nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-11-20T11:10:25Zhttps://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/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/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.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1544Resolve "Overview page displaying mixed information"2023-11-23T09:01:04ZMohammad NakhaeeResolve "Overview page displaying mixed information"Closes #1769Closes #1769Mohammad NakhaeeMohammad Nakhaeehttps://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/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/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/1539Improvement excited state workflows MethodNormalizer2023-11-07T10:28:48ZJose PizarroImprovement excited state workflows MethodNormalizerIn a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that ...In a recent merge for the `SimulationWorkflow.normalize()`, a different ordering was introduced for writting the inputs. I then adapted the MethodNormalizer part handling GW, BSE, XS workflows to handle these potential issues, such that now it scans the inputs and searches for one having the keyword `'method'` in the name.Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1537Resolve "MOF App"2023-11-03T12:12:32ZDinga WonankeResolve "MOF App"Closes #1766
We have built a MOF app by adding quantities to config/model.py, which is a simple layout for exploring MOFs and properties in NOMAD. The app currently
1. displays a periodic table containing all atoms and their number of i...Closes #1766
We have built a MOF app by adding quantities to config/model.py, which is a simple layout for exploring MOFs and properties in NOMAD. The app currently
1. displays a periodic table containing all atoms and their number of instances in the MOF subset
2. displays a table illustrating the type of metal SBUs and the number of each present.
3. four histograms displaying
i. pore limiting diameter
ii. largest cavity diameter
iii. accessible surface area
iv. void fractions.
We still need to have a discussion about the following.
1. Whether to create two apps, one for experimental data and the other for computed data or merge everything into a single MOF app.
2. Add scatter plots for preliminary analysis. The main issue is that quantities extracted from the porosity normalisers are stored in topology meanwhile scattered plots can currently be done only on quantities found in data. A plan discussion will be made at some point in the future.Dinga WonankeDinga Wonankehttps://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 Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1534Resolve "Searching from Upload does not behave as expected"2023-11-07T06:23:51ZLauri HimanenResolve "Searching from Upload does not behave as expected"Closes #1756Closes #1756Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1533Resolve "Cannot plot a Datetime Quantity"2023-11-17T13:47:56ZMohammad NakhaeeResolve "Cannot plot a Datetime Quantity"Closes #1754Closes #1754Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1532Resolve "Wrong entry type"2023-11-23T12:55:28ZMohammad NakhaeeResolve "Wrong entry type"Closes #1764Closes #1764Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1531Use ruff as linter2023-11-06T10:47:12ZAhmed IlyasUse ruff as linterThis replaces `pylint` with `ruff-pylint`. I have removed the `pylint` checks in CI and QA and updated the docs.
Once this is merged, I can also post on `nomad-developers` and recommend people to get the `ruff` extensions for vscode/py...This replaces `pylint` with `ruff-pylint`. I have removed the `pylint` checks in CI and QA and updated the docs.
Once this is merged, I can also post on `nomad-developers` and recommend people to get the `ruff` extensions for vscode/pycharm etc. That would also give people some time to transition towards using `ruff` tooling.Ahmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1530Resolve "DataTextParser inheriting from TextParser"2023-11-03T12:29:07ZAlvin Noe LadinesResolve "DataTextParser inheriting from TextParser"Closes #1655Closes #1655Alvin Noe LadinesAlvin Noe Ladines