diff --git a/requirements-dev.txt b/requirements-dev.txt index ed29159b333811a78cd55bb86c819742d2f9b103..c2915e9e7a7c5f48fb8685553d41fcb5e1324cec 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,402 +1,397 @@ -# -# This file is autogenerated by pip-compile with Python 3.9 -# by the following command: -# -# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt --pip-args='--prefer-binary' pyproject.toml requirements.txt -# +# This file was autogenerated by uv via the following command: +# uv pip compile --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 -r requirements.txt, sphinx -alembic==1.13.1 # via -r requirements.txt, jupyterhub -amqp==5.2.0 # via -r requirements.txt, kombu +alabaster==0.7.16 # via sphinx, -r requirements.txt +alembic==1.13.1 # 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==4.3.0 # via -r requirements.txt, httpx, jupyter-server, starlette, watchfiles -anytree==2.12.1 # via -r requirements.txt, pynxtools -appnope==0.1.4 # via -r requirements.txt, ipykernel -argon2-cffi==23.1.0 # via -r requirements.txt, jupyter-server -argon2-cffi-bindings==21.2.0 # via -r requirements.txt, argon2-cffi -arrow==1.3.0 # via -r requirements.txt, isoduration -asciitree==0.3.3 # via -r requirements.txt, zarr -ase==3.19.3 # via -r requirements.txt, asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase +anyio==4.4.0 # via httpx, jupyter-server, starlette, watchfiles, -r requirements.txt +anytree==2.12.1 # via pynxtools, -r requirements.txt +argon2-cffi==23.1.0 # via jupyter-server, -r requirements.txt +argon2-cffi-bindings==21.2.0 # via argon2-cffi, -r requirements.txt +arrow==1.3.0 # via isoduration, -r requirements.txt +asciitree==0.3.3 # via zarr, -r requirements.txt +ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, pynxtools, 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) -asteval==0.9.33 # via -r requirements.txt, lmfit +asteval==0.9.33 # via lmfit, -r requirements.txt astroid==3.2.2 # via nomad-lab (pyproject.toml) -asttokens==2.4.1 # via -r requirements.txt, devtools, stack-data -async-generator==1.10 # via -r requirements.txt, jupyterhub -async-lru==2.0.4 # via -r requirements.txt, jupyterlab +asttokens==2.4.1 # via devtools, stack-data, -r requirements.txt +async-generator==1.10 # via jupyterhub, -r requirements.txt +async-lru==2.0.4 # via jupyterlab, -r requirements.txt atpublic==4.1.0 # via aiosmtpd -attrs==23.2.0 # via -r requirements.txt, aiosmtpd, jsonschema, pytest -babel==2.15.0 # via -r requirements.txt, jupyterlab-server, mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx +attrs==23.2.0 # via aiosmtpd, jsonschema, pytest, -r requirements.txt +babel==2.15.0 # via jupyterlab-server, mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx, -r requirements.txt backports-tarfile==1.1.1 # 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, nbconvert, nomad-lab (pyproject.toml) -billiard==4.2.0 # via -r requirements.txt, celery -biopython==1.83 # via -r requirements.txt, mdanalysis +beautifulsoup4==4.12.3 # via nbconvert, -r requirements.txt, nomad-lab (pyproject.toml) +billiard==4.2.0 # via celery, -r requirements.txt +biopython==1.83 # via mdanalysis, -r requirements.txt bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml) -bleach==6.1.0 # via -r requirements.txt, nbconvert -blinker==1.8.2 # via -r requirements.txt, flask -blosc2==2.5.1 # via -r requirements.txt, tables +bleach==6.1.0 # via nbconvert, -r requirements.txt +blinker==1.8.2 # via flask, -r requirements.txt +blosc2==2.5.1 # via tables, -r requirements.txt build==1.2.1 # via nomad-lab (pyproject.toml) cachetools==5.3.3 # via -r requirements.txt, nomad-lab (pyproject.toml) celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -certifi==2024.2.2 # via -r requirements.txt, elasticsearch, httpcore, httpx, netcdf4, requests -certipy==0.1.3 # via -r requirements.txt, jupyterhub -cffi==1.16.0 # via -r requirements.txt, argon2-cffi-bindings, 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-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pynxtools, uvicorn -click-default-group==1.2.4 # via -r requirements.txt, pynxtools -click-didyoumean==0.3.1 # via -r requirements.txt, celery -click-plugins==1.1.1 # via -r requirements.txt, celery -click-repl==0.3.0 # via -r requirements.txt, celery -cloudpickle==3.0.0 # via -r requirements.txt, dask +certifi==2024.2.2 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt +certipy==0.1.3 # via jupyterhub, -r requirements.txt +cffi==1.16.0 # via argon2-cffi-bindings, cryptography, -r requirements.txt +cftime==1.6.3 # via netcdf4, -r requirements.txt +charset-normalizer==3.3.2 # via requests, -r requirements.txt +click==8.1.7 # via asr, celery, click-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, pynxtools, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml) +click-default-group==1.2.4 # via pynxtools, -r requirements.txt +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 +cloudpickle==3.0.0 # via dask, -r requirements.txt colorama==0.4.6 # via mkdocs-material, twine -comm==0.2.2 # via -r requirements.txt, ipykernel, ipywidgets -commonmark==0.9.1 # via -r requirements.txt, recommonmark -contourpy==1.2.1 # via -r requirements.txt, matplotlib -coverage==7.5.1 # via pytest-cov -cryptography==42.0.7 # via -r requirements.txt, jwcrypto, pyjwt, pyopenssl, rfc3161ng -cycler==0.12.1 # via -r requirements.txt, matplotlib -dask[array]==2024.5.1 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem, rosettasciio -debugpy==1.8.1 # via -r requirements.txt, ipykernel -decorator==5.1.1 # via -r requirements.txt, ipyparallel, ipython, validators -defusedxml==0.7.1 # via -r requirements.txt, nbconvert -deprecation==2.1.0 # via -r requirements.txt, python-keycloak +comm==0.2.2 # via ipykernel, ipywidgets, -r requirements.txt +commonmark==0.9.1 # via recommonmark, -r requirements.txt +contourpy==1.2.1 # via matplotlib, -r requirements.txt +coverage==7.5.2 # via pytest-cov +cryptography==42.0.7 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage, -r requirements.txt +cycler==0.12.1 # via matplotlib, -r requirements.txt +dask==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio, -r requirements.txt +debugpy==1.8.1 # via ipykernel, -r requirements.txt +decorator==5.1.1 # via ipyparallel, ipython, validators, -r requirements.txt +defusedxml==0.7.1 # via nbconvert, -r requirements.txt +deprecation==2.1.0 # via python-keycloak, -r requirements.txt devtools==0.12.2 # via nomad-lab (pyproject.toml) -diffpy-structure==3.1.0 # via -r requirements.txt, diffsims, kikuchipy, orix -diffsims==0.5.2 # via -r requirements.txt, kikuchipy, pyxem -dill==0.3.8 # via -r requirements.txt, hyperspy, lmfit -dnspython==2.6.1 # via -r requirements.txt, email-validator, pymongo -docker==7.1.0 # via -r requirements.txt, dockerspawner +diffpy-structure==3.1.0 # via diffsims, kikuchipy, orix, -r requirements.txt +diffsims==0.5.2 # via kikuchipy, pyxem, -r requirements.txt +dill==0.3.8 # via hyperspy, lmfit, -r requirements.txt +dnspython==2.6.1 # via email-validator, pymongo, -r requirements.txt +docker==7.1.0 # via dockerspawner, -r requirements.txt dockerspawner==13.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) docstring-parser==0.16 # via -r requirements.txt, nomad-lab (pyproject.toml) -docutils==0.21.2 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx -elasticsearch==7.17.1 # via -r requirements.txt, elasticsearch-dsl, nomad-lab (pyproject.toml) +docutils==0.21.2 # via m2r, readme-renderer, recommonmark, sphinx, -r requirements.txt +elasticsearch==7.17.1 # via elasticsearch-dsl, -r requirements.txt, nomad-lab (pyproject.toml) elasticsearch-dsl==7.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -email-validator==1.3.1 # via -r requirements.txt, optimade -entrypoints==0.4 # via -r requirements.txt, ipyparallel -escapism==1.0.1 # via -r requirements.txt, dockerspawner +email-validator==1.3.1 # via optimade, -r requirements.txt +entrypoints==0.4 # via ipyparallel, -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 -r requirements.txt, openpyxl -exceptiongroup==1.2.1 # via -r requirements.txt, anyio, ipython +et-xmlfile==1.1.0 # via openpyxl, -r requirements.txt +exceptiongroup==1.2.1 # via anyio, ipython, -r requirements.txt execnet==2.1.1 # via pytest-xdist -executing==2.0.1 # via -r requirements.txt, devtools, stack-data -f90wrap==0.2.14 # via -r requirements.txt, quippy-ase -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 -fastjsonschema==2.19.1 # via -r requirements.txt, nbformat +executing==2.0.1 # via devtools, stack-data, -r requirements.txt +f90wrap==0.2.14 # via quippy-ase, -r requirements.txt +fabio==2024.4.0 # via pyfai, silx, -r requirements.txt +fastapi==0.99.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) +fasteners==0.19 # via mdanalysis, zarr, -r requirements.txt +fastjsonschema==2.19.1 # via nbformat, -r requirements.txt filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -findiff==0.10.0 # via -r requirements.txt, pynxtools-stm -flask==3.0.3 # via -r requirements.txt, asr -flatdict==3.4.0 # via -r requirements.txt, ifes-apt-tc-data-modeling, pynxtools-em -fonttools==4.51.0 # via -r requirements.txt, matplotlib -fqdn==1.5.1 # via -r requirements.txt, jsonschema -fsspec==2024.5.0 # via -r requirements.txt, dask, hyperspy -future==1.0.0 # via -r requirements.txt, uncertainties +findiff==0.10.0 # via pynxtools-stm, -r requirements.txt +flask==3.0.3 # via asr, -r requirements.txt +flatdict==4.0.1 # via ifes-apt-tc-data-modeling, pynxtools-em, -r requirements.txt +fonttools==4.52.1 # via matplotlib, -r requirements.txt +fqdn==1.5.1 # via jsonschema, -r requirements.txt +fsspec==2024.5.0 # via dask, hyperspy, -r requirements.txt +future==1.0.0 # via uncertainties, -r requirements.txt ghp-import==2.1.0 # via mkdocs -gitdb==4.0.11 # via -r requirements.txt, gitpython -gitpython==3.1.43 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nomad-lab (pyproject.toml) -greenlet==3.0.3 # via -r requirements.txt, sqlalchemy -griddataformats==1.0.2 # via -r requirements.txt, mdanalysis -gsd==3.2.1 # via -r requirements.txt, mdanalysis +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 +griddataformats==1.0.2 # via mdanalysis, -r requirements.txt +gsd==3.2.1 # via mdanalysis, -r requirements.txt gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -h11==0.14.0 # via -r requirements.txt, httpcore, uvicorn -h5grove[fastapi]==1.3.0 # via -r requirements.txt, jupyterlab-h5web, nomad-lab (pyproject.toml) -h5py==3.11.0 # via -r requirements.txt, fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx -hdf5plugin==4.4.0 # via -r requirements.txt, fabio +h11==0.14.0 # via httpcore, uvicorn, -r requirements.txt +h5grove==1.3.0 # via jupyterlab-h5web, -r requirements.txt, nomad-lab (pyproject.toml) +h5py==3.11.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx, -r requirements.txt, nomad-lab (pyproject.toml) +hdf5plugin==4.4.0 # via fabio, -r requirements.txt hjson==3.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) html5lib==1.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -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, jupyterlab, nomad-lab (pyproject.toml) -hyperspy==1.7.6 # via -r requirements.txt, kikuchipy, pyxem -idna==3.7 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests -ifes-apt-tc-data-modeling==0.2.2 # via -r requirements.txt, pynxtools-apm -igor2==0.5.2 # via -r requirements.txt, pynxtools-xps -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, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, keyring, markdown, mkdocs, mkdocs-get-deps, nbconvert, nomad-lab (pyproject.toml), pynxtools, sphinx, twine -importlib-resources==6.4.0 # via -r requirements.txt, matplotlib, spglib +httpcore==1.0.5 # via httpx, -r requirements.txt +httptools==0.6.1 # via uvicorn, -r requirements.txt +httpx==0.27.0 # via jupyterlab, -r requirements.txt, nomad-lab (pyproject.toml) +hyperspy==1.7.5 # via kikuchipy, pyxem, -r requirements.txt +idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt +ifes-apt-tc-data-modeling==0.2.2 # via pynxtools-apm, -r requirements.txt +igor2==0.5.2 # via pynxtools-xps, -r requirements.txt +imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image, -r requirements.txt +imagesize==1.4.1 # via sphinx, -r requirements.txt +importlib-metadata==7.1.0 # via build, dask, flask, hyperspy, jupyter-client, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, keyring, markdown, mkdocs, mkdocs-get-deps, nbconvert, pynxtools, sphinx, twine, -r requirements.txt, nomad-lab (pyproject.toml) +importlib-resources==6.4.0 # via matplotlib, spglib, -r requirements.txt inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -ipykernel==6.29.4 # via -r requirements.txt, ipyparallel, jupyter, jupyter-console, jupyterlab, qtconsole -ipyparallel==8.8.0 # via -r requirements.txt, hyperspy -ipython==8.18.1 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, ipywidgets, jupyter-console, pynxtools-xrd -ipywidgets==8.1.2 # via -r requirements.txt, jupyter -isodate==0.6.1 # via -r requirements.txt, rdflib -isoduration==20.11.0 # via -r requirements.txt, jsonschema -itsdangerous==2.2.0 # via -r requirements.txt, flask, nomad-lab (pyproject.toml) +ipykernel==6.29.4 # via ipyparallel, jupyter, jupyter-console, jupyterlab, qtconsole, -r requirements.txt +ipyparallel==8.8.0 # via hyperspy, -r requirements.txt +ipython==8.18.1 # via hyperspy, ipykernel, ipyparallel, ipywidgets, jupyter-console, pynxtools-xrd, -r requirements.txt +ipywidgets==8.1.2 # via jupyter, -r requirements.txt +isodate==0.6.1 # via rdflib, -r requirements.txt +isoduration==20.11.0 # via jsonschema, -r requirements.txt +itsdangerous==2.2.0 # via flask, -r requirements.txt, nomad-lab (pyproject.toml) jaraco-classes==3.4.0 # via keyring jaraco-context==5.3.0 # via keyring jaraco-functools==4.0.1 # via keyring -jedi==0.19.1 # via -r requirements.txt, ipython -jinja2==3.1.4 # via -r requirements.txt, flask, hyperspy, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, mkdocs, mkdocs-macros-plugin, mkdocs-material, nbconvert, sphinx +jedi==0.19.1 # via ipython, -r requirements.txt +jeepney==0.8.0 # via keyring, secretstorage +jinja2==3.1.4 # via flask, hyperspy, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, mkdocs, mkdocs-macros-plugin, mkdocs-material, nbconvert, sphinx, -r requirements.txt jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -joblib==1.4.2 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn -json5==0.9.25 # via -r requirements.txt, jupyterlab-server -jsonpointer==2.4 # via -r requirements.txt, jsonschema -jsonschema[format,format-nongpl]==4.17.3 # via -r requirements.txt, jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, nomad-lab (pyproject.toml), oauthenticator -jupyter==1.0.0 # via -r requirements.txt, ifes-apt-tc-data-modeling -jupyter-client==8.6.2 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-console, jupyter-server, nbclient, qtconsole -jupyter-console==6.6.3 # via -r requirements.txt, jupyter -jupyter-core==5.7.2 # via -r requirements.txt, ipykernel, jupyter-client, jupyter-console, jupyter-server, jupyterlab, nbclient, nbconvert, nbformat, qtconsole -jupyter-events==0.5.0 # via -r requirements.txt, jupyter-server -jupyter-lsp==2.2.5 # via -r requirements.txt, jupyterlab -jupyter-server==2.5.0 # via -r requirements.txt, jupyter-lsp, jupyterlab, jupyterlab-h5web, jupyterlab-server, notebook, notebook-shim -jupyter-server-terminals==0.5.3 # via -r requirements.txt, jupyter-server -jupyter-telemetry==0.1.0 # via -r requirements.txt, jupyterhub -jupyterhub==4.0.2 # via -r requirements.txt, dockerspawner, nomad-lab (pyproject.toml), oauthenticator -jupyterlab==4.1.6 # via -r requirements.txt, ifes-apt-tc-data-modeling, notebook -jupyterlab-h5web==11.1.0 # via -r requirements.txt, ifes-apt-tc-data-modeling -jupyterlab-pygments==0.3.0 # via -r requirements.txt, nbconvert -jupyterlab-server==2.24.0 # via -r requirements.txt, jupyterlab, notebook -jupyterlab-widgets==3.0.10 # via -r requirements.txt, ipywidgets -jwcrypto==1.5.6 # via -r requirements.txt, python-keycloak +joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn, -r requirements.txt +json5==0.9.25 # via jupyterlab-server, -r requirements.txt +jsonpointer==2.4 # via jsonschema, -r requirements.txt +jsonschema==4.17.3 # via jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml) +jupyter==1.0.0 # via ifes-apt-tc-data-modeling, -r requirements.txt +jupyter-client==8.6.2 # via ipykernel, ipyparallel, jupyter-console, jupyter-server, nbclient, qtconsole, -r requirements.txt +jupyter-console==6.6.3 # via jupyter, -r requirements.txt +jupyter-core==5.7.2 # via ipykernel, jupyter-client, jupyter-console, jupyter-server, jupyterlab, nbclient, nbconvert, nbformat, qtconsole, -r requirements.txt +jupyter-events==0.5.0 # via jupyter-server, -r requirements.txt +jupyter-lsp==2.2.5 # via jupyterlab, -r requirements.txt +jupyter-server==2.5.0 # via jupyter-lsp, jupyterlab, jupyterlab-h5web, jupyterlab-server, notebook, notebook-shim, -r requirements.txt +jupyter-server-terminals==0.5.3 # via jupyter-server, -r requirements.txt +jupyter-telemetry==0.1.0 # via jupyterhub, -r requirements.txt +jupyterhub==4.0.2 # via dockerspawner, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml) +jupyterlab==4.1.6 # via ifes-apt-tc-data-modeling, notebook, -r requirements.txt +jupyterlab-h5web==11.1.0 # via ifes-apt-tc-data-modeling, -r requirements.txt +jupyterlab-pygments==0.3.0 # via nbconvert, -r requirements.txt +jupyterlab-server==2.24.0 # via jupyterlab, notebook, -r requirements.txt +jupyterlab-widgets==3.0.10 # via ipywidgets, -r requirements.txt +jwcrypto==1.5.6 # via python-keycloak, -r requirements.txt keyring==25.2.1 # via twine -kikuchipy==0.9.0 # via -r requirements.txt, pynxtools-em -kiwisolver==1.4.5 # via -r requirements.txt, matplotlib -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 -lmfit==1.3.1 # via -r requirements.txt, pyxem -locket==1.0.0 # via -r requirements.txt, partd -lxml==5.2.2 # via -r requirements.txt, fabio, lxml-html-clean, nomad-lab (pyproject.toml), pynxtools +kikuchipy==0.9.0 # via pynxtools-em, -r requirements.txt +kiwisolver==1.4.5 # via matplotlib, -r requirements.txt +kombu==5.3.7 # via celery, -r requirements.txt +lark==1.1.9 # via optimade, -r requirements.txt +latexcodec==3.0.0 # via pybtex, -r requirements.txt +llvmlite==0.42.0 # via numba, -r requirements.txt +lmfit==1.3.1 # via pyxem, -r requirements.txt +locket==1.0.0 # via partd, -r requirements.txt +lxml==5.2.2 # via fabio, lxml-html-clean, pynxtools, -r requirements.txt, nomad-lab (pyproject.toml) lxml-html-clean==0.1.1 # via -r requirements.txt, nomad-lab (pyproject.toml) m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -mako==1.3.5 # via -r requirements.txt, alembic +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 -r requirements.txt, jinja2, mako, mkdocs, nbconvert, nomad-lab (pyproject.toml), werkzeug +markupsafe==2.1.5 # via jinja2, mako, mkdocs, nbconvert, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml) matid==2.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -matplotlib==3.8.4 # via -r requirements.txt, ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay -matplotlib-inline==0.1.7 # via -r requirements.txt, ipykernel, ipython -matplotlib-scalebar==0.8.1 # via -r requirements.txt, orix -mda-xdrlib==0.2.0 # via -r requirements.txt, pyedr +matplotlib==3.8.4 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay, -r requirements.txt +matplotlib-inline==0.1.7 # via ipykernel, ipython, -r requirements.txt +matplotlib-scalebar==0.8.1 # via orix, -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 -r requirements.txt, mkdocs, mkdocs-get-deps, pynxtools -mistune==3.0.2 # via -r requirements.txt, m2r, nbconvert +mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps, pynxtools, -r requirements.txt +mistune==3.0.2 # via m2r, nbconvert, -r requirements.txt mkdocs==1.6.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml) mkdocs-click==0.8.1 # via nomad-lab (pyproject.toml) mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-git-revision-date-localized-plugin==1.2.5 # 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==9.5.24 # via nomad-lab (pyproject.toml) +mkdocs-material==9.5.25 # 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 -r requirements.txt, mdanalysis +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 -r requirements.txt, optimade -monty==2024.5.24 # via -r requirements.txt, pymatgen +mongomock==4.1.2 # via optimade, -r requirements.txt +monty==2024.5.24 # via pymatgen, -r requirements.txt more-itertools==10.2.0 # via jaraco-classes, jaraco-functools, pytest -mpmath==1.3.0 # via -r requirements.txt, sympy -mrcfile==1.5.0 # via -r requirements.txt, griddataformats -msgpack==1.0.8 # via -r requirements.txt, blosc2, mmtf-python, nomad-lab (pyproject.toml) +mpmath==1.3.0 # via sympy, -r requirements.txt +mrcfile==1.5.0 # via griddataformats, -r requirements.txt +msgpack==1.0.8 # via blosc2, 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) -natsort==8.4.0 # via -r requirements.txt, hyperspy -nbclient==0.10.0 # via -r requirements.txt, nbconvert -nbconvert==7.16.4 # via -r requirements.txt, jupyter, jupyter-server -nbformat==5.10.4 # via -r requirements.txt, jupyter-server, nbclient, nbconvert -ndindex==1.8 # via -r requirements.txt, blosc2 -nest-asyncio==1.6.0 # via -r requirements.txt, ipykernel +natsort==8.4.0 # via hyperspy, -r requirements.txt +nbclient==0.10.0 # via nbconvert, -r requirements.txt +nbconvert==7.16.4 # via jupyter, jupyter-server, -r requirements.txt +nbformat==5.10.4 # via jupyter-server, nbclient, nbconvert, -r requirements.txt +ndindex==1.8 # via blosc2, -r requirements.txt +nest-asyncio==1.6.0 # via ipykernel, -r requirements.txt netcdf4==1.6.5 # via -r requirements.txt, nomad-lab (pyproject.toml) -networkx==2.6.3 # via -r requirements.txt, matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image +networkx==2.6.3 # via matid, mdanalysis, pymatgen, radioactivedecay, scikit-image, -r requirements.txt, nomad-lab (pyproject.toml) nh3==0.2.17 # via readme-renderer -niondata==0.15.5 # via -r requirements.txt, nionswift, nionswift-io -nionswift==0.16.8 # via -r requirements.txt, pynxtools-em -nionswift-io==0.15.1 # via -r requirements.txt, nionswift -nionui==0.6.11 # via -r requirements.txt, nionswift -nionutils==0.4.10 # via -r requirements.txt, niondata, nionswift, nionswift-io, nionui -notebook==7.1.3 # via -r requirements.txt, jupyter -notebook-shim==0.2.4 # via -r requirements.txt, jupyterlab, notebook +niondata==0.15.5 # via nionswift, nionswift-io, -r requirements.txt +nionswift==0.16.8 # via pynxtools-em, -r requirements.txt +nionswift-io==0.15.1 # via nionswift, -r requirements.txt +nionui==0.6.11 # via nionswift, -r requirements.txt +nionutils==0.4.10 # via niondata, nionswift, nionswift-io, nionui, -r requirements.txt +notebook==7.1.3 # via jupyter, -r requirements.txt +notebook-shim==0.2.4 # via jupyterlab, notebook, -r requirements.txt nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml) -numba==0.59.1 # via -r requirements.txt, diffsims, hyperspy, kikuchipy, orix, pyxem, sparse -numcodecs==0.12.1 # via -r requirements.txt, zarr -numexpr==2.10.0 # via -r requirements.txt, hyperspy, pyfai, pyxem, tables -numpy==1.22.4 # via -r requirements.txt, ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, igor2, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, zarr -numpy-quaternion==2023.0.3 # via -r requirements.txt, orix +numba==0.59.1 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse, -r requirements.txt +numcodecs==0.12.1 # via zarr, -r requirements.txt +numexpr==2.10.0 # via hyperspy, pyfai, pyxem, tables, -r requirements.txt +numpy==1.22.4 # via ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, igor2, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, zarr, -r requirements.txt, nomad-lab (pyproject.toml) +numpy-quaternion==2023.0.3 # via orix, -r requirements.txt oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -oauthlib==3.2.2 # via -r requirements.txt, jupyterhub +oauthlib==3.2.2 # via jupyterhub, -r requirements.txt 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==0.12.1.post0 # via -r requirements.txt, diffsims, kikuchipy, pyxem -orjson==3.10.3 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml) -packaging==24.0 # via -r requirements.txt, build, dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mkdocs, mongomock, nbconvert, pint, plotly, pooch, pytest, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb +optimade==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml) +orix==0.12.1.post0 # via diffsims, kikuchipy, pyxem, -r requirements.txt +orjson==3.10.3 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) +packaging==24.0 # via build, dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mkdocs, mongomock, nbconvert, pint, plotly, pooch, pytest, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb, -r requirements.txt paginate==0.5.6 # via mkdocs-material -palettable==3.3.3 # via -r requirements.txt, pymatgen -pamela==1.1.0 # via -r requirements.txt, jupyterhub -pandas==1.5.3 # via -r requirements.txt, ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray -pandocfilters==1.5.1 # via -r requirements.txt, nbconvert +palettable==3.3.3 # via pymatgen, -r requirements.txt +pamela==1.1.0 # via jupyterhub, -r requirements.txt +pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, -r requirements.txt, nomad-lab (pyproject.toml) +pandocfilters==1.5.1 # via nbconvert, -r requirements.txt 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==1.4.2 # via -r requirements.txt, dask +parso==0.8.4 # via jedi, -r requirements.txt +partd==1.4.2 # via dask, -r requirements.txt pathspec==0.12.1 # via mkdocs -pexpect==4.9.0 # via -r requirements.txt, ipython -phonopy==2.23.1 # via -r requirements.txt, asr -pillow==10.0.1 # via -r requirements.txt, fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image -pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab (pyproject.toml), pynxtools-xps, rosettasciio +pexpect==4.9.0 # via ipython, -r requirements.txt +phonopy==2.23.1 # via asr, -r requirements.txt +pillow==10.3.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image, -r requirements.txt +pint==0.17 # via hyperspy, pynxtools-xps, rosettasciio, -r requirements.txt, nomad-lab (pyproject.toml) pkginfo==1.10.0 # via twine -platformdirs==4.2.2 # via -r requirements.txt, jupyter-core, mkdocs-get-deps, pooch, xraydb -plotly==5.22.0 # via -r requirements.txt, asr, pymatgen +platformdirs==4.2.2 # via jupyter-core, mkdocs-get-deps, pooch, xraydb, -r requirements.txt +plotly==5.22.0 # via asr, pymatgen, -r requirements.txt pluggy==0.13.1 # via pytest -ply==3.11 # via -r requirements.txt, pycifrw -pooch==1.8.1 # via -r requirements.txt, kikuchipy, orix -prettytable==3.10.0 # via -r requirements.txt, hyperspy -prometheus-client==0.20.0 # via -r requirements.txt, jupyter-server, jupyterhub -prompt-toolkit==3.0.43 # via -r requirements.txt, click-repl, ipython, jupyter-console -psutil==5.9.8 # via -r requirements.txt, diffsims, ipykernel, ipyparallel, pyxem -ptyprocess==0.7.0 # via -r requirements.txt, pexpect, terminado -pure-eval==0.2.2 # via -r requirements.txt, stack-data +ply==3.11 # via pycifrw, -r requirements.txt +pooch==1.8.1 # via kikuchipy, orix, -r requirements.txt +prettytable==3.10.0 # via hyperspy, -r requirements.txt +prometheus-client==0.20.0 # via jupyter-server, jupyterhub, -r requirements.txt +prompt-toolkit==3.0.43 # via click-repl, ipython, jupyter-console, -r requirements.txt +psutil==5.9.8 # via diffsims, ipykernel, ipyparallel, pyxem, -r requirements.txt +ptyprocess==0.7.0 # via pexpect, terminado, -r requirements.txt +pure-eval==0.2.2 # via stack-data, -r requirements.txt py==1.11.0 # via pytest, pytest-forked -py-cpuinfo==9.0.0 # via -r requirements.txt, blosc2, tables -pyasn1==0.6.0 # via -r requirements.txt, pyasn1-modules, rfc3161ng -pyasn1-modules==0.4.0 # via -r requirements.txt, rfc3161ng +py-cpuinfo==9.0.0 # via blosc2, tables, -r requirements.txt +pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng, -r requirements.txt +pyasn1-modules==0.4.0 # via rfc3161ng, -r requirements.txt pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370 # via -r requirements.txt, nomad-lab (pyproject.toml) -pybtex==0.24.0 # via -r requirements.txt, pymatgen -pycifrw==4.4.6 # via -r requirements.txt, diffpy-structure +pybtex==0.24.0 # via pymatgen, -r requirements.txt +pycifrw==4.4.6 # via diffpy-structure, -r requirements.txt 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 -pyfai==2024.5.0 # via -r requirements.txt, pyxem -pygments==2.18.0 # via -r requirements.txt, devtools, ipython, jupyter-console, mkdocs-material, nbconvert, qtconsole, readme-renderer, sphinx -pyjwt[crypto]==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -pymatgen==2023.9.25 # via -r requirements.txt, asr, nomad-lab (pyproject.toml) +pycparser==2.22 # via cffi, -r requirements.txt +pydantic==1.10.15 # via fastapi, optimade, -r requirements.txt, nomad-lab (pyproject.toml) +pyedr==0.8.0 # via panedr, -r requirements.txt +pyfai==2024.5.0 # via pyxem, -r requirements.txt +pygments==2.18.0 # via devtools, ipython, jupyter-console, mkdocs-material, nbconvert, qtconsole, readme-renderer, sphinx, -r requirements.txt +pyjwt==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml) +pymatgen==2023.9.25 # via asr, -r requirements.txt, nomad-lab (pyproject.toml) pymdown-extensions==10.8.1 # via mkdocs-material -pymongo==4.6.3 # via -r requirements.txt, mongoengine, nomad-lab (pyproject.toml), optimade -pynxtools[apm,convert,ellips,em,mpes,stm,xps,xrd]==0.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd -pynxtools-apm==0.1.1 # via -r requirements.txt, pynxtools -pynxtools-ellips==0.0.2 # via -r requirements.txt, pynxtools -pynxtools-em==0.1.1 # via -r requirements.txt, pynxtools -pynxtools-mpes==0.0.3 # via -r requirements.txt, pynxtools -pynxtools-stm==1.0.4 # via -r requirements.txt, pynxtools -pynxtools-xps==0.2.2 # via -r requirements.txt, pynxtools -pynxtools-xrd==0.0.1 # via -r requirements.txt, pynxtools -pyopenssl==24.1.0 # via -r requirements.txt, certipy -pyparsing==3.1.2 # via -r requirements.txt, matplotlib, rdflib +pymongo==4.6.3 # via mongoengine, optimade, -r requirements.txt, nomad-lab (pyproject.toml) +pynxtools==0.3.1 # via pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd, -r requirements.txt, nomad-lab (pyproject.toml) +pynxtools-apm==0.1.1 # via pynxtools, -r requirements.txt +pynxtools-ellips==0.0.2 # via pynxtools, -r requirements.txt +pynxtools-em==0.1.1 # via pynxtools, -r requirements.txt +pynxtools-mpes==0.0.3 # via pynxtools, -r requirements.txt +pynxtools-stm==1.0.4 # via pynxtools, -r requirements.txt +pynxtools-xps==0.2.2 # via pynxtools, -r requirements.txt +pynxtools-xrd==0.0.1 # via pynxtools, -r requirements.txt +pyopenssl==24.1.0 # 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 -r requirements.txt, jsonschema -pytest==5.4.3 # via nomad-lab (pyproject.toml), pytest-cov, pytest-forked, pytest-timeout, pytest-xdist +pyrsistent==0.20.0 # via jsonschema, -r requirements.txt +pytest==5.4.3 # via pytest-cov, pytest-forked, pytest-timeout, pytest-xdist, nomad-lab (pyproject.toml) pytest-cov==2.7.1 # via nomad-lab (pyproject.toml) pytest-forked==1.6.0 # via pytest-xdist pytest-timeout==1.4.2 # via nomad-lab (pyproject.toml) pytest-xdist==1.34.0 # via nomad-lab (pyproject.toml) -python-box==6.1.0 # via -r requirements.txt, rosettasciio -python-dateutil==2.9.0.post0 # via -r requirements.txt, arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng, rosettasciio -python-dotenv==1.0.1 # via -r requirements.txt, uvicorn +python-box==6.1.0 # via rosettasciio, -r requirements.txt +python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng, rosettasciio, -r requirements.txt +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 -r requirements.txt, jupyter-events, jupyter-telemetry, nomad-lab (pyproject.toml) +python-json-logger==2.0.2 # via jupyter-events, jupyter-telemetry, -r requirements.txt, nomad-lab (pyproject.toml) python-keycloak==4.0.0 # 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-multipart==0.0.9 # via -r requirements.txt, nomad-lab (pyproject.toml) -pytz==2024.1 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab (pyproject.toml), pandas -pywavelets==1.6.0 # via -r requirements.txt, scikit-image -pyxem==0.16.0 # via -r requirements.txt, pynxtools-em -pyyaml==6.0.1 # via -r requirements.txt, dask, hyperspy, jupyter-events, kikuchipy, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, rosettasciio, uvicorn +pytz==2024.1 # via mkdocs-git-revision-date-localized-plugin, nionswift, pandas, -r requirements.txt, nomad-lab (pyproject.toml) +pywavelets==1.6.0 # via scikit-image, -r requirements.txt +pyxem==0.16.0 # via pynxtools-em, -r requirements.txt +pyyaml==6.0.1 # via dask, hyperspy, jupyter-events, kikuchipy, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, rosettasciio, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml) pyyaml-env-tag==0.1 # via mkdocs pyzeo==0.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml) -pyzmq==26.0.3 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server, qtconsole -qtconsole==5.5.2 # via -r requirements.txt, jupyter -qtpy==2.4.1 # via -r requirements.txt, qtconsole +pyzmq==26.0.3 # via ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server, qtconsole, -r requirements.txt +qtconsole==5.5.2 # via jupyter, -r requirements.txt +qtpy==2.4.1 # via qtconsole, -r requirements.txt quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml) -radioactivedecay==0.5.0 # via -r requirements.txt, ifes-apt-tc-data-modeling +radioactivedecay==0.5.0 # via ifes-apt-tc-data-modeling, -r requirements.txt 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 recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml) regex==2024.5.15 # via mkdocs-material -requests==2.32.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, jupyterlab-server, mkdocs-material, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, twine -requests-toolbelt==1.0.0 # via -r requirements.txt, python-gitlab, python-keycloak, twine +requests==2.32.2 # via docker, hyperspy, jupyterhub, jupyterlab-server, mkdocs-material, oauthenticator, optimade, pooch, pybis, 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) -rfc3339-validator==0.1.4 # via -r requirements.txt, jsonschema +rfc3339-validator==0.1.4 # via jsonschema, -r requirements.txt rfc3986==2.0.0 # via twine -rfc3986-validator==0.1.1 # via -r requirements.txt, jsonschema -rfc3987==1.3.8 # via -r requirements.txt, jsonschema +rfc3986-validator==0.1.1 # via jsonschema, -r requirements.txt +rfc3987==1.3.8 # via jsonschema, -r requirements.txt rope==0.21.0 # via nomad-lab (pyproject.toml) -rosettasciio==0.4 # via -r requirements.txt, pynxtools-em -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 +rosettasciio==0.4 # via pynxtools-em, -r requirements.txt +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==0.4.5 # 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==1.5.0 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem -scipy==1.13.1 # via -r requirements.txt, ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb -send2trash==1.8.3 # via -r requirements.txt, jupyter-server -sentinels==1.0.0 # via -r requirements.txt, mongomock -silx==2.1.0 # via -r requirements.txt, pyfai -six==1.16.0 # via -r requirements.txt, anytree, asttokens, basicauth, bleach, 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==0.15.4 # via -r requirements.txt, hyperspy -spglib==2.4.0 # via -r requirements.txt, asr, matid, phonopy, pymatgen -sphinx==7.3.7 # 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 -sphinxcontrib-htmlhelp==2.0.5 # via -r requirements.txt, sphinx -sphinxcontrib-jsmath==1.0.1 # via -r requirements.txt, sphinx -sphinxcontrib-qthelp==1.0.7 # via -r requirements.txt, sphinx -sphinxcontrib-serializinghtml==1.1.10 # via -r requirements.txt, sphinx -sqlalchemy==2.0.30 # via -r requirements.txt, alembic, jupyterhub, xraydb -stack-data==0.6.3 # via -r requirements.txt, ipython -starlette==0.27.0 # via -r requirements.txt, fastapi +scikit-image==0.19.3 # via hyperspy, kikuchipy, pyxem, -r requirements.txt +scikit-learn==1.5.0 # via kikuchipy, matid, pyxem, -r requirements.txt, nomad-lab (pyproject.toml) +scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, -r requirements.txt, nomad-lab (pyproject.toml) +secretstorage==3.3.3 # via keyring +send2trash==1.8.3 # via jupyter-server, -r requirements.txt +sentinels==1.0.0 # via mongomock, -r requirements.txt +setuptools==70.0.0 # via radioactivedecay, -r requirements.txt +silx==2.1.0 # via pyfai, -r requirements.txt +six==1.16.0 # via anytree, asttokens, basicauth, bleach, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, pytest-xdist, 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 +sparse==0.15.4 # via hyperspy, -r requirements.txt +spglib==2.4.0 # via asr, matid, phonopy, pymatgen, -r requirements.txt +sphinx==7.3.7 # 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-jsmath==1.0.1 # via sphinx, -r requirements.txt +sphinxcontrib-qthelp==1.0.7 # via sphinx, -r requirements.txt +sphinxcontrib-serializinghtml==1.1.10 # via sphinx, -r requirements.txt +sqlalchemy==2.0.30 # via alembic, jupyterhub, xraydb, -r requirements.txt +stack-data==0.6.3 # via ipython, -r requirements.txt +starlette==0.27.0 # via fastapi, -r requirements.txt structlog==24.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -sympy==1.12 # via -r requirements.txt, findiff, hyperspy, pymatgen, radioactivedecay -tables==3.9.2 # via -r requirements.txt, ifes-apt-tc-data-modeling -tabulate==0.8.9 # via -r requirements.txt, nomad-lab (pyproject.toml), pybis, pymatgen -tenacity==8.3.0 # via -r requirements.txt, plotly +sympy==1.12 # via findiff, hyperspy, pymatgen, radioactivedecay, -r requirements.txt +tables==3.9.2 # via ifes-apt-tc-data-modeling, -r requirements.txt +tabulate==0.8.9 # via pybis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml) +tenacity==8.3.0 # via plotly, -r requirements.txt termcolor==2.4.0 # via mkdocs-macros-plugin -terminado==0.18.1 # via -r requirements.txt, jupyter-server, jupyter-server-terminals -texttable==1.7.0 # via -r requirements.txt, pybis -threadpoolctl==3.5.0 # via -r requirements.txt, mdanalysis, scikit-learn -tifffile==2024.5.22 # via -r requirements.txt, h5grove, hyperspy, scikit-image -tinycss2==1.3.0 # via -r requirements.txt, nbconvert -tomli==2.0.1 # via -r requirements.txt, build, jupyterlab, mypy, sphinx -toolz==0.12.1 # via -r requirements.txt, dask, hyperspy, partd +terminado==0.18.1 # via jupyter-server, jupyter-server-terminals, -r requirements.txt +texttable==1.7.0 # via pybis, -r requirements.txt +threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt +tifffile==2024.5.22 # via h5grove, hyperspy, scikit-image, -r requirements.txt +tinycss2==1.3.0 # via nbconvert, -r requirements.txt +tomli==2.0.1 # via build, jupyterlab, mypy, sphinx, -r requirements.txt +toolz==0.12.1 # via dask, hyperspy, partd, -r requirements.txt toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml) -tornado==6.4 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyter-server, jupyterhub, jupyterlab, notebook, terminado -tqdm==4.66.4 # via -r requirements.txt, diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine -traitlets==5.14.3 # via -r requirements.txt, comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-console, jupyter-core, jupyter-events, jupyter-server, jupyter-telemetry, jupyterhub, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat, qtconsole -traits==6.4.3 # via -r requirements.txt, hyperspy, pyxem -transforms3d==0.4.1 # via -r requirements.txt, diffsims, pyxem +tornado==6.4 # via ipykernel, ipyparallel, jupyter-client, jupyter-server, jupyterhub, jupyterlab, notebook, terminado, -r requirements.txt +tqdm==4.66.4 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine, -r requirements.txt +traitlets==5.14.3 # via comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-console, jupyter-core, jupyter-events, jupyter-server, jupyter-telemetry, jupyterhub, jupyterlab, matplotlib-inline, nbclient, nbconvert, nbformat, qtconsole, -r requirements.txt +traits==6.4.3 # via hyperspy, pyxem, -r requirements.txt +transforms3d==0.4.1 # via diffsims, pyxem, -r requirements.txt 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 -r requirements.txt, arrow -typing-extensions==4.12.0 # via -r requirements.txt, alembic, anyio, asgiref, astroid, async-lru, fastapi, ipython, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn -typish==1.9.3 # via -r requirements.txt, nptyping -tzdata==2024.1 # via -r requirements.txt, celery -tzlocal==5.2 # via -r requirements.txt, nionswift, pynxtools-em -uncertainties==3.1.7 # via -r requirements.txt, lmfit, pymatgen +types-python-dateutil==2.9.0.20240316 # via arrow, -r requirements.txt +typing-extensions==4.12.0 # via alembic, anyio, asgiref, astroid, async-lru, fastapi, ipython, jwcrypto, kombu, mypy, pydantic, sqlalchemy, starlette, uvicorn, -r requirements.txt +typish==1.9.3 # via nptyping, -r requirements.txt +tzdata==2024.1 # via celery, -r requirements.txt +tzlocal==5.2 # via nionswift, pynxtools-em, -r requirements.txt +uncertainties==3.1.7 # via lmfit, pymatgen, -r requirements.txt unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml) -uri-template==1.3.0 # via -r requirements.txt, jsonschema -urllib3==1.26.18 # via -r requirements.txt, docker, elasticsearch, pybis, requests -uv==0.2.2 # via nomad-lab (pyproject.toml) -uvicorn[standard]==0.29.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml) -uvloop==0.19.0 # via -r requirements.txt, uvicorn +uri-template==1.3.0 # via jsonschema, -r requirements.txt +urllib3==1.26.18 # via docker, elasticsearch, pybis, requests, -r requirements.txt +uv==0.2.4 # via nomad-lab (pyproject.toml) +uvicorn==0.29.0 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) +uvloop==0.19.0 # via uvicorn, -r requirements.txt validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml) -vine==5.1.0 # via -r requirements.txt, amqp, celery, kombu +vine==5.1.0 # via amqp, celery, kombu, -r requirements.txt watchdog==4.0.1 # via mkdocs -watchfiles==0.21.0 # via -r requirements.txt, uvicorn -wcwidth==0.2.13 # via -r requirements.txt, prettytable, prompt-toolkit, pytest -webcolors==1.13 # via -r requirements.txt, jsonschema -webencodings==0.5.1 # via -r requirements.txt, bleach, html5lib, tinycss2 -websocket-client==1.8.0 # via -r requirements.txt, jupyter-server -websockets==12.0 # via -r requirements.txt, uvicorn -werkzeug==3.0.3 # via -r requirements.txt, flask -widgetsnbextension==4.0.10 # via -r requirements.txt, ipywidgets +watchfiles==0.22.0 # via uvicorn, -r requirements.txt +wcwidth==0.2.13 # via prettytable, prompt-toolkit, pytest, -r requirements.txt +webcolors==1.13 # via jsonschema, -r requirements.txt +webencodings==0.5.1 # via bleach, html5lib, tinycss2, -r requirements.txt +websocket-client==1.8.0 # via jupyter-server, -r requirements.txt +websockets==12.0 # via uvicorn, -r requirements.txt +werkzeug==3.0.3 # via flask, -r requirements.txt +widgetsnbextension==4.0.10 # via ipywidgets, -r requirements.txt wrapt==1.16.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -xarray==2023.12.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps -xmltodict==0.13.0 # via -r requirements.txt, ifes-apt-tc-data-modeling, pynxtools-em -xraydb==4.5.4 # via -r requirements.txt, pynxtools-em -zarr==2.17.1 # via -r requirements.txt, hyperspy -zipp==3.18.2 # via -r requirements.txt, importlib-metadata, importlib-resources +xarray==2023.12.0 # via pynxtools, pynxtools-mpes, pynxtools-xps, -r requirements.txt, nomad-lab (pyproject.toml) +xmltodict==0.13.0 # via ifes-apt-tc-data-modeling, pynxtools-em, -r requirements.txt +xraydb==4.5.4 # via pynxtools-em, -r requirements.txt +zarr==2.17.1 # via hyperspy, -r requirements.txt +zipp==3.19.0 # via importlib-metadata, importlib-resources, -r requirements.txt zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml) - -# The following packages are considered to be unsafe in a requirements file: -# setuptools diff --git a/requirements.txt b/requirements.txt index f9954581b968a15f47793704590dca35550a4578..edf2fa30f00b713925909bb0aae0a044c15861a7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,21 +1,16 @@ -# -# 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 --pip-args='--prefer-binary' dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml -# +# This file was autogenerated by uv via the following command: +# uv pip compile --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==1.13.1 # via jupyterhub amqp==5.2.0 # via kombu aniso8601==9.0.1 # via nomad-lab (pyproject.toml) -anyio==4.3.0 # via httpx, jupyter-server, starlette, watchfiles +anyio==4.4.0 # via httpx, jupyter-server, starlette, watchfiles anytree==2.12.1 # via pynxtools -appnope==0.1.4 # via ipykernel argon2-cffi==23.1.0 # via jupyter-server argon2-cffi-bindings==21.2.0 # via argon2-cffi arrow==1.3.0 # via isoduration asciitree==0.3.3 # via zarr -ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools, quippy-ase +ase==3.19.3 # via asr, ifes-apt-tc-data-modeling, matid, pynxtools, quippy-ase, nomad-lab (pyproject.toml) asgiref==3.8.1 # via nomad-lab (pyproject.toml) asr==0.4.1 # via nomad-lab (pyproject.toml) asteval==0.9.33 # via lmfit @@ -29,7 +24,7 @@ basicauth==0.4.1 # via nomad-lab (pyproject.toml) beautifulsoup4==4.12.3 # via nbconvert, nomad-lab (pyproject.toml) billiard==4.2.0 # via celery biopython==1.83 # via mdanalysis -bitarray==2.9.2 # via nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml) +bitarray==2.9.2 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml) bleach==6.1.0 # via nbconvert blinker==1.8.2 # via flask blosc2==2.5.1 # via tables @@ -40,7 +35,7 @@ certipy==0.1.3 # via jupyterhub cffi==1.16.0 # via argon2-cffi-bindings, cryptography cftime==1.6.3 # via netcdf4 charset-normalizer==3.3.2 # via requests -click==8.1.7 # via asr, celery, click-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn +click==8.1.7 # via asr, celery, click-default-group, click-didyoumean, click-plugins, click-repl, dask, flask, pynxtools, uvicorn, nomad-lab (pyproject.toml) click-default-group==1.2.4 # via pynxtools click-didyoumean==0.3.1 # via celery click-plugins==1.1.1 # via celery @@ -51,7 +46,7 @@ commonmark==0.9.1 # via recommonmark contourpy==1.2.1 # via matplotlib cryptography==42.0.7 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng cycler==0.12.1 # via matplotlib -dask[array]==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio +dask==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio debugpy==1.8.1 # via ipykernel decorator==5.1.1 # via ipyparallel, ipython, validators defusedxml==0.7.1 # via nbconvert @@ -80,8 +75,8 @@ fastjsonschema==2.19.1 # via nbformat filelock==3.3.1 # via nomad-lab (pyproject.toml) findiff==0.10.0 # via pynxtools-stm flask==3.0.3 # via asr -flatdict==3.4.0 # via ifes-apt-tc-data-modeling, pynxtools-em -fonttools==4.51.0 # via matplotlib +flatdict==4.0.1 # via ifes-apt-tc-data-modeling, pynxtools-em +fonttools==4.52.1 # via matplotlib fqdn==1.5.1 # via jsonschema fsspec==2024.5.0 # via dask, hyperspy future==1.0.0 # via uncertainties @@ -92,21 +87,21 @@ griddataformats==1.0.2 # via mdanalysis gsd==3.2.1 # via mdanalysis gunicorn==21.2.0 # via nomad-lab (pyproject.toml) h11==0.14.0 # via httpcore, uvicorn -h5grove[fastapi]==1.3.0 # via jupyterlab-h5web, nomad-lab (pyproject.toml) -h5py==3.11.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx +h5grove==1.3.0 # via jupyterlab-h5web, nomad-lab (pyproject.toml) +h5py==3.11.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, jupyterlab-h5web, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, silx, nomad-lab (pyproject.toml) hdf5plugin==4.4.0 # via fabio hjson==3.1.0 # via nomad-lab (pyproject.toml) html5lib==1.1 # via nomad-lab (pyproject.toml) httpcore==1.0.5 # via httpx httptools==0.6.1 # via uvicorn httpx==0.27.0 # via jupyterlab, nomad-lab (pyproject.toml) -hyperspy==1.7.6 # via kikuchipy, pyxem +hyperspy==1.7.5 # via kikuchipy, pyxem idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests ifes-apt-tc-data-modeling==0.2.2 # via pynxtools-apm igor2==0.5.2 # via pynxtools-xps 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, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, nbconvert, nomad-lab (pyproject.toml), pynxtools, sphinx +importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyter-lsp, jupyterhub, jupyterlab, jupyterlab-server, nbconvert, pynxtools, sphinx, nomad-lab (pyproject.toml) importlib-resources==6.4.0 # via matplotlib, spglib inflection==0.5.1 # via nomad-lab (pyproject.toml) ipykernel==6.29.4 # via ipyparallel, jupyter, jupyter-console, jupyterlab, qtconsole @@ -122,7 +117,7 @@ jmespath==1.0.1 # via nomad-lab (pyproject.toml) joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn json5==0.9.25 # via jupyterlab-server jsonpointer==2.4 # via jsonschema -jsonschema[format,format-nongpl]==4.17.3 # via jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, nomad-lab (pyproject.toml), oauthenticator +jsonschema==4.17.3 # via jupyter-events, jupyter-telemetry, jupyterlab-server, nbformat, oauthenticator, nomad-lab (pyproject.toml) jupyter==1.0.0 # via ifes-apt-tc-data-modeling jupyter-client==8.6.2 # via ipykernel, ipyparallel, jupyter-console, jupyter-server, nbclient, qtconsole jupyter-console==6.6.3 # via jupyter @@ -132,7 +127,7 @@ jupyter-lsp==2.2.5 # via jupyterlab jupyter-server==2.5.0 # via jupyter-lsp, jupyterlab, jupyterlab-h5web, jupyterlab-server, notebook, notebook-shim jupyter-server-terminals==0.5.3 # via jupyter-server jupyter-telemetry==0.1.0 # via jupyterhub -jupyterhub==4.0.2 # via dockerspawner, nomad-lab (pyproject.toml), oauthenticator +jupyterhub==4.0.2 # via dockerspawner, oauthenticator, nomad-lab (pyproject.toml) jupyterlab==4.1.6 # via ifes-apt-tc-data-modeling, notebook jupyterlab-h5web==11.1.0 # via ifes-apt-tc-data-modeling jupyterlab-pygments==0.3.0 # via nbconvert @@ -147,7 +142,7 @@ latexcodec==3.0.0 # via pybtex llvmlite==0.42.0 # via numba lmfit==1.3.1 # via pyxem locket==1.0.0 # via partd -lxml==5.2.2 # via fabio, lxml-html-clean, nomad-lab (pyproject.toml), pynxtools +lxml==5.2.2 # via fabio, lxml-html-clean, pynxtools, nomad-lab (pyproject.toml) lxml-html-clean==0.1.1 # via nomad-lab (pyproject.toml) m2r==0.2.1 # via nomad-lab (pyproject.toml) mako==1.3.5 # via alembic @@ -174,7 +169,7 @@ nbformat==5.10.4 # via jupyter-server, nbclient, nbconvert ndindex==1.8 # via blosc2 nest-asyncio==1.6.0 # via ipykernel netcdf4==1.6.5 # via nomad-lab (pyproject.toml) -networkx==2.6.3 # via matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image +networkx==2.6.3 # via matid, mdanalysis, pymatgen, radioactivedecay, scikit-image, nomad-lab (pyproject.toml) niondata==0.15.5 # via nionswift, nionswift-io nionswift==0.16.8 # via pynxtools-em nionswift-io==0.15.1 # via nionswift @@ -186,18 +181,18 @@ nptyping==1.4.4 # via nomad-lab (pyproject.toml) numba==0.59.1 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse numcodecs==0.12.1 # via zarr numexpr==2.10.0 # via hyperspy, pyfai, pyxem, tables -numpy==1.22.4 # via ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, igor2, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, zarr +numpy==1.22.4 # via ase, biopython, blosc2, cftime, contourpy, dask, diffsims, f90wrap, fabio, findiff, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, igor2, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pycifrw, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, xraydb, zarr, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml) numpy-quaternion==2023.0.3 # via orix 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) +optimade==0.22.1 # via nomad-lab (pyproject.toml) orix==0.12.1.post0 # via diffsims, kikuchipy, pyxem orjson==3.10.3 # via h5grove, nomad-lab (pyproject.toml) packaging==24.0 # via dask, deprecation, f90wrap, gunicorn, hyperspy, ipykernel, jupyter-server, jupyterhub, jupyterlab, jupyterlab-server, matplotlib, mdanalysis, mongomock, nbconvert, pint, plotly, pooch, qtconsole, qtpy, scikit-image, silx, sphinx, tables, xarray, xraydb palettable==3.3.3 # via pymatgen pamela==1.1.0 # via jupyterhub -pandas==1.5.3 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray +pandas==1.5.3 # via ifes-apt-tc-data-modeling, panedr, pybis, pymatgen, pynxtools, radioactivedecay, xarray, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml) pandocfilters==1.5.1 # via nbconvert panedr==0.8.0 # via nomad-lab (pyproject.toml) parmed==4.2.2 # via nomad-lab (pyproject.toml) @@ -205,8 +200,8 @@ parso==0.8.4 # via jedi partd==1.4.2 # via dask pexpect==4.9.0 # via ipython phonopy==2.23.1 # via asr -pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image -pint==0.17 # via hyperspy, nomad-lab (pyproject.toml), pynxtools-xps, rosettasciio +pillow==10.3.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image +pint==0.17 # via hyperspy, pynxtools-xps, rosettasciio, nomad-lab (pyproject.toml) platformdirs==4.2.2 # via jupyter-core, pooch, xraydb plotly==5.22.0 # via asr, pymatgen ply==3.11 # via pycifrw @@ -224,14 +219,14 @@ pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88a pybtex==0.24.0 # via pymatgen pycifrw==4.4.6 # via diffpy-structure pycparser==2.22 # via cffi -pydantic==1.10.15 # via fastapi, nomad-lab (pyproject.toml), optimade +pydantic==1.10.15 # via fastapi, optimade, nomad-lab (pyproject.toml) pyedr==0.8.0 # via panedr pyfai==2024.5.0 # via pyxem pygments==2.18.0 # via ipython, jupyter-console, nbconvert, qtconsole, sphinx -pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml) +pyjwt==2.6.0 # via nomad-lab (pyproject.toml) pymatgen==2023.9.25 # via asr, nomad-lab (pyproject.toml) -pymongo==4.6.3 # via mongoengine, nomad-lab (pyproject.toml), optimade -pynxtools[apm,convert,ellips,em,mpes,stm,xps,xrd]==0.3.1 # via nomad-lab (pyproject.toml), pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd +pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml) +pynxtools==0.3.1 # via pynxtools-apm, pynxtools-ellips, pynxtools-em, pynxtools-mpes, pynxtools-stm, pynxtools-xps, pynxtools-xrd, nomad-lab (pyproject.toml) pynxtools-apm==0.1.1 # via pynxtools pynxtools-ellips==0.0.2 # via pynxtools pynxtools-em==0.1.1 # via pynxtools @@ -250,10 +245,10 @@ python-keycloak==4.0.0 # 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==0.0.9 # via nomad-lab (pyproject.toml) -pytz==2024.1 # via nionswift, nomad-lab (pyproject.toml), pandas +pytz==2024.1 # via nionswift, pandas, nomad-lab (pyproject.toml) pywavelets==1.6.0 # via scikit-image pyxem==0.16.0 # via pynxtools-em -pyyaml==6.0.1 # via dask, hyperspy, jupyter-events, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn +pyyaml==6.0.1 # via dask, hyperspy, jupyter-events, kikuchipy, phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn, nomad-lab (pyproject.toml) pyzeo==0.1.5 # via nomad-lab (pyproject.toml) pyzmq==26.0.3 # via ipykernel, ipyparallel, jupyter-client, jupyter-console, jupyter-server, qtconsole qtconsole==5.5.2 # via jupyter @@ -263,7 +258,7 @@ radioactivedecay==0.5.0 # via ifes-apt-tc-data-modeling rdflib==5.0.0 # via nomad-lab (pyproject.toml) rdkit==2023.9.5 # via nomad-lab (pyproject.toml) recommonmark==0.7.1 # via nomad-lab (pyproject.toml) -requests==2.32.2 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, jupyterlab-server, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx +requests==2.32.2 # via docker, hyperspy, jupyterhub, jupyterlab-server, oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), nomad-lab (pyproject.toml) requests-toolbelt==1.0.0 # via python-keycloak rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml) rfc3339-validator==0.1.4 # via jsonschema @@ -274,10 +269,11 @@ ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen ruamel-yaml-clib==0.2.8 # via ruamel-yaml runstats==2.0.0 # via nomad-lab (pyproject.toml) scikit-image==0.19.3 # via hyperspy, kikuchipy, pyxem -scikit-learn==1.5.0 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem -scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb +scikit-learn==1.5.0 # via kikuchipy, matid, pyxem, nomad-lab (pyproject.toml) +scipy==1.13.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, nomad-lab (pyproject.toml) send2trash==1.8.3 # via jupyter-server sentinels==1.0.0 # via mongomock +setuptools==70.0.0 # via radioactivedecay silx==2.1.0 # via pyfai six==1.16.0 # via anytree, asttokens, basicauth, bleach, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators smmap==5.0.1 # via gitdb @@ -299,7 +295,7 @@ starlette==0.27.0 # via fastapi structlog==24.1.0 # via nomad-lab (pyproject.toml) sympy==1.12 # via findiff, hyperspy, pymatgen, radioactivedecay tables==3.9.2 # via ifes-apt-tc-data-modeling -tabulate==0.8.9 # via nomad-lab (pyproject.toml), pybis, pymatgen +tabulate==0.8.9 # via pybis, pymatgen, nomad-lab (pyproject.toml) tenacity==8.3.0 # via plotly terminado==0.18.1 # via jupyter-server, jupyter-server-terminals texttable==1.7.0 # via pybis @@ -323,11 +319,11 @@ uncertainties==3.1.7 # via lmfit, pymatgen unidecode==1.3.2 # via nomad-lab (pyproject.toml) uri-template==1.3.0 # via jsonschema urllib3==1.26.18 # via docker, elasticsearch, pybis, requests -uvicorn[standard]==0.29.0 # via h5grove, nomad-lab (pyproject.toml) +uvicorn==0.29.0 # via h5grove, nomad-lab (pyproject.toml) uvloop==0.19.0 # via uvicorn validators==0.18.2 # via nomad-lab (pyproject.toml) vine==5.1.0 # via amqp, celery, kombu -watchfiles==0.21.0 # via uvicorn +watchfiles==0.22.0 # via uvicorn wcwidth==0.2.13 # via prettytable, prompt-toolkit webcolors==1.13 # via jsonschema webencodings==0.5.1 # via bleach, html5lib, tinycss2 @@ -336,12 +332,9 @@ websockets==12.0 # via uvicorn werkzeug==3.0.3 # via flask widgetsnbextension==4.0.10 # via ipywidgets wrapt==1.16.0 # via nomad-lab (pyproject.toml) -xarray==2023.12.0 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps +xarray==2023.12.0 # via pynxtools, pynxtools-mpes, pynxtools-xps, nomad-lab (pyproject.toml) xmltodict==0.13.0 # via ifes-apt-tc-data-modeling, pynxtools-em xraydb==4.5.4 # via pynxtools-em zarr==2.17.1 # via hyperspy -zipp==3.18.2 # via importlib-metadata, importlib-resources +zipp==3.19.0 # via importlib-metadata, importlib-resources zipstream-new==1.1.5 # via nomad-lab (pyproject.toml) - -# The following packages are considered to be unsafe in a requirements file: -# setuptools