diff --git a/pyproject.toml b/pyproject.toml index d4dce2596e034256202e2142a9d6fb6b6a76ef47..07ff15aff1312c04c70b5457e3369a8fd107b13f 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', - 'uv', + 'uv>=0.2.35', 'pycodestyle', 'pytest-asyncio', 'pytest-cov>=2.7.1', diff --git a/requirements-dev.txt b/requirements-dev.txt index 8798de4d40b98c08fc3c0718775331a2493124b6..cbc5d59c83c271de7c8762076e9cdff83b34990b 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -1,5 +1,5 @@ # This file was autogenerated by uv via the following command: -# uv pip compile -p 3.11 --python-platform linux --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt requirements.txt pyproject.toml +# uv pip compile --universal --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==1.0.0 # via sphinx, -r requirements.txt alembic==1.13.2 # via jupyterhub, -r requirements.txt @@ -17,7 +17,7 @@ async-property==0.2.2 # via python-keycloak, -r requirements.txt atpublic==5.0 # via aiosmtpd attrs==24.2.0 # via aiosmtpd, jsonschema, -r requirements.txt babel==2.16.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-material, sphinx, -r requirements.txt -backports-tarfile==1.2.0 # via jaraco-context +backports-tarfile==1.2.0 ; python_version < '3.12.0' # via jaraco-context bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml) basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml) beautifulsoup4==4.12.3 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -30,14 +30,14 @@ cachetools==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) certifi==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt certipy==0.1.3 # via jupyterhub, -r requirements.txt -cffi==1.17.0 # via cryptography, -r requirements.txt +cffi==1.17.0 ; platform_python_implementation != 'PyPy' # via cryptography, -r requirements.txt cftime==1.6.4 # 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, flask, mkdocs, mkdocs-click, 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 -colorama==0.4.6 # via mkdocs-material, twine +colorama==0.4.6 # via build, click, mkdocs, mkdocs-material, pytest, sphinx, tqdm, twine, uvicorn, -r requirements.txt commonmark==0.9.1 # via recommonmark, -r requirements.txt contourpy==1.2.1 # via matplotlib, -r requirements.txt coverage==7.6.1 # via pytest-cov @@ -69,7 +69,7 @@ fqdn==1.5.1 # via jsonschema, -r requirements.txt ghp-import==2.1.0 # via mkdocs 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 +greenlet==3.0.3 ; (python_version < '3.13' and platform_machine == 'AMD64') or (python_version < '3.13' and platform_machine == 'WIN32') or (python_version < '3.13' and platform_machine == 'aarch64') or (python_version < '3.13' and platform_machine == 'amd64') or (python_version < '3.13' and platform_machine == 'ppc64le') or (python_version < '3.13' and platform_machine == 'win32') or (python_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy, -r requirements.txt griddataformats==1.0.2 # via mdanalysis, -r requirements.txt gsd==3.3.0 # via mdanalysis, -r requirements.txt gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -92,7 +92,7 @@ itsdangerous==2.2.0 # via flask, -r requirements.txt, nomad-lab (pyproject jaraco-classes==3.4.0 # via keyring jaraco-context==5.3.0 # via keyring jaraco-functools==4.0.2 # via keyring -jeepney==0.8.0 # via keyring, secretstorage +jeepney==0.8.0 ; sys_platform == 'linux' # via keyring, secretstorage jinja2==3.1.4 # via flask, 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 mdanalysis, pymatgen, scikit-learn, -r requirements.txt @@ -153,7 +153,7 @@ orjson==3.10.7 # via h5grove, -r requirements.txt, nomad-lab (pyproje packaging==24.1 # via build, deprecation, f90wrap, gunicorn, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt paginate==0.5.6 # via mkdocs-material palettable==3.3.3 # via pymatgen, -r requirements.txt -pamela==1.1.0 # via jupyterhub, -r requirements.txt +pamela==1.2.0 ; sys_platform != 'win32' # via jupyterhub, -r requirements.txt pandas==1.5.3 # via nomad-openbis, panedr, pymatgen, 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) @@ -167,11 +167,12 @@ plotly==5.23.0 # via asr, pymatgen, -r requirements.txt pluggy==1.5.0 # via pytest prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt prompt-toolkit==3.0.47 # via click-repl, -r requirements.txt +psutil==6.0.0 ; sys_platform == 'win32' # via jupyterhub, -r requirements.txt pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng, -r requirements.txt pyasn1-modules==0.4.0 # via rfc3161ng, -r requirements.txt pybtex==0.24.0 # via pymatgen, -r requirements.txt pycodestyle==2.12.1 # via nomad-lab (pyproject.toml) -pycparser==2.22 # via cffi, -r requirements.txt +pycparser==2.22 ; platform_python_implementation != 'PyPy' # via cffi, -r requirements.txt pydantic==1.10.17 # via fastapi, optimade, -r requirements.txt, nomad-lab (pyproject.toml) pyedr==0.8.0 # via panedr, -r requirements.txt pygments==2.18.0 # via devtools, mkdocs-material, readme-renderer, sphinx, -r requirements.txt @@ -196,8 +197,11 @@ python-json-logger==2.0.2 # via jupyter-telemetry, -r requirements.txt, nomad-l python-keycloak==4.3.0 # 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-magic-bin==0.4.14 ; sys_platform == 'win32' # 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 mkdocs-git-revision-date-localized-plugin, pandas, -r requirements.txt, nomad-lab (pyproject.toml) +pywin32==306 ; sys_platform == 'win32' # via docker, -r requirements.txt +pywin32-ctypes==0.2.2 ; sys_platform == 'win32' # via keyring pyyaml==6.0.2 # via mkdocs, mkdocs-get-deps, mkdocs-macros-plugin, phonopy, pybtex, pymdown-extensions, pyyaml-env-tag, uvicorn, -r requirements.txt, nomad-lab (pyproject.toml) pyyaml-env-tag==0.1 # via mkdocs quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -214,12 +218,12 @@ rfc3986==2.0.0 # via twine rfc3987==1.3.8 # via jsonschema, -r requirements.txt rope==0.21.0 # via nomad-lab (pyproject.toml) 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 +ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt ruff==0.5.7 # via nomad-lab (pyproject.toml) runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) scikit-learn==1.5.1 # via matid, -r requirements.txt, nomad-lab (pyproject.toml) scipy==1.14.0 # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml) -secretstorage==3.3.3 # via keyring +secretstorage==3.3.3 ; sys_platform == 'linux' # via keyring sentinels==1.0.0 # via mongomock, -r requirements.txt six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5lib, isodate, pybtex, python-dateutil, rdflib, rfc3339-validator, validators, -r requirements.txt smmap==5.0.1 # via gitdb, -r requirements.txt @@ -258,15 +262,15 @@ uncertainties==3.2.2 # via pymatgen, -r requirements.txt unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml) uri-template==1.3.0 # via jsonschema, -r requirements.txt urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt -uv==0.2.34 # via nomad-lab (pyproject.toml) +uv==0.2.35 # via nomad-lab (pyproject.toml) uvicorn==0.30.5 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) -uvloop==0.19.0 # via uvicorn, -r requirements.txt +uvloop==0.19.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn, -r requirements.txt validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml) vine==5.1.0 # via amqp, celery, kombu, -r requirements.txt watchdog==4.0.1 # via mkdocs watchfiles==0.23.0 # via uvicorn, -r requirements.txt wcwidth==0.2.13 # via prompt-toolkit, -r requirements.txt -webcolors==24.6.0 # via jsonschema, -r requirements.txt +webcolors==24.8.0 # 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 diff --git a/requirements.txt b/requirements.txt index dbe9d170c55717f43ee004818de8636ff6813d53..95517735275fc5ce718bb75be1d61980cfcd447c 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,5 +1,5 @@ # This file was autogenerated by uv via the following command: -# uv pip compile -p 3.11 --python-platform linux --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml pyproject.toml +# uv pip compile --universal --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==1.0.0 # via sphinx alembic==1.13.2 # via jupyterhub amqp==5.2.0 # via kombu @@ -24,13 +24,14 @@ cachetools==5.4.0 # via nomad-lab (pyproject.toml) celery==5.4.0 # via nomad-lab (pyproject.toml) certifi==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests certipy==0.1.3 # via jupyterhub -cffi==1.17.0 # via cryptography +cffi==1.17.0 ; platform_python_implementation != 'PyPy' # via cryptography cftime==1.6.4 # via netcdf4 charset-normalizer==3.3.2 # via requests click==8.1.7 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, 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 +colorama==0.4.6 ; sys_platform == 'win32' or platform_system == 'Windows' # via click, sphinx, tqdm, uvicorn commonmark==0.9.1 # via recommonmark contourpy==1.2.1 # via matplotlib cryptography==43.0.0 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng @@ -56,7 +57,7 @@ fonttools==4.53.1 # via matplotlib fqdn==1.5.1 # via jsonschema gitdb==4.0.11 # via gitpython gitpython==3.1.43 # via nomad-lab (pyproject.toml) -greenlet==3.0.3 # via sqlalchemy +greenlet==3.0.3 ; (python_version < '3.13' and platform_machine == 'AMD64') or (python_version < '3.13' and platform_machine == 'WIN32') or (python_version < '3.13' and platform_machine == 'aarch64') or (python_version < '3.13' and platform_machine == 'amd64') or (python_version < '3.13' and platform_machine == 'ppc64le') or (python_version < '3.13' and platform_machine == 'win32') or (python_version < '3.13' and platform_machine == 'x86_64') # via sqlalchemy griddataformats==1.0.2 # via mdanalysis gsd==3.3.0 # via mdanalysis gunicorn==21.2.0 # via nomad-lab (pyproject.toml) @@ -117,7 +118,7 @@ optimade==0.22.1 # via nomad-lab (pyproject.toml) orjson==3.10.7 # via h5grove, nomad-lab (pyproject.toml) packaging==24.1 # via deprecation, f90wrap, gunicorn, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, sphinx, xarray palettable==3.3.3 # via pymatgen -pamela==1.1.0 # via jupyterhub +pamela==1.2.0 ; sys_platform != 'win32' # via jupyterhub pandas==1.5.3 # via nomad-openbis, panedr, pymatgen, 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) @@ -127,10 +128,11 @@ pint==0.17 # via nomad-lab (pyproject.toml) plotly==5.23.0 # via asr, pymatgen prometheus-client==0.20.0 # via jupyterhub prompt-toolkit==3.0.47 # via click-repl +psutil==6.0.0 ; sys_platform == 'win32' # via jupyterhub pyasn1==0.6.0 # via pyasn1-modules, rfc3161ng pyasn1-modules==0.4.0 # via rfc3161ng pybtex==0.24.0 # via pymatgen -pycparser==2.22 # via cffi +pycparser==2.22 ; platform_python_implementation != 'PyPy' # via cffi pydantic==1.10.17 # via fastapi, optimade, nomad-lab (pyproject.toml) pyedr==0.8.0 # via panedr pygments==2.18.0 # via sphinx @@ -146,8 +148,10 @@ python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml) python-keycloak==4.3.0 # 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-magic-bin==0.4.14 ; sys_platform == 'win32' # via nomad-lab (pyproject.toml) python-multipart==0.0.9 # via nomad-lab (pyproject.toml) pytz==2024.1 # via pandas, nomad-lab (pyproject.toml) +pywin32==306 ; sys_platform == 'win32' # via docker pyyaml==6.0.2 # via phonopy, pybtex, uvicorn, nomad-lab (pyproject.toml) quippy-ase==0.9.14 # via nomad-lab (pyproject.toml) rdflib==5.0.0 # via nomad-lab (pyproject.toml) @@ -159,7 +163,7 @@ rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml) rfc3339-validator==0.1.4 # via jsonschema rfc3987==1.3.8 # via jsonschema ruamel-yaml==0.18.6 # via jupyter-telemetry, oauthenticator, pymatgen -ruamel-yaml-clib==0.2.8 # via ruamel-yaml +ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml runstats==2.0.0 # via nomad-lab (pyproject.toml) scikit-learn==1.5.1 # via matid, nomad-lab (pyproject.toml) scipy==1.14.0 # via ase, griddataformats, matid, mdanalysis, pymatgen, scikit-learn, nomad-lab (pyproject.toml) @@ -199,12 +203,12 @@ unidecode==1.3.2 # via nomad-lab (pyproject.toml) uri-template==1.3.0 # via jsonschema urllib3==1.26.19 # via docker, elasticsearch, nomad-openbis, requests uvicorn==0.30.5 # via h5grove, nomad-lab (pyproject.toml) -uvloop==0.19.0 # via uvicorn +uvloop==0.19.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn validators==0.18.2 # via nomad-lab (pyproject.toml) vine==5.1.0 # via amqp, celery, kombu watchfiles==0.23.0 # via uvicorn wcwidth==0.2.13 # via prompt-toolkit -webcolors==24.6.0 # via jsonschema +webcolors==24.8.0 # via jsonschema webencodings==0.5.1 # via html5lib websockets==12.0 # via uvicorn werkzeug==3.0.3 # via flask diff --git a/scripts/generate_python_dependencies.sh b/scripts/generate_python_dependencies.sh index 4080f1644b890e980227e4346dc733952e37f175..eeb5d4a03b0a35486fb988129621dc5c968c4b39 100755 --- a/scripts/generate_python_dependencies.sh +++ b/scripts/generate_python_dependencies.sh @@ -15,14 +15,14 @@ project_dir=$(dirname $(dirname $(realpath $0))) cd $project_dir -uv pip compile -U -p 3.11 --python-platform linux --annotation-style=line \ +uv pip compile -U --universal --annotation-style=line \ --extra=infrastructure --extra=parsing \ --output-file=requirements.txt \ dependencies/nomad-dos-fingerprints/pyproject.toml \ dependencies/parsers/eelsdb/pyproject.toml \ pyproject.toml -uv pip compile -U -p 3.11 --python-platform linux --annotation-style=line \ +uv pip compile -U --universal --annotation-style=line \ --extra=dev --extra=infrastructure --extra=parsing \ --output-file=requirements-dev.txt \ requirements.txt \