diff --git a/default_plugins.txt b/default_plugins.txt index c038db129c6142b1ea28e21865bb3d82c63a189c..3b2dff35c945ca65ff32c57953ed8c1bd4f2e59e 100644 --- a/default_plugins.txt +++ b/default_plugins.txt @@ -11,7 +11,7 @@ git+https://github.com/nomad-coe/nomad-normalizer-plugin-soap.git@develop git+https://github.com/nomad-coe/nomad-normalizer-plugin-spectra.git@develop git+https://github.com/nomad-coe/nomad-normalizer-plugin-system.git@develop git+https://github.com/nomad-coe/nomad-normalizer-plugin-simulation-workflow.git@develop -git+https://github.com/nomad-coe/electronic-parsers.git@91bd91814eb3c663ac6dc64730f0fa1bee503ea9 -git+https://github.com/nomad-coe/atomistic-parsers.git@6e907aa4da0767d23450ff472118e63799101788 -git+https://github.com/nomad-coe/workflow-parsers.git@872eabb8dd53584278df26519a72d63652bad098 -git+https://github.com/nomad-coe/database-parsers.git@a82707377bd59f244739772803337c3a09615948 +git+https://github.com/nomad-coe/electronic-parsers.git@develop +git+https://github.com/nomad-coe/atomistic-parsers.git@develop +git+https://github.com/nomad-coe/workflow-parsers.git@master +git+https://github.com/nomad-coe/database-parsers.git@master diff --git a/requirements-dev.txt b/requirements-dev.txt index 920c1f4d67ba145109f8ea257dcb4e4ab462a8a3..b1e74edad113e730ae391658cacccab39652971a 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -25,7 +25,7 @@ bitarray==2.9.2 # via -r requirements.txt, nomad-lab (pyproject.toml) build==1.2.1 # 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==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt +certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -r requirements.txt certipy==0.1.3 # via jupyterhub, -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 @@ -55,7 +55,7 @@ escapism==1.0.1 # via dockerspawner, -r requirements.txt 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 +executing==2.1.0 # via devtools 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) @@ -102,7 +102,7 @@ kombu==5.4.0 # via celery, -r requirements.txt lark==1.2.2 # via optimade, -r requirements.txt latexcodec==3.0.0 # via pybtex, -r requirements.txt lxml==5.3.0 # via lxml-html-clean, -r requirements.txt, nomad-lab (pyproject.toml) -lxml-html-clean==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml) +lxml-html-clean==0.2.2 # 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==3.7 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions @@ -113,13 +113,13 @@ mda-xdrlib==0.2.0 # via mdanalysis, pyedr, -r requirements.txt mdanalysis==2.7.0 # via -r requirements.txt, nomad-lab (pyproject.toml) mergedeep==1.3.4 # via mkdocs, mkdocs-get-deps 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==1.6.1 # 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==1.2.7 # 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==9.5.33 # 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) mmtf-python==1.1.3 # via mdanalysis, -r requirements.txt @@ -156,7 +156,7 @@ 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==4.2.2 # via mkdocs-get-deps -plotly==5.23.0 # via pymatgen, -r requirements.txt +plotly==5.24.0 # via 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 @@ -211,7 +211,7 @@ 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_full_version < '3.13' and platform_python_implementation == 'CPython' # via ruamel-yaml, -r requirements.txt -ruff==0.6.2 # via nomad-lab (pyproject.toml) +ruff==0.6.3 # 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==1.14.1 # via ase, griddataformats, mdanalysis, pymatgen, scikit-learn, -r requirements.txt, nomad-lab (pyproject.toml) @@ -239,7 +239,7 @@ 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==2024.8.28 # via h5grove, -r requirements.txt +tifffile==2024.8.30 # 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 @@ -254,8 +254,8 @@ tzdata==2024.1 # via celery, pandas, -r requirements.txt 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==0.4.0 # via nomad-lab (pyproject.toml) +urllib3==1.26.20 # via docker, elasticsearch, nomad-openbis, requests, -r requirements.txt +uv==0.4.2 # 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) diff --git a/requirements-plugins.txt b/requirements-plugins.txt index a385d6428c6e828d2d1511bd5eb00fb8ac1c82ac..d9ed7e4fe3f893bc063a0080a8ca57d3ca3cd94f 100644 --- a/requirements-plugins.txt +++ b/requirements-plugins.txt @@ -14,7 +14,7 @@ asteval==1.0.2 # via lmfit asttokens==2.4.1 # via stack-data, -c requirements-dev.txt async-lru==2.0.4 # via jupyterlab async-property==0.2.2 # via python-keycloak, -c requirements-dev.txt -atomisticparsers @ git+https://github.com/nomad-coe/atomistic-parsers.git@6e907aa4da0767d23450ff472118e63799101788 # via -r default_plugins.txt +atomisticparsers @ git+https://github.com/nomad-coe/atomistic-parsers.git@cedaf4191abe315001f6b55a9690dcd21116e9b7 # via -r default_plugins.txt attrs==24.2.0 # via jsonschema, -c requirements-dev.txt babel==2.16.0 # via jupyterlab-server, -c requirements-dev.txt beautifulsoup4==4.12.3 # via nbconvert, -c requirements-dev.txt @@ -23,7 +23,7 @@ bleach==6.1.0 # via nbconvert blinker==1.8.2 # via flask blosc2==2.7.1 # via tables cachetools==5.5.0 # via nomad-lab, -c requirements-dev.txt -certifi==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests, -c requirements-dev.txt +certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests, -c requirements-dev.txt cffi==1.17.0 # 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 @@ -36,7 +36,7 @@ contourpy==1.3.0 # via matplotlib, -c requirements-dev.txt cryptography==43.0.0 # via jwcrypto, rfc3161ng, -c requirements-dev.txt cycler==0.12.1 # via matplotlib, -c requirements-dev.txt dask==2024.8.1 # via hyperspy, kikuchipy, orix, pyxem, rosettasciio -databaseparsers @ git+https://github.com/nomad-coe/database-parsers.git@a82707377bd59f244739772803337c3a09615948 # via -r default_plugins.txt +databaseparsers @ git+https://github.com/nomad-coe/database-parsers.git@defb8c2604e55d9421e8dcc03e86f06752920874 # via -r default_plugins.txt debugpy==1.8.5 # via ipykernel decorator==5.1.1 # via ipyparallel, ipython, -c requirements-dev.txt defusedxml==0.7.1 # via nbconvert @@ -47,10 +47,10 @@ dill==0.3.8 # via hyperspy, lmfit docstring-parser==0.16 # via nomad-lab, -c requirements-dev.txt elasticsearch==7.17.1 # via elasticsearch-dsl, -c requirements-dev.txt elasticsearch-dsl==7.4.0 # via nomad-lab, -c requirements-dev.txt -electronicparsers @ git+https://github.com/nomad-coe/electronic-parsers.git@91bd91814eb3c663ac6dc64730f0fa1bee503ea9 # via -r default_plugins.txt +electronicparsers @ git+https://github.com/nomad-coe/electronic-parsers.git@696b0e8d68a61c149c9da415f29b3662e96291f0 # via -r default_plugins.txt entrypoints==0.4 # via ipyparallel et-xmlfile==1.1.0 # via openpyxl, -c requirements-dev.txt -executing==2.0.1 # via stack-data, -c requirements-dev.txt +executing==2.1.0 # via stack-data, -c requirements-dev.txt fabio==2024.4.0 # via pyfai, silx fairmat-readers-xrd==0.0.6 # via pynxtools-xrd fasteners==0.19 # via mdanalysis, zarr, -c requirements-dev.txt @@ -112,7 +112,7 @@ llvmlite==0.43.0 # via numba lmfit==1.3.2 # via pyxem locket==1.0.0 # via partd lxml==5.3.0 # via atomisticparsers, electronicparsers, fabio, lxml-html-clean, nomad-lab, pynxtools, workflowparsers, -c requirements-dev.txt -lxml-html-clean==0.2.1 # via nomad-lab, perovskite-solar-cell-database, -c requirements-dev.txt +lxml-html-clean==0.2.2 # via nomad-lab, perovskite-solar-cell-database, -c requirements-dev.txt markupsafe==2.1.5 # via jinja2, nbconvert, werkzeug, -c requirements-dev.txt matid==2.1.2 # via nomad-lab, nomad-simulations, -c requirements-dev.txt matplotlib==3.9.2 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay, -c requirements-dev.txt @@ -176,7 +176,7 @@ phonopy==2.11.0 # via asr, workflowparsers 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==4.2.2 # via jupyter-core, pooch, xraydb, -c requirements-dev.txt -plotly==5.23.0 # via asr, pymatgen, -c requirements-dev.txt +plotly==5.24.0 # via asr, pymatgen, -c requirements-dev.txt pooch==1.8.2 # via kikuchipy, orix prettytable==3.11.0 # via hyperspy prometheus-client==0.20.0 # via jupyter-server, -c requirements-dev.txt @@ -249,7 +249,7 @@ tabulate==0.8.9 # via pymatgen, -c requirements-dev.txt tenacity==9.0.0 # via plotly, -c requirements-dev.txt terminado==0.18.1 # via jupyter-server, jupyter-server-terminals threadpoolctl==3.5.0 # via mdanalysis, scikit-learn, -c requirements-dev.txt -tifffile==2024.8.28 # via h5grove, hyperspy, scikit-image, -c requirements-dev.txt +tifffile==2024.8.30 # via h5grove, hyperspy, scikit-image, -c requirements-dev.txt tinycss2==1.3.0 # via nbconvert toolz==0.12.1 # via dask, hyperspy, partd toposort==1.10 # via nomad-lab, -c requirements-dev.txt @@ -266,14 +266,14 @@ tzlocal==5.2 # via nionswift, pynxtools-em uncertainties==3.2.2 # via lmfit, pymatgen, -c requirements-dev.txt unidecode==1.3.2 # via nomad-lab, -c requirements-dev.txt uri-template==1.3.0 # via jsonschema, -c requirements-dev.txt -urllib3==1.26.19 # via elasticsearch, requests, -c requirements-dev.txt +urllib3==1.26.20 # via elasticsearch, requests, -c requirements-dev.txt wcwidth==0.2.13 # via prettytable, prompt-toolkit, -c requirements-dev.txt webcolors==24.8.0 # via jsonschema, -c requirements-dev.txt webencodings==0.5.1 # via bleach, tinycss2, -c requirements-dev.txt websocket-client==1.8.0 # via jupyter-server werkzeug==3.0.4 # via flask widgetsnbextension==4.0.13 # via ipywidgets -workflowparsers @ git+https://github.com/nomad-coe/workflow-parsers.git@872eabb8dd53584278df26519a72d63652bad098 # via -r default_plugins.txt +workflowparsers @ git+https://github.com/nomad-coe/workflow-parsers.git@cb33c02468b1c38e9f94fd05a3180c121531902b # via -r default_plugins.txt wrapt==1.16.0 # via nomad-lab, -c requirements-dev.txt xarray==2024.7.0 # via nomad-lab, pynxtools, pynxtools-mpes, pynxtools-xps, workflowparsers, -c requirements-dev.txt xmltodict==0.13.0 # via fairmat-readers-xrd, ifes-apt-tc-data-modeling, pynxtools-em, pynxtools-xrd diff --git a/requirements.txt b/requirements.txt index 37631e02723784d2c19104976816fda185cd38b2..f251ba1713c5a530b49e4dc0bd3c3e9bc9c5ef89 100644 --- a/requirements.txt +++ b/requirements.txt @@ -19,7 +19,7 @@ billiard==4.2.0 # via celery bitarray==2.9.2 # via nomad-dos-fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nomad-lab (pyproject.toml) cachetools==5.5.0 # via nomad-lab (pyproject.toml) celery==5.4.0 # via nomad-lab (pyproject.toml) -certifi==2024.7.4 # via elasticsearch, httpcore, httpx, netcdf4, requests +certifi==2024.8.30 # via elasticsearch, httpcore, httpx, netcdf4, requests certipy==0.1.3 # via jupyterhub cffi==1.17.0 ; platform_python_implementation != 'PyPy' # via cryptography cftime==1.6.4 # via netcdf4 @@ -84,7 +84,7 @@ kombu==5.4.0 # via celery lark==1.2.2 # via optimade latexcodec==3.0.0 # via pybtex lxml==5.3.0 # via lxml-html-clean, nomad-lab (pyproject.toml) -lxml-html-clean==0.2.1 # via nomad-lab (pyproject.toml) +lxml-html-clean==0.2.2 # 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 @@ -118,7 +118,7 @@ panedr==0.8.0 # via nomad-lab (pyproject.toml) parmed==4.2.2 # via nomad-lab (pyproject.toml) pillow==10.4.0 # via matplotlib, rdkit pint==0.17 # via nomad-lab (pyproject.toml) -plotly==5.23.0 # via pymatgen +plotly==5.24.0 # via 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 @@ -181,7 +181,7 @@ tabulate==0.8.9 # via nomad-openbis, pymatgen, nomad-lab (pyproject.to tenacity==9.0.0 # via plotly texttable==1.7.0 # via nomad-openbis threadpoolctl==3.5.0 # via mdanalysis, scikit-learn -tifffile==2024.8.28 # via h5grove +tifffile==2024.8.30 # via h5grove toposort==1.10 # via nomad-lab (pyproject.toml) tornado==6.4.1 # via jupyterhub tqdm==4.66.5 # via mdanalysis, pyedr, pymatgen @@ -193,7 +193,7 @@ tzdata==2024.1 # via celery, pandas 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 +urllib3==1.26.20 # via docker, elasticsearch, nomad-openbis, requests uvicorn==0.30.6 # via h5grove, nomad-lab (pyproject.toml) uvloop==0.20.0 ; platform_python_implementation != 'PyPy' and sys_platform != 'cygwin' and sys_platform != 'win32' # via uvicorn validators==0.18.2 # via nomad-lab (pyproject.toml)