diff --git a/pyproject.toml b/pyproject.toml
index f4da17da608d74013a0dd25b7abcac5af48c4c90..b51c8aacf622457bdca8aa2baddcf2e00b806c11 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -28,7 +28,7 @@ dependencies = [
'jmespath>=0.10.0',
'lxml>=5.2',
'lxml-html-clean>=0.1.0',
- 'matid>=2.1.2',
+ 'matid>=2.1.3',
'nptyping~=1.4.4',
'numpy>=1.22.4,<2.0.0',
'openpyxl>=3.0.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index a2b20c19e6efa4aa7417344525ccf2fb830b9519..699212f89d12a391b147a8f7c64fed0a5630df18 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -5,7 +5,7 @@ alabaster==1.0.0 # via sphinx, -r requirements.txt
alembic==1.13.3 # via jupyterhub, -r requirements.txt
amqp==5.2.0 # via kombu, -r requirements.txt
aniso8601==9.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-anyio==4.6.0 # via httpx, starlette, watchfiles, -r requirements.txt
+anyio==4.6.2 # via httpx, starlette, watchfiles, -r requirements.txt
arrow==1.3.0 # via isoduration, -r requirements.txt
ase==3.22.1 # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
asgiref==3.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -19,7 +19,7 @@ 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==4.2.1 # via celery, -r requirements.txt
-bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
+bitarray==2.9.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
cachetools==5.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt
@@ -34,7 +34,7 @@ click-repl==0.3.0 # via celery, -r requirements.txt
colorama==0.4.6 # via click, mkdocs, mkdocs-material, pytest, sphinx, tqdm, uvicorn, -r requirements.txt
commonmark==0.9.1 # via recommonmark, -r requirements.txt
contourpy==1.3.0 # via matplotlib, -r requirements.txt
-coverage==7.6.2 # via pytest-cov
+coverage==7.6.3 # via pytest-cov
cryptography==43.0.1 # via certipy, jwcrypto, pyjwt, rfc3161ng, -r requirements.txt
cycler==0.12.1 # via matplotlib, -r requirements.txt
decorator==5.1.1 # via validators, -r requirements.txt
@@ -97,7 +97,7 @@ m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic, -r requirements.txt
markdown==3.7 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
markupsafe==3.0.1 # via jinja2, mako, mkdocs, -r requirements.txt, nomad-lab (pyproject.toml)
-matid==2.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
+matid==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, pymatgen, -r requirements.txt
mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps
@@ -107,7 +107,7 @@ mkdocs-click==0.8.1 # via nomad-lab (pyproject.toml)
mkdocs-get-deps==0.2.0 # via mkdocs
mkdocs-git-revision-date-localized-plugin==1.2.9 # via nomad-lab (pyproject.toml)
mkdocs-glightbox==0.4.0 # via nomad-lab (pyproject.toml)
-mkdocs-macros-plugin==1.3.4 # via nomad-lab (pyproject.toml)
+mkdocs-macros-plugin==1.3.5 # via nomad-lab (pyproject.toml)
mkdocs-material==9.5.40 # 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)
@@ -120,7 +120,7 @@ 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)
netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, pymatgen, -r requirements.txt
+networkx==3.4.1 # via matid, pymatgen, -r requirements.txt
nomad-openbis==1.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
numpy==1.26.4 # via ase, cftime, contourpy, h5grove, h5py, matid, matplotlib, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -156,7 +156,7 @@ pyjwt==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
pymatgen==2024.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
pymdown-extensions==10.11.2 # via mkdocs-material
pymongo==4.6.3 # via mongoengine, optimade, -r requirements.txt, nomad-lab (pyproject.toml)
-pyparsing==3.1.4 # via matplotlib, rdflib, -r requirements.txt
+pyparsing==3.2.0 # via matplotlib, rdflib, -r requirements.txt
pyrsistent==0.20.0 # via jsonschema, -r requirements.txt
pytest==7.4.4 # via pytest-asyncio, pytest-cov, pytest-split, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml)
pytest-asyncio==0.23.8 # via nomad-lab (pyproject.toml)
@@ -174,7 +174,7 @@ python-magic==0.4.24 # via -r requirements.txt, nomad-lab (pyproject.toml)
python-magic-bin==0.4.14 ; sys_platform == 'win32' # via -r requirements.txt, nomad-lab (pyproject.toml)
python-multipart==0.0.12 # via -r requirements.txt, nomad-lab (pyproject.toml)
pytz==2024.2 # via mkdocs-git-revision-date-localized-plugin, mongomock, pandas, -r requirements.txt, nomad-lab (pyproject.toml)
-pywin32==307 ; sys_platform == 'win32' # via docker, -r requirements.txt
+pywin32==308 ; sys_platform == 'win32' # via docker, -r requirements.txt
pyyaml==6.0.2 # via mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, pybtex, pymdown-extensions, pyyaml-env-tag, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
pyyaml-env-tag==0.1 # via mkdocs
rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -200,7 +200,7 @@ sniffio==1.3.1 # via anyio, httpx, -r requirements.txt
snowballstemmer==2.2.0 # via sphinx, -r requirements.txt
soupsieve==2.6 # via beautifulsoup4, -r requirements.txt
spglib==2.5.0 # via matid, pymatgen, -r requirements.txt
-sphinx==8.0.2 # via recommonmark, -r requirements.txt
+sphinx==8.1.3 # via recommonmark, -r requirements.txt
sphinxcontrib-applehelp==2.0.0 # via sphinx, -r requirements.txt
sphinxcontrib-devhelp==2.0.0 # via sphinx, -r requirements.txt
sphinxcontrib-htmlhelp==2.1.0 # via sphinx, -r requirements.txt
@@ -210,7 +210,7 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx, -r requirements.txt
sqlalchemy==2.0.35 # via alembic, jupyterhub, -r requirements.txt
starlette==0.27.0 # via fastapi, -r requirements.txt
structlog==24.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-super-collections==0.5.0 # via mkdocs-macros-plugin
+super-collections==0.5.3 # via mkdocs-macros-plugin
sympy==1.13.3 # via pymatgen, -r requirements.txt
tabulate==0.8.9 # via nomad-openbis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
tenacity==9.0.0 # via plotly, -r requirements.txt
diff --git a/requirements-plugins.txt b/requirements-plugins.txt
index a6e3b1f2465cc64a6f0d17afda323f5a983b4afc..d1d13bc8af764b42b5e72ac1cf47786c77539368 100644
--- a/requirements-plugins.txt
+++ b/requirements-plugins.txt
@@ -1,7 +1,7 @@
# This file was autogenerated by uv via the following command:
# uv pip compile --universal -p 3.11 --annotation-style=line --output-file=requirements-plugins.txt --unsafe-package nomad-lab -c requirements-dev.txt default_plugins.txt
aniso8601==9.0.1 # via nomad-lab, -c requirements-dev.txt
-anyio==4.6.0 # via httpx, jupyter-server, -c requirements-dev.txt
+anyio==4.6.2 # via httpx, jupyter-server, -c requirements-dev.txt
anytree==2.12.1 # via pynxtools
appnope==0.1.4 ; platform_system == 'Darwin' # via ipykernel
argon2-cffi==23.1.0 # via jupyter-server
@@ -17,7 +17,7 @@ async-property==0.2.2 # via python-keycloak, -c requirements-dev.txt
attrs==24.2.0 # via jsonschema, -c requirements-dev.txt
babel==2.16.0 # via jupyterlab-server, -c requirements-dev.txt
beautifulsoup4==4.12.3 # via nbconvert, -c requirements-dev.txt
-bitarray==2.9.2 # via nomad-lab, -c requirements-dev.txt
+bitarray==2.9.3 # via nomad-lab, -c requirements-dev.txt
bleach==6.1.0 # via nbconvert
blinker==1.8.2 # via flask
blosc2==2.7.1 # via tables
@@ -112,7 +112,7 @@ locket==1.0.0 # via partd
lxml==5.3.0 # via fabio, lxml-html-clean, nomad-lab, nomad-parser-plugins-atomistic, nomad-parser-plugins-electronic, nomad-parser-plugins-workflow, pynxtools, -c requirements-dev.txt
lxml-html-clean==0.3.1 # via nomad-lab, perovskite-solar-cell-database, -c requirements-dev.txt
markupsafe==3.0.1 # via jinja2, nbconvert, werkzeug, -c requirements-dev.txt
-matid==2.1.2 # via nomad-lab, nomad-simulations, -c requirements-dev.txt
+matid==2.1.3 # via nomad-lab, nomad-simulations, -c requirements-dev.txt
matplotlib==3.9.2 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay, -c requirements-dev.txt
matplotlib-inline==0.1.7 # via ipykernel, ipython
matplotlib-scalebar==0.8.1 # via orix
@@ -132,7 +132,7 @@ nbformat==5.10.4 # via jupyter-server, nbclient, nbconvert
ndindex==1.9.2 # via blosc2
nest-asyncio==1.6.0 # via ipykernel
netcdf4==1.6.5 # via nomad-parser-plugins-electronic, -c requirements-dev.txt
-networkx==3.3 # via matid, nomad-schema-plugin-simulation-workflow, pymatgen, radioactivedecay, scikit-image, -c requirements-dev.txt
+networkx==3.4.1 # via matid, nomad-schema-plugin-simulation-workflow, pymatgen, radioactivedecay, scikit-image, -c requirements-dev.txt
niondata==15.6.3 # via nionswift, nionswift-io
nionswift==16.11.0 # via pynxtools-em
nionswift-io==15.2.1 # via nionswift
@@ -208,7 +208,7 @@ pynxtools-raman==0.0.1 # via pynxtools
pynxtools-stm==1.0.5 # via pynxtools
pynxtools-xps==0.4.2 # via pynxtools
pynxtools-xrd==0.0.2 # via pynxtools
-pyparsing==3.1.4 # via matplotlib, -c requirements-dev.txt
+pyparsing==3.2.0 # via matplotlib, -c requirements-dev.txt
pyrsistent==0.20.0 # via jsonschema, -c requirements-dev.txt
python-box==7.2.0 # via rosettasciio
python-dateutil==2.9.0.post0 # via arrow, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, matplotlib, pandas, rfc3161ng, rosettasciio, -c requirements-dev.txt
@@ -216,7 +216,7 @@ python-json-logger==2.0.2 # via jupyter-events, -c requirements-dev.txt
python-keycloak==4.6.2 # via nomad-lab, -c requirements-dev.txt
python-magic==0.4.24 # via nomad-lab, -c requirements-dev.txt
pytz==2024.2 # via nionswift, nomad-lab, pandas, -c requirements-dev.txt
-pywin32==307 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' # via jupyter-core, -c requirements-dev.txt
+pywin32==308 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' # via jupyter-core, -c requirements-dev.txt
pywinpty==2.0.13 ; os_name == 'nt' # via jupyter-server, jupyter-server-terminals, terminado
pyxem==0.16.0 # via pynxtools-em
pyyaml==6.0.2 # via dask, hyperspy, jupyter-events, kikuchipy, nomad-lab, nomad-parser-plugins-electronic, phonopy, pybtex, pynxtools, rosettasciio, -c requirements-dev.txt
diff --git a/requirements.txt b/requirements.txt
index 3329858a4828b6c391dc0822355f25dfb438f962..5d44e05d3df6f6f42e12f7eee6c5b0c7bd1ca54d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,7 +4,7 @@ alabaster==1.0.0 # via sphinx
alembic==1.13.3 # via jupyterhub
amqp==5.2.0 # via kombu
aniso8601==9.0.1 # via nomad-lab (pyproject.toml)
-anyio==4.6.0 # via httpx, starlette, watchfiles
+anyio==4.6.2 # via httpx, starlette, watchfiles
arrow==1.3.0 # via isoduration
ase==3.22.1 # via matid, nomad-lab (pyproject.toml)
asgiref==3.8.1 # via nomad-lab (pyproject.toml)
@@ -16,7 +16,7 @@ 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)
billiard==4.2.1 # via celery
-bitarray==2.9.2 # via nomad-lab (pyproject.toml)
+bitarray==2.9.3 # via nomad-lab (pyproject.toml)
cachetools==5.5.0 # via nomad-lab (pyproject.toml)
celery==5.4.0 # via nomad-lab (pyproject.toml)
certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests
@@ -86,7 +86,7 @@ lxml-html-clean==0.3.1 # via nomad-lab (pyproject.toml)
m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic
markupsafe==3.0.1 # via jinja2, mako
-matid==2.1.2 # via nomad-lab (pyproject.toml)
+matid==2.1.3 # via nomad-lab (pyproject.toml)
matplotlib==3.9.2 # via ase, pymatgen
mda-xdrlib==0.2.0 # via pyedr
mistune==3.0.2 # via m2r
@@ -96,7 +96,7 @@ monty==2024.7.30 # via pymatgen
mpmath==1.3.0 # via sympy
msgpack==1.1.0 # via nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via nomad-lab (pyproject.toml)
-networkx==3.3 # via matid, pymatgen
+networkx==3.4.1 # via matid, pymatgen
nomad-openbis==1.0.0 # via nomad-lab (pyproject.toml)
nptyping==1.4.4 # via nomad-lab (pyproject.toml)
numpy==1.26.4 # via ase, cftime, contourpy, h5grove, h5py, matid, matplotlib, netcdf4, nptyping, pandas, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-lab (pyproject.toml)
@@ -127,7 +127,7 @@ pygments==2.18.0 # via sphinx
pyjwt==2.6.0 # via nomad-lab (pyproject.toml)
pymatgen==2024.5.1 # via nomad-lab (pyproject.toml)
pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml)
-pyparsing==3.1.4 # via matplotlib, rdflib
+pyparsing==3.2.0 # via matplotlib, rdflib
pyrsistent==0.20.0 # via jsonschema
python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, jupyterhub, matplotlib, nomad-openbis, pandas, rfc3161ng
python-dotenv==1.0.1 # via uvicorn
@@ -138,7 +138,7 @@ python-magic==0.4.24 # via nomad-lab (pyproject.toml)
python-magic-bin==0.4.14 ; sys_platform == 'win32' # via nomad-lab (pyproject.toml)
python-multipart==0.0.12 # via nomad-lab (pyproject.toml)
pytz==2024.2 # via mongomock, pandas, nomad-lab (pyproject.toml)
-pywin32==307 ; sys_platform == 'win32' # via docker
+pywin32==308 ; sys_platform == 'win32' # via docker
pyyaml==6.0.2 # via pybtex, uvicorn, nomad-lab (pyproject.toml)
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
rdkit==2023.9.5 # via nomad-lab (pyproject.toml)
@@ -160,7 +160,7 @@ sniffio==1.3.1 # via anyio, httpx
snowballstemmer==2.2.0 # via sphinx
soupsieve==2.6 # via beautifulsoup4
spglib==2.5.0 # via matid, pymatgen
-sphinx==8.0.2 # via recommonmark
+sphinx==8.1.3 # via recommonmark
sphinxcontrib-applehelp==2.0.0 # via sphinx
sphinxcontrib-devhelp==2.0.0 # via sphinx
sphinxcontrib-htmlhelp==2.1.0 # via sphinx
diff --git a/tests/normalizing/test_material.py b/tests/normalizing/test_material.py
index d845fcf8d5e4096d165706b0fa7dcae276c9a265..c2b9289da2f68eb3c767fcfd0c2ea6bbf058dcb1 100644
--- a/tests/normalizing/test_material.py
+++ b/tests/normalizing/test_material.py
@@ -421,7 +421,7 @@ two_d_split_expected = Atoms(
pbc=[True, True, False],
)
two_d_swap = Atoms(
- symbols=['B', 'N'],
+ symbols=['B', 'H'],
positions=[
[0, 0, 0],
[-0.6, 0.3, 0],
@@ -430,7 +430,7 @@ two_d_swap = Atoms(
pbc=True,
)
two_d_swap_expected = Atoms(
- symbols=['B', 'N'],
+ symbols=['B', 'H'],
positions=[
[0, 0, 0.67082039],
[0, 0, 0],
@@ -464,7 +464,10 @@ def test_conventional_structure(atoms, expected, monkeypatch):
"""Tests that the conventional structure has the correct form."""
monkeypatch.setattr(
'nomad.normalizing.topology.top_50k_material_ids',
- {'upphbIG7rwgpi5sAvc9-z3GT1MCO': 1, 'nikqWRhuLtW8p8rPILRL60yQlf1C': 1},
+ {
+ 'nikqWRhuLtW8p8rPILRL60yQlf1C': 1,
+ 'R2G5lRApZZD9dzBpXcZXbGQbsZDi': 1,
+ },
)
entry = get_template_for_structure(atoms)
topology = entry.results.material.topology