from nomad.utils import deep_get
+
from tests.utils import assert_at_least, assert_url_query_args, build_url
n_code_names = results.Simulation.program_name.a_elasticsearch[
diff --git a/tests/app/v1/routers/test_auth.py b/tests/app/v1/routers/test_auth.py
index 2c5e3e67c8f42da033bc0c1bc716025638f89d63..c814260a3c4b502c8c841b09a2cb1fd2eb1302fe 100644
--- a/tests/app/v1/routers/test_auth.py
+++ b/tests/app/v1/routers/test_auth.py
@@ -16,9 +16,8 @@
# limitations under the License.
#
-from urllib.parse import urlencode
-
import pytest
+from urllib.parse import urlencode
def perform_get_token_test(client, http_method, status_code, username, password):
diff --git a/tests/app/v1/routers/test_datasets.py b/tests/app/v1/routers/test_datasets.py
index 7153ee770a9b3a076f6f7072354924a2d0f7deff..36cd3de91c9161be75af1930c91b5a729102d73e 100644
--- a/tests/app/v1/routers/test_datasets.py
+++ b/tests/app/v1/routers/test_datasets.py
@@ -16,16 +16,16 @@
# limitations under the License.
#
-from datetime import datetime
-from urllib.parse import urlencode
-
import pytest
+from urllib.parse import urlencode
+from datetime import datetime
-from nomad import processing
-from nomad.app.v1.models import Any_, Query
from nomad.datamodel import Dataset
+from nomad import processing
from nomad.search import search
+from nomad.app.v1.models import Query, Any_
from nomad.utils.exampledata import ExampleData
+
from tests.fixtures.users import admin_user_id
from .common import assert_response
diff --git a/tests/app/v1/routers/test_entries.py b/tests/app/v1/routers/test_entries.py
index 36985eb08f55098d5930560ca4707427e14f710a..fbdfaaae175e5ccf8289ba8a3f503aca1df93711 100644
--- a/tests/app/v1/routers/test_entries.py
+++ b/tests/app/v1/routers/test_entries.py
@@ -16,37 +16,37 @@
# limitations under the License.
#
+import pytest
+from urllib.parse import urlencode
+import zipfile
import io
import json
-import zipfile
-from urllib.parse import urlencode
-
-import pytest
from nomad.metainfo.elasticsearch_extension import entry_type, schema_separator
from nomad.utils.exampledata import ExampleData
-from tests.test_files import append_raw_files, example_mainfile_contents # noqa: F401
+
+from tests.test_files import example_mainfile_contents, append_raw_files # noqa: F401
from tests.variables import python_schema_name
from .common import (
aggregation_exclude_from_search_test_parameters,
- aggregation_test_parameters,
- aggregation_test_parameters_default,
- assert_aggregation_response,
- assert_aggregations,
+ assert_response,
assert_base_metadata_response,
- assert_browser_download_headers,
- assert_metadata_response,
- assert_pagination,
assert_query_response,
+ assert_metadata_response,
assert_required,
- assert_response,
+ assert_aggregations,
+ assert_pagination,
+ assert_browser_download_headers,
+ post_query_test_parameters,
get_query_test_parameters,
+ perform_owner_test,
owner_test_parameters,
pagination_test_parameters,
+ aggregation_test_parameters,
+ aggregation_test_parameters_default,
+ assert_aggregation_response,
perform_entries_metadata_test,
- perform_owner_test,
- post_query_test_parameters,
)
"""
diff --git a/tests/app/v1/routers/test_entries_archive_edit.py b/tests/app/v1/routers/test_entries_archive_edit.py
index ba9903ebde1018599934eccc59a914e1243c6f9b..8a2e90107dbffd9b62c3d1d9677d5627e4ed7559 100644
--- a/tests/app/v1/routers/test_entries_archive_edit.py
+++ b/tests/app/v1/routers/test_entries_archive_edit.py
@@ -17,7 +17,6 @@
#
import json
-
import pytest
from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
diff --git a/tests/app/v1/routers/test_entries_edit.py b/tests/app/v1/routers/test_entries_edit.py
index 1d3db4a4df67d2a0e8bd2479212a3c2708f84692..cd793d3fb4c43a5696bf9dc7800296de9b254b88 100644
--- a/tests/app/v1/routers/test_entries_edit.py
+++ b/tests/app/v1/routers/test_entries_edit.py
@@ -16,22 +16,22 @@
# limitations under the License.
#
-from datetime import datetime
-
import pytest
+from datetime import datetime
-from nomad import processing as proc
-from nomad import utils
-from nomad.datamodel import Dataset
from nomad.search import search
+from nomad.datamodel import Dataset
+from nomad import processing as proc, utils
from nomad.utils.exampledata import ExampleData
+
from tests.app.v1.routers.common import assert_response
from tests.processing.test_edit_metadata import (
- all_admin_entry_metadata,
- all_coauthor_entry_metadata,
assert_metadata_edited,
+ all_coauthor_entry_metadata,
+ all_admin_entry_metadata,
)
+
logger = utils.get_logger(__name__)
diff --git a/tests/app/v1/routers/test_federation.py b/tests/app/v1/routers/test_federation.py
index 3b8d8284b51d58ccdd43b54bd5b1db150f616b88..cb990557fa7cc14b526542074f65c298a93002cb 100644
--- a/tests/app/v1/routers/test_federation.py
+++ b/tests/app/v1/routers/test_federation.py
@@ -1,10 +1,9 @@
+import requests
import json
+import pytest
+from copy import deepcopy
import logging
import zlib
-from copy import deepcopy
-
-import pytest
-import requests
from nomad.config import config
from nomad.utils.structlogging import LogstashFormatter
diff --git a/tests/app/v1/routers/test_graph.py b/tests/app/v1/routers/test_graph.py
index 5a12924f66a284f8d3af88036857ed051cf8b171..38f0670da8450ba2d01a751becf298292fd8ff79 100644
--- a/tests/app/v1/routers/test_graph.py
+++ b/tests/app/v1/routers/test_graph.py
@@ -18,11 +18,11 @@
import pytest
-from nomad.datamodel import EntryArchive
-from nomad.datamodel.metainfo import SCHEMA_IMPORT_ERROR, simulationworkflowschema
from nomad.graph.graph_reader import EntryReader, Token
+from nomad.datamodel import EntryArchive
from nomad.utils.exampledata import ExampleData
from tests.archive.test_archive import assert_dict
+from nomad.datamodel.metainfo import simulationworkflowschema, SCHEMA_IMPORT_ERROR
# try:
# from rich.pretty import pprint
diff --git a/tests/app/v1/routers/test_materials.py b/tests/app/v1/routers/test_materials.py
index a1e998720b957664a3542fda24169942467dabae..8490f3972414ba175a2859c228572d4a20aa92af 100644
--- a/tests/app/v1/routers/test_materials.py
+++ b/tests/app/v1/routers/test_materials.py
@@ -16,27 +16,27 @@
# limitations under the License.
#
-from urllib.parse import urlencode
-
import pytest
+from urllib.parse import urlencode
-from nomad.datamodel import results
from nomad.metainfo.elasticsearch_extension import material_entry_type
+from nomad.datamodel import results
+
from tests.test_files import example_mainfile_contents # noqa: F401
from .common import (
aggregation_exclude_from_search_test_parameters,
- aggregation_test_parameters_default,
- assert_aggregation_response,
- assert_metadata_response,
assert_pagination,
+ assert_metadata_response,
assert_required,
- get_query_test_parameters,
- owner_test_parameters,
- pagination_test_parameters,
perform_metadata_test,
perform_owner_test,
+ owner_test_parameters,
post_query_test_parameters,
+ get_query_test_parameters,
+ pagination_test_parameters,
+ aggregation_test_parameters_default,
+ assert_aggregation_response,
)
"""
diff --git a/tests/app/v1/routers/test_metainfo.py b/tests/app/v1/routers/test_metainfo.py
index a34cb5be582d0e6cd8327987cfd4953f36ff45e2..8d4e2e78a44cde6573f411aac933f685601869d8 100644
--- a/tests/app/v1/routers/test_metainfo.py
+++ b/tests/app/v1/routers/test_metainfo.py
@@ -21,11 +21,11 @@ from zipfile import ZipFile
import pytest
-from nomad.app.v1.routers.metainfo import store_package_definition
from nomad.config import config
-from nomad.datamodel import ClientContext, EntryArchive
-from nomad.metainfo import MetainfoReferenceError, MSection
-from nomad.utils import create_uuid, generate_entry_id
+from nomad.app.v1.routers.metainfo import store_package_definition
+from nomad.datamodel import EntryArchive, ClientContext
+from nomad.metainfo import MSection, MetainfoReferenceError
+from nomad.utils import generate_entry_id, create_uuid
from tests.processing.test_data import run_processing
diff --git a/tests/app/v1/routers/test_suggestions.py b/tests/app/v1/routers/test_suggestions.py
index 093c20ed7eb23f288efbd91dfe87bb89e1cdd657..937aad115af73b98413d9863cb7a857940bd35f2 100644
--- a/tests/app/v1/routers/test_suggestions.py
+++ b/tests/app/v1/routers/test_suggestions.py
@@ -27,10 +27,8 @@ to assert for certain aspects in the responses.
"""
import pytest
-
from nomad.metainfo.elasticsearch_extension import entry_type
from nomad.utils.exampledata import ExampleData
-
from .common import assert_response
diff --git a/tests/app/v1/routers/test_systems.py b/tests/app/v1/routers/test_systems.py
index 6b76eb777c317dfd6b6bf06550c4258914f08c3e..debb8bdef085c2f6a3950386e9cbb53c7a161309 100644
--- a/tests/app/v1/routers/test_systems.py
+++ b/tests/app/v1/routers/test_systems.py
@@ -19,21 +19,21 @@
import re
from io import BytesIO, StringIO
-import ase.io
-import numpy as np
import pytest
+import numpy as np
+import ase.io
from ase import Atoms as ASEAtoms
-from nomad.app.v1.routers.systems import FormatFeature, WrapModeEnum, format_map
+from nomad.units import ureg
+from nomad.normalizing.common import ase_atoms_from_nomad_atoms
from nomad.datamodel.datamodel import EntryArchive
+from nomad.datamodel.results import Results, Material, System
from nomad.datamodel.metainfo import runschema
from nomad.datamodel.metainfo.system import Atoms
-from nomad.datamodel.results import Material, Results, System
-from nomad.normalizing.common import ase_atoms_from_nomad_atoms
-from nomad.units import ureg
from nomad.utils.exampledata import ExampleData
+from nomad.app.v1.routers.systems import format_map, FormatFeature, WrapModeEnum
-from .common import assert_browser_download_headers, assert_response
+from .common import assert_response, assert_browser_download_headers
def ase_atoms(content, format):
diff --git a/tests/app/v1/routers/uploads/test_basic_uploads.py b/tests/app/v1/routers/uploads/test_basic_uploads.py
index a31f7ca2c20bdeadacf48f723536ef0954810e6f..6546dd8b7de3dc9e640f652c67ef7a5cef99d2ca 100644
--- a/tests/app/v1/routers/uploads/test_basic_uploads.py
+++ b/tests/app/v1/routers/uploads/test_basic_uploads.py
@@ -18,12 +18,12 @@
import io
import os
-import tempfile
import time
import zipfile
-from collections.abc import Iterable
from datetime import datetime
+import tempfile
from typing import Any
+from collections.abc import Iterable
import pytest
import requests
@@ -41,15 +41,15 @@ from tests.app.v1.routers.common import (
assert_response,
perform_get,
)
-from tests.config.models.test_plugins import (
- mock_example_upload_entry_point,
- mock_plugin_package,
-)
from tests.processing.test_edit_metadata import (
all_admin_metadata,
all_coauthor_metadata,
assert_metadata_edited,
)
+from tests.config.models.test_plugins import (
+ mock_plugin_package,
+ mock_example_upload_entry_point,
+)
from tests.test_files import (
assert_upload_files,
empty_file,
diff --git a/tests/app/v1/test_models.py b/tests/app/v1/test_models.py
index 9210f75d212792c627643cf23845572c02f11926..7328abd09346fd1dd42729f3ed36ddaa844e4396 100644
--- a/tests/app/v1/test_models.py
+++ b/tests/app/v1/test_models.py
@@ -17,16 +17,14 @@
#
from __future__ import annotations
-
-import sys
-
import pytest
-import yaml
from pydantic import BaseModel, Field, ValidationError
+import yaml
+import sys
+from nomad.utils import strip
from nomad.app.v1.models.graph import GraphRequest
from nomad.app.v1.models.graph.utils import generate_request_model, mapped
-from nomad.utils import strip
@pytest.fixture()
diff --git a/tests/app/v1/test_utils.py b/tests/app/v1/test_utils.py
index 5ed2c55176c8fc573420fafce25fa53937d0f9d3..ba6fd19fcfec71d55476496d73df32b2bd351f87 100644
--- a/tests/app/v1/test_utils.py
+++ b/tests/app/v1/test_utils.py
@@ -1,5 +1,4 @@
import pytest
-
from nomad.app.v1.utils import get_query_keys
diff --git a/tests/archive/test_archive.py b/tests/archive/test_archive.py
index 0c35c9b5b0b8b7d3e89a829d6e5c1c1b2efd2768..84e133d29ac6157ee8e34a80767e3a002e0f3ae3 100644
--- a/tests/archive/test_archive.py
+++ b/tests/archive/test_archive.py
@@ -15,42 +15,42 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import json
-import os.path
from datetime import datetime
-from io import BytesIO
from typing import Any
-
-import msgpack
import pytest
+import msgpack
+from io import BytesIO
+import os.path
+import json
+
import yaml
from nomad import utils
-from nomad.archive import (
- ArchiveQueryError,
- RequiredReader,
- compute_required_with_referenced,
- create_partial_archive,
- query_archive,
- read_archive,
- read_partial_archive_from_mongo,
- read_partial_archives_from_mongo,
- write_archive,
- write_partial_archive_to_mongo,
-)
-from nomad.archive.converter import convert_archive
-from nomad.archive.storage import _decode, _entries_per_block, to_json
from nomad.config import config
-from nomad.datamodel import ClientContext, EntryArchive
+from nomad.archive.converter import convert_archive
from nomad.metainfo import (
- Context,
- MetainfoError,
- MProxy,
MSection,
Quantity,
- QuantityReference,
Reference,
SubSection,
+ QuantityReference,
+ MetainfoError,
+ Context,
+ MProxy,
+)
+from nomad.datamodel import EntryArchive, ClientContext
+from nomad.archive.storage import _decode, _entries_per_block, to_json
+from nomad.archive import (
+ write_archive,
+ read_archive,
+ ArchiveQueryError,
+ query_archive,
+ write_partial_archive_to_mongo,
+ read_partial_archive_from_mongo,
+ read_partial_archives_from_mongo,
+ create_partial_archive,
+ compute_required_with_referenced,
+ RequiredReader,
)
from nomad.utils.exampledata import ExampleData
diff --git a/tests/archive/test_storage.py b/tests/archive/test_storage.py
index 6ce614b53e82aac86d9a5570a4b2801352312cee..4a2de3dbf6bce3c2e3b9ab8bfd8553060b55f3f7 100644
--- a/tests/archive/test_storage.py
+++ b/tests/archive/test_storage.py
@@ -5,7 +5,10 @@ import msgpack
import msgspec.msgpack
import pytest
-from nomad.archive.storage_v2 import ArchiveDict, ArchiveList
+from nomad.archive.storage_v2 import (
+ ArchiveList,
+ ArchiveDict,
+)
def generate_random_json(depth=10, width=4, simple=False):
diff --git a/tests/config/models/test_plugins.py b/tests/config/models/test_plugins.py
index 7d702f33e7f539100f52c98b90559b31bac11af3..a7d2f42ebb06ad971cd2aa00d806058927a4b68c 100644
--- a/tests/config/models/test_plugins.py
+++ b/tests/config/models/test_plugins.py
@@ -18,13 +18,12 @@
import os
import tempfile
-
import pytest
-
from nomad.config import Config
+
from nomad.config.models.plugins import (
- APIEntryPoint,
ExampleUploadEntryPoint,
+ APIEntryPoint,
UploadResource,
)
diff --git a/tests/config/models/test_ui.py b/tests/config/models/test_ui.py
index 606e9af0fb35890d54785ef54811806a8b562e34..ce0626c7c885db5ad1184e7f0cddef0da262e6a5 100644
--- a/tests/config/models/test_ui.py
+++ b/tests/config/models/test_ui.py
@@ -22,13 +22,13 @@ from nomad.config.models.ui import (
App,
Axis,
AxisQuantity,
- Column,
Columns,
+ Column,
+ Rows,
RowActions,
- RowActionURL,
RowDetails,
- Rows,
RowSelection,
+ RowActionURL,
)
diff --git a/tests/conftest.py b/tests/conftest.py
index a72d3e2687faca5ff45a9fbf00d1cf1e27a3da6a..66c1faa36e993a27d4cc28b2a6ae6296e83f52ef 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -16,17 +16,17 @@
# limitations under the License.
#
import builtins
-import logging
-import os
-import socketserver
-import tempfile
+from pathlib import Path
+from io import StringIO
+import pytest
import time
+import os
+import logging
import warnings
-from io import StringIO
-from pathlib import Path
+import tempfile
-import pytest
from fastapi.testclient import TestClient
+import socketserver
from nomad.config import config
from nomad.config.models.plugins import Schema, add_plugin, remove_plugin
@@ -35,8 +35,8 @@ from nomad.config.models.plugins import Schema, add_plugin, remove_plugin
config.logstash.enabled = False # noqa: E402 # this must be set *before* the other modules are imported
from nomad import utils
-from nomad.app.main import app
from nomad.utils import structlogging
+from nomad.app.main import app
# Set up pytest to pass control to the debugger on an exception.
if os.getenv('_PYTEST_RAISE', '0') != '0':
@@ -68,8 +68,8 @@ pytest_plugins = (
)
-import structlog
from structlog.testing import LogCapture
+import structlog
@pytest.fixture(scope='function')
diff --git a/tests/data/schemas/nomadschemaexample/schema.py b/tests/data/schemas/nomadschemaexample/schema.py
index 2f076b6d5734b77ccdad44b834aa11142d8beba3..2bf501f0067643332f9dd9d0f98312a11d090b1e 100644
--- a/tests/data/schemas/nomadschemaexample/schema.py
+++ b/tests/data/schemas/nomadschemaexample/schema.py
@@ -1,17 +1,16 @@
-import numpy as np
-
-from nomad.datamodel.data import EntryData
-from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
from nomad.metainfo import (
- Datetime,
- MEnum,
- MSection,
- Package,
Quantity,
+ Package,
Section,
- SectionProxy,
+ MEnum,
+ Datetime,
+ MSection,
SubSection,
+ SectionProxy,
)
+from nomad.datamodel.data import EntryData
+from nomad.datamodel.metainfo.annotations import ELNAnnotation, ELNComponentEnum
+import numpy as np
m_package = Package()
diff --git a/tests/datamodel/metainfo/test_annotations.py b/tests/datamodel/metainfo/test_annotations.py
index fb1208394b8348cc54a73facb400d8b366df3a71..2d0f472f42072296571776a88c3d9d122e7e51b0 100644
--- a/tests/datamodel/metainfo/test_annotations.py
+++ b/tests/datamodel/metainfo/test_annotations.py
@@ -19,13 +19,13 @@
import pytest
from pydantic import ValidationError
+from nomad.metainfo import Quantity
from nomad.datamodel.metainfo.annotations import (
- ELNAnnotation,
PlotAnnotation,
+ ELNAnnotation,
PlotlyGraphObjectAnnotation,
)
from nomad.datamodel.metainfo.plot import PlotlyError
-from nomad.metainfo import Quantity
@pytest.mark.parametrize(
diff --git a/tests/datamodel/metainfo/test_plotly.py b/tests/datamodel/metainfo/test_plotly.py
index 038cffbd0e329d4233c8d64c0dcab992dbffbcff..63d6daf2176827b663d4130701745b7d1af9c27c 100644
--- a/tests/datamodel/metainfo/test_plotly.py
+++ b/tests/datamodel/metainfo/test_plotly.py
@@ -1,5 +1,4 @@
import json
-
from tests.normalizing.conftest import run_processing
diff --git a/tests/datamodel/metainfo/test_substance.py b/tests/datamodel/metainfo/test_substance.py
index 6b30e54d32b7e67e459cbe769f27e29082fb3128..78c63e39a54c7ba8257f95167652b4698bb1b8a3 100644
--- a/tests/datamodel/metainfo/test_substance.py
+++ b/tests/datamodel/metainfo/test_substance.py
@@ -16,13 +16,12 @@
# limitations under the License.
#
-import json
from collections.abc import Iterable
-
import pytest
+import json
-from nomad.datamodel.metainfo.basesections import v1 as basesections
from tests.normalizing.conftest import run_processing
+from nomad.datamodel.metainfo.basesections import v1 as basesections
class MockResponse:
diff --git a/tests/datamodel/test_context.py b/tests/datamodel/test_context.py
index f8250df5fbd4d35c3590721e94b72b204d4bb80d..189753fec57af51ca1be6ab8d1fa6f588c5db9e5 100644
--- a/tests/datamodel/test_context.py
+++ b/tests/datamodel/test_context.py
@@ -16,20 +16,20 @@
# limitations under the License.
#
-import json
import os
-import re
import pytest
+import json
+import re
-from nomad import files, processing, utils
+from nomad import utils, files, processing
+from nomad.metainfo.metainfo import MSection
+from nomad.parsing.parser import ArchiveParser
from nomad.datamodel import Context
-from nomad.datamodel.context import ClientContext, ServerContext, parse_path
+from nomad.datamodel.context import ServerContext, ClientContext, parse_path
from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
+from nomad.processing import Upload, Entry, ProcessStatus
from nomad.datamodel.metainfo import runschema
-from nomad.metainfo.metainfo import MSection
-from nomad.parsing.parser import ArchiveParser
-from nomad.processing import Entry, ProcessStatus, Upload
@pytest.fixture(scope='module')
diff --git a/tests/datamodel/test_datamodel.py b/tests/datamodel/test_datamodel.py
index e0b263d41e6b0ed67e9ba8fb4b1c38b8a1587c26..306f2ad7c94a1992608a75410009b80c9e9ffa3c 100644
--- a/tests/datamodel/test_datamodel.py
+++ b/tests/datamodel/test_datamodel.py
@@ -21,12 +21,11 @@ A generator for random test calculations.
"""
import random
-
-import pytest
from essential_generators import DocumentGenerator
+import pytest
-from nomad.datamodel.metainfo import SCHEMA_IMPORT_ERROR, runschema
from nomad.parsing.parsers import parser_dict
+from nomad.datamodel.metainfo import runschema, SCHEMA_IMPORT_ERROR
number_of = 20
@@ -73,7 +72,7 @@ low_numbers_for_geometries = [1, 2, 2, 3, 3, 4, 4]
@pytest.mark.skipif(runschema is None, reason=SCHEMA_IMPORT_ERROR)
def test_common_metainfo():
from runschema.run import Run
- from runschema.system import Atoms, System
+ from runschema.system import System, Atoms
run = Run()
system = run.m_create(System)
@@ -84,8 +83,8 @@ def test_common_metainfo():
@pytest.mark.skipif(runschema is None, reason=SCHEMA_IMPORT_ERROR)
def test_vasp_metainfo():
- from electronicparsers.vasp.metainfo import vasp # noqa: F401
from runschema.run import Run
+ from electronicparsers.vasp.metainfo import vasp # noqa: F401
run = Run()
assert 'vasp_src_date' in run.m_def.all_quantities
diff --git a/tests/datamodel/test_hdf5.py b/tests/datamodel/test_hdf5.py
index 427b20ccd2b33db0263e020afc0601fb431500f3..bbdb88e143b4ca15d350410e413cf282231e0417 100644
--- a/tests/datamodel/test_hdf5.py
+++ b/tests/datamodel/test_hdf5.py
@@ -16,18 +16,19 @@
# limitations under the License.
#
+import pytest
+import numpy as np
import os
-
import h5py
-import numpy as np
-import pytest
from nomad import files, processing
-from nomad.datamodel import EntryArchive, EntryData, EntryMetadata
+from nomad.datamodel import EntryData, EntryArchive, EntryMetadata
from nomad.datamodel.context import ServerContext
-from nomad.datamodel.hdf5 import HDF5Dataset, HDF5Reference
from nomad.metainfo import Quantity
+from nomad.datamodel.hdf5 import HDF5Reference, HDF5Dataset
+
+
external_file = 'tests/data/datamodel/context.h5'
diff --git a/tests/datamodel/test_metadata.py b/tests/datamodel/test_metadata.py
index 0d6c40fd9fb6bd13f6e3890956dd397d042ac2b8..09cc397ba545f6498c6ba1dea1a59487955a9e5d 100644
--- a/tests/datamodel/test_metadata.py
+++ b/tests/datamodel/test_metadata.py
@@ -16,16 +16,15 @@
# limitations under the License.
#
-from datetime import datetime
-
-import numpy as np
import pytest
+import numpy as np
+from datetime import datetime
import pytz
-from nomad.datamodel import EntryData
-from nomad.datamodel.datamodel import EntryArchive, EntryMetadata, SearchableQuantity
-from nomad.metainfo import Datetime, MEnum, MSection, Quantity, SubSection
+from nomad.metainfo import Quantity, MSection, SubSection, Datetime, MEnum
+from nomad.datamodel.datamodel import EntryMetadata, SearchableQuantity, EntryArchive
from nomad.metainfo.elasticsearch_extension import schema_separator
+from nomad.datamodel import EntryData
from tests.variables import python_schema_name
diff --git a/tests/datamodel/test_schema.py b/tests/datamodel/test_schema.py
index c06f260122cab7664f40ab2adc3940c1425e60fa..17ccdea3ab84a0a3eb396270e7183376ecd0c421 100644
--- a/tests/datamodel/test_schema.py
+++ b/tests/datamodel/test_schema.py
@@ -17,21 +17,21 @@
#
import os.path
-
import pytest
+from nomad.metainfo import MetainfoError
from nomad.datamodel.context import ServerContext
-from nomad.datamodel.data import AuthorReference, Query, UserReference
from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
-from nomad.datamodel.metainfo.annotations import valid_eln_components, valid_eln_types
-from nomad.metainfo import MetainfoError
+from nomad.datamodel.data import UserReference, AuthorReference, Query
+from nomad.datamodel.metainfo.annotations import valid_eln_types, valid_eln_components
from nomad.metainfo.data_type import Datatype
from nomad.parsing.parser import ArchiveParser
from nomad.processing.data import Upload
from nomad.utils import get_logger, strip
-from tests.metainfo.test_yaml_schema import yaml_to_package
+
from tests.normalizing.conftest import run_normalize
from tests.test_files import create_test_upload_files
+from tests.metainfo.test_yaml_schema import yaml_to_package
def test_schema_processing(raw_files_function, no_warn):
diff --git a/tests/examples/test_archive_query.py b/tests/examples/test_archive_query.py
index 5cad68b2d008bcc4dabad27cddd706c87f2f1e40..86c0eaf8446d3bc4f06c1137a6faa7416c51ff00 100644
--- a/tests/examples/test_archive_query.py
+++ b/tests/examples/test_archive_query.py
@@ -16,13 +16,14 @@
# limitations under the License.
#
-import importlib
import os.path
+import importlib
import sys
from nomad.utils.exampledata import ExampleData
-from tests.normalizing.conftest import run_normalize
+
from tests.parsing.test_parsing import run_singular_parser
+from tests.normalizing.conftest import run_normalize
from tests.test_client import async_api_v1 # noqa: F401
diff --git a/tests/examples/test_docs.py b/tests/examples/test_docs.py
index ef1a43720d217ff262683120194593a606e4bd26..e8b737a9fbc0a21a85cd8e5d7893d0b0a5080697 100644
--- a/tests/examples/test_docs.py
+++ b/tests/examples/test_docs.py
@@ -1,12 +1,12 @@
+import yaml
import json
import os.path
-import yaml
-
from nomad.metainfo import Package
from nomad.units import ureg
-from tests.normalizing.conftest import run_normalize
+
from tests.parsing.test_parsing import run_singular_parser
+from tests.normalizing.conftest import run_normalize
def _file(path):
diff --git a/tests/examples/test_metainfo.py b/tests/examples/test_metainfo.py
index 739280867837e9d5cf4ef9ccf9d6fb1844f29468..3c42051e03012def7b8162e687854b8f7910e246 100644
--- a/tests/examples/test_metainfo.py
+++ b/tests/examples/test_metainfo.py
@@ -1,7 +1,7 @@
-import os
import runpy
-
import pytest
+import os
+
prefix = os.path.join(__file__, '../../../examples/metainfo')
diff --git a/tests/fixtures/data.py b/tests/fixtures/data.py
index d5000b0c381251ea99c04fd1fbf1908c08d5f788..a041704c3547aff25501c360938984cd02f39064 100644
--- a/tests/fixtures/data.py
+++ b/tests/fixtures/data.py
@@ -17,6 +17,7 @@ from nomad.datamodel.datamodel import SearchableQuantity
from nomad.metainfo.elasticsearch_extension import schema_separator
from nomad.processing import ProcessStatus
from nomad.utils.exampledata import ExampleData
+from tests.variables import python_schema_name, yaml_schema_name, yaml_schema_root
from tests.normalizing.conftest import run_normalize
from tests.parsing import test_parsing
from tests.processing import test_data as test_processing
@@ -26,7 +27,6 @@ from tests.utils import (
create_template_upload_file,
set_upload_entry_metadata,
)
-from tests.variables import python_schema_name, yaml_schema_name, yaml_schema_root
@pytest.fixture(scope='session')
diff --git a/tests/fixtures/group_uploads.py b/tests/fixtures/group_uploads.py
index 290b2b6d0b44eb83eb8533be38b48528687f7d6d..b0d8109c89dfc6a64e179ae0e36233d505ff6331 100644
--- a/tests/fixtures/group_uploads.py
+++ b/tests/fixtures/group_uploads.py
@@ -11,7 +11,6 @@ Values:
"""
from collections.abc import Sequence
-
import pytest
from nomad.utils.exampledata import ExampleData
diff --git a/tests/graph/test_definition_reader.py b/tests/graph/test_definition_reader.py
index 354f9fc00e38e17b3f63649fa45476bf35c942da..f67385897f1c1994fd2602742007eb02aff75e4d 100644
--- a/tests/graph/test_definition_reader.py
+++ b/tests/graph/test_definition_reader.py
@@ -21,8 +21,8 @@ import pytest
from nomad.graph.graph_reader import DefinitionReader
from nomad.metainfo import (
- MSection,
Package,
+ MSection,
Quantity,
Reference,
SectionProxy,
diff --git a/tests/graph/test_graph_reader.py b/tests/graph/test_graph_reader.py
index d6f9d75cd2a38a1a978894c08620a68dad10b005..ebcdc887caf49afd4a80c6b9011198caed2622ba 100644
--- a/tests/graph/test_graph_reader.py
+++ b/tests/graph/test_graph_reader.py
@@ -22,17 +22,17 @@ from datetime import datetime
import pytest
import yaml
-from nomad.datamodel import EntryArchive
from nomad.graph.graph_reader import (
EntryReader,
+ UploadReader,
+ UserReader,
FileSystemReader,
- GeneralReader,
MongoReader,
+ GeneralReader,
Token,
- UploadReader,
- UserReader,
)
from nomad.graph.lazy_wrapper import LazyWrapper
+from nomad.datamodel import EntryArchive
from nomad.utils.exampledata import ExampleData
from tests.normalizing.conftest import simulationworkflowschema
diff --git a/tests/metainfo/test_attributes.py b/tests/metainfo/test_attributes.py
index 32db3438decb3c5868d99cf098d2d3bc88ea25ed..13edf2b9d098a417b6ad9508697a78415bcff20c 100644
--- a/tests/metainfo/test_attributes.py
+++ b/tests/metainfo/test_attributes.py
@@ -18,20 +18,20 @@
import datetime
-import numpy as np
import pytest
+import numpy as np
import pytz
from nomad.metainfo import (
- Attribute,
- Datetime,
- MEnum,
MSection,
Quantity,
+ Attribute,
+ MEnum,
Reference,
+ Datetime,
Section,
)
-from nomad.metainfo.metainfo import Definition, MQuantity
+from nomad.metainfo.metainfo import MQuantity, Definition
from nomad.metainfo.util import validate_allowable_unit
from nomad.units import ureg
diff --git a/tests/metainfo/test_data_frames.py b/tests/metainfo/test_data_frames.py
index 9f1ee888517fef141fb712af31c1f3be6a728c50..b32aff08671e22390339e73d0185c3bbb333f609 100644
--- a/tests/metainfo/test_data_frames.py
+++ b/tests/metainfo/test_data_frames.py
@@ -2,13 +2,22 @@ import datetime
import numpy as np
import pandas as pd
-import pytest
import xarray as xr
+import pytest
-from nomad.metainfo.data_frames import DataFrameTemplate, ValuesTemplate
-from nomad.metainfo.metainfo import Datetime, MEnum, MSection, Package
+from nomad.metainfo.metainfo import (
+ MSection,
+ Package,
+ MEnum,
+ Datetime,
+)
+from nomad.metainfo.data_frames import (
+ ValuesTemplate,
+ DataFrameTemplate,
+)
from nomad.units import ureg
+
m_package = Package()
# Values
diff --git a/tests/metainfo/test_elasticsearch_extension.py b/tests/metainfo/test_elasticsearch_extension.py
index e9aafb1575baa292c688786fd5d8429d380f1a99..6001560fb83995648c7700bef1f1b31b6c0e4583 100644
--- a/tests/metainfo/test_elasticsearch_extension.py
+++ b/tests/metainfo/test_elasticsearch_extension.py
@@ -17,28 +17,28 @@
#
from datetime import date
-
-import numpy as np
import pytest
+import numpy as np
from elasticsearch_dsl import Keyword
from nomad.config import config
+from nomad.utils.exampledata import ExampleData
from nomad.datamodel.datamodel import SearchableQuantity
-from nomad.metainfo import Datetime, MEnum, MSection, Quantity, SubSection, Unit
+from nomad.metainfo import MSection, Quantity, SubSection, Datetime, Unit, MEnum
from nomad.metainfo.elasticsearch_extension import (
Elasticsearch,
create_indices,
- create_searchable_quantity,
- entry_index,
- entry_type,
index_entries_with_materials,
+ entry_type,
+ material_type,
material_entry_type,
+ entry_index,
material_index,
- material_type,
+ create_searchable_quantity,
)
-from nomad.utils.exampledata import ExampleData
-from tests.app.v1.routers.common import perform_quantity_search_test
+
from tests.fixtures.infrastructure import clear_elastic_infra
+from tests.app.v1.routers.common import perform_quantity_search_test
@pytest.fixture(scope='module')
diff --git a/tests/metainfo/test_full_storage_quantity.py b/tests/metainfo/test_full_storage_quantity.py
index e08520aad6f4c8e7d27574b015acba2424922218..9acb42dcf198b1c1b404dda216cd464160a31381 100644
--- a/tests/metainfo/test_full_storage_quantity.py
+++ b/tests/metainfo/test_full_storage_quantity.py
@@ -18,12 +18,12 @@
import pytest
from nomad.metainfo import (
- Attribute,
- MetainfoError,
MSection,
Quantity,
- Section,
+ Attribute,
SubSection,
+ MetainfoError,
+ Section,
)
from nomad.metainfo.util import MQuantity
from nomad.units import ureg
diff --git a/tests/metainfo/test_hash_id.py b/tests/metainfo/test_hash_id.py
index 6e2b678431a1432dd43dce2d6475071a190e8e90..3c3e44bb2e08569e30e48a0236f148d6b0109e2b 100644
--- a/tests/metainfo/test_hash_id.py
+++ b/tests/metainfo/test_hash_id.py
@@ -1,4 +1,4 @@
-from nomad.metainfo import MEnum, MSection, Quantity
+from nomad.metainfo import Quantity, MSection, MEnum
def simple_quantity():
diff --git a/tests/metainfo/test_metainfo.py b/tests/metainfo/test_metainfo.py
index 394d44b588d6d341075f5eefde1857f2bfa15e26..ea08bba6ca3b6af8324e339dd3db219f178e9207 100644
--- a/tests/metainfo/test_metainfo.py
+++ b/tests/metainfo/test_metainfo.py
@@ -20,33 +20,40 @@
# in-depth tests in test_* files of the same module.
from math import isnan
-
+import pytest
import numpy as np
import pandas as pd
import pint.quantity
-import pytest
-from nomad.metainfo import (
- Annotation,
- AnnotationModel,
- DefinitionAnnotation,
- SectionAnnotation,
-)
-from nomad.metainfo.example import SCC, Parsing, Run, System, SystemHash, VaspRun
-from nomad.metainfo.example import m_package as example_package
from nomad.metainfo.metainfo import (
- Definition,
- DeriveError,
- MCategory,
- MetainfoError,
MSection,
- Package,
- Quantity,
+ MCategory,
Section,
+ Quantity,
SubSection,
+ Definition,
+ Package,
+ DeriveError,
+ MetainfoError,
derived,
)
+from nomad.metainfo import (
+ Annotation,
+ DefinitionAnnotation,
+ SectionAnnotation,
+ AnnotationModel,
+)
+from nomad.metainfo.example import (
+ Run,
+ VaspRun,
+ System,
+ SystemHash,
+ Parsing,
+ SCC,
+ m_package as example_package,
+)
from nomad.units import ureg
+
from tests.metainfo import MTypes
diff --git a/tests/metainfo/test_mongodb_extension.py b/tests/metainfo/test_mongodb_extension.py
index ff1687b7660e10954fc98b88fc9283ddd9160b32..3f03c65a6dc97bb47f92e9532971d2e31d38b5f3 100644
--- a/tests/metainfo/test_mongodb_extension.py
+++ b/tests/metainfo/test_mongodb_extension.py
@@ -17,11 +17,9 @@
#
import json
-
import numpy as np
-
-from nomad.metainfo import MSection, Quantity, Section, SubSection
-from nomad.metainfo.mongoengine_extension import Mongo, MongoDocument
+from nomad.metainfo import MSection, Section, Quantity, SubSection
+from nomad.metainfo.mongoengine_extension import MongoDocument, Mongo
class B(MSection):
diff --git a/tests/metainfo/test_package.py b/tests/metainfo/test_package.py
index 583ccb35e6996ba10de5dc7825cb4eaa82795ed4..75d70c3d2c77a30e94bb0c38c65f83585e52b350 100644
--- a/tests/metainfo/test_package.py
+++ b/tests/metainfo/test_package.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
-from nomad.metainfo import MSection, Package
+from nomad.metainfo import Package, MSection
m_package = Package(aliases=['nomad.datamodel.test_package'])
diff --git a/tests/metainfo/test_quantities.py b/tests/metainfo/test_quantities.py
index 0e6842b2d32fd941bbf2525a576b4d2c217c342f..ad39b0e06313fce8e2dfffb4b6845d420cd79adb 100644
--- a/tests/metainfo/test_quantities.py
+++ b/tests/metainfo/test_quantities.py
@@ -24,14 +24,14 @@ import pytest
import pytz
from nomad.metainfo.metainfo import (
- JSON,
- URL,
Bytes,
Capitalized,
Datetime,
Dimension,
+ JSON,
MSection,
Quantity,
+ URL,
Unit,
units,
)
diff --git a/tests/metainfo/test_references.py b/tests/metainfo/test_references.py
index 8a7f14a00a67c4cac18a049e50c84fa4b6ab52c2..c9f20fcc985f1ecdc725f3abbe401a6e92fc1e53 100644
--- a/tests/metainfo/test_references.py
+++ b/tests/metainfo/test_references.py
@@ -16,26 +16,25 @@
# limitations under the License.
#
-import os.path
from typing import cast
-
import pytest
+import os.path
-from nomad.datamodel import AuthorReference, UserReference
+from nomad.datamodel import UserReference, AuthorReference
from nomad.metainfo import (
- Context,
- File,
- MetainfoReferenceError,
- MProxy,
MSection,
- Package,
Quantity,
- QuantityReference,
- Reference,
Section,
SubSection,
+ MProxy,
+ Reference,
+ QuantityReference,
+ File,
+ MetainfoReferenceError,
+ Package as MetainfoPackage,
+ Context,
+ Package,
)
-from nomad.metainfo import Package as MetainfoPackage
class Referenced(MSection):
@@ -384,7 +383,7 @@ def test_def_reference():
@pytest.mark.parametrize('mainfile', ['intra-entry', 'inter-entry'])
def test_parse_with_references(mainfile):
- from nomad.client import normalize_all, parse
+ from nomad.client import parse, normalize_all
entry_archive = parse(
os.path.join(
diff --git a/tests/metainfo/test_sections.py b/tests/metainfo/test_sections.py
index 7ed0276321249910bf0acb51232b3b50504d17b6..04de671f982ab274ef5ac1f6c363b12a04cad2ab 100644
--- a/tests/metainfo/test_sections.py
+++ b/tests/metainfo/test_sections.py
@@ -22,7 +22,7 @@
import pytest
from nomad.metainfo import MSection
-from nomad.metainfo.metainfo import Package, Quantity, Section, SubSection
+from nomad.metainfo.metainfo import Package, Quantity, SubSection, Section
def test_base_section():
@@ -251,7 +251,7 @@ def test_path():
assert SubSection.used_sections[ChildSection.m_def] == [EntryArchive.child]
assert ChildSection.m_def.path == 'child'
- from nomad.datamodel.metainfo.workflow import Task, Workflow
+ from nomad.datamodel.metainfo.workflow import Workflow, Task
assert Workflow.m_def.path == 'workflow2'
assert Task.m_def.path == '__no_archive_path__'
diff --git a/tests/metainfo/test_to_dict.py b/tests/metainfo/test_to_dict.py
index 8c296a8868d559c7dea801d4bfebb38cfcb75dfa..91e2288fabdfb7fd847774e941682d114c5b9206 100644
--- a/tests/metainfo/test_to_dict.py
+++ b/tests/metainfo/test_to_dict.py
@@ -16,16 +16,16 @@
# limitations under the License.
#
-import numpy as np
import pytest
+import numpy as np
import yaml
from nomad.app.v1.routers.metainfo import (
get_package_by_section_definition_id,
store_package_definition,
)
-from nomad.metainfo import MCategory, MSection, Quantity, SubSection
-from nomad.metainfo.metainfo import Definition, MEnum, Package, Reference
+from nomad.metainfo import MSection, MCategory, Quantity, SubSection
+from nomad.metainfo.metainfo import Package, MEnum, Reference, Definition
# resolve_references are tested in .test_references
# type specific serialization is tested in .test_quantities
diff --git a/tests/metainfo/test_yaml_schema.py b/tests/metainfo/test_yaml_schema.py
index 950d8927c61b1ef84704caeb952c150034381599..67df9908508c25b5a6885ebe8279250379346687 100644
--- a/tests/metainfo/test_yaml_schema.py
+++ b/tests/metainfo/test_yaml_schema.py
@@ -20,18 +20,18 @@ import numpy as np
import pytest
import yaml
+from nomad.utils import strip
from nomad.metainfo import (
- Context,
- MetainfoError,
- MProxy,
- MSection,
Package,
+ MSection,
Quantity,
Reference,
- Section,
SubSection,
+ Section,
+ MProxy,
+ MetainfoError,
+ Context,
)
-from nomad.utils import strip
m_package = Package()
diff --git a/tests/mkdocs/test_mkdocs_metainfo.py b/tests/mkdocs/test_mkdocs_metainfo.py
index 368288ff1cc8caf825772a45b86aeaf8981ef3d8..0ddda157dadb66ecc0281d78d5e470be3432f5a5 100644
--- a/tests/mkdocs/test_mkdocs_metainfo.py
+++ b/tests/mkdocs/test_mkdocs_metainfo.py
@@ -19,7 +19,7 @@
import pytest
-from nomad.metainfo import Datetime, MSection, Package, Quantity, Reference
+from nomad.metainfo import MSection, Quantity, Datetime, Reference, Package
from nomad.mkdocs.metainfo import (
get_property_description,
get_property_type_info,
diff --git a/tests/mkdocs/test_mkdocs_pydantic.py b/tests/mkdocs/test_mkdocs_pydantic.py
index 15a9bda32ebfc639342c8f1f0ce92092d2a4736f..1183cde07a3666fd3c4c219e5bc0a71d17810255 100644
--- a/tests/mkdocs/test_mkdocs_pydantic.py
+++ b/tests/mkdocs/test_mkdocs_pydantic.py
@@ -17,18 +17,17 @@
#
from enum import Enum
-from typing import Annotated, Literal, Optional, Union # type: ignore
-
import pytest
+from typing import Union, Optional
+from typing import Literal, Annotated # type: ignore
from pydantic import BaseModel, Field
-
from nomad.config.models.ui import WidgetHistogram, WidgetTerms
from nomad.mkdocs.pydantic import (
- get_field_default,
- get_field_deprecated,
+ get_field_type_info,
get_field_description,
+ get_field_default,
get_field_options,
- get_field_type_info,
+ get_field_deprecated,
)
diff --git a/tests/normalizing/conftest.py b/tests/normalizing/conftest.py
index c9c926b861409de40f92b0f30362de8e13718788..eac8d840eca71208d5b717f40e8b2e5114a99048 100644
--- a/tests/normalizing/conftest.py
+++ b/tests/normalizing/conftest.py
@@ -15,47 +15,53 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import re
from collections import defaultdict
-from typing import Any
-from warnings import warn
-
-import ase.build
import numpy as np
+from typing import Any
import pytest
from ase import Atoms
+import ase.build
+import re
+from warnings import warn
-from nomad.datamodel import ArchiveSection, EntryArchive
-from nomad.datamodel.context import ServerContext
-from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
-from nomad.datamodel.metainfo import runschema, simulationworkflowschema
+from nomad.units import ureg
+from nomad.utils import get_logger
+from nomad.normalizing import normalizers
+from nomad.metainfo import SubSection, Quantity
+from nomad.datamodel import EntryArchive, ArchiveSection
+from nomad.datamodel.results import (
+ Relation,
+ SymmetryNew as Symmetry,
+ Cell,
+ WyckoffSet,
+ System as ResultSystem,
+)
+from nomad.datamodel.optimade import Species
+from nomad.normalizing.common import cell_from_ase_atoms, nomad_atoms_from_ase_atoms
+from nomad.datamodel.metainfo.simulation.method import CoreHole
+from nomad.datamodel.metainfo.workflow import Workflow
from nomad.datamodel.metainfo.measurements import (
- EELSMeasurement,
- Instrument,
Measurement,
Sample,
+ EELSMeasurement,
Spectrum,
+ Instrument,
)
-from nomad.datamodel.metainfo.simulation.method import CoreHole
-from nomad.datamodel.metainfo.workflow import Workflow
-from nomad.datamodel.optimade import Species
-from nomad.datamodel.results import Cell, EELSInstrument, Relation, WyckoffSet
-from nomad.datamodel.results import SymmetryNew as Symmetry
-from nomad.datamodel.results import System as ResultSystem
-from nomad.metainfo import Quantity, SubSection
-from nomad.normalizing import normalizers
-from nomad.normalizing.common import cell_from_ase_atoms, nomad_atoms_from_ase_atoms
+from nomad.datamodel.results import EELSInstrument
+
+from nomad.datamodel.context import ServerContext
+from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
from nomad.parsing.parser import ArchiveParser
from nomad.processing.data import Upload
-from nomad.units import ureg
-from nomad.utils import get_logger
-from tests.parsing.test_parsing import (
- parse_file,
- parsed_example, # noqa: F401
- parsed_template_example, # noqa: F401
- parsed_vasp_example, # noqa: F401
-)
+from tests.parsing.test_parsing import parsed_vasp_example # noqa: F401
+from tests.parsing.test_parsing import parsed_template_example # noqa: F401
+from tests.parsing.test_parsing import parsed_example # noqa: F401
+from tests.parsing.test_parsing import parse_file
from tests.test_files import create_test_upload_files
+from nomad.datamodel.metainfo import (
+ simulationworkflowschema,
+ runschema,
+)
def run_normalize(entry_archive: EntryArchive) -> EntryArchive:
diff --git a/tests/normalizing/test_entry_type_and_name.py b/tests/normalizing/test_entry_type_and_name.py
index dffa84450dda6ebb4a292a09a2e706e4744ae2ef..c0b4ba6a327a6defde96e39c33d7eb7f9cd34193 100644
--- a/tests/normalizing/test_entry_type_and_name.py
+++ b/tests/normalizing/test_entry_type_and_name.py
@@ -16,9 +16,7 @@
# limitations under the License.
#
import pytest
-
import tests
-
from .conftest import run_normalize
diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py
index ab422266ef3aa1d335eae0318ad627944779e1bd..c2b9289da2f68eb3c767fcfd0c2ea6bbf058dcb1 100644
--- a/tests/normalizing/test_material.py
+++ b/tests/normalizing/test_material.py
@@ -16,18 +16,18 @@
# limitations under the License.
#
-import ase.build
import numpy as np
import pytest
from ase import Atoms
+import ase.build
from matid.symmetry.wyckoffset import WyckoffSet # pylint: disable=import-error
+from nomad.units import ureg
from nomad import atomutils
from nomad.config import config
-from nomad.datamodel.results import ElementalComposition
-from nomad.normalizing.common import ase_atoms_from_nomad_atoms
-from nomad.units import ureg
from nomad.utils import hash
+from nomad.normalizing.common import ase_atoms_from_nomad_atoms
+from nomad.datamodel.results import ElementalComposition
from tests.normalizing.conftest import get_template_for_structure
diff --git a/tests/normalizing/test_metainfo.py b/tests/normalizing/test_metainfo.py
index 815ad7df3a7882c324e4bf9b79655b3b0405bc93..6fc097c0538354edfb6e2e99f2e87386acbfb943 100644
--- a/tests/normalizing/test_metainfo.py
+++ b/tests/normalizing/test_metainfo.py
@@ -17,9 +17,9 @@
#
import numpy as np
-from nomad.client import normalize_all
-from nomad.datamodel import EntryArchive, EntryData
+from nomad.datamodel import EntryData, EntryArchive
from nomad.metainfo import Quantity, SubSection
+from nomad.client import normalize_all
def test_normalizer_level():
diff --git a/tests/normalizing/test_method.py b/tests/normalizing/test_method.py
index 1f9992a15b47f9d19a6f8b11eb990aa0027e6866..483753d8e65c234b4ab841cadf39ad6c3632eed5 100644
--- a/tests/normalizing/test_method.py
+++ b/tests/normalizing/test_method.py
@@ -17,9 +17,8 @@
#
import numpy as np
-import pytest
-
from nomad.units import ureg
+import pytest
def approx(value, abs=0, rel=1e-6):
diff --git a/tests/normalizing/test_properties.py b/tests/normalizing/test_properties.py
index 9ad5ae24b2daf9179cab3d23ca33be0686e844fc..ad82111b390280fb02528becf149458c473bcca5 100644
--- a/tests/normalizing/test_properties.py
+++ b/tests/normalizing/test_properties.py
@@ -19,20 +19,20 @@
import numpy as np
import pytest
-from nomad.datamodel.metainfo import SCHEMA_IMPORT_ERROR, simulationworkflowschema
from nomad.units import ureg
from .conftest import (
- add_template_band_structure,
+ get_template_dft,
add_template_dos,
+ get_template_dos,
+ add_template_band_structure,
+ get_template_band_structure,
add_template_magnetic_shielding,
- add_template_magnetic_susceptibility,
add_template_spin_spin_coupling,
- get_template_band_structure,
- get_template_dft,
- get_template_dos,
+ add_template_magnetic_susceptibility,
run_normalize,
)
+from nomad.datamodel.metainfo import simulationworkflowschema, SCHEMA_IMPORT_ERROR
def test_eels(eels):
diff --git a/tests/normalizing/test_topology.py b/tests/normalizing/test_topology.py
index 5940d8e8e9e8c1cbce921ca7adee123c90175eb2..552949f1400c26e99927c556b8dae4382357c1e6 100644
--- a/tests/normalizing/test_topology.py
+++ b/tests/normalizing/test_topology.py
@@ -16,35 +16,34 @@
# limitations under the License.
#
-from collections import defaultdict
-
import numpy as np
+from collections import defaultdict
import pytest
-
from nomad.datamodel.metainfo import runschema
+
from nomad.units import ureg
from tests.normalizing.conftest import ( # noqa: F401
- boron_nitride,
- boron_nitride_topology,
- check_template_active_orbitals,
- conv_bcc,
- conv_fcc,
- get_template_active_orbitals,
- get_template_computation,
get_template_for_structure,
get_template_topology,
- graphene,
- graphene_topology,
- mos2,
- mos2_topology,
+ conv_bcc,
+ conv_fcc,
rattle,
run_normalize,
- single_cr_surface_topology,
- single_cu_surface_topology,
stack,
+ surf,
+ single_cu_surface_topology,
+ single_cr_surface_topology,
stacked_cu_ni_surface_topology,
+ graphene,
+ graphene_topology,
+ boron_nitride,
+ boron_nitride_topology,
+ mos2,
+ mos2_topology,
stacked_graphene_boron_nitride_topology,
- surf,
+ get_template_active_orbitals,
+ check_template_active_orbitals,
+ get_template_computation,
)
diff --git a/tests/parsing/test_archive_parser.py b/tests/parsing/test_archive_parser.py
index e577bbb0681973c580f493dcbc1e74ca96cc5782..b9666aa564265de69aeb7d5bb64f9dcada4f8245 100644
--- a/tests/parsing/test_archive_parser.py
+++ b/tests/parsing/test_archive_parser.py
@@ -16,15 +16,14 @@
# limitations under the License.
#
+import pytest
import json
import os
import os.path
-import pytest
-
from nomad.config import config
-from nomad.datamodel import Context, EntryArchive
from nomad.parsing.parser import ArchiveParser
+from nomad.datamodel import EntryArchive, Context
def test_archive_parser(raw_files_function):
diff --git a/tests/parsing/test_file_parser.py b/tests/parsing/test_file_parser.py
index d3a6e0a32c56d6c7f0443a8b54be2f3688dce1fa..b9ffdb65d35da55ddf0a24a7ee6469172d463012 100644
--- a/tests/parsing/test_file_parser.py
+++ b/tests/parsing/test_file_parser.py
@@ -1,15 +1,14 @@
+import pytest
import numpy as np
import pint
-import pytest
-
-from nomad.datamodel.metainfo.system import Atoms
from nomad.parsing.file_parser import (
- FileParser,
- ParsePattern,
- Quantity,
TextParser,
+ Quantity,
+ ParsePattern,
XMLParser,
+ FileParser,
)
+from nomad.datamodel.metainfo.system import Atoms
class TestFileParser:
diff --git a/tests/parsing/test_mapping_parser.py b/tests/parsing/test_mapping_parser.py
index a772a8b08cc1e8d9d00c5d9a99b281c1754d6563..555587fab2626c22b5324989d82f5bee7c7b921f 100644
--- a/tests/parsing/test_mapping_parser.py
+++ b/tests/parsing/test_mapping_parser.py
@@ -1,27 +1,28 @@
-from copy import deepcopy
-from typing import Any
-
-import numpy as np
import pytest
+import numpy as np
+from typing import Any
+from copy import deepcopy
-from nomad.datamodel import ArchiveSection
-from nomad.datamodel.metainfo.annotations import Mapper as MapperAnnotation
from nomad.metainfo import Quantity, SubSection
+from nomad.datamodel.metainfo.annotations import Mapper as MapperAnnotation
from nomad.parsing.file_parser.mapping_parser import (
- MAPPING_ANNOTATION_KEY,
- Data,
- HDF5Parser,
- Mapper,
MappingParser,
+ XMLParser,
MetainfoParser,
- Path,
- PathParser,
+ HDF5Parser,
TextParser,
+ Path,
Transformer,
- XMLParser,
+ Data,
+ Mapper,
+ PathParser,
+ MAPPING_ANNOTATION_KEY,
+)
+from nomad.parsing.file_parser.text_parser import (
+ TextParser as TextFileParser,
+ Quantity as TextQuantity,
)
-from nomad.parsing.file_parser.text_parser import Quantity as TextQuantity
-from nomad.parsing.file_parser.text_parser import TextParser as TextFileParser
+from nomad.datamodel import ArchiveSection
class BSection(ArchiveSection):
diff --git a/tests/parsing/test_parsing.py b/tests/parsing/test_parsing.py
index 176679775b011990a7309df94b7dea15d2bc2e1f..adfbece7378ccc90039d204d6b9a42ca1e502ba5 100644
--- a/tests/parsing/test_parsing.py
+++ b/tests/parsing/test_parsing.py
@@ -19,13 +19,13 @@
import json
import os
from shutil import copyfile
-from unittest.mock import MagicMock, patch
+from unittest.mock import patch, MagicMock
import pytest
from nomad import files, utils
from nomad.datamodel import EntryArchive
-from nomad.parsing import BrokenParser, MatchingParser, MatchingParserInterface
+from nomad.parsing import BrokenParser, MatchingParserInterface, MatchingParser
from nomad.parsing.parsers import match_parser, parser_dict, parsers, run_parser
from nomad.utils import dump_json
diff --git a/tests/parsing/test_tabular.py b/tests/parsing/test_tabular.py
index 7acf5017b8cbd3856ac4b7bb958a30f752878888..50572e427ec98ce49c453fa9a94f75dfdf682317 100644
--- a/tests/parsing/test_tabular.py
+++ b/tests/parsing/test_tabular.py
@@ -16,23 +16,23 @@
# limitations under the License.
#
-import datetime
+import pytest
import os
import os.path
import re
-
-import pytest
+import datetime
import yaml
-from nomad import files
from nomad.config import config
-from nomad.datamodel.context import ClientContext
from nomad.datamodel.datamodel import EntryArchive, EntryMetadata
-from nomad.parsing.parser import ArchiveParser
+from nomad.datamodel.context import ClientContext
from nomad.parsing.tabular import read_table_data
-from nomad.processing import Entry, ProcessStatus, Upload
from nomad.utils import generate_entry_id, strip
+from nomad.parsing.parser import ArchiveParser
from tests.normalizing.conftest import run_normalize
+from nomad.processing import Upload, Entry
+from nomad.processing import ProcessStatus
+from nomad import files
def quantity_generator(quantity_name, header_name, shape, to_dict=False):
diff --git a/tests/processing/test_base.py b/tests/processing/test_base.py
index 45fbe4560311a106976ca52e1cd65509564333f2..d1e2cf8ca3767bbfee3336a1135456f9e683e479 100644
--- a/tests/processing/test_base.py
+++ b/tests/processing/test_base.py
@@ -15,20 +15,20 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import pytest
import random
-import threading
import time
+import threading
from typing import Any
-import pytest
-from mongoengine import IntField, ListField, StringField
+from mongoengine import StringField, IntField, ListField
from nomad.processing.base import (
Proc,
ProcessAlreadyRunning,
- ProcessStatus,
process,
process_local,
+ ProcessStatus,
)
random.seed(0)
diff --git a/tests/processing/test_data.py b/tests/processing/test_data.py
index d538f39a91a3f52cfd8128a1bbbeda7da4edf1fd..f32e0f14690757dfc44239645b754759ac376542 100644
--- a/tests/processing/test_data.py
+++ b/tests/processing/test_data.py
@@ -16,39 +16,39 @@
# limitations under the License.
#
-import json
+from collections.abc import Generator
+import pytest
import os.path
import re
import shutil
import zipfile
-from collections.abc import Generator
-
-import pytest
+import json
import yaml
-from nomad import infrastructure, utils
-from nomad.archive import read_partial_archive_from_mongo, to_json
+from nomad import utils, infrastructure
from nomad.config import config
from nomad.config.models.config import BundleImportSettings
+from nomad.archive import read_partial_archive_from_mongo, to_json
+from nomad.files import UploadFiles, StagingUploadFiles, PublicUploadFiles
+from nomad.parsing.parser import Parser
+from nomad.parsing import parsers
from nomad.datamodel import ServerContext
from nomad.datamodel.data import EntryData
-from nomad.datamodel.datamodel import ArchiveSection, EntryArchive, EntryData
-from nomad.files import PublicUploadFiles, StagingUploadFiles, UploadFiles
from nomad.metainfo import Package, Quantity, Reference, SubSection
-from nomad.parsing import parsers
-from nomad.parsing.parser import Parser
-from nomad.processing import Entry, ProcessStatus, Upload
-from nomad.search import refresh as search_refresh
-from nomad.search import search
+from nomad.processing import Upload, Entry, ProcessStatus
+from nomad.search import search, refresh as search_refresh
from nomad.utils.exampledata import ExampleData
+from nomad.datamodel.datamodel import EntryArchive, EntryData, ArchiveSection
+
+from tests.test_search import assert_search_upload
from tests.test_files import (
assert_upload_files,
- example_file_aux,
example_file_mainfile,
+ example_file_aux,
)
-from tests.test_search import assert_search_upload
from tests.utils import create_template_upload_file, set_upload_entry_metadata
+
# Package with some metainfo schemas used only for testing.
m_package = Package(name='test_schemas')
diff --git a/tests/processing/test_edit_metadata.py b/tests/processing/test_edit_metadata.py
index 96963944b85296fcf2e4c2418964f14ca579a514..6d53da2b890cc7743bfbb0f527e40ff97713dbc0 100644
--- a/tests/processing/test_edit_metadata.py
+++ b/tests/processing/test_edit_metadata.py
@@ -15,17 +15,18 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
+import pytest
from datetime import datetime
-import pytest
from fastapi.exceptions import RequestValidationError
from nomad import datamodel, metainfo
from nomad.metainfo.data_type import Datatype
-from nomad.processing import MetadataEditRequestHandler, Upload
+from nomad.processing import Upload, MetadataEditRequestHandler
from nomad.processing.data import editable_metadata, mongo_upload_metadata
from nomad.search import search
+
all_coauthor_metadata = dict(
# All attributes which a coauthor+ can edit
upload_name='a humble upload name',
diff --git a/tests/processing/test_rfc3161.py b/tests/processing/test_rfc3161.py
index 28f1bcc80ba94bbadbdc0bd0192b2e84786cd96a..e559a53246882e5154175d2a570a6bc61bd8ca48 100644
--- a/tests/processing/test_rfc3161.py
+++ b/tests/processing/test_rfc3161.py
@@ -23,9 +23,9 @@ import httpx
import pytest
import rfc3161ng
-from nomad.archive import read_archive, to_json, write_archive
+from nomad.archive import write_archive, read_archive, to_json
from nomad.datamodel.datamodel import RFC3161Timestamp
-from nomad.processing.data import Entry, get_rfc3161_token
+from nomad.processing.data import get_rfc3161_token, Entry
@pytest.mark.parametrize(
diff --git a/tests/states/archives/create_archives.py b/tests/states/archives/create_archives.py
index 0b53682f6dbcf3b0d580c005c09522d197edcf6c..bcee46b0a307349c098720aed9eb54741e85b34a 100644
--- a/tests/states/archives/create_archives.py
+++ b/tests/states/archives/create_archives.py
@@ -17,7 +17,6 @@
#
import math
-
from nomad.utils.exampledata import create_entry_archive
diff --git a/tests/states/entry.py b/tests/states/entry.py
index bbd97182e0c9389beb0731d255391002118eb053..767a77b37087849e30d2dfa81b850bf6edb45490 100644
--- a/tests/states/entry.py
+++ b/tests/states/entry.py
@@ -17,12 +17,10 @@
#
import json
-
-from nomad import files, infrastructure
-from nomad.processing import Upload
+from nomad import infrastructure, files
from nomad.utils.exampledata import ExampleData, create_entry_archive
-
from .archives.create_archives import archive_dft_bulk
+from nomad.processing import Upload
def dft():
diff --git a/tests/states/search.py b/tests/states/search.py
index 6a53a211cc259d5579aa653b461a6c9ab2ff5864..e3ef1fc19c585b0ceb5f4cea7d443f897b0047af 100644
--- a/tests/states/search.py
+++ b/tests/states/search.py
@@ -16,11 +16,10 @@
# limitations under the License.
#
from datetime import datetime, timedelta
-
from nomad import infrastructure
-from nomad.atomutils import chemical_symbols
-from nomad.units import ureg
from nomad.utils import create_uuid
+from nomad.units import ureg
+from nomad.atomutils import chemical_symbols
from nomad.utils.exampledata import ExampleData
material_h2o = {
diff --git a/tests/states/uploads.py b/tests/states/uploads.py
index a79aa893b8bcb3aac07d135887748803d01aca5b..52ae1ed4e99129aef629545183df7d84693ee127 100644
--- a/tests/states/uploads.py
+++ b/tests/states/uploads.py
@@ -16,12 +16,11 @@
# limitations under the License.
#
-from nomad import files, infrastructure
+from nomad import infrastructure, files
from nomad.processing import Upload
from nomad.utils.exampledata import ExampleData
-
from .archives.create_archives import archive_dft_bulk
-from .groups import delete_group, init_gui_test_groups
+from .groups import init_gui_test_groups, delete_group
default_access = {'coauthors': ['scooper'], 'reviewers': ['ttester']}
twin_access = {
diff --git a/tests/test_atomutils.py b/tests/test_atomutils.py
index e9dc5f5561a5d24803bcc0369b5a081cc73b5ecc..97655c0eded200dafd7bea8bf237a0bf35a3dd85 100644
--- a/tests/test_atomutils.py
+++ b/tests/test_atomutils.py
@@ -16,9 +16,8 @@
# limitations under the License.
#
import pytest
-
from nomad.atomutils import Formula
-from nomad.datamodel.results import ElementalComposition, Material
+from nomad.datamodel.results import Material, ElementalComposition
@pytest.mark.parametrize(
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 1350894136449b375906f4937adf8020ef4cfaf0..3ee028698b5e5098b2761c0f25f3066d413e869e 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -16,22 +16,20 @@
# limitations under the License.
#
-import datetime
+import pytest
+import click.testing
import json
import os
-import tempfile
+import datetime
import time
+import tempfile
-import click.testing
-import pytest
-
-from nomad import files
-from nomad import processing as proc
-from nomad.cli import cli
-from nomad.cli.cli import POPO
+from nomad import processing as proc, files
from nomad.config import config
-from nomad.processing import Entry, ProcessStatus, Upload
from nomad.search import search
+from nomad.cli import cli
+from nomad.cli.cli import POPO
+from nomad.processing import Upload, Entry, ProcessStatus
from nomad.utils.exampledata import ExampleData
# TODO there is much more to test
diff --git a/tests/test_client.py b/tests/test_client.py
index 35211bf701cd3aeed9391f3b6dc89707a19b5e68..ce2f246cf51093841b4501c02b84b1874c05897f 100644
--- a/tests/test_client.py
+++ b/tests/test_client.py
@@ -15,23 +15,28 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-import json
import os
-import pytest
from httpx import AsyncClient
+import pytest
+import json
+
from pydantic import ValidationError
from nomad.app.main import app
from nomad.client.archive import ArchiveQuery
from nomad.datamodel import EntryArchive, User
-from nomad.datamodel.metainfo import SCHEMA_IMPORT_ERROR, runschema
-from nomad.datamodel.metainfo.annotations import Rule, Rules
+from nomad.datamodel.metainfo import runschema, SCHEMA_IMPORT_ERROR
+from nomad.datamodel.metainfo.annotations import (
+ Rule,
+ Rules,
+)
from nomad.metainfo import MSection, SubSection
from nomad.utils.json_transformer import Transformer
from tests.fixtures.users import users
from tests.processing import test_data as test_processing
+
# TODO: more tests
diff --git a/tests/test_common.py b/tests/test_common.py
index 432be865b7eb05c5376cb65f6fda6915865fbda0..919538e69ef708a3e7d1fcec9b9ac4a090f83316 100644
--- a/tests/test_common.py
+++ b/tests/test_common.py
@@ -17,8 +17,7 @@
#
import pytest
-
-from nomad.common import is_safe_path, is_safe_relative_path
+from nomad.common import is_safe_relative_path, is_safe_path
@pytest.mark.parametrize(
diff --git a/tests/test_config.py b/tests/test_config.py
index 20fbe5d18f437c9b80ab850331410861264a4da8..7cc0f5070576d2c59b4fed4bd1acf8cebadb24e2 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -18,13 +18,12 @@
import os
import re
-
import pytest
import yaml
from pydantic import ValidationError
from nomad.config import load_config
-from nomad.config.models.plugins import Parser, ParserEntryPoint, Schema
+from nomad.config.models.plugins import Parser, Schema, ParserEntryPoint
from nomad.utils import flatten_dict
from .utils import assert_log
diff --git a/tests/test_doi.py b/tests/test_doi.py
index bcb4e61df01b8f202029b884856f0fb0976f3f22..60498040f7d707584a64bc152bcaf5729b268f54 100644
--- a/tests/test_doi.py
+++ b/tests/test_doi.py
@@ -15,12 +15,10 @@
# See the License for the specific language governing permissions and
# limitations under the License.
#
-from unittest.mock import MagicMock
-
-import pytest
-
from nomad.config import config
from nomad.doi import DOI, DOIException
+import pytest
+from unittest.mock import MagicMock
def test_create(mongo_function, user1, no_warn):
diff --git a/tests/test_files.py b/tests/test_files.py
index e2ca1d432ffd9f22b104eb4356b5d3b2a0d6a01b..519be1ec049b27579b1d9c2ac7ae1eb6c482678b 100644
--- a/tests/test_files.py
+++ b/tests/test_files.py
@@ -16,33 +16,31 @@
# limitations under the License.
#
-import itertools
+from typing import Any
+from collections.abc import Generator, Iterable
+from datetime import datetime
import os
import os.path
-import pathlib
-import re
import shutil
-import zipfile
-from collections.abc import Generator, Iterable
-from datetime import datetime
-from typing import Any
-
import pytest
+import itertools
+import zipfile
+import re
+import pathlib
from nomad import datamodel, utils
-from nomad.archive import to_json
from nomad.config import config
+from nomad.archive import to_json
from nomad.files import (
DirectoryObject,
PathObject,
- PublicUploadFiles,
- StagingUploadFiles,
- UploadFiles,
- empty_archive_file_size,
empty_zip_file_size,
+ empty_archive_file_size,
)
+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]
diff --git a/tests/test_logtransfer.py b/tests/test_logtransfer.py
index 122c727b07a823fff4cd0d3293b405c4f687c394..b67262fbeedf50b7db7a447f8e0e58da2374c5fb 100644
--- a/tests/test_logtransfer.py
+++ b/tests/test_logtransfer.py
@@ -1,12 +1,11 @@
-import json
import logging
-import os.path
-
+import json
import pytest
+import os.path
from nomad import config, utils
-from nomad.logtransfer import transfer_logs
from nomad.utils import structlogging
+from nomad.logtransfer import transfer_logs
@pytest.fixture(scope='function')
diff --git a/tests/test_search.py b/tests/test_search.py
index 0e6eeb1f709b52d9fff347b04f1f0a243ffe8edf..319dcbac437aa0c5ffe236838613beb43cea1598 100644
--- a/tests/test_search.py
+++ b/tests/test_search.py
@@ -17,9 +17,9 @@
#
import json
-from collections.abc import Iterable
from datetime import datetime
from typing import Any
+from collections.abc import Iterable
import pytest
@@ -41,8 +41,15 @@ from nomad.metainfo.elasticsearch_extension import (
)
from nomad.metainfo.metainfo import Datetime, Quantity
from nomad.metainfo.util import MEnum
-from nomad.search import AuthenticationRequiredError as ARE
-from nomad.search import quantity_values, refresh, search, update_by_query
+from nomad.search import (
+ AuthenticationRequiredError as ARE,
+)
+from nomad.search import (
+ quantity_values,
+ refresh,
+ search,
+ update_by_query,
+)
from nomad.utils import deep_get
from nomad.utils.exampledata import ExampleData
from tests.variables import python_schema_name, yaml_schema_name
diff --git a/tests/test_test.py b/tests/test_test.py
index ef2353b7ac48692678fcf6afcc0de6017e366d3d..bbca3fb46962648c5bad3662940c5f5101f761d5 100644
--- a/tests/test_test.py
+++ b/tests/test_test.py
@@ -16,9 +16,8 @@
# limitations under the License.
#
-import logging
-
import pytest
+import logging
@pytest.fixture()
diff --git a/tests/test_utils.py b/tests/test_utils.py
index 11f38f65f18387fd3e9db8633888d4009e239b69..5d7339d68ef2b5de9c272aee1def2468d504d7ed 100644
--- a/tests/test_utils.py
+++ b/tests/test_utils.py
@@ -16,24 +16,24 @@
# limitations under the License.
#
-import time
from importlib.metadata import PackageNotFoundError
-
-import pandas as pd
+import time
import pytest
+import pandas as pd
-from nomad import files, utils
+from nomad import utils
from nomad.metainfo.metainfo import MSection, Quantity, SubSection
+from nomad import files
from nomad.processing import Upload
from nomad.utils import (
- dataframe_to_dict,
- deep_get,
- dict_to_dataframe,
- flatten_dict,
nomad_distro_metadata,
- prune_dict,
- rebuild_dict,
structlogging,
+ flatten_dict,
+ rebuild_dict,
+ prune_dict,
+ deep_get,
+ dict_to_dataframe,
+ dataframe_to_dict,
)
diff --git a/tests/utils.py b/tests/utils.py
index c24fe475952acda078d98d74bebfc980be751012..253200de91c69f246f6f7245885fd250315dca8a 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -23,7 +23,6 @@ import urllib.parse
import zipfile
from logging import LogRecord
from typing import Any
-
import pytest