diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js index f0ce594a42a677bc1bd32d932160567548f3d442..e985fbd18e8d099ef451ed0aba8066e289b88372 100644 --- a/gui/tests/artifacts.js +++ b/gui/tests/artifacts.js @@ -103398,7 +103398,7 @@ window.nomadArtifacts = { "xps": { "short_description": "An example for analyzing XPS data.", "description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS SLE files into NeXus.", - "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter", + "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter:master", "cmd": null, "image_pull_policy": "Always", "privileged": false, diff --git a/nomad/config/north.py b/nomad/config/north.py index bbfa9623beb9a099ca15ede22e006172bcd31eb5..3aa5aa7201d38702dedac21c49ba114b535344af 100644 --- a/nomad/config/north.py +++ b/nomad/config/north.py @@ -266,7 +266,7 @@ class NORTH(NomadSettings): 'xps': NORTHTool( short_description='An example for analyzing XPS data.', description='Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS SLE files into NeXus.', - image='gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter', + image='gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter:master', path_prefix='lab/tree', icon='jupyter_logo.svg', mount_path='/home/jovyan', diff --git a/ops/kubernetes/nomad/updatevalues.py b/ops/kubernetes/nomad/updatevalues.py index 617d7f4a1e2371b43dafc7f2d2770deda153e0f3..3a4ba1e04cbb611021e9cc435059a3ec5b0cd637 100644 --- a/ops/kubernetes/nomad/updatevalues.py +++ b/ops/kubernetes/nomad/updatevalues.py @@ -2,6 +2,7 @@ # includes the following: # - populating jupyterhub.singleUser.profileList with NORTH tools +from typing import Any, Dict import os from sys import stdout, argv from ruamel.yaml import YAML @@ -15,33 +16,56 @@ yaml.allow_duplicate_keys = True with open(file_path, 'r') as file: data = yaml.load(file) -profile_list = ( - data.setdefault('jupyterhub', {}) - .setdefault('singleuser', {}) - .setdefault('profileList', []) -) -for name, tool in config.north.tools.filtered_items(): - profile = next( - (profile for profile in profile_list if profile['display_name'] == name), None +# Profiles currently break how NOMAD interacts with JupyterHub, so we're only using +# the extraImages to feed the prePuller +generate_profiles = False + +if generate_profiles: + profile_list = ( + data.setdefault('jupyterhub', {}) + .setdefault('singleuser', {}) + .setdefault('profileList', []) ) - if profile is None: - profile = dict() - profile_list.append(profile) - - profile.update( - dict( - display_name=name, - description=tool.description, - kubespawner_override=dict( - image=tool.image, image_pull_policy=tool.image_pull_policy - ), + for name, tool in config.north.tools.filtered_items(): + profile = next( + (profile for profile in profile_list if profile['display_name'] == name), + None, ) - ) + if profile is None: + profile = dict() + profile_list.append(profile) + + profile.update( + dict( + display_name=name, + description=tool.description, + kubespawner_override=dict( + image=tool.image, + image_pull_policy=tool.image_pull_policy, + ), + ) + ) + + if tool.path_prefix: + profile['kubespawner_override']['default_url'] = tool.path_prefix + if tool.cmd: + profile['kubespawner_override']['cmd'] = tool.cmd + if tool.privileged: + profile['kubespawner_override']['privileged'] = tool.privileged + +else: + pre_puller = data.setdefault('jupyterhub', {}).setdefault('prePuller', {}) + extra_images: Dict[str, Any] = {} + pre_puller['extraImages'] = extra_images + + for name, tool in config.north.tools.filtered_items(): + try: + image_name, image_tag = tool.image.rsplit(':', 1) + except ValueError: + image_name, image_tag = tool.image, 'latest' + + extra_images[name] = dict(name=image_name, tag=image_tag) - if tool.path_prefix: - profile['kubespawner_override']['default_url'] = tool.path_prefix - if tool.cmd: - profile['kubespawner_override']['cmd'] = tool.cmd if len(argv) == 2: with open(argv[1], 'w') as file: diff --git a/ops/kubernetes/nomad/values.yaml b/ops/kubernetes/nomad/values.yaml index 33d7f3677a4b12f51660090ee2aa1c47dbb5e82c..6835cc20f3358a58f5cdb53db476dba9bcf58efd 100644 --- a/ops/kubernetes/nomad/values.yaml +++ b/ops/kubernetes/nomad/values.yaml @@ -155,12 +155,11 @@ nomad: limitConnections: 32 limitConnectionsApi: 8 hosts: - - nomad-lab.eu - className: "" - annotations: - nginx.ingress.kubernetes.io/ssl-redirect: "false" - nginx.ingress.kubernetes.io/proxy-body-size: "32g" + - nomad-lab.eu className: '' + annotations: + nginx.ingress.kubernetes.io/ssl-redirect: 'false' + nginx.ingress.kubernetes.io/proxy-body-size: 32g tls: [] # Additional volumes on the output Deployment definition. @@ -185,7 +184,7 @@ nomad: ## Everything concerning the nginx that serves the gui, proxies the api # It is run via NodePort service proxy: - path: "/fairdi/nomad/latest" + path: /fairdi/nomad/latest timeout: 60 editTimeout: 60 connectionTimeout: 10 @@ -385,97 +384,6 @@ jupyterhub: pullPolicy: Always storage: type: none - profileList: - - display_name: jupyter - description: "### **Jupyter Notebook**: The Classic Notebook Interface\n\nThe\ - \ Jupyter Notebook is the original web application for creating and sharing\ - \ computational documents. It offers a simple, streamlined, document-centric\ - \ experience." - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:latest - image_pull_policy: Always - default_url: lab/tree - - display_name: nionswift - description: Run Nion Swift to analyze data. - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop - image_pull_policy: Always - - display_name: nexustools - description: Includes multiple NeXus tools for visualization and analysis. - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop - image_pull_policy: Always - - display_name: ellips - description: This example presents the capabilities of the NOMAD platform to - store and standardize ellipsometry data. It shows the generation of a NeXus - file according to the [NXellipsometry](https://manual.nexusformat.org/classes/contributed_definitions/NXellipsometry.html#nxellipsometry) - application definition and a successive analysis of a SiO2 on Si Psi/Delta - measurement. - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/ellips-jupyter - image_pull_policy: Always - default_url: lab/tree - - display_name: mpes - description: "This example presents the capabilities of the NOMAD platform to\ - \ store and standardize multi photoemission spectroscopy (MPES) experimental\ - \ data. It contains three major examples:\n\n- Taking a pre-binned file, here\ - \ stored in a h5 file, and converting it into the standardized MPES NeXus\ - \ format. There exists a [NeXus application definition for MPES](https://manual.nexusformat.org/classes/contributed_definitions/NXmpes.html#nxmpes)\ - \ which details the internal structure of such a file.\n- Binning of raw data\ - \ (see [here](https://www.nature.com/articles/s41597-020-00769-8) for additional\ - \ resources) into a h5 file and consecutively generating a NeXus file from\ - \ it.\n- An analysis example using data in the NeXus format and employing\ - \ the [pyARPES](https://github.com/chstan/arpes) analysis tool to reproduce\ - \ the main findings of [this paper](https://arxiv.org/pdf/2107.07158.pdf)." - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop - image_pull_policy: Always - - display_name: xps - description: Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) - spectra and converting SPECS SLE files into NeXus. - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter - image_pull_policy: Always - default_url: lab/tree - - display_name: sts - description: 'This example is for two types of experiments: Scanning Tunneling - Microscopy (STM) and Scanning Tunneling Spectroscopy (STS) from Scanning Probe - Microscopy. It can transform the data from files generated by a the nanonis - software into the NeXus application definition NXsts. The example contains - data files from the two specific nanonis software versions generic 5e and - generic 4.5.' - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter - image_pull_policy: Always - default_url: lab/tree - - display_name: webtop - description: Baseline webtop image for test - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop - image_pull_policy: Always - - display_name: apmtools - description: "Miscellaneous tools from the atom probe community:\nCurrently\ - \ APTyzer, paraprobe-toolbox, and APAV" - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop - image_pull_policy: Always - - display_name: fiji - description: ImageJ and Fiji with amongst others several electron-microscopy - specific plug-ins - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop - image_pull_policy: Always - - display_name: frwr - description: FRWR3 in-line holography/focus series reconstruction code - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop - image_pull_policy: Always - - display_name: abtem - description: VESTA, GPAW, and abTEM configured in one container for simulating - images and diffraction patterns in transmission electron microscopy - kubespawner_override: - image: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop - image_pull_policy: Always hub: extraEnv: NOMAD_NORTH_HUB_SERVICE_API_TOKEN: @@ -527,10 +435,6 @@ jupyterhub: if spawner.handler.current_user.name != 'nomad-service': # Do nothing, will only launch the default image with no volumes. - # Only the nomad-service can launch specialized tools with mounted volumes - if spawner.name: - spawner.log.error(f'The {spawner.name} server is not allowed to start this way, raise an error') - raise NotImplementedError('Only the nomad-service can launch specialized tools.') return user_home = spawner.user_options.get('user_home') @@ -577,7 +481,7 @@ jupyterhub: cull: enabled: true - timeout: 900 + timeout: 86400 # 24 hours every: 600 removeNamedServers: true @@ -588,7 +492,43 @@ jupyterhub: pullPolicy: Always continuous: enabled: false - + extraImages: + jupyter: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter + tag: latest + nionswift: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop + tag: latest + nexustools: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop + tag: latest + ellips: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/ellips-jupyter + tag: latest + mpes: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop + tag: latest + xps: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter + tag: master + sts: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter + tag: latest + webtop: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop + tag: latest + apmtools: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop + tag: latest + fiji: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop + tag: latest + frwr: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop + tag: latest + abtem: + name: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop + tag: latest scheduling: userScheduler: enabled: false diff --git a/ops/kubernetes/values.yaml b/ops/kubernetes/values.yaml index 8a5de798558488c1e8a1d854c91e525148a14fe6..4bd569c4d8e9ca2e8f015ea6a3305303048855e3 100644 --- a/ops/kubernetes/values.yaml +++ b/ops/kubernetes/values.yaml @@ -85,7 +85,7 @@ nomad: ingress: enabled: true limitConnections: 32 - limitConnectionsApi: 8 + limitConnectionsApi: 16 className: "nginx" annotations: cert-manager.io/cluster-issuer: "letsencrypt-production" diff --git a/requirements-dev.txt b/requirements-dev.txt index 8b7e870070aae1d3f995c363385a7e1eb946f118..292843e01e8ae44348dc4a8bd8f36132fc824784 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -2,20 +2,19 @@ # This file is autogenerated by pip-compile with Python 3.9 # by the following command: # -# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt --resolver=backtracking pyproject.toml requirements.txt +# pip-compile --annotation-style=line --extra=dev --extra=infrastructure --extra=parsing --output-file=requirements-dev.txt --pip-args='--prefer-binary' pyproject.toml requirements.txt # aiosmtpd==1.4.4.post2 # via nomad-lab (pyproject.toml) alabaster==0.7.12 # via -r requirements.txt, sphinx alembic==1.9.1 # via -r requirements.txt, jupyterhub amqp==5.1.1 # via -r requirements.txt, kombu -aniso8601==7.0.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +aniso8601==7.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) anyio==3.6.2 # via -r requirements.txt, httpcore, starlette, watchfiles -appdirs==1.4.4 # via virtualenv appnope==0.1.4 # via -r requirements.txt, ipykernel, ipython arrow==1.2.3 # via -r requirements.txt, isoduration asciitree==0.3.3 # via -r requirements.txt, zarr -ase==3.19.0 # via -r requirements.txt, asr, ifes-apt-tc-data-modeling, matid, nomad-lab, nomad-lab (pyproject.toml), quippy-ase -asgiref==3.6.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +ase==3.19.0 # via -r requirements.txt, asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), quippy-ase +asgiref==3.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml) asr==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml) asteval==0.9.31 # via -r requirements.txt, lmfit astroid==2.11.7 # via nomad-lab (pyproject.toml), pylint @@ -26,26 +25,25 @@ atpublic==3.1.1 # via aiosmtpd attrs==22.2.0 # via -r requirements.txt, aiosmtpd, cattrs, jsonschema, pytest, requests-cache babel==2.11.0 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, sphinx backcall==0.2.0 # via -r requirements.txt, ipython -bagit==1.8.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) -basicauth==0.4.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) -bcrypt==3.2.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +bagit==1.8.1 # via -r requirements.txt, nomad-lab (pyproject.toml) +basicauth==0.4.1 # via -r requirements.txt, nomad-lab (pyproject.toml) +bcrypt==3.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml) beautifulsoup4==4.11.1 # via -r requirements.txt, bs4 billiard==3.6.4.0 # via -r requirements.txt, celery biopython==1.80 # via -r requirements.txt, mdanalysis -bitarray==2.3.5 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +bitarray==2.3.5 # via -r requirements.txt, nomad-lab (pyproject.toml) bleach==5.0.1 # via readme-renderer -bs4==0.0.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +bs4==0.0.1 # via -r requirements.txt, nomad-lab (pyproject.toml) build==0.9.0 # via nomad-lab (pyproject.toml), pip-tools -cachetools==4.2.4 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +cachetools==4.2.4 # via -r requirements.txt, nomad-lab (pyproject.toml) cattrs==22.2.0 # via -r requirements.txt, requests-cache -celery[redis]==5.2.7 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +celery[redis]==5.2.7 # via -r requirements.txt, nomad-lab (pyproject.toml) certifi==2022.12.7 # via -r requirements.txt, elasticsearch, httpcore, httpx, requests certipy==0.1.3 # via -r requirements.txt, jupyterhub cffi==1.15.1 # via -r requirements.txt, bcrypt, cryptography -cfgv==3.4.0 # via pre-commit cftime==1.6.2 # via -r requirements.txt, netcdf4 charset-normalizer==2.0.12 # via -r requirements.txt, requests -click==8.1.3 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, flask, mkdocs, mkdocs-click, nomad-lab, nomad-lab (pyproject.toml), pip-tools, uvicorn +click==8.1.3 # via -r requirements.txt, asr, celery, click-didyoumean, click-plugins, click-repl, flask, mkdocs, mkdocs-click, nomad-lab (pyproject.toml), pip-tools, uvicorn click-didyoumean==0.3.0 # via -r requirements.txt, celery click-plugins==1.1.1 # via -r requirements.txt, celery click-repl==0.2.0 # via -r requirements.txt, celery @@ -54,7 +52,7 @@ colorama==0.4.6 # via twine comm==0.1.4 # via -r requirements.txt, ipywidgets commonmark==0.9.1 # via -r requirements.txt, recommonmark coverage==6.5.0 # via pytest-cov -cryptography==39.0.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng, secretstorage +cryptography==39.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng cycler==0.11.0 # via -r requirements.txt, matplotlib dask[array]==2022.2.0 # via -r requirements.txt, hyperspy, kikuchipy, orix, pyxem debugpy==1.6.5 # via -r requirements.txt, ipykernel @@ -63,17 +61,15 @@ devtools==0.8.0 # via nomad-lab (pyproject.toml) diffpy-structure==3.1.0 # via -r requirements.txt, diffsims, kikuchipy, orix diffsims==0.5.2 # via -r requirements.txt, kikuchipy, pyxem dill==0.3.6 # via -r requirements.txt, hyperspy, pylint -distlib==0.3.8 # via virtualenv dnspython==2.2.1 # via -r requirements.txt, email-validator, pymongo docker==6.0.1 # via -r requirements.txt, dockerspawner -dockerspawner==12.1.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) -docstring-parser==0.12 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +dockerspawner==12.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) +docstring-parser==0.12 # via -r requirements.txt, nomad-lab (pyproject.toml) docutils==0.19 # via -r requirements.txt, m2r, readme-renderer, recommonmark, sphinx ecdsa==0.18.0 # via -r requirements.txt, python-jose -elasticsearch==7.17.1 # via -r requirements.txt, elasticsearch-dsl, nomad-lab, nomad-lab (pyproject.toml) -elasticsearch-dsl==7.4.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +elasticsearch==7.17.1 # via -r requirements.txt, elasticsearch-dsl, nomad-lab (pyproject.toml) +elasticsearch-dsl==7.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) email-validator==1.3.0 # via -r requirements.txt, optimade -emmet-core==0.48.4 # via -r requirements.txt, mp-api entrypoints==0.4 # via -r requirements.txt, ipyparallel, jupyter-client, numcodecs escapism==1.0.1 # via -r requirements.txt, dockerspawner essential-generators==1.0 # via nomad-lab (pyproject.toml) @@ -83,9 +79,9 @@ execnet==1.9.0 # via pytest-xdist executing==0.10.0 # via devtools f90wrap==0.2.13 # via -r requirements.txt, quippy-ase fabio==2023.6.0 # via -r requirements.txt, pyfai, silx -fastapi==0.92.0 # via -r requirements.txt, h5grove, nomad-lab, nomad-lab (pyproject.toml) +fastapi==0.92.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml) fasteners==0.18 # via -r requirements.txt, mdanalysis, zarr -filelock==3.3.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +filelock==3.3.1 # via -r requirements.txt, nomad-lab (pyproject.toml) flask==2.2.2 # via -r requirements.txt, asr flatdict==4.0.1 # via -r requirements.txt fonttools==4.38.0 # via -r requirements.txt, matplotlib @@ -94,26 +90,25 @@ fsspec==2022.11.0 # via -r requirements.txt, dask, hyperspy future==0.18.2 # via -r requirements.txt, uncertainties ghp-import==2.1.0 # via mkdocs gitdb==4.0.10 # via -r requirements.txt, gitpython -gitpython==3.1.24 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nomad-lab, nomad-lab (pyproject.toml) +gitpython==3.1.24 # via -r requirements.txt, mkdocs-git-revision-date-localized-plugin, nomad-lab (pyproject.toml) greenlet==2.0.1 # via -r requirements.txt, sqlalchemy griddataformats==0.7.0 # via -r requirements.txt, mdanalysis gsd==2.7.0 # via -r requirements.txt, mdanalysis -gunicorn==21.2.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +gunicorn==21.2.0 # via -r requirements.txt, nomad-lab (pyproject.toml) h11==0.14.0 # via -r requirements.txt, httpcore, uvicorn h5grove[fastapi]==1.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml) -h5py==3.6.0 # via -r requirements.txt, h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools (dependencies/parsers/nexus/pyproject.toml), silx +h5py==3.6.0 # via -r requirements.txt, h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, silx hjson==3.0.2 # via -r requirements.txt, nomad-lab (pyproject.toml) html5lib==1.1 # via -r requirements.txt, nomad-lab (pyproject.toml) httpcore==0.16.3 # via -r requirements.txt, httpx httptools==0.5.0 # via -r requirements.txt, uvicorn httpx==0.23.3 # via -r requirements.txt, nomad-lab (pyproject.toml) -hyperspy==1.7.5 # via -r requirements.txt, kikuchipy, pynxtools (dependencies/parsers/nexus/pyproject.toml), pyxem -identify==2.5.35 # via pre-commit +hyperspy==1.7.5 # via -r requirements.txt, kikuchipy, pyxem idna==3.4 # via -r requirements.txt, anyio, email-validator, jsonschema, requests, rfc3986 ifes-apt-tc-data-modeling==0.0.9 # via -r requirements.txt imageio==2.24.0 # via -r requirements.txt, hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image imagesize==1.4.1 # via -r requirements.txt, sphinx -importlib-metadata==4.13.0 # via -r requirements.txt, flask, hyperspy, jupyterhub, keyring, markdown, mkdocs, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), sphinx, twine +importlib-metadata==4.13.0 # via -r requirements.txt, flask, hyperspy, jupyterhub, keyring, markdown, mkdocs, nomad-lab (pyproject.toml), sphinx, twine inflection==0.5.1 # via -r requirements.txt, nomad-lab (pyproject.toml) ipykernel==6.16.2 # via -r requirements.txt, ipyparallel ipyparallel==8.4.1 # via -r requirements.txt, hyperspy @@ -122,12 +117,12 @@ ipywidgets==8.1.1 # via -r requirements.txt, pyxem isodate==0.6.1 # via -r requirements.txt, rdflib isoduration==20.11.0 # via -r requirements.txt, jsonschema isort==4.3.21 # via pylint -itsdangerous==2.1.2 # via -r requirements.txt, flask, nomad-lab, nomad-lab (pyproject.toml) +itsdangerous==2.1.2 # via -r requirements.txt, flask, nomad-lab (pyproject.toml) jaraco-classes==3.2.3 # via keyring jedi==0.18.2 # via -r requirements.txt, ipython jinja2==3.0.3 # via -r requirements.txt, flask, hyperspy, jupyterhub, mkdocs, mkdocs-macros-plugin, mkdocs-material, sphinx -jmespath==0.10.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) -joblib==1.1.0 # via -r requirements.txt, mdanalysis, nomad-lab, pymatgen, scikit-learn +jmespath==0.10.0 # via -r requirements.txt, nomad-lab (pyproject.toml) +joblib==1.1.0 # via -r requirements.txt, mdanalysis, pymatgen, scikit-learn jsonpointer==2.3 # via -r requirements.txt, jsonschema jsonschema[format]==4.17.3 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator jupyter-client==7.4.8 # via -r requirements.txt, ipykernel, ipyparallel @@ -155,8 +150,8 @@ matplotlib==3.5.3 # via -r requirements.txt, ase, asr, diffsims, hypersp matplotlib-inline==0.1.6 # via -r requirements.txt, ipykernel, ipython matplotlib-scalebar==0.8.1 # via -r requirements.txt, orix mccabe==0.6.1 # via pylint -mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) -memoization==0.4.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +mdanalysis==2.5.0 # via -r requirements.txt, nomad-lab (pyproject.toml) +memoization==0.4.0 # via -r requirements.txt, nomad-lab (pyproject.toml) mergedeep==1.3.4 # via -r requirements.txt, mkdocs mistune==2.0.4 # via -r requirements.txt, m2r mkdocs==1.3.0 # via mkdocs-git-revision-date-localized-plugin, mkdocs-macros-plugin, mkdocs-material, mkdocs-redirects, nomad-lab (pyproject.toml) @@ -168,14 +163,14 @@ mkdocs-material==8.2.8 # via nomad-lab (pyproject.toml) mkdocs-material-extensions==1.3.1 # via mkdocs-material, nomad-lab (pyproject.toml) mkdocs-redirects==1.2.0 # via nomad-lab (pyproject.toml) mmtf-python==1.1.3 # via -r requirements.txt, mdanalysis -mongoengine==0.25.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +mongoengine==0.25.0 # via -r requirements.txt, nomad-lab (pyproject.toml) mongomock==4.1.2 # via -r requirements.txt, optimade monty==2022.9.9 # via -r requirements.txt, pymatgen more-itertools==9.0.0 # via jaraco-classes, pytest mpmath==1.2.1 # via -r requirements.txt, sympy mrcfile==1.4.3 # via -r requirements.txt, griddataformats -msgpack==1.0.4 # via -r requirements.txt, mmtf-python, mp-api, nomad-lab (pyproject.toml) -mypy==1.0.1 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +msgpack==1.0.4 # via -r requirements.txt, mmtf-python, nomad-lab (pyproject.toml) +mypy==1.0.1 # via nomad-lab (pyproject.toml) mypy-extensions==0.4.3 # via mypy names==0.3.0 # via nomad-lab (pyproject.toml) natsort==8.2.0 # via -r requirements.txt, hyperspy @@ -187,44 +182,39 @@ nionswift==0.16.8 # via -r requirements.txt nionswift-io==0.15.1 # via -r requirements.txt, nionswift nionui==0.6.11 # via -r requirements.txt, nionswift nionutils==0.4.8 # via -r requirements.txt, niondata, nionswift, nionswift-io, nionui -nomad-lab @ git+https://github.com/nomad-coe/nomad.git@develop # via -r requirements.txt, nomad-schema-plugin-run, nomad-schema-plugin-simulation-workflow, simulationparsers -nomad-schema-plugin-run @ git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop # via -r requirements.txt, nomad-schema-plugin-simulation-workflow, simulationparsers -nomad-schema-plugin-simulation-workflow @ git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop # via -r requirements.txt -nodeenv==1.8.0 # via pre-commit -nptyping==1.4.4 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +nptyping==1.4.4 # via -r requirements.txt, nomad-lab (pyproject.toml) numba==0.56.4 # via -r requirements.txt, diffsims, hyperspy, kikuchipy, orix, pyxem, sparse numcodecs==0.10.2 # via -r requirements.txt, zarr numexpr==2.8.4 # via -r requirements.txt, hyperspy, pyfai -numpy==1.22.4 # via -r requirements.txt, ase, biopython, cftime, dask, diffsims, f90wrap, fabio, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyfai, pymatgen, pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tifffile, xarray, zarr +numpy==1.22.4 # via -r requirements.txt, ase, biopython, cftime, dask, diffsims, f90wrap, fabio, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyfai, pymatgen, pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tifffile, xarray, zarr numpy-quaternion==2022.4.3 # via -r requirements.txt, orix -oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +oauthenticator==15.1.0 # via -r requirements.txt, nomad-lab (pyproject.toml) oauthlib==3.2.2 # via -r requirements.txt, jupyterhub openpyxl==3.1.2 # via -r requirements.txt, nomad-lab (pyproject.toml) optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab (pyproject.toml) orix==0.11.1 # via -r requirements.txt, diffsims, kikuchipy, pyxem orjson==3.9.4 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml) -packaging==24.0 # via -r requirements.txt, build, dask, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, pooch, pytest, scikit-image, sphinx +packaging==23.0 # via -r requirements.txt, build, dask, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mkdocs, mongomock, pint, pooch, pytest, scikit-image, sphinx palettable==3.3.0 # via -r requirements.txt, pymatgen pamela==1.0.0 # via -r requirements.txt, jupyterhub -pandas==1.3.5 # via -r requirements.txt, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), xarray +pandas==1.3.5 # via -r requirements.txt, ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, xarray panedr==0.2 # via -r requirements.txt, nomad-lab (pyproject.toml) parmed==3.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) parso==0.8.3 # via -r requirements.txt, jedi partd==1.3.0 # via -r requirements.txt, dask -passlib==1.7.4 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +passlib==1.7.4 # via -r requirements.txt, nomad-lab (pyproject.toml) pep517==0.13.0 # via build pexpect==4.8.0 # via -r requirements.txt, ipython -phonopy==2.11.0 # via -r requirements.txt, asr, nomad-lab (pyproject.toml) +phonopy==2.11.0 # via -r requirements.txt, asr pickleshare==0.7.5 # via -r requirements.txt, ipython pillow==9.4.0 # via -r requirements.txt, imageio, matplotlib, nionswift, scikit-image -pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab, nomad-lab (pyproject.toml) +pint==0.17 # via -r requirements.txt, hyperspy, nomad-lab (pyproject.toml) pip-tools==6.13.0 # via nomad-lab (pyproject.toml) pkginfo==1.8.3 # via twine platformdirs==3.1.1 # via -r requirements.txt, pooch, pylint, requests-cache plotly==5.11.0 # via -r requirements.txt, asr, pymatgen pluggy==0.13.1 # via pytest pooch==1.7.0 # via -r requirements.txt, kikuchipy, orix -pre-commit==2.20.0 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) prettytable==3.6.0 # via -r requirements.txt, hyperspy prometheus-client==0.15.0 # via -r requirements.txt, jupyterhub prompt-toolkit==3.0.36 # via -r requirements.txt, click-repl, ipython @@ -238,23 +228,23 @@ pybtex==0.24.0 # via -r requirements.txt, pymatgen pycifrw==4.4.5 # via -r requirements.txt, diffpy-structure pycodestyle==2.8.0 # via nomad-lab (pyproject.toml) pycparser==2.21 # via -r requirements.txt, cffi -pydantic==1.10.9 # via -r requirements.txt, fastapi, nomad-lab, nomad-lab (pyproject.toml), optimade +pydantic==1.10.9 # via -r requirements.txt, fastapi, nomad-lab (pyproject.toml), optimade pyfai==2023.9.0 # via -r requirements.txt, pyxem pygments==2.14.0 # via -r requirements.txt, ipython, mkdocs-material, readme-renderer, sphinx pyjwt[crypto]==2.6.0 # via -r requirements.txt, nomad-lab (pyproject.toml) pylint==2.13.9 # via nomad-lab (pyproject.toml), pylint-mongoengine, pylint-plugin-utils pylint-mongoengine==0.4.0 # via nomad-lab (pyproject.toml) pylint-plugin-utils==0.7 # via nomad-lab (pyproject.toml), pylint-mongoengine -pymatgen==2023.9.25 # via -r requirements.txt, asr, nomad-lab, nomad-lab (pyproject.toml) +pymatgen==2023.9.25 # via -r requirements.txt, asr, nomad-lab (pyproject.toml) pymdown-extensions==9.7 # via mkdocs-material -pymongo==4.3.3 # via -r requirements.txt, mongoengine, nomad-lab, nomad-lab (pyproject.toml), optimade +pymongo==4.3.3 # via -r requirements.txt, mongoengine, nomad-lab (pyproject.toml), optimade pyopenssl==23.0.0 # via -r requirements.txt, certipy pyparsing==3.0.9 # via -r requirements.txt, matplotlib, rdflib pyrsistent==0.19.3 # via -r requirements.txt, jsonschema -pytest==5.4.3 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), pytest-cov, pytest-forked, pytest-timeout, pytest-xdist -pytest-cov==2.7.1 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +pytest==5.4.3 # via nomad-lab (pyproject.toml), pytest-cov, pytest-forked, pytest-timeout, pytest-xdist +pytest-cov==2.7.1 # via nomad-lab (pyproject.toml) pytest-forked==1.6.0 # via pytest-xdist -pytest-timeout==1.4.2 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +pytest-timeout==1.4.2 # via nomad-lab (pyproject.toml) pytest-xdist==1.34.0 # via nomad-lab (pyproject.toml) python-dateutil==2.8.2 # via -r requirements.txt, arrow, elasticsearch-dsl, ghp-import, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, mkdocs-macros-plugin, pandas, pybis, rfc3161ng python-dotenv==0.21.0 # via -r requirements.txt, uvicorn @@ -265,47 +255,45 @@ python-keycloak==0.26.1 # 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-multipart==0.0.5 # via -r requirements.txt, nomad-lab (pyproject.toml) -pytz==2022.7.1 # via -r requirements.txt, babel, celery, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab (pyproject.toml), pandas, pynxtools (dependencies/parsers/nexus/pyproject.toml) +pytz==2022.7.1 # via -r requirements.txt, babel, celery, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab (pyproject.toml), pandas pytz-deprecation-shim==0.1.0.post0 # via -r requirements.txt, tzlocal pywavelets==1.3.0 # via -r requirements.txt, scikit-image -pyxem==0.15.1 # via -r requirements.txt, pynxtools (dependencies/parsers/nexus/pyproject.toml) -pyyaml==6.0 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pre-commit, pybtex, pynxtools (dependencies/parsers/nexus/pyproject.toml), pyyaml-env-tag, uvicorn +pyxem==0.15.1 # via -r requirements.txt +pyyaml==6.0 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-macros-plugin, nomad-lab (pyproject.toml), phonopy, pybtex, pyyaml-env-tag, uvicorn pyyaml-env-tag==0.1 # via mkdocs pyzeo==0.1.4 # via -r requirements.txt, nomad-lab (pyproject.toml) pyzmq==25.0.0 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client quippy-ase==0.9.14 # via -r requirements.txt, nomad-lab (pyproject.toml) radioactivedecay==0.4.17 # via -r requirements.txt, ifes-apt-tc-data-modeling -rdflib==5.0.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +rdflib==5.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) readme-renderer==37.3 # via twine -recommonmark==0.7.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +recommonmark==0.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml) redis==4.4.2 # via -r requirements.txt, celery -requests==2.28.2 # via -r requirements.txt, docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), python-gitlab, python-keycloak, requests-cache, requests-toolbelt, rfc3161ng, sphinx, twine -requests-cache==1.0.1 # via -r requirements.txt, pynxtools (dependencies/parsers/nexus/pyproject.toml) +requests==2.28.2 # via -r requirements.txt, docker, hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-cache, requests-toolbelt, rfc3161ng, sphinx, twine +requests-cache==1.0.1 # via -r requirements.txt requests-toolbelt==0.10.1 # via python-gitlab, twine -rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +rfc3161ng==2.1.3 # via -r requirements.txt, nomad-lab (pyproject.toml) rfc3339-validator==0.1.4 # via -r requirements.txt, jsonschema rfc3986[idna2008]==1.5.0 # via -r requirements.txt, httpx, twine rfc3987==1.3.8 # via -r requirements.txt, jsonschema rope==0.21.0 # via nomad-lab (pyproject.toml) rsa==4.9 # via -r requirements.txt, python-jose -ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, oauthenticator, pymatgen +ruamel-yaml==0.17.21 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator, pymatgen ruamel-yaml-clib==0.2.7 # via -r requirements.txt, ruamel-yaml -ruff==0.1.8 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +ruff==0.1.8 # via nomad-lab (pyproject.toml) runstats==2.0.0 # via -r requirements.txt, nomad-lab (pyproject.toml) scikit-image==0.19.3 # via -r requirements.txt, hyperspy, kikuchipy, pyxem scikit-learn==1.0.2 # via -r requirements.txt, kikuchipy, matid, nomad-lab (pyproject.toml), pyxem -scipy==1.7.1 # via -r requirements.txt, ase, diffsims, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), pyxem, radioactivedecay, scikit-image, scikit-learn, sparse -secretstorage==3.3.3 # via keyring +scipy==1.7.1 # via -r requirements.txt, ase, diffsims, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse sentinels==1.0.0 # via -r requirements.txt, mongomock silx==1.1.2 # via -r requirements.txt, pyfai -simulationparsers @ git+https://github.com/nomad-coe/simulation-parsers.git@develop # via -r requirements.txt -six==1.16.0 # via -r requirements.txt, asttokens, basicauth, bcrypt, bleach, click-repl, diffpy-structure, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, pytest-xdist, python-dateutil, python-multipart, rdflib, rfc3339-validator, url-normalize, validators, virtualenv +six==1.16.0 # via -r requirements.txt, asttokens, basicauth, bcrypt, bleach, click-repl, diffpy-structure, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, pytest-xdist, python-dateutil, python-multipart, rdflib, rfc3339-validator, url-normalize, validators smmap==5.0.0 # via -r requirements.txt, gitdb sniffio==1.3.0 # via -r requirements.txt, anyio, httpcore, httpx snowballstemmer==2.2.0 # via -r requirements.txt, sphinx soupsieve==2.3.2.post1 # via -r requirements.txt, beautifulsoup4 sparse==0.13.0 # via -r requirements.txt, hyperspy -spglib==2.0.2 # via -r requirements.txt, asr, emmet-core, matid, phonopy, pymatgen +spglib==2.0.2 # via -r requirements.txt, asr, matid, phonopy, pymatgen sphinx==5.3.0 # via -r requirements.txt, recommonmark sphinxcontrib-applehelp==1.0.2 # via -r requirements.txt, sphinx sphinxcontrib-devhelp==1.0.2 # via -r requirements.txt, sphinx @@ -315,18 +303,17 @@ sphinxcontrib-qthelp==1.0.3 # via -r requirements.txt, sphinx sphinxcontrib-serializinghtml==1.1.5 # via -r requirements.txt, sphinx sqlalchemy==1.4.46 # via -r requirements.txt, alembic, jupyterhub starlette==0.25.0 # via -r requirements.txt, fastapi -structlog==22.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +structlog==22.3.0 # via -r requirements.txt, nomad-lab (pyproject.toml) sympy==1.10.1 # via -r requirements.txt, hyperspy, pymatgen, radioactivedecay -tabulate==0.8.9 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml), pybis, pymatgen +tabulate==0.8.9 # via -r requirements.txt, nomad-lab (pyproject.toml), pybis, pymatgen tenacity==8.1.0 # via -r requirements.txt, plotly termcolor==2.1.0 # via mkdocs-macros-plugin texttable==1.7.0 # via -r requirements.txt, pybis threadpoolctl==3.1.0 # via -r requirements.txt, mdanalysis, scikit-learn tifffile==2021.11.2 # via -r requirements.txt, h5grove, hyperspy, scikit-image -toml==0.10.2 # via pre-commit tomli==2.0.1 # via build, mypy, pep517, pylint toolz==0.12.0 # via -r requirements.txt, dask, hyperspy, partd -toposort==1.9 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +toposort==1.9 # via -r requirements.txt, nomad-lab (pyproject.toml) tornado==6.2 # via -r requirements.txt, ipykernel, ipyparallel, jupyter-client, jupyterhub tqdm==4.64.1 # via -r requirements.txt, diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pymatgen, twine traitlets==5.8.1 # via -r requirements.txt, comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline @@ -334,24 +321,19 @@ traits==6.4.1 # via -r requirements.txt, hyperspy transforms3d==0.4.1 # via -r requirements.txt, diffsims, pyxem twine==3.4.2 # via nomad-lab (pyproject.toml) typed-ast==1.4.2 # via nomad-lab (pyproject.toml) -types-pytz==2022.7.0.0 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) -types-pyyaml==6.0.12.1 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) -types-requests==2.28.11.16 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) -types-urllib3==1.26.25.8 # via types-requests -typing-extensions==4.4.0 # via -r requirements.txt, astroid, emmet-core, gitpython, mp-api, mypy, numcodecs, pydantic, pylint, starlette +typing-extensions==4.4.0 # via -r requirements.txt, astroid, gitpython, mypy, numcodecs, pydantic, pylint, starlette typish==1.9.3 # via -r requirements.txt, nptyping tzdata==2023.3 # via -r requirements.txt, pytz-deprecation-shim tzlocal==4.3 # via -r requirements.txt, nionswift uncertainties==3.1.7 # via -r requirements.txt, lmfit, pymatgen -unidecode==1.3.2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +unidecode==1.3.2 # via -r requirements.txt, nomad-lab (pyproject.toml) uri-template==1.2.0 # via -r requirements.txt, jsonschema url-normalize==1.4.3 # via -r requirements.txt, requests-cache -urllib3==1.26.14 # via -r requirements.txt, docker, elasticsearch, requests, requests-cache +urllib3==1.26.14 # via -r requirements.txt, docker, elasticsearch, pybis, requests, requests-cache uvicorn[standard]==0.20.0 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml) uvloop==0.17.0 # via -r requirements.txt, uvicorn -validators==0.18.2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +validators==0.18.2 # via -r requirements.txt, nomad-lab (pyproject.toml) vine==5.0.0 # via -r requirements.txt, amqp, celery, kombu -virtualenv==20.4.7 # via pre-commit watchdog==2.1.9 # via mkdocs watchfiles==0.18.1 # via -r requirements.txt, uvicorn wcwidth==0.2.5 # via -r requirements.txt, prettytable, prompt-toolkit, pytest @@ -363,11 +345,11 @@ werkzeug==2.2.2 # via -r requirements.txt, flask wheel==0.38.4 # via pip-tools widgetsnbextension==4.0.9 # via -r requirements.txt, ipywidgets wrapt==1.12.1 # via -r requirements.txt, astroid, nomad-lab (pyproject.toml) -xarray==0.20.2 # via -r requirements.txt, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +xarray==0.20.2 # via -r requirements.txt, nomad-lab (pyproject.toml) zarr==2.12.0 # via -r requirements.txt, hyperspy zipfile37==0.1.3 # via -r requirements.txt zipp==3.11.0 # via -r requirements.txt, importlib-metadata -zipstream-new==1.1.5 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml) +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: # pip diff --git a/requirements.txt b/requirements.txt index 3ecd0be9346d3187525199a263a3c8fd803e8f92..8c69d3eff21f189aa76e64894df3083e55b79021 100644 --- a/requirements.txt +++ b/requirements.txt @@ -7,7 +7,7 @@ alabaster==0.7.12 # via sphinx alembic==1.9.1 # via jupyterhub amqp==5.1.1 # via kombu -aniso8601==7.0.0 # via nomad-lab, nomad-lab (pyproject.toml) +aniso8601==7.0.0 # via nomad-lab (pyproject.toml) anyio==3.6.2 # via httpcore, starlette, watchfiles appnope==0.1.4 # via ipykernel, ipython arrow==1.2.3 # via isoduration @@ -21,9 +21,9 @@ async-timeout==4.0.2 # via redis attrs==22.2.0 # via cattrs, jsonschema, requests-cache babel==2.11.0 # via sphinx backcall==0.2.0 # via ipython -bagit==1.8.1 # via nomad-lab, nomad-lab (pyproject.toml) -basicauth==0.4.1 # via nomad-lab, nomad-lab (pyproject.toml) -bcrypt==3.2.0 # via nomad-lab, nomad-lab (pyproject.toml) +bagit==1.8.1 # via nomad-lab (pyproject.toml) +basicauth==0.4.1 # via nomad-lab (pyproject.toml) +bcrypt==3.2.0 # via nomad-lab (pyproject.toml) beautifulsoup4==4.11.1 # via bs4 billiard==3.6.4.0 # via celery biopython==1.80 # via mdanalysis @@ -37,14 +37,14 @@ certipy==0.1.3 # via jupyterhub cffi==1.15.1 # via bcrypt, cryptography cftime==1.6.2 # via netcdf4 charset-normalizer==2.0.12 # via requests -click==8.1.3 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nomad-lab, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), uvicorn +click==8.1.3 # via asr, celery, click-didyoumean, click-plugins, click-repl, flask, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), uvicorn click-didyoumean==0.3.0 # via celery click-plugins==1.1.1 # via celery click-repl==0.2.0 # via celery cloudpickle==2.2.0 # via dask comm==0.1.4 # via ipywidgets commonmark==0.9.1 # via recommonmark -cryptography==39.0.0 # via nomad-lab, nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng +cryptography==39.0.0 # via nomad-lab (pyproject.toml), pyjwt, pyopenssl, rfc3161ng cycler==0.11.0 # via matplotlib dask[array]==2022.2.0 # via hyperspy, kikuchipy, orix, pyxem debugpy==1.6.5 # via ipykernel @@ -54,23 +54,22 @@ diffsims==0.5.2 # via kikuchipy, pyxem dill==0.3.6 # via hyperspy dnspython==2.2.1 # via email-validator, pymongo docker==6.0.1 # via dockerspawner -dockerspawner==12.1.0 # via nomad-lab, nomad-lab (pyproject.toml) -docstring-parser==0.12 # via nomad-lab, nomad-lab (pyproject.toml) +dockerspawner==12.1.0 # via nomad-lab (pyproject.toml) +docstring-parser==0.12 # via nomad-lab (pyproject.toml) docutils==0.19 # via m2r, recommonmark, sphinx ecdsa==0.18.0 # via python-jose -elasticsearch==7.17.1 # via elasticsearch-dsl, nomad-lab, nomad-lab (pyproject.toml) -elasticsearch-dsl==7.4.0 # via nomad-lab, nomad-lab (pyproject.toml) +elasticsearch==7.17.1 # via elasticsearch-dsl, nomad-lab (pyproject.toml) +elasticsearch-dsl==7.4.0 # via nomad-lab (pyproject.toml) email-validator==1.3.0 # via optimade -emmet-core==0.48.4 # via mp-api entrypoints==0.4 # via ipyparallel, jupyter-client, numcodecs escapism==1.0.1 # via dockerspawner et-xmlfile==1.1.0 # via openpyxl exceptiongroup==1.2.0 # via cattrs f90wrap==0.2.13 # via quippy-ase fabio==2023.6.0 # via pyfai, silx -fastapi==0.92.0 # via h5grove, nomad-lab, nomad-lab (pyproject.toml) +fastapi==0.92.0 # via h5grove, nomad-lab (pyproject.toml) fasteners==0.18 # via mdanalysis, zarr -filelock==3.3.1 # via nomad-lab, nomad-lab (pyproject.toml) +filelock==3.3.1 # via nomad-lab (pyproject.toml) flask==2.2.2 # via asr flatdict==4.0.1 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) fonttools==4.38.0 # via matplotlib @@ -78,11 +77,11 @@ fqdn==1.5.1 # via jsonschema fsspec==2022.11.0 # via dask, hyperspy future==0.18.2 # via uncertainties gitdb==4.0.10 # via gitpython -gitpython==3.1.24 # via nomad-lab, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +gitpython==3.1.24 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) greenlet==2.0.1 # via sqlalchemy griddataformats==0.7.0 # via mdanalysis gsd==2.7.0 # via mdanalysis -gunicorn==21.2.0 # via nomad-lab, nomad-lab (pyproject.toml) +gunicorn==21.2.0 # via nomad-lab (pyproject.toml) h11==0.14.0 # via httpcore, uvicorn h5grove[fastapi]==1.3.0 # via nomad-lab (pyproject.toml) h5py==3.6.0 # via h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab (pyproject.toml), orix, phonopy, pyfai, pynxtools (dependencies/parsers/nexus/pyproject.toml), silx @@ -90,7 +89,7 @@ hjson==3.0.2 # via nomad-lab (pyproject.toml) html5lib==1.1 # via nomad-lab (pyproject.toml) httpcore==0.16.3 # via httpx httptools==0.5.0 # via uvicorn -httpx==0.23.3 # via nomad-lab, nomad-lab (pyproject.toml) +httpx==0.23.3 # via nomad-lab (pyproject.toml) hyperspy==1.7.5 # via kikuchipy, pynxtools (dependencies/parsers/nexus/pyproject.toml), pyxem idna==3.4 # via anyio, email-validator, jsonschema, requests, rfc3986 ifes-apt-tc-data-modeling==0.0.9 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) @@ -104,11 +103,11 @@ ipython==7.34.0 # via hyperspy, ipykernel, ipyparallel, ipywidgets ipywidgets==8.1.1 # via pyxem isodate==0.6.1 # via rdflib isoduration==20.11.0 # via jsonschema -itsdangerous==2.1.2 # via flask, nomad-lab, nomad-lab (pyproject.toml) +itsdangerous==2.1.2 # via flask, nomad-lab (pyproject.toml) jedi==0.18.2 # via ipython jinja2==3.0.3 # via flask, hyperspy, jupyterhub, sphinx -jmespath==0.10.0 # via nomad-lab, nomad-lab (pyproject.toml) -joblib==1.1.0 # via mdanalysis, nomad-lab, pymatgen, scikit-learn +jmespath==0.10.0 # via nomad-lab (pyproject.toml) +joblib==1.1.0 # via mdanalysis, pymatgen, scikit-learn jsonpointer==2.3 # via jsonschema jsonschema[format]==4.17.3 # via jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator jupyter-client==7.4.8 # via ipykernel, ipyparallel @@ -132,17 +131,17 @@ matid==2.0.0.dev2 # via nomad-lab (pyproject.toml) matplotlib==3.5.3 # via ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay matplotlib-inline==0.1.6 # via ipykernel, ipython matplotlib-scalebar==0.8.1 # via orix -mdanalysis==2.5.0 # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab, nomad-lab (pyproject.toml) -memoization==0.4.0 # via nomad-lab, nomad-lab (pyproject.toml) +mdanalysis==2.5.0 # via nomad-lab (pyproject.toml) +memoization==0.4.0 # via nomad-lab (pyproject.toml) mergedeep==1.3.4 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) mistune==2.0.4 # via m2r mmtf-python==1.1.3 # via mdanalysis -mongoengine==0.25.0 # via nomad-lab, nomad-lab (pyproject.toml) +mongoengine==0.25.0 # via nomad-lab (pyproject.toml) mongomock==4.1.2 # via optimade monty==2022.9.9 # via pymatgen mpmath==1.2.1 # via sympy mrcfile==1.4.3 # via griddataformats -msgpack==1.0.4 # via mmtf-python, nomad-lab, nomad-lab (pyproject.toml) +msgpack==1.0.4 # via mmtf-python, nomad-lab (pyproject.toml) natsort==8.2.0 # via hyperspy nest-asyncio==1.5.6 # via ipykernel, jupyter-client netcdf4==1.5.4 # via nomad-lab (pyproject.toml) @@ -152,16 +151,13 @@ nionswift==0.16.8 # via pynxtools (dependencies/parsers/nexus/pyproject. nionswift-io==0.15.1 # via nionswift nionui==0.6.11 # via nionswift nionutils==0.4.8 # via niondata, nionswift, nionswift-io, nionui -nomad-lab @ git+https://github.com/nomad-coe/nomad.git@develop # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-schema-plugin-run, nomad-schema-plugin-simulation-workflow, simulationparsers, workflowparsers (dependencies/parsers/workflow/pyproject.toml) -nomad-schema-plugin-run @ git+https://github.com/nomad-coe/nomad-schema-plugin-run.git@develop # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-schema-plugin-simulation-workflow, simulationparsers, workflowparsers (dependencies/parsers/workflow/pyproject.toml) -nomad-schema-plugin-simulation-workflow @ git+https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow.git@develop # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml) -nptyping==1.4.4 # via nomad-lab, nomad-lab (pyproject.toml) +nptyping==1.4.4 # via nomad-lab (pyproject.toml) numba==0.56.4 # via diffsims, hyperspy, kikuchipy, orix, pyxem, sparse numcodecs==0.10.2 # via zarr numexpr==2.8.4 # via hyperspy, pyfai numpy==1.22.4 # via ase, biopython, cftime, dask, diffsims, f90wrap, fabio, griddataformats, gsd, h5grove, h5py, hyperspy, ifes-apt-tc-data-modeling, imageio, kikuchipy, lmfit, matid, matplotlib, mdanalysis, mrcfile, netcdf4, niondata, nionswift, nionswift-io, nionui, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml), nptyping, numba, numcodecs, numexpr, numpy-quaternion, orix, pandas, phonopy, pyfai, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), pywavelets, pyxem, quippy-ase, radioactivedecay, scikit-image, scikit-learn, scipy, silx, sparse, spglib, tifffile, xarray, zarr numpy-quaternion==2022.4.3 # via orix -oauthenticator==15.1.0 # via nomad-lab, nomad-lab (pyproject.toml) +oauthenticator==15.1.0 # via nomad-lab (pyproject.toml) oauthlib==3.2.2 # via jupyterhub openpyxl==3.1.2 # via nomad-lab (pyproject.toml) optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml) @@ -170,17 +166,17 @@ orjson==3.9.4 # via h5grove, nomad-lab (pyproject.toml) packaging==23.0 # via dask, docker, gunicorn, hyperspy, ipykernel, jupyterhub, matplotlib, mdanalysis, mongomock, pint, pooch, scikit-image, sphinx palettable==3.3.0 # via pymatgen pamela==1.0.0 # via jupyterhub -pandas==1.3.5 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), xarray +pandas==1.3.5 # via eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), ifes-apt-tc-data-modeling, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), xarray panedr==0.2 # via nomad-lab (pyproject.toml) parmed==3.0.0 # via nomad-lab (pyproject.toml) parso==0.8.3 # via jedi partd==1.3.0 # via dask -passlib==1.7.4 # via nomad-lab, nomad-lab (pyproject.toml) +passlib==1.7.4 # via nomad-lab (pyproject.toml) pexpect==4.8.0 # via ipython -phonopy==2.11.0 # via asr, nomad-lab (pyproject.toml) +phonopy==2.11.0 # via asr pickleshare==0.7.5 # via ipython pillow==9.4.0 # via imageio, matplotlib, nionswift, scikit-image -pint==0.17 # via hyperspy, nomad-lab, nomad-lab (pyproject.toml) +pint==0.17 # via hyperspy, nomad-lab (pyproject.toml) platformdirs==3.1.1 # via pooch, requests-cache plotly==5.11.0 # via asr, pymatgen pooch==1.7.0 # via kikuchipy, orix @@ -195,24 +191,24 @@ pybis @ git+https://github.com/FAIRmat-NFDI/fairmat-pybis.git # via nomad-lab ( pybtex==0.24.0 # via pymatgen pycifrw==4.4.5 # via diffpy-structure pycparser==2.21 # via cffi -pydantic==1.10.9 # via fastapi, nomad-lab, nomad-lab (pyproject.toml), optimade +pydantic==1.10.9 # via fastapi, nomad-lab (pyproject.toml), optimade pyfai==2023.9.0 # via pyxem pygments==2.14.0 # via ipython, sphinx -pyjwt[crypto]==2.6.0 # via nomad-lab, nomad-lab (pyproject.toml) -pymatgen==2023.9.25 # via asr, nomad-lab, nomad-lab (pyproject.toml) -pymongo==4.3.3 # via mongoengine, nomad-lab, nomad-lab (pyproject.toml), optimade +pyjwt[crypto]==2.6.0 # via nomad-lab (pyproject.toml) +pymatgen==2023.9.25 # via asr, nomad-lab (pyproject.toml) +pymongo==4.3.3 # via mongoengine, nomad-lab (pyproject.toml), optimade pyopenssl==23.0.0 # via certipy pyparsing==3.0.9 # via matplotlib, rdflib pyrsistent==0.19.3 # via jsonschema python-dateutil==2.8.2 # via arrow, elasticsearch-dsl, hyperspy, ipyparallel, jupyter-client, jupyterhub, matplotlib, pandas, pybis, rfc3161ng python-dotenv==0.21.0 # via uvicorn python-jose==3.3.0 # via python-keycloak -python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab, nomad-lab (pyproject.toml) -python-keycloak==0.26.1 # via nomad-lab, nomad-lab (pyproject.toml) -python-logstash==0.4.6 # via nomad-lab, nomad-lab (pyproject.toml) -python-magic==0.4.24 # via nomad-lab, nomad-lab (pyproject.toml) -python-multipart==0.0.5 # via nomad-lab, nomad-lab (pyproject.toml) -pytz==2022.7.1 # via babel, celery, nionswift, nomad-lab, nomad-lab (pyproject.toml), pandas, pynxtools (dependencies/parsers/nexus/pyproject.toml) +python-json-logger==2.0.2 # via jupyter-telemetry, nomad-lab (pyproject.toml) +python-keycloak==0.26.1 # 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-multipart==0.0.5 # via nomad-lab (pyproject.toml) +pytz==2022.7.1 # via babel, celery, nionswift, nomad-lab (pyproject.toml), pandas, pynxtools (dependencies/parsers/nexus/pyproject.toml) pytz-deprecation-shim==0.1.0.post0 # via tzlocal pywavelets==1.3.0 # via scikit-image pyxem==0.15.1 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) @@ -221,32 +217,31 @@ pyzeo==0.1.4 # via nomad-lab (pyproject.toml) pyzmq==25.0.0 # via ipykernel, ipyparallel, jupyter-client quippy-ase==0.9.14 # via nomad-lab (pyproject.toml) radioactivedecay==0.4.17 # via ifes-apt-tc-data-modeling -rdflib==5.0.0 # via nomad-lab, nomad-lab (pyproject.toml) -recommonmark==0.7.1 # via nomad-lab, nomad-lab (pyproject.toml) +rdflib==5.0.0 # via nomad-lab (pyproject.toml) +recommonmark==0.7.1 # via nomad-lab (pyproject.toml) redis==4.4.2 # via celery -requests==2.28.2 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, mp-api, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), python-keycloak, requests-cache, rfc3161ng, sphinx +requests==2.28.2 # via docker, eelsdbconverter (dependencies/parsers/eelsdb/pyproject.toml), hyperspy, jupyterhub, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), python-keycloak, requests-cache, rfc3161ng, sphinx requests-cache==1.0.1 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) -rfc3161ng==2.1.3 # via nomad-lab, nomad-lab (pyproject.toml) +rfc3161ng==2.1.3 # via nomad-lab (pyproject.toml) rfc3339-validator==0.1.4 # via jsonschema rfc3986[idna2008]==1.5.0 # via httpx rfc3987==1.3.8 # via jsonschema rsa==4.9 # via python-jose ruamel-yaml==0.17.21 # via jupyter-telemetry, oauthenticator, pymatgen ruamel-yaml-clib==0.2.7 # via ruamel-yaml -runstats==2.0.0 # via nomad-lab, nomad-lab (pyproject.toml) +runstats==2.0.0 # via nomad-lab (pyproject.toml) scikit-image==0.19.3 # via hyperspy, kikuchipy, pyxem -scikit-learn==1.0.2 # via kikuchipy, matid, nomad-lab, nomad-lab (pyproject.toml), pyxem -scipy==1.7.1 # via ase, atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), diffsims, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse +scikit-learn==1.0.2 # via kikuchipy, matid, nomad-lab (pyproject.toml), pyxem +scipy==1.7.1 # via ase, diffsims, griddataformats, hyperspy, kikuchipy, lmfit, matid, mdanalysis, niondata, nionswift, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pynxtools (dependencies/parsers/nexus/pyproject.toml), pyxem, radioactivedecay, scikit-image, scikit-learn, sparse sentinels==1.0.0 # via mongomock silx==1.1.2 # via pyfai -simulationparsers @ git+https://github.com/nomad-coe/simulation-parsers.git@develop # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), electronicparsers (dependencies/parsers/electronic/pyproject.toml) six==1.16.0 # via basicauth, bcrypt, click-repl, diffpy-structure, ecdsa, elasticsearch-dsl, griddataformats, html5lib, isodate, latexcodec, pybtex, python-dateutil, python-multipart, rdflib, rfc3339-validator, url-normalize, validators smmap==5.0.0 # via gitdb sniffio==1.3.0 # via anyio, httpcore, httpx snowballstemmer==2.2.0 # via sphinx soupsieve==2.3.2.post1 # via beautifulsoup4 sparse==0.13.0 # via hyperspy -spglib==2.0.2 # via asr, emmet-core, matid, phonopy, pymatgen +spglib==2.0.2 # via asr, matid, phonopy, pymatgen sphinx==5.3.0 # via recommonmark sphinxcontrib-applehelp==1.0.2 # via sphinx sphinxcontrib-devhelp==1.0.2 # via sphinx @@ -256,15 +251,15 @@ sphinxcontrib-qthelp==1.0.3 # via sphinx sphinxcontrib-serializinghtml==1.1.5 # via sphinx sqlalchemy==1.4.46 # via alembic, jupyterhub starlette==0.25.0 # via fastapi -structlog==22.3.0 # via nomad-lab, nomad-lab (pyproject.toml) +structlog==22.3.0 # via nomad-lab (pyproject.toml) sympy==1.10.1 # via hyperspy, pymatgen, radioactivedecay -tabulate==0.8.9 # via nomad-lab, nomad-lab (pyproject.toml), pybis, pymatgen +tabulate==0.8.9 # via nomad-lab (pyproject.toml), pybis, pymatgen tenacity==8.1.0 # via plotly texttable==1.7.0 # via pybis threadpoolctl==3.1.0 # via mdanalysis, scikit-learn tifffile==2021.11.2 # via h5grove, hyperspy, scikit-image toolz==0.12.0 # via dask, hyperspy, partd -toposort==1.9 # via nomad-lab, nomad-lab (pyproject.toml) +toposort==1.9 # via nomad-lab (pyproject.toml) tornado==6.2 # via ipykernel, ipyparallel, jupyter-client, jupyterhub tqdm==4.64.1 # via diffsims, hyperspy, ipyparallel, kikuchipy, mdanalysis, orix, pymatgen traitlets==5.8.1 # via comm, ipykernel, ipyparallel, ipython, ipywidgets, jupyter-client, jupyter-core, jupyter-telemetry, jupyterhub, matplotlib-inline @@ -275,13 +270,13 @@ typish==1.9.3 # via nptyping tzdata==2023.3 # via pytz-deprecation-shim tzlocal==4.3 # via nionswift, pynxtools (dependencies/parsers/nexus/pyproject.toml) uncertainties==3.1.7 # via lmfit, pymatgen -unidecode==1.3.2 # via nomad-lab, nomad-lab (pyproject.toml) +unidecode==1.3.2 # via nomad-lab (pyproject.toml) uri-template==1.2.0 # via jsonschema url-normalize==1.4.3 # via requests-cache urllib3==1.26.14 # via docker, elasticsearch, pybis, requests, requests-cache -uvicorn[standard]==0.20.0 # via h5grove, nomad-lab, nomad-lab (pyproject.toml) +uvicorn[standard]==0.20.0 # via h5grove, nomad-lab (pyproject.toml) uvloop==0.17.0 # via uvicorn -validators==0.18.2 # via nomad-lab, nomad-lab (pyproject.toml) +validators==0.18.2 # via nomad-lab (pyproject.toml) vine==5.0.0 # via amqp, celery, kombu watchfiles==0.18.1 # via uvicorn wcwidth==0.2.5 # via prettytable, prompt-toolkit @@ -291,12 +286,12 @@ websocket-client==1.4.2 # via docker websockets==10.4 # via uvicorn werkzeug==2.2.2 # via flask widgetsnbextension==4.0.9 # via ipywidgets -wrapt==1.12.1 # via nomad-lab, nomad-lab (pyproject.toml) -xarray==0.20.2 # via nomad-lab, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) +wrapt==1.12.1 # via nomad-lab (pyproject.toml) +xarray==0.20.2 # via nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml) zarr==2.12.0 # via hyperspy zipfile37==0.1.3 # via pynxtools (dependencies/parsers/nexus/pyproject.toml) zipp==3.11.0 # via importlib-metadata -zipstream-new==1.1.5 # via nomad-lab, nomad-lab (pyproject.toml) +zipstream-new==1.1.5 # via nomad-lab (pyproject.toml) # The following packages are considered to be unsafe in a requirements file: # setuptools diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh index 273bdd566d0f22a0fd34ba3a7b236a0314e7809c..fb033199c1f90b6eae2f6b73afe37f8cef5f23cb 100755 --- a/scripts/check_python_dependencies.sh +++ b/scripts/check_python_dependencies.sh @@ -14,25 +14,30 @@ project_dir=$(dirname $(dirname $(realpath $0))) cd $project_dir -set -x # echo on +# backup +cp requirements.txt requirements.txt.tmp +cp requirements-dev.txt requirements-dev.txt.tmp -pip-compile --resolver=backtracking --quiet --annotation-style=line \ +pip-compile --resolver=backtracking --annotation-style=line \ --extra=infrastructure --extra=parsing \ - --output-file=requirements.txt.tmp \ + --output-file=requirements.txt \ + --pip-args="--prefer-binary" \ dependencies/nomad-dos-fingerprints/pyproject.toml \ dependencies/parsers/eelsdb/pyproject.toml \ dependencies/parsers/nexus/pyproject.toml \ pyproject.toml -diff requirements.txt requirements.txt.tmp +diff requirements.txt.tmp requirements.txt -pip-compile --resolver=backtracking --quiet --annotation-style=line \ +pip-compile --resolver=backtracking --annotation-style=line \ --extra=dev --extra=infrastructure --extra=parsing \ - --output-file=requirements-dev.txt.tmp \ + --output-file=requirements-dev.txt \ + --pip-args="--prefer-binary" \ requirements.txt \ pyproject.toml -diff requirements-dev.txt requirements-dev.txt.tmp +diff requirements-dev.txt.tmp requirements-dev.txt # cleanup -rm requirements.txt.tmp requirements-dev.txt.tmp +mv requirements.txt.tmp requirements.txt +mv requirements-dev.txt.tmp requirements-dev.txt