Tags: FAIRmat-NFDI/pynxtools-apm
Tags
Apm app niac changes (#37) * Initial code for a simple NOMAD app for atom probe * Fixed appname, installed for a py3.11.11 nomad dev pyenv * Minor edits on the app * Edits to the documentation in prep for apmapp * precommit updated * Configuration for parsing dictionary of controlled keyword - value pairs with information from AP Suite / IVAS * Implementation skeleton for YAML IVAS/APSuite parser * Using pynxtools with custom NeXus definitions to enable that NOMAD can detect these * Added an optional deps group nomad to assure that an installation of pynxtools-apm does not actively modify the environment with versions of these that nomad needs, otherwise nomad did not start reporting that h5grove was unable to load pydantic_settings * Working first version of the Cameca-specific parsing to NeXus * Bumped ruff * minor edits * Edits on configuration in response to how cameca example worked in nomad * Bugfixes, mainly type conversions for apm_app * Refactored event records * edits * fix imprecise statement * Several bugfixes for apm_app cameca examples, heuristics for leap model and pulse mode * bugfix leap model heuristics * Last changes before switching to refactored NXapm, which might break some paths in the parser as apm-specific base classes were heavily reassessed in preparation for NIAC revision of NXapm to become accepted in the standard * Using refactored NXapm, possibly BREAKING CHANGE, next through testing with run-throughs * Fix #35 via #32 * Fixes NOMAD APM example * run_number now a countable * Updated config paths as caused by changes in the definitions because of feedback from the NIAC Autumn 2024 code camp * Must not downgrade any longer h5grove when using the particular combination nomad a1610f8b, pynxtools e314454b, pynxtools-apm da799ac * Generated working NOMAD dev environment with pynx-core and pynxtools-em * Completed the bugfixes on the generic APM example, next steps: i) run all examples, ii) finalize code for the APM-specific search app * Remove trailing whitespace * Bugfixing tests in CICD and reverting the removal of dependency pynxtools that was removed during the development as tests were run in a specifically customized pyenv * Carried over changes on the custom ELN schema to the right place, this explains also and fixes why at some point there were still custom ELN schema templates used with the .nxdl ending that is no longer accepted by NOMAD and because of which parsing errors happened * Updated test script * Couple of more fixes for apm, parsing into NOMAD fine now, normalizer issus need to be fixed in pynxtools/nomad/schema.py * Additional test Jesse * Updated examples data and generic example of a custom ELN * Citation, pyproject, deps * Removed app code for reasons of phasing, added nomad_dependency test * Updating devs as pynx v0.10.1 arrived * removed app due to phasing --------- Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>
Bring in NOMAD examples (#27) * Nexus eln examples * Updates north + pynxtools apm test branch * Implementing fixes for EM and APM examples in NOMAD * Pluginise pynxtools * initial commit for nomad entrypoints * typo fix in MANIFEST.in * bring in additional changes from SprintNomadBaseSectionEmApmFixes branch * add integration tests for nomad example entrypoints * linting of entrypoints * missing closing bracket * return archive dict in testing function * fix pyproject.toml * use relative path in tests * bump ruff to >v0.6 * update dev-requirements and pre-commit * platform-independent dev-requirements * update dev-requirements * use resource in ExampleUploadEntryPoint * linting * ruff 0.8 formatting * bump ruff * update nomad exmaple tests * move some test functionality to pynxtools * update MANIFEST * simplify nomad import test in test_nomad_examples * CI: install nomad with infrastructure extra and test also with python 3.12 * fix typo in CI/CD * update pynxtools dependency * update pynxtools in dev-requirements --------- Co-authored-by: Sherjeel Shabih <sshabih@physik.hu-berlin.de> Co-authored-by: Florian Dobener <florian.dobener@physik.hu-berlin.de> Co-authored-by: Sandor Brockhauser <sandor.brockhauser@physik.hu-berlin.de> Co-authored-by: Markus Kuehbach <kuehbach@fhi-berlin.mpg.de> Co-authored-by: mkuehbach <markus.kuehbach@physik.hu-berlin.de>