diff --git a/Dockerfile b/Dockerfile
index 7084a7029a94427835dbee9b334613a9de57e8e6..670321e788dfcc19215872851cb8dafca45f48a3 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -126,9 +126,6 @@ ARG SETUPTOOLS_SCM_PRETEND_VERSION='0.0'
# Build documentation
-# This is a temporary workaround because atomisticparsers installs an older version
-# of nomad-lab via pip install git+...still containing pynxtools as a submodule
-RUN pip uninstall -y pynxtools
RUN pip install ".[parsing,infrastructure,dev]"
RUN ./scripts/generate_docs_artifacts.sh \
@@ -174,14 +171,6 @@ RUN pip install --progress-bar off --prefer-binary -r requirements.txt
# install
COPY --from=dev_python /app/dist/nomad-lab-*.tar.gz .
RUN pip install nomad-lab-*.tar.gz
-# This is a temporary workaround because atomisticparsers installs an older version
-# of nomad-lab via pip install git+...still containing pynxtools as a submodule.
-RUN pip uninstall -y pynxtools
-RUN pip install pynxtools[convert]
-# This is a temporary workaround because pynxtools installs an incompatible
-# version of h5grove
-RUN pip uninstall -y h5grove
-RUN pip install h5grove[fastapi]==1.3.0
# Reduce the size of the packages
RUN find /usr/local/lib/python3.9/ -type d -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + \
diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index bd59789aa0ddc414002407951d51dbf9a3f24f80..5ec6ea6e0c1e5d06adaf69bb449ab0b7b58e8bcb 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -39983,18 +39983,14 @@ window.nomadArtifacts = {
"type_data": [
"apm",
"ellips",
- "em_nion",
- "em_om",
- "em_spctrscpy",
+ "em",
"example",
- "hall",
"json_map",
"json_yml",
"mpes",
+ "srd",
"sts",
- "transmission",
- "xps",
- "xrd"
+ "xps"
]
}
},
@@ -40014,23 +40010,65 @@ window.nomadArtifacts = {
"type": {
"type_kind": "Enum",
"type_data": [
+ "NXapm",
+ "NXapm_composition_space_results",
+ "NXapm_compositionspace_config",
+ "NXapm_compositionspace_results",
+ "NXapm_paraprobe_clusterer_config",
+ "NXapm_paraprobe_clusterer_results",
+ "NXapm_paraprobe_distancer_config",
+ "NXapm_paraprobe_distancer_results",
+ "NXapm_paraprobe_intersector_config",
+ "NXapm_paraprobe_intersector_results",
+ "NXapm_paraprobe_nanochem_config",
+ "NXapm_paraprobe_nanochem_results",
+ "NXapm_paraprobe_ranger_config",
+ "NXapm_paraprobe_ranger_results",
+ "NXapm_paraprobe_selector_config",
+ "NXapm_paraprobe_selector_results",
+ "NXapm_paraprobe_spatstat_config",
+ "NXapm_paraprobe_spatstat_results",
+ "NXapm_paraprobe_surfacer_config",
+ "NXapm_paraprobe_surfacer_results",
+ "NXapm_paraprobe_tessellator_config",
+ "NXapm_paraprobe_tessellator_results",
+ "NXapm_paraprobe_transcoder_config",
+ "NXapm_paraprobe_transcoder_results",
"NXarchive",
"NXarpes",
"NXcanSAS",
+ "NXcxi_ptycho",
"NXdirecttof",
+ "NXdispersive_material",
+ "NXellipsometry",
+ "NXem",
"NXfluo",
"NXindirecttof",
"NXiqproc",
+ "NXiv_temp",
+ "NXlab_electro_chemo_mechanical_preparation",
+ "NXlab_sample_mounting",
"NXlauetof",
"NXmonopd",
+ "NXmpes",
+ "NXms",
+ "NXms_score_config",
+ "NXms_score_results",
"NXmx",
+ "NXopt",
+ "NXraman",
"NXrefscan",
"NXreftof",
+ "NXroot",
"NXsas",
"NXsastof",
"NXscan",
+ "NXsensor_scan",
+ "NXsnsevent",
+ "NXsnshisto",
"NXspe",
"NXsqom",
+ "NXsts",
"NXstxm",
"NXtas",
"NXtofnpd",
@@ -40039,6 +40077,7 @@ window.nomadArtifacts = {
"NXtomo",
"NXtomophase",
"NXtomoproc",
+ "NXtransmission",
"NXxas",
"NXxasproc",
"NXxbase",
@@ -40047,215 +40086,9 @@ window.nomadArtifacts = {
"NXxlaue",
"NXxlaueplate",
"NXxnb",
- "NXxrot",
- "NXaberration",
- "NXaberration_model",
- "NXaberration_model_ceos",
- "NXaberration_model_nion",
- "NXactivity",
- "NXactuator",
- "NXadc",
- "NXamplifier",
- "NXaperture_em",
- "NXapm",
- "NXapm_composition_space_results",
- "NXapm_input_ranging",
- "NXapm_input_reconstruction",
- "NXapm_paraprobe_config_clusterer",
- "NXapm_paraprobe_config_distancer",
- "NXapm_paraprobe_config_intersector",
- "NXapm_paraprobe_config_nanochem",
- "NXapm_paraprobe_config_ranger",
- "NXapm_paraprobe_config_selector",
- "NXapm_paraprobe_config_spatstat",
- "NXapm_paraprobe_config_surfacer",
- "NXapm_paraprobe_config_tessellator",
- "NXapm_paraprobe_config_transcoder",
- "NXapm_paraprobe_results_clusterer",
- "NXapm_paraprobe_results_distancer",
- "NXapm_paraprobe_results_intersector",
- "NXapm_paraprobe_results_nanochem",
- "NXapm_paraprobe_results_ranger",
- "NXapm_paraprobe_results_selector",
- "NXapm_paraprobe_results_spatstat",
- "NXapm_paraprobe_results_surfacer",
- "NXapm_paraprobe_results_tessellator",
- "NXapm_paraprobe_results_transcoder",
- "NXbeam_path",
- "NXbeam_splitter",
- "NXbias_spectroscopy",
- "NXcalibration",
- "NXcg_alpha_complex",
- "NXcg_cylinder_set",
- "NXcg_ellipsoid_set",
- "NXcg_face_list_data_structure",
- "NXcg_geodesic_mesh",
- "NXcg_grid",
- "NXcg_half_edge_data_structure",
- "NXcg_hexahedron_set",
- "NXcg_marching_cubes",
- "NXcg_parallelogram_set",
- "NXcg_point_set",
- "NXcg_polygon_set",
- "NXcg_polyhedron_set",
- "NXcg_polyline_set",
- "NXcg_primitive_set",
- "NXcg_roi_set",
- "NXcg_sphere_set",
- "NXcg_tetrahedron_set",
- "NXcg_triangle_set",
- "NXcg_triangulated_surface_mesh",
- "NXcg_unit_normal_set",
- "NXchamber",
- "NXchemical_composition",
- "NXchemical_process",
- "NXcircuit",
- "NXcircuit_board",
- "NXclustering",
- "NXcollectioncolumn",
- "NXcomponent_em",
- "NXcontainer",
- "NXcoordinate_system",
- "NXcoordinate_system_set",
- "NXcorrector_cs",
- "NXcrystal_structure",
- "NXcs_computer",
- "NXcs_cpu",
- "NXcs_cpu_obj",
- "NXcs_cpu_sys",
- "NXcs_filter_boolean_mask",
- "NXcs_gpu",
- "NXcs_gpu_obj",
- "NXcs_gpu_sys",
- "NXcs_io_obj",
- "NXcs_io_sys",
- "NXcs_mm_obj",
- "NXcs_mm_sys",
- "NXcs_prng",
- "NXcs_profiling",
- "NXcs_profiling_event",
- "NXcsg",
- "NXcxi_ptycho",
- "NXdac",
- "NXdata_mpes",
- "NXdata_mpes_detector",
- "NXdeflector",
- "NXdelocalization",
- "NXdispersion",
- "NXdispersion_function",
- "NXdispersion_repeated_parameter",
- "NXdispersion_single_parameter",
- "NXdispersion_table",
- "NXdispersive_material",
- "NXdistortion",
- "NXebeam_column",
- "NXelectron_level",
- "NXelectronanalyser",
- "NXelectrostatic_kicker",
- "NXellipsometry",
- "NXem",
- "NXem_adf",
- "NXem_base",
- "NXem_conventions",
- "NXem_conventions_ebsd",
- "NXem_correlation",
- "NXem_ebsd",
- "NXem_eds",
- "NXem_eels",
- "NXem_img",
- "NXem_method",
- "NXem_msr",
- "NXem_sim",
- "NXenergydispersion",
- "NXevent_data_em",
- "NXevent_data_em_set",
- "NXfabrication",
- "NXfiber",
- "NXgraph_edge_set",
- "NXgraph_node_set",
- "NXgraph_root",
- "NXibeam_column",
- "NXidentifier",
- "NXimage_c_set",
- "NXimage_r_set",
- "NXimage_r_set_diff",
- "NXimage_set",
- "NXinteraction_vol_em",
- "NXion",
- "NXisocontour",
- "NXiv_bias",
- "NXiv_temp",
- "NXlab_electro_chemo_mechanical_preparation",
- "NXlab_sample_mounting",
- "NXlens_em",
- "NXlens_opt",
- "NXlockin",
- "NXmagnetic_kicker",
- "NXmanipulator",
- "NXmatch_filter",
- "NXmpes",
- "NXms",
- "NXms_feature_set",
- "NXms_ipf",
- "NXms_ipf_set",
- "NXms_mtex_config",
- "NXms_odf",
- "NXms_odf_set",
- "NXms_pf",
- "NXms_pf_set",
- "NXms_recon",
- "NXms_score_config",
- "NXms_score_results",
- "NXms_snapshot",
- "NXms_snapshot_set",
- "NXopt",
- "NXoptical_system_em",
- "NXpeak",
- "NXphysical_process",
- "NXpid",
- "NXpolarizer_opt",
- "NXpositioner_sts",
- "NXprocess_mpes",
- "NXprogram",
- "NXpulser_apm",
- "NXpump",
- "NXquadric",
- "NXquadrupole_magnet",
- "NXreflectron",
- "NXregion",
- "NXregistration",
- "NXresolution",
- "NXroi",
- "NXrotation_set",
- "NXsample_component_set",
- "NXsample_history",
- "NXscanbox_em",
- "NXsensor_scan",
- "NXsensor_sts",
- "NXseparator",
- "NXserialized",
- "NXsimilarity_grouping",
- "NXsingle_crystal",
- "NXslip_system_set",
- "NXsnsevent",
- "NXsnshisto",
- "NXsolenoid_magnet",
- "NXsolid_geometry",
- "NXspatial_filter",
- "NXspectrum_set",
- "NXspin_rotator",
- "NXspindispersion",
- "NXstage_lab",
- "NXsts",
- "NXsubsampling_filter",
- "NXsubstance",
- "NXtransmission",
- "NXunit_cell",
- "NXwaveplate",
"NXxpcs",
- "NXxrd",
"NXxrd_pan",
- "NXroot"
+ "NXxrot"
]
}
},
@@ -102868,47 +102701,6 @@ window.nomadArtifacts = {
]
}
},
- {
- "authors": [
- "Sbail\u00f2, Luigi",
- "Scheffler, Matthias",
- "Ghiringhelli, Luca M."
- ],
- "email": "ghiringhelli@fhi-berlin.mpg.de",
- "title": "Querying the NOMAD Archive and performing artificial-intelligence modeling",
- "description": "In this tutorial, we demonstrate how to query the NOMAD Archive from the NOMAD Analytics toolkit. We then show examples of machine learning analysis performed on the retrieved data set.",
- "notebook_name": "query_nomad_archive.ipynb",
- "url": "https://gitlab.mpcdf.mpg.de/nomad-lab/analytics-query-nomad-archive",
- "link": "https://analytics-toolkit.nomad-coe.eu/hub/user-redirect/notebooks/tutorials/query_nomad_archive.ipynb",
- "link_public": "https://analytics-toolkit.nomad-coe.eu/public/user-redirect/notebooks/tutorials/query_nomad_archive.ipynb",
- "updated": "2022-04-06",
- "flags": {
- "featured": true,
- "top_of_list": false
- },
- "labels": {
- "application_section": [
- "Analysing the content of the Archive"
- ],
- "application_system": [
- "Ternaries"
- ],
- "category": [
- "query_tutorial"
- ],
- "ai_methods": [
- "Unsupervised learning",
- "Supervised learning",
- "Regression",
- "Clustering",
- "Dimension reduction",
- "Random forest"
- ],
- "platform": [
- "jupyter"
- ]
- }
- },
{
"authors": [
"Langer, Marcel F."
diff --git a/nomad/datamodel/metainfo/eln/nexus_data_converter.py b/nomad/datamodel/metainfo/eln/nexus_data_converter.py
index c3207ec08beca2549c830bc55f0c1a5a71b3cce6..0448da52e1a75f166e7379bb1cf12fb635f4bace 100644
--- a/nomad/datamodel/metainfo/eln/nexus_data_converter.py
+++ b/nomad/datamodel/metainfo/eln/nexus_data_converter.py
@@ -10,7 +10,9 @@ try:
from pynxtools.dataconverter import convert as pynxtools_converter
from pynxtools.dataconverter import writer as pynxtools_writer
from pynxtools.dataconverter.template import Template
- from pynxtools.nexus.nexus import get_app_defs_names # pylint: disable=import-error
+ from pynxtools.definitions.dev_tools.utils.nxdl_utils import (
+ get_app_defs_names, # pylint: disable=import-error
+ )
except ImportError:
NEXUS_AVAILABLE = False
pass
@@ -172,7 +174,7 @@ class NexusDataConverter(EntryData):
)
nxdl = Quantity(
- type=MEnum(get_app_defs_names() if NEXUS_AVAILABLE else []),
+ type=MEnum(sorted(list(set(get_app_defs_names()))) if NEXUS_AVAILABLE else []),
description='The nxdl needed for running the Nexus converter.',
a_eln=dict(component='AutocompleteEditQuantity'),
)
diff --git a/nomad/metainfo/elasticsearch_extension.py b/nomad/metainfo/elasticsearch_extension.py
index 4fe00726f562b144a9500e294c1c082d59009517..6deac6fcb3570994dac602544c22d006eab23d63 100644
--- a/nomad/metainfo/elasticsearch_extension.py
+++ b/nomad/metainfo/elasticsearch_extension.py
@@ -157,23 +157,25 @@ sub-sections as if they were direct sub-sections.
"""
import math
+import re
+from collections import defaultdict
from typing import (
- Union,
+ TYPE_CHECKING,
Any,
+ Callable,
+ DefaultDict,
Dict,
- cast,
- Set,
List,
- Callable,
- Tuple,
Optional,
- DefaultDict,
+ Set,
+ Tuple,
+ Union,
+ cast,
)
-from collections import defaultdict
+
import numpy as np
-from pint import Quantity as PintQuantity
-import re
from elasticsearch_dsl import Q
+from pint import Quantity as PintQuantity
from nomad import utils
from nomad.config import config
@@ -181,24 +183,22 @@ from nomad.config.models.plugins import Schema, Parser, SchemaPackageEntryPoint
from nomad.metainfo.util import MTypes
from .metainfo import (
- MSectionBound,
- Section,
- Quantity,
- MSection,
- MEnum,
Datetime,
- Reference,
- DefinitionAnnotation,
Definition,
+ DefinitionAnnotation,
+ MEnum,
+ MSection,
+ MSectionBound,
+ Package,
+ Quantity,
QuantityReference,
+ Reference,
+ Section,
Unit,
- Package,
)
-from typing import TYPE_CHECKING
-
if TYPE_CHECKING:
- from nomad.datamodel.datamodel import SearchableQuantity, EntryArchive
+ from nomad.datamodel.datamodel import EntryArchive, SearchableQuantity
schema_separator = '#'
dtype_separator = '#'
@@ -1603,17 +1603,25 @@ def create_searchable_quantity(
value_field_name = get_searchable_quantity_value_field(annotation)
if value_field_name is None:
return None
+
if mapping == 'text':
value = str(value)
elif mapping == 'date':
value = Datetime.serialize(section, quantity_def, value)
elif mapping == 'long':
- value = int(value)
+ if isinstance(value, PintQuantity):
+ value = int(value.m)
+ elif isinstance(value, dict):
+ return None
+ else:
+ value = int(value)
elif mapping == 'boolean':
value = bool(value)
elif mapping == 'double':
if isinstance(value, PintQuantity):
value = float(value.m)
+ elif isinstance(value, dict):
+ return None
else:
value = float(value)
if math.isnan(value):
diff --git a/nomad/metainfo/metainfo.py b/nomad/metainfo/metainfo.py
index ae8bcd2bd1ed92652ff045fa115548de0997ea01..4fb7155e2981421f63b2efebe8bb5b4d9b759cb2 100644
--- a/nomad/metainfo/metainfo.py
+++ b/nomad/metainfo/metainfo.py
@@ -18,7 +18,6 @@
from __future__ import annotations
import base64
-from copy import deepcopy
import importlib
import inspect
import itertools
@@ -26,11 +25,13 @@ import json
import re
import sys
from collections.abc import Iterable as IterableABC
+from copy import deepcopy
from functools import reduce
from typing import (
Any,
- Callable as TypingCallable,
+ ClassVar,
Dict,
+ Generator,
Iterable,
List,
Optional,
@@ -39,9 +40,10 @@ from typing import (
Type,
TypeVar,
Union,
- Generator,
cast,
- ClassVar,
+)
+from typing import (
+ Callable as TypingCallable,
)
import docstring_parser
@@ -49,7 +51,7 @@ import jmespath
import numpy as np
import pandas as pd
import pint
-from pydantic import parse_obj_as, ValidationError, BaseModel, Field
+from pydantic import BaseModel, Field, ValidationError, parse_obj_as
from nomad.config import config
from nomad.metainfo.util import (
@@ -1946,6 +1948,12 @@ class MSection(
if dimension == 0:
attr_value = self.__set_normalize(tgt_attr, attr_value)
elif dimension == 1:
+ if isinstance(tgt_attr.shape[0], str) and (
+ not isinstance(attr_value, IterableABC)
+ or isinstance(attr_value, str)
+ ):
+ if tgt_attr.shape[0].startswith('0') or '*' in tgt_attr.shape[0]:
+ attr_value = [attr_value]
if isinstance(attr_value, str) or not isinstance(
attr_value, IterableABC
):
diff --git a/nomad/metainfo/nexus.py b/nomad/metainfo/nexus.py
index 80b9f0366470e0e702669096cae6d59da2eb6471..e9192c837ecbc7fb830c7d6be76e0cb9c817a4bd 100644
--- a/nomad/metainfo/nexus.py
+++ b/nomad/metainfo/nexus.py
@@ -23,7 +23,7 @@ import sys
# noinspection PyPep8Naming
import xml.etree.ElementTree as ET
-from typing import Dict, List, Optional, Set, Union
+from typing import Dict, List, Optional, Union
import numpy as np
@@ -41,7 +41,6 @@ from nomad.metainfo import (
Definition,
MEnum,
Package,
- Property,
Quantity,
Section,
SubSection,
@@ -81,6 +80,18 @@ __NX_TYPES = { # Primitive Types, 'ISO8601' is the only type not defined here
'NX_BINARY': Bytes,
'NX_DATE_TIME': Datetime,
}
+__NX_ATTR_TYPES = {
+ 'NX_COMPLEX': float,
+ 'NX_FLOAT': float,
+ 'NX_CHAR': str,
+ 'NX_BOOLEAN': bool,
+ 'NX_INT': int,
+ 'NX_UINT': int,
+ 'NX_NUMBER': float,
+ 'NX_POSINT': int,
+ 'NX_BINARY': Bytes,
+ 'NX_DATE_TIME': Datetime,
+}
class NXUnitSet:
@@ -225,7 +236,7 @@ def __to_section(name: str, **kwargs) -> Section:
"""
Returns the 'existing' metainfo section for a given top-level nexus base-class name.
- This function ensures that sections for these base-classes are only created one.
+ This function ensures that sections for these base-classes are only created once.
This allows to access the metainfo section even before it is generated from the base
class nexus definition.
"""
@@ -314,7 +325,7 @@ def __create_attributes(xml_node: ET.Element, definition: Union[Section, Quantit
nx_type = nx_enum
nx_shape: List[str] = []
else:
- nx_type = __NX_TYPES[attribute.get('type', 'NX_CHAR')] # type: ignore
+ nx_type = __NX_ATTR_TYPES[attribute.get('type', 'NX_CHAR')] # type: ignore
has_bound = False
has_bound |= 'minOccurs' in attribute.attrib
has_bound |= 'maxOccurs' in attribute.attrib
@@ -325,7 +336,8 @@ def __create_attributes(xml_node: ET.Element, definition: Union[Section, Quantit
nx_max_occurs = '*'
nx_shape = [f'{nx_min_occurs}..{nx_max_occurs}']
else:
- nx_shape = []
+ # Default is to allow any shape
+ nx_shape = ['0..*']
m_attribute = Attribute(
name=name, variable=__if_template(name), shape=nx_shape, type=nx_type
@@ -340,7 +352,7 @@ def __create_attributes(xml_node: ET.Element, definition: Union[Section, Quantit
def __add_additional_attributes(definition: Definition):
- if 'm_nx_data_path' not in definition.all_attributes:
+ if 'm_nx_data_path' not in definition.attributes:
definition.attributes.append(
Attribute(
name='m_nx_data_path',
@@ -352,7 +364,7 @@ def __add_additional_attributes(definition: Definition):
)
)
- if 'm_nx_data_file' not in definition.all_attributes:
+ if 'm_nx_data_file' not in definition.attributes:
definition.attributes.append(
Attribute(
name='m_nx_data_file',
@@ -639,7 +651,7 @@ def __add_section_from_nxdl(xml_node: ET.Element) -> Optional[Section]:
__logger.error(
'Fail to generate metainfo.',
target_name=xml_node.attrib['name'],
- exe_info=str(err),
+ exc_info=str(err),
)
return None
@@ -732,15 +744,20 @@ def init_nexus_metainfo():
nexus_metainfo_package.init_metainfo()
# Add additional NOMAD specific attributes (nx_data_path, nx_data_file, nx_mean, ...)
- sections: Set[Section] = set()
- quantities: Set[Quantity] = set()
- for section in __section_definitions.values():
- sections.add(section.inherited_sections[0])
- quantities.update(section.all_quantities.values())
- for definition in sections:
- __add_additional_attributes(definition)
- for definition in quantities:
- __add_additional_attributes(definition)
+ # This needs to be done in the right order, base sections first.
+ visited_definitions = set()
+ sections = list()
+ for definition, _, _, _ in nexus_metainfo_package.m_traverse():
+ if isinstance(definition, Section):
+ for section in reversed([definition] + definition.all_base_sections):
+ if section not in visited_definitions:
+ visited_definitions.add(section)
+ sections.append(section)
+
+ for section in sections:
+ __add_additional_attributes(section)
+ for quantity in section.quantities:
+ __add_additional_attributes(quantity)
# We skip the Python code generation for now and offer Python classes as variables
# TO DO not necessary right now, could also be done case-by-case by the nexus parser
diff --git a/nomad/normalizing/metainfo.py b/nomad/normalizing/metainfo.py
index 81fdf44b1fbbd54b09b4c86f35d914cae37b0758..4ab8107ccf11d964e135f81cf3f5e2ee347d4dd7 100644
--- a/nomad/normalizing/metainfo.py
+++ b/nomad/normalizing/metainfo.py
@@ -33,7 +33,7 @@ class MetainfoNormalizer(Normalizer):
except Exception:
pass
- if normalize:
+ if normalize and callable(normalize):
try:
normalize(archive, logger)
except Exception as e:
diff --git a/nomad/parsing/nexus/nexus.py b/nomad/parsing/nexus/nexus.py
index 759c263999bc16403c076ca844b291031bc299c4..81f116d89fba65e42f4b514df461f188e7921e99 100644
--- a/nomad/parsing/nexus/nexus.py
+++ b/nomad/parsing/nexus/nexus.py
@@ -16,9 +16,9 @@
# limitations under the License.
#
-import xml.etree.ElementTree as ET
from typing import Optional, Set
+import lxml.etree as ET
import numpy as np
try:
@@ -138,7 +138,7 @@ class NexusParser(Parser):
self._sample_class_refs[key] = []
def _collect_class(self, current: MSection):
- class_name = current.m_def.name
+ class_name = current.m_def.more.get('nx_type')
if (
class_name in self._sample_class_refs
and current not in self._sample_class_refs[class_name]
@@ -151,9 +151,6 @@ class NexusParser(Parser):
"""
Populate attributes and fields
"""
- if not self.nxs_fname and hdf_node:
- self.nxs_fname = hdf_node.file.filename.split('/')[-1]
-
if depth < len(nx_path):
# it is an attribute of either field or group
nx_attr = nx_path[depth]
@@ -176,7 +173,7 @@ class NexusParser(Parser):
attr_value = hdf_node.attrs[attr_name]
if not isinstance(attr_value, str):
if isinstance(attr_value, np.ndarray):
- attr_value = [value for value in attr_value]
+ attr_value = attr_value.tolist()
if len(attr_value) == 1:
attr_value = attr_value[0]
@@ -188,17 +185,29 @@ class NexusParser(Parser):
current.m_set_section_attribute(attr_name, attr_value)
else:
parent_html_name = nx_path[-2].get('name')
+
parent_instance_name = hdf_node.name.split('/')[-1] + '__field'
parent_field_name = parent_html_name + '__field'
- metainfo_def = resolve_variadic_name(
- current.m_def.all_properties, parent_field_name
- )
+
+ metainfo_def = None
+ try:
+ metainfo_def = resolve_variadic_name(
+ current.m_def.all_properties, parent_field_name
+ )
+ except ValueError as exc:
+ self._logger.warning(
+ f'{current.m_def} has no suitable property for {parent_field_name}',
+ target_name=attr_name,
+ exc_info=exc,
+ )
+
if parent_field_name in current.__dict__:
quantity = current.__dict__[parent_field_name]
if isinstance(quantity, dict):
quantity = quantity[parent_instance_name]
else:
quantity = None
+
current.m_set_quantity_attribute(
metainfo_def, attr_name, attr_value, quantity=quantity
)
@@ -206,7 +215,7 @@ class NexusParser(Parser):
self._logger.warning(
'Error while setting attribute.',
target_name=attr_name,
- exe_info=str(e),
+ exc_info=e,
)
else:
# it is a field
@@ -233,12 +242,6 @@ class NexusParser(Parser):
]
)
field = field_stats[0]
- if np.isnan(field):
- self._logger.warning(
- 'NaN value is not set for field ',
- target_name=field_name + '[' + data_instance_name + ']',
- )
- return
# check if unit is given
unit = hdf_node.attrs.get('units', None)
@@ -287,7 +290,7 @@ class NexusParser(Parser):
self._logger.warning(
'Error while setting field.',
target_name=field_name,
- exe_info=str(e),
+ exc_info=e,
)
def __nexus_populate(self, params: dict, attr=None): # pylint: disable=W0613
@@ -303,9 +306,6 @@ class NexusParser(Parser):
hdf_path: str = hdf_info['hdf_path']
hdf_node = hdf_info['hdf_node']
- if not self.nxs_fname and hdf_node:
- self.nxs_fname = hdf_node.file.filename.split('/')[-1]
-
if nx_path is None:
return
@@ -317,12 +317,12 @@ class NexusParser(Parser):
current = _to_section(name, nx_def, nx_node, current)
self._collect_class(current)
depth += 1
- current_hdf_path = current_hdf_path + (
- '/' + name if depth < len(nx_path) else ''
- )
- current.m_set_section_attribute('m_nx_data_path', current_hdf_path)
-
- current.m_set_section_attribute('m_nx_data_file', self.nxs_fname)
+ if depth < len(nx_path):
+ current_hdf_path = current_hdf_path + ('/' + name)
+ if nx_node is not None and isinstance(nx_node, ET._Element):
+ if nx_node.tag.endswith('group'):
+ current.m_set_section_attribute('m_nx_data_path', current_hdf_path)
+ current.m_set_section_attribute('m_nx_data_file', self.nxs_fname)
self._populate_data(depth, nx_path, nx_def, hdf_node, current)
def get_sub_element_names(self, elem: MSection):
@@ -362,15 +362,18 @@ class NexusParser(Parser):
for sample in self._sample_class_refs['NXsample']:
if sample.get('atom_types__field') is not None:
- if isinstance(sample.atom_types__field, list):
- atomlist = sample.atom_types__field
+ atom_types = sample.atom_types__field['atom_types__field'].value
+ if isinstance(atom_types, list):
+ atomlist = atom_types
else:
- atomlist = sample.atom_types__field.replace(' ', '').split(',')
+ atomlist = atom_types.replace(' ', '').split(',')
# Caution: The element list will be overwritten
# in case a single chemical formula is found
material.elements = list(set(material.elements) | set(atomlist))
if sample.get('chemical_formula__field') is not None:
- chemical_formulas.add(sample.chemical_formula__field)
+ chemical_formulas.add(
+ sample.chemical_formula__field['chemical_formula__field'].value
+ )
for class_ref in (
'NXsample_component',
@@ -378,11 +381,17 @@ class NexusParser(Parser):
):
for section in self._sample_class_refs[class_ref]:
if section.get('chemical_formula__field') is not None:
- chemical_formulas.add(section.chemical_formula__field)
+ chemical_formulas.add(
+ section.chemical_formula__field['chemical_formula__field'].value
+ )
for substance in self._sample_class_refs['NXsubstance']:
if substance.get('molecular_formula_hill__field') is not None:
- chemical_formulas.add(substance.molecular_formula_hill__field)
+ chemical_formulas.add(
+ substance.molecular_formula_hill__field[
+ 'molecular_formula_hill__field'
+ ].value
+ )
return chemical_formulas
@@ -427,6 +436,7 @@ class NexusParser(Parser):
self._clear_class_refs()
if mainfile.endswith('nxs'):
+ *_, self.nxs_fname = mainfile.rsplit('/', 1)
nexus_helper = read_nexus.HandleNexus(logger, mainfile)
nexus_helper.process_nexus_master_file(self.__nexus_populate)
else:
diff --git a/pyproject.toml b/pyproject.toml
index 23571ec71b6cf7d9681bdb857c094b1e41c4342d..ce34cebb61826b94e3dbb09f6ad443f8a412dac3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -66,10 +66,10 @@ parsing = [
'h5py==3.11.0',
'netCDF4==1.6.5',
'pybis@git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370',
- 'pynxtools[convert]==0.1.1',
+ 'pynxtools[convert]==0.3.1',
'pyzeo==0.1.5',
'quippy-ase==0.9.14',
- 'rdkit',
+ 'rdkit==2023.9.5',
]
infrastructure = [
'asgiref~=3.5',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 530b0633fea24cb2b442d543019663780ee6d028..ed29159b333811a78cd55bb86c819742d2f9b103 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,148 +1,181 @@
-# This file was autogenerated by uv via the following command:
-# uv pip compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
+#
+# 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' pyproject.toml requirements.txt
+#
aiosmtpd==1.4.6 # via nomad-lab (pyproject.toml)
-alabaster==0.7.16 # via sphinx, -r requirements.txt
-alembic==1.13.1 # via jupyterhub, -r requirements.txt
-amqp==5.2.0 # via kombu, -r requirements.txt
+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 httpx, starlette, watchfiles, -r requirements.txt
-arrow==1.3.0 # via isoduration, -r requirements.txt
-asciitree==0.3.3 # via zarr, -r requirements.txt
-ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, pynxtools, quippy-ase, -r requirements.txt, nomad-lab (pyproject.toml)
+anyio==4.3.0 # via -r requirements.txt, httpx, jupyter-server, starlette, watchfiles
+anytree==2.12.1 # via -r requirements.txt, pynxtools
+appnope==0.1.4 # via -r requirements.txt, ipykernel
+argon2-cffi==23.1.0 # via -r requirements.txt, jupyter-server
+argon2-cffi-bindings==21.2.0 # via -r requirements.txt, argon2-cffi
+arrow==1.3.0 # via -r requirements.txt, isoduration
+asciitree==0.3.3 # via -r requirements.txt, zarr
+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==0.9.32 # via lmfit, -r requirements.txt
+asteval==0.9.33 # via -r requirements.txt, lmfit
astroid==3.2.2 # via nomad-lab (pyproject.toml)
-asttokens==2.4.1 # via devtools, stack-data, -r requirements.txt
-async-generator==1.10 # via jupyterhub, -r requirements.txt
+asttokens==2.4.1 # via -r requirements.txt, devtools, stack-data
+async-generator==1.10 # via -r requirements.txt, jupyterhub
+async-lru==2.0.4 # via -r requirements.txt, jupyterlab
atpublic==4.1.0 # via aiosmtpd
-attrs==23.2.0 # via aiosmtpd, jsonschema, pytest, -r requirements.txt
-babel==2.15.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx, -r requirements.txt
+attrs==23.2.0 # via -r requirements.txt, aiosmtpd, jsonschema, pytest
+babel==2.15.0 # via -r requirements.txt, jupyterlab-server, mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx
backports-tarfile==1.1.1 # 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)
-beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
-billiard==4.2.0 # via celery, -r requirements.txt
-biopython==1.83 # via mdanalysis, -r requirements.txt
+beautifulsoup4==4.12.3 # via -r requirements.txt, nbconvert, 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==1.8.2 # via flask, -r requirements.txt
-blosc2==2.5.1 # via tables, -r requirements.txt
+bleach==6.1.0 # via -r requirements.txt, nbconvert
+blinker==1.8.2 # via -r requirements.txt, flask
+blosc2==2.5.1 # via -r requirements.txt, tables
build==1.2.1 # via nomad-lab (pyproject.toml)
cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-certifi==2024.2.2 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt
-certipy==0.1.3 # via jupyterhub, -r requirements.txt
-cffi==1.16.0 # via cryptography, -r requirements.txt
-cftime==1.6.3 # via netcdf4, -r requirements.txt
-charset-normalizer==3.3.2 # via requests, -r requirements.txt
-click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, pynxtools, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
-click-didyoumean==0.3.1 # via celery, -r requirements.txt
-click-plugins==1.1.1 # via celery, -r requirements.txt
-click-repl==0.3.0 # via celery, -r requirements.txt
-cloudpickle==3.0.0 # via dask, hyperspy, -r requirements.txt
+certifi==2024.2.2 # via -r requirements.txt, elasticsearch, httpcore, httpx, netcdf4, requests
+certipy==0.1.3 # via -r requirements.txt, jupyterhub
+cffi==1.16.0 # via -r requirements.txt, argon2-cffi-bindings, 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-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pynxtools, uvicorn
+click-default-group==1.2.4 # via -r requirements.txt, pynxtools
+click-didyoumean==0.3.1 # via -r requirements.txt, celery
+click-plugins==1.1.1 # via -r requirements.txt, celery
+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
-commonmark==0.9.1 # via recommonmark, -r requirements.txt
-contourpy==1.2.1 # via matplotlib, -r requirements.txt
+comm==0.2.2 # via -r requirements.txt, ipykernel, ipywidgets
+commonmark==0.9.1 # via -r requirements.txt, recommonmark
+contourpy==1.2.1 # via -r requirements.txt, matplotlib
coverage==7.5.1 # via pytest-cov
-cryptography==42.0.7 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage, -r requirements.txt
-cycler==0.12.1 # via matplotlib, -r requirements.txt
-dask==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio, -r requirements.txt
-decorator==5.1.1 # via ipython, validators, -r requirements.txt
-deprecation==2.1.0 # via python-keycloak, -r requirements.txt
+cryptography==42.0.7 # via -r requirements.txt, jwcrypto, pyjwt, pyopenssl, rfc3161ng
+cycler==0.12.1 # via -r requirements.txt, matplotlib
+dask[array]==2024.5.1 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem, rosettasciio
+debugpy==1.8.1 # via -r requirements.txt, ipykernel
+decorator==5.1.1 # via -r requirements.txt, ipyparallel, ipython, validators
+defusedxml==0.7.1 # via -r requirements.txt, nbconvert
+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 diffsims, kikuchipy, orix, -r requirements.txt
-diffsims==0.5.2 # via kikuchipy, pyxem, -r requirements.txt
-dill==0.3.8 # via lmfit, -r requirements.txt
-dnspython==2.6.1 # via email-validator, pymongo, -r requirements.txt
-docker==7.0.0 # via dockerspawner, -r requirements.txt
+diffpy-structure==3.1.0 # via -r requirements.txt, diffsims, kikuchipy, orix
+diffsims==0.5.2 # via -r requirements.txt, kikuchipy, pyxem
+dill==0.3.8 # via -r requirements.txt, hyperspy, lmfit
+dnspython==2.6.1 # via -r requirements.txt, email-validator, pymongo
+docker==7.1.0 # via -r requirements.txt, dockerspawner
dockerspawner==13.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
docstring-parser==0.16 # via -r requirements.txt, nomad-lab (pyproject.toml)
-docutils==0.21.2 # via m2r, readme-renderer, recommonmark, sphinx, -r requirements.txt
-elasticsearch==7.17.1 # via elasticsearch-dsl, -r requirements.txt, nomad-lab (pyproject.toml)
+docutils==0.21.2 # 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==1.3.1 # via optimade, -r requirements.txt
-escapism==1.0.1 # via dockerspawner, -r requirements.txt
+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 openpyxl, -r requirements.txt
-exceptiongroup==1.2.1 # via anyio, ipython, -r requirements.txt
+et-xmlfile==1.1.0 # via -r requirements.txt, openpyxl
+exceptiongroup==1.2.1 # via -r requirements.txt, anyio, ipython
execnet==2.1.1 # via pytest-xdist
-executing==2.0.1 # via devtools, stack-data, -r requirements.txt
-f90wrap==0.2.14 # via quippy-ase, -r requirements.txt
-fabio==2024.4.0 # via pyfai, silx, -r requirements.txt
-fastapi==0.99.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-fasteners==0.19 # via mdanalysis, zarr, -r requirements.txt
+executing==2.0.1 # via -r requirements.txt, devtools, stack-data
+f90wrap==0.2.14 # via -r requirements.txt, quippy-ase
+fabio==2024.4.0 # 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
+fastjsonschema==2.19.1 # via -r requirements.txt, nbformat
filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-findiff==0.10.0 # via pynxtools-stm, -r requirements.txt
-flask==3.0.3 # via asr, -r requirements.txt
-flatdict==4.0.1 # via pynxtools, -r requirements.txt
-fonttools==4.51.0 # via matplotlib, -r requirements.txt
-fqdn==1.5.1 # via jsonschema, -r requirements.txt
-fsspec==2024.5.0 # via dask, -r requirements.txt
-future==1.0.0 # via uncertainties, -r requirements.txt
+findiff==0.10.0 # via -r requirements.txt, pynxtools-stm
+flask==3.0.3 # via -r requirements.txt, asr
+flatdict==3.4.0 # via -r requirements.txt, ifes-apt-tc-data-modeling, pynxtools-em
+fonttools==4.51.0 # via -r requirements.txt, matplotlib
+fqdn==1.5.1 # via -r requirements.txt, jsonschema
+fsspec==2024.5.0 # via -r requirements.txt, dask, hyperspy
+future==1.0.0 # via -r requirements.txt, uncertainties
ghp-import==2.1.0 # via mkdocs
-gitdb==4.0.11 # via gitpython, -r requirements.txt
-gitpython==3.1.43 # via mkdocs-git-revision-date-localized-plugin, pynxtools, -r requirements.txt, nomad-lab (pyproject.toml)
-greenlet==3.0.3 # via sqlalchemy, -r requirements.txt
-griddataformats==1.0.2 # via mdanalysis, -r requirements.txt
-gsd==3.2.1 # via mdanalysis, -r requirements.txt
+gitdb==4.0.11 # via -r requirements.txt, gitpython
+gitpython==3.1.43 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nomad-lab (pyproject.toml)
+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 httpcore, uvicorn, -r requirements.txt
-h5grove==1.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-h5py==3.11.0 # via fabio, h5grove, hdf5plugin, ifes-apt-tc-data-modeling, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, silx, -r requirements.txt, nomad-lab (pyproject.toml)
-hdf5plugin==4.4.0 # via fabio, -r requirements.txt
+h11==0.14.0 # via -r requirements.txt, httpcore, uvicorn
+h5grove[fastapi]==1.3.0 # via -r requirements.txt, jupyterlab-h5web, nomad-lab (pyproject.toml)
+h5py==3.11.0 # via -r requirements.txt, fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, 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==1.0.5 # via httpx, -r requirements.txt
-httptools==0.6.1 # via uvicorn, -r requirements.txt
-httpx==0.27.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-hyperspy==2.1.0 # via kikuchipy, pynxtools, pyxem, -r requirements.txt
-idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt
-ifes-apt-tc-data-modeling==0.1 # via pynxtools, -r requirements.txt
-imageio==2.34.1 # via kikuchipy, nionswift, nionswift-io, nionui, scikit-image, -r requirements.txt
-imagesize==1.4.1 # via sphinx, -r requirements.txt
-importlib-metadata==7.1.0 # via build, dask, flask, hyperspy, jupyterhub, keyring, markdown, mkdocs, mkdocs-get-deps, pynxtools, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml)
-importlib-resources==6.4.0 # via matplotlib, spglib, -r requirements.txt
+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, jupyterlab, nomad-lab (pyproject.toml)
+hyperspy==1.7.6 # via -r requirements.txt, kikuchipy, pyxem
+idna==3.7 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests
+ifes-apt-tc-data-modeling==0.2.2 # via -r requirements.txt, pynxtools-apm
+igor2==0.5.2 # via -r requirements.txt, pynxtools-xps
+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==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, keyring, markdown, mkdocs, mkdocs-get-deps, nbconvert, nomad-lab (pyproject.toml), pynxtools, sphinx, twine
+importlib-resources==6.4.0 # via -r requirements.txt, matplotlib, spglib
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-ipython==8.18.1 # via pynxtools-stm, -r requirements.txt
-isodate==0.6.1 # via rdflib, -r requirements.txt
-isoduration==20.11.0 # via jsonschema, -r requirements.txt
-itsdangerous==2.2.0 # via flask, -r requirements.txt, nomad-lab (pyproject.toml)
+ipykernel==6.29.4 # via -r requirements.txt, ipyparallel, jupyter, jupyter-console, jupyterlab, qtconsole
+ipyparallel==8.8.0 # via -r requirements.txt, hyperspy
+ipython==8.18.1 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, ipywidgets, jupyter-console, pynxtools-xrd
+ipywidgets==8.1.2 # via -r requirements.txt, jupyter
+isodate==0.6.1 # via -r requirements.txt, rdflib
+isoduration==20.11.0 # via -r requirements.txt, jsonschema
+itsdangerous==2.2.0 # via -r requirements.txt, flask, nomad-lab (pyproject.toml)
jaraco-classes==3.4.0 # via keyring
jaraco-context==5.3.0 # via keyring
jaraco-functools==4.0.1 # via keyring
-jedi==0.19.1 # via ipython, -r requirements.txt
-jeepney==0.8.0 # via keyring, secretstorage
-jinja2==3.1.4 # via flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx, -r requirements.txt
+jedi==0.19.1 # via -r requirements.txt, ipython
+jinja2==3.1.4 # via -r requirements.txt, flask, hyperspy, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, mkdocs, mkdocs-macros-plugin, mkdocs-material, nbconvert, sphinx
jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn, -r requirements.txt
-jsonpointer==2.4 # via jsonschema, -r requirements.txt
-jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml)
-jupyter-telemetry==0.1.0 # via jupyterhub, -r requirements.txt
-jupyterhub==4.0.2 # via dockerspawner, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml)
-jwcrypto==1.5.6 # via python-keycloak, -r requirements.txt
+joblib==1.4.2 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn
+json5==0.9.25 # via -r requirements.txt, jupyterlab-server
+jsonpointer==2.4 # via -r requirements.txt, jsonschema
+jsonschema[format,format-nongpl]==4.17.3 # via -r requirements.txt, jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, nomad-lab (pyproject.toml), oauthenticator
+jupyter==1.0.0 # via -r requirements.txt, ifes-apt-tc-data-modeling
+jupyter-client==8.6.2 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-console, jupyter-server, nbclient, qtconsole
+jupyter-console==6.6.3 # via -r requirements.txt, jupyter
+jupyter-core==5.7.2 # via -r requirements.txt, ipykernel, jupyter-client, jupyter-console, jupyter-server, jupyterlab, nbclient, nbconvert, nbformat, qtconsole
+jupyter-events==0.5.0 # via -r requirements.txt, jupyter-server
+jupyter-lsp==2.2.5 # via -r requirements.txt, jupyterlab
+jupyter-server==2.5.0 # via -r requirements.txt, jupyter-lsp, jupyterlab, jupyterlab-h5web, jupyterlab-server, notebook, notebook-shim
+jupyter-server-terminals==0.5.3 # via -r requirements.txt, jupyter-server
+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==4.1.6 # via -r requirements.txt, ifes-apt-tc-data-modeling, notebook
+jupyterlab-h5web==11.1.0 # via -r requirements.txt, ifes-apt-tc-data-modeling
+jupyterlab-pygments==0.3.0 # via -r requirements.txt, nbconvert
+jupyterlab-server==2.24.0 # via -r requirements.txt, jupyterlab, notebook
+jupyterlab-widgets==3.0.10 # via -r requirements.txt, ipywidgets
+jwcrypto==1.5.6 # via -r requirements.txt, python-keycloak
keyring==25.2.1 # via twine
-kikuchipy==0.8.7 # via pynxtools, -r requirements.txt
-kiwisolver==1.4.5 # via matplotlib, -r requirements.txt
-kombu==5.3.7 # via celery, -r requirements.txt
-lark==1.1.9 # via optimade, -r requirements.txt
-latexcodec==3.0.0 # via pybtex, -r requirements.txt
-llvmlite==0.42.0 # via numba, -r requirements.txt
-lmfit==1.3.1 # via pyxem, -r requirements.txt
-locket==1.0.0 # via partd, -r requirements.txt
-lxml==5.2.2 # via fabio, lxml-html-clean, -r requirements.txt, nomad-lab (pyproject.toml)
+kikuchipy==0.9.0 # via -r requirements.txt, pynxtools-em
+kiwisolver==1.4.5 # via -r requirements.txt, matplotlib
+kombu==5.3.7 # 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==1.3.1 # via -r requirements.txt, pyxem
+locket==1.0.0 # via -r requirements.txt, partd
+lxml==5.2.2 # via -r requirements.txt, fabio, lxml-html-clean, nomad-lab (pyproject.toml), pynxtools
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==1.3.5 # via alembic, -r requirements.txt
+mako==1.3.5 # via -r requirements.txt, alembic
markdown==3.6 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
-markupsafe==2.1.5 # via jinja2, mako, mkdocs, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml)
+markupsafe==2.1.5 # via -r requirements.txt, jinja2, mako, mkdocs, nbconvert, nomad-lab (pyproject.toml), werkzeug
matid==2.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-matplotlib==3.8.4 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay, -r requirements.txt
-matplotlib-inline==0.1.7 # via ipython, -r requirements.txt
-matplotlib-scalebar==0.8.1 # via orix, -r requirements.txt
-mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
+matplotlib==3.8.4 # via -r requirements.txt, ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
+matplotlib-inline==0.1.7 # via -r requirements.txt, ipykernel, ipython
+matplotlib-scalebar==0.8.1 # via -r requirements.txt, orix
+mda-xdrlib==0.2.0 # via -r requirements.txt, pyedr
mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps, pynxtools, -r requirements.txt
-mistune==3.0.2 # via m2r, -r requirements.txt
+mergedeep==1.3.4 # via -r requirements.txt, mkdocs, mkdocs-get-deps, pynxtools
+mistune==3.0.2 # via -r requirements.txt, m2r, nbconvert
mkdocs==1.6.0 # 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-get-deps==0.2.0 # via mkdocs
@@ -152,197 +185,218 @@ mkdocs-macros-plugin==1.0.5 # via nomad-lab (pyproject.toml)
mkdocs-material==9.5.24 # via nomad-lab (pyproject.toml)
mkdocs-material-extensions==1.3.1 # via mkdocs-material, nomad-lab (pyproject.toml)
mkdocs-redirects==1.2.1 # via nomad-lab (pyproject.toml)
-mmtf-python==1.1.3 # via mdanalysis, -r requirements.txt
+mmtf-python==1.1.3 # via -r requirements.txt, mdanalysis
mongoengine==0.28.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-mongomock==4.1.2 # via optimade, -r requirements.txt
-monty==2024.5.15 # via pymatgen, -r requirements.txt
+mongomock==4.1.2 # via -r requirements.txt, optimade
+monty==2024.5.24 # via -r requirements.txt, pymatgen
more-itertools==10.2.0 # via jaraco-classes, jaraco-functools, pytest
-mpmath==1.3.0 # via sympy, -r requirements.txt
-mrcfile==1.5.0 # via griddataformats, -r requirements.txt
-msgpack==1.0.8 # via blosc2, mmtf-python, -r requirements.txt, nomad-lab (pyproject.toml)
+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==1.0.0 # via mypy
names==0.3.0 # via nomad-lab (pyproject.toml)
-natsort==8.4.0 # via hyperspy, -r requirements.txt
-ndindex==1.8 # via blosc2, -r requirements.txt
+natsort==8.4.0 # via -r requirements.txt, hyperspy
+nbclient==0.10.0 # via -r requirements.txt, nbconvert
+nbconvert==7.16.4 # via -r requirements.txt, jupyter, jupyter-server
+nbformat==5.10.4 # via -r requirements.txt, jupyter-server, nbclient, nbconvert
+ndindex==1.8 # via -r requirements.txt, blosc2
+nest-asyncio==1.6.0 # via -r requirements.txt, ipykernel
netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-networkx==2.6.3 # via matid, mdanalysis, pymatgen, radioactivedecay, scikit-image, -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 nionswift, nionswift-io, -r requirements.txt
-nionswift==0.16.8 # via pynxtools, -r requirements.txt
-nionswift-io==0.15.1 # via nionswift, -r requirements.txt
-nionui==0.6.11 # via nionswift, -r requirements.txt
-nionutils==0.4.10 # via niondata, nionswift, nionswift-io, nionui, -r requirements.txt
+niondata==0.15.5 # via -r requirements.txt, nionswift, nionswift-io
+nionswift==0.16.8 # via -r requirements.txt, pynxtools-em
+nionswift-io==0.15.1 # via -r requirements.txt, nionswift
+nionui==0.6.11 # via -r requirements.txt, nionswift
+nionutils==0.4.10 # via -r requirements.txt, niondata, nionswift, nionswift-io, nionui
+notebook==7.1.3 # via -r requirements.txt, jupyter
+notebook-shim==0.2.4 # via -r requirements.txt, jupyterlab, notebook
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-numba==0.59.1 # via diffsims, kikuchipy, orix, pyxem, -r requirements.txt
-numcodecs==0.12.1 # via zarr, -r requirements.txt
-numexpr==2.10.0 # via pyfai, pyxem, tables, -r requirements.txt
-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, nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, shapely, silx, spglib, tables, tifffile, xarray, zarr, -r requirements.txt, nomad-lab (pyproject.toml)
-numpy-quaternion==2023.0.3 # via orix, -r requirements.txt
+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, igor2, 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, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, 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 jupyterhub, -r requirements.txt
+oauthlib==3.2.2 # via -r requirements.txt, jupyterhub
openpyxl==3.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-optimade==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-orix==0.12.1.post0 # via diffsims, kikuchipy, pyxem, -r requirements.txt
-orjson==3.10.3 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-packaging==24.0 # via build, dask, deprecation, docker, f90wrap, gunicorn, hyperspy, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pooch, pytest, scikit-image, silx, sphinx, tables, xarray, -r requirements.txt
+optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+orix==0.12.1.post0 # via -r requirements.txt, diffsims, kikuchipy, pyxem
+orjson==3.10.3 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
+packaging==24.0 # via -r requirements.txt, build, dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mkdocs, mongomock, nbconvert, pint, plotly, pooch, pytest, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb
paginate==0.5.6 # via mkdocs-material
-palettable==3.3.3 # via pymatgen, -r requirements.txt
-pamela==1.1.0 # via jupyterhub, -r requirements.txt
-pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
+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, radioactivedecay, xarray
+pandocfilters==1.5.1 # via -r requirements.txt, nbconvert
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 jedi, -r requirements.txt
-partd==1.4.2 # via dask, -r requirements.txt
+parso==0.8.4 # via -r requirements.txt, jedi
+partd==1.4.2 # via -r requirements.txt, dask
pathspec==0.12.1 # via mkdocs
-pexpect==4.9.0 # via ipython, -r requirements.txt
-phonopy==2.23.1 # via asr, -r requirements.txt
-pillow==10.3.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image, -r requirements.txt
-pint==0.17 # via hyperspy, rosettasciio, -r requirements.txt, nomad-lab (pyproject.toml)
+pexpect==4.9.0 # via -r requirements.txt, ipython
+phonopy==2.23.1 # via -r requirements.txt, asr
+pillow==10.0.1 # via -r requirements.txt, fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image
+pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab (pyproject.toml), pynxtools-xps, rosettasciio
pkginfo==1.10.0 # via twine
-platformdirs==4.2.2 # via mkdocs-get-deps, pooch, -r requirements.txt
-plotly==5.22.0 # via asr, pymatgen, -r requirements.txt
+platformdirs==4.2.2 # via -r requirements.txt, jupyter-core, mkdocs-get-deps, pooch, xraydb
+plotly==5.22.0 # via -r requirements.txt, asr, pymatgen
pluggy==0.13.1 # via pytest
-ply==3.11 # via pycifrw, -r requirements.txt
-pooch==1.8.1 # via hyperspy, kikuchipy, orix, pyxem, -r requirements.txt
-prettytable==3.10.0 # via hyperspy, -r requirements.txt
-prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt
-prompt-toolkit==3.0.43 # via click-repl, ipython, -r requirements.txt
-psutil==5.9.8 # via diffsims, pyxem, -r requirements.txt
-ptyprocess==0.7.0 # via pexpect, -r requirements.txt
-pure-eval==0.2.2 # via stack-data, -r requirements.txt
+ply==3.11 # via -r requirements.txt, pycifrw
+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, jupyter-server, jupyterhub
+prompt-toolkit==3.0.43 # via -r requirements.txt, click-repl, ipython, jupyter-console
+psutil==5.9.8 # via -r requirements.txt, diffsims, ipykernel, ipyparallel, pyxem
+ptyprocess==0.7.0 # via -r requirements.txt, pexpect, terminado
+pure-eval==0.2.2 # via -r requirements.txt, stack-data
py==1.11.0 # via pytest, pytest-forked
-py-cpuinfo==9.0.0 # via blosc2, tables, -r requirements.txt
-pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng, -r requirements.txt
-pyasn1-modules==0.4.0 # via rfc3161ng, -r requirements.txt
+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@91039c2a1df364c88ab7e284b59c43ec42f18370 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pybtex==0.24.0 # via pymatgen, -r requirements.txt
-pycifrw==4.4.6 # via diffpy-structure, -r requirements.txt
+pybtex==0.24.0 # via -r requirements.txt, pymatgen
+pycifrw==4.4.6 # via -r requirements.txt, diffpy-structure
pycodestyle==2.11.1 # via nomad-lab (pyproject.toml)
-pycparser==2.22 # via cffi, -r requirements.txt
-pydantic==1.10.15 # via fastapi, optimade, -r requirements.txt, nomad-lab (pyproject.toml)
-pyedr==0.8.0 # via panedr, -r requirements.txt
-pyfai==2023.9.0 # via pyxem, -r requirements.txt
-pygments==2.18.0 # via devtools, ipython, mkdocs-material, readme-renderer, sphinx, -r requirements.txt
-pyjwt==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pymatgen==2023.9.25 # via asr, -r requirements.txt, nomad-lab (pyproject.toml)
+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==2024.5.0 # via -r requirements.txt, pyxem
+pygments==2.18.0 # via -r requirements.txt, devtools, ipython, jupyter-console, mkdocs-material, nbconvert, qtconsole, 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==10.8.1 # via mkdocs-material
-pymongo==4.6.3 # via mongoengine, optimade, -r requirements.txt, nomad-lab (pyproject.toml)
-pynxtools==0.1.1 # via pynxtools-mpes, pynxtools-stm, pynxtools-xps, -r requirements.txt, nomad-lab (pyproject.toml)
-pynxtools-mpes==0.0.3 # via pynxtools, -r requirements.txt
-pynxtools-stm==1.0.1 # via pynxtools, -r requirements.txt
-pynxtools-xps==0.0.3 # via pynxtools, -r requirements.txt
-pyopenssl==24.1.0 # via certipy, -r requirements.txt
-pyparsing==3.1.2 # via matplotlib, rdflib, -r requirements.txt
+pymongo==4.6.3 # via -r requirements.txt, mongoengine, nomad-lab (pyproject.toml), optimade
+pynxtools[apm,convert,ellips,em,mpes,stm,xps,xrd]==0.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd
+pynxtools-apm==0.1.1 # via -r requirements.txt, pynxtools
+pynxtools-ellips==0.0.2 # via -r requirements.txt, pynxtools
+pynxtools-em==0.1.1 # via -r requirements.txt, pynxtools
+pynxtools-mpes==0.0.3 # via -r requirements.txt, pynxtools
+pynxtools-stm==1.0.4 # via -r requirements.txt, pynxtools
+pynxtools-xps==0.2.2 # via -r requirements.txt, pynxtools
+pynxtools-xrd==0.0.1 # via -r requirements.txt, pynxtools
+pyopenssl==24.1.0 # via -r requirements.txt, certipy
+pyparsing==3.1.2 # via -r requirements.txt, matplotlib, rdflib
pyproject-hooks==1.1.0 # via build
-pyrsistent==0.20.0 # via jsonschema, -r requirements.txt
-pytest==5.4.3 # via pytest-cov, pytest-forked, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
+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-box==6.1.0 # via rosettasciio, -r requirements.txt
-python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng, rosettasciio, -r requirements.txt
-python-dotenv==1.0.1 # via uvicorn, -r requirements.txt
+python-box==6.1.0 # via -r requirements.txt, rosettasciio
+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, rosettasciio
+python-dotenv==1.0.1 # via -r requirements.txt, uvicorn
python-gitlab==2.10.1 # via nomad-lab (pyproject.toml)
-python-json-logger==2.0.2 # via jupyter-telemetry, -r requirements.txt, nomad-lab (pyproject.toml)
+python-json-logger==2.0.2 # via -r requirements.txt, jupyter-events, jupyter-telemetry, nomad-lab (pyproject.toml)
python-keycloak==4.0.0 # 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==0.0.9 # via -r requirements.txt, nomad-lab (pyproject.toml)
-pytz==2024.1 # via mkdocs-git-revision-date-localized-plugin, nionswift, pandas, pynxtools, -r requirements.txt, nomad-lab (pyproject.toml)
-pytz-deprecation-shim==0.1.0.post0 # via tzlocal, -r requirements.txt
-pywavelets==1.6.0 # via scikit-image, -r requirements.txt
-pyxem==0.18.0 # via pynxtools, -r requirements.txt
-pyyaml==6.0.1 # via dask, hyperspy, kikuchipy, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, rosettasciio, uvicorn, -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
+pywavelets==1.6.0 # via -r requirements.txt, scikit-image
+pyxem==0.16.0 # via -r requirements.txt, pynxtools-em
+pyyaml==6.0.1 # via -r requirements.txt, dask, hyperspy, jupyter-events, kikuchipy, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, rosettasciio, uvicorn
pyyaml-env-tag==0.1 # via mkdocs
pyzeo==0.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
+pyzmq==26.0.3 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server, qtconsole
+qtconsole==5.5.2 # via -r requirements.txt, jupyter
+qtpy==2.4.1 # via -r requirements.txt, qtconsole
quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml)
-radioactivedecay==0.5.0 # via ifes-apt-tc-data-modeling, -r requirements.txt
+radioactivedecay==0.5.0 # via -r requirements.txt, ifes-apt-tc-data-modeling
rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
rdkit==2023.9.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
readme-renderer==43.0 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
regex==2024.5.15 # via mkdocs-material
-requests==2.32.2 # via docker, hyperspy, jupyterhub, mkdocs-material, oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml)
-requests-toolbelt==1.0.0 # via python-gitlab, python-keycloak, twine, -r requirements.txt
+requests==2.32.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, jupyterlab-server, 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 jsonschema, -r requirements.txt
+rfc3339-validator==0.1.4 # via -r requirements.txt, jsonschema
rfc3986==2.0.0 # via twine
-rfc3987==1.3.8 # via jsonschema, -r requirements.txt
+rfc3986-validator==0.1.1 # via -r requirements.txt, jsonschema
+rfc3987==1.3.8 # via -r requirements.txt, jsonschema
rope==0.21.0 # via nomad-lab (pyproject.toml)
-rosettasciio==0.4 # via hyperspy, -r requirements.txt
-ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
-ruamel-yaml-clib==0.2.8 # via ruamel-yaml, -r requirements.txt
+rosettasciio==0.4 # via -r requirements.txt, pynxtools-em
+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==0.4.5 # via nomad-lab (pyproject.toml)
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-scikit-image==0.19.3 # via hyperspy, kikuchipy, pyxem, -r requirements.txt
-scikit-learn==1.5.0 # via kikuchipy, matid, pyxem, -r requirements.txt, nomad-lab (pyproject.toml)
-scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
-secretstorage==3.3.3 # via keyring
-sentinels==1.0.0 # via mongomock, -r requirements.txt
-setuptools==70.0.0 # via radioactivedecay, -r requirements.txt
-shapely==2.0.4 # via pyxem, -r requirements.txt
-silx==2.1.0 # via pyfai, -r requirements.txt
-six==1.16.0 # via asttokens, basicauth, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, pytest-xdist, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt
-smmap==5.0.1 # via gitdb, -r requirements.txt
-sniffio==1.3.1 # via anyio, httpx, -r requirements.txt
-snowballstemmer==2.2.0 # via sphinx, -r requirements.txt
-soupsieve==2.5 # via beautifulsoup4, -r requirements.txt
-spglib==2.4.0 # via asr, matid, phonopy, pymatgen, -r requirements.txt
-sphinx==7.3.7 # via recommonmark, -r requirements.txt
-sphinxcontrib-applehelp==1.0.8 # via sphinx, -r requirements.txt
-sphinxcontrib-devhelp==1.0.6 # via sphinx, -r requirements.txt
-sphinxcontrib-htmlhelp==2.0.5 # via sphinx, -r requirements.txt
-sphinxcontrib-jsmath==1.0.1 # via sphinx, -r requirements.txt
-sphinxcontrib-qthelp==1.0.7 # via sphinx, -r requirements.txt
-sphinxcontrib-serializinghtml==1.1.10 # via sphinx, -r requirements.txt
-sqlalchemy==2.0.30 # via alembic, jupyterhub, -r requirements.txt
-stack-data==0.6.3 # via ipython, -r requirements.txt
-starlette==0.27.0 # via fastapi, -r requirements.txt
+scikit-image==0.19.3 # via -r requirements.txt, hyperspy, kikuchipy, pyxem
+scikit-learn==1.5.0 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
+scipy==1.13.1 # via -r requirements.txt, ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb
+send2trash==1.8.3 # via -r requirements.txt, jupyter-server
+sentinels==1.0.0 # via -r requirements.txt, mongomock
+silx==2.1.0 # via -r requirements.txt, pyfai
+six==1.16.0 # via -r requirements.txt, anytree, asttokens, basicauth, bleach, 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==2.5 # via -r requirements.txt, beautifulsoup4
+sparse==0.15.4 # via -r requirements.txt, hyperspy
+spglib==2.4.0 # via -r requirements.txt, asr, matid, phonopy, pymatgen
+sphinx==7.3.7 # 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==1.0.7 # via -r requirements.txt, sphinx
+sphinxcontrib-serializinghtml==1.1.10 # via -r requirements.txt, sphinx
+sqlalchemy==2.0.30 # via -r requirements.txt, alembic, jupyterhub, xraydb
+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 findiff, hyperspy, pymatgen, radioactivedecay, -r requirements.txt
-tables==3.9.2 # via ifes-apt-tc-data-modeling, -r requirements.txt
-tabulate==0.8.9 # via pybis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
-tenacity==8.3.0 # via plotly, -r requirements.txt
+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==8.3.0 # via -r requirements.txt, plotly
termcolor==2.4.0 # via mkdocs-macros-plugin
-texttable==1.7.0 # via pybis, -r requirements.txt
-threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt
-tifffile==2024.5.22 # via h5grove, scikit-image, -r requirements.txt
-tomli==2.0.1 # via build, mypy, sphinx, -r requirements.txt
-toolz==0.12.1 # via dask, partd, -r requirements.txt
+terminado==0.18.1 # via -r requirements.txt, jupyter-server, jupyter-server-terminals
+texttable==1.7.0 # via -r requirements.txt, pybis
+threadpoolctl==3.5.0 # via -r requirements.txt, mdanalysis, scikit-learn
+tifffile==2024.5.22 # via -r requirements.txt, h5grove, hyperspy, scikit-image
+tinycss2==1.3.0 # via -r requirements.txt, nbconvert
+tomli==2.0.1 # via -r requirements.txt, build, jupyterlab, mypy, sphinx
+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 jupyterhub, -r requirements.txt
-tqdm==4.66.4 # via diffsims, hyperspy, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine, -r requirements.txt
-traitlets==5.14.3 # via ipython, jupyter-telemetry, jupyterhub, matplotlib-inline, -r requirements.txt
-traits==6.4.3 # via hyperspy, pyxem, -r requirements.txt
-transforms3d==0.4.1 # via diffsims, pyxem, -r requirements.txt
+tornado==6.4 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyter-server, jupyterhub, jupyterlab, notebook, terminado
+tqdm==4.66.4 # via -r requirements.txt, diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine
+traitlets==5.14.3 # via -r requirements.txt, comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-console, jupyter-core, jupyter-events, jupyter-server, jupyter-telemetry, jupyterhub, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat, qtconsole
+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==1.5.5 # via nomad-lab (pyproject.toml)
-types-python-dateutil==2.9.0.20240316 # via arrow, -r requirements.txt
-typing-extensions==4.11.0 # via alembic, anyio, asgiref, astroid, fastapi, ipython, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn, -r requirements.txt
-typish==1.9.3 # via nptyping, -r requirements.txt
-tzdata==2024.1 # via celery, pytz-deprecation-shim, -r requirements.txt
-tzlocal==4.3 # via nionswift, pynxtools, -r requirements.txt
-uncertainties==3.1.7 # via lmfit, pymatgen, -r requirements.txt
+types-python-dateutil==2.9.0.20240316 # via -r requirements.txt, arrow
+typing-extensions==4.12.0 # via -r requirements.txt, alembic, anyio, asgiref, astroid, async-lru, fastapi, ipython, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn
+typish==1.9.3 # via -r requirements.txt, nptyping
+tzdata==2024.1 # via -r requirements.txt, celery
+tzlocal==5.2 # via -r requirements.txt, nionswift, pynxtools-em
+uncertainties==3.1.7 # via -r requirements.txt, lmfit, pymatgen
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
-uri-template==1.3.0 # via jsonschema, -r requirements.txt
-urllib3==1.26.18 # via docker, elasticsearch, pybis, requests, -r requirements.txt
+uri-template==1.3.0 # via -r requirements.txt, jsonschema
+urllib3==1.26.18 # via -r requirements.txt, docker, elasticsearch, pybis, requests
uv==0.2.2 # via nomad-lab (pyproject.toml)
-uvicorn==0.29.0 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-uvloop==0.19.0 # via uvicorn, -r requirements.txt
+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==5.1.0 # via amqp, celery, kombu, -r requirements.txt
-watchdog==4.0.0 # via mkdocs
-watchfiles==0.21.0 # via uvicorn, -r requirements.txt
-wcwidth==0.2.13 # via prettytable, prompt-toolkit, pytest, -r requirements.txt
-webcolors==1.13 # via jsonschema, -r requirements.txt
-webencodings==0.5.1 # via html5lib, -r requirements.txt
-websockets==12.0 # via uvicorn, -r requirements.txt
-werkzeug==3.0.3 # via flask, -r requirements.txt
+vine==5.1.0 # via -r requirements.txt, amqp, celery, kombu
+watchdog==4.0.1 # 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, bleach, html5lib, tinycss2
+websocket-client==1.8.0 # via -r requirements.txt, jupyter-server
+websockets==12.0 # via -r requirements.txt, uvicorn
+werkzeug==3.0.3 # via -r requirements.txt, flask
+widgetsnbextension==4.0.10 # via -r requirements.txt, ipywidgets
wrapt==1.16.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-xarray==2023.12.0 # via pynxtools, pynxtools-mpes, pynxtools-xps, -r requirements.txt, nomad-lab (pyproject.toml)
-zarr==2.17.1 # via pyxem, -r requirements.txt
-zipfile37==0.1.3 # via pynxtools, -r requirements.txt
-zipp==3.18.2 # via importlib-metadata, importlib-resources, -r requirements.txt
+xarray==2023.12.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
+xmltodict==0.13.0 # via -r requirements.txt, ifes-apt-tc-data-modeling, pynxtools-em
+xraydb==4.5.4 # via -r requirements.txt, pynxtools-em
+zarr==2.17.1 # via -r requirements.txt, hyperspy
+zipp==3.18.2 # 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:
+# setuptools
diff --git a/requirements.txt b/requirements.txt
index f16f9bb343c178f15c287bf7771a8840bd90a2f7..f9954581b968a15f47793704590dca35550a4578 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,58 +1,73 @@
-# This file was autogenerated by uv via the following command:
-# uv pip compile --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
+#
+# 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' dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
+#
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
+anyio==4.3.0 # via httpx, jupyter-server, starlette, watchfiles
+anytree==2.12.1 # via pynxtools
+appnope==0.1.4 # via ipykernel
+argon2-cffi==23.1.0 # via jupyter-server
+argon2-cffi-bindings==21.2.0 # via argon2-cffi
arrow==1.3.0 # via isoduration
asciitree==0.3.3 # via zarr
-ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, pynxtools, quippy-ase, 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==0.9.32 # via lmfit
+asteval==0.9.33 # via lmfit
asttokens==2.4.1 # via stack-data
async-generator==1.10 # via jupyterhub
+async-lru==2.0.4 # via jupyterlab
attrs==23.2.0 # via jsonschema
-babel==2.15.0 # via sphinx
+babel==2.15.0 # via jupyterlab-server, sphinx
bagit==1.8.1 # via nomad-lab (pyproject.toml)
basicauth==0.4.1 # via nomad-lab (pyproject.toml)
-beautifulsoup4==4.12.3 # via nomad-lab (pyproject.toml)
+beautifulsoup4==4.12.3 # via nbconvert, nomad-lab (pyproject.toml)
billiard==4.2.0 # via celery
biopython==1.83 # via mdanalysis
-bitarray==2.9.2 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
+bitarray==2.9.2 # via nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
+bleach==6.1.0 # via nbconvert
blinker==1.8.2 # via flask
blosc2==2.5.1 # via tables
cachetools==5.3.3 # via nomad-lab (pyproject.toml)
celery==5.4.0 # via nomad-lab (pyproject.toml)
certifi==2024.2.2 # via elasticsearch, httpcore, httpx, netcdf4, requests
certipy==0.1.3 # via jupyterhub
-cffi==1.16.0 # via cryptography
+cffi==1.16.0 # via argon2-cffi-bindings, 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, pynxtools, uvicorn, nomad-lab (pyproject.toml)
+click==8.1.7 # via asr, celery, click-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn
+click-default-group==1.2.4 # via pynxtools
click-didyoumean==0.3.1 # via celery
click-plugins==1.1.1 # via celery
click-repl==0.3.0 # via celery
-cloudpickle==3.0.0 # via dask, hyperspy
+cloudpickle==3.0.0 # via dask
+comm==0.2.2 # via ipykernel, ipywidgets
commonmark==0.9.1 # via recommonmark
contourpy==1.2.1 # via matplotlib
cryptography==42.0.7 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng
cycler==0.12.1 # via matplotlib
-dask==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
-decorator==5.1.1 # via ipython, validators
+dask[array]==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
+debugpy==1.8.1 # via ipykernel
+decorator==5.1.1 # via ipyparallel, ipython, validators
+defusedxml==0.7.1 # via nbconvert
deprecation==2.1.0 # via python-keycloak
diffpy-structure==3.1.0 # via diffsims, kikuchipy, orix
diffsims==0.5.2 # via kikuchipy, pyxem
-dill==0.3.8 # via lmfit
+dill==0.3.8 # via hyperspy, lmfit
dnspython==2.6.1 # via email-validator, pymongo
-docker==7.0.0 # via dockerspawner
+docker==7.1.0 # via dockerspawner
dockerspawner==13.0.0 # via nomad-lab (pyproject.toml)
docstring-parser==0.16 # via nomad-lab (pyproject.toml)
docutils==0.21.2 # 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==1.3.1 # via optimade
+entrypoints==0.4 # via ipyparallel
escapism==1.0.1 # via dockerspawner
et-xmlfile==1.1.0 # via openpyxl
exceptiongroup==1.2.1 # via anyio, ipython
@@ -61,51 +76,70 @@ f90wrap==0.2.14 # via quippy-ase
fabio==2024.4.0 # via pyfai, silx
fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml)
fasteners==0.19 # via mdanalysis, zarr
+fastjsonschema==2.19.1 # via nbformat
filelock==3.3.1 # via nomad-lab (pyproject.toml)
findiff==0.10.0 # via pynxtools-stm
flask==3.0.3 # via asr
-flatdict==4.0.1 # via pynxtools
+flatdict==3.4.0 # via ifes-apt-tc-data-modeling, pynxtools-em
fonttools==4.51.0 # via matplotlib
fqdn==1.5.1 # via jsonschema
-fsspec==2024.5.0 # via dask
+fsspec==2024.5.0 # via dask, hyperspy
future==1.0.0 # via uncertainties
gitdb==4.0.11 # via gitpython
-gitpython==3.1.43 # via pynxtools, nomad-lab (pyproject.toml)
+gitpython==3.1.43 # via nomad-lab (pyproject.toml)
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==1.3.0 # via nomad-lab (pyproject.toml)
-h5py==3.11.0 # via fabio, h5grove, hdf5plugin, ifes-apt-tc-data-modeling, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, silx, nomad-lab (pyproject.toml)
+h5grove[fastapi]==1.3.0 # via jupyterlab-h5web, nomad-lab (pyproject.toml)
+h5py==3.11.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, 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==1.0.5 # via httpx
httptools==0.6.1 # via uvicorn
-httpx==0.27.0 # via nomad-lab (pyproject.toml)
-hyperspy==2.1.0 # via kikuchipy, pynxtools, pyxem
+httpx==0.27.0 # via jupyterlab, nomad-lab (pyproject.toml)
+hyperspy==1.7.6 # via kikuchipy, pyxem
idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests
-ifes-apt-tc-data-modeling==0.1 # via pynxtools
-imageio==2.34.1 # via kikuchipy, nionswift, nionswift-io, nionui, scikit-image
+ifes-apt-tc-data-modeling==0.2.2 # via pynxtools-apm
+igor2==0.5.2 # via pynxtools-xps
+imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via sphinx
-importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyterhub, pynxtools, sphinx, nomad-lab (pyproject.toml)
+importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, nbconvert, nomad-lab (pyproject.toml), pynxtools, sphinx
importlib-resources==6.4.0 # via matplotlib, spglib
inflection==0.5.1 # via nomad-lab (pyproject.toml)
-ipython==8.18.1 # via pynxtools-stm
+ipykernel==6.29.4 # via ipyparallel, jupyter, jupyter-console, jupyterlab, qtconsole
+ipyparallel==8.8.0 # via hyperspy
+ipython==8.18.1 # via hyperspy, ipykernel, ipyparallel, ipywidgets, jupyter-console, pynxtools-xrd
+ipywidgets==8.1.2 # via jupyter
isodate==0.6.1 # via rdflib
isoduration==20.11.0 # via jsonschema
itsdangerous==2.2.0 # via flask, nomad-lab (pyproject.toml)
jedi==0.19.1 # via ipython
-jinja2==3.1.4 # via flask, hyperspy, jupyterhub, sphinx
+jinja2==3.1.4 # via flask, hyperspy, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, nbconvert, sphinx
jmespath==1.0.1 # via nomad-lab (pyproject.toml)
joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn
+json5==0.9.25 # via jupyterlab-server
jsonpointer==2.4 # via jsonschema
-jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, nomad-lab (pyproject.toml)
+jsonschema[format,format-nongpl]==4.17.3 # via jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, nomad-lab (pyproject.toml), oauthenticator
+jupyter==1.0.0 # via ifes-apt-tc-data-modeling
+jupyter-client==8.6.2 # via ipykernel, ipyparallel, jupyter-console, jupyter-server, nbclient, qtconsole
+jupyter-console==6.6.3 # via jupyter
+jupyter-core==5.7.2 # via ipykernel, jupyter-client, jupyter-console, jupyter-server, jupyterlab, nbclient, nbconvert, nbformat, qtconsole
+jupyter-events==0.5.0 # via jupyter-server
+jupyter-lsp==2.2.5 # via jupyterlab
+jupyter-server==2.5.0 # via jupyter-lsp, jupyterlab, jupyterlab-h5web, jupyterlab-server, notebook, notebook-shim
+jupyter-server-terminals==0.5.3 # via jupyter-server
jupyter-telemetry==0.1.0 # via jupyterhub
-jupyterhub==4.0.2 # via dockerspawner, oauthenticator, nomad-lab (pyproject.toml)
+jupyterhub==4.0.2 # via dockerspawner, nomad-lab (pyproject.toml), oauthenticator
+jupyterlab==4.1.6 # via ifes-apt-tc-data-modeling, notebook
+jupyterlab-h5web==11.1.0 # via ifes-apt-tc-data-modeling
+jupyterlab-pygments==0.3.0 # via nbconvert
+jupyterlab-server==2.24.0 # via jupyterlab, notebook
+jupyterlab-widgets==3.0.10 # via ipywidgets
jwcrypto==1.5.6 # via python-keycloak
-kikuchipy==0.8.7 # via pynxtools
+kikuchipy==0.9.0 # via pynxtools-em
kiwisolver==1.4.5 # via matplotlib
kombu==5.3.7 # via celery
lark==1.1.9 # via optimade
@@ -113,68 +147,75 @@ latexcodec==3.0.0 # via pybtex
llvmlite==0.42.0 # via numba
lmfit==1.3.1 # via pyxem
locket==1.0.0 # via partd
-lxml==5.2.2 # via fabio, lxml-html-clean, nomad-lab (pyproject.toml)
+lxml==5.2.2 # via fabio, lxml-html-clean, nomad-lab (pyproject.toml), pynxtools
lxml-html-clean==0.1.1 # via nomad-lab (pyproject.toml)
m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic
-markupsafe==2.1.5 # via jinja2, mako, werkzeug
+markupsafe==2.1.5 # via jinja2, mako, nbconvert, werkzeug
matid==2.0.1 # via nomad-lab (pyproject.toml)
matplotlib==3.8.4 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
-matplotlib-inline==0.1.7 # via ipython
+matplotlib-inline==0.1.7 # 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)
mergedeep==1.3.4 # via pynxtools
-mistune==3.0.2 # via m2r
+mistune==3.0.2 # via m2r, nbconvert
mmtf-python==1.1.3 # via mdanalysis
mongoengine==0.28.2 # via nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade
-monty==2024.5.15 # via pymatgen
+monty==2024.5.24 # 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
+nbclient==0.10.0 # via nbconvert
+nbconvert==7.16.4 # via jupyter, jupyter-server
+nbformat==5.10.4 # via jupyter-server, nbclient, nbconvert
ndindex==1.8 # via blosc2
+nest-asyncio==1.6.0 # via ipykernel
netcdf4==1.6.5 # via nomad-lab (pyproject.toml)
-networkx==2.6.3 # via matid, mdanalysis, pymatgen, radioactivedecay, scikit-image, 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==0.16.8 # via pynxtools-em
nionswift-io==0.15.1 # via nionswift
nionui==0.6.11 # via nionswift
nionutils==0.4.10 # via niondata, nionswift, nionswift-io, nionui
+notebook==7.1.3 # via jupyter
+notebook-shim==0.2.4 # via jupyterlab, notebook
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
-numba==0.59.1 # via diffsims, kikuchipy, orix, pyxem
+numba==0.59.1 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse
numcodecs==0.12.1 # via zarr
-numexpr==2.10.0 # via 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, nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, shapely, silx, spglib, tables, tifffile, xarray, zarr, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
+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, igor2, 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, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, 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==0.22.1 # via nomad-lab (pyproject.toml)
+optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml)
orix==0.12.1.post0 # via diffsims, kikuchipy, pyxem
orjson==3.10.3 # via h5grove, nomad-lab (pyproject.toml)
-packaging==24.0 # via dask, deprecation, docker, f90wrap, gunicorn, hyperspy, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, pooch, scikit-image, silx, sphinx, tables, xarray
+packaging==24.0 # via dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mongomock, nbconvert, pint, plotly, pooch, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb
palettable==3.3.3 # via pymatgen
pamela==1.1.0 # via jupyterhub
-pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
+pandas==1.5.3 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray
+pandocfilters==1.5.1 # via nbconvert
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==1.4.2 # via dask
pexpect==4.9.0 # via ipython
phonopy==2.23.1 # via asr
-pillow==10.3.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image
-pint==0.17 # via hyperspy, rosettasciio, nomad-lab (pyproject.toml)
-platformdirs==4.2.2 # via pooch
+pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image
+pint==0.17 # via hyperspy, nomad-lab (pyproject.toml), pynxtools-xps, rosettasciio
+platformdirs==4.2.2 # via jupyter-core, pooch, xraydb
plotly==5.22.0 # via asr, pymatgen
ply==3.11 # via pycifrw
-pooch==1.8.1 # via hyperspy, kikuchipy, orix, pyxem
+pooch==1.8.1 # via 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, pyxem
-ptyprocess==0.7.0 # via pexpect
+prometheus-client==0.20.0 # via jupyter-server, jupyterhub
+prompt-toolkit==3.0.43 # via click-repl, ipython, jupyter-console
+psutil==5.9.8 # via diffsims, ipykernel, ipyparallel, pyxem
+ptyprocess==0.7.0 # via pexpect, terminado
pure-eval==0.2.2 # via stack-data
py-cpuinfo==9.0.0 # via blosc2, tables
pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng
@@ -183,60 +224,67 @@ pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88a
pybtex==0.24.0 # via pymatgen
pycifrw==4.4.6 # via diffpy-structure
pycparser==2.22 # via cffi
-pydantic==1.10.15 # via fastapi, optimade, nomad-lab (pyproject.toml)
+pydantic==1.10.15 # via fastapi, nomad-lab (pyproject.toml), optimade
pyedr==0.8.0 # via panedr
-pyfai==2023.9.0 # via pyxem
-pygments==2.18.0 # via ipython, sphinx
-pyjwt==2.6.0 # via nomad-lab (pyproject.toml)
+pyfai==2024.5.0 # via pyxem
+pygments==2.18.0 # via ipython, jupyter-console, nbconvert, qtconsole, sphinx
+pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml)
pymatgen==2023.9.25 # via asr, nomad-lab (pyproject.toml)
-pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml)
-pynxtools==0.1.1 # via pynxtools-mpes, pynxtools-stm, pynxtools-xps, nomad-lab (pyproject.toml)
+pymongo==4.6.3 # via mongoengine, nomad-lab (pyproject.toml), optimade
+pynxtools[apm,convert,ellips,em,mpes,stm,xps,xrd]==0.3.1 # via nomad-lab (pyproject.toml), pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd
+pynxtools-apm==0.1.1 # via pynxtools
+pynxtools-ellips==0.0.2 # via pynxtools
+pynxtools-em==0.1.1 # via pynxtools
pynxtools-mpes==0.0.3 # via pynxtools
-pynxtools-stm==1.0.1 # via pynxtools
-pynxtools-xps==0.0.3 # via pynxtools
+pynxtools-stm==1.0.4 # via pynxtools
+pynxtools-xps==0.2.2 # via pynxtools
+pynxtools-xrd==0.0.1 # via pynxtools
pyopenssl==24.1.0 # via certipy
pyparsing==3.1.2 # via matplotlib, rdflib
pyrsistent==0.20.0 # via jsonschema
python-box==6.1.0 # via rosettasciio
-python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, jupyterhub, matplotlib, pandas, pybis, rfc3161ng, rosettasciio
+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-json-logger==2.0.2 # via jupyter-events, jupyter-telemetry, nomad-lab (pyproject.toml)
python-keycloak==4.0.0 # 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==0.0.9 # via nomad-lab (pyproject.toml)
-pytz==2024.1 # via nionswift, pandas, pynxtools, nomad-lab (pyproject.toml)
-pytz-deprecation-shim==0.1.0.post0 # via tzlocal
+pytz==2024.1 # via nionswift, nomad-lab (pyproject.toml), pandas
pywavelets==1.6.0 # via scikit-image
-pyxem==0.18.0 # via pynxtools
-pyyaml==6.0.1 # via dask, hyperspy, kikuchipy, phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn, nomad-lab (pyproject.toml)
+pyxem==0.16.0 # via pynxtools-em
+pyyaml==6.0.1 # via dask, hyperspy, jupyter-events, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn
pyzeo==0.1.5 # via nomad-lab (pyproject.toml)
+pyzmq==26.0.3 # via ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server, qtconsole
+qtconsole==5.5.2 # via jupyter
+qtpy==2.4.1 # via qtconsole
quippy-ase==0.9.14 # via nomad-lab (pyproject.toml)
radioactivedecay==0.5.0 # via ifes-apt-tc-data-modeling
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
rdkit==2023.9.5 # via nomad-lab (pyproject.toml)
recommonmark==0.7.1 # via nomad-lab (pyproject.toml)
-requests==2.32.2 # via docker, hyperspy, jupyterhub, oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
+requests==2.32.2 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, jupyterlab-server, 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-validator==0.1.1 # via jsonschema
rfc3987==1.3.8 # via jsonschema
-rosettasciio==0.4 # via hyperspy
+rosettasciio==0.4 # via pynxtools-em
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==1.5.0 # via kikuchipy, matid, pyxem, nomad-lab (pyproject.toml)
-scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, nomad-lab (pyproject.toml)
+scikit-learn==1.5.0 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
+scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb
+send2trash==1.8.3 # via jupyter-server
sentinels==1.0.0 # via mongomock
-setuptools==70.0.0 # via radioactivedecay
-shapely==2.0.4 # via pyxem
silx==2.1.0 # via pyfai
-six==1.16.0 # via asttokens, basicauth, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
+six==1.16.0 # via anytree, asttokens, basicauth, bleach, 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==2.5 # via beautifulsoup4
+sparse==0.15.4 # via hyperspy
spglib==2.4.0 # via asr, matid, phonopy, pymatgen
sphinx==7.3.7 # via recommonmark
sphinxcontrib-applehelp==1.0.8 # via sphinx
@@ -245,47 +293,55 @@ sphinxcontrib-htmlhelp==2.0.5 # via sphinx
sphinxcontrib-jsmath==1.0.1 # via sphinx
sphinxcontrib-qthelp==1.0.7 # via sphinx
sphinxcontrib-serializinghtml==1.1.10 # via sphinx
-sqlalchemy==2.0.30 # via alembic, jupyterhub
+sqlalchemy==2.0.30 # via alembic, jupyterhub, xraydb
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 pybis, pymatgen, nomad-lab (pyproject.toml)
+tabulate==0.8.9 # via nomad-lab (pyproject.toml), pybis, pymatgen
tenacity==8.3.0 # via plotly
+terminado==0.18.1 # via jupyter-server, jupyter-server-terminals
texttable==1.7.0 # via pybis
threadpoolctl==3.5.0 # via mdanalysis, scikit-learn
-tifffile==2024.5.22 # via h5grove, scikit-image
-tomli==2.0.1 # via sphinx
-toolz==0.12.1 # via dask, partd
+tifffile==2024.5.22 # via h5grove, hyperspy, scikit-image
+tinycss2==1.3.0 # via nbconvert
+tomli==2.0.1 # via jupyterlab, sphinx
+toolz==0.12.1 # via dask, hyperspy, partd
toposort==1.10 # via nomad-lab (pyproject.toml)
-tornado==6.4 # via jupyterhub
-tqdm==4.66.4 # via diffsims, hyperspy, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem
-traitlets==5.14.3 # via ipython, jupyter-telemetry, jupyterhub, matplotlib-inline
+tornado==6.4 # via ipykernel, ipyparallel, jupyter-client, jupyter-server, jupyterhub, jupyterlab, notebook, terminado
+tqdm==4.66.4 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem
+traitlets==5.14.3 # via comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-console, jupyter-core, jupyter-events, jupyter-server, jupyter-telemetry, jupyterhub, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat, qtconsole
traits==6.4.3 # via hyperspy, pyxem
transforms3d==0.4.1 # via diffsims, pyxem
types-python-dateutil==2.9.0.20240316 # via arrow
-typing-extensions==4.11.0 # via alembic, anyio, asgiref, fastapi, ipython, jwcrypto, kombu, pydantic, sqlalchemy, starlette, uvicorn
+typing-extensions==4.12.0 # via alembic, anyio, asgiref, async-lru, fastapi, ipython, jwcrypto, kombu, pydantic, sqlalchemy, starlette, uvicorn
typish==1.9.3 # via nptyping
-tzdata==2024.1 # via celery, pytz-deprecation-shim
-tzlocal==4.3 # via nionswift, pynxtools
+tzdata==2024.1 # via celery
+tzlocal==5.2 # via nionswift, pynxtools-em
uncertainties==3.1.7 # via lmfit, pymatgen
unidecode==1.3.2 # via nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema
urllib3==1.26.18 # via docker, elasticsearch, pybis, requests
-uvicorn==0.29.0 # via h5grove, nomad-lab (pyproject.toml)
+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==5.1.0 # 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
+webencodings==0.5.1 # via bleach, html5lib, tinycss2
+websocket-client==1.8.0 # via jupyter-server
websockets==12.0 # via uvicorn
werkzeug==3.0.3 # via flask
+widgetsnbextension==4.0.10 # via ipywidgets
wrapt==1.16.0 # via nomad-lab (pyproject.toml)
-xarray==2023.12.0 # via pynxtools, pynxtools-mpes, pynxtools-xps, nomad-lab (pyproject.toml)
-zarr==2.17.1 # via pyxem
-zipfile37==0.1.3 # via pynxtools
+xarray==2023.12.0 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps
+xmltodict==0.13.0 # via ifes-apt-tc-data-modeling, pynxtools-em
+xraydb==4.5.4 # via pynxtools-em
+zarr==2.17.1 # via hyperspy
zipp==3.18.2 # 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:
+# setuptools
diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh
index 276ed31737058d641120d39e7164d01469dfac69..f6aa37b5c165f29ed71cae32fad05612a442fc6e 100755
--- a/scripts/check_python_dependencies.sh
+++ b/scripts/check_python_dependencies.sh
@@ -14,6 +14,9 @@ project_dir=$(dirname $(dirname $(realpath $0)))
cd $project_dir
+# do no support git install for pynxtools
+grep pynxtools pyproject.toml | grep "@git+" 1>&2
+
# backup
cp requirements.txt requirements.txt.tmp
cp requirements-dev.txt requirements-dev.txt.tmp
diff --git a/scripts/setup_dev_env.sh b/scripts/setup_dev_env.sh
index 7a89bd96b7ed8fdbb0135051f18e9620480acb7e..23d14cec4e10e438c1f2436e21c422d4cabe4093 100755
--- a/scripts/setup_dev_env.sh
+++ b/scripts/setup_dev_env.sh
@@ -17,7 +17,6 @@ rm -rf site
# Install nomad
pip install --prefer-binary -r requirements-dev.txt
-pip uninstall -y pynxtools
pip install -e ".[infrastructure,parsing,dev]"
# Build documentation
diff --git a/tests/data/parsers/nexus/SiO2onSi.ellips.nxs b/tests/data/parsers/nexus/SiO2onSi.ellips.nxs
index 31516e6ed681320a5223a7672ed75d116af7dcbe..dcb645cd9392c3ebff92dbeac5c690012c636f2b 100644
Binary files a/tests/data/parsers/nexus/SiO2onSi.ellips.nxs and b/tests/data/parsers/nexus/SiO2onSi.ellips.nxs differ