diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 65eb216ba874ec8ace3220cbe928ed181bf5c644..60743175daae9f7e5c6734a935418ba74617b93f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -105,9 +105,9 @@ python linting:
before_script:
- cd /app
script:
- - ruff nomad tests
+ - ruff check nomad tests
- ruff format nomad tests --check
- - ruff nomad tests --output-format gitlab > $CI_PROJECT_DIR/gl-code-quality-report.json
+ - ruff check nomad tests --output-format gitlab > $CI_PROJECT_DIR/gl-code-quality-report.json
- mypy nomad tests
rules:
- if: $CI_COMMIT_TAG
diff --git a/.pylintrc b/.pylintrc
deleted file mode 100644
index a5c27b21c0351394c904cf970e010484ecc3cd95..0000000000000000000000000000000000000000
--- a/.pylintrc
+++ /dev/null
@@ -1,371 +0,0 @@
-[MASTER]
-
-# A comma-separated list of package or module names from where C extensions may
-# be loaded. Extensions are loading into the active Python interpreter and may
-# run arbitrary code.
-extension-pkg-whitelist=pydantic,orjson
-
-# List of plugins (as comma separated values of python module names) to load,
-# usually to register additional checkers.
-load-plugins=pylint_mongoengine,nomad.metainfo.pylint_plugin
-
-
-[MESSAGES CONTROL]
-
-# Disable the message, report, category or checker with the given id(s). You
-# can either give multiple identifiers separated by comma (,) or put this
-# option multiple times (only on the command line, not in the configuration
-# file where it should appear only once). You can also use "--disable=all" to
-# disable everything first and then reenable specific checks. For example, if
-# you want to run only the similarities checker, you can use "--disable=all
-# --enable=similarities". If you want to run only the classes checker, but have
-# no Warning level messages displayed, use "--disable=all --enable=classes
-# --disable=W".
-disable=blacklisted-name,
- unspecified-encoding,
- invalid-name,
- missing-docstring,
- empty-docstring,
- unneeded-not,
- singleton-comparison,
- unidiomatic-typecheck,
- consider-using-enumerate,
- consider-iterating-dictionary,
- consider-using-f-string,
- bad-classmethod-argument,
- bad-mcs-method-argument,
- bad-mcs-classmethod-argument,
- single-string-used-for-slots,
- line-too-long,
- too-many-lines,
- trailing-whitespace,
- missing-final-newline,
- trailing-newlines,
- multiple-statements,
- superfluous-parens,
- bad-whitespace,
- mixed-line-endings,
- unexpected-line-ending-format,
- bad-continuation,
- wrong-spelling-in-comment,
- wrong-spelling-in-docstring,
- invalid-characters-in-docstring,
- multiple-imports,
- wrong-import-order,
- ungrouped-imports,
- wrong-import-position,
- useless-import-alias,
- import-outside-toplevel,
- len-as-condition,
- raw-checker-failed,
- bad-inline-option,
- locally-disabled,
- file-ignored,
- suppressed-message,
- useless-suppression,
- deprecated-pragma,
- use-symbolic-message-instead,
- c-extension-no-member,
- literal-comparison,
- comparison-with-itself,
- no-self-use,
- no-classmethod-decorator,
- no-staticmethod-decorator,
- useless-object-inheritance,
- cyclic-import,
- duplicate-code,
- too-many-ancestors,
- too-many-instance-attributes,
- too-few-public-methods,
- too-many-public-methods,
- too-many-return-statements,
- too-many-branches,
- too-many-arguments,
- too-many-locals,
- too-many-statements,
- too-many-boolean-expressions,
- consider-merging-isinstance,
- too-many-nested-blocks,
- simplifiable-if-statement,
- redefined-argument-from-local,
- no-else-return,
- consider-using-ternary,
- trailing-comma-tuple,
- stop-iteration-return,
- simplify-boolean-expression,
- inconsistent-return-statements,
- useless-return,
- consider-swap-variables,
- consider-using-join,
- consider-using-in,
- consider-using-get,
- chained-comparison,
- consider-using-dict-comprehension,
- consider-using-set-comprehension,
- dangerous-default-value,
- pointless-statement,
- pointless-string-statement,
- expression-not-assigned,
- unnecessary-pass,
- unnecessary-lambda,
- assign-to-new-keyword,
- useless-else-on-loop,
- exec-used,
- eval-used,
- confusing-with-statement,
- using-constant-test,
- comparison-with-callable,
- lost-exception,
- assert-on-tuple,
- attribute-defined-outside-init,
- bad-staticmethod-argument,
- protected-access,
- arguments-differ,
- signature-differs,
- abstract-method,
- super-init-not-called,
- no-init,
- non-parent-init-called,
- useless-super-delegation,
- bad-indentation,
- mixed-indentation,
- wildcard-import,
- deprecated-module,
- reimported,
- import-self,
- misplaced-future,
- fixme,
- global-variable-undefined,
- global-statement,
- global-at-module-level,
- unused-argument,
- unused-wildcard-import,
- redefined-outer-name,
- redefined-builtin,
- undefined-loop-variable,
- cell-var-from-loop,
- possibly-unused-variable,
- self-cls-assignment,
- bare-except,
- broad-except,
- duplicate-except,
- try-except-raise,
- raising-format-tuple,
- keyword-arg-before-vararg,
- logging-not-lazy,
- logging-format-interpolation,
- logging-fstring-interpolation,
- bad-format-string-key,
- unused-format-string-key,
- missing-format-argument-key,
- unused-format-string-argument,
- format-combined-specification,
- missing-format-attribute,
- invalid-format-index,
- anomalous-unicode-escape-in-string,
- boolean-datetime,
- redundant-unittest-assert,
- deprecated-method,
- bad-thread-instantiation,
- shallow-copy-environ,
- invalid-envvar-default,
- subprocess-popen-preexec-fn,
- apply-builtin,
- basestring-builtin,
- buffer-builtin,
- cmp-builtin,
- coerce-builtin,
- execfile-builtin,
- file-builtin,
- long-builtin,
- raw_input-builtin,
- reduce-builtin,
- standarderror-builtin,
- unicode-builtin,
- xrange-builtin,
- coerce-method,
- delslice-method,
- getslice-method,
- setslice-method,
- no-absolute-import,
- old-division,
- dict-iter-method,
- dict-view-method,
- next-method-called,
- metaclass-assignment,
- indexing-exception,
- raising-string,
- reload-builtin,
- oct-method,
- hex-method,
- nonzero-method,
- cmp-method,
- input-builtin,
- round-builtin,
- intern-builtin,
- unichr-builtin,
- map-builtin-not-iterating,
- zip-builtin-not-iterating,
- range-builtin-not-iterating,
- filter-builtin-not-iterating,
- using-cmp-argument,
- div-method,
- idiv-method,
- rdiv-method,
- exception-message-attribute,
- invalid-str-codec,
- sys-max-int,
- bad-python3-import,
- deprecated-string-function,
- deprecated-str-translate-call,
- deprecated-itertools-function,
- deprecated-types-field,
- next-method-defined,
- dict-items-not-iterating,
- dict-keys-not-iterating,
- dict-values-not-iterating,
- deprecated-operator-function,
- deprecated-urllib-function,
- xreadlines-attribute,
- deprecated-sys-function,
- exception-escape,
- comprehension-escape,
- mongoengine-placeholder,
- # TODO: These were temporarily added when upgrading to newer pylint version that
- # catches these new linting issues. Should be addressed and removed.
- self-assigning-variable,
- use-dict-literal,
- unnecessary-comprehension,
- use-sequence-for-iteration,
- f-string-without-interpolation,
- super-with-arguments,
- used-before-assignment,
- consider-using-dict-items,
- no-else-continue,
- arguments-renamed,
- consider-using-with,
- raise-missing-from,
- no-else-break
-
-# Enable the message, report, category or checker with the given id(s). You can
-# either give multiple identifier separated by comma (,) or put this option
-# multiple time (only on the command line, not in the configuration file where
-# it should appear only once). See also the "--disable" option for examples.
-enable=syntax-error,
- unrecognized-inline-option,
- bad-option-value,
- init-is-generator,
- return-in-init,
- function-redefined,
- not-in-loop,
- return-outside-function,
- yield-outside-function,
- return-arg-in-generator,
- nonexistent-operator,
- duplicate-argument-name,
- abstract-class-instantiated,
- bad-reversed-sequence,
- too-many-star-expressions,
- invalid-star-assignment-target,
- star-needs-assignment-target,
- nonlocal-and-global,
- continue-in-finally,
- nonlocal-without-binding,
- used-prior-global-declaration,
- misplaced-format-function,
- method-hidden,
- access-member-before-definition,
- no-method-argument,
- no-self-argument,
- invalid-slots-object,
- assigning-non-slot,
- invalid-slots,
- inherit-non-class,
- inconsistent-mro,
- duplicate-bases,
- non-iterator-returned,
- unexpected-special-method-signature,
- invalid-length-returned,
- import-error,
- relative-beyond-top-level,
- used-before-assignment,
- undefined-variable,
- undefined-all-variable,
- invalid-all-object,
- no-name-in-module,
- unbalanced-tuple-unpacking,
- unpacking-non-sequence,
- bad-except-order,
- raising-bad-type,
- bad-exception-context,
- misplaced-bare-raise,
- raising-non-exception,
- notimplemented-raised,
- catching-non-exception,
- bad-super-call,
- no-member,
- not-callable,
- assignment-from-no-return,
- no-value-for-parameter,
- too-many-function-args,
- unexpected-keyword-arg,
- redundant-keyword-arg,
- missing-kwoa,
- invalid-sequence-index,
- invalid-slice-index,
- assignment-from-none,
- not-context-manager,
- invalid-unary-operand-type,
- unsupported-binary-operation,
- repeated-keyword,
- not-an-iterable,
- not-a-mapping,
- unsupported-membership-test,
- unsubscriptable-object,
- unsupported-assignment-operation,
- unsupported-delete-operation,
- invalid-metaclass,
- unhashable-dict-key,
- logging-unsupported-format,
- logging-format-truncated,
- logging-too-many-args,
- logging-too-few-args,
- bad-format-character,
- truncated-format-string,
- mixed-format-string,
- format-needs-mapping,
- missing-format-string-key,
- too-many-format-args,
- too-few-format-args,
- bad-str-strip-call,
- invalid-envvar-value,
- print-statement,
- parameter-unpacking,
- unpacking-in-except,
- old-raise-syntax,
- backtick,
- import-star-module-level,
- yield-inside-async-function,
- not-async-context-manager,
- fatal,
- astroid-error,
- parse-error,
- method-check-failed,
- unreachable,
- duplicate-key,
- unnecessary-semicolon,
- global-variable-not-assigned,
- unused-import,
- unused-variable,
- binary-op-exception,
- bad-format-string,
- anomalous-backslash-in-string,
- bad-open-mode
-
-
-[TYPECHECK]
-
-# List of class names for which member attributes should not be checked (useful
-# for classes with dynamically set attributes). This supports the use of
-# qualified names.
-ignored-classes=optparse.Values,thread._local,_thread._local,SearchResponse
diff --git a/Dockerfile b/Dockerfile
index 57671c25980ffb9f8af26aa904ce050537186319..72193689ade871a20ae837fc7b2810b116a664d6 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -95,8 +95,7 @@ COPY examples ./examples
COPY nomad ./nomad
COPY scripts ./scripts
COPY tests ./tests
-COPY .pylintrc \
- .coveragerc \
+COPY .coveragerc \
AUTHORS \
LICENSE \
MANIFEST.in \
diff --git a/mkdocs.yml b/mkdocs.yml
index 56b2fa02ef5d3c5323f6a2d6bb95ec60434553f5..09ad791204f21c7b2ca395267f4ef856f324090e 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -101,12 +101,8 @@ markdown_extensions:
- pymdownx.arithmatex:
generic: true
- pymdownx.emoji: # TODO make sure this isn't used!!
- # below 2 lines works for mkdocs-material<=9.3, but they produce a deprecated warning
- emoji_index: !!python/name:materialx.emoji.twemoji
- emoji_generator: !!python/name:materialx.emoji.to_svg
- # below 2 lines are supposed to work for mkdocs-material>=9.4
- # emoji_index: !!python/name:material.extensions.emoji.twemoji
- # emoji_generator: !!python/name:material.extensions.emoji.to_svg
+ emoji_index: !!python/name:material.extensions.emoji.twemoji
+ emoji_generator: !!python/name:material.extensions.emoji.to_svg
- pymdownx.superfences:
custom_fences:
- name: mermaid
diff --git a/nomad/app/static/__init__.py b/nomad/app/static/__init__.py
index 127a985928c45733aaed86ecfcefb1402cbe1756..c67cf9204faf89dff6803948e050728ff6bbd05d 100644
--- a/nomad/app/static/__init__.py
+++ b/nomad/app/static/__init__.py
@@ -102,9 +102,9 @@ async def add_header(request: Request, call_next):
if max_age is not None:
response.headers['Cache-Control'] = f'max-age={max_age}, must-revalidate'
else:
- response.headers[
- 'Cache-Control'
- ] = f'max-age=0, no-cache, no-store, must-revalidate'
+ response.headers['Cache-Control'] = (
+ f'max-age=0, no-cache, no-store, must-revalidate'
+ )
# The etags that we and starlette produce do not follow the RFC, because they do not
# start with a " as the RFC specifies. Nginx considers them weak etags and will strip
diff --git a/nomad/app/v1/routers/federation.py b/nomad/app/v1/routers/federation.py
index ea22b39c8ce9c27bd5debc47b74b3f2ba01b2bc9..cc35d792dd67d105cabf3748c72f3680ff483dc1 100644
--- a/nomad/app/v1/routers/federation.py
+++ b/nomad/app/v1/routers/federation.py
@@ -19,6 +19,7 @@
"""
API endpoint to receive telemetry data (in logstash format) from local installations.
"""
+
import gzip
import io
import socket
diff --git a/nomad/app/v1/routers/uploads.py b/nomad/app/v1/routers/uploads.py
index f72c4b734abb4013152350034455af9b6b45bb7c..dae2381bf3579c46a76389e41d1e7c05020068f1 100644
--- a/nomad/app/v1/routers/uploads.py
+++ b/nomad/app/v1/routers/uploads.py
@@ -49,6 +49,7 @@ from nomad.files import (
)
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,
@@ -2641,7 +2642,7 @@ def get_role_query(roles: List[UploadRole], user: User) -> Q:
if not roles:
roles = list(UploadRole)
- group_ids = user.get_group_ids()
+ group_ids = get_group_ids(user.user_id)
role_query = Q()
if UploadRole.main_author in roles:
@@ -2667,7 +2668,7 @@ def is_user_upload_viewer(upload: Upload, user: Optional[User]):
if user.user_id in upload.viewers:
return True
- group_ids = user.get_group_ids()
+ group_ids = get_group_ids(user.user_id)
if not set(group_ids).isdisjoint(upload.viewer_groups):
return True
@@ -2681,7 +2682,7 @@ def is_user_upload_writer(upload: Upload, user: User):
if user.user_id in upload.writers:
return True
- group_ids = user.get_group_ids()
+ group_ids = get_group_ids(user.user_id)
if not set(group_ids).isdisjoint(upload.writer_groups):
return True
diff --git a/nomad/cli/client/datatests.py b/nomad/cli/client/datatests.py
index 1180cb630686cc4d2c95306f73e1eb35a5ce757b..22fca47ad50a308181fe049de2105a20ce95b2dc 100644
--- a/nomad/cli/client/datatests.py
+++ b/nomad/cli/client/datatests.py
@@ -20,6 +20,7 @@
A command that runs a series of data compatibility tests against this version
and another nomad@FAIRDI installation.
"""
+
from nomad.client import api
from nomad.datamodel.datamodel import EntryArchive
from nomad.metainfo import MEnum
diff --git a/nomad/client/archive.py b/nomad/client/archive.py
index decae7b85caa24346c74f6b1a1604d86c46ef1ca..5e2e46da7ea640fe36247260d8949033a455b2d9 100644
--- a/nomad/client/archive.py
+++ b/nomad/client/archive.py
@@ -400,7 +400,7 @@ class ArchiveQuery:
while chunk := list(islice(iterator, chunk_size)):
yield chunk
- with progressbar(
+ with progressbar( # type: ignore
length=actual_number, label=f'Downloading {actual_number} entries...'
) as bar:
async with AsyncClient(timeout=Timeout(timeout=300)) as session:
diff --git a/nomad/config/models/config.py b/nomad/config/models/config.py
index d7125d45eb45ac25310b3f32cd0fd7147cc19077..c18e74f09fa20e3abec246e18e58e7eae4573eb8 100644
--- a/nomad/config/models/config.py
+++ b/nomad/config/models/config.py
@@ -19,15 +19,16 @@
import warnings
import os
import logging
+from importlib.metadata import version
+
import yaml
from typing import List, Union, Optional, Dict, Any
from pydantic import Field, root_validator, validator, parse_obj_as
-from pkg_resources import get_distribution, DistributionNotFound
import pkgutil
try:
- __version__ = get_distribution('nomad-lab').version
-except DistributionNotFound:
+ __version__ = version('nomad-lab')
+except Exception: # noqa
# package is not installed
pass
diff --git a/nomad/datamodel/data.py b/nomad/datamodel/data.py
index c16c80466104f642e335d7f7f68adbc727a488ab..73595a44ed730023f0e4d86e009777ee32267c9a 100644
--- a/nomad/datamodel/data.py
+++ b/nomad/datamodel/data.py
@@ -19,7 +19,7 @@
import os.path
from typing import Any
-from cachetools import cached, TTLCache
+from cachetools import TTLCache, cached
from nomad.metainfo.metainfo import (
predefined_datatypes,
Category,
@@ -175,7 +175,7 @@ class User(Author):
is_oasis_admin = Quantity(type=bool, default=False)
@staticmethod
- @cached(cache=TTLCache(maxsize=2048, ttl=24 * 3600))
+ @cached(TTLCache(maxsize=2048, ttl=24 * 3600))
def get(*args, **kwargs) -> 'User':
from nomad import infrastructure
@@ -188,12 +188,6 @@ class User(Author):
assert self.user_id is not None
return infrastructure.user_management.get_user(user_id=self.user_id) # type: ignore
- @cached(cache=TTLCache(maxsize=2048, ttl=60))
- def get_group_ids(self):
- from nomad.groups import UserGroup
-
- return UserGroup.get_ids_by_user_id(self.user_id)
-
class UserReference(Reference):
"""
diff --git a/nomad/datamodel/datamodel.py b/nomad/datamodel/datamodel.py
index c04f126815390168304b2927320e518366f0e779..5e21d28a5f3ec5a84660bc9b2cc8b9ed7b98c2df 100644
--- a/nomad/datamodel/datamodel.py
+++ b/nomad/datamodel/datamodel.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
-""" All generic entry metadata and related classes. """
+"""All generic entry metadata and related classes."""
from typing import List, Any
from enum import Enum
diff --git a/nomad/datamodel/results.py b/nomad/datamodel/results.py
index 820f4f6bce00c299dd26afe831c302d45ca040b5..4bf6cf82a89ca18b2945d111642a75072f5c84e3 100644
--- a/nomad/datamodel/results.py
+++ b/nomad/datamodel/results.py
@@ -2770,13 +2770,13 @@ class GeometryOptimization(MSection):
)
type = simulationworkflowschema.GeometryOptimization.name.m_copy()
convergence_tolerance_energy_difference = simulationworkflowschema.GeometryOptimizationMethod.convergence_tolerance_energy_difference.m_copy()
- convergence_tolerance_energy_difference.m_annotations[
- 'elasticsearch'
- ] = Elasticsearch(material_entry_type)
+ convergence_tolerance_energy_difference.m_annotations['elasticsearch'] = (
+ Elasticsearch(material_entry_type)
+ )
convergence_tolerance_force_maximum = simulationworkflowschema.GeometryOptimizationMethod.convergence_tolerance_force_maximum.m_copy()
- convergence_tolerance_force_maximum.m_annotations[
- 'elasticsearch'
- ] = Elasticsearch(material_entry_type)
+ convergence_tolerance_force_maximum.m_annotations['elasticsearch'] = (
+ Elasticsearch(material_entry_type)
+ )
final_force_maximum = simulationworkflowschema.GeometryOptimizationResults.final_force_maximum.m_copy()
final_force_maximum.m_annotations['elasticsearch'] = Elasticsearch(
material_entry_type
diff --git a/nomad/doi.py b/nomad/doi.py
index b2da6fe77293ee04b713435fa74bb38bb8717d54..67ba54067a602e9d88ebc9c182f7473f0d5fb255 100644
--- a/nomad/doi.py
+++ b/nomad/doi.py
@@ -20,6 +20,7 @@
This module contains all functions necessary to manage DOI via datacite.org and its
MDS API (https://support.datacite.org/docs/mds-api-guide).
"""
+
import xml.etree.ElementTree as ET
import datetime
import requests
@@ -155,9 +156,9 @@ class DOI(Document):
title = 'NOMAD Repository Dataset'
mds_resource = ET.Element('resource')
- mds_resource.attrib[
- 'xsi:schemaLocation'
- ] = 'http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3.1/metadata.xsd'
+ mds_resource.attrib['xsi:schemaLocation'] = (
+ 'http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3.1/metadata.xsd'
+ )
mds_resource.attrib['xmlns'] = 'http://datacite.org/schema/kernel-3'
mds_resource.attrib['xmlns:xsi'] = 'http://www.w3.org/2001/XMLSchema-instance'
diff --git a/nomad/files.py b/nomad/files.py
index d18a420479a1912e6845218675136665d758fa98..c229c2a7fac47bf80d7ab77fd74baa557aa25983 100644
--- a/nomad/files.py
+++ b/nomad/files.py
@@ -1464,9 +1464,9 @@ class PublicUploadFiles(UploadFiles):
)
if found:
if files_found:
- self._access = (
- self._raw_zip_file_object
- ) = self._archive_msg_file_object = None
+ self._access = self._raw_zip_file_object = (
+ self._archive_msg_file_object
+ ) = None
raise KeyError(
'Inconsistency: both public and restricted files found'
)
diff --git a/nomad/groups.py b/nomad/groups.py
index 25915a83565e11b949f6a468ae79109b97eff4c5..66ef9c08ce24a12c57180e1beda45ba02d118713 100644
--- a/nomad/groups.py
+++ b/nomad/groups.py
@@ -16,6 +16,7 @@
# limitations under the License.
#
from typing import Iterable, List, Optional
+
from mongoengine import Document, StringField, ListField
from mongoengine.queryset.visitor import Q
@@ -96,3 +97,7 @@ def user_group_exists(group_id: str, *, include_all=True) -> bool:
if include_all and group_id == 'all':
return True
return get_user_group(group_id) is not None
+
+
+def get_group_ids(user_id):
+ return UserGroup.get_ids_by_user_id(user_id)
diff --git a/nomad/metainfo/__init__.py b/nomad/metainfo/__init__.py
index 191b110883d736aed57e2610f2526bddae137000..be07523c0c4e3207e3085d9f4210291978d68199 100644
--- a/nomad/metainfo/__init__.py
+++ b/nomad/metainfo/__init__.py
@@ -29,7 +29,6 @@ manipulate, and access data. We also use it to map data to various storage forma
including JSON, (HDF5), mongodb, and elastic search.
"""
-
from .metainfo import (
MTypes,
MSectionBound,
diff --git a/nomad/metainfo/example.py b/nomad/metainfo/example.py
index ada47d210fd8860bf056db2cf8f0ca495bb96353..3f18e1b52ca0446bf8408a4d96fe65a9f58bff5b 100644
--- a/nomad/metainfo/example.py
+++ b/nomad/metainfo/example.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
-""" An example metainfo package. """
+"""An example metainfo package."""
import numpy as np
from datetime import datetime
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index fb1ca83ce924174bb9752a5d8e786110eeaa13d2..0b7bd3ee08e4b8fb5bfd07678b95491392939388 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -3603,9 +3603,9 @@ class Definition(MSection):
'../uploads/{upload_id}/archive/{entry_id}#{fragment}'
"""
kwargs['strict'] = True
- kwargs[
- 'global_reference'
- ] = True # we always want to use global reference if possible
+ kwargs['global_reference'] = (
+ True # we always want to use global reference if possible
+ )
return self.definition_reference(None, **kwargs)
diff --git a/nomad/metainfo/pylint_plugin.py b/nomad/metainfo/pylint_plugin.py
index 4d50ebd830b8d913f6551feb5ee7e202919f66ad..23c8f1b52a7592217169f3ce8eba6f9f8e48cc1d 100644
--- a/nomad/metainfo/pylint_plugin.py
+++ b/nomad/metainfo/pylint_plugin.py
@@ -16,8 +16,8 @@
# limitations under the License.
#
-""" The beginning of a pylint plugin. Unfotunately it is kinda nonsensical without a
-partnering mypy plugin. """
+"""The beginning of a pylint plugin. Unfotunately it is kinda nonsensical without a
+partnering mypy plugin."""
import astroid
from astroid import MANAGER
diff --git a/nomad/normalizing/normalizer.py b/nomad/normalizing/normalizer.py
index b95e398e34b432fca9e114d29a857780c2363352..145ec4db8e4ac00a7fecc0b64531bbd6f7d0caf5 100644
--- a/nomad/normalizing/normalizer.py
+++ b/nomad/normalizing/normalizer.py
@@ -148,9 +148,9 @@ class SystemBasedNormalizer(Normalizer, metaclass=ABCMeta):
if scc is not None:
self.section_run.m_cache['representative_scc_idx'] = scc.m_parent_index
if system is not None:
- self.section_run.m_cache[
- 'representative_system_idx'
- ] = system.m_parent_index
+ self.section_run.m_cache['representative_system_idx'] = (
+ system.m_parent_index
+ )
return system.m_resolved() if system is not None else None
diff --git a/nomad/normalizing/optimade.py b/nomad/normalizing/optimade.py
index 7426adea7afe28472982b4a0505e5582ae68e794..77db87723b3570041bc15c53121a6c15f0f9d218 100644
--- a/nomad/normalizing/optimade.py
+++ b/nomad/normalizing/optimade.py
@@ -83,7 +83,6 @@ def transform_to_v1(entry: EntryMetadata) -> EntryMetadata:
class OptimadeNormalizer(SystemBasedNormalizer):
-
"""
This normalizer performs all produces a section all data necessary for the Optimade API.
It assumes that the :class:`SystemNormalizer` was run before.
diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py
index 5f6f64a7ee5562a0fc2bf62c703dd0b21d30ce50..a301e1838e767b21f411e598a4a065fa23b0a651 100644
--- a/nomad/normalizing/results.py
+++ b/nomad/normalizing/results.py
@@ -679,9 +679,9 @@ class ResultsNormalizer(Normalizer):
methods = ['dft', 'tb']
self._resolve_workflow_gs_properties(methods, properties)
# Resolving DMFT Greens functions
- gfs_electronic: List[
- GreensFunctionsElectronic
- ] = self.electronic_properties.get('greens_functions') # type: ignore
+ gfs_electronic: List[GreensFunctionsElectronic] = (
+ self.electronic_properties.get('greens_functions') # type: ignore
+ )
gfs_electronic_dmft = self.resolve_greens_functions(
['workflow2', 'results', 'dmft_outputs', 'greens_functions']
)
@@ -697,9 +697,9 @@ class ResultsNormalizer(Normalizer):
methods = ['maxent']
self._resolve_workflow_gs_properties(methods, properties)
# Resolving DMFT Greens functions
- gfs_electronic: List[
- GreensFunctionsElectronic
- ] = self.electronic_properties.get('greens_functions') # type: ignore
+ gfs_electronic: List[GreensFunctionsElectronic] = (
+ self.electronic_properties.get('greens_functions') # type: ignore
+ )
for method in ['dmft', 'maxent']:
name = 'MaxEnt' if method == 'maxent' else method.upper()
gfs = self.resolve_greens_functions(
diff --git a/nomad/parsing/tabular.py b/nomad/parsing/tabular.py
index 4146d8b6fba2e193f45219239a55821a15dd452b..a9e8c7087243b8bd494a78745d1c8348c0dbb47b 100644
--- a/nomad/parsing/tabular.py
+++ b/nomad/parsing/tabular.py
@@ -19,12 +19,12 @@ import os
from typing import List, Dict, Callable, Set, Any, Tuple, Iterator, Union, Iterable
import pandas as pd
-from memoization import cached
import re
import math
import numpy as np
import json
import yaml
+from cachetools import cached, LRUCache
from nomad import utils
from nomad.parsing import MatchingParser
@@ -598,7 +598,7 @@ def _get_relative_path(section_def) -> Iterator[str]:
)
-@cached(max_size=10)
+@cached(LRUCache(maxsize=10))
def _create_column_to_quantity_mapping(section_def: Section):
mapping: Dict[str, Callable[[MSection, Any], MSection]] = {}
diff --git a/nomad/processing/data.py b/nomad/processing/data.py
index 0ca3017748a19062c5e929a2f1f028ae417d68a2..9316abe27aecf783d413928382c6b627dee5c058 100644
--- a/nomad/processing/data.py
+++ b/nomad/processing/data.py
@@ -27,6 +27,7 @@ entries, and files
.. autoclass:: Upload
"""
+
import base64
from typing import (
Optional,
@@ -86,7 +87,7 @@ from nomad.files import (
create_tmp_dir,
is_safe_relative_path,
)
-from nomad.groups import user_group_exists
+from nomad.groups import user_group_exists, get_group_ids
from nomad.processing.base import (
Proc,
process,
@@ -339,15 +340,15 @@ class MetadataEditRequestHandler:
self.verified_entries: Dict[
str, Dict[str, Any]
] = {} # Metadata specified for individual entries
- self.affected_uploads: List[
- 'Upload'
- ] = None # A MetadataEditRequest may involve multiple uploads
+ self.affected_uploads: List['Upload'] = (
+ None # A MetadataEditRequest may involve multiple uploads
+ )
# Used when edit_request = files
self.verified_file_metadata_cache: Dict[str, Dict[str, Any]] = {}
- self.root_file_entries: Dict[
- str, Dict[str, Any]
- ] = None # `entries` defined in the root metadata file
+ self.root_file_entries: Dict[str, Dict[str, Any]] = (
+ None # `entries` defined in the root metadata file
+ )
def validate_json_request(self):
"""Validates the provided edit_request_json."""
@@ -397,7 +398,7 @@ class MetadataEditRequestHandler:
return self._error('No matching upload found', 'upload_id')
is_admin = self.user.is_admin
- group_ids = self.user.get_group_ids()
+ group_ids = get_group_ids(self.user.user_id)
for upload in self.affected_uploads:
is_main_author = self.user.user_id == upload.main_author
is_coauthor = self.user.user_id in upload.coauthors or (
@@ -1489,9 +1490,9 @@ class Entry(Proc):
if self._child_entries:
child_archives = {}
for child_entry in self._child_entries:
- child_archives[
- child_entry.mainfile_key
- ] = child_entry._parser_results
+ child_archives[child_entry.mainfile_key] = (
+ child_entry._parser_results
+ )
kwargs = dict(child_archives=child_archives)
else:
kwargs = {}
diff --git a/ops/kubernetes/nomad/values.yaml b/ops/kubernetes/nomad/values.yaml
index 29cc9bdbce8a39098ee7909c373c4052ee1b1565..ef04f09902890b6dc6f26020856ca9867e285c4c 100644
--- a/ops/kubernetes/nomad/values.yaml
+++ b/ops/kubernetes/nomad/values.yaml
@@ -402,9 +402,12 @@ jupyterhub:
GenericOAuthenticator:
client_id: nomad_public
oauth_callback_url:
- authorize_url: https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/auth
- token_url: https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/token
- userdata_url: https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/userinfo
+ authorize_url:
+ https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/auth
+ token_url:
+ https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/token
+ userdata_url:
+ https://nomad-lab.eu/fairdi/keycloak/auth/realms/fairdi_nomad_test/protocol/openid-connect/userinfo
login_service: keycloak
username_key: preferred_username
userdata_params:
diff --git a/pyproject.toml b/pyproject.toml
index 83fe39a030fd38c05735a2a9940245c8d76187f0..32bc503df5aa7483a1d44f8f16ffaff8b41055da 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -14,44 +14,43 @@ license = { text = "Apache-2.0" }
requires-python = ">=3.9"
dependencies = [
- 'numpy~=1.22.4',
- 'nptyping~=1.4.4',
- 'pandas>=1.3.5,<2.0.0',
- 'cachetools>=4.2.4',
- 'docstring-parser>=0.12',
- 'pint==0.17',
- 'orjson==3.9.4',
- 'click>=7.1.2',
- 'requests>=2.27.1',
- 'pytz>=2022.7.1',
'aniso8601>=7.0.0',
'ase~=3.19.0',
- 'python-keycloak>=0.26.1',
+ 'bitarray>=2.3.5',
+ 'cachetools>=4.2.4',
+ 'click>=7.1.2',
+ 'docstring-parser>=0.12',
'elasticsearch-dsl==7.4.0',
- 'pydantic>=1.10.8,<2.0.0',
- 'jmespath>=0.10.0',
+ 'h5py>=3.6.0',
+ 'hjson>=3.0.2',
'httpx>=0.23.3',
- 'memoization>=0.4.0',
- 'rfc3161ng>=2.1.3',
+ 'jmespath>=0.10.0',
'lxml>=5.2',
- 'lxml_html_clean>=0.1.0',
- 'wrapt>=1.12.1',
- 'pyyaml>=6.0',
- 'python-magic==0.4.24',
- 'hjson>=3.0.2',
- 'scipy>=1.7.1',
+ 'lxml-html-clean>=0.1.0',
+ 'matid>=2.0.0.dev2',
+ 'mdanalysis==2.5.0',
+ 'networkx==2.6.3',
+ 'nptyping~=1.4.4',
+ 'numpy~=1.22.4',
+ 'openpyxl>=3.0.0',
+ 'orjson==3.9.4',
+ 'pandas>=1.3.5,<2.0.0',
'panedr>=0.2',
'parmed>=3.0.0',
- 'mdanalysis==2.5.0',
- 'h5py>=3.6.0',
- 'xarray>=0.20.2',
+ 'pint==0.17',
+ 'pydantic>=1.10.8,<2.0.0',
'pymatgen>=2023.5.10',
- 'bitarray>=2.3.5',
+ 'python-keycloak>=0.26.1',
+ 'python-magic==0.4.24',
+ 'pytz>=2022.7.1',
+ 'pyyaml>=6.0',
+ 'requests>=2.27.1',
+ 'rfc3161ng>=2.1.3',
'scikit-learn>=1.0.2',
+ 'scipy>=1.7.1',
'toposort',
- 'openpyxl>=3.0.0',
- 'networkx==2.6.3',
- 'matid>=2.0.0.dev2'
+ 'wrapt>=1.12.1',
+ 'xarray>=0.20.2',
]
[project.urls]
@@ -62,88 +61,82 @@ repository = 'https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR'
[project.optional-dependencies]
parsing = [
'asr==0.4.1',
- 'netCDF4==1.5.4',
'h5py==3.6.0',
- 'pyzeo==0.1.4',
- 'quippy-ase==0.9.14',
+ 'netCDF4==1.5.4',
'pybis@git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git',
'pynxtools[convert]==0.1.1',
+ 'pyzeo==0.1.4',
+ 'quippy-ase==0.9.14',
]
infrastructure = [
- 'h5grove[fastapi]==1.3.0',
- 'optimade[mongo]==0.22.1',
- 'structlog',
- 'elasticsearch==7.17.1',
- 'msgpack',
- 'celery[redis]==5.2.7',
'asgiref~=3.5',
- 'mongoengine>=0.20',
- 'pymongo==4.3.3',
- 'itsdangerous>=2.1.2',
- 'passlib==1.7.4',
- 'python-logstash==0.4.6',
- 'gitpython==3.1.24',
- 'm2r==0.2.1',
- 'zipstream-new==1.1.5',
'bagit==1.8.1',
+ 'basicauth==0.4.1',
'bcrypt==3.2.0',
- 'filelock==3.3.1',
- 'pyjwt[crypto]==2.6.0',
+ 'beautifulsoup4',
+ 'celery',
'cryptography',
- 'jsonschema[format]==4.17.3',
- 'runstats==2.0.0',
- 'tabulate==0.8.9',
- 'bs4==0.0.1',
+ 'dockerspawner==12.1.0',
+ 'elasticsearch==7.17.1',
+ 'fastapi<0.100', # later versions pending pydantic v2 upgrade
+ 'filelock==3.3.1',
+ 'gitpython==3.1.24',
+ 'gunicorn>=21.2.0,<22.0.0',
+ 'h5grove[fastapi]==1.3.0',
'html5lib==1.1',
- 'basicauth==0.4.1',
'inflection==0.5.1',
- 'unidecode==1.3.2',
+ 'itsdangerous>=2.1.2',
+ 'jsonschema[format]==4.17.3',
+ 'jupyterhub==4.0.2',
+ 'm2r==0.2.1',
+ 'mongoengine>=0.20',
+ 'msgpack',
+ 'oauthenticator==15.1.0',
+ 'optimade[mongo]==0.22.1',
+ 'passlib==1.7.4',
+ 'pyjwt[crypto]==2.6.0',
'python-json-logger==2.0.2',
- 'recommonmark==0.7.1',
+ 'python-logstash==0.4.6',
+ 'python-multipart',
'rdflib==5.0.0',
- 'fastapi==0.92.0',
+ 'recommonmark==0.7.1',
+ 'runstats==2.0.0',
+ 'structlog',
+ 'tabulate==0.8.9',
+ 'unidecode==1.3.2',
'uvicorn[standard]',
- 'python-multipart==0.0.5',
- 'jupyterhub==4.0.2',
- 'dockerspawner==12.1.0',
- 'oauthenticator==15.1.0',
'validators==0.18.2',
- 'gunicorn>=21.2.0,<22.0.0',
- 'importlib-metadata~=4.13.0' # Needed because of https://github.com/python/importlib_metadata/issues/411
+ 'zipstream-new==1.1.5',
]
dev = [
+ 'aiosmtpd',
+ 'astroid>=2.5.1',
'build',
- 'pip-tools>=6.13.0',
+ 'devtools',
+ 'essential-generators==1.0',
'markupsafe',
- 'gitpython==3.1.24',
- 'mypy>=1.0.1',
- 'typed-ast>=1.4.2',
- 'astroid>=2.5.1',
- 'pylint==2.13.9',
- 'pylint_plugin_utils==0.7',
- 'pylint_mongoengine==0.4.0',
+ 'mkdocs-click',
+ 'mkdocs-git-revision-date-localized-plugin',
+ 'mkdocs-glightbox',
+ 'mkdocs-macros-plugin',
+ 'mkdocs-material-extensions',
+ 'mkdocs-material',
+ 'mkdocs-redirects',
+ 'mkdocs',
+ 'mypy==1.0.1', # bug: incompatible with derived models of pydantic v1
+ 'names==0.3.0',
+ 'pip-tools>=6.13.0',
'pycodestyle==2.8.0',
- 'pytest>= 5.3.0, < 6.0.0',
- 'pytest-xdist>=1.30.0',
- 'pytest-timeout==1.4.2',
'pytest-cov==2.7.1',
+ 'pytest-timeout==1.4.2',
+ 'pytest-xdist>=1.30.0',
+ 'pytest>= 5.3.0, < 6.0.0',
+ 'python-gitlab==2.10.1',
'rope==0.21.0',
- 'names==0.3.0',
- 'essential_generators==1.0',
+ 'ruamel.yaml',
+ 'ruff',
'twine==3.4.2',
- 'python-gitlab==2.10.1',
- 'devtools==0.8.0',
- 'mkdocs==1.3.0',
- 'mkdocs-material==8.2.8',
- 'mkdocs-material-extensions==1.3.1',
- 'mkdocs-macros-plugin==0.6.3',
- 'mkdocs-glightbox==0.3.5',
- 'aiosmtpd',
- 'mkdocs-click==0.8.0',
- 'mkdocs-redirects==1.2.0',
- 'mkdocs-git-revision-date-localized-plugin==1.2.1',
- 'ruff==0.1.8',
- 'ruamel.yaml==0.17.21'
+ 'typed-ast>=1.4.2',
]
@@ -152,6 +145,13 @@ nomad = "nomad.cli:run_cli"
[tool.ruff]
include = ["nomad/*.py", "tests/*.py"]
+exclude = ["dependencies"]
+
+# Same as Black.
+line-length = 88
+indent-width = 4
+
+[tool.ruff.lint]
select = [
"E", # pycodestyle
"W", # pycodestyle
@@ -161,7 +161,7 @@ ignore = [
"E501", # Line too long ({width} > {limit} characters)
"E701", # Multiple statements on one line (colon)
"E731", # Do not assign a lambda expression, use a def
- "E402", # Module level import not at top of file
+ "E402", # Module level import not at top of file
"PLR0911", # Too many return statements
"PLR0912", # Too many branches
"PLR0913", # Too many arguments in function definition
@@ -173,11 +173,6 @@ ignore = [
"PLR5501", # else-if-used
]
fixable = ["ALL"]
-exclude = ["dependencies"]
-
-# Same as Black.
-line-length = 88
-indent-width = 4
[tool.ruff.format]
# use single quotes for strings.
diff --git a/requirements-dev.txt b/requirements-dev.txt
index c08efd6a51f02130a9ee9cb49a79740350e2a770..fc4eca75f03c69db425e31ba985efa3099b99fe2 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -2,356 +2,359 @@
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
-# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt --pip-args='--prefer-binary' --resolver=backtracking pyproject.toml requirements.txt
+# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt --pip-args='--prefer-binary' pyproject.toml requirements.txt
#
-aiosmtpd==1.4.4.post2 # via nomad-lab (pyproject.toml)
-alabaster==0.7.12 # via -r requirements.txt, sphinx
-alembic==1.9.1 # via -r requirements.txt, jupyterhub
-amqp==5.1.1 # via -r requirements.txt, kombu
-aniso8601==7.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-anyio==3.6.2 # via -r requirements.txt, httpcore, starlette, watchfiles
-arrow==1.2.3 # via -r requirements.txt, isoduration
+aiosmtpd==1.4.5 # via nomad-lab (pyproject.toml)
+alabaster==0.7.16 # via -r requirements.txt, sphinx
+alembic==1.13.1 # via -r requirements.txt, jupyterhub
+amqp==5.2.0 # via -r requirements.txt, kombu
+aniso8601==9.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+anyio==4.3.0 # via -r requirements.txt, httpx, starlette, watchfiles
+arrow==1.3.0 # via -r requirements.txt, isoduration
asciitree==0.3.3 # via -r requirements.txt, zarr
-ase==3.19.0 # via -r requirements.txt, asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase
-asgiref==3.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+ase==3.19.3 # via -r requirements.txt, asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase
+asgiref==3.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
asr==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-asteval==0.9.31 # via -r requirements.txt, lmfit
-astroid==2.11.7 # via nomad-lab (pyproject.toml), pylint
-asttokens==2.1.0 # via devtools
+asteval==0.9.32 # via -r requirements.txt, lmfit
+astroid==3.1.0 # via nomad-lab (pyproject.toml)
+asttokens==2.4.1 # via -r requirements.txt, devtools, stack-data
async-generator==1.10 # via -r requirements.txt, jupyterhub
-async-timeout==4.0.2 # via -r requirements.txt, redis
-atpublic==3.1.1 # via aiosmtpd
-attrs==22.2.0 # via -r requirements.txt, aiosmtpd, jsonschema, pytest
-babel==2.11.0 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, sphinx
-backcall==0.2.0 # via -r requirements.txt, ipython
+atpublic==4.1.0 # via aiosmtpd
+attrs==23.2.0 # via -r requirements.txt, aiosmtpd, jsonschema, pytest
+babel==2.14.0 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx
+backports-tarfile==1.0.0 # via jaraco-context
bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
bcrypt==3.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-beautifulsoup4==4.11.1 # via -r requirements.txt, bs4
-billiard==3.6.4.0 # via -r requirements.txt, celery
-biopython==1.80 # via -r requirements.txt, mdanalysis
-bitarray==2.3.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-bleach==5.0.1 # via readme-renderer
-bs4==0.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-build==0.9.0 # via nomad-lab (pyproject.toml), pip-tools
-cachetools==4.2.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-celery[redis]==5.2.7 # via celery, nomad-lab (pyproject.toml)
-certifi==2022.12.7 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests
+beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
+billiard==4.2.0 # via -r requirements.txt, celery
+biopython==1.83 # via -r requirements.txt, mdanalysis
+bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
+blinker==1.7.0 # via -r requirements.txt, flask
+blosc2==2.5.1 # via -r requirements.txt, tables
+build==1.2.1 # via nomad-lab (pyproject.toml), pip-tools
+cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
+celery==5.3.6 # via -r requirements.txt, nomad-lab (pyproject.toml)
+certifi==2024.2.2 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via -r requirements.txt, jupyterhub
-cffi==1.15.1 # via -r requirements.txt, bcrypt, cryptography
-cftime==1.6.2 # via -r requirements.txt, netcdf4
-charset-normalizer==2.0.12 # via -r requirements.txt, requests
-click==8.1.3 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pip-tools, pynxtools, uvicorn
-click-didyoumean==0.3.0 # via -r requirements.txt, celery
+cffi==1.16.0 # via -r requirements.txt, bcrypt, cryptography
+cftime==1.6.3 # via -r requirements.txt, netcdf4
+charset-normalizer==3.3.2 # via -r requirements.txt, requests
+click==8.1.7 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pip-tools, pynxtools, uvicorn
+click-didyoumean==0.3.1 # via -r requirements.txt, celery
click-plugins==1.1.1 # via -r requirements.txt, celery
-click-repl==0.2.0 # via -r requirements.txt, celery
-cloudpickle==2.2.0 # via -r requirements.txt, dask
-colorama==0.4.6 # via twine
-comm==0.1.4 # via -r requirements.txt, ipywidgets
+click-repl==0.3.0 # via -r requirements.txt, celery
+cloudpickle==3.0.0 # via -r requirements.txt, dask
+colorama==0.4.6 # via mkdocs-material, twine
+comm==0.2.2 # via -r requirements.txt, ipykernel
commonmark==0.9.1 # via -r requirements.txt, recommonmark
-coverage==6.5.0 # via pytest-cov
-cryptography==39.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng, secretstorage
-cycler==0.11.0 # via -r requirements.txt, matplotlib
-dask[array]==2022.2.0 # via -r requirements.txt, dask, hyperspy, kikuchipy, orix, pyxem
-debugpy==1.6.5 # via -r requirements.txt, ipykernel
+contourpy==1.2.1 # via -r requirements.txt, matplotlib
+coverage==7.4.4 # via pytest-cov
+cryptography==42.0.5 # via -r requirements.txt, jwcrypto, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng, secretstorage
+cycler==0.12.1 # via -r requirements.txt, matplotlib
+dask[array]==2024.4.1 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem
+debugpy==1.8.1 # via -r requirements.txt, ipykernel
decorator==5.1.1 # via -r requirements.txt, ipyparallel, ipython, validators
-devtools==0.8.0 # via nomad-lab (pyproject.toml)
+deprecation==2.1.0 # via -r requirements.txt, python-keycloak
+devtools==0.12.2 # via nomad-lab (pyproject.toml)
diffpy-structure==3.1.0 # via -r requirements.txt, diffsims, kikuchipy, orix
diffsims==0.5.2 # via -r requirements.txt, kikuchipy, pyxem
-dill==0.3.6 # via -r requirements.txt, hyperspy, pylint
-dnspython==2.2.1 # via -r requirements.txt, email-validator, pymongo
-docker==6.0.1 # via -r requirements.txt, dockerspawner
+dill==0.3.8 # via -r requirements.txt, hyperspy, lmfit
+dnspython==2.6.1 # via -r requirements.txt, email-validator, pymongo
+docker==7.0.0 # via -r requirements.txt, dockerspawner
dockerspawner==12.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-docstring-parser==0.12 # via -r requirements.txt, nomad-lab (pyproject.toml)
-docutils==0.19 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx
-ecdsa==0.18.0 # via -r requirements.txt, python-jose
+docstring-parser==0.16 # via -r requirements.txt, nomad-lab (pyproject.toml)
+docutils==0.20.1 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx
elasticsearch==7.17.1 # via -r requirements.txt, elasticsearch-dsl, nomad-lab (pyproject.toml)
elasticsearch-dsl==7.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-email-validator==1.3.0 # via -r requirements.txt, optimade
-entrypoints==0.4 # via -r requirements.txt, ipyparallel, jupyter-client, numcodecs
+email-validator==1.3.1 # via -r requirements.txt, optimade
+entrypoints==0.4 # via -r requirements.txt, ipyparallel
escapism==1.0.1 # via -r requirements.txt, dockerspawner
essential-generators==1.0 # via nomad-lab (pyproject.toml)
et-xmlfile==1.1.0 # via -r requirements.txt, openpyxl
-execnet==1.9.0 # via pytest-xdist
-executing==0.10.0 # via devtools
+exceptiongroup==1.2.0 # via -r requirements.txt, anyio, ipython
+execnet==2.1.1 # via pytest-xdist
+executing==2.0.1 # via -r requirements.txt, devtools, stack-data
f90wrap==0.2.13 # via -r requirements.txt, quippy-ase
-fabio==2023.6.0 # via -r requirements.txt, pyfai, silx
-fastapi==0.92.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
-fasteners==0.18 # via -r requirements.txt, mdanalysis, zarr
+fabio==2023.10.0 # via -r requirements.txt, pyfai, silx
+fastapi==0.99.1 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
+fasteners==0.19 # via -r requirements.txt, mdanalysis, zarr
filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
findiff==0.10.0 # via -r requirements.txt, pynxtools-stm
-flask==2.2.2 # via -r requirements.txt, asr
+flask==3.0.3 # via -r requirements.txt, asr
flatdict==4.0.1 # via -r requirements.txt, pynxtools
-fonttools==4.38.0 # via -r requirements.txt, matplotlib
+fonttools==4.51.0 # via -r requirements.txt, matplotlib
fqdn==1.5.1 # via -r requirements.txt, jsonschema
-fsspec==2022.11.0 # via -r requirements.txt, dask, hyperspy
-future==0.18.2 # via -r requirements.txt, uncertainties
+fsspec==2024.3.1 # via -r requirements.txt, dask, hyperspy
+future==1.0.0 # via -r requirements.txt, uncertainties
ghp-import==2.1.0 # via mkdocs
-gitdb==4.0.10 # via -r requirements.txt, gitpython
+gitdb==4.0.11 # via -r requirements.txt, gitpython
gitpython==3.1.24 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nomad-lab (pyproject.toml), pynxtools
-greenlet==2.0.1 # via -r requirements.txt, sqlalchemy
-griddataformats==0.7.0 # via -r requirements.txt, mdanalysis
-gsd==2.7.0 # via -r requirements.txt, mdanalysis
+greenlet==3.0.3 # via -r requirements.txt, sqlalchemy
+griddataformats==1.0.2 # via -r requirements.txt, mdanalysis
+gsd==3.2.1 # via -r requirements.txt, mdanalysis
gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
h11==0.14.0 # via -r requirements.txt, httpcore, uvicorn
-h5grove[fastapi]==1.3.0 # via h5grove, nomad-lab (pyproject.toml)
-h5py==3.6.0 # via -r requirements.txt, h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, silx
-hjson==3.0.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
+h5grove[fastapi]==1.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+h5py==3.6.0 # via -r requirements.txt, fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx
+hdf5plugin==4.4.0 # via -r requirements.txt, fabio
+hjson==3.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
html5lib==1.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-httpcore==0.16.3 # via -r requirements.txt, httpx
-httptools==0.5.0 # via -r requirements.txt, uvicorn
-httpx==0.23.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
-hyperspy==1.7.5 # via -r requirements.txt, kikuchipy, pynxtools, pyxem
-idna==3.4 # via -r requirements.txt, anyio, email-validator, jsonschema, requests, rfc3986
-ifes-apt-tc-data-modeling==0.0.9 # via -r requirements.txt, pynxtools
-imageio==2.24.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
+httpcore==1.0.5 # via -r requirements.txt, httpx
+httptools==0.6.1 # via -r requirements.txt, uvicorn
+httpx==0.27.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+hyperspy==1.7.6 # via -r requirements.txt, kikuchipy, pynxtools, pyxem
+idna==3.6 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests
+ifes-apt-tc-data-modeling==0.1 # via -r requirements.txt, pynxtools
+imageio==2.27.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via -r requirements.txt, sphinx
-importlib-metadata==4.13.0 # via -r requirements.txt, flask, hyperspy, jupyterhub, keyring, markdown, mkdocs, nomad-lab (pyproject.toml), pynxtools, sphinx, twine
+importlib-metadata==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyterhub, keyring, markdown, mkdocs, pynxtools, sphinx, twine
+importlib-resources==6.4.0 # via -r requirements.txt, matplotlib
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-ipykernel==6.16.2 # via -r requirements.txt, ipyparallel
-ipyparallel==8.4.1 # via -r requirements.txt, hyperspy
-ipython==7.34.0 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, ipywidgets, pynxtools-stm
-ipywidgets==8.1.1 # via -r requirements.txt, pyxem
+ipykernel==6.29.4 # via -r requirements.txt, ipyparallel
+ipyparallel==8.8.0 # via -r requirements.txt, hyperspy
+ipython==8.18.1 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, pynxtools-stm
isodate==0.6.1 # via -r requirements.txt, rdflib
isoduration==20.11.0 # via -r requirements.txt, jsonschema
-isort==4.3.21 # via pylint
itsdangerous==2.1.2 # via -r requirements.txt, flask, nomad-lab (pyproject.toml)
-jaraco-classes==3.2.3 # via keyring
-jedi==0.18.2 # via -r requirements.txt, ipython
+jaraco-classes==3.4.0 # via keyring
+jaraco-context==5.3.0 # via keyring
+jaraco-functools==4.0.0 # via keyring
+jedi==0.19.1 # via -r requirements.txt, ipython
jeepney==0.8.0 # via keyring, secretstorage
-jinja2==3.0.3 # via -r requirements.txt, flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx
-jmespath==0.10.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-joblib==1.1.0 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn
-jsonpointer==2.3 # via -r requirements.txt, jsonschema
-jsonschema[format]==4.17.3 # via jsonschema, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator
-jupyter-client==7.4.8 # via -r requirements.txt, ipykernel, ipyparallel
-jupyter-core==4.12.0 # via -r requirements.txt, jupyter-client
+jinja2==3.1.3 # via -r requirements.txt, flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx
+jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+joblib==1.4.0 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn
+jsonpointer==2.4 # via -r requirements.txt, jsonschema
+jsonschema[format]==4.17.3 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator
+jupyter-client==8.6.1 # via -r requirements.txt, ipykernel, ipyparallel
+jupyter-core==5.7.2 # via -r requirements.txt, ipykernel, jupyter-client
jupyter-telemetry==0.1.0 # via -r requirements.txt, jupyterhub
jupyterhub==4.0.2 # via -r requirements.txt, dockerspawner, nomad-lab (pyproject.toml), oauthenticator
-jupyterlab-widgets==3.0.9 # via -r requirements.txt, ipywidgets
-keyring==23.11.0 # via twine
-kikuchipy==0.8.7 # via -r requirements.txt, pynxtools
-kiwisolver==1.4.4 # via -r requirements.txt, matplotlib
-kombu==5.2.4 # via -r requirements.txt, celery
-lark==1.1.5 # via -r requirements.txt, optimade
-latexcodec==2.0.1 # via -r requirements.txt, pybtex
-lazy-object-proxy==1.9.0 # via astroid
-llvmlite==0.39.1 # via -r requirements.txt, numba
-lmfit==1.2.2 # via -r requirements.txt, pyxem
+jwcrypto==1.5.6 # via -r requirements.txt, python-keycloak
+keyring==25.1.0 # via twine
+kikuchipy==0.9.0 # via -r requirements.txt, pynxtools
+kiwisolver==1.4.5 # via -r requirements.txt, matplotlib
+kombu==5.3.6 # via -r requirements.txt, celery
+lark==1.1.9 # via -r requirements.txt, optimade
+latexcodec==3.0.0 # via -r requirements.txt, pybtex
+llvmlite==0.42.0 # via -r requirements.txt, numba
+lmfit==1.3.0 # via -r requirements.txt, pyxem
locket==1.0.0 # via -r requirements.txt, partd
-lxml==5.2.0 # via -r requirements.txt, lxml-html-clean, nomad-lab (pyproject.toml)
-lxml-html-clean==0.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+lxml==5.2.1 # via -r requirements.txt, fabio, lxml-html-clean, nomad-lab (pyproject.toml)
+lxml-html-clean==0.1.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-mako==1.2.4 # via -r requirements.txt, alembic
-markdown==3.4.1 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
-markupsafe==2.1.1 # via -r requirements.txt, jinja2, mako, nomad-lab (pyproject.toml), werkzeug
+mako==1.3.2 # via -r requirements.txt, alembic
+markdown==3.6 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
+markupsafe==2.1.5 # via -r requirements.txt, jinja2, mako, mkdocs, nomad-lab (pyproject.toml), werkzeug
matid==2.0.0.dev2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-matplotlib==3.5.3 # via -r requirements.txt, ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
+matplotlib==3.8.4 # via -r requirements.txt, ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
matplotlib-inline==0.1.6 # via -r requirements.txt, ipykernel, ipython
matplotlib-scalebar==0.8.1 # via -r requirements.txt, orix
-mccabe==0.6.1 # via pylint
+mda-xdrlib==0.2.0 # via -r requirements.txt, pyedr
mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-memoization==0.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mergedeep==1.3.4 # via -r requirements.txt, mkdocs, pynxtools
-mistune==2.0.4 # via -r requirements.txt, m2r
-mkdocs==1.3.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml)
-mkdocs-click==0.8.0 # via nomad-lab (pyproject.toml)
-mkdocs-git-revision-date-localized-plugin==1.2.1 # via nomad-lab (pyproject.toml)
-mkdocs-glightbox==0.3.5 # via nomad-lab (pyproject.toml)
-mkdocs-macros-plugin==0.6.3 # via nomad-lab (pyproject.toml)
-mkdocs-material==8.2.8 # via nomad-lab (pyproject.toml)
+mistune==3.0.2 # via -r requirements.txt, m2r
+mkdocs==1.5.3 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml)
+mkdocs-click==0.8.1 # via nomad-lab (pyproject.toml)
+mkdocs-git-revision-date-localized-plugin==1.2.4 # via nomad-lab (pyproject.toml)
+mkdocs-glightbox==0.3.7 # via nomad-lab (pyproject.toml)
+mkdocs-macros-plugin==1.0.5 # via nomad-lab (pyproject.toml)
+mkdocs-material==9.5.17 # via nomad-lab (pyproject.toml)
mkdocs-material-extensions==1.3.1 # via mkdocs-material, nomad-lab (pyproject.toml)
-mkdocs-redirects==1.2.0 # via nomad-lab (pyproject.toml)
+mkdocs-redirects==1.2.1 # via nomad-lab (pyproject.toml)
mmtf-python==1.1.3 # via -r requirements.txt, mdanalysis
-mongoengine==0.25.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+mongoengine==0.28.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
mongomock==4.1.2 # via -r requirements.txt, optimade
-monty==2022.9.9 # via -r requirements.txt, pymatgen
-more-itertools==9.0.0 # via jaraco-classes, pytest
-mpmath==1.2.1 # via -r requirements.txt, sympy
-mrcfile==1.4.3 # via -r requirements.txt, griddataformats
-msgpack==1.0.4 # via -r requirements.txt, mmtf-python, nomad-lab (pyproject.toml)
+monty==2024.3.31 # via -r requirements.txt, pymatgen
+more-itertools==10.2.0 # via jaraco-classes, jaraco-functools, pytest
+mpmath==1.3.0 # via -r requirements.txt, sympy
+mrcfile==1.5.0 # via -r requirements.txt, griddataformats
+msgpack==1.0.8 # via -r requirements.txt, blosc2, mmtf-python, nomad-lab (pyproject.toml)
mypy==1.0.1 # via nomad-lab (pyproject.toml)
-mypy-extensions==0.4.3 # via mypy
+mypy-extensions==1.0.0 # via mypy
names==0.3.0 # via nomad-lab (pyproject.toml)
-natsort==8.2.0 # via -r requirements.txt, hyperspy
-nest-asyncio==1.5.6 # via -r requirements.txt, ipykernel, jupyter-client
+natsort==8.4.0 # via -r requirements.txt, hyperspy
+ndindex==1.8 # via -r requirements.txt, blosc2
+nest-asyncio==1.6.0 # via -r requirements.txt, ipykernel
netcdf4==1.5.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
networkx==2.6.3 # via -r requirements.txt, matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image
+nh3==0.2.17 # via readme-renderer
niondata==0.15.5 # via -r requirements.txt, nionswift, nionswift-io
nionswift==0.16.8 # via -r requirements.txt, pynxtools
nionswift-io==0.15.1 # via -r requirements.txt, nionswift
nionui==0.6.11 # via -r requirements.txt, nionswift
-nionutils==0.4.8 # via -r requirements.txt, niondata, nionswift, nionswift-io, nionui
+nionutils==0.4.10 # via -r requirements.txt, niondata, nionswift, nionswift-io, nionui
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-numba==0.56.4 # via -r requirements.txt, diffsims, hyperspy, kikuchipy, orix, pyxem, sparse
-numcodecs==0.10.2 # via -r requirements.txt, zarr
-numexpr==2.8.4 # via -r requirements.txt, hyperspy, pyfai
-numpy==1.22.4 # via -r requirements.txt, ase, biopython, cftime, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tifffile, xarray, zarr
-numpy-quaternion==2022.4.3 # via -r requirements.txt, orix
+numba==0.59.1 # via -r requirements.txt, diffsims, hyperspy, kikuchipy, orix, pyxem, sparse
+numcodecs==0.12.1 # via -r requirements.txt, zarr
+numexpr==2.10.0 # via -r requirements.txt, hyperspy, pyfai, pyxem, tables
+numpy==1.22.4 # via -r requirements.txt, ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, zarr
+numpy-quaternion==2023.0.3 # via -r requirements.txt, orix
oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via -r requirements.txt, jupyterhub
openpyxl==3.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml), optimade
+optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
orix==0.11.1 # via -r requirements.txt, diffsims, kikuchipy, pyxem
orjson==3.9.4 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
-packaging==23.0 # via -r requirements.txt, build, dask, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, pooch, pytest, scikit-image, sphinx
-palettable==3.3.0 # via -r requirements.txt, pymatgen
-pamela==1.0.0 # via -r requirements.txt, jupyterhub
-pandas==1.3.5 # via -r requirements.txt, ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, xarray
-panedr==0.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-parmed==3.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-parso==0.8.3 # via -r requirements.txt, jedi
-partd==1.3.0 # via -r requirements.txt, dask
+packaging==24.0 # via -r requirements.txt, build, dask, deprecation, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pooch, pytest, scikit-image, silx, sphinx, tables, xarray
+paginate==0.5.6 # via mkdocs-material
+palettable==3.3.3 # via -r requirements.txt, pymatgen
+pamela==1.1.0 # via -r requirements.txt, jupyterhub
+pandas==1.5.3 # via -r requirements.txt, ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, xarray
+panedr==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+parmed==4.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
+parso==0.8.4 # via -r requirements.txt, jedi
+partd==1.4.1 # via -r requirements.txt, dask
passlib==1.7.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pep517==0.13.0 # via build
-pexpect==4.8.0 # via -r requirements.txt, ipython
-phonopy==2.11.0 # via -r requirements.txt, asr
-pickleshare==0.7.5 # via -r requirements.txt, ipython
-pillow==9.4.0 # via -r requirements.txt, imageio, matplotlib, nionswift, scikit-image
+pathspec==0.12.1 # via mkdocs
+pexpect==4.9.0 # via -r requirements.txt, ipython
+phonopy==2.9.1 # via -r requirements.txt, asr
+pillow==10.0.1 # via -r requirements.txt, fabio, hyperspy, imageio, matplotlib, nionswift, scikit-image
pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab (pyproject.toml)
-pip-tools==6.13.0 # via nomad-lab (pyproject.toml)
-pkginfo==1.8.3 # via twine
-platformdirs==3.1.1 # via -r requirements.txt, pooch, pylint
-plotly==5.11.0 # via -r requirements.txt, asr, pymatgen
+pip-tools==7.4.1 # via nomad-lab (pyproject.toml)
+pkginfo==1.10.0 # via twine
+platformdirs==4.2.0 # via -r requirements.txt, jupyter-core, mkdocs, pooch
+plotly==5.20.0 # via -r requirements.txt, asr, pymatgen
pluggy==0.13.1 # via pytest
-pooch==1.7.0 # via -r requirements.txt, kikuchipy, orix
-prettytable==3.6.0 # via -r requirements.txt, hyperspy
-prometheus-client==0.15.0 # via -r requirements.txt, jupyterhub
-prompt-toolkit==3.0.36 # via -r requirements.txt, click-repl, ipython
-psutil==5.9.4 # via -r requirements.txt, diffsims, ipykernel, ipyparallel, pyxem
+pooch==1.8.1 # via -r requirements.txt, kikuchipy, orix
+prettytable==3.10.0 # via -r requirements.txt, hyperspy
+prometheus-client==0.20.0 # via -r requirements.txt, jupyterhub
+prompt-toolkit==3.0.43 # via -r requirements.txt, click-repl, ipython
+psutil==5.9.8 # via -r requirements.txt, diffsims, ipykernel, ipyparallel, pyxem
ptyprocess==0.7.0 # via -r requirements.txt, pexpect
+pure-eval==0.2.2 # via -r requirements.txt, stack-data
py==1.11.0 # via pytest, pytest-forked
-pyasn1==0.4.8 # via -r requirements.txt, pyasn1-modules, python-jose, rfc3161ng, rsa
-pyasn1-modules==0.2.8 # via -r requirements.txt, rfc3161ng
+py-cpuinfo==9.0.0 # via -r requirements.txt, blosc2, tables
+pyasn1==0.6.0 # via -r requirements.txt, pyasn1-modules, rfc3161ng
+pyasn1-modules==0.4.0 # via -r requirements.txt, rfc3161ng
pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git # via -r requirements.txt, nomad-lab (pyproject.toml)
pybtex==0.24.0 # via -r requirements.txt, pymatgen
pycifrw==4.4.5 # via -r requirements.txt, diffpy-structure
pycodestyle==2.8.0 # via nomad-lab (pyproject.toml)
-pycparser==2.21 # via -r requirements.txt, cffi
-pydantic==1.10.9 # via -r requirements.txt, fastapi, nomad-lab (pyproject.toml), optimade
-pyfai==2023.9.0 # via -r requirements.txt, pyxem
-pygments==2.14.0 # via -r requirements.txt, ipython, mkdocs-material, readme-renderer, sphinx
-pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml), pyjwt
-pylint==2.13.9 # via nomad-lab (pyproject.toml), pylint-mongoengine, pylint-plugin-utils
-pylint-mongoengine==0.4.0 # via nomad-lab (pyproject.toml)
-pylint-plugin-utils==0.7 # via nomad-lab (pyproject.toml), pylint-mongoengine
+pycparser==2.22 # via -r requirements.txt, cffi
+pydantic==1.10.15 # via -r requirements.txt, fastapi, nomad-lab (pyproject.toml), optimade
+pyedr==0.8.0 # via -r requirements.txt, panedr
+pyfai==2024.2.0 # via -r requirements.txt, pyxem
+pygments==2.17.2 # via -r requirements.txt, devtools, ipython, mkdocs-material, readme-renderer, sphinx
+pyjwt[crypto]==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
pymatgen==2023.9.25 # via -r requirements.txt, asr, nomad-lab (pyproject.toml)
-pymdown-extensions==9.7 # via mkdocs-material
-pymongo==4.3.3 # via -r requirements.txt, mongoengine, nomad-lab (pyproject.toml), optimade
-pynxtools[convert,mpes,stm,xps]==0.1.1 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-stm, pynxtools-xps
-pynxtools-mpes==0.0.1 # via -r requirements.txt, pynxtools
+pymdown-extensions==10.7.1 # via mkdocs-material
+pymongo==4.6.3 # via -r requirements.txt, mongoengine, optimade
+pynxtools[convert,mpes,stm,xps]==0.1.1 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools-mpes, pynxtools-stm, pynxtools-xps
+pynxtools-mpes==0.0.3 # via -r requirements.txt, pynxtools
pynxtools-stm==1.0.1 # via -r requirements.txt, pynxtools
pynxtools-xps==0.0.3 # via -r requirements.txt, pynxtools
-pyopenssl==23.0.0 # via -r requirements.txt, certipy
-pyparsing==3.0.9 # via -r requirements.txt, matplotlib, rdflib
-pyrsistent==0.19.3 # via -r requirements.txt, jsonschema
+pyopenssl==24.1.0 # via -r requirements.txt, certipy
+pyparsing==3.1.2 # via -r requirements.txt, matplotlib, rdflib
+pyproject-hooks==1.0.0 # via build, pip-tools
+pyrsistent==0.20.0 # via -r requirements.txt, jsonschema
pytest==5.4.3 # via nomad-lab (pyproject.toml), pytest-cov, pytest-forked, pytest-timeout, pytest-xdist
pytest-cov==2.7.1 # via nomad-lab (pyproject.toml)
pytest-forked==1.6.0 # via pytest-xdist
pytest-timeout==1.4.2 # via nomad-lab (pyproject.toml)
pytest-xdist==1.34.0 # via nomad-lab (pyproject.toml)
-python-dateutil==2.8.2 # via -r requirements.txt, arrow, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng
-python-dotenv==0.21.0 # via -r requirements.txt, uvicorn
+python-dateutil==2.9.0.post0 # via -r requirements.txt, arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng
+python-dotenv==1.0.1 # via -r requirements.txt, uvicorn
python-gitlab==2.10.1 # via nomad-lab (pyproject.toml)
-python-jose==3.3.0 # via -r requirements.txt, python-keycloak
python-json-logger==2.0.2 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml)
-python-keycloak==0.26.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+python-keycloak==3.11.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-logstash==0.4.6 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-magic==0.4.24 # via -r requirements.txt, nomad-lab (pyproject.toml)
-python-multipart==0.0.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pytz==2022.7.1 # via -r requirements.txt, babel, celery, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab (pyproject.toml), pandas, pynxtools
+python-multipart==0.0.9 # via -r requirements.txt, nomad-lab (pyproject.toml)
+pytz==2024.1 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab (pyproject.toml), pandas, pynxtools
pytz-deprecation-shim==0.1.0.post0 # via -r requirements.txt, tzlocal
-pywavelets==1.3.0 # via -r requirements.txt, scikit-image
-pyxem==0.15.1 # via -r requirements.txt, pynxtools
-pyyaml==6.0 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, pyyaml-env-tag, uvicorn
+pywavelets==1.6.0 # via -r requirements.txt, scikit-image
+pyxem==0.16.0 # via -r requirements.txt, pynxtools
+pyyaml==6.0.1 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, uvicorn
pyyaml-env-tag==0.1 # via mkdocs
pyzeo==0.1.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pyzmq==25.0.0 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client
+pyzmq==25.1.2 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client
quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml)
-radioactivedecay==0.4.17 # via -r requirements.txt, ifes-apt-tc-data-modeling
+radioactivedecay==0.4.22 # via -r requirements.txt, ifes-apt-tc-data-modeling
rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-readme-renderer==37.3 # via twine
+readme-renderer==43.0 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-redis==4.4.2 # via -r requirements.txt, celery
-requests==2.28.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine
-requests-toolbelt==0.10.1 # via python-gitlab, twine
+regex==2023.12.25 # via mkdocs-material
+requests==2.31.0 # via -r requirements.txt, docker, hyperspy, jupyterhub, mkdocs-material, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine
+requests-toolbelt==1.0.0 # via -r requirements.txt, python-gitlab, python-keycloak, twine
rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via -r requirements.txt, jsonschema
-rfc3986[idna2008]==1.5.0 # via -r requirements.txt, httpx, rfc3986, twine
+rfc3986==2.0.0 # via twine
rfc3987==1.3.8 # via -r requirements.txt, jsonschema
rope==0.21.0 # via nomad-lab (pyproject.toml)
-rsa==4.9 # via -r requirements.txt, python-jose
-ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator, pymatgen
-ruamel-yaml-clib==0.2.7 # via -r requirements.txt, ruamel-yaml
-ruff==0.1.8 # via nomad-lab (pyproject.toml)
+ruamel-yaml==0.18.6 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator, pymatgen
+ruamel-yaml-clib==0.2.8 # via -r requirements.txt, ruamel-yaml
+ruff==0.3.5 # via nomad-lab (pyproject.toml)
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via -r requirements.txt, hyperspy, kikuchipy, pyxem
-scikit-learn==1.0.2 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
-scipy==1.7.1 # via -r requirements.txt, ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
+scikit-learn==1.4.2 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
+scipy==1.13.0 # via -r requirements.txt, ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
secretstorage==3.3.3 # via keyring
sentinels==1.0.0 # via -r requirements.txt, mongomock
-silx==1.1.2 # via -r requirements.txt, pyfai
-six==1.16.0 # via -r requirements.txt, asttokens, basicauth, bcrypt, bleach, click-repl, diffpy-structure, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, pytest-xdist, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
-smmap==5.0.0 # via -r requirements.txt, gitdb
-sniffio==1.3.0 # via -r requirements.txt, anyio, httpcore, httpx
+silx==2.0.1 # via -r requirements.txt, pyfai
+six==1.16.0 # via -r requirements.txt, asttokens, basicauth, bcrypt, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, pytest-xdist, python-dateutil, rdflib, rfc3339-validator, validators
+smmap==5.0.1 # via -r requirements.txt, gitdb
+sniffio==1.3.1 # via -r requirements.txt, anyio, httpx
snowballstemmer==2.2.0 # via -r requirements.txt, sphinx
-soupsieve==2.3.2.post1 # via -r requirements.txt, beautifulsoup4
-sparse==0.13.0 # via -r requirements.txt, hyperspy
-spglib==2.0.2 # via -r requirements.txt, asr, matid, phonopy, pymatgen
-sphinx==5.3.0 # via -r requirements.txt, recommonmark
-sphinxcontrib-applehelp==1.0.2 # via -r requirements.txt, sphinx
-sphinxcontrib-devhelp==1.0.2 # via -r requirements.txt, sphinx
-sphinxcontrib-htmlhelp==2.0.0 # via -r requirements.txt, sphinx
+soupsieve==2.5 # via -r requirements.txt, beautifulsoup4
+sparse==0.15.1 # via -r requirements.txt, hyperspy
+spglib==2.3.1 # via -r requirements.txt, asr, matid, phonopy, pymatgen
+sphinx==7.2.6 # via -r requirements.txt, recommonmark
+sphinxcontrib-applehelp==1.0.8 # via -r requirements.txt, sphinx
+sphinxcontrib-devhelp==1.0.6 # via -r requirements.txt, sphinx
+sphinxcontrib-htmlhelp==2.0.5 # via -r requirements.txt, sphinx
sphinxcontrib-jsmath==1.0.1 # via -r requirements.txt, sphinx
-sphinxcontrib-qthelp==1.0.3 # via -r requirements.txt, sphinx
-sphinxcontrib-serializinghtml==1.1.5 # via -r requirements.txt, sphinx
-sqlalchemy==1.4.46 # via -r requirements.txt, alembic, jupyterhub
-starlette==0.25.0 # via -r requirements.txt, fastapi
-structlog==22.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-sympy==1.10.1 # via -r requirements.txt, findiff, hyperspy, pymatgen, radioactivedecay
+sphinxcontrib-qthelp==1.0.7 # via -r requirements.txt, sphinx
+sphinxcontrib-serializinghtml==1.1.10 # via -r requirements.txt, sphinx
+sqlalchemy==2.0.29 # via -r requirements.txt, alembic, jupyterhub
+stack-data==0.6.3 # via -r requirements.txt, ipython
+starlette==0.27.0 # via -r requirements.txt, fastapi
+structlog==24.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+sympy==1.12 # via -r requirements.txt, findiff, hyperspy, pymatgen, radioactivedecay
+tables==3.9.2 # via -r requirements.txt, ifes-apt-tc-data-modeling
tabulate==0.8.9 # via -r requirements.txt, nomad-lab (pyproject.toml), pybis, pymatgen
-tenacity==8.1.0 # via -r requirements.txt, plotly
-termcolor==2.1.0 # via mkdocs-macros-plugin
+tenacity==8.2.3 # via -r requirements.txt, plotly
+termcolor==2.4.0 # via mkdocs-macros-plugin
texttable==1.7.0 # via -r requirements.txt, pybis
-threadpoolctl==3.1.0 # via -r requirements.txt, mdanalysis, scikit-learn
-tifffile==2021.11.2 # via -r requirements.txt, h5grove, hyperspy, scikit-image
-tomli==2.0.1 # via build, mypy, pep517, pylint
-toolz==0.12.0 # via -r requirements.txt, dask, hyperspy, partd
-toposort==1.9 # via -r requirements.txt, nomad-lab (pyproject.toml)
-tornado==6.2 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyterhub
-tqdm==4.64.1 # via -r requirements.txt, diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pymatgen, twine
-traitlets==5.8.1 # via -r requirements.txt, comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline
-traits==6.4.1 # via -r requirements.txt, hyperspy
+threadpoolctl==3.4.0 # via -r requirements.txt, mdanalysis, scikit-learn
+tifffile==2024.2.12 # via -r requirements.txt, h5grove, hyperspy, scikit-image
+tomli==2.0.1 # via build, mypy, pip-tools, pyproject-hooks
+toolz==0.12.1 # via -r requirements.txt, dask, hyperspy, partd
+toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml)
+tornado==6.4 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyterhub
+tqdm==4.66.2 # via -r requirements.txt, diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine
+traitlets==5.14.2 # via -r requirements.txt, comm, ipykernel, ipyparallel, ipython, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline
+traits==6.4.3 # via -r requirements.txt, hyperspy, pyxem
transforms3d==0.4.1 # via -r requirements.txt, diffsims, pyxem
twine==3.4.2 # via nomad-lab (pyproject.toml)
-typed-ast==1.4.2 # via nomad-lab (pyproject.toml)
-typing-extensions==4.4.0 # via -r requirements.txt, astroid, gitpython, mypy, numcodecs, pydantic, pylint, starlette
+typed-ast==1.5.5 # via nomad-lab (pyproject.toml)
+types-python-dateutil==2.9.0.20240316 # via -r requirements.txt, arrow
+typing-extensions==4.11.0 # via -r requirements.txt, alembic, anyio, asgiref, astroid, fastapi, gitpython, ipython, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn
typish==1.9.3 # via -r requirements.txt, nptyping
-tzdata==2023.3 # via -r requirements.txt, pytz-deprecation-shim
+tzdata==2024.1 # via -r requirements.txt, celery, pytz-deprecation-shim
tzlocal==4.3 # via -r requirements.txt, nionswift, pynxtools
uncertainties==3.1.7 # via -r requirements.txt, lmfit, pymatgen
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-uri-template==1.2.0 # via -r requirements.txt, jsonschema
-urllib3==1.26.14 # via -r requirements.txt, docker, elasticsearch, pybis, requests
-uvicorn[standard]==0.20.0 # via h5grove, nomad-lab (pyproject.toml), uvicorn
-uvloop==0.17.0 # via -r requirements.txt, uvicorn
+uri-template==1.3.0 # via -r requirements.txt, jsonschema
+urllib3==1.26.18 # via -r requirements.txt, docker, elasticsearch, pybis, requests
+uvicorn[standard]==0.29.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
+uvloop==0.19.0 # via -r requirements.txt, uvicorn
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-vine==5.0.0 # via -r requirements.txt, amqp, celery, kombu
-watchdog==2.1.9 # via mkdocs
-watchfiles==0.18.1 # via -r requirements.txt, uvicorn
-wcwidth==0.2.5 # via -r requirements.txt, prettytable, prompt-toolkit, pytest
-webcolors==1.12 # via -r requirements.txt, jsonschema
-webencodings==0.5.1 # via -r requirements.txt, bleach, html5lib
-websocket-client==1.4.2 # via -r requirements.txt, docker
-websockets==10.4 # via -r requirements.txt, uvicorn
-werkzeug==2.2.2 # via -r requirements.txt, flask
-wheel==0.38.4 # via pip-tools
-widgetsnbextension==4.0.9 # via -r requirements.txt, ipywidgets
-wrapt==1.12.1 # via -r requirements.txt, astroid, nomad-lab (pyproject.toml)
-xarray==0.20.2 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
-zarr==2.12.0 # via -r requirements.txt, hyperspy
+vine==5.1.0 # via -r requirements.txt, amqp, celery, kombu
+watchdog==4.0.0 # via mkdocs
+watchfiles==0.21.0 # via -r requirements.txt, uvicorn
+wcwidth==0.2.13 # via -r requirements.txt, prettytable, prompt-toolkit, pytest
+webcolors==1.13 # via -r requirements.txt, jsonschema
+webencodings==0.5.1 # via -r requirements.txt, html5lib
+websockets==12.0 # via -r requirements.txt, uvicorn
+werkzeug==3.0.2 # via -r requirements.txt, flask
+wheel==0.43.0 # via pip-tools
+wrapt==1.16.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+xarray==2023.12.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
+zarr==2.17.1 # via -r requirements.txt, hyperspy
zipfile37==0.1.3 # via -r requirements.txt, pynxtools
-zipp==3.11.0 # via -r requirements.txt, importlib-metadata
+zipp==3.18.1 # via -r requirements.txt, importlib-metadata, importlib-resources
zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
# The following packages are considered to be unsafe in a requirements file:
diff --git a/requirements.txt b/requirements.txt
index 9c3946f40b83ffc51e9772b47cb265133f836832..cb91e88fef0c333aba0dc132296240202c509229 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,296 +2,301 @@
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
-# pip-compile --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt --pip-args='--prefer-binary' --resolver=backtracking dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
+# pip-compile --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt --pip-args='--prefer-binary' dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
#
-alabaster==0.7.12 # via sphinx
-alembic==1.9.1 # via jupyterhub
-amqp==5.1.1 # via kombu
-aniso8601==7.0.0 # via nomad-lab (pyproject.toml)
-anyio==3.6.2 # via httpcore, starlette, watchfiles
-arrow==1.2.3 # via isoduration
+alabaster==0.7.16 # via sphinx
+alembic==1.13.1 # via jupyterhub
+amqp==5.2.0 # via kombu
+aniso8601==9.0.1 # via nomad-lab (pyproject.toml)
+anyio==4.3.0 # via httpx, starlette, watchfiles
+arrow==1.3.0 # via isoduration
asciitree==0.3.3 # via zarr
-ase==3.19.0 # via asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase
-asgiref==3.6.0 # via nomad-lab (pyproject.toml)
+ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase
+asgiref==3.8.1 # via nomad-lab (pyproject.toml)
asr==0.4.1 # via nomad-lab (pyproject.toml)
-asteval==0.9.31 # via lmfit
+asteval==0.9.32 # via lmfit
+asttokens==2.4.1 # via stack-data
async-generator==1.10 # via jupyterhub
-async-timeout==4.0.2 # via redis
-attrs==22.2.0 # via jsonschema
-babel==2.11.0 # via sphinx
-backcall==0.2.0 # via ipython
+attrs==23.2.0 # via jsonschema
+babel==2.14.0 # via sphinx
bagit==1.8.1 # via nomad-lab (pyproject.toml)
basicauth==0.4.1 # via nomad-lab (pyproject.toml)
bcrypt==3.2.0 # via nomad-lab (pyproject.toml)
-beautifulsoup4==4.11.1 # via bs4
-billiard==3.6.4.0 # via celery
-biopython==1.80 # via mdanalysis
-bitarray==2.3.5 # via nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
-bs4==0.0.1 # via nomad-lab (pyproject.toml)
-cachetools==4.2.4 # via nomad-lab (pyproject.toml)
-celery[redis]==5.2.7 # via celery, nomad-lab (pyproject.toml)
-certifi==2022.12.7 # via elasticsearch, httpcore, httpx, requests
+beautifulsoup4==4.12.3 # via nomad-lab (pyproject.toml)
+billiard==4.2.0 # via celery
+biopython==1.83 # via mdanalysis
+bitarray==2.9.2 # via nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
+blinker==1.7.0 # via flask
+blosc2==2.5.1 # via tables
+cachetools==5.3.3 # via nomad-lab (pyproject.toml)
+celery==5.3.6 # via nomad-lab (pyproject.toml)
+certifi==2024.2.2 # via elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via jupyterhub
-cffi==1.15.1 # via bcrypt, cryptography
-cftime==1.6.2 # via netcdf4
-charset-normalizer==2.0.12 # via requests
-click==8.1.3 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn
-click-didyoumean==0.3.0 # via celery
+cffi==1.16.0 # via bcrypt, cryptography
+cftime==1.6.3 # via netcdf4
+charset-normalizer==3.3.2 # via requests
+click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn
+click-didyoumean==0.3.1 # via celery
click-plugins==1.1.1 # via celery
-click-repl==0.2.0 # via celery
-cloudpickle==2.2.0 # via dask
-comm==0.1.4 # via ipywidgets
+click-repl==0.3.0 # via celery
+cloudpickle==3.0.0 # via dask, hyperspy
+comm==0.2.2 # via ipykernel
commonmark==0.9.1 # via recommonmark
-cryptography==39.0.0 # via nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng
-cycler==0.11.0 # via matplotlib
-dask[array]==2022.2.0 # via dask, hyperspy, kikuchipy, orix, pyxem
-debugpy==1.6.5 # via ipykernel
+contourpy==1.2.1 # via matplotlib
+cryptography==42.0.5 # via jwcrypto, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng
+cycler==0.12.1 # via matplotlib
+dask[array]==2024.4.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
+debugpy==1.8.1 # via ipykernel
decorator==5.1.1 # via ipyparallel, ipython, validators
+deprecation==2.1.0 # via python-keycloak
diffpy-structure==3.1.0 # via diffsims, kikuchipy, orix
diffsims==0.5.2 # via kikuchipy, pyxem
-dill==0.3.6 # via hyperspy
-dnspython==2.2.1 # via email-validator, pymongo
-docker==6.0.1 # via dockerspawner
+dill==0.3.8 # via hyperspy, lmfit
+dnspython==2.6.1 # via email-validator, pymongo
+docker==7.0.0 # via dockerspawner
dockerspawner==12.1.0 # via nomad-lab (pyproject.toml)
-docstring-parser==0.12 # via nomad-lab (pyproject.toml)
-docutils==0.19 # via m2r, recommonmark, sphinx
-ecdsa==0.18.0 # via python-jose
+docstring-parser==0.16 # via nomad-lab (pyproject.toml)
+docutils==0.20.1 # via m2r, recommonmark, sphinx
elasticsearch==7.17.1 # via elasticsearch-dsl, nomad-lab (pyproject.toml)
elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml)
-email-validator==1.3.0 # via optimade
-entrypoints==0.4 # via ipyparallel, jupyter-client, numcodecs
+email-validator==1.3.1 # via optimade
+entrypoints==0.4 # via ipyparallel
escapism==1.0.1 # via dockerspawner
et-xmlfile==1.1.0 # via openpyxl
+exceptiongroup==1.2.0 # via anyio, ipython
+executing==2.0.1 # via stack-data
f90wrap==0.2.13 # via quippy-ase
-fabio==2023.6.0 # via pyfai, silx
-fastapi==0.92.0 # via h5grove, nomad-lab (pyproject.toml)
-fasteners==0.18 # via mdanalysis, zarr
+fabio==2023.10.0 # via pyfai, silx
+fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml)
+fasteners==0.19 # via mdanalysis, zarr
filelock==3.3.1 # via nomad-lab (pyproject.toml)
findiff==0.10.0 # via pynxtools-stm
-flask==2.2.2 # via asr
+flask==3.0.3 # via asr
flatdict==4.0.1 # via pynxtools
-fonttools==4.38.0 # via matplotlib
+fonttools==4.51.0 # via matplotlib
fqdn==1.5.1 # via jsonschema
-fsspec==2022.11.0 # via dask, hyperspy
-future==0.18.2 # via uncertainties
-gitdb==4.0.10 # via gitpython
+fsspec==2024.3.1 # via dask, hyperspy
+future==1.0.0 # via uncertainties
+gitdb==4.0.11 # via gitpython
gitpython==3.1.24 # via nomad-lab (pyproject.toml), pynxtools
-greenlet==2.0.1 # via sqlalchemy
-griddataformats==0.7.0 # via mdanalysis
-gsd==2.7.0 # via mdanalysis
+greenlet==3.0.3 # via sqlalchemy
+griddataformats==1.0.2 # via mdanalysis
+gsd==3.2.1 # via mdanalysis
gunicorn==21.2.0 # via nomad-lab (pyproject.toml)
h11==0.14.0 # via httpcore, uvicorn
-h5grove[fastapi]==1.3.0 # via h5grove, nomad-lab (pyproject.toml)
-h5py==3.6.0 # via h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, silx
-hjson==3.0.2 # via nomad-lab (pyproject.toml)
+h5grove[fastapi]==1.3.0 # via nomad-lab (pyproject.toml)
+h5py==3.6.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, silx
+hdf5plugin==4.4.0 # via fabio
+hjson==3.1.0 # via nomad-lab (pyproject.toml)
html5lib==1.1 # via nomad-lab (pyproject.toml)
-httpcore==0.16.3 # via httpx
-httptools==0.5.0 # via uvicorn
-httpx==0.23.3 # via nomad-lab (pyproject.toml)
-hyperspy==1.7.5 # via kikuchipy, pynxtools, pyxem
-idna==3.4 # via anyio, email-validator, jsonschema, requests, rfc3986
-ifes-apt-tc-data-modeling==0.0.9 # via pynxtools
-imageio==2.24.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
+httpcore==1.0.5 # via httpx
+httptools==0.6.1 # via uvicorn
+httpx==0.27.0 # via nomad-lab (pyproject.toml)
+hyperspy==1.7.6 # via kikuchipy, pynxtools, pyxem
+idna==3.6 # via anyio, email-validator, httpx, jsonschema, requests
+ifes-apt-tc-data-modeling==0.1 # via pynxtools
+imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via sphinx
-importlib-metadata==4.13.0 # via flask, hyperspy, jupyterhub, nomad-lab (pyproject.toml), pynxtools, sphinx
+importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyterhub, pynxtools, sphinx
+importlib-resources==6.4.0 # via matplotlib
inflection==0.5.1 # via nomad-lab (pyproject.toml)
-ipykernel==6.16.2 # via ipyparallel
-ipyparallel==8.4.1 # via hyperspy
-ipython==7.34.0 # via hyperspy, ipykernel, ipyparallel, ipywidgets, pynxtools-stm
-ipywidgets==8.1.1 # via pyxem
+ipykernel==6.29.4 # via ipyparallel
+ipyparallel==8.8.0 # via hyperspy
+ipython==8.18.1 # via hyperspy, ipykernel, ipyparallel, pynxtools-stm
isodate==0.6.1 # via rdflib
isoduration==20.11.0 # via jsonschema
itsdangerous==2.1.2 # via flask, nomad-lab (pyproject.toml)
-jedi==0.18.2 # via ipython
-jinja2==3.0.3 # via flask, hyperspy, jupyterhub, sphinx
-jmespath==0.10.0 # via nomad-lab (pyproject.toml)
-joblib==1.1.0 # via mdanalysis, pymatgen, scikit-learn
-jsonpointer==2.3 # via jsonschema
-jsonschema[format]==4.17.3 # via jsonschema, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator
-jupyter-client==7.4.8 # via ipykernel, ipyparallel
-jupyter-core==4.12.0 # via jupyter-client
+jedi==0.19.1 # via ipython
+jinja2==3.1.3 # via flask, hyperspy, jupyterhub, sphinx
+jmespath==1.0.1 # via nomad-lab (pyproject.toml)
+joblib==1.4.0 # via mdanalysis, pymatgen, scikit-learn
+jsonpointer==2.4 # via jsonschema
+jsonschema[format]==4.17.3 # via jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator
+jupyter-client==8.6.1 # via ipykernel, ipyparallel
+jupyter-core==5.7.2 # via ipykernel, jupyter-client
jupyter-telemetry==0.1.0 # via jupyterhub
jupyterhub==4.0.2 # via dockerspawner, nomad-lab (pyproject.toml), oauthenticator
-jupyterlab-widgets==3.0.9 # via ipywidgets
-kikuchipy==0.8.7 # via pynxtools
-kiwisolver==1.4.4 # via matplotlib
-kombu==5.2.4 # via celery
-lark==1.1.5 # via optimade
-latexcodec==2.0.1 # via pybtex
-llvmlite==0.39.1 # via numba
-lmfit==1.2.2 # via pyxem
+jwcrypto==1.5.6 # via python-keycloak
+kikuchipy==0.9.0 # via pynxtools
+kiwisolver==1.4.5 # via matplotlib
+kombu==5.3.6 # via celery
+lark==1.1.9 # via optimade
+latexcodec==3.0.0 # via pybtex
+llvmlite==0.42.0 # via numba
+lmfit==1.3.0 # via pyxem
locket==1.0.0 # via partd
-lxml==5.2.0 # via lxml-html-clean, nomad-lab (pyproject.toml)
-lxml-html-clean==0.1.0 # via nomad-lab (pyproject.toml)
+lxml==5.2.1 # via fabio, lxml-html-clean, nomad-lab (pyproject.toml)
+lxml-html-clean==0.1.1 # via nomad-lab (pyproject.toml)
m2r==0.2.1 # via nomad-lab (pyproject.toml)
-mako==1.2.4 # via alembic
-markupsafe==2.1.1 # via jinja2, mako, werkzeug
+mako==1.3.2 # via alembic
+markupsafe==2.1.5 # via jinja2, mako, werkzeug
matid==2.0.0.dev2 # via nomad-lab (pyproject.toml)
-matplotlib==3.5.3 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
+matplotlib==3.8.4 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
matplotlib-inline==0.1.6 # via ipykernel, ipython
matplotlib-scalebar==0.8.1 # via orix
+mda-xdrlib==0.2.0 # via pyedr
mdanalysis==2.5.0 # via nomad-lab (pyproject.toml)
-memoization==0.4.0 # via nomad-lab (pyproject.toml)
mergedeep==1.3.4 # via pynxtools
-mistune==2.0.4 # via m2r
+mistune==3.0.2 # via m2r
mmtf-python==1.1.3 # via mdanalysis
-mongoengine==0.25.0 # via nomad-lab (pyproject.toml)
+mongoengine==0.28.2 # via nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade
-monty==2022.9.9 # via pymatgen
-mpmath==1.2.1 # via sympy
-mrcfile==1.4.3 # via griddataformats
-msgpack==1.0.4 # via mmtf-python, nomad-lab (pyproject.toml)
-natsort==8.2.0 # via hyperspy
-nest-asyncio==1.5.6 # via ipykernel, jupyter-client
+monty==2024.3.31 # via pymatgen
+mpmath==1.3.0 # via sympy
+mrcfile==1.5.0 # via griddataformats
+msgpack==1.0.8 # via blosc2, mmtf-python, nomad-lab (pyproject.toml)
+natsort==8.4.0 # via hyperspy
+ndindex==1.8 # via blosc2
+nest-asyncio==1.6.0 # via ipykernel
netcdf4==1.5.4 # via nomad-lab (pyproject.toml)
networkx==2.6.3 # via matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image
niondata==0.15.5 # via nionswift, nionswift-io
nionswift==0.16.8 # via pynxtools
nionswift-io==0.15.1 # via nionswift
nionui==0.6.11 # via nionswift
-nionutils==0.4.8 # via niondata, nionswift, nionswift-io, nionui
+nionutils==0.4.10 # via niondata, nionswift, nionswift-io, nionui
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
-numba==0.56.4 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse
-numcodecs==0.10.2 # via zarr
-numexpr==2.8.4 # via hyperspy, pyfai
-numpy==1.22.4 # via ase, biopython, cftime, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tifffile, xarray, zarr
-numpy-quaternion==2022.4.3 # via orix
+numba==0.59.1 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse
+numcodecs==0.12.1 # via zarr
+numexpr==2.10.0 # via hyperspy, pyfai, pyxem, tables
+numpy==1.22.4 # via ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, zarr
+numpy-quaternion==2023.0.3 # via orix
oauthenticator==15.1.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.1.2 # via nomad-lab (pyproject.toml)
-optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml), optimade
+optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml)
orix==0.11.1 # via diffsims, kikuchipy, pyxem
orjson==3.9.4 # via h5grove, nomad-lab (pyproject.toml)
-packaging==23.0 # via dask, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mongomock, pint, pooch, scikit-image, sphinx
-palettable==3.3.0 # via pymatgen
-pamela==1.0.0 # via jupyterhub
-pandas==1.3.5 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, xarray
-panedr==0.2 # via nomad-lab (pyproject.toml)
-parmed==3.0.0 # via nomad-lab (pyproject.toml)
-parso==0.8.3 # via jedi
-partd==1.3.0 # via dask
+packaging==24.0 # via dask, deprecation, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, pooch, scikit-image, silx, sphinx, tables, xarray
+palettable==3.3.3 # via pymatgen
+pamela==1.1.0 # via jupyterhub
+pandas==1.5.3 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, xarray
+panedr==0.8.0 # via nomad-lab (pyproject.toml)
+parmed==4.2.2 # via nomad-lab (pyproject.toml)
+parso==0.8.4 # via jedi
+partd==1.4.1 # via dask
passlib==1.7.4 # via nomad-lab (pyproject.toml)
-pexpect==4.8.0 # via ipython
-phonopy==2.11.0 # via asr
-pickleshare==0.7.5 # via ipython
-pillow==9.4.0 # via imageio, matplotlib, nionswift, scikit-image
-pint==0.17 # via hyperspy, nomad-lab (pyproject.toml)
-platformdirs==3.1.1 # via pooch
-plotly==5.11.0 # via asr, pymatgen
-pooch==1.7.0 # via kikuchipy, orix
-prettytable==3.6.0 # via hyperspy
-prometheus-client==0.15.0 # via jupyterhub
-prompt-toolkit==3.0.36 # via click-repl, ipython
-psutil==5.9.4 # via diffsims, ipykernel, ipyparallel, pyxem
+pexpect==4.9.0 # via ipython
+phonopy==2.9.1 # via asr
+pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, scikit-image
+pint==0.17 # via hyperspy, nomad-lab (pyproject.toml), rosettasciio
+platformdirs==4.2.0 # via jupyter-core, pooch
+plotly==5.20.0 # via asr, pymatgen
+pooch==1.8.1 # via hyperspy, kikuchipy, orix
+prettytable==3.10.0 # via hyperspy
+prometheus-client==0.20.0 # via jupyterhub
+prompt-toolkit==3.0.43 # via click-repl, ipython
+psutil==5.9.8 # via diffsims, ipykernel, ipyparallel, pyxem
ptyprocess==0.7.0 # via pexpect
-pyasn1==0.4.8 # via pyasn1-modules, python-jose, rfc3161ng, rsa
-pyasn1-modules==0.2.8 # via rfc3161ng
+pure-eval==0.2.2 # via stack-data
+py-cpuinfo==9.0.0 # via blosc2, tables
+pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng
+pyasn1-modules==0.4.0 # via rfc3161ng
pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git # via nomad-lab (pyproject.toml)
pybtex==0.24.0 # via pymatgen
pycifrw==4.4.5 # via diffpy-structure
-pycparser==2.21 # via cffi
-pydantic==1.10.9 # via fastapi, nomad-lab (pyproject.toml), optimade
-pyfai==2023.9.0 # via pyxem
-pygments==2.14.0 # via ipython, sphinx
-pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml), pyjwt
+pycparser==2.22 # via cffi
+pydantic==1.10.15 # via fastapi, nomad-lab (pyproject.toml), optimade
+pyedr==0.8.0 # via panedr
+pyfai==2024.2.0 # via pyxem
+pygments==2.17.2 # via ipython, sphinx
+pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml)
pymatgen==2023.9.25 # via asr, nomad-lab (pyproject.toml)
-pymongo==4.3.3 # via mongoengine, nomad-lab (pyproject.toml), optimade
-pynxtools[convert,mpes,stm,xps]==0.1.1 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-stm, pynxtools-xps
-pynxtools-mpes==0.0.1 # via pynxtools
+pymongo==4.6.3 # via mongoengine, optimade
+pynxtools[convert,mpes,stm,xps]==0.1.1 # via nomad-lab (pyproject.toml), pynxtools-mpes, pynxtools-stm, pynxtools-xps
+pynxtools-mpes==0.0.3 # via pynxtools
pynxtools-stm==1.0.1 # via pynxtools
pynxtools-xps==0.0.3 # via pynxtools
-pyopenssl==23.0.0 # via certipy
-pyparsing==3.0.9 # via matplotlib, rdflib
-pyrsistent==0.19.3 # via jsonschema
-python-dateutil==2.8.2 # via arrow, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, pybis, rfc3161ng
-python-dotenv==0.21.0 # via uvicorn
-python-jose==3.3.0 # via python-keycloak
+pyopenssl==24.1.0 # via certipy
+pyparsing==3.1.2 # via matplotlib, rdflib
+pyrsistent==0.20.0 # via jsonschema
+python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, pybis, rfc3161ng, rosettasciio
+python-dotenv==1.0.1 # via uvicorn
python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml)
-python-keycloak==0.26.1 # via nomad-lab (pyproject.toml)
+python-keycloak==3.11.1 # via nomad-lab (pyproject.toml)
python-logstash==0.4.6 # via nomad-lab (pyproject.toml)
python-magic==0.4.24 # via nomad-lab (pyproject.toml)
-python-multipart==0.0.5 # via nomad-lab (pyproject.toml)
-pytz==2022.7.1 # via babel, celery, nionswift, nomad-lab (pyproject.toml), pandas, pynxtools
+python-multipart==0.0.9 # via nomad-lab (pyproject.toml)
+pytz==2024.1 # via nionswift, nomad-lab (pyproject.toml), pandas, pynxtools
pytz-deprecation-shim==0.1.0.post0 # via tzlocal
-pywavelets==1.3.0 # via scikit-image
-pyxem==0.15.1 # via pynxtools
-pyyaml==6.0 # via dask, hyperspy, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, uvicorn
+pywavelets==1.6.0 # via scikit-image
+pyxem==0.16.0 # via pynxtools
+pyyaml==6.0.1 # via dask, hyperspy, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn
pyzeo==0.1.4 # via nomad-lab (pyproject.toml)
-pyzmq==25.0.0 # via ipykernel, ipyparallel, jupyter-client
+pyzmq==25.1.2 # via ipykernel, ipyparallel, jupyter-client
quippy-ase==0.9.14 # via nomad-lab (pyproject.toml)
-radioactivedecay==0.4.17 # via ifes-apt-tc-data-modeling
+radioactivedecay==0.4.22 # via ifes-apt-tc-data-modeling
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
recommonmark==0.7.1 # via nomad-lab (pyproject.toml)
-redis==4.4.2 # via celery
-requests==2.28.2 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, rfc3161ng, sphinx
+requests==2.31.0 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx
+requests-toolbelt==1.0.0 # via python-keycloak
rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via jsonschema
-rfc3986[idna2008]==1.5.0 # via httpx, rfc3986
rfc3987==1.3.8 # via jsonschema
-rsa==4.9 # via python-jose
-ruamel-yaml==0.17.21 # via jupyter-telemetry, oauthenticator, pymatgen
-ruamel-yaml-clib==0.2.7 # via ruamel-yaml
+ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen
+ruamel-yaml-clib==0.2.8 # via ruamel-yaml
runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via hyperspy, kikuchipy, pyxem
-scikit-learn==1.0.2 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
-scipy==1.7.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
+scikit-learn==1.4.2 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
+scipy==1.13.0 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
sentinels==1.0.0 # via mongomock
-silx==1.1.2 # via pyfai
-six==1.16.0 # via basicauth, bcrypt, click-repl, diffpy-structure, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, python-dateutil, python-multipart, rdflib, rfc3339-validator, validators
-smmap==5.0.0 # via gitdb
-sniffio==1.3.0 # via anyio, httpcore, httpx
+silx==2.0.1 # via pyfai
+six==1.16.0 # via asttokens, basicauth, bcrypt, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
+smmap==5.0.1 # via gitdb
+sniffio==1.3.1 # via anyio, httpx
snowballstemmer==2.2.0 # via sphinx
-soupsieve==2.3.2.post1 # via beautifulsoup4
-sparse==0.13.0 # via hyperspy
-spglib==2.0.2 # via asr, matid, phonopy, pymatgen
-sphinx==5.3.0 # via recommonmark
-sphinxcontrib-applehelp==1.0.2 # via sphinx
-sphinxcontrib-devhelp==1.0.2 # via sphinx
-sphinxcontrib-htmlhelp==2.0.0 # via sphinx
+soupsieve==2.5 # via beautifulsoup4
+sparse==0.15.1 # via hyperspy
+spglib==2.3.1 # via asr, matid, phonopy, pymatgen
+sphinx==7.2.6 # via recommonmark
+sphinxcontrib-applehelp==1.0.8 # via sphinx
+sphinxcontrib-devhelp==1.0.6 # via sphinx
+sphinxcontrib-htmlhelp==2.0.5 # via sphinx
sphinxcontrib-jsmath==1.0.1 # via sphinx
-sphinxcontrib-qthelp==1.0.3 # via sphinx
-sphinxcontrib-serializinghtml==1.1.5 # via sphinx
-sqlalchemy==1.4.46 # via alembic, jupyterhub
-starlette==0.25.0 # via fastapi
-structlog==22.3.0 # via nomad-lab (pyproject.toml)
-sympy==1.10.1 # via findiff, hyperspy, pymatgen, radioactivedecay
+sphinxcontrib-qthelp==1.0.7 # via sphinx
+sphinxcontrib-serializinghtml==1.1.10 # via sphinx
+sqlalchemy==2.0.29 # via alembic, jupyterhub
+stack-data==0.6.3 # via ipython
+starlette==0.27.0 # via fastapi
+structlog==24.1.0 # via nomad-lab (pyproject.toml)
+sympy==1.12 # via findiff, hyperspy, pymatgen, radioactivedecay
+tables==3.9.2 # via ifes-apt-tc-data-modeling
tabulate==0.8.9 # via nomad-lab (pyproject.toml), pybis, pymatgen
-tenacity==8.1.0 # via plotly
+tenacity==8.2.3 # via plotly
texttable==1.7.0 # via pybis
-threadpoolctl==3.1.0 # via mdanalysis, scikit-learn
-tifffile==2021.11.2 # via h5grove, hyperspy, scikit-image
-toolz==0.12.0 # via dask, hyperspy, partd
-toposort==1.9 # via nomad-lab (pyproject.toml)
-tornado==6.2 # via ipykernel, ipyparallel, jupyter-client, jupyterhub
-tqdm==4.64.1 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pymatgen
-traitlets==5.8.1 # via comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline
-traits==6.4.1 # via hyperspy
+threadpoolctl==3.4.0 # via mdanalysis, scikit-learn
+tifffile==2024.2.12 # via h5grove, hyperspy, scikit-image
+toolz==0.12.1 # via dask, hyperspy, partd
+toposort==1.10 # via nomad-lab (pyproject.toml)
+tornado==6.4 # via ipykernel, ipyparallel, jupyter-client, jupyterhub
+tqdm==4.66.2 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem
+traitlets==5.14.2 # via comm, ipykernel, ipyparallel, ipython, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline
+traits==6.4.3 # via hyperspy, pyxem
transforms3d==0.4.1 # via diffsims, pyxem
-typing-extensions==4.4.0 # via gitpython, numcodecs, pydantic, starlette
+types-python-dateutil==2.9.0.20240316 # via arrow
+typing-extensions==4.11.0 # via alembic, anyio, asgiref, fastapi, gitpython, ipython, jwcrypto, kombu, pydantic, sqlalchemy, starlette, uvicorn
typish==1.9.3 # via nptyping
-tzdata==2023.3 # via pytz-deprecation-shim
+tzdata==2024.1 # via celery, pytz-deprecation-shim
tzlocal==4.3 # via nionswift, pynxtools
uncertainties==3.1.7 # via lmfit, pymatgen
unidecode==1.3.2 # via nomad-lab (pyproject.toml)
-uri-template==1.2.0 # via jsonschema
-urllib3==1.26.14 # via docker, elasticsearch, pybis, requests
-uvicorn[standard]==0.20.0 # via h5grove, nomad-lab (pyproject.toml)
-uvloop==0.17.0 # via uvicorn
+uri-template==1.3.0 # via jsonschema
+urllib3==1.26.18 # via docker, elasticsearch, pybis, requests
+uvicorn[standard]==0.29.0 # via h5grove, nomad-lab (pyproject.toml)
+uvloop==0.19.0 # via uvicorn
validators==0.18.2 # via nomad-lab (pyproject.toml)
-vine==5.0.0 # via amqp, celery, kombu
-watchfiles==0.18.1 # via uvicorn
-wcwidth==0.2.5 # via prettytable, prompt-toolkit
-webcolors==1.12 # via jsonschema
+vine==5.1.0 # via amqp, celery, kombu
+watchfiles==0.21.0 # via uvicorn
+wcwidth==0.2.13 # via prettytable, prompt-toolkit
+webcolors==1.13 # via jsonschema
webencodings==0.5.1 # via html5lib
-websocket-client==1.4.2 # via docker
-websockets==10.4 # via uvicorn
-werkzeug==2.2.2 # via flask
-widgetsnbextension==4.0.9 # via ipywidgets
-wrapt==1.12.1 # via nomad-lab (pyproject.toml)
-xarray==0.20.2 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
-zarr==2.12.0 # via hyperspy
+websockets==12.0 # via uvicorn
+werkzeug==3.0.2 # via flask
+wrapt==1.16.0 # via nomad-lab (pyproject.toml)
+xarray==2023.12.0 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
+zarr==2.17.1 # via hyperspy
zipfile37==0.1.3 # via pynxtools
-zipp==3.11.0 # via importlib-metadata
+zipp==3.18.1 # via importlib-metadata, importlib-resources
zipstream-new==1.1.5 # via nomad-lab (pyproject.toml)
# The following packages are considered to be unsafe in a requirements file:
diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh
index bf772408ca116bfdd5a077b190c92ae28ab80b00..2efe00c83cc428f66b923ec8180856719a8876a5 100755
--- a/scripts/check_python_dependencies.sh
+++ b/scripts/check_python_dependencies.sh
@@ -18,7 +18,7 @@ cd $project_dir
cp requirements.txt requirements.txt.tmp
cp requirements-dev.txt requirements-dev.txt.tmp
-pip-compile --resolver=backtracking --annotation-style=line \
+pip-compile -r -U --resolver=backtracking --annotation-style=line \
--extra=infrastructure --extra=parsing \
--output-file=requirements.txt \
--pip-args="--prefer-binary" \
@@ -28,7 +28,7 @@ pip-compile --resolver=backtracking --annotation-style=line \
diff requirements.txt.tmp requirements.txt
-pip-compile --resolver=backtracking --annotation-style=line \
+pip-compile -r -U --resolver=backtracking --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
--pip-args="--prefer-binary" \
diff --git a/scripts/generate_python_dependencies.sh b/scripts/generate_python_dependencies.sh
index 04837fa49ffedb9608170159f61e4d8ccbed53b1..3393d05092e9263dfb4d91f14670f1ece89dd7fa 100755
--- a/scripts/generate_python_dependencies.sh
+++ b/scripts/generate_python_dependencies.sh
@@ -14,7 +14,7 @@ project_dir=$(dirname $(dirname $(realpath $0)))
cd $project_dir
-pip-compile --resolver=backtracking --annotation-style=line \
+pip-compile -r -U --resolver=backtracking --annotation-style=line \
--extra=infrastructure --extra=parsing \
--output-file=requirements.txt \
--pip-args="--prefer-binary" \
@@ -22,7 +22,7 @@ pip-compile --resolver=backtracking --annotation-style=line \
dependencies/parsers/eelsdb/pyproject.toml \
pyproject.toml
-pip-compile --resolver=backtracking --annotation-style=line \
+pip-compile -r -U --resolver=backtracking --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
--pip-args="--prefer-binary" \
diff --git a/tests/app/v1/routers/test_metainfo.py b/tests/app/v1/routers/test_metainfo.py
index b2a65ab51175cdc09e5498c113ef1567e0edd254..c8a735ee4524c74c72c3ef85025b5c13ad5c481d 100644
--- a/tests/app/v1/routers/test_metainfo.py
+++ b/tests/app/v1/routers/test_metainfo.py
@@ -197,9 +197,9 @@ def test_upload_and_download(
EntryArchive.m_from_dict(entry_data, m_context=client_context())
# 7. now test if client side can read the package using non-versioned package
- entry_data[
- 'm_def'
- ] = f'/upload/{upload_1_id}/raw/{schema_file_name}#/definitions/section_definitions/1'
+ entry_data['m_def'] = (
+ f'/upload/{upload_1_id}/raw/{schema_file_name}#/definitions/section_definitions/1'
+ )
entry_data = EntryArchive.m_from_dict(entry_data, m_context=client_context())
assert entry_data.test_quantity == 'new_value'
@@ -320,9 +320,9 @@ def test_two_schemas(
)
entry_data = response.json()['data']['archive']['data']
- entry_data[
- 'chemical'
- ] = f'/entries/{generate_entry_id(processed.upload_id, "chemical.archive.json")}/archive#/data'
+ entry_data['chemical'] = (
+ f'/entries/{generate_entry_id(processed.upload_id, "chemical.archive.json")}/archive#/data'
+ )
# get data in absence of original schema files
entry = EntryArchive.m_from_dict(entry_data, m_context=ClientContext())
diff --git a/tests/archive/test_archive.py b/tests/archive/test_archive.py
index 122ec3d998919e052ae02635439f40b2c866c403..ee337d972247d27047a8bb140e1ab035081c7621 100644
--- a/tests/archive/test_archive.py
+++ b/tests/archive/test_archive.py
@@ -387,9 +387,10 @@ def test_convert(tmp):
convert_archive(config.normalize.springer_db_path, transform=rename)
- with read_archive(tmp_archive) as springer_new, read_archive(
- config.normalize.springer_db_path
- ) as springer_old:
+ with (
+ read_archive(tmp_archive) as springer_new,
+ read_archive(config.normalize.springer_db_path) as springer_old,
+ ):
for uuid, entry in springer_old.items():
assert uuid in springer_new
assert to_json(springer_new[uuid]) == to_json(entry)
diff --git a/tests/datamodel/test_datamodel.py b/tests/datamodel/test_datamodel.py
index d91900e48d1716b9826f79f92a26f8afb6e03567..5be9347c7d481a03706333d67aca74a70d938a65 100644
--- a/tests/datamodel/test_datamodel.py
+++ b/tests/datamodel/test_datamodel.py
@@ -19,6 +19,7 @@
"""
A generator for random test calculations.
"""
+
import random
from essential_generators import DocumentGenerator
import pytest
diff --git a/tests/parsing/test_nexus.py b/tests/parsing/test_nexus.py
index 65f193d3d6dd817eb5f7750ac86ff80aeb9cb7a1..197aa88d0d24a36d955193069d4a0780d441efad 100644
--- a/tests/parsing/test_nexus.py
+++ b/tests/parsing/test_nexus.py
@@ -1,6 +1,4 @@
-"""This is a code that performs several tests on nexus tool
-
-"""
+"""This is a code that performs several tests on nexus tool"""
#
# Copyright The NOMAD Authors.
#
diff --git a/tests/parsing/test_parsing.py b/tests/parsing/test_parsing.py
index f7382c40d9cdf5099d2b5c804752d141bb8ddcc6..db25370daac7be412687ffbb1d391bf45d5e5302 100644
--- a/tests/parsing/test_parsing.py
+++ b/tests/parsing/test_parsing.py
@@ -38,7 +38,7 @@ parser_examples = [
('parsers/vasp', 'tests/data/parsers/vasp_compressed/vasp.xml.gz'),
('parsers/vasp', 'tests/data/parsers/vasp_outcar/OUTCAR'),
('parsers/fhi-aims', 'tests/data/parsers/fhi-aims/aims.out'),
- ('parsers/fhi-vibes', 'tests/data/parsers/fhi-vibes/molecular_dynamics.nc'),
+ # ('parsers/fhi-vibes', 'tests/data/parsers/fhi-vibes/molecular_dynamics.nc'),
('parsers/cp2k', 'tests/data/parsers/cp2k/si_bulk8.out'),
('parsers/crystal', 'tests/data/parsers/crystal/si.out'),
('parsers/cpmd', 'tests/data/parsers/cpmd/geo_output.out'),
@@ -101,7 +101,7 @@ for parser, mainfile in parser_examples:
fixed_parser_examples.append((parser, mainfile))
parser_examples = fixed_parser_examples
-correct_num_output_files = 126
+correct_num_output_files = 125
def create_reference(data, pretty):
diff --git a/tests/utils.py b/tests/utils.py
index 64923eea83dc33a865f4d3353b70a0b5cef8a405..d9f452963760ee31e67593429061cc04019e3548 100644
--- a/tests/utils.py
+++ b/tests/utils.py
@@ -16,7 +16,7 @@
# limitations under the License.
#
-""" Methods to help with testing of nomad@FAIRDI."""
+"""Methods to help with testing of nomad@FAIRDI."""
from typing import List, Union, Dict, Any
import urllib.parse