nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-11T14:04:41Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1719Draft: bump dependencies for pandas and scipy2024-03-11T14:04:41ZAhmed IlyasDraft: bump dependencies for pandas and scipyAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1718Documentation: Tiny improvement and typo fix2024-03-11T13:14:18ZFabian SchöppachDocumentation: Tiny improvement and typo fixhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1704Draft: Full refactoring of `run` into `data`2024-03-11T12:30:43ZJose PizarroDraft: Full refactoring of `run` into `data`We need to keep track of the changes in files somewhere.
Closes #1728We need to keep track of the changes in files somewhere.
Closes #1728https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1713Fixes from review comments2024-03-11T08:07:21ZAlvin Noe LadinesFixes from review commentsSome fixes to address @jrudz review.Some fixes to address @jrudz review.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1692Changed config to use the new archive writer by default.2024-03-09T03:03:52ZMarkus ScheidgenChanged config to use the new archive writer by default.Changelog: AddedChangelog: AddedMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1629Draft: Pynxtools as dependency2024-03-08T09:07:45ZFlorian DobenerDraft: Pynxtools as dependencyThis PR remoevs pynxtools (aka nexus parser) as a submodule and adds it as a python dependency to `pyproject.toml`.This PR remoevs pynxtools (aka nexus parser) as a submodule and adds it as a python dependency to `pyproject.toml`.Florian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1701Implement a rate limit in archive query2024-03-07T14:39:06ZTheodore ChangImplement a rate limit in archive queryTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1712copy local path to temp directory2024-03-07T12:54:20ZAhmed Ilyascopy local path to temp directoryIf a local path is provided, copy it to a temp dir before importing. Otherwise when the upload is deleted, the original local path file ends up getting deleted too.If a local path is provided, copy it to a temp dir before importing. Otherwise when the upload is deleted, the original local path file ends up getting deleted too.Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1695Resolve "conversion of ArchiveQuery to dataframe works only for the last call...2024-03-07T12:40:21ZAmir GolparvarResolve "conversion of ArchiveQuery to dataframe works only for the last call of the downloaded entries"Closes #1909Closes #1909Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1708Resolve "Reloading link bugs out"2024-03-07T10:07:30ZLauri HimanenResolve "Reloading link bugs out"Closes #1918Closes #1918Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1711Add raw_path_exists method to ClientContext2024-03-06T14:23:57ZSarthak KapoorAdd raw_path_exists method to ClientContext`nomad.datamodel.Context` has a `raw_path_exists` method which needs to implemented in it's child classes. But this implementation is missing in one of the child classes `ClientContext`. The current MR fixes it.
_Why is this needed?_ Wh...`nomad.datamodel.Context` has a `raw_path_exists` method which needs to implemented in it's child classes. But this implementation is missing in one of the child classes `ClientContext`. The current MR fixes it.
_Why is this needed?_ When testing a schema class locally using pytest, the context associated with the archive is of class `ClientContext`. If the schema uses `archive.m_context.raw_path_exists(filepath)` in normalize, the test fails as the method is not implemented.Sarthak KapoorSarthak Kapoorhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1709updated submodules and gui artifacts2024-03-05T14:30:33ZJoseph Rudzinskiupdated submodules and gui artifactsCloses #1921Closes #1921Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1707Resolve "CP2K parser failure"2024-03-05T11:52:22ZNathan DaelmanResolve "CP2K parser failure"- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1705Draft: Resolve "CP2K parser failure"2024-03-05T11:19:33ZNathan DaelmanDraft: Resolve "CP2K parser failure"- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919- Update `CP2K` parser with header patch
- Update `Phonopy` parser with non-canonical hexagonal cell patch
Closes #1919Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1703Reverted automated re-lableing of sub sections in archive browser and ELN.2024-03-04T16:33:41ZMarkus ScheidgenReverted automated re-lableing of sub sections in archive browser and ELN.https://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/1702Resolve "errors in the gui whenquantitities are of type=np.float64 and no uni...2024-03-04T15:04:11ZMarkus ScheidgenResolve "errors in the gui whenquantitities are of type=np.float64 and no unit given"Closes #1913Closes #1913https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1694Resolve "ArchiveQuery sends to many requests."2024-03-04T13:01:35ZTheodore ChangResolve "ArchiveQuery sends to many requests."Closes #1905Closes #1905Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1689saving and loading nexus schema instead of building it from NXDL to save abou...2024-03-01T17:42:48ZSandor Brockhausersaving and loading nexus schema instead of building it from NXDL to save about 50%https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1698WIP2024-03-01T15:15:12ZMarkus ScheidgenWIP