diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 11ca0c7eea2a5ac4ac83ed38f753aa5177f13e2d..6da592a30a5bce5383f63157c1509e2086b36933 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -147,6 +147,22 @@ check python dependencies:
- when: manual
allow_failure: true
+check helm chart:
+ stage: test
+ image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
+ script:
+ - scripts/check_helm_chart.sh
+ after_script:
+ - >
+ if [ $CI_JOB_STATUS == 'failed' ]; then
+ echo 'Make sure that the helm chart values.yaml has been updated and committed by running'
+ echo './scripts/update_hem_chart.sh'
+ fi
+ rules:
+ - if: $CI_COMMIT_TAG
+ when: never
+ - when: on_success
+
check gui artifacts:
stage: test
image: ${CI_REGISTRY_IMAGE}/dev_python:${DOCKER_TAG}
diff --git a/docs/howto/oasis/migrate.md b/docs/howto/oasis/migrate.md
index 6ef3acfaf055cc6b28011688d047133918d1eb1b..e893eab11faec69e4ab9682815e650bae56b05ca 100644
--- a/docs/howto/oasis/migrate.md
+++ b/docs/howto/oasis/migrate.md
@@ -66,6 +66,30 @@ For changing the minor or major version, please check the [migration steps](#mig
## Migration steps
+### to 1.2.2
+
+We upgraded the Jupyterhub version used for NORTH from 1.0.2 to 4.0.2. By default the
+Jupyterhub database is persisted in the `nomad_oasis_north` container. If you want to
+keep the database (e.g. to not loose any open tools), you will have to upgrade the database.
+Update the NOMAD docker image version and restart the Oasis like this:
+
+```
+docker compose down
+docker compose pull
+docker copmose run north python -m jupyterhub upgrade
+docker compose up -d
+```
+
+Alternatively, you can delete the `nomad_oasis_north` container and start with a fresh
+database. Make sure that all north tools are stopped and removed.
+
+```
+docker compose down
+docker rm nomad_oasis_north
+docker compose pull
+docker compose up -d
+```
+
### to 1.2.0
- We introduced the plugin mechanism. There are now more options to control which schemas
diff --git a/gui/public/pyiron_logo.png b/gui/public/pyiron_logo.png
new file mode 100644
index 0000000000000000000000000000000000000000..f3fb087817bdf45cd7fdcfc3f3d7687c47f5e279
Binary files /dev/null and b/gui/public/pyiron_logo.png differ
diff --git a/gui/tests/artifacts.js b/gui/tests/artifacts.js
index bafe358be1f5862297ad81a63efa529828dd4529..e985fbd18e8d099ef451ed0aba8066e289b88372 100644
--- a/gui/tests/artifacts.js
+++ b/gui/tests/artifacts.js
@@ -103273,58 +103273,56 @@ window.nomadArtifacts = {
},
"northTools": {
"jupyter": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/jupyterlab:prod",
- "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.",
"short_description": "Basic jupyter run with an empty notebook or on given notebook file.",
+ "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.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:latest",
"cmd": null,
- "with_path": true,
+ "image_pull_policy": "Always",
+ "privileged": false,
"path_prefix": "lab/tree",
- "mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "with_path": true,
"file_extensions": [
"ipynb"
],
+ "mount_path": "/home/jovyan",
+ "icon": "jupyter_logo.svg",
"maintainer": [
{
"name": "Markus Scheidgen",
"email": "markus.scheidgen@physik.hu-berlin.de"
- },
- {
- "name": "Some-one Else",
- "email": "markus.scheidgen@physik.hu-berlin.de"
}
],
- "privileged": false,
"external_mounts": []
},
"nionswift": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop",
- "description": "Run Nion Swift to analyze data.",
"short_description": "Run NionSwift to analyze data as well as prepare focus series reconstructions",
+ "description": "Run Nion Swift to analyze data.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nionswift-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": null,
- "file_extensions": [],
"maintainer": [
{
"name": "Sherjeel Shabih",
"email": "sherjeel.shabih@hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"nexustools": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop",
- "description": "Includes multiple NeXus tools for visualization and analysis.",
"short_description": null,
+ "description": "Includes multiple NeXus tools for visualization and analysis.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/nexus-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
- "mount_path": "/config",
- "icon": null,
+ "with_path": false,
"file_extensions": [
"nxs",
"nx",
@@ -103335,28 +103333,31 @@ window.nomadArtifacts = {
"hdf",
"ipynb"
],
+ "mount_path": "/config",
+ "icon": null,
"maintainer": [
{
"name": "Sandor Brockhauser",
"email": "sandor.brockhauser@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"ellips": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/ellips-jupyter",
- "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.",
"short_description": "An example for analyzing ellipsometric data.",
+ "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.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/ellips-jupyter",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": false,
"path_prefix": "lab/tree",
- "mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "with_path": false,
"file_extensions": [
"ipynb",
"nxs"
],
+ "mount_path": "/home/jovyan",
+ "icon": "jupyter_logo.svg",
"maintainer": [
{
"name": "Florian Dobener",
@@ -103367,48 +103368,50 @@ window.nomadArtifacts = {
"email": "emminger.carola@physik.hu-berlin.de"
}
],
- "privileged": false,
"external_mounts": []
},
"mpes": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop",
- "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).",
"short_description": "An example for analyzing mpes data.",
+ "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).",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/mpes/webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
- "mount_path": "/config",
- "icon": null,
+ "with_path": false,
"file_extensions": [
"ipynb",
"nxs",
"h5",
"hdf5"
],
+ "mount_path": "/config",
+ "icon": null,
"maintainer": [
{
"name": "Florian Dobener",
"email": "florian.dobener@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"xps": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/north/xps/jupyter",
- "description": "Includes tools for analyzing X-ray Photoelectron Spectroscopy (XPS) spectra and converting SPECS SLE files into NeXus.",
"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:master",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": false,
"path_prefix": "lab/tree",
- "mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "with_path": false,
"file_extensions": [
"ipynb",
"nxs",
"h5",
"hdf5"
],
+ "mount_path": "/home/jovyan",
+ "icon": "jupyter_logo.svg",
"maintainer": [
{
"name": "Florian Dobener",
@@ -103423,126 +103426,131 @@ window.nomadArtifacts = {
"email": "rubel.mozumder@physik.hu-berlin.de"
}
],
- "privileged": false,
"external_mounts": []
},
"sts": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter",
- "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.",
"short_description": "An example for analyzing SPM (STM / STS) experiment.",
+ "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.",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/sts-jupyter",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": false,
"path_prefix": "lab/tree",
- "mount_path": "/home/jovyan",
- "icon": "jupyter_logo.svg",
+ "with_path": false,
"file_extensions": [
"ipynb",
"nxs",
"h5",
"hdf5"
],
+ "mount_path": "/home/jovyan",
+ "icon": "jupyter_logo.svg",
"maintainer": [
{
"name": "Rubel Mozumder",
"email": "rubel.mozumder@physik.hu-berlin.de"
}
],
- "privileged": false,
"external_mounts": []
},
"webtop": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop",
- "description": "Baseline webtop image for test",
"short_description": null,
+ "description": "Baseline webtop image for test",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": null,
- "file_extensions": [],
"maintainer": [
{
"name": "Sherjeel Shabih",
"email": "sherjeel.shabih@hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"apmtools": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop",
- "description": "Miscellaneous tools from the atom probe community:\nCurrently APTyzer, paraprobe-toolbox, and APAV",
"short_description": "An example for analyzing atom probe data.",
+ "description": "Miscellaneous tools from the atom probe community:\nCurrently APTyzer, paraprobe-toolbox, and APAV",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/apmtools-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": "jupyter_logo.svg",
- "file_extensions": [],
"maintainer": [
{
"name": "Markus K\u00fchbach",
"email": "markus.kuehbach@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"fiji": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop",
- "description": "ImageJ and Fiji with amongst others several electron-microscopy specific plug-ins",
"short_description": "ImageJ and Fiji for image processing",
+ "description": "ImageJ and Fiji with amongst others several electron-microscopy specific plug-ins",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/fiji-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": "jupyter_logo.svg",
- "file_extensions": [],
"maintainer": [
{
"name": "Markus K\u00fchbach",
"email": "markus.kuehbach@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"frwr": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop",
- "description": "FRWR3 in-line holography/focus series reconstruction code",
"short_description": "Inline electron holography by C. Koch",
+ "description": "FRWR3 in-line holography/focus series reconstruction code",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/frwr-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": "jupyter_logo.svg",
- "file_extensions": [],
"maintainer": [
{
"name": "Markus K\u00fchbach",
"email": "markus.kuehbach@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
},
"abtem": {
- "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop",
- "description": "VESTA, GPAW, and abTEM configured in one container for simulating images and diffraction patterns in transmission electron microscopy",
"short_description": "Electronic structure supported image simulation for transmission electron microscopy.",
+ "description": "VESTA, GPAW, and abTEM configured in one container for simulating images and diffraction patterns in transmission electron microscopy",
+ "image": "gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/abtem-webtop",
"cmd": null,
- "with_path": false,
+ "image_pull_policy": "Always",
+ "privileged": true,
"path_prefix": null,
+ "with_path": false,
+ "file_extensions": [],
"mount_path": "/config",
"icon": "jupyter_logo.svg",
- "file_extensions": [],
"maintainer": [
{
"name": "Markus K\u00fchbach",
"email": "markus.kuehbach@physik.hu-berlin.de"
}
],
- "privileged": true,
"external_mounts": []
}
},
diff --git a/nomad/app/v1/routers/north.py b/nomad/app/v1/routers/north.py
index be57d7eab21fca13596818e7d5118e6b70543ce8..7df361a9958e0223fc335e95b48790166b2754c6 100644
--- a/nomad/app/v1/routers/north.py
+++ b/nomad/app/v1/routers/north.py
@@ -29,6 +29,7 @@ from nomad import config
from nomad.config.north import NORTHTool
from nomad.utils import strip, get_logger, slugify
from nomad.processing import Upload
+from nomad.app.v1.routers.auth import generate_simple_token
from .auth import create_user_dependency, oauth2_scheme
from ..models import User, HTTPExceptionModel
from ..utils import create_responses
@@ -159,7 +160,6 @@ async def get_tool(
)
async def start_tool(
tool: ToolModel = Depends(tool),
- access_token: str = Depends(oauth2_scheme),
user: User = Depends(create_user_dependency(required=True)),
upload_id: Optional[str] = None,
):
@@ -238,6 +238,9 @@ async def start_tool(
)
url = f'{config.hub_url()}/api/users/{user.username}/servers/{tool.name}'
+ access_token = generate_simple_token(
+ user_id=user.user_id, expires_in=config.north.nomad_access_token_expiry_time
+ )
body = {
'tool': {'image': tool.image, 'cmd': tool.cmd, 'privileged': tool.privileged},
'environment': {
diff --git a/nomad/config/north.py b/nomad/config/north.py
index 43ab0144425761dbf83b6eabe2901d9bc44fde64..3aa5aa7201d38702dedac21c49ba114b535344af 100644
--- a/nomad/config/north.py
+++ b/nomad/config/north.py
@@ -46,18 +46,60 @@ class NORTHExternalMount(BaseModel):
class NORTHTool(BaseModel):
- image: str
- description: str = None
- short_description: str = None
- cmd: str = None
- with_path: bool = False
- path_prefix: str = None
- mount_path: str = None
- icon: str = None
- file_extensions: List[str] = []
- maintainer: List[NORTHToolMaintainer] = []
- privileged: bool = False
- external_mounts: List[NORTHExternalMount] = []
+ short_description: str = Field(
+ None,
+ description='A short description of the tool, e.g. shown in the NOMAD GUI.',
+ )
+ description: str = Field(
+ None, description='A description of the tool, e.g. shown in the NOMAD GUI.'
+ )
+ image: str = Field(
+ None, description='The docker image (incl. tags) to use for the tool.'
+ )
+ cmd: str = Field(
+ None, description='The container cmd that is passed to the spawner.'
+ )
+ image_pull_policy: str = Field(
+ 'Always', description='The image pull policy used in k8s deployments.'
+ )
+ privileged: bool = Field(
+ False, description='Whether the tool needs to run in privileged mode.'
+ )
+ path_prefix: str = Field(
+ None,
+ description=(
+ 'An optional path prefix that is added to the container URL to '
+ 'reach the tool, e.g. "lab/tree" for jupyterlab.'
+ ),
+ )
+ with_path: bool = Field(
+ False,
+ description=(
+ 'Whether the tool supports a path to a file or directory. '
+ 'This also enables tools to be launched from files in the NOMAD UI.'
+ ),
+ )
+ file_extensions: List[str] = Field(
+ [],
+ description='The file extensions of files that this tool should be launchable for.',
+ )
+ mount_path: str = Field(
+ None,
+ description=(
+ 'The path in the container where uploads and work directories will be mounted, '
+ 'e.g. /home/jovyan for Jupyter containers.'
+ ),
+ )
+ icon: str = Field(
+ None,
+ description='A URL to an icon that is used to represent the tool in the NOMAD UI.',
+ )
+ maintainer: List[NORTHToolMaintainer] = Field(
+ [], description='The maintainers of the tool.'
+ )
+ external_mounts: List[NORTHExternalMount] = Field(
+ [], description='Additional mounts to be added to tool containers.'
+ )
class NORTHTools(Options):
@@ -107,14 +149,25 @@ class NORTH(NomadSettings):
None, description='The NOMAD app host name that spawned containers use.'
)
windows = Field(True, description='Enable windows OS hacks.')
+ nomad_access_token_expiry_time: int = Field(
+ 24 * 3600,
+ description=(
+ 'All tools are run with an access token for the NOMAD api in the NOMAD_CLIENT_ACCESS_TOKEN '
+ 'environment variable. This token will be automatically used by the nomad-lab Python package, '
+ 'e.g. if you use the ArchiveQuery to access data. '
+ 'This option sets the amount of seconds that this token is valid for.'
+ ),
+ )
tools: NORTHTools = Field(
NORTHTools(
+ include=None,
+ exclude=['pyiron'],
options={
'jupyter': NORTHTool(
short_description='Basic jupyter run with an empty notebook or on given notebook file.',
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.',
- image='gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/jupyterlab:prod',
+ image='gitlab-registry.mpcdf.mpg.de/nomad-lab/north/jupyter:latest',
path_prefix='lab/tree',
with_path=True,
mount_path='/home/jovyan',
@@ -124,11 +177,23 @@ class NORTH(NomadSettings):
NORTHToolMaintainer(
name='Markus Scheidgen',
email='markus.scheidgen@physik.hu-berlin.de',
- ),
+ )
+ ],
+ ),
+ 'pyiron': NORTHTool(
+ short_description='Jupyterlab with pyiron installed.',
+ description='## Pyiron: Complex workflows made easy\n\nFrom rapid prototyping to high performance computing in material science. [Homepage](https://pyiron.org/).',
+ image='pyiron/pyiron:latest',
+ path_prefix='lab/tree',
+ with_path=True,
+ mount_path='/home/jovyan',
+ icon='pyiron_logo.png',
+ file_extensions=['ipynb'],
+ maintainer=[
NORTHToolMaintainer(
- name='Some-one Else',
+ name='Markus Scheidgen',
email='markus.scheidgen@physik.hu-berlin.de',
- ),
+ )
],
),
'nionswift': NORTHTool(
@@ -201,7 +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',
@@ -303,7 +368,7 @@ class NORTH(NomadSettings):
)
],
),
- }
+ },
),
description='The available north tools. Either the tools definitions as dict or a path to a .json file.',
)
diff --git a/nomad/jupyterhub_config.py b/nomad/jupyterhub_config.py
index c023eb62e21030a086c2b79d31225bbbf2834f0e..418b75afc3774c7aaaaba5160c5c400d6c39617c 100644
--- a/nomad/jupyterhub_config.py
+++ b/nomad/jupyterhub_config.py
@@ -77,13 +77,13 @@ def pre_spawn(spawner):
c.Spawner.pre_spawn_hook = pre_spawn
# configure nomad service
-c.JupyterHub.services = [
+c.JupyterHub.services.append(
{
'name': 'nomad-service',
'admin': True,
'api_token': config.north.hub_service_api_token,
}
-]
+)
# Allow named single-user servers per user (Default: False)
c.JupyterHub.allow_named_servers = True
@@ -117,6 +117,7 @@ c.GenericOAuthenticator.username_key = 'preferred_username'
c.GenericOAuthenticator.scope = ['openid', 'profile']
c.Authenticator.auto_login = True
c.Authenticator.enable_auth_state = True
+c.Ahtenticator.allow_all = True
# configure docker spawner
diff --git a/ops/kubernetes/nomad-prod-develop.yaml b/ops/kubernetes/nomad-prod-develop.yaml
index 52e600b2d05638b355a537091919e74b28a64034..565cf041f9e6228bf513641643d774ebfc1d6c78 100644
--- a/ops/kubernetes/nomad-prod-develop.yaml
+++ b/ops/kubernetes/nomad-prod-develop.yaml
@@ -41,7 +41,7 @@ nomad:
memory: "8Gi"
jupyterhub:
- fullnameOverride: "nomad-prod-staging-north"
+ fullnameOverride: "nomad-prod-develop-north"
hub:
baseUrl: "/prod/v1/develop/north"
config:
diff --git a/ops/kubernetes/nomad/Chart.lock b/ops/kubernetes/nomad/Chart.lock
index c79e2d604f329394c58607d48f1406950fa31e0c..ca21ee2e9c5a86a58143822d20db2476a7ba537a 100644
--- a/ops/kubernetes/nomad/Chart.lock
+++ b/ops/kubernetes/nomad/Chart.lock
@@ -10,6 +10,6 @@ dependencies:
version: 14.0.4
- name: jupyterhub
repository: https://jupyterhub.github.io/helm-chart/
- version: 1.2.0
-digest: sha256:75cf4c73a86fb9a6ca46cbfd7676d20600c64932659c30b36d4b494170a7b6d0
-generated: "2024-02-08T20:14:29.044024+01:00"
+ version: 3.2.1
+digest: sha256:f77e87c16f5417c9ba3d30143451035d6b570c5eb9d736589069e31e26ab5adf
+generated: "2024-02-26T13:51:48.48639+01:00"
diff --git a/ops/kubernetes/nomad/Chart.yaml b/ops/kubernetes/nomad/Chart.yaml
index 22860c0caeaddb7d2f7e167c33d8d664b0976b05..e7adb99ecfc6c950a41f6f39b7fc4b253f478863 100644
--- a/ops/kubernetes/nomad/Chart.yaml
+++ b/ops/kubernetes/nomad/Chart.yaml
@@ -37,7 +37,7 @@ dependencies:
version: 14.0.4
repository: oci://registry-1.docker.io/bitnamicharts
- name: jupyterhub
- version: "1.2.0"
+ version: "3.2.1"
repository: "https://jupyterhub.github.io/helm-chart/"
condition: nomad.config.north.enabled
diff --git a/ops/kubernetes/nomad/updatevalues.py b/ops/kubernetes/nomad/updatevalues.py
new file mode 100644
index 0000000000000000000000000000000000000000..3a4ba1e04cbb611021e9cc435059a3ec5b0cd637
--- /dev/null
+++ b/ops/kubernetes/nomad/updatevalues.py
@@ -0,0 +1,74 @@
+# Updates the values.yaml file based on the nomad configuration. Currently this
+# 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
+from nomad import config
+
+dir_path = os.path.dirname(os.path.realpath(__file__))
+file_path = os.path.join(dir_path, 'values.yaml')
+
+yaml = YAML()
+yaml.allow_duplicate_keys = True
+with open(file_path, 'r') as file:
+ data = yaml.load(file)
+
+# 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', [])
+ )
+ 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 len(argv) == 2:
+ with open(argv[1], 'w') as file:
+ yaml.dump(data, file)
+else:
+ yaml.dump(data, stdout)
diff --git a/ops/kubernetes/nomad/values.yaml b/ops/kubernetes/nomad/values.yaml
index ac2cba4fee1aa8045b283998904535d7a5fad996..6835cc20f3358a58f5cdb53db476dba9bcf58efd 100644
--- a/ops/kubernetes/nomad/values.yaml
+++ b/ops/kubernetes/nomad/values.yaml
@@ -2,8 +2,8 @@
# This is a YAML-formatted file.
# Declare variables to be passed into your templates.
roll: false
-nameOverride: ""
-fullnameOverride: ""
+nameOverride: ''
+fullnameOverride: ''
serviceAccount:
# Specifies whether a service account should be created
@@ -14,42 +14,33 @@ serviceAccount:
annotations: {}
# The name of the service account to use.
# If not set and create is true, a name is generated using the fullname template
- name: ""
+ name: ''
nomad:
enabled: true
image:
repository: gitlab-registry.mpcdf.mpg.de/nomad-lab/nomad-fair
- tag: "latest"
+ tag: latest
pullPolicy: Always
imagePullSecrets: []
-
- # Default values for nomad.
- # This is a YAML-formatted file.
- # Declare variables to be passed into your templates.
-
- # GLOBAL parameters
- enabled: false
-
- ## Default values for nomad@FAIRDI
config:
version:
- label: "latest"
+ label: latest
isTest: false
isBeta: false
usesBetaData: false
- officialUrl: "https://nomad-lab.eu/prod/v1/gui"
+ officialUrl: https://nomad-lab.eu/prod/v1/gui
meta:
- service: "app"
- homepage: "https://nomad-lab.eu"
- source_url: "https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR"
- maintainer_email: "markus.scheidgen@physik.hu-berlin.de"
+ service: app
+ homepage: https://nomad-lab.eu
+ source_url: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR
+ maintainer_email: markus.scheidgen@physik.hu-berlin.de
api:
## Secret used as cryptographic seed
- secret: "defaultApiSecret"
+ secret: defaultApiSecret
## Limit of unpublished uploads per user, except admin user
uploadLimit: 10
@@ -63,15 +54,15 @@ nomad:
## There are two routing modes "queue" and "worker". The "queue" routing will use a general
# task queue and spread calc processing task over worker instances. The "worker" routing
# will send all tasks related to an upload to the same worker
- routing: "queue"
+ routing: queue
timeout: 7200
acks_late: false
mail:
enabled: false
- host: "localhost"
+ host: localhost
port: 25
- from: "support@nomad-lab.eu"
+ from: support@nomad-lab.eu
client:
username: admin
@@ -93,17 +84,17 @@ nomad:
datacite:
enabled: false
- prefix: "10.17172"
+ prefix: '10.17172'
## A common name/prefix for all dbs and indices.
dbname: fairdi_nomad_latest
mongo:
- host: ""
+ host: ''
port: 27017
elastic:
- host: ""
+ host: ''
port: 9200
timeout: 60
bulkTimeout: 600
@@ -113,16 +104,16 @@ nomad:
logstash:
enabled: true
port: 5000
- host: ""
+ host: ''
keycloak:
- serverExternalUrl: "https://nomad-lab.eu/fairdi/keycloak/auth/"
- serverUrl: "https://nomad-lab.eu/keycloak/auth/"
- realmName: "fairdi_nomad_test"
- username: "admin"
- clientId: "nomad_public"
- guiClientId: "nomad_public"
- admin_user_id: "00000000-0000-0000-0000-000000000000"
+ serverExternalUrl: https://nomad-lab.eu/fairdi/keycloak/auth/
+ serverUrl: https://nomad-lab.eu/keycloak/auth/
+ realmName: fairdi_nomad_test
+ username: admin
+ clientId: nomad_public
+ guiClientId: nomad_public
+ admin_user_id: 00000000-0000-0000-0000-000000000000
## Everything concerning the data that is used by the service
volumes:
@@ -140,7 +131,7 @@ nomad:
north:
enabled: false
- hubServiceApiToken: "secret-token"
+ hubServiceApiToken: secret-token
gui:
## This variable is used in the GUI to show or hide additional information
@@ -148,16 +139,27 @@ nomad:
## automatically gz based on header
gzip: true
+ proxy:
+ # Set a nodePort to create a NodePort service instead of ClusterIP. Also set a nodeIP for the externalIP.
+ timeout: 120
+ editTimeout: 1800
+ external:
+ host: nomad-lab.eu
+ port: 80
+ path: /fairdi/nomad/latest
+ https: true
+
+
ingress:
enabled: false
limitConnections: 32
limitConnectionsApi: 8
hosts:
- - nomad-lab.eu
- className: ""
+ - nomad-lab.eu
+ className: ''
annotations:
- nginx.ingress.kubernetes.io/ssl-redirect: "false"
- nginx.ingress.kubernetes.io/proxy-body-size: "32g"
+ nginx.ingress.kubernetes.io/ssl-redirect: 'false'
+ nginx.ingress.kubernetes.io/proxy-body-size: 32g
tls: []
# Additional volumes on the output Deployment definition.
@@ -182,7 +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
@@ -196,8 +198,8 @@ nomad:
tag: 1.13.9-alpine
pullPolicy: IfNotPresent
- command: ["nginx"]
- args: ["-g", "daemon off;"]
+ command: [nginx]
+ args: [-g, daemon off;]
imagePullSecrets: []
@@ -379,7 +381,7 @@ jupyterhub:
type: ClusterIP
singleuser:
image:
- pullPolicy: "Always"
+ pullPolicy: Always
storage:
type: none
hub:
@@ -416,13 +418,13 @@ jupyterhub:
hub_service_api_token = os.getenv('NOMAD_NORTH_HUB_SERVICE_API_TOKEN')
# configure nomad service
- c.JupyterHub.services = [
+ c.JupyterHub.services.append(
{
"name": "nomad-service",
"admin": True,
"api_token": hub_service_api_token,
}
- ]
+ )
async def pre_spawn_hook(spawner):
await spawner.load_user_options()
@@ -433,10 +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')
@@ -479,10 +477,11 @@ jupyterhub:
spawner.uid = 0
c.Spawner.pre_spawn_hook = pre_spawn_hook
+ c.OAuthenticator.allow_all = True
cull:
enabled: true
- timeout: 3600
+ timeout: 86400 # 24 hours
every: 600
removeNamedServers: true
@@ -490,10 +489,46 @@ jupyterhub:
hook:
enabled: true
image:
- pullPolicy: "Always"
+ 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/pyproject.toml b/pyproject.toml
index d3dcfb2c8131bf9f77bb7bfe8a1317588c34bcf1..5ec11c8d4a78f26b87474c0b867405b8fab02f82 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -102,7 +102,7 @@ infrastructure = [
'fastapi==0.92.0',
'uvicorn[standard]',
'python-multipart==0.0.5',
- 'jupyterhub==1.4.2',
+ 'jupyterhub==4.0.2',
'dockerspawner==12.1.0',
'oauthenticator==15.1.0',
'validators==0.18.2',
@@ -140,7 +140,8 @@ dev = [
'mkdocs-click==0.8.0',
'mkdocs-redirects==1.2.0',
'mkdocs-git-revision-date-localized-plugin==1.2.1',
- 'ruff==0.1.8'
+ 'ruff==0.1.8',
+ 'ruamel.yaml==0.17.21'
]
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 5be4fda0fcb64af24d4e7d85f8d85aa0f8fd1cf6..292843e01e8ae44348dc4a8bd8f36132fc824784 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -2,18 +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
+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
@@ -24,25 +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
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
@@ -51,7 +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
@@ -62,14 +63,14 @@ diffsims==0.5.2 # via -r requirements.txt, kikuchipy, pyxem
dill==0.3.6 # via -r requirements.txt, hyperspy, pylint
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
-entrypoints==0.4 # via -r requirements.txt, ipyparallel, jupyter-client, jupyterhub, numcodecs
+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)
et-xmlfile==1.1.0 # via -r requirements.txt, openpyxl
@@ -78,9 +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
@@ -89,26 +90,26 @@ 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, nomad-lab (pyproject.toml)
-h5py==3.6.0 # via -r requirements.txt, h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab, nomad-lab (pyproject.toml), orix, phonopy, pyfai, silx
-hjson==3.0.2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-html5lib==1.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+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, 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, nomad-lab (pyproject.toml)
+httpx==0.23.3 # via -r requirements.txt, nomad-lab (pyproject.toml)
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, keyring, markdown, mkdocs, nomad-lab, nomad-lab (pyproject.toml), sphinx, twine
-inflection==0.5.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+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
ipython==7.34.0 # via -r requirements.txt, hyperspy, ipykernel, ipyparallel, ipywidgets
@@ -116,19 +117,18 @@ 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
-jeepney==0.8.0 # via keyring, secretstorage
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, nomad-lab (pyproject.toml), oauthenticator
+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
jupyter-core==4.12.0 # via -r requirements.txt, jupyter-client
jupyter-telemetry==0.1.0 # via -r requirements.txt, jupyterhub
-jupyterhub==1.4.2 # via -r requirements.txt, dockerspawner, nomad-lab, nomad-lab (pyproject.toml), oauthenticator
+jupyterhub==4.0.2 # via -r requirements.txt, dockerspawner, nomad-lab (pyproject.toml), oauthenticator
jupyterlab-widgets==3.0.9 # via -r requirements.txt, ipywidgets
keyring==23.11.0 # via twine
kikuchipy==0.8.7 # via -r requirements.txt
@@ -140,18 +140,18 @@ lazy-object-proxy==1.9.0 # via astroid
llvmlite==0.39.1 # via -r requirements.txt, numba
lmfit==1.2.2 # via -r requirements.txt, pyxem
locket==1.0.0 # via -r requirements.txt, partd
-lxml==4.7.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-m2r==0.2.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+lxml==4.7.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
+m2r==0.2.1 # via -r requirements.txt, nomad-lab (pyproject.toml)
mako==1.2.4 # via -r requirements.txt, alembic
markdown==3.4.1 # via mkdocs, mkdocs-click, mkdocs-material, pymdown-extensions
markupsafe==2.1.1 # via -r requirements.txt, jinja2, mako, nomad-lab (pyproject.toml), werkzeug
-matid==2.0.0.dev2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+matid==2.0.0.dev2 # via -r requirements.txt, nomad-lab (pyproject.toml)
matplotlib==3.5.3 # via -r requirements.txt, ase, asr, diffsims, hyperspy, kikuchipy, matplotlib-scalebar, mdanalysis, orix, phonopy, pyfai, pymatgen, pyxem, radioactivedecay
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)
@@ -163,55 +163,52 @@ 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, nomad-lab, nomad-lab (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
nest-asyncio==1.5.6 # via -r requirements.txt, ipykernel, jupyter-client
netcdf4==1.5.4 # via -r requirements.txt, nomad-lab (pyproject.toml)
-networkx==2.6.3 # via -r requirements.txt, matid, mdanalysis, nomad-lab, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image
+networkx==2.6.3 # via -r requirements.txt, matid, mdanalysis, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image
niondata==0.15.5 # via -r requirements.txt, nionswift, nionswift-io
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
-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, nomad-lab (pyproject.toml)
-optimade[mongo]==0.22.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+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, nomad-lab (pyproject.toml)
-packaging==24.0 # via -r requirements.txt, build, dask, docker, gunicorn, hyperspy, ipykernel, matplotlib, mdanalysis, mkdocs, mongomock, pint, pooch, pytest, scikit-image, sphinx
+orjson==3.9.4 # via -r requirements.txt, h5grove, nomad-lab (pyproject.toml)
+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, ifes-apt-tc-data-modeling, nomad-lab, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, xarray
-panedr==0.2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-parmed==3.0.0 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+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
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
@@ -231,16 +228,16 @@ 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, nomad-lab (pyproject.toml)
+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
@@ -253,45 +250,43 @@ python-dateutil==2.8.2 # via -r requirements.txt, arrow, elasticsearch-dsl, g
python-dotenv==0.21.0 # via -r requirements.txt, uvicorn
python-gitlab==2.10.1 # via nomad-lab (pyproject.toml)
python-jose==3.3.0 # via -r requirements.txt, python-keycloak
-python-json-logger==2.0.2 # via -r requirements.txt, jupyter-telemetry, nomad-lab, nomad-lab (pyproject.toml)
-python-keycloak==0.26.1 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-python-logstash==0.4.6 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-python-magic==0.4.24 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-python-multipart==0.0.5 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
-pytz==2022.7.1 # via -r requirements.txt, babel, celery, mkdocs-git-revision-date-localized-plugin, nionswift, nomad-lab, nomad-lab (pyproject.toml), pandas
+python-json-logger==2.0.2 # via -r requirements.txt, jupyter-telemetry, nomad-lab (pyproject.toml)
+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
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
-pyyaml==6.0 # via -r requirements.txt, dask, hyperspy, kikuchipy, mkdocs, mkdocs-macros-plugin, nomad-lab, nomad-lab (pyproject.toml), phonopy, pybtex, pyyaml-env-tag, uvicorn
+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, hyperspy, jupyterhub, nomad-lab, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, python-gitlab, python-keycloak, requests-cache, requests-toolbelt, rfc3161ng, sphinx, twine
+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)
-runstats==2.0.0 # via -r requirements.txt, nomad-lab, 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, 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, nomad-lab (pyproject.toml), orix, pyfai, pymatgen, pyxem, radioactivedecay, scikit-image, scikit-learn, sparse
-secretstorage==3.3.3 # via keyring
+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, 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
smmap==5.0.0 # via -r requirements.txt, gitdb
sniffio==1.3.0 # via -r requirements.txt, anyio, httpcore, httpx
@@ -308,9 +303,9 @@ 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, nomad-lab (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
@@ -318,7 +313,7 @@ threadpoolctl==3.1.0 # via -r requirements.txt, mdanalysis, scikit-learn
tifffile==2021.11.2 # via -r requirements.txt, h5grove, hyperspy, scikit-image
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
@@ -331,13 +326,13 @@ 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, pybis, requests, requests-cache
-uvicorn[standard]==0.20.0 # via -r requirements.txt, h5grove, nomad-lab, nomad-lab (pyproject.toml)
+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
watchdog==2.1.9 # via mkdocs
watchfiles==0.18.1 # via -r requirements.txt, uvicorn
@@ -349,12 +344,12 @@ websockets==10.4 # via -r requirements.txt, uvicorn
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, nomad-lab (pyproject.toml)
-xarray==0.20.2 # via -r requirements.txt, nomad-lab, nomad-lab (pyproject.toml)
+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)
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 6761ecddc37b3039890e3d087c4c86394929537c..8c69d3eff21f189aa76e64894df3083e55b79021 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -2,48 +2,49 @@
# This file is autogenerated by pip-compile with Python 3.9
# by the following command:
#
-# pip-compile --annotation-style=line --extra=infrastructure --extra=parsing --output-file=requirements.txt --resolver=backtracking dependencies/nomad-dos-fingerprints/pyproject.toml dependencies/parsers/atomistic/pyproject.toml dependencies/parsers/database/pyproject.toml dependencies/parsers/eelsdb/pyproject.toml dependencies/parsers/electronic/pyproject.toml dependencies/parsers/nexus/pyproject.toml dependencies/parsers/workflow/pyproject.toml pyproject.toml
+# pip-compile --annotation-style=line --extra=infrastructure --extra=parsing --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
#
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
asciitree==0.3.3 # via zarr
-ase==3.19.0 # via asr, ifes-apt-tc-data-modeling, matid, nomad-lab, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), quippy-ase
-asgiref==3.6.0 # via nomad-lab, nomad-lab (pyproject.toml)
-asr==0.4.1 # via nomad-lab (pyproject.toml), workflowparsers (dependencies/parsers/workflow/pyproject.toml)
+ase==3.19.0 # via asr, ifes-apt-tc-data-modeling, matid, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), quippy-ase
+asgiref==3.6.0 # via nomad-lab (pyproject.toml)
+asr==0.4.1 # via nomad-lab (pyproject.toml)
asteval==0.9.31 # via lmfit
async-generator==1.10 # via jupyterhub
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
-bitarray==2.3.5 # via nomad-lab, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
-bs4==0.0.1 # via nomad-lab, nomad-lab (pyproject.toml)
-cachetools==4.2.4 # via nomad-lab, nomad-lab (pyproject.toml)
+bitarray==2.3.5 # via nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/pyproject.toml)
+bs4==0.0.1 # via nomad-lab (pyproject.toml)
+cachetools==4.2.4 # via nomad-lab (pyproject.toml)
cattrs==22.2.0 # via requests-cache
-celery[redis]==5.2.7 # via nomad-lab, nomad-lab (pyproject.toml)
+celery[redis]==5.2.7 # via nomad-lab (pyproject.toml)
certifi==2022.12.7 # via elasticsearch, httpcore, httpx, requests
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
@@ -53,22 +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
-entrypoints==0.4 # via ipyparallel, jupyter-client, jupyterhub, numcodecs
+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
@@ -76,43 +77,43 @@ 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, nomad-lab (pyproject.toml)
-h5py==3.6.0 # via electronicparsers (dependencies/parsers/electronic/pyproject.toml), h5grove, hyperspy, ifes-apt-tc-data-modeling, kikuchipy, nionswift, nomad-lab, nomad-lab (pyproject.toml), orix, phonopy, pyfai, silx
-hjson==3.0.2 # via nomad-lab, nomad-lab (pyproject.toml)
-html5lib==1.1 # via nomad-lab, nomad-lab (pyproject.toml)
+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
+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)
imageio==2.24.0 # via hyperspy, kikuchipy, nionswift, nionswift-io, nionui, scikit-image
imagesize==1.4.1 # via sphinx
-importlib-metadata==4.13.0 # via flask, hyperspy, nomad-lab, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), sphinx
-inflection==0.5.1 # via nomad-lab, nomad-lab (pyproject.toml)
+importlib-metadata==4.13.0 # via flask, hyperspy, jupyterhub, nomad-lab (pyproject.toml), pynxtools (dependencies/parsers/nexus/pyproject.toml), sphinx
+inflection==0.5.1 # via nomad-lab (pyproject.toml)
ipykernel==6.16.2 # via ipyparallel
ipyparallel==8.4.1 # via hyperspy
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, nomad-lab (pyproject.toml), oauthenticator
+jsonschema[format]==4.17.3 # via jupyter-telemetry, nomad-lab (pyproject.toml), oauthenticator
jupyter-client==7.4.8 # via ipykernel, ipyparallel
jupyter-core==4.12.0 # via jupyter-client
jupyter-telemetry==0.1.0 # via jupyterhub
-jupyterhub==1.4.2 # via dockerspawner, nomad-lab, nomad-lab (pyproject.toml), oauthenticator
+jupyterhub==4.0.2 # via dockerspawner, nomad-lab (pyproject.toml), oauthenticator
jupyterlab-widgets==3.0.9 # via ipywidgets
kikuchipy==0.8.7 # via pynxtools (dependencies/parsers/nexus/pyproject.toml)
kiwisolver==1.4.4 # via matplotlib
@@ -122,63 +123,60 @@ latexcodec==2.0.1 # via pybtex
llvmlite==0.39.1 # via numba
lmfit==1.2.2 # via pyxem
locket==1.0.0 # via partd
-lxml==4.7.1 # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab, nomad-lab (pyproject.toml)
-m2r==0.2.1 # via nomad-lab, nomad-lab (pyproject.toml)
+lxml==4.7.1 # via nomad-lab (pyproject.toml)
+m2r==0.2.1 # via nomad-lab (pyproject.toml)
mako==1.2.4 # via alembic
markupsafe==2.1.1 # via jinja2, mako, werkzeug
-matid==2.0.0.dev2 # via nomad-lab, nomad-lab (pyproject.toml)
+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 electronicparsers (dependencies/parsers/electronic/pyproject.toml), nomad-lab (pyproject.toml)
-networkx==2.6.3 # via matid, mdanalysis, nomad-lab, nomad-lab (pyproject.toml), pymatgen, radioactivedecay, scikit-image
+netcdf4==1.5.4 # 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 (dependencies/parsers/nexus/pyproject.toml)
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, nomad-lab (pyproject.toml), nomad_dos_fingerprints (dependencies/nomad-dos-fingerprints/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 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, nomad-lab (pyproject.toml)
-optimade[mongo]==0.22.1 # via nomad-lab, nomad-lab (pyproject.toml)
+openpyxl==3.1.2 # via nomad-lab (pyproject.toml)
+optimade[mongo]==0.22.1 # via nomad-lab (pyproject.toml)
orix==0.11.1 # via diffsims, kikuchipy, pyxem
-orjson==3.9.4 # via h5grove, nomad-lab, nomad-lab (pyproject.toml)
-packaging==24.0 # via dask, docker, gunicorn, hyperspy, ipykernel, matplotlib, mdanalysis, mongomock, pint, pooch, scikit-image, sphinx
+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, nomad-lab (pyproject.toml), panedr, pybis, pymatgen, xarray
-panedr==0.2 # via atomisticparsers (dependencies/parsers/atomistic/pyproject.toml), nomad-lab, nomad-lab (pyproject.toml)
-parmed==3.0.0 # via nomad-lab, nomad-lab (pyproject.toml)
+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, workflowparsers (dependencies/parsers/workflow/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
@@ -193,51 +191,50 @@ 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)
-pyyaml==6.0 # via dask, electronicparsers (dependencies/parsers/electronic/pyproject.toml), hyperspy, kikuchipy, nomad-lab, nomad-lab (pyproject.toml), phonopy, pybtex, uvicorn
+pyyaml==6.0 # via dask, hyperspy, kikuchipy, nomad-lab (pyproject.toml), phonopy, pybtex, pynxtools (dependencies/parsers/nexus/pyproject.toml), uvicorn
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, nomad-lab, nomad-lab (pyproject.toml), oauthenticator, optimade, pooch, pybis, pymatgen, 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
@@ -254,15 +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
@@ -273,13 +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
@@ -289,12 +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_helm_chart.sh b/scripts/check_helm_chart.sh
new file mode 100755
index 0000000000000000000000000000000000000000..f840fd21217b23593dbc7412fb37745a05b47557
--- /dev/null
+++ b/scripts/check_helm_chart.sh
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+set -e
+set -x # echo on
+
+working_dir=$(pwd)
+project_dir=$(dirname $(dirname $(realpath $0)))
+
+cd $project_dir
+
+mkdir tmp
+
+python ops/kubernetes/nomad/updatevalues.py > tmp/helm-values.yaml
+diff ops/kubernetes/nomad/values.yaml tmp/helm-values.yaml
+
+# cleanup
+rm -rf tmp
diff --git a/scripts/check_python_dependencies.sh b/scripts/check_python_dependencies.sh
index b6680a822c1b76a66881b6375e4a0fc5068d1a87..fb033199c1f90b6eae2f6b73afe37f8cef5f23cb 100755
--- a/scripts/check_python_dependencies.sh
+++ b/scripts/check_python_dependencies.sh
@@ -1,5 +1,12 @@
#!/bin/sh
+# For now we exclude the following dependencies, because they import an older version
+# of nomad-lab causing inevitable conflicts.
+# dependencies/parsers/atomistic/pyproject.toml \
+# dependencies/parsers/database/pyproject.toml \
+# dependencies/parsers/electronic/pyproject.toml \
+# dependencies/parsers/workflow/pyproject.toml \
+
set -e
working_dir=$(pwd)
@@ -7,28 +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/atomistic/pyproject.toml \
- dependencies/parsers/database/pyproject.toml \
dependencies/parsers/eelsdb/pyproject.toml \
- dependencies/parsers/electronic/pyproject.toml \
dependencies/parsers/nexus/pyproject.toml \
- dependencies/parsers/workflow/pyproject.toml 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
diff --git a/scripts/generate_python_dependencies.sh b/scripts/generate_python_dependencies.sh
index df678273e99d0139a2a75c528fbf846cd0335ae7..91de80c94df001abd8b50e73dd7386723c12a2fa 100755
--- a/scripts/generate_python_dependencies.sh
+++ b/scripts/generate_python_dependencies.sh
@@ -1,5 +1,12 @@
#!/bin/sh
+# For now we exclude the following dependencies, because they import an older version
+# of nomad-lab causing inevitable conflicts.
+# dependencies/parsers/atomistic/pyproject.toml \
+# dependencies/parsers/database/pyproject.toml \
+# dependencies/parsers/electronic/pyproject.toml \
+# dependencies/parsers/workflow/pyproject.toml \
+
set -e
working_dir=$(pwd)
@@ -10,18 +17,16 @@ cd $project_dir
pip-compile --resolver=backtracking --annotation-style=line \
--extra=infrastructure --extra=parsing \
--output-file=requirements.txt \
+ --pip-args="--prefer-binary" \
dependencies/nomad-dos-fingerprints/pyproject.toml \
- dependencies/parsers/atomistic/pyproject.toml \
- dependencies/parsers/database/pyproject.toml \
dependencies/parsers/eelsdb/pyproject.toml \
- dependencies/parsers/electronic/pyproject.toml \
dependencies/parsers/nexus/pyproject.toml \
- dependencies/parsers/workflow/pyproject.toml pyproject.toml
-
+ pyproject.toml
pip-compile --resolver=backtracking --annotation-style=line \
--extra=dev --extra=infrastructure --extra=parsing \
--output-file=requirements-dev.txt \
+ --pip-args="--prefer-binary" \
requirements.txt \
pyproject.toml
diff --git a/scripts/update_helm_chart.sh b/scripts/update_helm_chart.sh
new file mode 100755
index 0000000000000000000000000000000000000000..a58bff4d03443aff3f9f5d82ed26951f75b39551
--- /dev/null
+++ b/scripts/update_helm_chart.sh
@@ -0,0 +1,10 @@
+#!/bin/sh
+
+set -e
+
+working_dir=$(pwd)
+project_dir=$(dirname $(dirname $(realpath $0)))
+
+cd $project_dir
+
+python ops/kubernetes/nomad/updatevalues.py ops/kubernetes/nomad/values.yaml