diff --git a/pyproject.toml b/pyproject.toml index 7e6892b89346c34a42e4e9a809fffadeb08da244..23571ec71b6cf7d9681bdb857c094b1e41c4342d 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -125,7 +125,7 @@ dev = [ 'mkdocs', 'mypy==1.0.1', # bug: incompatible with derived models of pydantic v1 'names==0.3.0', - 'pip-tools>=6.13.0', + 'uv', 'pycodestyle', 'pytest-cov==2.7.1', 'pytest-timeout==1.4.2', diff --git a/requirements-dev.txt b/requirements-dev.txt index fbbdb51f68611fdef3592a5be010a1380b8138ce..530b0633fea24cb2b442d543019663780ee6d028 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,362 +1,348 @@ -# -# 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 -# -aiosmtpd==1.4.5 # 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 +# 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 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, starlette, watchfiles -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==4.3.0 # via httpx, starlette, watchfiles, -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==0.9.32 # via -r requirements.txt, lmfit -astroid==3.2.0 # 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 +asteval==0.9.32 # via lmfit, -r requirements.txt +astroid==3.2.2 # via nomad-lab (pyproject.toml) +asttokens==2.4.1 # via devtools, stack-data, -r requirements.txt +async-generator==1.10 # via jupyterhub, -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, 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 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, nomad-lab (pyproject.toml) -billiard==4.2.0 # via -r requirements.txt, celery -biopython==1.83 # via -r requirements.txt, mdanalysis +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) -blinker==1.8.2 # via -r requirements.txt, flask -blosc2==2.5.1 # via -r requirements.txt, tables -build==1.2.1 # via nomad-lab (pyproject.toml), pip-tools +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, cryptography -cftime==1.6.3 # via -r requirements.txt, netcdf4 -charset-normalizer==3.3.2 # via -r requirements.txt, requests -click==8.1.7 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pip-tools, pynxtools, uvicorn -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 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-didyoumean, click-plugins, click-repl, dask, flask, mkdocs, mkdocs-click, pynxtools, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml) +click-didyoumean==0.3.1 # via celery, -r requirements.txt +click-plugins==1.1.1 # via celery, -r requirements.txt +click-repl==0.3.0 # via celery, -r requirements.txt +cloudpickle==3.0.0 # via dask, hyperspy, -r requirements.txt colorama==0.4.6 # via mkdocs-material, twine -comm==0.2.2 # via -r requirements.txt, ipykernel -commonmark==0.9.1 # via -r requirements.txt, recommonmark -contourpy==1.2.1 # via -r requirements.txt, matplotlib +commonmark==0.9.1 # via recommonmark, -r requirements.txt +contourpy==1.2.1 # via matplotlib, -r requirements.txt coverage==7.5.1 # via pytest-cov -cryptography==42.0.7 # via -r requirements.txt, jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage -cycler==0.12.1 # via -r requirements.txt, matplotlib -dask[array]==2024.5.0 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem -debugpy==1.8.1 # via -r requirements.txt, ipykernel -decorator==5.1.1 # via -r requirements.txt, ipyparallel, ipython, validators -deprecation==2.1.0 # via -r requirements.txt, python-keycloak +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 +decorator==5.1.1 # via ipython, validators, -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==7.0.0 # 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 lmfit, -r requirements.txt +dnspython==2.6.1 # via email-validator, pymongo, -r requirements.txt +docker==7.0.0 # 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 +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 +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 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==4.0.1 # via -r requirements.txt, pynxtools -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 pynxtools, -r requirements.txt +fonttools==4.51.0 # via matplotlib, -r requirements.txt +fqdn==1.5.1 # via jsonschema, -r requirements.txt +fsspec==2024.5.0 # via dask, -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), pynxtools -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, pynxtools, -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, nomad-lab (pyproject.toml) -h5py==3.11.0 # via -r requirements.txt, fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, 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 -r requirements.txt, nomad-lab (pyproject.toml) +h5py==3.11.0 # via fabio, h5grove, hdf5plugin, ifes-apt-tc-data-modeling, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, 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 +httpcore==1.0.5 # via httpx, -r requirements.txt +httptools==0.6.1 # via uvicorn, -r requirements.txt httpx==0.27.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -hyperspy==1.7.6 # via -r requirements.txt, kikuchipy, pynxtools, pyxem -idna==3.7 # via -r requirements.txt, anyio, email-validator, httpx, jsonschema, requests -ifes-apt-tc-data-modeling==0.1 # via -r requirements.txt, pynxtools -imageio==2.27.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image -imagesize==1.4.1 # via -r requirements.txt, sphinx -importlib-metadata==7.1.0 # via -r requirements.txt, build, dask, flask, hyperspy, jupyter-client, jupyterhub, keyring, markdown, mkdocs, mkdocs-get-deps, nomad-lab (pyproject.toml), pynxtools, sphinx, twine -importlib-resources==6.4.0 # via -r requirements.txt, matplotlib, spglib +hyperspy==2.1.0 # via kikuchipy, pynxtools, pyxem, -r requirements.txt +idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt +ifes-apt-tc-data-modeling==0.1 # via pynxtools, -r requirements.txt +imageio==2.34.1 # via 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, jupyterhub, keyring, markdown, mkdocs, mkdocs-get-deps, 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 -ipyparallel==8.8.0 # via -r requirements.txt, hyperspy -ipython==8.18.1 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, pynxtools-stm -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) +ipython==8.18.1 # via pynxtools-stm, -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 +jedi==0.19.1 # via ipython, -r requirements.txt jeepney==0.8.0 # via keyring, secretstorage -jinja2==3.1.4 # via -r requirements.txt, flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx +jinja2==3.1.4 # via flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx, -r requirements.txt jmespath==1.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -joblib==1.4.2 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn -jsonpointer==2.4 # via -r requirements.txt, jsonschema -jsonschema[format]==4.17.3 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator -jupyter-client==8.6.1 # via -r requirements.txt, ipykernel, ipyparallel -jupyter-core==5.7.2 # via -r requirements.txt, ipykernel, jupyter-client -jupyter-telemetry==0.1.0 # via -r requirements.txt, jupyterhub -jupyterhub==4.0.2 # via -r requirements.txt, dockerspawner, nomad-lab (pyproject.toml), oauthenticator -jwcrypto==1.5.6 # via -r requirements.txt, python-keycloak +joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn, -r requirements.txt +jsonpointer==2.4 # via jsonschema, -r requirements.txt +jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml) +jupyter-telemetry==0.1.0 # via jupyterhub, -r requirements.txt +jupyterhub==4.0.2 # via dockerspawner, oauthenticator, -r requirements.txt, nomad-lab (pyproject.toml) +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 -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) +kikuchipy==0.8.7 # via pynxtools, -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, -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, nomad-lab (pyproject.toml), werkzeug +markupsafe==2.1.5 # via jinja2, mako, mkdocs, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml) matid==2.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) -matplotlib==3.8.4 # 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 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 +mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps, pynxtools, -r requirements.txt +mistune==3.0.2 # via m2r, -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==9.5.23 # via nomad-lab (pyproject.toml) +mkdocs-material==9.5.24 # 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==2024.5.15 # via -r requirements.txt, pymatgen +mongomock==4.1.2 # via optimade, -r requirements.txt +monty==2024.5.15 # 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 -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 +ndindex==1.8 # via blosc2, -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 -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 +niondata==0.15.5 # via nionswift, nionswift-io, -r requirements.txt +nionswift==0.16.8 # via pynxtools, -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 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, 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, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, zarr -numpy-quaternion==2023.0.3 # via -r requirements.txt, orix +numba==0.59.1 # via diffsims, kikuchipy, orix, pyxem, -r requirements.txt +numcodecs==0.12.1 # via zarr, -r requirements.txt +numexpr==2.10.0 # via 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, 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, shapely, silx, spglib, tables, tifffile, xarray, 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, docker, f90wrap, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pooch, pytest, scikit-image, silx, sphinx, tables, xarray +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, docker, f90wrap, gunicorn, hyperspy, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pooch, pytest, scikit-image, silx, sphinx, tables, xarray, -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 +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) 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==2.9.1 # 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) -pip-tools==7.4.1 # via nomad-lab (pyproject.toml) +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, 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 -plotly==5.22.0 # via -r requirements.txt, asr, pymatgen +platformdirs==4.2.2 # via mkdocs-get-deps, pooch, -r requirements.txt +plotly==5.22.0 # via asr, pymatgen, -r requirements.txt pluggy==0.13.1 # via pytest -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, jupyterhub -prompt-toolkit==3.0.43 # via -r requirements.txt, click-repl, ipython -psutil==5.9.8 # via -r requirements.txt, diffsims, ipykernel, ipyparallel, pyxem -ptyprocess==0.7.0 # via -r requirements.txt, pexpect -pure-eval==0.2.2 # via -r requirements.txt, stack-data +ply==3.11 # via pycifrw, -r requirements.txt +pooch==1.8.1 # via hyperspy, kikuchipy, orix, pyxem, -r requirements.txt +prettytable==3.10.0 # via hyperspy, -r requirements.txt +prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt +prompt-toolkit==3.0.43 # via click-repl, ipython, -r requirements.txt +psutil==5.9.8 # via diffsims, pyxem, -r requirements.txt +ptyprocess==0.7.0 # via pexpect, -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==4.4.5 # 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==2024.2.0 # via -r requirements.txt, pyxem -pygments==2.18.0 # via -r requirements.txt, devtools, ipython, mkdocs-material, 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==2023.9.0 # via pyxem, -r requirements.txt +pygments==2.18.0 # via devtools, ipython, mkdocs-material, 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[convert,mpes,stm,xps]==0.1.1 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools-mpes, pynxtools-stm, pynxtools-xps -pynxtools-mpes==0.0.3 # via -r requirements.txt, pynxtools -pynxtools-stm==1.0.1 # via -r requirements.txt, pynxtools -pynxtools-xps==0.0.3 # via -r requirements.txt, pynxtools -pyopenssl==24.1.0 # via -r requirements.txt, certipy -pyparsing==3.1.2 # via -r requirements.txt, matplotlib, rdflib -pyproject-hooks==1.1.0 # via build, pip-tools -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 +pymongo==4.6.3 # via mongoengine, optimade, -r requirements.txt, nomad-lab (pyproject.toml) +pynxtools==0.1.1 # via pynxtools-mpes, pynxtools-stm, pynxtools-xps, -r requirements.txt, nomad-lab (pyproject.toml) +pynxtools-mpes==0.0.3 # via pynxtools, -r requirements.txt +pynxtools-stm==1.0.1 # via pynxtools, -r requirements.txt +pynxtools-xps==0.0.3 # 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 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-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 -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, 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-telemetry, nomad-lab (pyproject.toml) +python-json-logger==2.0.2 # via 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, pynxtools -pytz-deprecation-shim==0.1.0.post0 # via -r requirements.txt, tzlocal -pywavelets==1.6.0 # via -r requirements.txt, scikit-image -pyxem==0.16.0 # via -r requirements.txt, pynxtools -pyyaml==6.0.1 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pymdown-extensions, pynxtools, pynxtools-mpes, pyyaml-env-tag, uvicorn +pytz==2024.1 # via mkdocs-git-revision-date-localized-plugin, nionswift, pandas, pynxtools, -r requirements.txt, nomad-lab (pyproject.toml) +pytz-deprecation-shim==0.1.0.post0 # via tzlocal, -r requirements.txt +pywavelets==1.6.0 # via scikit-image, -r requirements.txt +pyxem==0.18.0 # via pynxtools, -r requirements.txt +pyyaml==6.0.1 # via dask, hyperspy, 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 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==2.31.0 # via -r requirements.txt, docker, hyperspy, jupyterhub, 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, 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 -rfc3987==1.3.8 # via -r requirements.txt, jsonschema +rfc3987==1.3.8 # via jsonschema, -r requirements.txt rope==0.21.0 # via nomad-lab (pyproject.toml) -ruamel-yaml==0.18.6 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator, pymatgen -ruamel-yaml-clib==0.2.8 # via -r requirements.txt, ruamel-yaml -ruff==0.4.4 # via nomad-lab (pyproject.toml) +rosettasciio==0.4 # via hyperspy, -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==1.4.2 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem -scipy==1.13.0 # via -r requirements.txt, ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse +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, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml) secretstorage==3.3.3 # via keyring -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, asttokens, basicauth, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, pytest-xdist, python-dateutil, rdflib, rfc3339-validator, validators -smmap==5.0.1 # via -r requirements.txt, gitdb -sniffio==1.3.1 # via -r requirements.txt, anyio, httpx -snowballstemmer==2.2.0 # via -r requirements.txt, sphinx -soupsieve==2.5 # via -r requirements.txt, beautifulsoup4 -sparse==0.15.1 # via -r requirements.txt, hyperspy -spglib==2.4.0 # 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 -stack-data==0.6.3 # via -r requirements.txt, ipython -starlette==0.27.0 # via -r requirements.txt, fastapi +sentinels==1.0.0 # via mongomock, -r requirements.txt +setuptools==70.0.0 # via radioactivedecay, -r requirements.txt +shapely==2.0.4 # via pyxem, -r requirements.txt +silx==2.1.0 # via pyfai, -r requirements.txt +six==1.16.0 # via asttokens, basicauth, 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 +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, -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 -texttable==1.7.0 # via -r requirements.txt, pybis -threadpoolctl==3.5.0 # via -r requirements.txt, mdanalysis, scikit-learn -tifffile==2024.5.10 # via -r requirements.txt, h5grove, hyperspy, scikit-image -tomli==2.0.1 # via -r requirements.txt, build, mypy, pip-tools, sphinx -toolz==0.12.1 # via -r requirements.txt, dask, hyperspy, partd +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, scikit-image, -r requirements.txt +tomli==2.0.1 # via build, mypy, sphinx, -r requirements.txt +toolz==0.12.1 # via dask, 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, jupyterhub -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, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline -traits==6.4.3 # via -r requirements.txt, hyperspy, pyxem -transforms3d==0.4.1 # via -r requirements.txt, diffsims, pyxem +tornado==6.4 # via jupyterhub, -r requirements.txt +tqdm==4.66.4 # via diffsims, hyperspy, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem, twine, -r requirements.txt +traitlets==5.14.3 # via ipython, jupyter-telemetry, jupyterhub, matplotlib-inline, -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==4.11.0 # via -r requirements.txt, alembic, anyio, asgiref, astroid, 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, pytz-deprecation-shim -tzlocal==4.3 # via -r requirements.txt, nionswift, pynxtools -uncertainties==3.1.7 # via -r requirements.txt, lmfit, pymatgen +types-python-dateutil==2.9.0.20240316 # via arrow, -r requirements.txt +typing-extensions==4.11.0 # via alembic, anyio, asgiref, astroid, 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, pytz-deprecation-shim, -r requirements.txt +tzlocal==4.3 # via nionswift, pynxtools, -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 -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==0.2.2 # 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==4.0.0 # 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, html5lib -websockets==12.0 # via -r requirements.txt, uvicorn -werkzeug==3.0.3 # via -r requirements.txt, flask -wheel==0.43.0 # via pip-tools +watchfiles==0.21.0 # 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 html5lib, -r requirements.txt +websockets==12.0 # via uvicorn, -r requirements.txt +werkzeug==3.0.3 # via flask, -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 -zarr==2.17.1 # via -r requirements.txt, hyperspy -zipfile37==0.1.3 # via -r requirements.txt, pynxtools -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) +zarr==2.17.1 # via pyxem, -r requirements.txt +zipfile37==0.1.3 # via pynxtools, -r requirements.txt +zipp==3.18.2 # 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: -# pip -# setuptools diff --git a/requirements.txt b/requirements.txt index dc0d328e46187b84d193f4cca8f838f5bf31db58..f16f9bb343c178f15c287bf7771a8840bd90a2f7 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,9 +1,5 @@ -# -# 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 @@ -11,7 +7,7 @@ aniso8601==9.0.1 # via nomad-lab (pyproject.toml) anyio==4.3.0 # via httpx, starlette, watchfiles 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==0.9.32 # via lmfit @@ -24,7 +20,7 @@ basicauth==0.4.1 # via nomad-lab (pyproject.toml) beautifulsoup4==4.12.3 # via nomad-lab (pyproject.toml) billiard==4.2.0 # via celery biopython==1.83 # via mdanalysis -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) blinker==1.8.2 # via flask blosc2==2.5.1 # via tables cachetools==5.3.3 # via nomad-lab (pyproject.toml) @@ -34,23 +30,21 @@ certipy==0.1.3 # via jupyterhub cffi==1.16.0 # via cryptography cftime==1.6.3 # via netcdf4 charset-normalizer==3.3.2 # via requests -click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, nomad-lab (pyproject.toml), pynxtools, uvicorn +click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, dask, flask, pynxtools, uvicorn, nomad-lab (pyproject.toml) click-didyoumean==0.3.1 # via celery click-plugins==1.1.1 # via celery click-repl==0.3.0 # via celery cloudpickle==3.0.0 # via dask, hyperspy -comm==0.2.2 # via ipykernel commonmark==0.9.1 # via recommonmark contourpy==1.2.1 # via matplotlib cryptography==42.0.7 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng cycler==0.12.1 # via matplotlib -dask[array]==2024.5.0 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio -debugpy==1.8.1 # via ipykernel -decorator==5.1.1 # via ipyparallel, ipython, validators +dask==2024.5.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio +decorator==5.1.1 # via ipython, validators deprecation==2.1.0 # via python-keycloak diffpy-structure==3.1.0 # via diffsims, kikuchipy, orix diffsims==0.5.2 # via kikuchipy, pyxem -dill==0.3.8 # via hyperspy, lmfit +dill==0.3.8 # via lmfit dnspython==2.6.1 # via email-validator, pymongo docker==7.0.0 # via dockerspawner dockerspawner==13.0.0 # via nomad-lab (pyproject.toml) @@ -59,7 +53,6 @@ docutils==0.21.2 # via m2r, recommonmark, sphinx elasticsearch==7.17.1 # via elasticsearch-dsl, nomad-lab (pyproject.toml) elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml) email-validator==1.3.1 # via optimade -entrypoints==0.4 # via ipyparallel escapism==1.0.1 # via dockerspawner et-xmlfile==1.1.0 # via openpyxl exceptiongroup==1.2.1 # via anyio, ipython @@ -74,34 +67,32 @@ flask==3.0.3 # via asr flatdict==4.0.1 # via pynxtools fonttools==4.51.0 # via matplotlib fqdn==1.5.1 # via jsonschema -fsspec==2024.5.0 # via dask, hyperspy +fsspec==2024.5.0 # via dask future==1.0.0 # via uncertainties gitdb==4.0.11 # via gitpython -gitpython==3.1.43 # via nomad-lab (pyproject.toml), pynxtools +gitpython==3.1.43 # via pynxtools, nomad-lab (pyproject.toml) greenlet==3.0.3 # via sqlalchemy 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 nomad-lab (pyproject.toml) -h5py==3.11.0 # via fabio, h5grove, hdf5plugin, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, silx +h5grove==1.3.0 # via nomad-lab (pyproject.toml) +h5py==3.11.0 # via fabio, h5grove, hdf5plugin, ifes-apt-tc-data-modeling, kikuchipy, nionswift, orix, phonopy, pyfai, pynxtools, pynxtools-mpes, pynxtools-xps, pyxem, rosettasciio, 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 nomad-lab (pyproject.toml) -hyperspy==1.7.6 # via kikuchipy, pynxtools, pyxem +hyperspy==2.1.0 # via kikuchipy, pynxtools, pyxem idna==3.7 # via anyio, email-validator, httpx, jsonschema, requests ifes-apt-tc-data-modeling==0.1 # via pynxtools -imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image +imageio==2.34.1 # via kikuchipy, nionswift, nionswift-io, nionui, scikit-image imagesize==1.4.1 # via sphinx -importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyter-client, jupyterhub, nomad-lab (pyproject.toml), pynxtools, sphinx +importlib-metadata==7.1.0 # via dask, flask, hyperspy, jupyterhub, 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 -ipyparallel==8.8.0 # via hyperspy -ipython==8.18.1 # via hyperspy, ipykernel, ipyparallel, pynxtools-stm +ipython==8.18.1 # via pynxtools-stm isodate==0.6.1 # via rdflib isoduration==20.11.0 # via jsonschema itsdangerous==2.2.0 # via flask, nomad-lab (pyproject.toml) @@ -110,13 +101,11 @@ jinja2==3.1.4 # via flask, hyperspy, jupyterhub, sphinx jmespath==1.0.1 # via nomad-lab (pyproject.toml) joblib==1.4.2 # via mdanalysis, pymatgen, scikit-learn jsonpointer==2.4 # via jsonschema -jsonschema[format]==4.17.3 # via jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator -jupyter-client==8.6.1 # via ipykernel, ipyparallel -jupyter-core==5.7.2 # via ipykernel, jupyter-client +jsonschema==4.17.3 # via jupyter-telemetry, oauthenticator, nomad-lab (pyproject.toml) 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) jwcrypto==1.5.6 # via python-keycloak -kikuchipy==0.9.0 # via pynxtools +kikuchipy==0.8.7 # via pynxtools kiwisolver==1.4.5 # via matplotlib kombu==5.3.7 # via celery lark==1.1.9 # via optimade @@ -131,7 +120,7 @@ mako==1.3.5 # via alembic markupsafe==2.1.5 # via jinja2, mako, werkzeug matid==2.0.1 # via nomad-lab (pyproject.toml) matplotlib==3.8.4 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay -matplotlib-inline==0.1.7 # via ipykernel, ipython +matplotlib-inline==0.1.7 # via ipython matplotlib-scalebar==0.8.1 # via orix mda-xdrlib==0.2.0 # via pyedr mdanalysis==2.5.0 # via nomad-lab (pyproject.toml) @@ -146,45 +135,45 @@ mrcfile==1.5.0 # via griddataformats msgpack==1.0.8 # via blosc2, mmtf-python, nomad-lab (pyproject.toml) natsort==8.4.0 # via hyperspy 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 nionswift-io==0.15.1 # via nionswift nionui==0.6.11 # via nionswift nionutils==0.4.10 # via niondata, nionswift, nionswift-io, nionui nptyping==1.4.4 # via nomad-lab (pyproject.toml) -numba==0.59.1 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse +numba==0.59.1 # via diffsims, kikuchipy, orix, pyxem 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, 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, pyedr, pyfai, pymatgen, pynxtools, pywavelets, pyxem, quippy-ase, radioactivedecay, rdkit, rosettasciio, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tables, tifffile, xarray, zarr +numexpr==2.10.0 # via 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, 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, shapely, silx, spglib, tables, tifffile, xarray, 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, docker, f90wrap, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, pooch, scikit-image, silx, sphinx, tables, xarray +packaging==24.0 # via dask, deprecation, docker, f90wrap, gunicorn, hyperspy, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, pooch, scikit-image, silx, sphinx, tables, xarray 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) panedr==0.8.0 # via nomad-lab (pyproject.toml) parmed==4.2.2 # via nomad-lab (pyproject.toml) parso==0.8.4 # via jedi partd==1.4.2 # via dask pexpect==4.9.0 # via ipython -phonopy==2.9.1 # via asr -pillow==10.0.1 # via fabio, hyperspy, imageio, matplotlib, nionswift, rdkit, scikit-image -pint==0.17 # via hyperspy, nomad-lab (pyproject.toml), rosettasciio -platformdirs==4.2.2 # via jupyter-core, pooch +phonopy==2.23.1 # via asr +pillow==10.3.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image +pint==0.17 # via hyperspy, rosettasciio, nomad-lab (pyproject.toml) +platformdirs==4.2.2 # via pooch plotly==5.22.0 # via asr, pymatgen -pooch==1.8.1 # via hyperspy, kikuchipy, orix +ply==3.11 # via pycifrw +pooch==1.8.1 # via hyperspy, kikuchipy, orix, pyxem prettytable==3.10.0 # via hyperspy prometheus-client==0.20.0 # via jupyterhub prompt-toolkit==3.0.43 # via click-repl, ipython -psutil==5.9.8 # via diffsims, ipykernel, ipyparallel, pyxem +psutil==5.9.8 # via diffsims, pyxem ptyprocess==0.7.0 # via pexpect pure-eval==0.2.2 # via stack-data py-cpuinfo==9.0.0 # via blosc2, tables @@ -192,60 +181,62 @@ pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng pyasn1-modules==0.4.0 # via rfc3161ng pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370 # via nomad-lab (pyproject.toml) pybtex==0.24.0 # via pymatgen -pycifrw==4.4.5 # via diffpy-structure +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==2024.2.0 # via pyxem +pyfai==2023.9.0 # via pyxem pygments==2.18.0 # via ipython, 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[convert,mpes,stm,xps]==0.1.1 # via nomad-lab (pyproject.toml), pynxtools-mpes, pynxtools-stm, pynxtools-xps +pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml) +pynxtools==0.1.1 # via pynxtools-mpes, pynxtools-stm, pynxtools-xps, nomad-lab (pyproject.toml) pynxtools-mpes==0.0.3 # via pynxtools pynxtools-stm==1.0.1 # via pynxtools pynxtools-xps==0.0.3 # via pynxtools pyopenssl==24.1.0 # via certipy pyparsing==3.1.2 # via matplotlib, rdflib pyrsistent==0.20.0 # via jsonschema -python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, pybis, rfc3161ng, rosettasciio +python-box==6.1.0 # via rosettasciio +python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, hyperspy, jupyterhub, matplotlib, pandas, pybis, rfc3161ng, rosettasciio python-dotenv==1.0.1 # via uvicorn python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml) 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, pynxtools +pytz==2024.1 # via nionswift, pandas, pynxtools, nomad-lab (pyproject.toml) pytz-deprecation-shim==0.1.0.post0 # via tzlocal pywavelets==1.6.0 # via scikit-image -pyxem==0.16.0 # via pynxtools -pyyaml==6.0.1 # via dask, hyperspy, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools, pynxtools-mpes, rosettasciio, uvicorn +pyxem==0.18.0 # via pynxtools +pyyaml==6.0.1 # via dask, hyperspy, 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 quippy-ase==0.9.14 # via nomad-lab (pyproject.toml) 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==2.31.0 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-keycloak, requests-toolbelt, rfc3161ng, sphinx +requests==2.32.2 # via docker, hyperspy, jupyterhub, 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 rfc3987==1.3.8 # via jsonschema +rosettasciio==0.4 # via hyperspy 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==1.4.2 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem -scipy==1.13.0 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse +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, pynxtools, pyxem, radioactivedecay, scikit-image, scikit-learn, nomad-lab (pyproject.toml) sentinels==1.0.0 # via mongomock +setuptools==70.0.0 # via radioactivedecay +shapely==2.0.4 # via pyxem silx==2.1.0 # via pyfai six==1.16.0 # via asttokens, basicauth, diffpy-structure, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators smmap==5.0.1 # via gitdb sniffio==1.3.1 # via anyio, httpx snowballstemmer==2.2.0 # via sphinx soupsieve==2.5 # via beautifulsoup4 -sparse==0.15.1 # via hyperspy spglib==2.4.0 # via asr, matid, phonopy, pymatgen sphinx==7.3.7 # via recommonmark sphinxcontrib-applehelp==1.0.8 # via sphinx @@ -260,17 +251,17 @@ 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 texttable==1.7.0 # via pybis threadpoolctl==3.5.0 # via mdanalysis, scikit-learn -tifffile==2024.5.10 # via h5grove, hyperspy, scikit-image +tifffile==2024.5.22 # via h5grove, scikit-image tomli==2.0.1 # via sphinx -toolz==0.12.1 # via dask, hyperspy, partd +toolz==0.12.1 # via dask, partd toposort==1.10 # via nomad-lab (pyproject.toml) -tornado==6.4 # via ipykernel, ipyparallel, jupyter-client, jupyterhub -tqdm==4.66.4 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem -traitlets==5.14.3 # via comm, ipykernel, ipyparallel, ipython, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline +tornado==6.4 # via jupyterhub +tqdm==4.66.4 # via diffsims, hyperspy, kikuchipy, mdanalysis, orix, pyedr, pymatgen, pyxem +traitlets==5.14.3 # via ipython, jupyter-telemetry, jupyterhub, matplotlib-inline traits==6.4.3 # via hyperspy, pyxem transforms3d==0.4.1 # via diffsims, pyxem types-python-dateutil==2.9.0.20240316 # via arrow @@ -282,7 +273,7 @@ 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 @@ -293,11 +284,8 @@ webencodings==0.5.1 # via html5lib websockets==12.0 # via uvicorn werkzeug==3.0.3 # via flask wrapt==1.16.0 # via nomad-lab (pyproject.toml) -xarray==2023.12.0 # via nomad-lab (pyproject.toml), pynxtools, pynxtools-mpes, pynxtools-xps -zarr==2.17.1 # via hyperspy +xarray==2023.12.0 # via pynxtools, pynxtools-mpes, pynxtools-xps, nomad-lab (pyproject.toml) +zarr==2.17.1 # via pyxem zipfile37==0.1.3 # via pynxtools zipp==3.18.2 # 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 diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh index 2efe00c83cc428f66b923ec8180856719a8876a5..276ed31737058d641120d39e7164d01469dfac69 100755 --- a/scripts/check_python_dependencies.sh +++ b/scripts/check_python_dependencies.sh @@ -18,20 +18,18 @@ cd $project_dir cp requirements.txt requirements.txt.tmp cp requirements-dev.txt requirements-dev.txt.tmp -pip-compile -r -U --resolver=backtracking --annotation-style=line \ +uv pip compile -q -U --annotation-style=line \ --extra=infrastructure --extra=parsing \ --output-file=requirements.txt \ - --pip-args="--prefer-binary" \ dependencies/nomad-dos-fingerprints/pyproject.toml \ dependencies/parsers/eelsdb/pyproject.toml \ pyproject.toml diff requirements.txt.tmp requirements.txt -pip-compile -r -U --resolver=backtracking --annotation-style=line \ +uv pip compile -q -U --annotation-style=line \ --extra=dev --extra=infrastructure --extra=parsing \ --output-file=requirements-dev.txt \ - --pip-args="--prefer-binary" \ requirements.txt \ pyproject.toml diff --git a/scripts/generate_python_dependencies.sh b/scripts/generate_python_dependencies.sh index 3393d05092e9263dfb4d91f14670f1ece89dd7fa..02890282fd762c6f6c305a2a7ce0e90f8cdf48a2 100755 --- a/scripts/generate_python_dependencies.sh +++ b/scripts/generate_python_dependencies.sh @@ -14,18 +14,17 @@ project_dir=$(dirname $(dirname $(realpath $0))) cd $project_dir -pip-compile -r -U --resolver=backtracking --annotation-style=line \ + +uv pip compile -U --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 -pip-compile -r -U --resolver=backtracking --annotation-style=line \ +uv pip compile -U --annotation-style=line \ --extra=dev --extra=infrastructure --extra=parsing \ --output-file=requirements-dev.txt \ - --pip-args="--prefer-binary" \ requirements.txt \ pyproject.toml