nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-12-04T09:55:26Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1578Draft: Resolve "rework TabularParser"2023-12-04T09:55:26ZAmir GolparvarDraft: Resolve "rework TabularParser"Closes #1806Closes #1806Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1577Remove redundant fixtures2023-12-21T11:56:54ZSascha KlawohnRemove redundant fixturesSeveral fixtures in conftest.py are redundant. Probably due to some historic change that never got cleaned up.Several fixtures in conftest.py are redundant. Probably due to some historic change that never got cleaned up.Sascha KlawohnSascha Klawohnhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1575Fixed performance problem when deciding visibility for entries.2023-12-01T14:05:28ZMarkus ScheidgenFixed performance problem when deciding visibility for entries.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1573Remove mdtraj2024-02-14T17:20:43ZAlvin Noe LadinesRemove mdtrajAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1569added rules for phosphites2023-11-30T08:01:25ZDinga Wonankeadded rules for phosphitesAdded a rule for phosphides
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Phttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1568docs: add documentation about ruff to plugin docs2023-12-21T14:02:57ZAhmed Ilyasdocs: add documentation about ruff to plugin docshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1565Resolve "MOF rules for nitrogen bonded to two metals"2023-11-29T06:09:36ZDinga WonankeResolve "MOF rules for nitrogen bonded to two metals"Here we changed our MOF deconstructor rule to be more general in how it deconstructs nitrogen containing systems. Initially, we assumed that a nitrogen atom in the sbu bound to only one metal. However, there are MOFs wherein a nitrogen b...Here we changed our MOF deconstructor rule to be more general in how it deconstructs nitrogen containing systems. Initially, we assumed that a nitrogen atom in the sbu bound to only one metal. However, there are MOFs wherein a nitrogen binds to two different metals. Hence we decided to update our porosity normaliser to capture such systems.Dinga WonankeDinga Wonankehttps://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/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/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/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/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/1545Added tutorial example upload.2023-11-28T11:24:34ZMarkus ScheidgenAdded tutorial example upload.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1541Add timer2023-12-20T16:25:56ZTheodore ChangAdd timerTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1540Small fixes2023-11-07T23:37:13ZTheodore ChangSmall fixesTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1535Provide possibility to return msection from xpath2023-11-03T11:07:13ZAlvin Noe LadinesProvide possibility to return msection from xpathAlvin Noe LadinesAlvin Noe Ladines