nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-28T14:17:40Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1759replaced tutorials.md w new version2024-03-28T14:17:40ZJoseph Rudzinskireplaced tutorials.md w new versionCloses #1959Closes #1959Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1751Add 'Visible for all' checkbox2024-03-28T10:43:50ZSascha KlawohnAdd 'Visible for all' checkboxSee #1948 for screenshots.
Closes #1948See #1948 for screenshots.
Closes #1948Sascha KlawohnSascha Klawohnhttps://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/1748Removed unit_system from display annotation2024-03-28T07:52:16ZLauri HimanenRemoved unit_system from display annotationCloses #1951Closes #1951Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1717Move pynxtools and plugins into parsing packages2024-03-27T17:30:38ZFlorian DobenerMove pynxtools and plugins into parsing packagesThis adds pynxtools and respective plugins to the `parsing` section of `pyproject.toml` and regenerates the requirements files with it. It also removes the nexus submodule as this is no longer needed.
This is a _hotfix_ to have the newe...This adds pynxtools and respective plugins to the `parsing` section of `pyproject.toml` and regenerates the requirements files with it. It also removes the nexus submodule as this is no longer needed.
This is a _hotfix_ to have the newest examples ready for DPG and proper pluginisation of pynxtools will be handled in !1629.
As discussed with @lukaspie @sanbrock.
ToDo:
- [x] Update `pynxtools==0.1.0`Florian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1758Fix magres parser2024-03-27T15:02:02ZJose PizarroFix magres parserHotfix from devs feedbackHotfix from devs feedbackJose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1622Resolve "Update heterogeneous catalysis app and results"2024-03-26T12:30:32ZJulia SchumannResolve "Update heterogeneous catalysis app and results"Closes #1840Closes #1840Julia SchumannJulia Schumannhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1754Resolve "root validator on FS config does not work properly"2024-03-25T17:10:46ZLauri HimanenResolve "root validator on FS config does not work properly"Closes #1949Closes #1949Lauri HimanenLauri Himanenhttps://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/1737Improving Install plugins docu2024-03-25T10:18:53ZJose PizarroImproving Install plugins docuCloses #1941
@aalbino would you mind reviewing these changes? I just wanted to improve a bit the description on how to add a plugin as a developer. I don't know whether the place for it is the best (because it is under How to > OASIS),...Closes #1941
@aalbino would you mind reviewing these changes? I just wanted to improve a bit the description on how to add a plugin as a developer. I don't know whether the place for it is the best (because it is under How to > OASIS), I just fixed the how to regarding us, developers :slight_smile:
Thanks!Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1744Added documentation for downloading files and data with curl.2024-03-22T16:42:37ZMarkus ScheidgenAdded documentation for downloading files and data with curl.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1749Resolve "h5grove app does correctly handle url encoding"2024-03-22T10:20:19ZMarkus ScheidgenResolve "h5grove app does correctly handle url encoding"Closes #1952Closes #1952https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1747Removed incorrect archive suffix default.2024-03-22T08:07:17ZLauri HimanenRemoved incorrect archive suffix default.Closes #1950Closes #1950Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1721Remove cache2024-03-21T15:05:25ZTheodore ChangRemove cacheTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1739Resolve "EditQuantities use global units instead of default units"2024-03-21T09:20:52ZLauri HimanenResolve "EditQuantities use global units instead of default units"Closes #1929Closes #1929https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1743Split fixtures from conftest2024-03-20T12:20:26ZSascha KlawohnSplit fixtures from conftestFor better management, extract fixtures from `tests/conftest.py` to appropriate files in `tests/fixtures/` and import them via `pytest_plugins`. Conftest should not directly import those modules too.
The remaining fixtures were left in ...For better management, extract fixtures from `tests/conftest.py` to appropriate files in `tests/fixtures/` and import them via `pytest_plugins`. Conftest should not directly import those modules too.
The remaining fixtures were left in conftest for now. Some might go into `fixtures/infrastructure.py`.
There are still a lot of fixtures in `fixtures/data.py`. Maybe they could be split further by type of data later.
Uploads connected to groups were moved to `fixtures/groups.py`. When groups and users have been merged, those uploads may be moved/merged together.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1742Added required parameter to post entry archive download API.2024-03-19T12:02:28ZMarkus ScheidgenAdded required parameter to post entry archive download API.Changelog: AddedChangelog: Addedhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1741Resolve "Config does not allow string loglevel like "INFO" anymore"2024-03-19T09:37:51ZMarkus ScheidgenResolve "Config does not allow string loglevel like "INFO" anymore"Closes #1944Closes #1944https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1730Add pytest options for faster local testing2024-03-18T10:05:01ZSascha KlawohnAdd pytest options for faster local testingThe `celery.inspect.().active()` broadcast used in the cleanup of fixture `worker` waits until timeout (default 1 s) is reached, which accumulates for each test with this fixture, e.g. about 14 min instead of 7 min on a laptop. Removal m...The `celery.inspect.().active()` broadcast used in the cleanup of fixture `worker` waits until timeout (default 1 s) is reached, which accumulates for each test with this fixture, e.g. about 14 min instead of 7 min on a laptop. Removal may lead to tasks still running during the next test.
This MR adds the pytest option `--celery-inspect-timeout`, which can be used to decrease the timeout for faster local testing.
It further adds the option `--fixture-filters` to run only tests that depend (directly or indirectly) on a list of fixtures and do not depend on fixtures prefixed with '!'.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1738Fixed typo.2024-03-18T08:22:16ZLauri HimanenFixed typo.Closes #1942Closes #1942Lauri HimanenLauri Himanen