nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-28T09:19:32Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1016Resolve "Add a automatically generated changelog to our git"2024-03-28T09:19:32ZMarkus ScheidgenResolve "Add a automatically generated changelog to our git"This adds automatically updated CHANGELOG.md to the project. The mechanism uses GitLabs build in [changelog mechanism](https://docs.gitlab.com/ee/api/repositories.html#add-changelog-data-to-a-changelog-file) and is triggered when a relea...This adds automatically updated CHANGELOG.md to the project. The mechanism uses GitLabs build in [changelog mechanism](https://docs.gitlab.com/ee/api/repositories.html#add-changelog-data-to-a-changelog-file) and is triggered when a release tag is added to git.
We have an automatically generated changelog in the repository file `CHANGELOG.md`.
This changelog is produced from commit messages and to maintain this file, you
need to write commit messages accordingly.
To trigger a changelog entry, your commit needs to end with a so called *git trailer*
called `Changelog`. A typical commit message for a changelog entry should look like this:
```
A brief one line title of the change.
A longer *markdown* formatted description of the change. Keep in mind that gitlab
will automatically link the changelog entry with this commit and a respective merge
requests. You do not need to manually link to any gitlab resources.
This could span multiple paragraphs. However, keep it short. Documentation should
go into the actual documentation, but you should mention breaks in backward compatibility,
deprecation of features, etc.
Changelog: Fixed
```
The trailer value (`Fixed` in the example) has to be one of the following values:
- `Fixed`, for bugfixes.
- `Added`, for new features.
- `Changed`, for general improvements, e.g. updated documentation, refactoring,
improving performance, etc.
These categories are consistent with (keepachangelog.com)[https://keepachangelog.com/].
For more information about the changelog generation read the [gitlab documentation](https://docs.gitlab.com/ee/api/repositories.html#add-changelog-data-to-a-changelog-file).
Closes #1223https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1750Added support for topologies with multiple roots and no atomic structure.2024-03-25T11:57:35ZLauri HimanenAdded support for topologies with multiple roots and no atomic structure.Closes #1953Closes #1953https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1733Resolve "add reference to elabftw parser"2024-03-15T00:49:13ZAmir GolparvarResolve "add reference to elabftw parser"Closes #1937Closes #1937Amir GolparvarAmir Golparvarhttps://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/1625Resolve "Attribute inheritance"2024-02-29T11:46:43ZMarkus ScheidgenResolve "Attribute inheritance"Closes #1845Closes #1845Markus ScheidgenMarkus Scheidgenhttps://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/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/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/1649Add coauthor, reviewer groups2024-01-29T13:47:24ZSascha KlawohnAdd coauthor, reviewer groups- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760- Add user groups, API `/groups`
- Add coauthor, reviewer groups
- Add writer, viewer groups
- Add groups to ES owner query
- Add tests for groups, uploads, search
Closes #1760Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1615Improved search bar2024-01-15T09:59:05ZLauri HimanenImproved search barCloses #1790, #1700Closes #1790, #1700Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1553Add computational core-hole metadata2023-12-20T06:12:10ZNathan DaelmanAdd computational core-hole metadataAdd `CoreHole` under `AtomParameters`, but with an interface to `AtomsGroup` and by extension topology.Add `CoreHole` under `AtomParameters`, but with an interface to `AtomsGroup` and by extension topology.Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1543Resolve "OpenBIS Integration"2023-12-07T09:17:36ZAmir GolparvarResolve "OpenBIS Integration"Closes #1768Closes #1768Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1576Added wrap mode option to the API endpoint for retrieving system geometries.2023-12-04T08:10:24ZLauri HimanenAdded wrap mode option to the API endpoint for retrieving system geometries.Closes #1804Closes #1804Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1542Resolve "Unit selection component"2023-12-01T06:01:20ZLauri HimanenResolve "Unit selection component"Closes #1758, #960Closes #1758, #960Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1285Resolve "Add Tight Binding Studio parser"2023-11-20T11:31:52ZMohammad NakhaeeResolve "Add Tight Binding Studio parser"Closes #1251Closes #1251Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1510Resolve "Search interface improvements"2023-11-01T06:55:21ZLauri HimanenResolve "Search interface improvements"Closes #1740Closes #1740Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1449New DOS schema2023-10-31T09:36:36ZJose PizarroNew DOS schemaAdded a new dos_electronic schema in run and results.Added a new dos_electronic schema in run and results.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1502Resolve "Workflow for chemical reaction steps"2023-10-23T16:51:59ZAlvin Noe LadinesResolve "Workflow for chemical reaction steps"Closes #1430Closes #1430Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1378Resolve "Plot support refactor"2023-10-17T14:37:35ZMohammad NakhaeeResolve "Plot support refactor"Closes #1554Closes #1554Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1482Exposed upload_name in the search, added suggestions for upload_name.2023-10-03T05:34:16ZLauri HimanenExposed upload_name in the search, added suggestions for upload_name.Closes #1708Closes #1708Lauri HimanenLauri Himanen