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@casperdcl casperdcl commented May 30, 2023

  • add acr module
  • add img.signa module
  • misc prc & img updates
  • fix/migrate pkg_resources => importlib_resources
  • misc code tidy
  • misc build/CI/framework/test updates
    • fix CI build & test workflow
    • add Py3.11, drop Py3.6 support
    • migrate setup.cfg => pyproject.toml
    • update pre-commit hooks

@casperdcl casperdcl added enhancement New feature or request framework labels May 30, 2023
@casperdcl casperdcl mentioned this pull request May 30, 2023
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@pjmark
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pjmark commented Jun 1, 2023

from me it is all good

@casperdcl
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Pushed lots of fixes, but left some errors (see https://github.com/NiftyPET/NIMPA/actions/runs/5193633461/jobs/9364422220) because I'm unsure about them

@casperdcl casperdcl force-pushed the devel branch 2 times, most recently from 6d52f61 to 700f7cf Compare June 19, 2023 22:54
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codecov bot commented Jun 19, 2023

Codecov Report

Merging #28 (08e0174) into master (f69c6ff) will increase coverage by 3.13%.
The diff coverage is 14.05%.

❗ Current head 08e0174 differs from pull request most recent head 308cf91. Consider uploading reports for the commit 308cf91 to get more accurate results

@@            Coverage Diff             @@
##           master      #28      +/-   ##
==========================================
+ Coverage    7.84%   10.98%   +3.13%     
==========================================
  Files           9       16       +7     
  Lines        2102     3131    +1029     
==========================================
+ Hits          165      344     +179     
- Misses       1937     2787     +850     
Impacted Files Coverage Δ
niftypet/nimpa/prc/__init__.py 100.00% <ø> (ø)
niftypet/nimpa/acr/templates.py 3.88% <3.88%> (ø)
niftypet/nimpa/img/gen.py 11.42% <5.00%> (-0.67%) ⬇️
niftypet/nimpa/acr/ioaux.py 6.50% <6.50%> (ø)
niftypet/nimpa/acr/analysis.py 10.18% <10.18%> (ø)
niftypet/nimpa/prc/prc.py 6.03% <13.04%> (+0.38%) ⬆️
niftypet/nimpa/prc/regseg.py 6.38% <13.33%> (+0.23%) ⬆️
niftypet/nimpa/img/signa.py 14.86% <14.86%> (ø)
niftypet/nimpa/acr/proc.py 21.62% <21.62%> (ø)
niftypet/nimpa/prc/imio.py 6.17% <29.41%> (+0.22%) ⬆️
... and 4 more

... and 1 file with indirect coverage changes

'''
# possible DICOM file extensions
ext = ('dcm', 'DCM', 'ima', 'IMA')
ext = 'dcm', 'ima'
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btw can this use dcmext ('dcm', 'ima', 'img') instead?

for f in chain(outdir.glob('*.nii*'), outdir.glob('*.json')):
# remove previous files
os.remove(f)
run([dcm2niix.bin, '-i', 'y', '-v', 'n', '-o', outdir, '-f', '%f_%s', str(indat)])
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this was 'f', '%f_%s' instead of '-f', '%f_%s'. Presumably latter is correct.

@casperdcl casperdcl merged commit f80a3d6 into master Jun 20, 2023
@casperdcl casperdcl deleted the devel branch June 20, 2023 21:17
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/tag v2.6.0 f80a3d6

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3 participants