diff --git a/dependencies/parsers/electronic b/dependencies/parsers/electronic index b818b633b8c25752520e765b191031b2f79805b4..72aa44b44b453255b7d16c480d4d2f5880f0e8f5 160000 --- a/dependencies/parsers/electronic +++ b/dependencies/parsers/electronic @@ -1 +1 @@ -Subproject commit b818b633b8c25752520e765b191031b2f79805b4 +Subproject commit 72aa44b44b453255b7d16c480d4d2f5880f0e8f5 diff --git a/pyproject.toml b/pyproject.toml index 6ceb4235474caf8feef10a88f5a3a4de530ec85e..7e6892b89346c34a42e4e9a809fffadeb08da244 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -64,8 +64,8 @@ repository = 'https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR' parsing = [ 'asr==0.4.1', 'h5py==3.11.0', - 'netCDF4==1.5.4', - 'pybis@git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git', + 'netCDF4==1.6.5', + 'pybis@git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git@91039c2a1df364c88ab7e284b59c43ec42f18370', 'pynxtools[convert]==0.1.1', 'pyzeo==0.1.5', 'quippy-ase==0.9.14', diff --git a/requirements-dev.txt b/requirements-dev.txt index 7eb0254f408d0db891eb657ca9b31731e549dc66..fbbdb51f68611fdef3592a5be010a1380b8138ce 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -34,7 +34,7 @@ blosc2==2.5.1 # via -r requirements.txt, tables build==1.2.1 # via nomad-lab (pyproject.toml), pip-tools 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, requests +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 @@ -84,7 +84,7 @@ 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==2024.3.1 # via -r requirements.txt, dask, hyperspy +fsspec==2024.5.0 # via -r requirements.txt, dask, hyperspy future==1.0.0 # via -r requirements.txt, uncertainties ghp-import==2.1.0 # via mkdocs gitdb==4.0.11 # via -r requirements.txt, gitpython @@ -160,13 +160,13 @@ 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==9.5.22 # via nomad-lab (pyproject.toml) +mkdocs-material==9.5.23 # 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 mongoengine==0.28.2 # via -r requirements.txt, nomad-lab (pyproject.toml) mongomock==4.1.2 # via -r requirements.txt, optimade -monty==2024.4.17 # via -r requirements.txt, pymatgen +monty==2024.5.15 # via -r requirements.txt, pymatgen 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 @@ -177,7 +177,7 @@ 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 -netcdf4==1.5.4 # via -r requirements.txt, nomad-lab (pyproject.toml) +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 nh3==0.2.17 # via readme-renderer niondata==0.15.5 # via -r requirements.txt, nionswift, nionswift-io @@ -227,7 +227,7 @@ 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 -pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git # via -r requirements.txt, nomad-lab (pyproject.toml) +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 pycodestyle==2.11.1 # via nomad-lab (pyproject.toml) @@ -275,7 +275,7 @@ 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==2024.5.10 # via mkdocs-material +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 rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml) @@ -354,7 +354,7 @@ 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==3.18.1 # via -r requirements.txt, importlib-metadata, importlib-resources +zipp==3.18.2 # via -r requirements.txt, importlib-metadata, importlib-resources 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: diff --git a/requirements.txt b/requirements.txt index f126c254230f00f7005314ba1917ab4a551d364b..dc0d328e46187b84d193f4cca8f838f5bf31db58 100644 --- a/requirements.txt +++ b/requirements.txt @@ -29,7 +29,7 @@ blinker==1.8.2 # via flask blosc2==2.5.1 # via tables cachetools==5.3.3 # via nomad-lab (pyproject.toml) celery==5.4.0 # via nomad-lab (pyproject.toml) -certifi==2024.2.2 # via elasticsearch, httpcore, httpx, requests +certifi==2024.2.2 # via elasticsearch, httpcore, httpx, netcdf4, requests certipy==0.1.3 # via jupyterhub cffi==1.16.0 # via cryptography cftime==1.6.3 # via netcdf4 @@ -74,7 +74,7 @@ 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==2024.3.1 # via dask, hyperspy +fsspec==2024.5.0 # via dask, hyperspy future==1.0.0 # via uncertainties gitdb==4.0.11 # via gitpython gitpython==3.1.43 # via nomad-lab (pyproject.toml), pynxtools @@ -140,14 +140,14 @@ mistune==3.0.2 # via m2r mmtf-python==1.1.3 # via mdanalysis mongoengine==0.28.2 # via nomad-lab (pyproject.toml) mongomock==4.1.2 # via optimade -monty==2024.4.17 # via pymatgen +monty==2024.5.15 # via pymatgen mpmath==1.3.0 # via sympy 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==1.5.4 # via nomad-lab (pyproject.toml) +netcdf4==1.6.5 # via nomad-lab (pyproject.toml) networkx==2.6.3 # via matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image niondata==0.15.5 # via nionswift, nionswift-io nionswift==0.16.8 # via pynxtools @@ -190,7 +190,7 @@ pure-eval==0.2.2 # via stack-data py-cpuinfo==9.0.0 # via blosc2, tables 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 # via nomad-lab (pyproject.toml) +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 pycparser==2.22 # via cffi @@ -296,7 +296,7 @@ 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 zipfile37==0.1.3 # via pynxtools -zipp==3.18.1 # via importlib-metadata, importlib-resources +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: