nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-03-03T09:50:09Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1126Resolve "Hyperlink to entry in scatter plot widget and hover details"2023-03-03T09:50:09ZJose Marquez PrietoResolve "Hyperlink to entry in scatter plot widget and hover details"Closes #1364Closes #1364Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1125Upgrade python version2023-03-07T08:23:58ZMarkus ScheidgenUpgrade python versionUpgraded nomad-lab to Python 3.9 and bumped a few dependency version.
Changelog: Changed
- updated to python 3.9
- only bumped what was necessary in this first step
- add a mypy.ini to remove longer and longer arg-based config from pyl...Upgraded nomad-lab to Python 3.9 and bumped a few dependency version.
Changelog: Changed
- updated to python 3.9
- only bumped what was necessary in this first step
- add a mypy.ini to remove longer and longer arg-based config from pylint calls
- some minor code fixes due to new version of mypy and pylint
With 3.9, i mean that we now build and run with 3.9. The min required is only 3.8. I guess, we could go even higher, if this is successful.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1123Check existance of `m_proxy_value` for references.2023-02-28T13:24:51ZTheodore ChangCheck existance of `m_proxy_value` for references.Check existance of `m_proxy_value` for references as the criterion.
Use existance of `m_proxy_value` as the criterion of reference detection. Proxies will be automatically resolved which changes its type.
Changelog: Fixed
Closes #1365Check existance of `m_proxy_value` for references as the criterion.
Use existance of `m_proxy_value` as the criterion of reference detection. Proxies will be automatically resolved which changes its type.
Changelog: Fixed
Closes #1365Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1122Running linters and type checks in the background in vscode2023-03-10T00:07:29ZAdam FeketeRunning linters and type checks in the background in vscodeCloses #1356
Vscode using [specific precedence](https://code.visualstudio.com/docs/getstarted/settings#_settings-precedence) to load setting.
In short: the workspace setting overrides the user's settings.
Solution:
- remove setting...Closes #1356
Vscode using [specific precedence](https://code.visualstudio.com/docs/getstarted/settings#_settings-precedence) to load setting.
In short: the workspace setting overrides the user's settings.
Solution:
- remove settings which related to enabling test to run any time when a file has been saved/modified (this could create high load and shorter battery time).
- add a few lines to the documentation to encourage individual users to turn it on in their users settings because at the end it is a good practice to do contiuons testing...Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1121Minor fix workflow visualizer2023-02-27T15:56:53ZAlvin Noe LadinesMinor fix workflow visualizerAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1120Resolve "Add GUI Annotation Examples to Documentation"2023-03-13T09:55:08ZMohammad NakhaeeResolve "Add GUI Annotation Examples to Documentation"Closes #1335Closes #1335Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1118Minor workflow visualizer fix2023-02-25T20:51:20ZAlvin Noe LadinesMinor workflow visualizer fixFix link in workflow visualizerFix link in workflow visualizerAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1116Resolve "Tabular parser - using column and row modes together only works for ...2023-03-13T13:41:43ZAmir GolparvarResolve "Tabular parser - using column and row modes together only works for children repeated sections"The top most section that inherits from TableData enforces that all the subsequent subsections should retain the same mode of operation as the top most section. For example, when top most section is annotated with column mode, then all s...The top most section that inherits from TableData enforces that all the subsequent subsections should retain the same mode of operation as the top most section. For example, when top most section is annotated with column mode, then all sub-sections should be annotated with column mode as well. This causes some limitations when implementing a mixed mode in an ELN YAML/JSON file.
Closes #1354Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1115Fixed issue with displaying band structures and brillouin zone for entries wi...2023-02-24T08:42:42ZLauri HimanenFixed issue with displaying band structures and brillouin zone for entries with missing reciprocal cell.Fixed issue with displaying band structures and Brillouin zone for entries that are missing the reciprocal cell.
Closes #1246Fixed issue with displaying band structures and Brillouin zone for entries that are missing the reciprocal cell.
Closes #1246Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1114Resolve "North fiji tool crashing at stratup"2023-02-23T11:08:03ZAdam FeketeResolve "North fiji tool crashing at stratup"Closes #1358Closes #1358Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1113Workflow fix2023-02-22T20:37:23ZAlvin Noe LadinesWorkflow fixImplement various small fixes and improvements to the workflow visualizerImplement various small fixes and improvements to the workflow visualizerAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1110Add Feature for Plotting Scalar Values in XYPlot2023-02-23T06:45:34ZHampus NaesstroemAdd Feature for Plotting Scalar Values in XYPlotAdded feature for plotting scalars from repeating subsections
Closes #1333
The following yaml:
```yaml
definitions:
name: My Plot Test
sections:
MySection:
base_section: nomad.datamodel.data.ArchiveSection
quantiti...Added feature for plotting scalars from repeating subsections
Closes #1333
The following yaml:
```yaml
definitions:
name: My Plot Test
sections:
MySection:
base_section: nomad.datamodel.data.ArchiveSection
quantities:
x_value:
type: int
y_value:
type: int
y2_value:
type: int
MyTopSection:
base_section: nomad.datamodel.data.EntryData
m_annotations:
plot:
- label: My values
x: my_sections/:/x_value
y:
- my_sections/:/y_value
- my_sections/:/y2_value
sub_sections:
my_sections:
section: MySection
repeats: True
data:
m_def: MyTopSection
my_sections:
- x_value: 1
y_value: -1
y2_value: -5
- x_value: 2
y_value: -2
y2_value: -4
- x_value: 3
y_value: -3
y2_value: -3
- x_value: 4
y_value: -4
y2_value: -2
- x_value: 5
y_value: -5
y2_value: -1
```
No gives the following plot:
![image](/uploads/aada2a647b300ca9625d0cbbf6d1bddc/image.png)Hampus NaesstroemHampus Naesstroemhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1109Small fixes to prepare for the production deployment.2023-03-01T06:31:36ZMarkus ScheidgenSmall fixes to prepare for the production deployment.There is still a couple of issues that need to be adressed before publishing v1.1.7 to the production deployment of nomad.
- [x] The k8s value for north.enabled is not working.
- [x] There should be error handling in the app start to de...There is still a couple of issues that need to be adressed before publishing v1.1.7 to the production deployment of nomad.
- [x] The k8s value for north.enabled is not working.
- [x] There should be error handling in the app start to deal with breaking changes in `env.js`. Otherwise, users are stuck with old implementations in the service worker.
- [x] #1095Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1108BSE and Core-hole methods, Spectra metainfo and [exciting, OCEAN, Quantum Esp...2023-03-13T04:01:39ZJose PizarroBSE and Core-hole methods, Spectra metainfo and [exciting, OCEAN, Quantum Espresso XSpectra]First set of tasks in #1316First set of tasks in #1316Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1106Adjust asap parser matching spec2023-02-21T12:59:36ZAlvin Noe LadinesAdjust asap parser matching specCloses #1348Closes #1348Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1105Resolve ".volumes folder structure is missing from nomad-oasis.zip"2023-02-21T12:53:14ZAdam FeketeResolve ".volumes folder structure is missing from nomad-oasis.zip"Closes #1350Closes #1350Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1104Resolve "Pydantic models for UI config."2023-02-27T14:06:50ZLauri HimanenResolve "Pydantic models for UI config."Closes #1257, #1334.Closes #1257, #1334.Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1103Resolve "NORTH: the updated tool image has not been updated on the deployment"2023-02-21T12:53:55ZAdam FeketeResolve "NORTH: the updated tool image has not been updated on the deployment"Closes #1347Closes #1347Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1102Fixed issue with retrieving entry_id from older entries.2023-02-17T11:22:40ZLauri HimanenFixed issue with retrieving entry_id from older entries.Closes #1344Closes #1344https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1101Resolve "Add Feature for Creating Workflow in ELN"2023-03-05T16:29:59ZHampus NaesstroemResolve "Add Feature for Creating Workflow in ELN"Closes #1346Closes #1346