diff --git a/pyproject.toml b/pyproject.toml
index f414282769aa6f344c25bac13cd9780983a1c5f6..b873257cd0e06590e26b0c3a1ad8ae3d10e9f283 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -72,10 +72,8 @@ infrastructure = [
'asgiref~=3.5',
'bagit==1.8.1',
'basicauth==0.4.1',
- 'bcrypt==3.2.0',
'beautifulsoup4',
'celery',
- 'cryptography',
'dockerspawner==13.0.0',
'elasticsearch==7.17.1',
'fastapi<0.100', # later versions pending pydantic v2 upgrade
@@ -93,7 +91,6 @@ infrastructure = [
'msgpack',
'oauthenticator==15.1.0',
'optimade[mongo]==0.22.1',
- 'passlib==1.7.4',
'pyjwt[crypto]==2.6.0',
'python-json-logger==2.0.2',
'python-logstash==0.4.6',
@@ -126,7 +123,7 @@ dev = [
'mypy==1.0.1', # bug: incompatible with derived models of pydantic v1
'names==0.3.0',
'pip-tools>=6.13.0',
- 'pycodestyle==2.8.0',
+ 'pycodestyle',
'pytest-cov==2.7.1',
'pytest-timeout==1.4.2',
'pytest-xdist>=1.30.0',
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 28402e87adf87142c51884b8f33e61d8ad7a6de4..0f5d54d1d77db4aa57a0284367974ddf155ff742 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -25,7 +25,6 @@ babel==2.14.0 # via -r requirements.txt, mkdocs-git-revision-date-lo
backports-tarfile==1.0.0 # via jaraco-context
bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-bcrypt==3.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
billiard==4.2.0 # via -r requirements.txt, celery
biopython==1.83 # via -r requirements.txt, mdanalysis
@@ -37,7 +36,7 @@ cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
celery==5.3.6 # via -r requirements.txt, nomad-lab (pyproject.toml)
certifi==2024.2.2 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via -r requirements.txt, jupyterhub
-cffi==1.16.0 # via -r requirements.txt, bcrypt, cryptography
+cffi==1.16.0 # via -r requirements.txt, cryptography
cftime==1.6.3 # via -r requirements.txt, netcdf4
charset-normalizer==3.3.2 # via -r requirements.txt, requests
click==8.1.7 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pip-tools, pynxtools, uvicorn
@@ -50,7 +49,7 @@ comm==0.2.2 # via -r requirements.txt, ipykernel
commonmark==0.9.1 # via -r requirements.txt, recommonmark
contourpy==1.2.1 # via -r requirements.txt, matplotlib
coverage==7.4.4 # via pytest-cov
-cryptography==42.0.5 # via -r requirements.txt, jwcrypto, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng, secretstorage
+cryptography==42.0.5 # via -r requirements.txt, jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage
cycler==0.12.1 # via -r requirements.txt, matplotlib
dask[array]==2024.4.1 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem
debugpy==1.8.1 # via -r requirements.txt, ipykernel
@@ -76,7 +75,7 @@ exceptiongroup==1.2.0 # via -r requirements.txt, anyio, ipython
execnet==2.1.1 # via pytest-xdist
executing==2.0.1 # via -r requirements.txt, devtools, stack-data
f90wrap==0.2.13 # via -r requirements.txt, quippy-ase
-fabio==2023.10.0 # via -r requirements.txt, pyfai, silx
+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
filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
@@ -104,12 +103,12 @@ httpcore==1.0.5 # via -r requirements.txt, httpx
httptools==0.6.1 # via -r requirements.txt, uvicorn
httpx==0.27.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
hyperspy==1.7.6 # via -r requirements.txt, kikuchipy, pynxtools, pyxem
-idna==3.6 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests
+idna==3.7 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests
ifes-apt-tc-data-modeling==0.1 # via -r requirements.txt, pynxtools
imageio==2.27.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via -r requirements.txt, sphinx
importlib-metadata==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyterhub, keyring, markdown, mkdocs, pynxtools, sphinx, twine
-importlib-resources==6.4.0 # via -r requirements.txt, matplotlib
+importlib-resources==6.4.0 # via -r requirements.txt, matplotlib, spglib
inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
ipykernel==6.29.4 # via -r requirements.txt, ipyparallel
ipyparallel==8.8.0 # via -r requirements.txt, hyperspy
@@ -135,7 +134,7 @@ jwcrypto==1.5.6 # via -r requirements.txt, python-keycloak
keyring==25.1.0 # via twine
kikuchipy==0.9.0 # via -r requirements.txt, pynxtools
kiwisolver==1.4.5 # via -r requirements.txt, matplotlib
-kombu==5.3.6 # via -r requirements.txt, celery
+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
@@ -195,7 +194,7 @@ oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via -r requirements.txt, jupyterhub
openpyxl==3.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
-orix==0.11.1 # via -r requirements.txt, diffsims, kikuchipy, pyxem
+orix==0.12.0 # via -r requirements.txt, diffsims, kikuchipy, pyxem
orjson==3.10.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
packaging==24.0 # via -r requirements.txt, build, dask, deprecation, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pooch, pytest, scikit-image, silx, sphinx, tables, xarray
paginate==0.5.6 # via mkdocs-material
@@ -206,7 +205,6 @@ panedr==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
parmed==4.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml)
parso==0.8.4 # via -r requirements.txt, jedi
partd==1.4.1 # via -r requirements.txt, dask
-passlib==1.7.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
pathspec==0.12.1 # via mkdocs
pexpect==4.9.0 # via -r requirements.txt, ipython
phonopy==2.9.1 # via -r requirements.txt, asr
@@ -231,7 +229,7 @@ pyasn1-modules==0.4.0 # via -r requirements.txt, rfc3161ng
pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git # via -r requirements.txt, nomad-lab (pyproject.toml)
pybtex==0.24.0 # via -r requirements.txt, pymatgen
pycifrw==4.4.5 # via -r requirements.txt, diffpy-structure
-pycodestyle==2.8.0 # via nomad-lab (pyproject.toml)
+pycodestyle==2.11.1 # via 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
@@ -285,7 +283,7 @@ rfc3987==1.3.8 # via -r requirements.txt, jsonschema
rope==0.21.0 # via nomad-lab (pyproject.toml)
ruamel-yaml==0.18.6 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator, pymatgen
ruamel-yaml-clib==0.2.8 # via -r requirements.txt, ruamel-yaml
-ruff==0.3.5 # via nomad-lab (pyproject.toml)
+ruff==0.3.7 # via nomad-lab (pyproject.toml)
runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml)
scikit-image==0.19.3 # via -r requirements.txt, hyperspy, kikuchipy, pyxem
scikit-learn==1.4.2 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem
@@ -293,13 +291,13 @@ scipy==1.13.0 # via -r requirements.txt, ase, diffsims, findiff, gri
secretstorage==3.3.3 # via keyring
sentinels==1.0.0 # via -r requirements.txt, mongomock
silx==2.0.1 # via -r requirements.txt, pyfai
-six==1.16.0 # via -r requirements.txt, asttokens, basicauth, bcrypt, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, pytest-xdist, python-dateutil, rdflib, rfc3339-validator, validators
+six==1.16.0 # via -r requirements.txt, asttokens, basicauth, 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==0.15.1 # via -r requirements.txt, hyperspy
-spglib==2.3.1 # via -r requirements.txt, asr, matid, phonopy, pymatgen
+spglib==2.4.0 # via -r requirements.txt, asr, matid, phonopy, pymatgen
sphinx==7.2.6 # via -r requirements.txt, recommonmark
sphinxcontrib-applehelp==1.0.8 # via -r requirements.txt, sphinx
sphinxcontrib-devhelp==1.0.6 # via -r requirements.txt, sphinx
diff --git a/requirements.txt b/requirements.txt
index ca95c112e3f71bffb27687be47b0c86266ae1844..ade7bbef828c66bbad27d61f48ffe095132fa18d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -21,7 +21,6 @@ attrs==23.2.0 # via jsonschema
babel==2.14.0 # via sphinx
bagit==1.8.1 # via nomad-lab (pyproject.toml)
basicauth==0.4.1 # via nomad-lab (pyproject.toml)
-bcrypt==3.2.0 # via nomad-lab (pyproject.toml)
beautifulsoup4==4.12.3 # via nomad-lab (pyproject.toml)
billiard==4.2.0 # via celery
biopython==1.83 # via mdanalysis
@@ -32,7 +31,7 @@ cachetools==5.3.3 # via nomad-lab (pyproject.toml)
celery==5.3.6 # via nomad-lab (pyproject.toml)
certifi==2024.2.2 # via elasticsearch, httpcore, httpx, requests
certipy==0.1.3 # via jupyterhub
-cffi==1.16.0 # via bcrypt, cryptography
+cffi==1.16.0 # via cryptography
cftime==1.6.3 # via netcdf4
charset-normalizer==3.3.2 # via requests
click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn
@@ -43,7 +42,7 @@ cloudpickle==3.0.0 # via dask, hyperspy
comm==0.2.2 # via ipykernel
commonmark==0.9.1 # via recommonmark
contourpy==1.2.1 # via matplotlib
-cryptography==42.0.5 # via jwcrypto, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng
+cryptography==42.0.5 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng
cycler==0.12.1 # via matplotlib
dask[array]==2024.4.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio
debugpy==1.8.1 # via ipykernel
@@ -66,7 +65,7 @@ et-xmlfile==1.1.0 # via openpyxl
exceptiongroup==1.2.0 # via anyio, ipython
executing==2.0.1 # via stack-data
f90wrap==0.2.13 # via quippy-ase
-fabio==2023.10.0 # via pyfai, silx
+fabio==2024.4.0 # via pyfai, silx
fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml)
fasteners==0.19 # via mdanalysis, zarr
filelock==3.3.1 # via nomad-lab (pyproject.toml)
@@ -93,12 +92,12 @@ httpcore==1.0.5 # via httpx
httptools==0.6.1 # via uvicorn
httpx==0.27.0 # via nomad-lab (pyproject.toml)
hyperspy==1.7.6 # via kikuchipy, pynxtools, pyxem
-idna==3.6 # via anyio, email-validator, httpx, jsonschema, requests
+idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests
ifes-apt-tc-data-modeling==0.1 # via pynxtools
imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via sphinx
importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyterhub, pynxtools, sphinx
-importlib-resources==6.4.0 # via matplotlib
+importlib-resources==6.4.0 # via matplotlib, spglib
inflection==0.5.1 # via nomad-lab (pyproject.toml)
ipykernel==6.29.4 # via ipyparallel
ipyparallel==8.8.0 # via hyperspy
@@ -119,7 +118,7 @@ jupyterhub==4.0.2 # via dockerspawner, nomad-lab (pyproject.toml), oauth
jwcrypto==1.5.6 # via python-keycloak
kikuchipy==0.9.0 # via pynxtools
kiwisolver==1.4.5 # via matplotlib
-kombu==5.3.6 # via celery
+kombu==5.3.7 # via celery
lark==1.1.9 # via optimade
latexcodec==3.0.0 # via pybtex
llvmlite==0.42.0 # via numba
@@ -165,7 +164,7 @@ oauthenticator==15.1.0 # via nomad-lab (pyproject.toml)
oauthlib==3.2.2 # via jupyterhub
openpyxl==3.1.2 # via nomad-lab (pyproject.toml)
optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml)
-orix==0.11.1 # via diffsims, kikuchipy, pyxem
+orix==0.12.0 # via diffsims, kikuchipy, pyxem
orjson==3.10.0 # via h5grove, nomad-lab (pyproject.toml)
packaging==24.0 # via dask, deprecation, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, pooch, scikit-image, silx, sphinx, tables, xarray
palettable==3.3.3 # via pymatgen
@@ -175,7 +174,6 @@ panedr==0.8.0 # via nomad-lab (pyproject.toml)
parmed==4.2.2 # via nomad-lab (pyproject.toml)
parso==0.8.4 # via jedi
partd==1.4.1 # via dask
-passlib==1.7.4 # via nomad-lab (pyproject.toml)
pexpect==4.9.0 # via ipython
phonopy==2.9.1 # via asr
pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, scikit-image
@@ -241,13 +239,13 @@ scikit-learn==1.4.2 # via kikuchipy, matid, nomad-lab (pyproject.toml), py
scipy==1.13.0 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
sentinels==1.0.0 # via mongomock
silx==2.0.1 # via pyfai
-six==1.16.0 # via asttokens, basicauth, bcrypt, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators
+six==1.16.0 # via asttokens, basicauth, 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==0.15.1 # via hyperspy
-spglib==2.3.1 # via asr, matid, phonopy, pymatgen
+spglib==2.4.0 # via asr, matid, phonopy, pymatgen
sphinx==7.2.6 # via recommonmark
sphinxcontrib-applehelp==1.0.8 # via sphinx
sphinxcontrib-devhelp==1.0.6 # via sphinx