FAIRmat-NFDI / pynxtools-em / 14063963400
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Em app niac changes (#106)

* Minor linting

* Manual upgrading of ruff to lint prior commit correctly

* precommit updated

* Editing entrypoint emapp

* Refactored generic custom ELN taking the demands of the Koch group as an example

* Generated working NOMAD dev environment with pynxtools and pynxtools-apm

* Editing of configuration tables to integrate feedback from NIAC Autumn 2024 code camp discussions

* Replacements of many common hdf5 pathes and patterns that have changed as a consequence of the changes from code camp and using the new definitions

* Swopping and harmonization of concepts and terms using the name fragment identifier and removal of NXidentifier

* Bugfix arithmetics of axes

* EMD parsing fine, bumped ruff

* Excluded py3.9 from pytest

* Fixing gatan examples, fine-tuning of serialization for serializing and concatenating multiple custom concepts that have no place in NeXus into a string such as optics/operation_mode

* Image parsers for TFS, Hitachi, TEScan, JEOL, point electronic, and protochips ZIP so far look okay

* Fix bug that the Hitachi parsers throw when offered content not matching its specification because of a variable not set

* Fixed Oxford instrument examples EBSD and Viteshs microstructure working again with IPF color plots

* Made fixes in further EBSD examples, removed all explicit calls for template @NX_class to enforce that the algorithm needs to find these alone and if not expose a missing attribute via missing default plots as a bug

* Switched off HdfFiveDreamThreedLegacyParser, first set of tests on EM examples done, the parser generates NeXus files. In the next step, first developments from pynxtools, specifically update_defs and ConsiderIdentifier branches should be merged in and used to run all these examples in NOMAD and fix remaining bugs

* Added a ipynb with a script to aggregate all unique warnings from the corpus of examples, fixes for several of the warnings where the pathes in the template... (continued)

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Jobs
ID Job ID Ran Files Coverage
1 14063963400.1 2
42.86
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2 14063963400.2 2
91.67
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3 14063963400.3 2
91.67
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4 14063963400.4 2
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5 14063963400.5 2
42.86
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Source Files on build 14063963400