APM refactoring / APMv2 #204
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…V, FAU/Erlangen's pyccapt calibration and ranging, and FAU/Erlangen's Matlab Atom probe Toolbox fig ranging definitions, currently deactivated ELN and configuration parsing also in the io_case initial check of the apm reader, these functionalities need to use the updated and refactored ifes_apt_tc_data_modeling library, which however as of 2023/12/31 has not yet been placed on pypi (but committed into the repo, that's why this commit works with a local py3.11.5 where the sitepackage ifes_apt_tc_data_modeling was modified manually to avoid frequent publishing of dysfunctional ifes version and test them here first, next steps: i) run the reader against all 150+ test cases, ii) fix bugs of these examples, iii) move changes to ifes library and publish that on pypi, iv) update pyproject toml, v) reactivate ELN and config parsing, vi) update apm definitions to use the refactored apm base classes, vii) integrate ruff changes, viii) commit on pynxtools master
…ge 176 dataset example case
…erage 58 elements, 5.9 billions ions in total, 77 projects from research of all major groups worldwide, next steps: iii) move to ifes, vi) nxdef refactor, v) eln, cfg parsing, RUN ALL and check proper annotation, styling, linting ruff
…have now plenty of real world examples to show and run these tools with
…cf052a34 to not tested developmental apm_refactoring
…workflow-related files in the NeXus file so that NOMAD is available could use them further, also added feedback of best practice metadata to report from T. Blum et al. from the geoscience community, next steps: i) fix eln parsing, ii) add 176case study specific citation code, iii) customize nomad schema, iv) runthrough
…mass spectrum database which is currently hosted on an AirTable (but no longer maintained), added ELN and I/O logic parsing to populate NXserialized artifacts which can be used for implementing a visualization of a information provenance (workflow) for NOMAD OASIS, added ELN parsing, fix i) except for user
…or charge_state_model
mkuehbach
requested review from
lukaspie,
domna,
sherjeelshabih,
sanbrock,
RubelMozumder and
RonHildebrandt
and removed request for
RubelMozumder
pynxtools/dataconverter/readers/apm/utils/apm_create_nx_default_plots.py
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Before this PR can be merged RUFF linting has to be used and the current state of this branch checked and merging master in again. All this is not a blocker though for the task of reviewing the implementation of the em parser as it is proposed in this PR. Also other em_ parsers will be removed but this will happen in a clean separate branch and PR to not clutter this PR further. |
…ctoring feature branch
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The code in this feature branch is taken as the starting point for the creation of the pynxtools-apm plugin. Ruff is also used now in this plugin replacing pylint and pycodestyle. |
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