nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-01-17T15:02:26Zhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1637documentation - minor, visual fix2024-01-17T15:02:26ZAdrianna Wojasdocumentation - minor, visual fix- updated screenshots
- softer shadows- updated screenshots
- softer shadowsAdrianna WojasAdrianna Wojashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1636Resolve "Update MatID"2024-01-17T12:32:43ZLauri HimanenResolve "Update MatID"Closes #1816Closes #1816Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1635Smaller cloud migration related issues.2024-02-12T10:44:11ZMarkus ScheidgenSmaller cloud migration related issues.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1634Fixed variable name in user defined quantities menu, removed unnecessary logg...2024-01-19T10:17:26ZLauri HimanenFixed variable name in user defined quantities menu, removed unnecessary logging.Closes #1847Closes #1847Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1633Update mpes, xps example and container registry url2024-02-13T08:50:23ZFlorian DobenerUpdate mpes, xps example and container registry url1. Changes the mpes container url to be used from the new [repository](https://gitlab.mpcdf.mpg.de/nomad-lab/north/mpes).
2. Updates the mpes example
3. Changes the xps container url to be used from the new [repository](https://gitlab.mp...1. Changes the mpes container url to be used from the new [repository](https://gitlab.mpcdf.mpg.de/nomad-lab/north/mpes).
2. Updates the mpes example
3. Changes the xps container url to be used from the new [repository](https://gitlab.mpcdf.mpg.de/nomad-lab/north/xps).
4. Updates the xps exampleFlorian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1632Adding magres parsing and schema2024-02-07T11:36:03ZJose PizarroAdding magres parsing and schemaCloses #1846
Related MR in Github:
- [nomad-schema-plugin-simulation-run](https://github.com/nomad-coe/nomad-schema-plugin-run/pull/2)
- [nomad-schema-simulation-workflow](https://github.com/nomad-coe/nomad-schema-plugin-simulation-wor...Closes #1846
Related MR in Github:
- [nomad-schema-plugin-simulation-run](https://github.com/nomad-coe/nomad-schema-plugin-run/pull/2)
- [nomad-schema-simulation-workflow](https://github.com/nomad-coe/nomad-schema-plugin-simulation-workflow/pull/3)
- [electronic-parsers](https://github.com/nomad-coe/electronic-parsers/pull/193)Jose PizarroJose Pizarrohttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1631Resolve "include and exclude the visible and the editable properties"2024-01-23T15:41:24ZMohammad NakhaeeResolve "include and exclude the visible and the editable properties"Closes #1852Closes #1852Mohammad NakhaeeMohammad Nakhaeehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1630Added gitlab ci tags to use cloud cicd runner.2024-02-12T10:44:06ZMarkus ScheidgenAdded gitlab ci tags to use cloud cicd runner.https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1629Draft: Pynxtools as dependency2024-03-08T09:07:45ZFlorian DobenerDraft: Pynxtools as dependencyThis PR remoevs pynxtools (aka nexus parser) as a submodule and adds it as a python dependency to `pyproject.toml`.This PR remoevs pynxtools (aka nexus parser) as a submodule and adds it as a python dependency to `pyproject.toml`.Florian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1628Resolve "Converter for json to and from pd dataframe"2024-02-29T10:43:49ZAmir GolparvarResolve "Converter for json to and from pd dataframe"- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849- [x] flatten json into a pandas dataframe
- [x] reconstruct dataframe to json
- [x] options: depth of the json to flatten
- [x] options: order resultant dataframe alphabetically or by a list of strings
Closes #1849Amir GolparvarAmir Golparvarhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1627Draft: Resolve "Refine building process of docker image"2024-01-23T09:15:56ZAdam FeketeDraft: Resolve "Refine building process of docker image"This MR suppose to fix multiple issues with the building process of the noamd docker image.
- [x] ~~Fix the python package dependency conflicts~~
- [x] ~~get rid of the circular dependencies of the submodules (closing: https://gitlab.m...This MR suppose to fix multiple issues with the building process of the noamd docker image.
- [x] ~~Fix the python package dependency conflicts~~
- [x] ~~get rid of the circular dependencies of the submodules (closing: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1579, @ahmil , @himanel1 )
solution: Adding the submodules dependency directly to the main pyproject.toml file. This way we do not rely on the submodules' dependencies. This method might change when these submodules are going to be a proper plugins.~~
- [x] ~~fix the issue with the pybis package (@amgo) Solution: remove it from the dependency and install it without its deps later. `pip install --no-deps pybis`~~
- [x] ~~remove unused/probelmatic pyscf package dependency (@ladinesa )~~
- [x] explicitly defining nomad user and using it propertly for the kubernetes' security context (@afekete) solution: using nomad user for both of the docker build stages
- [x] Using develop stage for debugging or as a replacement for the production image (closing: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/issues/1598, @mscheidg ) solution: combining the python and node build stage into a single stage to represent better a full dev environment. It can be used for running the test or the full application if needed.
- [x] ~~Pynxtools as dependency (closing: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1629, @dflor )~~
Update: all python dependency related fix has been removed from this MR.
Closes #1848Adam FeketeAdam Feketehttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1626added example function to calc summed mass from comp model2024-02-15T15:59:34ZJoseph Rudzinskiadded example function to calc summed mass from comp modelCloses #1844
@himanel1 I need your advice here. I created a mock function in atom_utils `get_summed_atomic_mass_from_computational_model` as a demonstration of how we should try to calculate the mass_density, maybe by default, but defi...Closes #1844
@himanel1 I need your advice here. I created a mock function in atom_utils `get_summed_atomic_mass_from_computational_model` as a demonstration of how we should try to calculate the mass_density, maybe by default, but definitely in the case where the atom types are unknown. However, I am not sure about the best way to implement this: I need access to the archive to grab the masses from the `atom_parameters` section, but in the topology normalizer, we currently don't have access to this at the point where we are calculating the cell.Joseph RudzinskiJoseph Rudzinskihttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1625Resolve "Attribute inheritance"2024-02-29T11:46:43ZMarkus ScheidgenResolve "Attribute inheritance"Closes #1845Closes #1845Markus ScheidgenMarkus Scheidgenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1624Draft: Refactor run.system as a base section2024-01-29T10:46:09ZNathan DaelmanDraft: Refactor run.system as a base sectionhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1623Draft: refactor run.system2024-01-04T11:04:45ZNathan DaelmanDraft: refactor run.systemApply refactoring of `run.system` toApply refactoring of `run.system` tohttps://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/1621Move run section to plugin2024-01-31T07:43:36ZAlvin Noe LadinesMove run section to pluginRemove all references to section run schema in nomad.datanodel.metainfo.simulation . These are moved to achema plugin. As an effect, all normalizers referencing the run section are also made plug ins together with their tests. In additio...Remove all references to section run schema in nomad.datanodel.metainfo.simulation . These are moved to achema plugin. As an effect, all normalizers referencing the run section are also made plug ins together with their tests. In addition, the results schema are now defined independently and not copied from run.Alvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1620sts and stm example update.2024-01-09T08:13:21ZRubel Mozumdersts and stm example update.- [x] Update example in nomad-remote-tools-hub
- [x] Modify the nomad scripts corresponding to the examples (STM and STS)
- [x] Mrege 158 in nomad-remote-tools-hub and update the hash of submodule remote-tool-hub in nomad.
PR: https:/...- [x] Update example in nomad-remote-tools-hub
- [x] Modify the nomad scripts corresponding to the examples (STM and STS)
- [x] Mrege 158 in nomad-remote-tools-hub and update the hash of submodule remote-tool-hub in nomad.
PR: https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-remote-tools-hub/-/merge_requests/158Florian DobenerFlorian Dobenerhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1619Fix quantum espresso parser2023-12-25T20:53:48ZAlvin Noe LadinesFix quantum espresso parserAlvin Noe LadinesAlvin Noe Ladineshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1618ci error on format failure2023-12-22T15:12:25ZAhmed Ilyasci error on format failureAhmed IlyasAhmed Ilyas