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Update fairmat branch with upstream main#332

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lukaspie merged 498 commits into
fairmatfrom
fairmat-main-updated
Feb 28, 2025
Merged

Update fairmat branch with upstream main#332
lukaspie merged 498 commits into
fairmatfrom
fairmat-main-updated

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@lukaspie

@lukaspie lukaspie commented Feb 17, 2025 •
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  1. Switched to fairmat branch and created new branch fairmat-main-updated from there
  2. Ran git merge upstream/main
  3. Resolved merge conflicts for ~150 files
  4. Remove instances of NXidentifier
  5. Remove instances of NXserialized
  6. Implement nameType="partial" wherever possible -> probably still missed sone instances
  7. Run make nyaml
  8. Run make nxdl

This introduced unexpected changes compared to upstream/main in the applications and base_classes files. Therefore, I checked out these files from upstream/main manually (by running git checkout upstream/main <file>) and then only applied these changes that we want to keep:

  • changed the copyright starting date for files that we recently merged into NIAC main, but where we had (unintentionally) set all starting dates to 2014. Like NXactivity, NXfabrication, etc. We should probably make a PR to NIAC where we make these starting dates correct as well. For this, I used the mentioned script by the way.
  • there are some files where we have additional modifications which we have not proposed or are not yet merged to NIAC, e.g. NXactuator has NXpid_controller. Here, I kept the NIAC formatting, but this still probably change when we make further changes in the YAML files on our side.
  • changes that are still open in NIAC PRs (see NXbeam, NXentry, NXdata, for example).

All nyaml files were generated with nyaml=0.2.1 which also leads to a diff compared to existing files.

lukaspie and others added 30 commits October 16, 2024 10:16
@lukaspie
format base classes and applications in accordance to existing NIAC v…
b939493 
…ersion

# Conflicts:
#	applications/NXarpes.nxdl.xml
#	applications/nyaml/NXarpes.yaml
#	base_classes/NXaperture.nxdl.xml
#	base_classes/NXbeam.nxdl.xml
#	base_classes/NXdata.nxdl.xml
#	base_classes/NXdetector.nxdl.xml
#	base_classes/NXentry.nxdl.xml
#	base_classes/NXenvironment.nxdl.xml
#	base_classes/NXinstrument.nxdl.xml
#	base_classes/NXroot.nxdl.xml
#	base_classes/NXsample.nxdl.xml
#	base_classes/NXsample_component.nxdl.xml
#	base_classes/NXsensor.nxdl.xml
#	base_classes/NXsource.nxdl.xml
#	base_classes/NXsubentry.nxdl.xml
#	base_classes/NXtransformations.nxdl.xml
#	base_classes/NXuser.nxdl.xml
#	base_classes/nyaml/NXaperture.yaml
#	base_classes/nyaml/NXbeam.yaml
#	base_classes/nyaml/NXdata.yaml
#	base_classes/nyaml/NXdetector.yaml
#	base_classes/nyaml/NXentry.yaml
#	base_classes/nyaml/NXenvironment.yaml
#	base_classes/nyaml/NXinstrument.yaml
#	base_classes/nyaml/NXmonochromator.yaml
#	base_classes/nyaml/NXprocess.yaml
#	base_classes/nyaml/NXroot.yaml
#	base_classes/nyaml/NXsample.yaml
#	base_classes/nyaml/NXsample_component.yaml
#	base_classes/nyaml/NXsensor.yaml
#	base_classes/nyaml/NXsource.yaml
#	base_classes/nyaml/NXsubentry.yaml
#	base_classes/nyaml/NXtransformations.yaml
#	base_classes/nyaml/NXuser.yaml
@lukaspie
revert unintentional changes from cherry-pick
4697d1c 
update copyright
@lukaspie
use unit example in NXmonochromator
0508826
@lukaspie
use unit example in NXmonochromator/wavelength_dispersion
5542cd2
@domna @lukaspie
Revert to older classes
2e301dc 
# Conflicts:
#	base_classes/NXaperture.nxdl.xml
#	base_classes/NXdetector.nxdl.xml
@RubelMozumder @lukaspie
Regeneration of the nexus file for fixing the changes coming from old…
bf182a2 
… version of yaml.

Removing unintensional comments

# Conflicts:
#	base_classes/NXbeam.nxdl.xml
#	base_classes/NXentry.nxdl.xml
#	base_classes/NXinstrument.nxdl.xml
#	base_classes/NXprocess.nxdl.xml
#	base_classes/NXsample.nxdl.xml
#	base_classes/NXsource.nxdl.xml
@lukaspie
Add NXfabrication to all MPES instrument-related base classes
b9daab2 
# Conflicts:
#	base_classes/NXinstrument.nxdl.xml
#	base_classes/NXsensor.nxdl.xml
#	base_classes/NXsource.nxdl.xml
#	base_classes/nyaml/NXdetector.yaml
#	base_classes/nyaml/NXinstrument.yaml
#	base_classes/nyaml/NXsensor.yaml
#	base_classes/nyaml/NXsource.yaml
@lukaspie
extend NXdetector/acquisition_mode
d386ca6 
# Conflicts:
#	contributed_definitions/nyaml/NXdetector.yaml
@lukaspie
change enum in NXdetector
81810fb 
# Conflicts:
#	base_classes/nyaml/NXdetector.yaml
@lukaspie
format base classes and applications in accordance to existing NIAC v…
41036b5 
…ersion

# Conflicts:
#	applications/NXarpes.nxdl.xml
#	applications/nyaml/NXarpes.yaml
#	base_classes/NXaperture.nxdl.xml
#	base_classes/NXbeam.nxdl.xml
#	base_classes/NXdata.nxdl.xml
#	base_classes/NXentry.nxdl.xml
#	base_classes/NXenvironment.nxdl.xml
#	base_classes/NXinstrument.nxdl.xml
#	base_classes/NXmonochromator.nxdl.xml
#	base_classes/NXroot.nxdl.xml
#	base_classes/NXsample.nxdl.xml
#	base_classes/NXsample_component.nxdl.xml
#	base_classes/NXsensor.nxdl.xml
#	base_classes/NXsource.nxdl.xml
#	base_classes/NXsubentry.nxdl.xml
#	base_classes/NXtransformations.nxdl.xml
#	base_classes/NXuser.nxdl.xml
#	base_classes/nyaml/NXaperture.yaml
#	base_classes/nyaml/NXbeam.yaml
#	base_classes/nyaml/NXdata.yaml
#	base_classes/nyaml/NXdetector.yaml
#	base_classes/nyaml/NXentry.yaml
#	base_classes/nyaml/NXenvironment.yaml
#	base_classes/nyaml/NXmonochromator.yaml
#	base_classes/nyaml/NXprocess.yaml
#	base_classes/nyaml/NXroot.yaml
#	base_classes/nyaml/NXsample.yaml
#	base_classes/nyaml/NXsample_component.yaml
#	base_classes/nyaml/NXsensor.yaml
#	base_classes/nyaml/NXsubentry.yaml
#	base_classes/nyaml/NXtransformations.yaml
#	base_classes/nyaml/NXuser.yaml
#	contributed_definitions/nyaml/NXinstrument.yaml
#	contributed_definitions/nyaml/NXsource.yaml
@lukaspie
revert unintentional changes from cherry-pick
d002c64
@lukaspie
fix copyright in NXdetector
12cc278
@lukaspie
move electron detector specifics to subclass
6cb6b83
@lukaspie
fix Nxelectron_detector
d2766df
@lukaspie
implement review suggestions
00bf64c
@lukaspie
simplify nxdl_utils.py
8495979
@lukaspie
minor fixes from review
7d851fb
@lukaspie
black formatting
301582d
@RubelMozumder
Name type.
1063abe
@prjemian
Merge pull request nexusformat#1497 from nexusformat/1380-how-to-vali…
979ec79 
…date-XML-files

show how to validate an XML file
@RubelMozumder
fix conflict.
fdf6c05
@lukaspie
black formatting
485cd0a
@lukaspie
refactor to use pathlib.Path(), add to UnicodeDecodeError
7e40c0d
@lukaspie
formatting
1201748
@lukaspie
isort
bdf0ed8
@lukaspie
Merge pull request nexusformat#1491 from FAIRmat-NFDI/name-type-parti…
ee1078b 
…al-in-dev-tools

`name_type="partial"`  in dev tools
@lukaspie
add identifierNAME to NXobject
abce47e
@lukaspie
typo fix
5290722
@lukaspie
add identifier to reserved prefixes
d00b007
@lukaspie
implement review from NXuser PR
0a5a797
RubelMozumder
RubelMozumder reviewed Feb 27, 2025
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LGTM, except the nameType issue. I also got 2-3 issue with data type. Nothing is very serious.

@lukaspie lukaspie mentioned this pull request Feb 27, 2025
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@lukaspie lukaspie mentioned this pull request Feb 27, 2025
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mkuehbach
mkuehbach reviewed Feb 27, 2025
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Comment thread contributed_definitions/nyaml/NXcg_marching_cubes.yaml
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Comment thread contributed_definitions/nyaml/NXstm.yaml
mkuehbach
mkuehbach requested changes Feb 27, 2025
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A few more comments mainly on contributed_definitions/nyaml

@lukaspie lukaspie force-pushed the fairmat-main-updated branch from ceeb510 to e297747 Compare February 28, 2025 11:20
mkuehbach
mkuehbach approved these changes Feb 28, 2025
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Nice work!

@lukaspie lukaspie merged commit 365d4d8 into fairmat Feb 28, 2025
@lukaspie lukaspie deleted the fairmat-main-updated branch February 28, 2025 15:45
@lukaspie lukaspie mentioned this pull request Mar 4, 2025
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@lukaspie lukaspie linked an issue Mar 4, 2025 that may be closed by this pull request
Fairmat definitions sync with NIAC 2025 #325
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@lukaspie lukaspie mentioned this pull request Mar 4, 2025
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@lukaspie lukaspie mentioned this pull request Aug 28, 2025
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@mkuehbach mkuehbach mkuehbach approved these changes

@RubelMozumder RubelMozumder RubelMozumder approved these changes

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Fairmat definitions sync with NIAC 2025

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@lukaspie @RubelMozumder @mkuehbach @domna @prjemian @rayosborn @phyy-nx @atomprobe-tc @PeterC-DLS