nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-11-21T12:46:32Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/856Resolve "Extended topology tests"2022-11-21T12:46:32ZThea DenellResolve "Extended topology tests"Closes #1077Closes #1077Thea DenellThea Denellhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/861Draft: Resolve "3rd-party ELN integration"2022-11-17T08:22:09ZMarkus ScheidgenDraft: Resolve "3rd-party ELN integration"Closes #896Closes #896Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/865Resolve "Workflow visualizer"2022-11-22T11:01:05ZAlvin Noe LadinesResolve "Workflow visualizer"Closes #1036Closes #1036https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/867Draft: Ikz eln into develop2023-12-21T08:50:16ZSebastian BruecknerDraft: Ikz eln into developUpdate ikz_eln to 1.1.5Update ikz_eln to 1.1.5Sebastian BruecknerSebastian Bruecknerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/868Draft: Resolve "Inherited subsections might break archive browser"2022-10-06T08:22:14ZMarkus ScheidgenDraft: Resolve "Inherited subsections might break archive browser"Closes #1108Closes #1108https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/876Draft: Resolve "Standard output / Log file "duplication" for Molecular Dynami...2022-10-11T12:10:00ZJoseph RudzinskiDraft: Resolve "Standard output / Log file "duplication" for Molecular Dynamics data from Gromacs"Closes #957
issue fixed by adjusting regex mainfile command for gromacsCloses #957
issue fixed by adjusting regex mainfile command for gromacsAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/883Nexus examples downloads2022-12-21T14:35:52ZMarkus ScheidgenNexus examples downloadsI replaced the downloads in `generate_example_uplods.sh` with respective downloads that are done during processing. We are about to drastically reduce the size of our images and I do not want to loose these gains immediately. This also f...I replaced the downloads in `generate_example_uplods.sh` with respective downloads that are done during processing. We are about to drastically reduce the size of our images and I do not want to loose these gains immediately. This also fixes some of the issues in the examples and triggers `.nxs` processing while processing ELNs.Sherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/896Added eln annotations to workflow2 sections.2022-12-14T08:19:23ZHampus NaesstroemAdded eln annotations to workflow2 sections.@mscheidg and @ladinesa I added eln annotations to the `Link`, `Task` and `TaskReference` sections in `nomad.datamodel.metainfo.workflow2`. I tested it together with the following yaml schema:
```yaml
definitions:
name: My custom schem...@mscheidg and @ladinesa I added eln annotations to the `Link`, `Task` and `TaskReference` sections in `nomad.datamodel.metainfo.workflow2`. I tested it together with the following yaml schema:
```yaml
definitions:
name: My custom schemas
sections:
my_workflow:
base_sections: [nomad.datamodel.metainfo.workflow2.Workflow, nomad.datamodel.data.EntryData]
```
And could create a workflow using the ELN:
![Screenshot_from_2022-10-20_16-22-26](/uploads/f15a3d8e23ea6c1e2652121855e2c636/Screenshot_from_2022-10-20_16-22-26.png)https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/899Enlarge client_max_body_size for north2023-02-17T13:56:49ZFlorian DobenerEnlarge client_max_body_size for northFor some examples we get the error `413 Request entity too large` which is related to a client_max_body_size which is too small in the nginx reverse proxy (https://github.com/jupyterlab/jupyterlab/issues/4214).
This MR sets the client_m...For some examples we get the error `413 Request entity too large` which is related to a client_max_body_size which is too small in the nginx reverse proxy (https://github.com/jupyterlab/jupyterlab/issues/4214).
This MR sets the client_max_body_size to 500mb to resolve this issue for deployments.
I'm not sure if the config change for k8s is sufficient the way I made it, since I'm not very experienced with it.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/902Resolve "Bi-directional metainfo references"2022-11-08T15:12:25ZTheodore ChangResolve "Bi-directional metainfo references"![RevisedCard](/uploads/ce8364890f036de0e2a49a0be13cf593/RevisedCard.mp4)![RevisedCard](/uploads/ce8364890f036de0e2a49a0be13cf593/RevisedCard.mp4)Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/906Draft: Resolve "Add MSD plot to overview page for MD"2022-10-26T07:38:07ZJoseph RudzinskiDraft: Resolve "Add MSD plot to overview page for MD"Closes #1144Closes #1144Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/925Draft: Added possibility to add new widgets, started adding edit dialog valia...2022-11-04T14:04:47ZMohammad NakhaeeDraft: Added possibility to add new widgets, started adding edit dialog valiation,...Added possibility to add new widgets, started adding edit dialog valiation, fixed issue with D3 plot ids.
Related #961Added possibility to add new widgets, started adding edit dialog valiation, fixed issue with D3 plot ids.
Related #961Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/926Draft: ALF parser2022-11-08T12:56:37ZJose PizarroDraft: ALF parserCloses #1155Closes #1155Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/928Draft: Resolve "Complex quantities in the metainfo"2022-11-23T20:10:48ZJose PizarroDraft: Resolve "Complex quantities in the metainfo"Closes #1126Closes #1126https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/935Draft: Resolve "FHI aims parser out of date"2022-11-09T15:38:23ZJose PizarroDraft: Resolve "FHI aims parser out of date"FHIaims regex for Fermi level now captures difference between older / newer code versions.
Closes #939FHIaims regex for Fermi level now captures difference between older / newer code versions.
Closes #939https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/940Draft: Resolve "Integrating Labfolder"2023-01-24T11:29:02ZAmir GolparvarDraft: Resolve "Integrating Labfolder"https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/947Draft: Resolve "GW metainfo and parsing for exciting and FHIaims"2022-11-14T11:01:27ZJose PizarroDraft: Resolve "GW metainfo and parsing for exciting and FHIaims"Closes #1131Closes #1131https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/953Draft: Resolve "Error in rendering ReferenceEditQuantity"2022-11-18T14:40:40ZMohammad NakhaeeDraft: Resolve "Error in rendering ReferenceEditQuantity"Closes #1149Closes #1149Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/960Improve parsing of trajectory in cpmd2022-12-07T15:56:46ZAlvin Noe LadinesImprove parsing of trajectory in cpmdCloses #1196Closes #1196https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/964Resolve "Switching to src layout"2022-12-02T09:56:18ZAdam FeketeResolve "Switching to src layout"Closes #1206
The main advantage of using src layout is that you can make sure that you are using the proper code during the test...Closes #1206
The main advantage of using src layout is that you can make sure that you are using the proper code during the test...Adam FeketeAdam Fekete