nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-02-27T09:39:41Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1683Add *.json/*.yaml config files for pynxtools readers2024-02-27T09:39:41ZFlorian DobenerAdd *.json/*.yaml config files for pynxtools readersSome readers have *.json files for configuration. This adds them to nomads `MANIFEST.in` so they are copied into the package.Some readers have *.json files for configuration. This adds them to nomads `MANIFEST.in` so they are copied into the package.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1646Resolve "Config option to disable optimade API."2024-02-26T11:46:23ZMarkus ScheidgenResolve "Config option to disable optimade API."Closes #1866Closes #1866https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1597Resolve "Defaul global unit system"2024-02-26T10:22:56ZMohammad NakhaeeResolve "Defaul global unit system"Closes #1666Closes #1666Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1684Resolve "Rendering of SubSection names in Gui"2024-03-04T15:56:57ZMohammad NakhaeeResolve "Rendering of SubSection names in Gui"Closes #1829Closes #1829Mohammad NakhaeeMohammad Nakhaeehttps://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/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/1638Adds Nomad's structlog logger to nexus dataconverter2024-02-22T15:06:45ZSherjeel ShabihAdds Nomad's structlog logger to nexus dataconverterSherjeel ShabihSherjeel Shabihhttps://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/1680Ensure RFC3161 server is reachable2024-02-21T18:53:59ZTheodore ChangEnsure RFC3161 server is reachableTheodore ChangTheodore Changhttps://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/1626added example function to calc summed mass from comp model2024-02-15T15:59:34ZJoseph Rudzinskiadded example function to calc summed mass from comp modelCloses #1844
@himanel1 I need your advice here. I created a mock function in atom_utils `get_summed_atomic_mass_from_computational_model` as a demonstration of how we should try to calculate the mass_density, maybe by default, but defi...Closes #1844
@himanel1 I need your advice here. I created a mock function in atom_utils `get_summed_atomic_mass_from_computational_model` as a demonstration of how we should try to calculate the mass_density, maybe by default, but definitely in the case where the atom types are unknown. However, I am not sure about the best way to implement this: I need access to the archive to grab the masses from the `atom_parameters` section, but in the topology normalizer, we currently don't have access to this at the point where we are calculating the cell.Joseph 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/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/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/1628Resolve "Converter for json to and from pd dataframe"2024-02-29T10:43:49ZAmir GolparvarResolve "Converter for json to and from pd dataframe"- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849Amir GolparvarAmir Golparvarhttps://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/1573Remove mdtraj2024-02-14T17:20:43ZAlvin Noe LadinesRemove mdtrajAlvin 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/1667Fixed broken links and typos.2024-02-13T11:45:26ZLauri HimanenFixed broken links and typos.Closes #1890Closes #1890Lauri HimanenLauri Himanen