nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-02-15T10:46:35Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1095Fixes to GUI reference bugs2023-02-15T10:46:35ZMarkus ScheidgenFixes to GUI reference bugsCloses #1328Closes #1328Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1094Resolve "Overview load problem when changing between entries"2023-02-15T06:34:52ZLauri HimanenResolve "Overview load problem when changing between entries"Closes #1338Closes #1338https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1092Fixed issue with not resetting entry context data on new entry load.2023-02-14T14:08:19ZLauri HimanenFixed issue with not resetting entry context data on new entry load.Closes #1338Closes #1338https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1085Prepare next release2023-02-14T13:16:25ZMarkus ScheidgenPrepare next releaseThis contains a few minor UX things in preparation of the next release. See the individual commits for more details.
This branch is also used as a release candidate that will be deployed to the beta/staging installation.This contains a few minor UX things in preparation of the next release. See the individual commits for more details.
This branch is also used as a release candidate that will be deployed to the beta/staging installation.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1091Resolve "GUI entered information in overview is not saved"2023-02-14T20:43:10ZLauri HimanenResolve "GUI entered information in overview is not saved"Closes #1329Closes #1329https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1090Resolve "quickfix: typo in scripts/build_sdist.sh"2023-02-13T14:32:44ZAdam FeketeResolve "quickfix: typo in scripts/build_sdist.sh"Closes #1330Closes #1330Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1083Make pytest and VSCode co-operate2023-02-13T12:52:53ZAdam FeketeMake pytest and VSCode co-operateIn vscode when you run the tests you need ask pytest to hand over control to vscode's debugger
This is necessary because in a case of an exception raises pytest "consumes" it
Closes #1298In vscode when you run the tests you need ask pytest to hand over control to vscode's debugger
This is necessary because in a case of an exception raises pytest "consumes" it
Closes #1298Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1089Resolve "Wrong URL path in API helper < > in the gui?"2023-02-13T11:41:28ZJose Marquez PrietoResolve "Wrong URL path in API helper < > in the gui?"Closes #1322Closes #1322Jose Marquez PrietoJose Marquez Prietohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1073Resolve "Plot Reference to Missing SubSection Crashes GUI"2023-02-13T07:20:40ZHampus NaesstroemResolve "Plot Reference to Missing SubSection Crashes GUI"### Aim
Closes #1313
Closes #1311
This means that:
1. Non-instantiated subsections will not be plotted until they are instantiated (Bug fix)
2. The paths for plot annotations now support a python like slice operator (`start:end`) (fe...### Aim
Closes #1313
Closes #1311
This means that:
1. Non-instantiated subsections will not be plotted until they are instantiated (Bug fix)
2. The paths for plot annotations now support a python like slice operator (`start:end`) (feature)
For example:
```yaml
plot:
- x: my_middle_sections/:/my_sub_sections/-2:/x
y: my_middle_sections/:/my_sub_sections/-2:/y
```
will plot data from the last two `my_sub_sections` of all the `my_middle_sections`.
This means that passing the following data:
```yaml
data:
m_def: '#/MyTopSection'
my_middle_sections:
- name: Middle 1
my_sub_sections:
- name: Sub 1
x: [0,1]
y: [1,2]
- name: Sub 2
x: [0,0.5]
y: [1,2]
- name: Sub 3
x: [0.2,0.4]
y: [1.5,3]
- name: Middle 2
my_sub_sections:
- name: Sub 1
x: [0.5,1]
y: [3,1]
- name: Sub 2
x: [0.5,1.5]
y: [-1,2]
```
Will give the following plot:
![image](/uploads/cc4ca842f677b1d5564dbb6da937a411/image.png)
### Tasks
- [x] Add tests:
- [x] Non-instantiated SubSection
- [x] Wildcard
- [x] Legend labels
- [x] Fix bugs:
- [x] GUI crash on non-instantiated subsection #1313
- [x] Add features:
- [x] Wildcard for repeating subsections #1311
- [x] Legend labels for repeating sections
- [x] Add documentation:
- [x] Information on how to use the new features
- [x] Adding links to plotly javascript docs
- [x] ~~Potentially a link to the plot examples?~~ → Will need new issueHampus NaesstroemHampus Naesstroemhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1079Resolve "Some weird things happen when using the reference quntity"2023-02-28T15:24:00ZMohammad NakhaeeResolve "Some weird things happen when using the reference quntity"Closes #1309Closes #1309Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/957New workflow visualizer2023-02-11T00:06:53ZAlvin Noe LadinesNew workflow visualizerImplementation of visualizer following the new workflow schema.Implementation of visualizer following the new workflow schema.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1082Added temporary fallback for name and type columns.2023-02-09T16:55:44ZMarkus ScheidgenAdded temporary fallback for name and type columns.If entries are not processed with v1.1. they have no
entry name or type. This emulates entry name and type as
discussed in #1178. This is only used if there
is no entry name or type from the processing.
Chnagelog: AddedIf entries are not processed with v1.1. they have no
entry name or type. This emulates entry name and type as
discussed in #1178. This is only used if there
is no entry name or type from the processing.
Chnagelog: AddedMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1078Hotfix GW workflow method section2023-02-09T14:04:49ZJose PizarroHotfix GW workflow method sectionFixed method normalizer to get starting_point and basis_set metainfo ONLY in the GW workflow entry
Deleted starting_point metainfo from GW run.methodFixed method normalizer to get starting_point and basis_set metainfo ONLY in the GW workflow entry
Deleted starting_point metainfo from GW run.methodJose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1081Resolve "Limit the number of list entries loaded within the Data tab of the G...2023-02-09T11:39:34ZLauri HimanenResolve "Limit the number of list entries loaded within the Data tab of the GUI overview page"Closes #1011Closes #1011https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1080Added categories to the example uploads dialog.2023-02-09T06:35:25ZMarkus ScheidgenAdded categories to the example uploads dialog.Added categories to the example uploads dialog.
Also added configuration switches to include/exclude
example based on configuration.
Changelog: AddedAdded categories to the example uploads dialog.
Also added configuration switches to include/exclude
example based on configuration.
Changelog: AddedAmir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1075Improved overview UX2023-02-09T06:28:52ZLauri HimanenImproved overview UXImproved overview UX.
Closes #1312Improved overview UX.
Closes #1312Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1062Resolve "Question: example for URLEditQuantity"2023-02-06T10:21:51ZAmir GolparvarResolve "Question: example for URLEditQuantity"URLEditQuantity is missing from the annotations.
Closes #1306URLEditQuantity is missing from the annotations.
Closes #1306Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1076Implement parsing of xml output in fleur2023-02-03T09:19:49ZAlvin Noe LadinesImplement parsing of xml output in fleurAddress user request for parsing of xml outputs in fleur.Address user request for parsing of xml outputs in fleur.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1060Resolve "selected entries does not work properly"2023-02-03T09:11:15ZMohammad NakhaeeResolve "selected entries does not work properly"Closes #1283Closes #1283Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1072Adds nexus eln yaml converter2023-02-03T08:49:59ZFlorian DobenerAdds nexus eln yaml converterMaybe it's better to integrate the two functions into `ElnYamlConverter` and create this class inside `NexusDataConverter`, but I wasn't sure how to properly do this. @sshabih Do you have an idea how to do this nicely, or do you think it...Maybe it's better to integrate the two functions into `ElnYamlConverter` and create this class inside `NexusDataConverter`, but I wasn't sure how to properly do this. @sshabih Do you have an idea how to do this nicely, or do you think it's just fine as as?
Other than that I still need to test this (Tested and works ✓)