nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2022-11-08T15:12:25Zhttps://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ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/935Draft: Resolve "FHI aims parser out of date"2022-11-09T15:38:23ZJose PizarroDraft: Resolve "FHI aims parser out of date"FHIaims regex for Fermi level now captures difference between older / newer code versions.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/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/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/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/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/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/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/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 Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/965Draft: Resolve "Building docs independently from the python package"2022-12-02T23:21:52ZAdam FeketeDraft: Resolve "Building docs independently from the python package"Closes #1207
The "compiled" documentation should not be part of the python source distribution.
Reasoning:
- we need the nomad package to build the documentation which actually should also contain the documentation... Currently the onl...Closes #1207
The "compiled" documentation should not be part of the python source distribution.
Reasoning:
- we need the nomad package to build the documentation which actually should also contain the documentation... Currently the only way to build the python sdist by building it twice.
- most of the other links on the gui are also pointing to external link
- it is more just a decimation of the usage of the gui...
- the link of the logo of the documentation redirect to a another page (central deployment) and not to the one where it was actually deployed.https://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/973Small ui fixes2022-12-08T06:46:14ZMarkus ScheidgenSmall ui fixeshttps://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/993generalization of md workflow2022-12-19T12:18:37ZJoseph Rudzinskigeneralization of md workflowfinished gromacs normalized workflow test, some system/method parsing info for lammps fixed, tests still fail
Closes #1199finished gromacs normalized workflow test, some system/method parsing info for lammps fixed, tests still fail
Closes #1199https://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/630Draft: Merge a collection of north and eln related contributions2022-12-21T14:36:11ZMarkus ScheidgenDraft: Merge a collection of north and eln related contributionshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/828Draft: Bring in latest Nexus features and corresponding ELNs2022-12-21T14:50:26ZSherjeel ShabihDraft: Bring in latest Nexus features and corresponding ELNsThis still does not have the IV_temp example. But I have tested it to work in a new nomad install.
TODOs:
- [ ] MPES container doesn't launch
- [x] Add IV temp example
- [x] Resolve dependency issues
- [ ] Make sure nexusparser function...This still does not have the IV_temp example. But I have tested it to work in a new nomad install.
TODOs:
- [ ] MPES container doesn't launch
- [x] Add IV temp example
- [x] Resolve dependency issues
- [ ] Make sure nexusparser functionality works on commit deployment
- [ ] Review by @kuehbachm
- [x] Review by @dflor
- [ ] Review by @ecaro
- [x] Update submodule for nomad-remote-tools
- [x] Update submodule for nomad-parser-nexus
- [x] Make issue for MetainfoError: Cannot serialize float64 quantitySherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1022Draft: Resolve "Matching parsers based on h5 (or similar) outputs"2023-01-05T16:36:15ZAlvin Noe LadinesDraft: Resolve "Matching parsers based on h5 (or similar) outputs"Closes #1268Closes #1268Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1012Draft: Fixed issues in the Formula class, added tests, improved the descripti...2023-01-12T13:46:12ZLauri HimanenDraft: Fixed issues in the Formula class, added tests, improved the description of formulas.Closes #1259Closes #1259https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/967Draft: Resolve "Updating electronic-parsers and fixing tests"2023-01-13T23:16:48ZAdam FeketeDraft: Resolve "Updating electronic-parsers and fixing tests"Closes #1208
- [x] update to latest version of electornic-parser
- [x] fix the previously bypassed tests
failing cases:
- [x] tests/parsing/test_parsing.py::test_parser[parsers/siesta-tests/data/parsers/siesta/Fe/out] FAILED
- [x] tes...Closes #1208
- [x] update to latest version of electornic-parser
- [x] fix the previously bypassed tests
failing cases:
- [x] tests/parsing/test_parsing.py::test_parser[parsers/siesta-tests/data/parsers/siesta/Fe/out] FAILED
- [x] tests/parsing/test_parsing.py::test_parser[parser/fleur-tests/data/parsers/fleur/out] FAILED
- [x] tests/parsing/test_parsing.py::test_match FAILED - this is easy to fix this
test cases with errors:
- [x] tests/normalizing/test_dos.py::test_dos_magnitude ERROR
- [x] tests/normalizing/test_system.py::test_normalizer[parsers/siesta-tests/data/parsers/siesta/Fe/out] ERROR
- [x] tests/normalizing/test_system.py::test_normalizer[parser/fleur-tests/data/parsers/fleur/out] ERROR