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Commit 7554334d authored by Markus Scheidgen's avatar Markus Scheidgen
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Merge branch 'release' into 'develop' 

Changed version requirements on some dependencies.

See merge request nomad-lab/nomad-FAIR!1384
parents dcf8842b 70d1d5a7
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pyproject.toml
+ 3
− 3
View file @ 7554334d
......@@ -15,19 +15,19 @@ requires-python = ">=3.9"
dependencies = [
'numpy~=1.22.4',
'nptyping~=1.4.4',
'pandas~=1.3.5',
'pandas>=1.3.5,<2.0.0',
'cachetools>=4.2.4',
'docstring-parser>=0.12',
'pint==0.17',
'orjson==3.6.0',
'click>=7.1.2',
'requests>=2.28.2',
'requests>=2.27.1',
'pytz>=2022.7.1',
'aniso8601>=7.0.0',
'ase~=3.19.0',
'python-keycloak>=0.26.1',
'elasticsearch-dsl==7.4.0',
'pydantic>=1.10.8',
'pydantic>=1.10.8,<2.0.0',
'jmespath>=0.10.0',
'httpx>=0.23.3',
'memoization>=0.4.0',
......
requirements-dev.txt
+ 104
− 102
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This diff is collapsed.
requirements.txt
+ 23
− 21
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#
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
# This file is autogenerated by pip-compile with python 3.9
# To update, run:
#
# 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
#
......@@ -9,13 +9,14 @@ alembic==1.9.1 # via jupyterhub
amqp==5.1.1 # via kombu
aniso8601==7.0.0 # via nomad-lab (pyproject.toml)
anyio==3.6.2 # via httpcore, jupyter-server, starlette, watchfiles
appnope==0.1.3 # via ipykernel, ipython
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), nomad-lab (pyproject.toml)
ase==3.19.0 # via asr, ifes-apt-tc-data-modeling, matid (dependencies/matid/pyproject.toml)
asgiref==3.6.0 # via nomad-lab (pyproject.toml)
asr==0.4.1 # via nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
asr==0.4.1 # via 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
......@@ -28,7 +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), nomad-lab (pyproject.toml)
bitarray==2.3.5 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/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)
......@@ -39,7 +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), nomad-lab (pyproject.toml), uvicorn
click==8.1.3 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nexusutils (dependencies/parsers/nexus/pyproject.toml), uvicorn
click-didyoumean==0.3.0 # via celery
click-plugins==1.1.1 # via celery
click-repl==0.2.0 # via celery
......@@ -77,13 +78,13 @@ 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), nomad-lab (pyproject.toml)
gitpython==3.1.24 # via nexusutils (dependencies/parsers/nexus/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, nomad-lab (pyproject.toml), phonopy
h5py==3.6.0 # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, 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
......@@ -125,13 +126,13 @@ 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), nomad-lab (pyproject.toml)
lxml==4.7.1 # via atomisticparsers (dependencies/parsers/atomistic/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), nomad-lab (pyproject.toml)
mdanalysis==2.5.0 # via atomisticparsers (dependencies/parsers/atomistic/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
......@@ -149,7 +150,7 @@ 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), nomad-lab (pyproject.toml)
netcdf4==1.5.4 # via electronicparsers (dependencies/parsers/electronic/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
......@@ -157,7 +158,7 @@ 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, 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, pywavelets, radioactivedecay, scikit-image, scikit-learn, scipy, sparse, spglib, tifffile, xarray, zarr
numpy==1.22.4 # via ase, biopython, cftime, dask, 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, 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)
......@@ -166,15 +167,15 @@ 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
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, nomad-lab (pyproject.toml), panedr, pymatgen, xarray
pandas==1.3.5 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, panedr, pymatgen, xarray
pandocfilters==1.5.0 # via nbconvert
panedr==0.2 # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab (pyproject.toml)
panedr==0.2 # via atomisticparsers (dependencies/parsers/atomistic/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, nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
phonopy==2.11.0 # via asr, 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)
......@@ -197,6 +198,7 @@ pymongo==3.12.1 # via mongoengine, nomad-lab (pyproject.toml), optimad
pyopenssl==23.0.0 # via certipy
pyparsing==3.0.9 # via matplotlib, mdtraj, rdflib
pyrsistent==0.19.3 # via jsonschema
pyscf==2.0.1 ; sys_platform == "darwin" # via electronicparsers (dependencies/parsers/electronic/pyproject.toml)
python-dateutil==2.8.2 # via arrow, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, rfc3161ng
python-dotenv==0.21.0 # via uvicorn
python-jose==3.3.0 # via python-keycloak
......@@ -205,16 +207,16 @@ 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), nomad-lab (pyproject.toml), pandas
pytz==2022.7.1 # via babel, celery, nexusutils (dependencies/parsers/nexus/pyproject.toml), pandas
pywavelets==1.3.0 # via scikit-image
pyyaml==6.0 # via dask, electronicparsers (dependencies/parsers/electronic/pyproject.toml), hyperspy, nomad-lab (pyproject.toml), phonopy, pybtex, uvicorn
pyyaml==6.0 # via dask, electronicparsers (dependencies/parsers/electronic/pyproject.toml), hyperspy, 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
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), nomad-lab (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), 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
......@@ -225,8 +227,8 @@ 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), nomad-lab (pyproject.toml)
scipy==1.7.1 # via ase, griddataformats, hyperspy, matid (dependencies/matid/pyproject.toml), mdanalysis, mdtraj, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image, scikit-learn, sparse
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
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
......@@ -280,7 +282,7 @@ 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==0.20.2 # via nexusutils (dependencies/parsers/nexus/pyproject.toml), nomad-lab (pyproject.toml)
xarray==0.20.2 # via nexusutils (dependencies/parsers/nexus/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)
......
scripts/generate_python_dependencies.sh
+ 1
− 1
View file @ 7554334d
......@@ -20,7 +20,7 @@ pip-compile --resolver=backtracking --annotation-style=line \
dependencies/parsers/workflow/pyproject.toml pyproject.toml
pip-compile ---resolver=backtracking -annotation-style=line \
pip-compile --resolver=backtracking --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
requirements.txt \
......
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