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create basic Github action #891

Merged
merged 11 commits into from
Apr 15, 2021
Merged

create basic Github action #891

merged 11 commits into from
Apr 15, 2021

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KrisThielemans
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@KrisThielemans
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KrisThielemans commented Apr 13, 2021

build is fine but tests fail due to a problem with finding data paths.

MR_TESTS_CPLUSPLUS https://github.com/SyneRBI/SIRF/runs/2336059007?check_suite_focus=true#step:7:760

/home/runner/work/SIRF/SIRF/data/examples/MR/simulated_MR_2D_cartesian_Grappa2.h5', errno = 2, error message = 'No such file or directory'

and confusingly using a different path in ERROR: test1.test_main https://github.com/SyneRBI/SIRF/runs/2336059007?check_suite_focus=true#step:7:837

sirf.Utilities.error: ??? "'File /home/runner/install/share/SIRF-2.2/data/examples/MR/simulated_MR_2D_cartesian_Grappa2.h5 not found' 

Also, we need to install coverage, see https://github.com/SyneRBI/SIRF/runs/2336059007?check_suite_focus=true#step:7:788

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previous run failed with download from Zenodo. hmmm.
https://github.com/SyneRBI/SIRF/runs/2336668850?check_suite_focus=true#step:6:12683

-- Downloading (if not already done)...
		Path:     /home/runner/work/SIRF/SIRF/data/examples/MR/zenodo/dicom_as_nifti.nii
		URL:      https://zenodo.org/record/3571228/files/dicom_as_nifti.nii?download=1
		MD5:      c5f5b519e5c032560ead912713479b53
-- [download 0% complete]
CMake Error at src/Synergistic/tests/CMakeLists.txt:24 (file):
  file DOWNLOAD HASH mismatch

    for file: [/home/runner/work/SIRF/SIRF/data/examples/MR/zenodo/dicom_as_nifti.nii]
      expected hash: [c5f5b519e5c032560ead912713479b53]
        actual hash: [d41d8cd98f00b204e9800998ecf8427e]
             status: [22;"HTTP response code said error"]

@KrisThielemans
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Checking the logs, sirf_env.sh sets

SIRF_PATH=/home/runner/work/SIRF/SIRF
# Where all binaries are installed
SIRF_INSTALL_PATH=/home/runner/install

implying that different tests go and find files in different places, which is probably not a great idea.

The next run will hopefully tell us where the files actually are.

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KrisThielemans commented Apr 14, 2021

This is now running ok, but we get an actual test failure in PET_TESTS_CPLUSPLUS_1, see https://github.com/SyneRBI/SIRF/runs/2346802199?check_suite_focus=true#step:7:1865

vector::_M_range_check: __n (which is 0) >= this->size() (which is 0)

All other tests work. (Currently just tested one configuration)

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This is working as it should. test failure is now reported in #892.

coverage and coveralls are currently not installed. Needs a fix for the issue in #709, #710 first anyway.

@KrisThielemans KrisThielemans linked an issue Apr 15, 2021 that may be closed by this pull request
@KrisThielemans KrisThielemans merged commit 843eb25 into master Apr 15, 2021
@KrisThielemans KrisThielemans deleted the GHA branch April 15, 2021 06:56
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