nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-11-28T12:54:04Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1564Fixed ferrocene deconstructor and added other deconstructing rules2023-11-28T12:54:04ZDinga WonankeFixed ferrocene deconstructor and added other deconstructing rulesWe added some new rules to make the porosity normaliser to become more robust in its deconstruction procedure. The following changes were included.
1. We added new changes to better deconstruct system containing ferrocene. we discovered ...We added some new rules to make the porosity normaliser to become more robust in its deconstruction procedure. The following changes were included.
1. We added new changes to better deconstruct system containing ferrocene. we discovered that although ferrocene is contains a metal, it is still and organic ligand consequently ferrocene building units will now be classed under organic sbu and organic ligand.
2. We also added a rule to deconstruct -COS systems. Initially the we deconstructed only from the metal-Sulphur bonds for such systems. Ideally, we need to break at the metal-carbon bonds for the sbus. So we have now fixed this.
3. Finally the deconstructor was not robust for systems containing metal-O-R-CO2-metal. We have not fixed this.Dinga WonankeDinga Wonankehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1563Add kmc method name2023-12-14T11:33:38ZNathan DaelmanAdd kmc method nameAdd `kMC` to the `results.method.method_name` enumeration, as a response to a user's request over at the [MatSci forum](https://matsci.org/t/adding-kmc-to-available-methods/52074).Add `kMC` to the `results.method.method_name` enumeration, as a response to a user's request over at the [MatSci forum](https://matsci.org/t/adding-kmc-to-available-methods/52074).Nathan DaelmanNathan Daelmanhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1562Added ignore_above config by default for all keyword fields.2023-11-29T12:05:15ZLauri HimanenAdded ignore_above config by default for all keyword fields.Closes #1787Closes #1787Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1561Resolve "Nexus search prototype"2023-12-05T07:25:41ZLauri HimanenResolve "Nexus search prototype"Closes #1776Closes #1776Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1560Fixed embedded youtube videos.2023-11-21T17:15:25ZMarkus ScheidgenFixed embedded youtube videos.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1559Draft: Resolve "Setting ReferenceEditQuantity to None in normalie"2023-11-21T15:40:30ZMohammad NakhaeeDraft: Resolve "Setting ReferenceEditQuantity to None in normalie"Closes #1707Closes #1707https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1558Resolve "Setting ReferenceEditQuantity to None in normalie"2023-11-27T12:24:43ZMohammad NakhaeeResolve "Setting ReferenceEditQuantity to None in normalie"Closes #1707Closes #1707Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1557Resolve "New entries in tabular parser should be picked up from label_quantity"2023-12-04T09:08:22ZAmir GolparvarResolve "New entries in tabular parser should be picked up from label_quantity"Closes #1786Closes #1786Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1556Quickfix TB merge2023-11-20T14:51:48ZJose PizarroQuickfix TB mergeQuick fix on the DMFT workflows in the electronic parsers.Quick fix on the DMFT workflows in the electronic parsers.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1555Enabled MOF app, fixed issue in MOF app layout, added MOF data to the tests.2023-11-20T11:10:25ZLauri HimanenEnabled MOF app, fixed issue in MOF app layout, added MOF data to the tests.Closes #1783Closes #1783https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1554move linting to the build stage2023-12-20T10:36:55ZAhmed Ilyasmove linting to the build stageAhmed IlyasAhmed Ilyashttps://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/1552Fixed issue with infinite recursion, added tests for recursive schema values.2023-11-15T12:19:50ZLauri HimanenFixed issue with infinite recursion, added tests for recursive schema values.Closes #1771Closes #1771Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1551Draft: Resolve "Representing notebooks as custom ELN schema"2024-02-22T08:29:54ZAdam FeketeDraft: Resolve "Representing notebooks as custom ELN schema"Closes #1549
Implementing notebook interface as a python schema.
Plan:
- create a separate repo for the plugins (separate the notebook schema from the ai-toolkit) like nomad-app-aitoolkit and nomad-app-notebooks
- add them to dependenci...Closes #1549
Implementing notebook interface as a python schema.
Plan:
- create a separate repo for the plugins (separate the notebook schema from the ai-toolkit) like nomad-app-aitoolkit and nomad-app-notebooks
- add them to dependencies as a submodule (I think this is mandatory for making sure it works.)
- the plugin will not be included into the python package but it will be integrated into the image by some Dockerfile magic
- create a custom nomad.yaml file for our different deployments (prod, staging, dev) which includes all the app configsAdam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1550Add pyflake and pyupgrade lints to ruff2023-11-23T09:24:29ZAhmed IlyasAdd pyflake and pyupgrade lints to ruff- Adds pyflakes and pyupgrade linting to ruff
- Pyflakes analyzes programs and detects various errors
- Pyupgrade: Modernizes Python code with new features and idioms.
The diff is very big but the changes are very trivial. (A lot of D...- Adds pyflakes and pyupgrade linting to ruff
- Pyflakes analyzes programs and detects various errors
- Pyupgrade: Modernizes Python code with new features and idioms.
The diff is very big but the changes are very trivial. (A lot of Dict -> dict and so on)Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1549Updates north submodule2024-01-31T08:11:47ZFlorian DobenerUpdates north submoduleThere was a problem with the example files download, because zenodo changed it's url from `.../record/` to `.../records/` which failed for curl, because it could not follow the redirect.There was a problem with the example files download, because zenodo changed it's url from `.../record/` to `.../records/` which failed for curl, because it could not follow the redirect.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1548Resolve "Python version in setup docs"2023-11-10T10:41:17ZSarthak KapoorResolve "Python version in setup docs"Closes #1777Closes #1777Sarthak KapoorSarthak Kapoorhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1547Add additional ruff check to print linting errors to console2023-11-09T14:30:07ZAhmed IlyasAdd additional ruff check to print linting errors to consoleThis MR adds an additional ruff check to the CI. Ruff is very fast so another 50ms doesn't harm us.
This way we will maintain the old behavior of having the linting errors in the console output in the linting pipeline in addition to ha...This MR adds an additional ruff check to the CI. Ruff is very fast so another 50ms doesn't harm us.
This way we will maintain the old behavior of having the linting errors in the console output in the linting pipeline in addition to having a Code Quality report in merge requests.Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1546Fixed issue with hashtag not being included in query string.2023-11-09T09:02:15ZLauri HimanenFixed issue with hashtag not being included in query string.Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1545Added tutorial example upload.2023-11-28T11:24:34ZMarkus ScheidgenAdded tutorial example upload.