nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-02-23T10:24:47Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1679Added a publish command and util deployment.2024-02-23T10:24:47ZMarkus ScheidgenAdded a publish command and util deployment.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1678Resolve "Scatter plots with multiple values per entry"2024-02-27T15:46:39ZLauri HimanenResolve "Scatter plots with multiple values per entry"Closes #1732Closes #1732Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1677Resolve "Upgrade the NORTH Jupyterhub"2024-03-13T15:40:53ZMarkus ScheidgenResolve "Upgrade the NORTH Jupyterhub"Closes #1897
Closes #1843Closes #1897
Closes #1843Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1676Resolve "Packages aliases in metainfo"2024-03-01T11:03:53ZMarkus ScheidgenResolve "Packages aliases in metainfo"This MR uses the `alias` property on `Package` definitions, e.g.
```python
m_package = Package(aliases=['some.other.python.package.name'])
class MySection(MSection):
...
m_package.__init__metainfo__()
```
I checked that you can now:
...This MR uses the `alias` property on `Package` definitions, e.g.
```python
m_package = Package(aliases=['some.other.python.package.name'])
class MySection(MSection):
...
m_package.__init__metainfo__()
```
I checked that you can now:
- [x] process an `.archive.json` file with an `"m_def": "some.other.python.package.name.MySection"` in it.
- [x] you can reprocess an entry that was previously processed and has an `"m_def": "some.other.python.package.name.MySection"` in the archive.
- [x] the gui shows the data for an entry with `"m_def": "some.other.python.package.name.MySection"` in it.
This should cover most cases when refactoring package names:
- using the ArchiveQuery on old data (or instantiating it otherwise)
- showing old data in the gui
There are use cases were this does not work:
- querying with for a python based section definition name as a search criteria
!!! This is only for refactoring python package names. This is not about changing sub-section names. This will require another MR.
!!! This also only works for packages that are known and loaded in the backend. Therefore, this only works for python packages in nomad-lab or plugins. It does not work for any uploaded ".yaml" schemas.
Closes #1886Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1675Added a simple locust load test script.2024-02-23T10:52:54ZMarkus ScheidgenAdded a simple locust load test script.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1674Remove CAS image after test2024-03-01T12:04:41ZSascha KlawohnRemove CAS image after testThe test `tests/datamodel/metainfo/eln/test_system.py::test_substance` left an SVG file (`cas_10101-63-0_image.svg`) after processing.
This MR removes the image at the end of the test, thereby also checking if it existed.The test `tests/datamodel/metainfo/eln/test_system.py::test_substance` left an SVG file (`cas_10101-63-0_image.svg`) after processing.
This MR removes the image at the end of the test, thereby also checking if it existed.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1673Fixed outdated gui test artifacts.2024-02-15T15:05:59ZMarkus ScheidgenFixed outdated gui test artifacts.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1672Add deprecation note on old run schema2024-02-15T08:56:10ZAlvin Noe LadinesAdd deprecation note on old run schemaAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1671Add `nexus-version.txt` to MANIFEST.in2024-02-14T18:43:37ZFlorian DobenerAdd `nexus-version.txt` to MANIFEST.inThe `nexus-version.txt` needs to be included to retrieve the nexus version in pynxtools.The `nexus-version.txt` needs to be included to retrieve the nexus version in pynxtools.Florian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1670Initial reorganization of parser docs2024-02-16T12:06:50ZAlvin Noe LadinesInitial reorganization of parser docsGeneralize nomad parser docs.Generalize nomad parser docs.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1669Transfer area c plugin docs2024-02-13T14:04:30ZJoseph RudzinskiTransfer area c plugin docsJoseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1668Resolve "Bug in extract_orbital TopologyNormalizer"2024-02-27T14:31:22ZNathan DaelmanResolve "Bug in extract_orbital TopologyNormalizer"Closes #1891Closes #1891Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1667Fixed broken links and typos.2024-02-13T11:45:26ZLauri HimanenFixed broken links and typos.Closes #1890Closes #1890Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1665Use runschema def for archive section run2024-02-15T13:59:36ZAlvin Noe LadinesUse runschema def for archive section runFix error in loading archive as a result of not explicitly defining archive section run using the new schema.Fix error in loading archive as a result of not explicitly defining archive section run using the new schema.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1664fixed active orbital error2024-02-09T12:35:36ZJoseph Rudzinskifixed active orbital errorCloses #1884
@ndaelman this may not be the most elegant solution (please make another suggestion if you'd like), but the old code/check:
```
active_orbitals_run = [
param.core_hole for param in atom_params if hasa...Closes #1884
@ndaelman this may not be the most elegant solution (please make another suggestion if you'd like), but the old code/check:
```
active_orbitals_run = [
param.core_hole for param in atom_params if hasattr(param, 'core_hole')
]
```
returns a list of None's in every case and always throws an errorJoseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1662Resolve "plotly config dictionary can't be fed in from normalize function"2024-02-22T13:00:07ZMohammad NakhaeeResolve "plotly config dictionary can't be fed in from normalize function"Closes #1857Closes #1857Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1661Do not lazy load schema plugin2024-02-08T10:46:03ZAlvin Noe LadinesDo not lazy load schema pluginIndeed the problem was caused by lazy loading the schemas. Disabled it now.Indeed the problem was caused by lazy loading the schemas. Disabled it now.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1660Resolve "Remove Perovskite Solar Cell Database Files"2024-02-09T15:01:06ZYaru WangResolve "Remove Perovskite Solar Cell Database Files"Closes #1870Closes #1870https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1659Fixed CP2K2024-02-06T12:30:54ZJose PizarroFixed CP2KCloses #1879Closes #1879Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1658Update parser ref2024-02-05T16:41:11ZAlvin Noe LadinesUpdate parser refAlvin Noe LadinesAlvin Noe Ladines