diff --git a/dependencies/normalizers/simulation/soap b/dependencies/normalizers/simulation/soap index f594bd6bbdcb275020a5109885bf6b613a76d9d1..05c632cb3e896a97c0e26a914ad42191444acc19 160000 --- a/dependencies/normalizers/simulation/soap +++ b/dependencies/normalizers/simulation/soap @@ -1 +1 @@ -Subproject commit f594bd6bbdcb275020a5109885bf6b613a76d9d1 +Subproject commit 05c632cb3e896a97c0e26a914ad42191444acc19 diff --git a/nomad/client/archive.py b/nomad/client/archive.py index 8bc9abf8cd7a086006dad3de32de4a6824f7f4b1..4e1f1f752f6309b4941948db00a6b85ee9a812e5 100644 --- a/nomad/client/archive.py +++ b/nomad/client/archive.py @@ -169,8 +169,7 @@ class ArchiveQuery: self._after: str = after self._results_max: int = results_max if results_max > 0 else 1000 self._page_size: int = min(page_size, 9999) if page_size > 0 else 100 - if self._page_size > self._results_max: - self._page_size = self._results_max + self._page_size = min(self._page_size, self._results_max) self._batch_size: int = batch_size if batch_size > 0 else 10 self._retry: int = retry if retry >= 0 else 4 self._sleep_time: float = sleep_time if sleep_time > 0.0 else 4.0 diff --git a/nomad/parsing/tabular.py b/nomad/parsing/tabular.py index 6820ad54222fa4d8ee3f0aed7ca2ea313d053ade..04b58160c73c461b0be562d2e4fec62e26ae3fb5 100644 --- a/nomad/parsing/tabular.py +++ b/nomad/parsing/tabular.py @@ -774,8 +774,9 @@ def parse_table(pd_dataframe, section_def: Section, logger): for col in list(df): try: no_of_stacked_section = int(col.split('.')[1]) - if no_of_stacked_section > max_no_of_repeated_columns: - max_no_of_repeated_columns = no_of_stacked_section + max_no_of_repeated_columns = max( + no_of_stacked_section, max_no_of_repeated_columns + ) except ValueError as e: logger.error( 'No dot (.) is allowed in the column name.', diff --git a/pyproject.toml b/pyproject.toml index 5a933d1f24900d8d7243e051bbdedc513778aa46..3553438bed01c2f4443fadcf9f826a6bf545b90b 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -67,7 +67,6 @@ parsing = [ 'h5py==3.11.0', 'netCDF4==1.6.5', 'nomad-openbis', - 'quippy-ase==0.9.14', 'rdkit==2023.9.5', 'python-magic-bin; sys_platform == "win32"', ] diff --git a/requirements-dev.txt b/requirements-dev.txt index 9b4f123c4d669ae4fd56a6f441fdd8b069f9cf44..fbac4f1283684e04b9363fed956d719dc35e68bc 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -7,17 +7,17 @@ amqp==5.2.0 # via kombu, -r requirements.txt aniso8601==9.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) anyio==4.4.0 # via httpx, starlette, watchfiles, -r requirements.txt arrow==1.3.0 # via isoduration, -r requirements.txt -ase==3.22.1 # via asr, matid, quippy-ase, -r requirements.txt, nomad-lab (pyproject.toml) +ase==3.22.1 # via asr, matid, -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) -astroid==3.3.1 # via nomad-lab (pyproject.toml) +astroid==3.3.2 # via nomad-lab (pyproject.toml) asttokens==2.4.1 # via devtools async-generator==1.10 # via jupyterhub, -r requirements.txt 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_version < '3.12.0' # 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) @@ -59,7 +59,6 @@ essential-generators==1.0 # via nomad-lab (pyproject.toml) et-xmlfile==1.1.0 # via openpyxl, -r requirements.txt execnet==2.1.1 # via pytest-xdist executing==2.0.1 # via devtools -f90wrap==0.2.15 # via quippy-ase, -r requirements.txt fastapi==0.99.1 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) fasteners==0.19 # via mdanalysis, -r requirements.txt filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -105,16 +104,16 @@ kaleido==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml) keyring==25.3.0 # via twine kiwisolver==1.4.5 # via matplotlib, -r requirements.txt kombu==5.4.0 # via celery, -r requirements.txt -lark==1.1.9 # via optimade, -r requirements.txt +lark==1.2.2 # via optimade, -r requirements.txt latexcodec==3.0.0 # via pybtex, -r requirements.txt -lxml==5.2.2 # via lxml-html-clean, -r requirements.txt, nomad-lab (pyproject.toml) +lxml==5.3.0 # via lxml-html-clean, -r requirements.txt, nomad-lab (pyproject.toml) lxml-html-clean==0.2.0 # 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 alembic, -r requirements.txt markdown==3.6 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions markupsafe==2.1.5 # via jinja2, mako, mkdocs, werkzeug, -r requirements.txt, nomad-lab (pyproject.toml) matid==2.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -matplotlib==3.9.1.post1 # via ase, asr, mdanalysis, phonopy, pymatgen, -r requirements.txt +matplotlib==3.9.2 # via ase, asr, mdanalysis, phonopy, pymatgen, -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 mkdocs, mkdocs-get-deps @@ -144,13 +143,13 @@ networkx==3.3 # via matid, mdanalysis, pymatgen, -r requirements.txt nh3==0.2.18 # via readme-renderer nomad-openbis==1.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml) -numpy==1.26.4 # via ase, biopython, cftime, contourpy, f90wrap, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, quippy-ase, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml) +numpy==1.26.4 # via ase, biopython, cftime, contourpy, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, -r requirements.txt, nomad-lab (pyproject.toml) oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) 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, f90wrap, gunicorn, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, plotly, pytest, sphinx, xarray, -r requirements.txt +packaging==24.1 # via build, deprecation, 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==1.2.0 ; sys_platform != 'win32' # via jupyterhub, -r requirements.txt @@ -158,7 +157,7 @@ pandas==1.5.3 # via nomad-openbis, panedr, pymatgen, xarray, -r requ panedr==0.8.0 # via -r requirements.txt, nomad-lab (pyproject.toml) parmed==4.2.2 # via -r requirements.txt, nomad-lab (pyproject.toml) pathspec==0.12.1 # via mkdocs -phonopy==2.26.6 # via asr, -r requirements.txt +phonopy==2.26.7 # via asr, -r requirements.txt 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 @@ -201,10 +200,9 @@ python-magic-bin==0.4.14 ; sys_platform == 'win32' # via -r requirements.txt, n 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 +pywin32-ctypes==0.2.3 ; 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) 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==44.0 # via twine @@ -219,7 +217,7 @@ 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_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt -ruff==0.5.7 # via nomad-lab (pyproject.toml) +ruff==0.6.0 # 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) @@ -229,7 +227,7 @@ six==1.16.0 # via asttokens, basicauth, elasticsearch-dsl, html5li 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 +soupsieve==2.6 # via beautifulsoup4, -r requirements.txt spglib==2.5.0 # via asr, matid, phonopy, pymatgen, -r requirements.txt sphinx==8.0.2 # via recommonmark, -r requirements.txt sphinxcontrib-applehelp==2.0.0 # via sphinx, -r requirements.txt @@ -241,13 +239,13 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx, -r requirements.txt sqlalchemy==2.0.32 # via alembic, jupyterhub, -r requirements.txt starlette==0.27.0 # via fastapi, -r requirements.txt structlog==24.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -sympy==1.13.1 # via pymatgen, -r requirements.txt +sympy==1.13.2 # via pymatgen, -r requirements.txt tabulate==0.8.9 # via nomad-openbis, pymatgen, -r requirements.txt, nomad-lab (pyproject.toml) tenacity==9.0.0 # via plotly, -r requirements.txt termcolor==2.4.0 # via mkdocs-macros-plugin texttable==1.7.0 # via nomad-openbis, -r requirements.txt threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -r requirements.txt -tifffile==2024.7.24 # via h5grove, -r requirements.txt +tifffile==2024.8.10 # via h5grove, -r requirements.txt 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 @@ -263,12 +261,12 @@ 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==0.2.35 # via nomad-lab (pyproject.toml) -uvicorn==0.30.5 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) +uv==0.2.36 # via nomad-lab (pyproject.toml) +uvicorn==0.30.6 # via h5grove, -r requirements.txt, nomad-lab (pyproject.toml) 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 +watchdog==4.0.2 # via mkdocs watchfiles==0.23.0 # via uvicorn, -r requirements.txt wcwidth==0.2.13 # via prompt-toolkit, -r requirements.txt webcolors==24.8.0 # via jsonschema, -r requirements.txt @@ -277,5 +275,5 @@ 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==2024.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -zipp==3.19.2 # via importlib-metadata, -r requirements.txt +zipp==3.20.0 # via importlib-metadata, -r requirements.txt zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab (pyproject.toml) diff --git a/requirements.txt b/requirements.txt index ee902e16efb822598a00807ee2a8624d55bd6e01..b8187f8b2d4dc64e0abb5f6cb2a5be9bbddee8dc 100644 --- a/requirements.txt +++ b/requirements.txt @@ -6,7 +6,7 @@ amqp==5.2.0 # via kombu aniso8601==9.0.1 # via nomad-lab (pyproject.toml) anyio==4.4.0 # via httpx, starlette, watchfiles arrow==1.3.0 # via isoduration -ase==3.22.1 # via asr, matid, quippy-ase, nomad-lab (pyproject.toml) +ase==3.22.1 # via asr, matid, nomad-lab (pyproject.toml) asgiref==3.8.1 # via nomad-lab (pyproject.toml) asr==0.4.1 # via nomad-lab (pyproject.toml) async-generator==1.10 # via jupyterhub @@ -48,7 +48,6 @@ elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml) email-validator==1.3.1 # via optimade escapism==1.0.1 # via dockerspawner et-xmlfile==1.1.0 # via openpyxl -f90wrap==0.2.15 # via quippy-ase fastapi==0.99.1 # via h5grove, nomad-lab (pyproject.toml) fasteners==0.19 # via mdanalysis filelock==3.3.1 # via nomad-lab (pyproject.toml) @@ -87,15 +86,15 @@ jwcrypto==1.5.6 # via python-keycloak kaleido==0.2.1 # via nomad-lab (pyproject.toml) kiwisolver==1.4.5 # via matplotlib kombu==5.4.0 # via celery -lark==1.1.9 # via optimade +lark==1.2.2 # via optimade latexcodec==3.0.0 # via pybtex -lxml==5.2.2 # via lxml-html-clean, nomad-lab (pyproject.toml) +lxml==5.3.0 # via lxml-html-clean, nomad-lab (pyproject.toml) lxml-html-clean==0.2.0 # via nomad-lab (pyproject.toml) m2r==0.2.1 # via nomad-lab (pyproject.toml) mako==1.3.5 # via alembic markupsafe==2.1.5 # via jinja2, mako, werkzeug matid==2.1.0 # via nomad-lab (pyproject.toml) -matplotlib==3.9.1.post1 # via ase, asr, mdanalysis, phonopy, pymatgen +matplotlib==3.9.2 # via ase, asr, mdanalysis, phonopy, pymatgen mda-xdrlib==0.2.0 # via pyedr mdanalysis==2.5.0 # via nomad-lab (pyproject.toml) mistune==3.0.2 # via m2r @@ -110,19 +109,19 @@ netcdf4==1.6.5 # via nomad-lab (pyproject.toml) networkx==3.3 # via matid, mdanalysis, pymatgen, nomad-lab (pyproject.toml) nomad-openbis==1.0.0 # via nomad-lab (pyproject.toml) nptyping==1.4.4 # via nomad-lab (pyproject.toml) -numpy==1.26.4 # via ase, biopython, cftime, contourpy, f90wrap, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, quippy-ase, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml) +numpy==1.26.4 # via ase, biopython, cftime, contourpy, griddataformats, gsd, h5grove, h5py, matid, matplotlib, mdanalysis, mrcfile, netcdf4, nptyping, pandas, phonopy, pyedr, pymatgen, rdkit, scikit-learn, scipy, spglib, tifffile, xarray, nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml) oauthenticator==15.1.0 # via nomad-lab (pyproject.toml) oauthlib==3.2.2 # via jupyterhub openpyxl==3.1.5 # via nomad-lab (pyproject.toml) 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 +packaging==24.1 # via deprecation, gunicorn, jupyterhub, matplotlib, mdanalysis, mongomock, pint, plotly, sphinx, xarray palettable==3.3.3 # via pymatgen 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) -phonopy==2.26.6 # via asr +phonopy==2.26.7 # via asr pillow==10.4.0 # via matplotlib, rdkit pint==0.17 # via nomad-lab (pyproject.toml) plotly==5.23.0 # via asr, pymatgen @@ -153,7 +152,6 @@ 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) rdkit==2023.9.5 # via nomad-lab (pyproject.toml) recommonmark==0.7.1 # via nomad-lab (pyproject.toml) @@ -172,7 +170,7 @@ six==1.16.0 # via basicauth, elasticsearch-dsl, html5lib, isodate, smmap==5.0.1 # via gitdb sniffio==1.3.1 # via anyio, httpx snowballstemmer==2.2.0 # via sphinx -soupsieve==2.5 # via beautifulsoup4 +soupsieve==2.6 # via beautifulsoup4 spglib==2.5.0 # via asr, matid, phonopy, pymatgen sphinx==8.0.2 # via recommonmark sphinxcontrib-applehelp==2.0.0 # via sphinx @@ -184,12 +182,12 @@ sphinxcontrib-serializinghtml==2.0.0 # via sphinx sqlalchemy==2.0.32 # via alembic, jupyterhub starlette==0.27.0 # via fastapi structlog==24.4.0 # via nomad-lab (pyproject.toml) -sympy==1.13.1 # via pymatgen +sympy==1.13.2 # via pymatgen tabulate==0.8.9 # via nomad-openbis, pymatgen, nomad-lab (pyproject.toml) tenacity==9.0.0 # via plotly texttable==1.7.0 # via nomad-openbis threadpoolctl==3.5.0 # via mdanalysis, scikit-learn -tifffile==2024.7.24 # via h5grove +tifffile==2024.8.10 # via h5grove toposort==1.10 # via nomad-lab (pyproject.toml) tornado==6.4.1 # via jupyterhub tqdm==4.66.5 # via mdanalysis, pyedr, pymatgen @@ -202,7 +200,7 @@ uncertainties==3.2.2 # via pymatgen 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) +uvicorn==0.30.6 # via h5grove, nomad-lab (pyproject.toml) 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 @@ -214,5 +212,5 @@ websockets==12.0 # via uvicorn werkzeug==3.0.3 # via flask wrapt==1.16.0 # via nomad-lab (pyproject.toml) xarray==2024.3.0 # via nomad-lab (pyproject.toml) -zipp==3.19.2 # via importlib-metadata +zipp==3.20.0 # via importlib-metadata zipstream-new==1.1.5 # via nomad-lab (pyproject.toml)