nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-07-19T06:30:19Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1408Resolve "Create archive file from ReferenceEditQuantity choosing among the ch...2023-07-19T06:30:19ZMohammad NakhaeeResolve "Create archive file from ReferenceEditQuantity choosing among the children classes of the defined type"Closes #1578Closes #1578Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1407Resolve "Keycloak client_id hardcoded in jupyterhub_config.py"2023-07-26T08:13:07ZJonas SchwabResolve "Keycloak client_id hardcoded in jupyterhub_config.py"Closes #1604Closes #1604Jonas SchwabJonas Schwabhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1406Resolve "Replace the celery-based example data usage with the ExampleData"2023-11-06T14:07:45ZAhmed IlyasResolve "Replace the celery-based example data usage with the ExampleData"Closes #1603Closes #1603Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1404small unit fix for ase atoms objects2023-07-17T09:23:23ZJames Darbysmall unit fix for ase atoms objectsCloses #1602.
As ase Atoms objects don't have attached units and expect Angstroms I think this should be the default behaviour.
@mscheidg please could you take a look at this?Closes #1602.
As ase Atoms objects don't have attached units and expect Angstroms I think this should be the default behaviour.
@mscheidg please could you take a look at this?https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1403Fixed broken links in the documentation.2023-07-12T12:21:43ZMarkus ScheidgenFixed broken links in the documentation.Changelog: FixedChangelog: Fixedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1402Changed dependency versions to increase compatibility.2023-07-12T13:00:41ZMarkus ScheidgenChanged dependency versions to increase compatibility.Changelog: ChangedChangelog: Changedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1401Added compression suport to quantum expresso mainfiles.2023-07-12T11:49:16ZMarkus ScheidgenAdded compression suport to quantum expresso mainfiles.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1399Changed the version of scikit-learn for better compatibility.2023-07-11T17:24:46ZMarkus ScheidgenChanged the version of scikit-learn for better compatibility.Changelog: ChangedChangelog: Changedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1398Documentation2023-07-11T16:45:38ZMarkus ScheidgenDocumentationhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1397Adds styling to H5web and small bug fixes in Nexus browsing2023-08-11T10:13:56ZSherjeel ShabihAdds styling to H5web and small bug fixes in Nexus browsingThis tries to get our current version of H5Web themed up to look better with Nomad.
Note: This branch can benefit from updating pynxtools submodule.This tries to get our current version of H5Web themed up to look better with Nomad.
Note: This branch can benefit from updating pynxtools submodule.Sherjeel ShabihSherjeel Shabihhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1396Added a new code contribution guide to the docs.2023-07-09T13:13:39ZMarkus ScheidgenAdded a new code contribution guide to the docs.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1395Changed xarray requirements to allow install in colab.2023-07-09T09:33:50ZMarkus ScheidgenChanged xarray requirements to allow install in colab.Changelog: ChangedChangelog: Changedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1394Fixed soap problems.2023-07-09T08:33:10ZMarkus ScheidgenFixed soap problems.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1393Added helm config options for plugins and normalize.2023-07-08T18:12:46ZMarkus ScheidgenAdded helm config options for plugins and normalize.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1391Added a soap normalizer normalizer.2023-07-08T10:01:31ZMarkus ScheidgenAdded a soap normalizer normalizer.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1390Added more learn documentation on data and schemas.2023-07-08T16:40:24ZMarkus ScheidgenAdded more learn documentation on data and schemas.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1388Integrate metrics to logtransfer2024-01-17T12:18:07ZDaniel LehmbergIntegrate metrics to logtransfer
Add a new class `Statistics` in `logtransfer.py` which is a thread process that regularly (currently daily) collects metrics/statistics and includes these into the logs from an Oasis such that they are eventually transferred to logstas...
Add a new class `Statistics` in `logtransfer.py` which is a thread process that regularly (currently daily) collects metrics/statistics and includes these into the logs from an Oasis such that they are eventually transferred to logstash on central.
The Statistics internally calls the info/ (FastAPI endpoint), collects the statistics and sends them to the logstash (proxy) server. It should be rather easy to include more statistics, e.g. queries to elastic search or mongodb).
* [x] Prefix for the statistics -- currently a "stats_" is prefixed to each entry -- would it be better to add an identifying field to the json?
* [x] Run only the Statistics service (i.e. without logstash proxy, and let this run on central -- this includes the central statistics in the same format to the ES index)
Closes #1705
Related: #886
(old issues #820 )https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1385Refactored Substance Base Sections2023-08-16T06:09:25ZHampus NaesstroemRefactored Substance Base SectionsSeparates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSect...Separates out `Substance` properties to a `SubstanceSection` class
Adds `SubstanceComponent` with `SubstanceSection` sub section
Moves `system` quantity from `Component` to inheriting `SystemComponent` class
Adds `PubChemSubstanceSection` which queries PubChem for substance information
Adds `PubChemSubstanceComponent` and `PubChemSubstance` analogous to `Substance`
Closes #1585https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1384Changed version requirements on some dependencies.2023-07-04T11:12:46ZMarkus ScheidgenChanged version requirements on some dependencies.We loosened some version requirements for key dependencies
to make it easier to install the nomad-lab pypi package.
Changelog: ChangedWe loosened some version requirements for key dependencies
to make it easier to install the nomad-lab pypi package.
Changelog: Changedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1383csv pandasResolve "problem with parsing extra_fields in elabftw parser"2023-07-07T08:32:24ZAmir Golparvarcsv pandasResolve "problem with parsing extra_fields in elabftw parser"Closes #1591Closes #1591Amir GolparvarAmir Golparvar