nomad-FAIR merge requestshttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests2024-03-08T09:07:45Zhttps://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/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 Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1617Resolve "Keep a clean gitlab project"2023-12-22T10:21:48ZMarkus ScheidgenResolve "Keep a clean gitlab project"https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1616Remove timers2023-12-21T20:19:18ZTheodore ChangRemove timersTheodore ChangTheodore Changhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1615Improved search bar2024-01-15T09:59:05ZLauri HimanenImproved search barCloses #1790, #1700Closes #1790, #1700Lauri HimanenLauri Himanenhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1614add link to migration how to in mkdocs.yml2023-12-21T11:28:03ZAhmed Ilyasadd link to migration how to in mkdocs.ymlAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1613add documentation for formatting2023-12-21T11:04:54ZAhmed Ilyasadd documentation for formattingAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1612add tabular description2023-12-20T20:08:37ZAhmed Ilyasadd tabular descriptionAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1611GitHub PR: Remove upwards pin2023-12-21T08:57:04ZMarkus ScheidgenGitHub PR: Remove upwards pinOriginal pull request on GitHub: https://github.com/nomad-coe/nomad/pull/91Original pull request on GitHub: https://github.com/nomad-coe/nomad/pull/91https://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1610autoformat python2023-12-21T09:38:03ZAhmed Ilyasautoformat pythonhttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1609manually fix type ignore2023-12-20T17:44:59ZAhmed Ilyasmanually fix type ignoreAhmed IlyasAhmed Ilyashttps://gitlab.mpcdf.mpg.de/nomad-lab/nomad-FAIR/-/merge_requests/1608revert import order2023-12-20T16:24:55ZAhmed Ilyasrevert import order