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Adding NOMAD APM app #34

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Adding NOMAD APM app #34

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e0ff30d
Initial code for a simple NOMAD app for atom probe
atomprobe-tc Jan 9, 2025
45ebb29
Fixed appname, installed for a py3.11.11 nomad dev pyenv
atomprobe-tc Jan 9, 2025
a9ae578
Minor edits on the app
atomprobe-tc Jan 10, 2025
192691a
Edits to the documentation in prep for apmapp
atomprobe-tc Jan 10, 2025
cf672b5
precommit updated
atomprobe-tc Jan 10, 2025
f005457
Configuration for parsing dictionary of controlled keyword - value pa…
mkuehbach Jan 25, 2025
54eed6e
Implementation skeleton for YAML IVAS/APSuite parser
atomprobe-tc Jan 26, 2025
7c77640
Using pynxtools with custom NeXus definitions to enable that NOMAD ca…
atomprobe-tc Jan 26, 2025
d587171
Added an optional deps group nomad to assure that an installation of …
atomprobe-tc Jan 26, 2025
d032dd4
Working first version of the Cameca-specific parsing to NeXus
atomprobe-tc Jan 27, 2025
66023fa
Bumped ruff
atomprobe-tc Jan 27, 2025
069d267
minor edits
atomprobe-tc Jan 27, 2025
f088889
Edits on configuration in response to how cameca example worked in nomad
atomprobe-tc Jan 28, 2025
f72395c
Bugfixes, mainly type conversions for apm_app
atomprobe-tc Jan 28, 2025
8936a45
Refactored event records
atomprobe-tc Jan 30, 2025
075c8b9
edits
atomprobe-tc Jan 30, 2025
04f5ac8
fix imprecise statement
atomprobe-tc Jan 30, 2025
94dc834
Several bugfixes for apm_app cameca examples, heuristics for leap mod…
atomprobe-tc Jan 30, 2025
3fee393
bugfix leap model heuristics
atomprobe-tc Jan 30, 2025
ffea6b0
Last changes before switching to refactored NXapm, which might break …
atomprobe-tc Jan 31, 2025
63f7eb5
Using refactored NXapm, possibly BREAKING CHANGE, next through testin…
atomprobe-tc Jan 31, 2025
1a2182f
Fix #35 via #32
atomprobe-tc Jan 31, 2025
12bd21b
Fixes NOMAD APM example
atomprobe-tc Feb 1, 2025
eaa800d
run_number now a countable
atomprobe-tc Feb 1, 2025
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4 changes: 2 additions & 2 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,9 @@
repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
rev: v0.8.0
rev: v0.9.3
hooks:
# Run the linter.
- id: ruff
# Run the formatter.
- id: ruff-format
- id: ruff-format
22 changes: 16 additions & 6 deletions .vscode/launch.json
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Original file line number Diff line number Diff line change
Expand Up @@ -9,17 +9,27 @@
"type": "python",
"request": "launch",
"cwd": "${workspaceFolder}",
"program": "../.py3.12.4/bin/dataconverter",
"program": "../../.py3.11.11/bin/dataconverter",
"args": [//workflow files str.str, hits.hits, root.root should be created via touch str.str ...
"tests/data/eln/eln_data.yaml",
"tests/data/eln/apm.oasis.specific.yaml",
"tests/data/apt/Si.apt",
"tests/data/rng/87D_1.rng",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/001.0.c4b1b412f46833ef7b72164858f3fa2daea60de212b2a62cd7121c07a92d5837.rhit.CRunHeader.dat.Parsed.cameca",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/019.0.8d12016f3d152ce8a02194b126bd6c896f517928dada673864e93e4dfc418738.root.CAnalysis.dat.Parsed.cameca",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/091.0.638c14a699bce8644b1df4690c86b5f0d2fdc60fc4cbfdeb8bc89def735193b6.rhit.CRunHeader.dat.Parsed.cameca",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/091.0.68466f6cc6a751a23126c82f8a5a04c9c91f1c7e03bb44e6d2c2c9375e07a624.root.CAnalysis.dat.Parsed.cameca",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/008.1.1f7a63e5a16239bcaebe71c8ac2812b5f6cdb1175f1a4618db7c9435c3ead06c.rhit.CRunHeader.dat.Parsed.cameca",
//"../../../../paper_paper_paper/scidat_nomad_apt/bb_analysis/analysis/harvest_examples/data/production/cameca/088.44.1444afcbc8114aa6832716877ea9dc3360968458ce1ce74bb4c9ea21f4fe8678.rhit.CRunHeader.dat.Parsed.cameca",
"examples/apm.oasis.specific.yaml",
"examples/eln_data.yaml",
"examples/Si.apt",
"examples/Si.RRNG",
"--reader",
"apm",
"--nxdl",
"NXapm",
"--output=tests/prod/apt.Si.apt.nxs"]
"--output=Si.nxs"],
//"--output=tests/prod/usa_idaho_boise.088.44.nxs"]
//"--output=tests/prod/usa_portland_grimm.091.0.nxs"]
//"--output=tests/prod/out_recon.nxs"]
//"--output=tests/prod/out_range.nxs"]
}
]
}
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