nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2023-11-03T11:19:42Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1536Draft: Resolve "MOF App"2023-11-03T11:19:42ZDinga WonankeDraft: Resolve "MOF App"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 t...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.
1. 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/1511Resolve "MOF App"2023-11-03T11:04:26ZDinga WonankeResolve "MOF App"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 th...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/524Draft: Catalysis oasis - merge to v1.0.02023-11-03T09:46:27ZFelix DietrichDraft: Catalysis oasis - merge to v1.0.0This branch adds metaschema information for catalysis experiments from FHI.
The changes for the GUI are here:
`gui/src/components/visualization/Catalysis.js`
`gui/src/components/archive/Overview.js`
The metaschema changes are here:
`nom...This branch adds metaschema information for catalysis experiments from FHI.
The changes for the GUI are here:
`gui/src/components/visualization/Catalysis.js`
`gui/src/components/archive/Overview.js`
The metaschema changes are here:
`nomad/datamodel/datamodel.py`
`nomad/datamodel/metainfo/measurements.py`
Before the merge, the changes in `nomad/config.py` have to be reverted, otherwise only four people can access NOMAD v1.0.0.v1.0.0 releaseMarkus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1529Draft: Replace pylint with ruff pylint2023-11-02T09:27:10ZAhmed IlyasDraft: Replace pylint with ruff pylintAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1356Draft: Attempt to fix python dependencies2023-11-01T10:42:20ZAdam FeketeDraft: Attempt to fix python dependenciesIt would be nice to relax the version dependencies in the `pyproject.toml` but fixing them in the `requirement.txt` files.
The main issue if we fix all the versions in `pyproject.toml`:
- Practically it is impossible to install `nomad-l...It would be nice to relax the version dependencies in the `pyproject.toml` but fixing them in the `requirement.txt` files.
The main issue if we fix all the versions in `pyproject.toml`:
- Practically it is impossible to install `nomad-lab` package into an existing python environment eg using a jupyter docker image...
- it doesn't make sense to uninstall and reinstall different version of numpy pandas just because you want to do a query...
- use `--no-dependencies` to ignore package dependencies but then it is hard to install the necessary packages manually...
- Obviously it is the easy way to setup an python environment from scratch but for that purpose you can use the `requirement.txt` filesAdam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1513Draft: Resolve "add centimeter and millimeter as custom units in NOMAD GUI"2023-10-24T06:31:05ZJulia SchumannDraft: Resolve "add centimeter and millimeter as custom units in NOMAD GUI"Closes #1743Closes #1743Julia SchumannJulia Schumannhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1501Draft: Resolve "Processing_logs and Entry Metadata cannot be retrieved from g...2023-10-16T09:12:49ZAmir GolparvarDraft: Resolve "Processing_logs and Entry Metadata cannot be retrieved from graph_model"Closes #1734Closes #1734Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1496Draft: Resolve "Workflow for chemical reaction steps"2023-10-16T09:07:46ZAlvin Noe LadinesDraft: Resolve "Workflow for chemical reaction steps"Closes #1430Closes #1430Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1494Simplified App config, improved handling of unexpected config fields, added...2023-10-16T08:46:59ZLauri HimanenSimplified App config, improved handling of unexpected config fields, added...Simplified App config, improved handling of unexpected config fields, added basic documentation for setting up apps.
Closes #1730Simplified App config, improved handling of unexpected config fields, added basic documentation for setting up apps.
Closes #1730Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1443tabular parser doc revision 12023-09-05T15:07:41ZAndrea Albinotabular parser doc revision 1Hi @mscheidg, @sbrueck
I started this MR from the need of some extensions of tabular parser documentation by @amgo.
I will try to shape it as an HowTo and move elsewhere the parts that go beyond an HowTo purpose.
An overarching Tutor...Hi @mscheidg, @sbrueck
I started this MR from the need of some extensions of tabular parser documentation by @amgo.
I will try to shape it as an HowTo and move elsewhere the parts that go beyond an HowTo purpose.
An overarching Tutorial issue #1653 is being opened by @hnaesstroem that will reference this HowTo.
A cascade of side info will probably fall in Learn within this MR, too.Andrea AlbinoAndrea Albinohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1416Draft: Testing apm-em-sprint14-p2 pynxtools and fixed incorrect references to...2023-08-17T15:43:26ZRubel MozumderDraft: Testing apm-em-sprint14-p2 pynxtools and fixed incorrect references to old...This is just for testing purposes Nothin elseThis is just for testing purposes Nothin elsehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1405Draft: Stm integration2023-08-17T15:42:57ZRubel MozumderDraft: Stm integrationhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1445Draft: Rebase stm integretion2023-08-17T15:39:26ZRubel MozumderDraft: Rebase stm integretionThis is a test purpose: whether changes are working or not.This is a test purpose: whether changes are working or not.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1270Draft: Resolve "Circular references in ELN lead to infinite processing"2023-08-16T09:18:40ZMohammad NakhaeeDraft: Resolve "Circular references in ELN lead to infinite processing"Closes #1381Closes #1381Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1382Draft: Resolve "plotly full support"2023-08-16T09:13:25ZMohammad NakhaeeDraft: Resolve "plotly full support"Closes #1588Closes #1588Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1271Draft: Updates north submodule2023-08-11T09:25:52ZFlorian DobenerDraft: Updates north submodulehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1203Use process based implementation for file matching2023-08-10T19:39:48ZTheodore ChangUse process based implementation for file matchingCloses #1396Closes #1396Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1371More development2023-08-10T12:59:52ZTheodore ChangMore developmentCloses #1180Closes #1180Theodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1372Draft: Resolve "Aggregations for custom quantities"2023-08-09T05:23:08ZLauri HimanenDraft: Resolve "Aggregations for custom quantities"Closes #1502Closes #1502Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1430Draft: Resolve "Problems with Gromacs parser from umbrella sampling simulation"2023-08-09T05:11:03ZJoseph RudzinskiDraft: Resolve "Problems with Gromacs parser from umbrella sampling simulation"Closes #1643
Not sure why the pipeline build did not even work here...?Closes #1643
Not sure why the pipeline build did not even work here...?Joseph RudzinskiJoseph Rudzinski