diff --git a/default_plugins.txt b/default_plugins.txt index 6936742e727ef5b0096d6a10fa88667d22adb005..254385cdd46c09aeab13cc1d245c019210305188 100644 --- a/default_plugins.txt +++ b/default_plugins.txt @@ -12,7 +12,7 @@ nomad-normalizer-plugin-spectra>=1.0 nomad-normalizer-plugin-system>=1.0 nomad-normalizer-plugin-simulation-workflow>=1.0 nomad-parser-plugins-electronic>=1.0 -nomad-parser-plugins-atomistic>=1.0 +nomad-parser-plugins-atomistic>=1.0.1 nomad-parser-plugins-workflow>=1.0 nomad-parser-plugins-database>=1.0 git+https://github.com/nomad-coe/nomad-parser-eelsdb.git@entry-point \ No newline at end of file diff --git a/gui/tests/env.js b/gui/tests/env.js index b26eaa2a299f27c9e6c62b37172c1812786f80c8..68c0f110044e5b18f86ddc423462d12622c971d9 100644 --- a/gui/tests/env.js +++ b/gui/tests/env.js @@ -4408,7 +4408,7 @@ window.nomadEnv = { "homepage": "https://github.com/nomad-coe/atomistic-parsers", "name": "atomisticparsers", "repository": null, - "version": "1.0" + "version": "1.0.1" }, "bandstructurenormalizer": { "description": "Band structure normalizer plugin for NOMAD.", diff --git a/requirements-dev.txt b/requirements-dev.txt index da9420bbaf68560c6ee95fa479a0b6be4e74940b..75a303300f310e4ad160472fc7f66ef067e59c15 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -16,7 +16,7 @@ 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 ; python_full_version < '3.12' # via jaraco-context +backports-tarfile==1.2.0 ; python_version < '3.12' # 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) @@ -26,7 +26,7 @@ build==1.2.2 # via nomad-lab (pyproject.toml) cachetools==5.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml) celery==5.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt -certipy==0.1.3 # via jupyterhub, -r requirements.txt +certipy==0.2.1 # via jupyterhub, -r requirements.txt cffi==1.17.1 ; 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 @@ -38,7 +38,7 @@ colorama==0.4.6 # via build, click, mkdocs, mkdocs-material, pytest, s commonmark==0.9.1 # via recommonmark, -r requirements.txt contourpy==1.3.0 # via matplotlib, -r requirements.txt coverage==7.6.1 # via pytest-cov -cryptography==43.0.1 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng, secretstorage, -r requirements.txt +cryptography==43.0.1 # via certipy, jwcrypto, pyjwt, rfc3161ng, secretstorage, -r requirements.txt cycler==0.12.1 # via matplotlib, -r requirements.txt decorator==5.1.1 # via validators, -r requirements.txt deprecation==2.1.0 # via python-keycloak, -r requirements.txt @@ -73,7 +73,7 @@ html5lib==1.1 # via -r requirements.txt, nomad-lab (pyproject.toml) httpcore==1.0.5 # via httpx, -r requirements.txt httptools==0.6.1 # via uvicorn, -r requirements.txt httpx==0.27.2 # via python-keycloak, -r requirements.txt, nomad-lab (pyproject.toml) -idna==3.8 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt +idna==3.10 # via anyio, email-validator, httpx, jsonschema, requests, -r requirements.txt imagesize==1.4.1 # via sphinx, -r requirements.txt importlib-metadata==7.1.0 # via keyring, twine, -r requirements.txt, nomad-lab (pyproject.toml) inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -115,7 +115,7 @@ mkdocs-click==0.8.1 # via nomad-lab (pyproject.toml) mkdocs-get-deps==0.2.0 # via mkdocs mkdocs-git-revision-date-localized-plugin==1.2.9 # 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-macros-plugin==1.2.0 # via nomad-lab (pyproject.toml) mkdocs-material==9.5.34 # 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) @@ -139,7 +139,7 @@ oauthlib==3.2.2 # via jupyterhub, -r requirements.txt openpyxl==3.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml) optimade==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml) orjson==3.10.7 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) -packaging==24.1 # via build, deprecation, gunicorn, jupyterhub, matplotlib, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt +packaging==24.1 # via build, deprecation, gunicorn, jupyterhub, matplotlib, mkdocs, mkdocs-macros-plugin, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt paginate==0.5.7 # via mkdocs-material palettable==3.3.3 # via pymatgen, -r requirements.txt pamela==1.2.0 ; sys_platform != 'win32' # via jupyterhub, -r requirements.txt @@ -150,7 +150,7 @@ pathspec==0.12.1 # via mkdocs pillow==10.4.0 # via matplotlib, rdkit, -r requirements.txt pint==0.17 # via -r requirements.txt, nomad-lab (pyproject.toml) pkginfo==1.11.1 # via twine -platformdirs==4.3.2 # via mkdocs-get-deps +platformdirs==4.3.3 # via mkdocs-get-deps plotly==5.24.1 # via pymatgen, -r requirements.txt pluggy==1.5.0 # via pytest prometheus-client==0.20.0 # via jupyterhub, -r requirements.txt @@ -168,7 +168,6 @@ pyjwt==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml) pymatgen==2024.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml) pymdown-extensions==10.9 # via mkdocs-material pymongo==4.6.3 # via mongoengine, optimade, -r requirements.txt, nomad-lab (pyproject.toml) -pyopenssl==24.2.1 # via certipy, -r requirements.txt pyparsing==3.1.4 # via matplotlib, rdflib, -r requirements.txt pyproject-hooks==1.1.0 # via build pyrsistent==0.20.0 # via jsonschema, -r requirements.txt @@ -182,7 +181,7 @@ python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, ghp-import 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 jupyter-telemetry, -r requirements.txt, nomad-lab (pyproject.toml) -python-keycloak==4.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml) +python-keycloak==4.4.0 # 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) @@ -205,8 +204,8 @@ 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 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt -ruff==0.6.4 # via nomad-lab (pyproject.toml) +ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt +ruff==0.6.5 # via nomad-lab (pyproject.toml) runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) scikit-learn==1.5.2 # via matid, -r requirements.txt, nomad-lab (pyproject.toml) scipy==1.14.1 # via ase, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml) @@ -235,7 +234,7 @@ termcolor==2.4.0 # via mkdocs-macros-plugin texttable==1.7.0 # via nomad-openbis, -r requirements.txt threadpoolctl==3.5.0 # via scikit-learn, -r requirements.txt tifffile==2024.8.30 # via h5grove, -r requirements.txt -tomli==2.0.1 ; python_full_version <= '3.11' # via coverage +tomli==2.0.1 ; python_full_version == '3.11' # via coverage toposort==1.10 # via -r requirements.txt, nomad-lab (pyproject.toml) tornado==6.4.1 # via jupyterhub, -r requirements.txt tqdm==4.66.5 # via pyedr, pymatgen, twine, -r requirements.txt @@ -250,7 +249,7 @@ 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==1.26.20 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt -uv==0.4.9 # via nomad-lab (pyproject.toml) +uv==0.4.10 # via nomad-lab (pyproject.toml) uvicorn==0.30.6 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) uvloop==0.20.0 ; 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) @@ -263,5 +262,5 @@ webencodings==0.5.1 # via html5lib, -r requirements.txt websockets==13.0.1 # via uvicorn, -r requirements.txt wrapt==1.16.0 # via -r requirements.txt, nomad-lab (pyproject.toml) xarray==2024.9.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -zipp==3.20.1 # via importlib-metadata, -r requirements.txt +zipp==3.20.2 # via importlib-metadata, -r requirements.txt zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml) diff --git a/requirements-plugins.txt b/requirements-plugins.txt index b8db7c7e62e71e1eefa67ac1daecfcf760b9cfd8..833184d264c91fd5532192053b99128e8287a49a 100644 --- a/requirements-plugins.txt +++ b/requirements-plugins.txt @@ -23,8 +23,7 @@ blinker==1.8.2 # via flask blosc2==2.7.1 # via tables cachetools==5.5.0 # via nomad-lab, -c requirements-dev.txt certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -c requirements-dev.txt -cffi==1.17.0 ; platform_python_implementation == 'PyPy' # via argon2-cffi-bindings, pyzmq, -c requirements-dev.txt -cffi==1.17.1 ; platform_python_implementation != 'PyPy' # via argon2-cffi-bindings, cryptography, pyzmq, -c requirements-dev.txt +cffi==1.17.1 # via argon2-cffi-bindings, cryptography, pyzmq, -c requirements-dev.txt cftime==1.6.4 # via netcdf4, -c requirements-dev.txt charset-normalizer==3.3.2 # via requests, -c requirements-dev.txt click==8.1.7 # via asr, click-default-group, dask, flask, nomad-lab, pynxtools, -c requirements-dev.txt @@ -70,7 +69,7 @@ hjson==3.1.0 # via nomad-lab, -c requirements-dev.txt httpcore==1.0.5 # via httpx, -c requirements-dev.txt httpx==0.27.2 # via jupyterlab, nomad-lab, python-keycloak, -c requirements-dev.txt hyperspy==1.7.5 # via kikuchipy, pyxem -idna==3.8 # via anyio, httpx, jsonschema, requests, -c requirements-dev.txt +idna==3.10 # via anyio, httpx, jsonschema, requests, -c requirements-dev.txt ifes-apt-tc-data-modeling==0.2.2 # via pynxtools-apm igor2==0.5.8 # via pynxtools-xps imageio==2.27.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image @@ -147,7 +146,7 @@ nomad-normalizer-plugin-simulation-workflow==1.0 # via -r default_plugins.txt nomad-normalizer-plugin-soap==1.0 # via -r default_plugins.txt nomad-normalizer-plugin-spectra==1.0 # via -r default_plugins.txt nomad-normalizer-plugin-system==1.0 # via -r default_plugins.txt -nomad-parser-plugins-atomistic==1.0 # via -r default_plugins.txt +nomad-parser-plugins-atomistic==1.0.1 # via -r default_plugins.txt nomad-parser-plugins-database==1.0 # via -r default_plugins.txt nomad-parser-plugins-electronic==1.0 # via -r default_plugins.txt nomad-parser-plugins-simulation==1.0.2 # via nomad-parser-plugins-atomistic, nomad-parser-plugins-electronic @@ -180,7 +179,7 @@ pexpect==4.9.0 ; sys_platform != 'emscripten' and sys_platform != 'win32' # via phonopy==2.11.0 # via asr, nomad-parser-plugins-workflow pillow==10.4.0 # via fabio, imageio, matplotlib, nionswift, rdkit, scikit-image, -c requirements-dev.txt pint==0.17 # via fairmat-readers-xrd, hyperspy, nomad-lab, pynxtools-xps, pynxtools-xrd, rosettasciio, -c requirements-dev.txt -platformdirs==4.3.2 # via jupyter-core, pooch, xraydb, -c requirements-dev.txt +platformdirs==4.3.3 # via jupyter-core, pooch, xraydb, -c requirements-dev.txt plotly==5.24.1 # via asr, pymatgen, -c requirements-dev.txt pooch==1.8.2 # via kikuchipy, orix prettytable==3.11.0 # via hyperspy @@ -213,7 +212,7 @@ pyrsistent==0.20.0 # via jsonschema, -c requirements-dev.txt python-box==7.2.0 # via rosettasciio python-dateutil==2.9.0.post0 # via arrow, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, matplotlib, pandas, rfc3161ng, rosettasciio, -c requirements-dev.txt python-json-logger==2.0.2 # via jupyter-events, -c requirements-dev.txt -python-keycloak==4.3.0 # via nomad-lab, -c requirements-dev.txt +python-keycloak==4.4.0 # via nomad-lab, -c requirements-dev.txt python-magic==0.4.24 # via nomad-lab, -c requirements-dev.txt pytz==2024.2 # via nionswift, nomad-lab, pandas, -c requirements-dev.txt pywin32==306 ; platform_python_implementation != 'PyPy' and sys_platform == 'win32' # via jupyter-core, -c requirements-dev.txt @@ -233,7 +232,7 @@ rfc3339-validator==0.1.4 # via jsonschema, -c requirements-dev.txt rfc3986-validator==0.1.1 # via jsonschema rosettasciio==0.6 # via pynxtools-em ruamel-yaml==0.18.6 # via pymatgen, -c requirements-dev.txt -ruamel-yaml-clib==0.2.8 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -c requirements-dev.txt +ruamel-yaml-clib==0.2.8 ; python_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -c requirements-dev.txt scikit-image==0.22.0 # via hyperspy, kikuchipy, pyxem scikit-learn==1.5.2 # via kikuchipy, matid, nomad-lab, pyxem, -c requirements-dev.txt scipy==1.14.1 # via ase, diffsims, findiff, griddataformats, hyperspy, kikuchipy, lmfit, mdanalysis, niondata, nionswift, nomad-lab, nomad-parser-plugins-atomistic, nomad-schema-plugin-simulation-workflow, orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse, xraydb, -c requirements-dev.txt @@ -282,7 +281,7 @@ xarray==2024.9.0 # via nomad-lab, nomad-parser-plugins-workflow, pynxto xmltodict==0.13.0 # via fairmat-readers-xrd, ifes-apt-tc-data-modeling, pynxtools-em, pynxtools-xrd xraydb==4.5.4 # via pynxtools-em zarr==2.18.2 ; platform_machine == 'AMD64' or platform_machine == 'x86_64' # via hyperspy -zipp==3.20.1 # via importlib-metadata, -c requirements-dev.txt +zipp==3.20.2 # via importlib-metadata, -c requirements-dev.txt # The following packages were excluded from the output: # nomad-lab diff --git a/requirements.txt b/requirements.txt index 1171ff5dfd1a3ff5b367df0644f5858e02cf59a3..8d4b6a8fa9ba2d9d878e983499eabe374377fc57 100644 --- a/requirements.txt +++ b/requirements.txt @@ -20,7 +20,7 @@ bitarray==2.9.2 # via nomad-lab (pyproject.toml) cachetools==5.5.0 # via nomad-lab (pyproject.toml) celery==5.4.0 # via nomad-lab (pyproject.toml) certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests -certipy==0.1.3 # via jupyterhub +certipy==0.2.1 # via jupyterhub cffi==1.17.1 ; platform_python_implementation != 'PyPy' # via cryptography cftime==1.6.4 # via netcdf4 charset-normalizer==3.3.2 # via requests @@ -31,7 +31,7 @@ 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==1.3.0 # via matplotlib -cryptography==43.0.1 # via jwcrypto, pyjwt, pyopenssl, rfc3161ng +cryptography==43.0.1 # via certipy, jwcrypto, pyjwt, rfc3161ng cycler==0.12.1 # via matplotlib decorator==5.1.1 # via validators deprecation==2.1.0 # via python-keycloak @@ -61,7 +61,7 @@ html5lib==1.1 # via nomad-lab (pyproject.toml) httpcore==1.0.5 # via httpx httptools==0.6.1 # via uvicorn httpx==0.27.2 # via python-keycloak, nomad-lab (pyproject.toml) -idna==3.8 # via anyio, email-validator, httpx, jsonschema, requests +idna==3.10 # via anyio, email-validator, httpx, jsonschema, requests imagesize==1.4.1 # via sphinx importlib-metadata==7.1.0 # via nomad-lab (pyproject.toml) inflection==0.5.1 # via nomad-lab (pyproject.toml) @@ -127,13 +127,12 @@ pygments==2.18.0 # via sphinx pyjwt==2.6.0 # via nomad-lab (pyproject.toml) pymatgen==2024.5.1 # via nomad-lab (pyproject.toml) pymongo==4.6.3 # via mongoengine, optimade, nomad-lab (pyproject.toml) -pyopenssl==24.2.1 # via certipy pyparsing==3.1.4 # via matplotlib, rdflib pyrsistent==0.20.0 # via jsonschema python-dateutil==2.9.0.post0 # via arrow, celery, elasticsearch-dsl, jupyterhub, matplotlib, nomad-openbis, pandas, rfc3161ng python-dotenv==1.0.1 # via uvicorn python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml) -python-keycloak==4.3.0 # via nomad-lab (pyproject.toml) +python-keycloak==4.4.0 # 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) @@ -150,7 +149,7 @@ 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 ; python_full_version < '3.13' and platform_python_implementation == 'CPython' # 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==1.5.2 # via matid, nomad-lab (pyproject.toml) scipy==1.14.1 # via ase, pymatgen, scikit-learn, nomad-lab (pyproject.toml) @@ -200,5 +199,5 @@ webencodings==0.5.1 # via html5lib websockets==13.0.1 # via uvicorn wrapt==1.16.0 # via nomad-lab (pyproject.toml) xarray==2024.9.0 # via nomad-lab (pyproject.toml) -zipp==3.20.1 # via importlib-metadata +zipp==3.20.2 # via importlib-metadata zipstream-new==1.1.5 # via nomad-lab (pyproject.toml)