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More CI checks #119

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More CI checks #119

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15701d8
[CI] minimal check on get_data()
KrisThielemans Sep 29, 2024
d372708
[CI] use existing petric.py
KrisThielemans Sep 29, 2024
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10 changes: 9 additions & 1 deletion .github/workflows/run.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -33,14 +33,22 @@ jobs:
shell: bash -el {0}
run: |
source /opt/SIRF-SuperBuild/INSTALL/bin/env_sirf.sh
curl -fsSL https://raw.githubusercontent.com/SyneRBI/PETRIC/main/petric.py > petric.py
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we need this line to overwrite any users' changes as per the README

Any modifications to petric.py are ignored.

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sure, but does tha tuse this run.yml? I guess it does. But then this isn't really CI.

anyway.

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@casperdcl casperdcl Sep 30, 2024 •
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yes all submission repos are a fork of this one, so they all use this run.yml.

  • pro: we all use the same petric.py
  • con: it's impossible for organisers to test changes to petric.py in CI
    • I've had to manually test any change(s)

We could de-sync forks from this repo, but I'd rather not (it might confuse participants)

dataset=Siemens_mMR_NEMA_IQ
curl -sfSL -o ${dataset}.zip https://petric.tomography.stfc.ac.uk/data/${dataset}.zip
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Suggested change
curl -sfSL -o ${dataset}.zip https://petric.tomography.stfc.ac.uk/data/${dataset}.zip
curl -fsSLO https://petric.tomography.stfc.ac.uk/data/${dataset}.zip

mkdir -p data; cd data; unzip -u ../${dataset}.zip; cd ..
test -f main.py || ln -s main_ISTA.py main.py
python <<EOF
import petric
from main import Submission, submission_callbacks
from cil.optimisation.algorithms import Algorithm
assert issubclass(Submission, Algorithm)
assert isinstance(submission_callbacks, list)
assert all(callable(callback) for callback in submission_callbacks)
srcdir, outdir, metrics = petric.data_dirs_metrics[0]
data = petric.get_data(srcdir)
assert data.OSEM_image.max() > 0
assert data.reference_image.max() > 0
assert data.FOV_mask.max() > 0
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may as well test init?

Suggested change
assert data.FOV_mask.max() > 0
assert data.FOV_mask.max() > 0
algo = Submission(data)

or maybe to avoid e.g. "could not find GPU"...

Suggested change
assert data.FOV_mask.max() > 0
assert data.FOV_mask.max() > 0
try:
algo = Submission(data)
except Exception:
from warnings import warn
warn("Submission.__init__ failed", RuntimeWarning, stacklevel=2)

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we'd want to have a dummy submission then. Not sure what a test tells us that we know will fail. Anyway, that'll all be for PETRIC 2.0... I suggest to do minor clean-up here, and merge it when all done.

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run(1) is even more likely to fail than __init__ due to lacking GPU... but true, we could add a warning for that too.

EOF
full:
if: startsWith(github.ref, 'refs/tags')
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