Merge branch 'fix-dependencies' into 'develop'

Changed dependency versions to increase compatibility.

See merge request !1402

pyproject.toml

@@ -32,8 +32,8 @@ dependencies = [
     'httpx>=0.23.3',
     'memoization>=0.4.0',
     'rfc3161ng>=2.1.3',
-    'lxml~=4.6',
-    'wrapt~=1.12.1',
+    'lxml>=4.6',
+    'wrapt>=1.12.1',
     'pyyaml>=6.0',
     'python-magic==0.4.24',
     'hjson>=3.0.2',

requirements.txt

 #
-# This file is autogenerated by pip-compile with python 3.9
-# To update, run:
+# 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 --resolver=backtracking dependencies/matid/pyproject.toml dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/atomistic/pyproject.toml dependencies/parsers/database/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml dependencies/parsers/electronic/pyproject.toml dependencies/parsers/nexus/pyproject.toml dependencies/parsers/workflow/pyproject.toml pyproject.toml
+#    pip-compile --annotation-style=line --config=pyproject.toml --extra=infrastructure --extra=parsing --output-file=requirements.txt --resolver=backtracking dependencies/matid/pyproject.toml dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/atomistic/pyproject.toml dependencies/parsers/database/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml dependencies/parsers/electronic/pyproject.toml dependencies/parsers/nexus/pyproject.toml dependencies/parsers/workflow/pyproject.toml pyproject.toml
 #
 alabaster==0.7.12         # via sphinx
 alembic==1.9.1            # via jupyterhub
@@ -14,9 +14,9 @@ argon2-cffi==21.3.0       # via jupyter-server, nbclassic, notebook
 argon2-cffi-bindings==21.2.0  # via argon2-cffi
 arrow==1.2.3              # via isoduration
 asciitree==0.3.3          # via zarr
-ase==3.19.0               # via asr, ifes-apt-tc-data-modeling, matid (dependencies/matid/pyproject.toml), quippy-ase
+ase==3.19.0               # via asr, ifes-apt-tc-data-modeling, matid (dependencies/matid/pyproject.toml), nomad-lab (pyproject.toml), quippy-ase
 asgiref==3.6.0            # via nomad-lab (pyproject.toml)
-asr==0.4.1                # via workflowparsers (dependencies/parsers/workflow/pyproject.toml)
+asr==0.4.1                # via nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
 astunparse==1.6.3         # via mdtraj
 async-generator==1.10     # via jupyterhub
 async-timeout==4.0.2      # via redis
@@ -29,7 +29,7 @@ bcrypt==3.2.0             # via nomad-lab (pyproject.toml)
 beautifulsoup4==4.11.1    # via bs4, nbconvert
 billiard==3.6.4.0         # via celery
 biopython==1.80           # via mdanalysis
-bitarray==2.3.5           # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
+bitarray==2.3.5           # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml)
 bleach==5.0.1             # via nbconvert
 bs4==0.0.1                # via nomad-lab (pyproject.toml)
 cachetools==4.2.4         # via nomad-lab (pyproject.toml)
@@ -40,7 +40,7 @@ certipy==0.1.3            # via jupyterhub
 cffi==1.15.1              # via argon2-cffi-bindings, bcrypt, cryptography
 cftime==1.6.2             # via netcdf4
 charset-normalizer==2.0.12  # via requests
-click==8.1.3              # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nexusutils (dependencies/parsers/nexus/pyproject.toml), uvicorn
+click==8.1.3              # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), uvicorn
 click-didyoumean==0.3.0   # via celery
 click-plugins==1.1.1      # via celery
 click-repl==0.2.0         # via celery
@@ -79,13 +79,13 @@ fqdn==1.5.1               # via jsonschema
 fsspec==2022.11.0         # via dask, hyperspy
 future==0.18.2            # via uncertainties
 gitdb==4.0.10             # via gitpython
-gitpython==3.1.24         # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
+gitpython==3.1.24         # via nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
 greenlet==2.0.1           # via sqlalchemy
 griddataformats==0.7.0    # via mdanalysis
 gsd==2.7.0                # via mdanalysis
 h11==0.14.0               # via httpcore, uvicorn
 h5grove==1.2.0            # via jupyterlab-h5web, nomad-lab (pyproject.toml)
-h5py==3.6.0               # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, phonopy, pyscf
+h5py==3.6.0               # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, nomad-lab (pyproject.toml), phonopy, pyscf
 hjson==3.0.2              # via nomad-lab (pyproject.toml)
 html5lib==1.1             # via nomad-lab (pyproject.toml)
 httpcore==0.16.3          # via httpx
@@ -127,13 +127,13 @@ lark==1.1.5               # via nexusutils (dependencies/parsers/nexus/pyproject
 latexcodec==2.0.1         # via pybtex
 llvmlite==0.39.1          # via numba
 locket==1.0.0             # via partd
-lxml==4.7.1               # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml)
+lxml==4.7.1               # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab (pyproject.toml)
 m2r==0.2.1                # via nomad-lab (pyproject.toml)
 mako==1.2.4               # via alembic
 markupsafe==2.1.1         # via jinja2, mako, nbconvert, werkzeug
 matplotlib==3.5.3         # via ase, asr, hyperspy, mdanalysis, phonopy, pymatgen, radioactivedecay
 matplotlib-inline==0.1.6  # via ipykernel, ipython
-mdanalysis==2.5.0         # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml)
+mdanalysis==2.5.0         # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab (pyproject.toml)
 mdtraj==1.9.6             # via nomad-lab (pyproject.toml)
 memoization==0.4.0        # via nomad-lab (pyproject.toml)
 mistune==2.0.4            # via m2r, nbconvert
@@ -151,7 +151,7 @@ nbclient==0.7.2           # via nbconvert
 nbconvert==7.2.7          # via jupyter-server, nbclassic, notebook
 nbformat==5.7.3           # via jupyter-server, nbclassic, nbclient, nbconvert, notebook
 nest-asyncio==1.5.6       # via ipykernel, jupyter-client, nbclassic, notebook
-netcdf4==1.5.4            # via electronicparsers (dependencies/parsers/electronic/pyproject.toml)
+netcdf4==1.5.4            # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
 networkx==2.6.3           # via matid (dependencies/matid/pyproject.toml), mdanalysis, pymatgen, radioactivedecay, scikit-image
 notebook==6.5.3           # via jupyterlab
 notebook-shim==0.2.2      # via nbclassic
@@ -159,7 +159,7 @@ nptyping==1.4.4           # via nomad-lab (pyproject.toml)
 numba==0.56.4             # via hyperspy, sparse
 numcodecs==0.10.2         # via zarr
 numexpr==2.8.4            # via hyperspy
-numpy==1.22.4             # via ase, biopython, cftime, dask, f90wrap, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, zarr
+numpy==1.22.4             # via ase, biopython, cftime, dask, f90wrap, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, matid (dependencies/matid/pyproject.toml), matplotlib, mdanalysis, mdtraj, mrcfile, netcdf4, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, pandas, phonopy, pymatgen, pyscf, pywavelets, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, zarr
 oauthenticator==15.1.0    # via nomad-lab (pyproject.toml)
 oauthlib==3.2.2           # via jupyterhub
 openpyxl==3.1.2           # via nomad-lab (pyproject.toml)
@@ -168,15 +168,15 @@ orjson==3.6.0             # via h5grove, nomad-lab (pyproject.toml)
 packaging==23.0           # via dask, docker, hyperspy, ipykernel, jupyter-server, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mongomock, nbconvert, pint, scikit-image, sphinx, xarray
 palettable==3.3.0         # via pymatgen
 pamela==1.0.0             # via jupyterhub
-pandas==1.3.5             # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, panedr, pymatgen, xarray
+pandas==1.3.5             # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pymatgen, xarray
 pandocfilters==1.5.0      # via nbconvert
-panedr==0.2               # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml)
+panedr==0.2               # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab (pyproject.toml)
 parmed==3.0.0             # via nomad-lab (pyproject.toml)
 parso==0.8.3              # via jedi
 partd==1.3.0              # via dask
 passlib==1.7.4            # via nomad-lab (pyproject.toml)
 pexpect==4.8.0            # via ipython
-phonopy==2.11.0           # via asr, workflowparsers (dependencies/parsers/workflow/pyproject.toml)
+phonopy==2.11.0           # via asr, nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
 pickleshare==0.7.5        # via ipython
 pillow==9.4.0             # via imageio, matplotlib, scikit-image
 pint==0.17                # via hyperspy, nomad-lab (pyproject.toml)
@@ -208,9 +208,9 @@ python-keycloak==0.26.1   # via nomad-lab (pyproject.toml)
 python-logstash==0.4.6    # via nomad-lab (pyproject.toml)
 python-magic==0.4.24      # via nomad-lab (pyproject.toml)
 python-multipart==0.0.5   # via nomad-lab (pyproject.toml)
-pytz==2022.7.1            # via babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), pandas
+pytz==2022.7.1            # via babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), pandas
 pywavelets==1.3.0         # via scikit-image
-pyyaml==6.0               # via dask, electronicparsers (dependencies/parsers/electronic/pyproject.toml), hyperspy, phonopy, pybtex, uvicorn
+pyyaml==6.0               # via dask, electronicparsers (dependencies/parsers/electronic/pyproject.toml), hyperspy, nomad-lab (pyproject.toml), phonopy, pybtex, uvicorn
 pyzeo==0.1.4              # via nomad-lab (pyproject.toml)
 pyzmq==25.0.0             # via ipykernel, ipyparallel, jupyter-client, jupyter-server, nbclassic, notebook
 quippy-ase==0.9.14        # via nomad-lab (pyproject.toml)
@@ -218,7 +218,7 @@ radioactivedecay==0.4.17  # via ifes-apt-tc-data-modeling
 rdflib==5.0.0             # via nomad-lab (pyproject.toml)
 recommonmark==0.7.1       # via nomad-lab (pyproject.toml)
 redis==4.4.2              # via celery
-requests==2.28.2          # via docker, hyperspy, jupyterhub, jupyterlab-server, mp-api, nexusutils (dependencies/parsers/nexus/pyproject.toml), oauthenticator, optimade, pymatgen, python-keycloak, requests-cache, rfc3161ng, sphinx
+requests==2.28.2          # via docker, hyperspy, jupyterhub, jupyterlab-server, mp-api, nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml), oauthenticator, optimade, pymatgen, python-keycloak, requests-cache, rfc3161ng, sphinx
 requests-cache==1.0.1     # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
 rfc3161ng==2.1.3          # via nomad-lab (pyproject.toml)
 rfc3339-validator==0.1.4  # via jsonschema
@@ -229,8 +229,8 @@ ruamel-yaml==0.17.21      # via jupyter-telemetry, oauthenticator, pymatgen
 ruamel-yaml-clib==0.2.7   # via ruamel-yaml
 runstats==2.0.0           # via nomad-lab (pyproject.toml)
 scikit-image==0.19.3      # via hyperspy
-scikit-learn==1.0.2       # via matid (dependencies/matid/pyproject.toml)
-scipy==1.7.1              # via ase, griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, pymatgen, pyscf, radioactivedecay, scikit-image, scikit-learn, sparse
+scikit-learn==1.0.2       # via matid (dependencies/matid/pyproject.toml), nomad-lab (pyproject.toml)
+scipy==1.7.1              # via ase, griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, pyscf, radioactivedecay, scikit-image, scikit-learn, sparse
 send2trash==1.8.0         # via jupyter-server, nbclassic, notebook
 sentinels==1.0.0          # via mongomock
 six==1.16.0               # via astunparse, basicauth, bcrypt, bleach, click-repl, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, python-dateutil, python-multipart, rdflib, rfc3339-validator, url-normalize, validators
@@ -284,7 +284,7 @@ websockets==10.4          # via uvicorn
 werkzeug==2.2.2           # via flask
 wheel==0.38.4             # via astunparse
 wrapt==1.12.1             # via nomad-lab (pyproject.toml)
-xarray==2023.1.0          # via nexusutils (dependencies/parsers/nexus/pyproject.toml)
+xarray==2023.1.0          # via nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
 zarr==2.12.0              # via hyperspy
 zipp==3.11.0              # via importlib-metadata
 zipstream-new==1.1.5      # via nomad-lab (pyproject.toml)