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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 da799acb

* 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... (continued)

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