diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 267a67c332a3d9fdce1a5340cd835ec49554eda1..d53cf660fdefa320b6119dfb662ac37451d847b7 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -375,7 +375,10 @@ build final image:
install tests:
stage: test
- image: python:3.9
+ parallel:
+ matrix:
+ - PYTHON_VERSION: ["3.9", "3.10", "3.11"]
+ image: python:${PYTHON_VERSION}
needs: ["build python package"]
variables:
UV_SYSTEM_PYTHON: true
diff --git a/Dockerfile b/Dockerfile
index 79f1d21ad59635308b317d621f45df38b63e55f2..a59347f2a3b294aec3fc197cc147648128511eaa 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -21,7 +21,7 @@
# https://docs.docker.com/engine/reference/builder/
FROM node:16.15 AS base_node
-FROM python:3.9-slim AS base_python
+FROM python:3.11-slim AS base_python
# Keeps Python from buffering stdout and stderr to avoid situations where
# the application crashes without emitting any logs due to buffering.
ENV PYTHONUNBUFFERED 1
@@ -200,9 +200,9 @@ COPY default_plugins.txt .
RUN uv pip install -r default_plugins.txt -c requirements.txt
# Reduce the size of the packages
-RUN find /usr/local/lib/python3.9/ -type d -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + \
- && find /usr/local/lib/python3.9/ -type d -name 'test' -exec rm -r '{}' + \
- && find /usr/local/lib/python3.9/site-packages/ -name '*.so' ! -path '*/h5py/*' ! -path '*/quippy*/*' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
+RUN find /usr/local/lib/python3.11/ -type d -name 'tests' ! -path '*/networkx/*' -exec rm -r '{}' + \
+ && find /usr/local/lib/python3.11/ -type d -name 'test' -exec rm -r '{}' + \
+ && find /usr/local/lib/python3.11/site-packages/ -name '*.so' ! -path '*/h5py/*' ! -path '*/quippy*/*' -print -exec sh -c 'file "{}" | grep -q "not stripped" && strip -s "{}"' \;
# ================================================================================
@@ -221,7 +221,7 @@ COPY --chown=nomad:1000 scripts/run-worker.sh .
COPY --chown=nomad:1000 nomad/jupyterhub_config.py ./nomad/jupyterhub_config.py
COPY --chown=nomad:1000 --from=dev_package /app/examples/data/uploads /app/examples/data/uploads
-COPY --chown=nomad:1000 --from=builder /usr/local/lib/python3.9/site-packages /usr/local/lib/python3.9/site-packages
+COPY --chown=nomad:1000 --from=builder /usr/local/lib/python3.11/site-packages /usr/local/lib/python3.11/site-packages
COPY --chown=nomad:1000 --from=builder /usr/local/share/jupyterhub /usr/local/share/jupyterhub
COPY --chown=nomad:1000 --from=builder /usr/local/share/jupyter /usr/local/share/jupyter
COPY --chown=nomad:1000 --from=builder /usr/local/bin/nomad /usr/local/bin/nomad
@@ -229,7 +229,7 @@ COPY --chown=nomad:1000 --from=builder /usr/local/bin/jupyter* /usr/local/bin/
RUN mkdir -p /app/.volumes/fs \
&& chown -R nomad:1000 /app \
- && chown -R nomad:1000 /usr/local/lib/python3.9/site-packages/nomad
+ && chown -R nomad:1000 /usr/local/lib/python3.11/site-packages/nomad
USER nomad
diff --git a/docs/howto/plugins/normalizers.md b/docs/howto/plugins/normalizers.md
index 890ea6a91902d9ae872e199e938ef92ecd121c12..43c897bafde06719a594e0fe0c34a74d5acd2a23 100644
--- a/docs/howto/plugins/normalizers.md
+++ b/docs/howto/plugins/normalizers.md
@@ -178,7 +178,7 @@ cd <normalizer-dir>
Either remove the installed normalizer and `pip install` the cloned version:
```shell
-rm -rf <path-to-your-python-env>/lib/python3.9/site-packages/<normalizer-module-name>
+rm -rf <path-to-your-python-env>/lib/python3.11/site-packages/<normalizer-module-name>
pip install -e .
```
@@ -189,4 +189,4 @@ PYTHONPATH=. nomad parse <path-to-example-file>
```
Alternatively, you can also do a full [developer setup](../develop/setup.md) of the NOMAD infrastructure and
-enhance the normalizer there.
\ No newline at end of file
+enhance the normalizer there.
diff --git a/docs/howto/plugins/parsers.md b/docs/howto/plugins/parsers.md
index 67a9d5c738291751e10dd05cd21ac9afbe0a866b..7bb3196230d685d3643d970e246a02b9344402b9 100644
--- a/docs/howto/plugins/parsers.md
+++ b/docs/howto/plugins/parsers.md
@@ -424,7 +424,7 @@ cd <parser-dir>
Either remove the installed parser and `pip install` the cloned version:
```shell
-rm -rf <path-to-your-python-env>/lib/python3.9/site-packages/<parser-module-name>
+rm -rf <path-to-your-python-env>/lib/python3.11/site-packages/<parser-module-name>
pip install -e .
```
diff --git a/docs/tutorial/develop_plugin.md b/docs/tutorial/develop_plugin.md
index 0026471de6bb32fdba6e02baf870157a701dff22..f60077d022d4e8ab55381d6edc2b571d8880d7bb 100644
--- a/docs/tutorial/develop_plugin.md
+++ b/docs/tutorial/develop_plugin.md
@@ -172,7 +172,7 @@ and the "Allow GitHub Actions to create and approve pull requests" options and c
Before we can start developing we recommend to create a virtual environment using Python 3.9
```sh
-python3.9 -m venv .pyenv
+python3.11 -m venv .pyenv
source .pyenv/bin/activate
```
diff --git a/nomad/app/v1/routers/systems.py b/nomad/app/v1/routers/systems.py
index ce0cf3957eba6a443848f9830ff4158b2f6b00db..36748041d27430c43d74e9282662dcbcd449a1be 100644
--- a/nomad/app/v1/routers/systems.py
+++ b/nomad/app/v1/routers/systems.py
@@ -17,6 +17,7 @@
#
from typing import Dict, List, Union
from io import StringIO, BytesIO
+import sys
from collections import OrderedDict
from enum import Enum
@@ -210,9 +211,15 @@ for format in format_map.values():
)
format_features = '\n'.join(format_features_list)
+if sys.version_info < (3, 11):
-class TempFormatEnum(str, Enum):
- pass
+ class TempFormatEnum(str, Enum):
+ pass
+else:
+ from enum import StrEnum
+
+ class TempFormatEnum(StrEnum):
+ pass
FormatEnum = TempFormatEnum(
@@ -239,8 +246,15 @@ wrap_mode_map: Dict[str, dict] = OrderedDict(
)
-class TempWrapModeEnum(str, Enum):
- pass
+if sys.version_info < (3, 11):
+
+ class TempWrapModeEnum(str, Enum):
+ pass
+else:
+ from enum import StrEnum
+
+ class TempWrapModeEnum(StrEnum):
+ pass
WrapModeEnum = TempWrapModeEnum(
@@ -334,7 +348,7 @@ Here is a brief rundown of the different features each format supports:
{format_features}""",
),
wrap_mode: WrapModeEnum = Query( # type: ignore
- default=WrapModeEnum.original,
+ default=WrapModeEnum.original, # type: ignore
description=f"""Determines how to handle atomic positions for the requested system. The available options are:
{wrap_mode_description}
@@ -437,13 +451,13 @@ Here is a brief rundown of the different features each format supports:
pass
# Handle wrap mode
- if wrap_mode == WrapModeEnum.wrap:
+ if wrap_mode == WrapModeEnum.wrap: # type: ignore
atoms.positions = wrap_positions(
atoms.positions.magnitude,
atoms.lattice_vectors.magnitude,
atoms.periodic,
)
- elif wrap_mode == WrapModeEnum.unwrap:
+ elif wrap_mode == WrapModeEnum.unwrap: # type: ignore
atoms.positions = unwrap_positions(
atoms.positions.magnitude,
atoms.lattice_vectors.magnitude,
diff --git a/requirements-dev.txt b/requirements-dev.txt
index d1fda4dd9940238632919ab11c4577ebc7890781..87ea1aa64ee33c75f125d7d183d13e6f7ffb0f68 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,5 @@
# This file was autogenerated by uv via the following command:
-# uv pip compile -p 3.9 --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
+# uv pip compile --universal --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml
aiosmtpd==1.4.6 # via nomad-lab (pyproject.toml)
alabaster==0.7.16 # via sphinx, -r requirements.txt
alembic==1.13.2 # via jupyterhub, -r requirements.txt
@@ -10,14 +10,14 @@ arrow==1.3.0 # via isoduration, -r requirements.txt
ase==3.22.1 # via asr, matid, quippy-ase, -r requirements.txt, nomad-lab (pyproject.toml)
asgiref==3.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
asr==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-astroid==3.2.2 # via nomad-lab (pyproject.toml)
+astroid==3.2.4 # via nomad-lab (pyproject.toml)
asttokens==2.4.1 # via devtools
async-generator==1.10 # via jupyterhub, -r requirements.txt
async-property==0.2.2 # via python-keycloak, -r requirements.txt
-atpublic==4.1.0 # via aiosmtpd
+atpublic==5.0 # via aiosmtpd
attrs==23.2.0 # via aiosmtpd, jsonschema, -r requirements.txt
babel==2.15.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx, -r requirements.txt
-backports-tarfile==1.2.0 # via jaraco-context
+backports-tarfile==1.2.0 ; python_version < '3.12' # 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)
@@ -26,22 +26,22 @@ biopython==1.84 # via mdanalysis, -r requirements.txt
bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
blinker==1.8.2 # via flask, -r requirements.txt
build==1.2.1 # via nomad-lab (pyproject.toml)
-cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
+cachetools==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2024.7.4 # 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
+cffi==1.16.0 ; platform_python_implementation != 'PyPy' # via cryptography, -r requirements.txt
cftime==1.6.4 # 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, flask, mkdocs, mkdocs-click, 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
-colorama==0.4.6 # via mkdocs-material, twine
+colorama==0.4.6 # via build, click, mkdocs, mkdocs-material, pytest, sphinx, tqdm, twine, uvicorn, -r requirements.txt
commonmark==0.9.1 # via recommonmark, -r requirements.txt
contourpy==1.2.1 # via matplotlib, -r requirements.txt
-coverage==7.5.4 # via pytest-cov
-cryptography==42.0.8 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, -r requirements.txt
+coverage==7.6.0 # via pytest-cov
+cryptography==43.0.0 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage, -r requirements.txt
cycler==0.12.1 # via matplotlib, -r requirements.txt
decorator==5.1.1 # via validators, -r requirements.txt
deprecation==2.1.0 # via python-keycloak, -r requirements.txt
@@ -57,7 +57,7 @@ email-validator==1.3.1 # via optimade, -r requirements.txt
escapism==1.0.1 # via dockerspawner, -r requirements.txt
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, pytest, -r requirements.txt
+exceptiongroup==1.2.2 ; python_version < '3.11' # via anyio, pytest, -r requirements.txt
execnet==2.1.1 # via pytest-xdist
executing==2.0.1 # via devtools
f90wrap==0.2.15 # via quippy-ase, -r requirements.txt
@@ -65,12 +65,12 @@ fastapi==0.99.1 # via h5grove, -r requirements.txt, nomad-lab (pyproje
fasteners==0.19 # via mdanalysis, -r requirements.txt
filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
flask==3.0.3 # via asr, -r requirements.txt
-fonttools==4.53.0 # via matplotlib, -r requirements.txt
+fonttools==4.53.1 # via matplotlib, -r requirements.txt
fqdn==1.5.1 # via jsonschema, -r requirements.txt
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, -r requirements.txt, nomad-lab (pyproject.toml)
-greenlet==3.0.3 # via sqlalchemy, -r requirements.txt
+greenlet==3.0.3 ; python_version < '3.13' and (platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64') # via sqlalchemy, -r requirements.txt
griddataformats==1.0.2 # via mdanalysis, -r requirements.txt
gsd==3.3.0 # via mdanalysis, -r requirements.txt
gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -85,7 +85,7 @@ httpx==0.27.0 # via python-keycloak, -r requirements.txt, nomad-lab
idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt
imagesize==1.4.1 # via sphinx, -r requirements.txt
importlib-metadata==7.1.0 # via build, flask, jupyterhub, keyring, markdown, mkdocs, mkdocs-get-deps, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml)
-importlib-resources==6.4.0 # via matplotlib, spglib, -r requirements.txt
+importlib-resources==6.4.0 ; python_version < '3.10' # via matplotlib, spglib, -r requirements.txt
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
iniconfig==2.0.0 # via pytest
isodate==0.6.1 # via rdflib, -r requirements.txt
@@ -94,6 +94,7 @@ itsdangerous==2.2.0 # via flask, -r requirements.txt, nomad-lab (pyproject
jaraco-classes==3.4.0 # via keyring
jaraco-context==5.3.0 # via keyring
jaraco-functools==4.0.1 # via keyring
+jeepney==0.8.0 ; sys_platform == 'linux' # via keyring, secretstorage
jinja2==3.1.4 # via flask, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx, -r requirements.txt
jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn, -r requirements.txt
@@ -114,7 +115,7 @@ mako==1.3.5 # via alembic, -r requirements.txt
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)
matid==2.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-matplotlib==3.9.0 # via ase, asr, mdanalysis, phonopy, pymatgen, -r requirements.txt
+matplotlib==3.9.1 # via ase, asr, mdanalysis, phonopy, pymatgen, -r requirements.txt
mda-xdrlib==0.2.0 # via pyedr, -r requirements.txt
mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps
@@ -125,23 +126,23 @@ mkdocs-get-deps==0.2.0 # via mkdocs
mkdocs-git-revision-date-localized-plugin==1.2.6 # via nomad-lab (pyproject.toml)
mkdocs-glightbox==0.4.0 # via nomad-lab (pyproject.toml)
mkdocs-macros-plugin==1.0.5 # via nomad-lab (pyproject.toml)
-mkdocs-material==9.5.28 # via nomad-lab (pyproject.toml)
+mkdocs-material==9.5.30 # 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
mongoengine==0.28.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade, -r requirements.txt
-monty==2024.5.24 # via pymatgen, -r requirements.txt
+monty==2024.7.12 # via pymatgen, -r requirements.txt
more-itertools==10.3.0 # via jaraco-classes, jaraco-functools
mpmath==1.3.0 # via sympy, -r requirements.txt
-mrcfile==1.5.0 # via griddataformats, -r requirements.txt
+mrcfile==1.5.3 # via griddataformats, -r requirements.txt
msgpack==1.0.8 # via mmtf-python, -r requirements.txt, 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)
netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml)
networkx==2.6.3 # via matid, mdanalysis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
-nh3==0.2.17 # via readme-renderer
+nh3==0.2.18 # via readme-renderer
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, biopython, cftime, contourpy, f90wrap, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, quippy-ase, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
@@ -153,38 +154,40 @@ orjson==3.10.6 # via h5grove, -r requirements.txt, nomad-lab (pyproje
packaging==24.1 # via build, deprecation, f90wrap, gunicorn, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt
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
+pamela==1.1.0 ; sys_platform != 'win32' # via jupyterhub, -r requirements.txt
pandas==1.5.3 # via nomad-openbis, panedr, pymatgen, xarray, -r requirements.txt, nomad-lab (pyproject.toml)
panedr==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
parmed==4.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
pathspec==0.12.1 # via mkdocs
-phonopy==2.25.0 # via asr, -r requirements.txt
+phonopy==2.26.6 # via asr, -r requirements.txt
pillow==10.4.0 # via matplotlib, rdkit, -r requirements.txt
pint==0.17 # via -r requirements.txt, nomad-lab (pyproject.toml)
pkginfo==1.11.1 # via twine
platformdirs==4.2.2 # via mkdocs-get-deps
-plotly==5.22.0 # via asr, pymatgen, -r requirements.txt
+plotly==5.23.0 # via asr, pymatgen, -r requirements.txt
pluggy==1.5.0 # via pytest
prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt
prompt-toolkit==3.0.47 # via click-repl, -r requirements.txt
+psutil==6.0.0 ; sys_platform == 'win32' # via jupyterhub, -r requirements.txt
pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng, -r requirements.txt
pyasn1-modules==0.4.0 # via rfc3161ng, -r requirements.txt
pybtex==0.24.0 # via pymatgen, -r requirements.txt
pycodestyle==2.12.0 # via nomad-lab (pyproject.toml)
-pycparser==2.22 # via cffi, -r requirements.txt
+pycparser==2.22 ; platform_python_implementation != 'PyPy' # via cffi, -r requirements.txt
pydantic==1.10.17 # via fastapi, optimade, -r requirements.txt, nomad-lab (pyproject.toml)
pyedr==0.8.0 # via panedr, -r requirements.txt
pygments==2.18.0 # via devtools, mkdocs-material, readme-renderer, sphinx, -r requirements.txt
pyjwt==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+pylibmagic==0.5.0 ; sys_platform == 'darwin' # via -r requirements.txt, nomad-lab (pyproject.toml)
pymatgen==2024.5.1 # via asr, -r requirements.txt, 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)
-pyopenssl==24.1.0 # via certipy, -r requirements.txt
+pyopenssl==24.2.1 # via certipy, -r requirements.txt
pyparsing==3.1.2 # via matplotlib, rdflib, -r requirements.txt
pyproject-hooks==1.1.0 # via build
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==0.23.7 # via nomad-lab (pyproject.toml)
+pytest-asyncio==0.23.8 # via nomad-lab (pyproject.toml)
pytest-cov==5.0.0 # via nomad-lab (pyproject.toml)
pytest-split==0.9.0 # via nomad-lab (pyproject.toml)
pytest-timeout==2.3.1 # via nomad-lab (pyproject.toml)
@@ -193,19 +196,22 @@ python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import
python-dotenv==1.0.1 # via uvicorn, -r requirements.txt
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-keycloak==4.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+python-keycloak==4.2.3 # 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-magic-bin==0.4.14 ; sys_platform == 'win32' # 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, pandas, -r requirements.txt, nomad-lab (pyproject.toml)
+pywin32==306 ; sys_platform == 'win32' # via docker, -r requirements.txt
+pywin32-ctypes==0.2.2 ; sys_platform == 'win32' # via keyring
pyyaml==6.0.1 # via mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, phonopy, pybtex, pymdown-extensions, pyyaml-env-tag, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml)
pyyaml-env-tag==0.1 # via mkdocs
quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml)
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
+readme-renderer==44.0 # via twine
recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-regex==2024.5.15 # via mkdocs-material
+regex==2024.7.24 # via mkdocs-material
requests==2.31.0 # via docker, jupyterhub, mkdocs-material, nomad-openbis, oauthenticator, optimade, 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
rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -214,36 +220,37 @@ rfc3986==2.0.0 # via twine
rfc3987==1.3.8 # via jsonschema, -r requirements.txt
rope==0.21.0 # via nomad-lab (pyproject.toml)
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
-ruff==0.5.4 # via nomad-lab (pyproject.toml)
+ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt
+ruff==0.5.5 # via nomad-lab (pyproject.toml)
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-learn==1.5.1 # via matid, -r requirements.txt, nomad-lab (pyproject.toml)
scipy==1.13.1 # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml)
+secretstorage==3.3.3 ; sys_platform == 'linux' # via keyring
sentinels==1.0.0 # via mongomock, -r requirements.txt
six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, 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
+spglib==2.5.0 # via asr, matid, phonopy, pymatgen, -r requirements.txt
+sphinx==7.4.7 # 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-htmlhelp==2.0.6 # 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-qthelp==1.0.8 # via sphinx, -r requirements.txt
sphinxcontrib-serializinghtml==1.1.10 # via sphinx, -r requirements.txt
sqlalchemy==2.0.31 # via alembic, jupyterhub, -r requirements.txt
starlette==0.27.0 # via fastapi, -r requirements.txt
-structlog==24.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
-sympy==1.12.1 # via pymatgen, -r requirements.txt
+structlog==24.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
+sympy==1.13.1 # via pymatgen, -r requirements.txt
tabulate==0.8.9 # via nomad-openbis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml)
-tenacity==8.4.2 # via plotly, -r requirements.txt
+tenacity==8.5.0 # via plotly, -r requirements.txt
termcolor==2.4.0 # via mkdocs-macros-plugin
texttable==1.7.0 # via nomad-openbis, -r requirements.txt
threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt
-tifffile==2024.7.2 # via h5grove, -r requirements.txt
-tomli==2.0.1 # via build, coverage, mypy, pytest, sphinx, -r requirements.txt
+tifffile==2024.7.24 # via h5grove, -r requirements.txt
+tomli==2.0.1 ; python_full_version <= '3.11.0a6' or python_version < '3.11' # via build, coverage, mypy, pytest, sphinx, -r requirements.txt
toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml)
tornado==6.4.1 # via jupyterhub, -r requirements.txt
tqdm==4.66.4 # via mdanalysis, pyedr, pymatgen, twine, -r requirements.txt
@@ -251,16 +258,16 @@ traitlets==5.14.3 # via jupyter-telemetry, jupyterhub, -r requirements.t
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==4.12.2 # via alembic, anyio, asgiref, astroid, fastapi, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn, -r requirements.txt
+typing-extensions==4.12.2 # via alembic, anyio, asgiref, astroid, fastapi, jwcrypto, kombu, mypy, pydantic, spglib, sqlalchemy, starlette, uvicorn, -r requirements.txt
typish==1.9.3 # via nptyping, -r requirements.txt
tzdata==2024.1 # via celery, -r requirements.txt
-uncertainties==3.2.1 # via pymatgen, -r requirements.txt
+uncertainties==3.2.2 # via pymatgen, -r requirements.txt
unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema, -r requirements.txt
urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt
-uv==0.2.21 # via nomad-lab (pyproject.toml)
-uvicorn==0.30.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
-uvloop==0.19.0 # via uvicorn, -r requirements.txt
+uv==0.2.29 # via nomad-lab (pyproject.toml)
+uvicorn==0.30.3 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml)
+uvloop==0.19.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn, -r requirements.txt
validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
vine==5.1.0 # via amqp, celery, kombu, -r requirements.txt
watchdog==4.0.1 # via mkdocs
diff --git a/requirements.txt b/requirements.txt
index 08656b154fc81be075d2b775d5f8eb479a7284db..2d9edb09161772a8c15e430796751d9067765a2d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
# This file was autogenerated by uv via the following command:
-# uv pip compile -p 3.9 --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
+# uv pip compile --universal --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml
alabaster==0.7.16 # via sphinx
alembic==1.13.2 # via jupyterhub
amqp==5.2.0 # via kombu
@@ -20,20 +20,21 @@ billiard==4.2.0 # via celery
biopython==1.84 # via mdanalysis
bitarray==2.9.2 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
blinker==1.8.2 # via flask
-cachetools==5.3.3 # via nomad-lab (pyproject.toml)
+cachetools==5.4.0 # via nomad-lab (pyproject.toml)
celery==5.4.0 # via nomad-lab (pyproject.toml)
certifi==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests
certipy==0.1.3 # via jupyterhub
-cffi==1.16.0 # via cryptography
+cffi==1.16.0 ; platform_python_implementation != 'PyPy' # via cryptography
cftime==1.6.4 # via netcdf4
charset-normalizer==3.3.2 # via requests
click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, uvicorn, nomad-lab (pyproject.toml)
click-didyoumean==0.3.1 # via celery
click-plugins==1.1.1 # via celery
click-repl==0.3.0 # via celery
+colorama==0.4.6 ; platform_system == 'Windows' or sys_platform == 'win32' # via click, sphinx, tqdm, uvicorn
commonmark==0.9.1 # via recommonmark
contourpy==1.2.1 # via matplotlib
-cryptography==42.0.8 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng
+cryptography==43.0.0 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng
cycler==0.12.1 # via matplotlib
decorator==5.1.1 # via validators
deprecation==2.1.0 # via python-keycloak
@@ -47,17 +48,17 @@ elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml)
email-validator==1.3.1 # via optimade
escapism==1.0.1 # via dockerspawner
et-xmlfile==1.1.0 # via openpyxl
-exceptiongroup==1.2.1 # via anyio
+exceptiongroup==1.2.2 ; python_version < '3.11' # via anyio
f90wrap==0.2.15 # via quippy-ase
fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml)
fasteners==0.19 # via mdanalysis
filelock==3.3.1 # via nomad-lab (pyproject.toml)
flask==3.0.3 # via asr
-fonttools==4.53.0 # via matplotlib
+fonttools==4.53.1 # via matplotlib
fqdn==1.5.1 # via jsonschema
gitdb==4.0.11 # via gitpython
gitpython==3.1.43 # via nomad-lab (pyproject.toml)
-greenlet==3.0.3 # via sqlalchemy
+greenlet==3.0.3 ; python_version < '3.13' and (platform_machine == 'AMD64' or platform_machine == 'WIN32' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'ppc64le' or platform_machine == 'win32' or platform_machine == 'x86_64') # via sqlalchemy
griddataformats==1.0.2 # via mdanalysis
gsd==3.3.0 # via mdanalysis
gunicorn==21.2.0 # via nomad-lab (pyproject.toml)
@@ -72,7 +73,7 @@ httpx==0.27.0 # via python-keycloak, nomad-lab (pyproject.toml)
idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests
imagesize==1.4.1 # via sphinx
importlib-metadata==7.1.0 # via flask, jupyterhub, sphinx, nomad-lab (pyproject.toml)
-importlib-resources==6.4.0 # via matplotlib, spglib
+importlib-resources==6.4.0 ; python_version < '3.10' # via matplotlib, spglib
inflection==0.5.1 # via nomad-lab (pyproject.toml)
isodate==0.6.1 # via rdflib
isoduration==20.11.0 # via jsonschema
@@ -95,16 +96,16 @@ m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.3.5 # via alembic
markupsafe==2.1.5 # via jinja2, mako, werkzeug
matid==2.0.1 # via nomad-lab (pyproject.toml)
-matplotlib==3.9.0 # via ase, asr, mdanalysis, phonopy, pymatgen
+matplotlib==3.9.1 # via ase, asr, mdanalysis, phonopy, pymatgen
mda-xdrlib==0.2.0 # via pyedr
mdanalysis==2.5.0 # via nomad-lab (pyproject.toml)
mistune==3.0.2 # via m2r
mmtf-python==1.1.3 # via mdanalysis
mongoengine==0.28.2 # via nomad-lab (pyproject.toml)
mongomock==4.1.2 # via optimade
-monty==2024.5.24 # via pymatgen
+monty==2024.7.12 # via pymatgen
mpmath==1.3.0 # via sympy
-mrcfile==1.5.0 # via griddataformats
+mrcfile==1.5.3 # via griddataformats
msgpack==1.0.8 # via mmtf-python, nomad-lab (pyproject.toml)
netcdf4==1.6.5 # via nomad-lab (pyproject.toml)
networkx==2.6.3 # via matid, mdanalysis, pymatgen, nomad-lab (pyproject.toml)
@@ -118,37 +119,41 @@ optimade==0.22.1 # via nomad-lab (pyproject.toml)
orjson==3.10.6 # via h5grove, nomad-lab (pyproject.toml)
packaging==24.1 # via deprecation, f90wrap, gunicorn, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, sphinx, xarray
palettable==3.3.3 # via pymatgen
-pamela==1.1.0 # via jupyterhub
+pamela==1.1.0 ; sys_platform != 'win32' # via jupyterhub
pandas==1.5.3 # via nomad-openbis, panedr, pymatgen, xarray, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml)
panedr==0.8.0 # via nomad-lab (pyproject.toml)
parmed==4.2.2 # via nomad-lab (pyproject.toml)
-phonopy==2.25.0 # via asr
+phonopy==2.26.6 # via asr
pillow==10.4.0 # via matplotlib, rdkit
pint==0.17 # via nomad-lab (pyproject.toml)
-plotly==5.22.0 # via asr, pymatgen
+plotly==5.23.0 # via asr, pymatgen
prometheus-client==0.20.0 # via jupyterhub
prompt-toolkit==3.0.47 # via click-repl
+psutil==6.0.0 ; sys_platform == 'win32' # via jupyterhub
pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng
pyasn1-modules==0.4.0 # via rfc3161ng
pybtex==0.24.0 # via pymatgen
-pycparser==2.22 # via cffi
+pycparser==2.22 ; platform_python_implementation != 'PyPy' # via cffi
pydantic==1.10.17 # via fastapi, optimade, nomad-lab (pyproject.toml)
pyedr==0.8.0 # via panedr
pygments==2.18.0 # via sphinx
pyjwt==2.6.0 # via nomad-lab (pyproject.toml)
+pylibmagic==0.5.0 ; sys_platform == 'darwin' # via nomad-lab (pyproject.toml)
pymatgen==2024.5.1 # via asr, nomad-lab (pyproject.toml)
pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml)
-pyopenssl==24.1.0 # via certipy
+pyopenssl==24.2.1 # via certipy
pyparsing==3.1.2 # via matplotlib, rdflib
pyrsistent==0.20.0 # via jsonschema
python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, jupyterhub, matplotlib, nomad-openbis, pandas, rfc3161ng
python-dotenv==1.0.1 # via uvicorn
python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml)
-python-keycloak==4.2.0 # via nomad-lab (pyproject.toml)
+python-keycloak==4.2.3 # 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-magic-bin==0.4.14 ; sys_platform == 'win32' # via nomad-lab (pyproject.toml)
python-multipart==0.0.9 # via nomad-lab (pyproject.toml)
pytz==2024.1 # via pandas, nomad-lab (pyproject.toml)
+pywin32==306 ; sys_platform == 'win32' # via docker
pyyaml==6.0.1 # via phonopy, pybtex, uvicorn, nomad-lab (pyproject.toml)
quippy-ase==0.9.14 # via nomad-lab (pyproject.toml)
rdflib==5.0.0 # via nomad-lab (pyproject.toml)
@@ -160,7 +165,7 @@ rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml)
rfc3339-validator==0.1.4 # via jsonschema
rfc3987==1.3.8 # via jsonschema
ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen
-ruamel-yaml-clib==0.2.8 # via ruamel-yaml
+ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml
runstats==2.0.0 # via nomad-lab (pyproject.toml)
scikit-learn==1.5.1 # via matid, nomad-lab (pyproject.toml)
scipy==1.13.1 # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, nomad-lab (pyproject.toml)
@@ -170,38 +175,38 @@ smmap==5.0.1 # via gitdb
sniffio==1.3.1 # via anyio, httpx
snowballstemmer==2.2.0 # via sphinx
soupsieve==2.5 # via beautifulsoup4
-spglib==2.4.0 # via asr, matid, phonopy, pymatgen
-sphinx==7.3.7 # via recommonmark
+spglib==2.5.0 # via asr, matid, phonopy, pymatgen
+sphinx==7.4.7 # via recommonmark
sphinxcontrib-applehelp==1.0.8 # via sphinx
sphinxcontrib-devhelp==1.0.6 # via sphinx
-sphinxcontrib-htmlhelp==2.0.5 # via sphinx
+sphinxcontrib-htmlhelp==2.0.6 # via sphinx
sphinxcontrib-jsmath==1.0.1 # via sphinx
-sphinxcontrib-qthelp==1.0.7 # via sphinx
+sphinxcontrib-qthelp==1.0.8 # via sphinx
sphinxcontrib-serializinghtml==1.1.10 # via sphinx
sqlalchemy==2.0.31 # via alembic, jupyterhub
starlette==0.27.0 # via fastapi
-structlog==24.2.0 # via nomad-lab (pyproject.toml)
-sympy==1.12.1 # via pymatgen
+structlog==24.4.0 # via nomad-lab (pyproject.toml)
+sympy==1.13.1 # via pymatgen
tabulate==0.8.9 # via nomad-openbis, pymatgen, nomad-lab (pyproject.toml)
-tenacity==8.4.2 # via plotly
+tenacity==8.5.0 # via plotly
texttable==1.7.0 # via nomad-openbis
threadpoolctl==3.5.0 # via mdanalysis, scikit-learn
-tifffile==2024.7.2 # via h5grove
-tomli==2.0.1 # via sphinx
+tifffile==2024.7.24 # via h5grove
+tomli==2.0.1 ; python_version < '3.11' # via sphinx
toposort==1.10 # via nomad-lab (pyproject.toml)
tornado==6.4.1 # via jupyterhub
tqdm==4.66.4 # via mdanalysis, pyedr, pymatgen
traitlets==5.14.3 # via jupyter-telemetry, jupyterhub
types-python-dateutil==2.9.0.20240316 # via arrow
-typing-extensions==4.12.2 # via alembic, anyio, asgiref, fastapi, jwcrypto, kombu, pydantic, sqlalchemy, starlette, uvicorn
+typing-extensions==4.12.2 # via alembic, anyio, asgiref, fastapi, jwcrypto, kombu, pydantic, spglib, sqlalchemy, starlette, uvicorn
typish==1.9.3 # via nptyping
tzdata==2024.1 # via celery
-uncertainties==3.2.1 # via pymatgen
+uncertainties==3.2.2 # via pymatgen
unidecode==1.3.2 # via nomad-lab (pyproject.toml)
uri-template==1.3.0 # via jsonschema
urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests
-uvicorn==0.30.1 # via h5grove, nomad-lab (pyproject.toml)
-uvloop==0.19.0 # via uvicorn
+uvicorn==0.30.3 # via h5grove, nomad-lab (pyproject.toml)
+uvloop==0.19.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn
validators==0.18.2 # via nomad-lab (pyproject.toml)
vine==5.1.0 # via amqp, celery, kombu
watchfiles==0.22.0 # via uvicorn
diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh
index 5c8c80fd5ffcea4a661074aa627a8dba64e0ebb4..c9412f00f1aeda908da8db07781bd76fe25b2d1f 100755
--- a/scripts/check_python_dependencies.sh
+++ b/scripts/check_python_dependencies.sh
@@ -21,7 +21,7 @@ grep pynxtools scripts/install_default_plugins.sh | grep "@git+" 1>&2
cp requirements.txt requirements.txt.tmp
cp requirements-dev.txt requirements-dev.txt.tmp
-uv pip compile -q -U --annotation-style=line \
+uv pip compile -q -U --universal --annotation-style=line \
--extra=infrastructure --extra=parsing \
--output-file=requirements.txt \
dependencies/nomad-dos-fingerprints/pyproject.toml \
@@ -30,7 +30,7 @@ uv pip compile -q -U --annotation-style=line \
diff requirements.txt.tmp requirements.txt
-uv pip compile -q -U --annotation-style=line \
+uv pip compile -q -U --universal --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
requirements.txt \
diff --git a/scripts/generate_python_dependencies.sh b/scripts/generate_python_dependencies.sh
index a08c88fdb9e7eb849a84b967a896a7fb1b382c75..eeb5d4a03b0a35486fb988129621dc5c968c4b39 100755
--- a/scripts/generate_python_dependencies.sh
+++ b/scripts/generate_python_dependencies.sh
@@ -15,14 +15,14 @@ project_dir=$(dirname $(dirname $(realpath $0)))
cd $project_dir
-uv pip compile -U -p 3.9 --annotation-style=line \
+uv pip compile -U --universal --annotation-style=line \
--extra=infrastructure --extra=parsing \
--output-file=requirements.txt \
dependencies/nomad-dos-fingerprints/pyproject.toml \
dependencies/parsers/eelsdb/pyproject.toml \
pyproject.toml
-uv pip compile -U -p 3.9 --annotation-style=line \
+uv pip compile -U --universal --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
requirements.txt \
diff --git a/tests/app/v1/routers/test_systems.py b/tests/app/v1/routers/test_systems.py
index 40beb917bac514fb283090be6d0ce436ac9e7118..fe261c95348a121c3ec87207d9c0dea6aefc88a5 100644
--- a/tests/app/v1/routers/test_systems.py
+++ b/tests/app/v1/routers/test_systems.py
@@ -400,31 +400,31 @@ def test_indices(path, filename, n_atoms, client, example_data_systems):
),
pytest.param(
'/run/0/system/3',
- WrapModeEnum.original,
+ WrapModeEnum.original, # type: ignore
[[-15, -15, -15], [17, 17, 17]],
id='original',
),
pytest.param(
'/run/0/system/3',
- WrapModeEnum.wrap,
+ WrapModeEnum.wrap, # type: ignore
[[0, 0, 0], [2, 2, 2]],
id='wrap, pbc=[1, 1, 1]',
),
pytest.param(
'/run/0/system/4',
- WrapModeEnum.wrap,
+ WrapModeEnum.wrap, # type: ignore
[[-15, -15, -15], [17, 17, 17]],
id='wrap, pbc=[0, 0, 0]',
),
pytest.param(
'/run/0/system/3',
- WrapModeEnum.unwrap,
+ WrapModeEnum.unwrap, # type: ignore
[[1.5, 1.5, 1.5], [3.5, 3.5, 3.5]],
id='unwrap, pbc=[1, 1, 1]',
),
pytest.param(
'/run/0/system/4',
- WrapModeEnum.unwrap,
+ WrapModeEnum.unwrap, # type: ignore
[[-15, -15, -15], [17, 17, 17]],
id='unwrap, pbc=[0, 0, 0]',
),