Port to CircleCI 2.0 #79
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Based on bids-apps/example#27.
Taking components from the FreeSurfer BIDS App.
git tag cannot be queried for the purpose of generating a name for the container cache.
Primarily to fix version of numpy for nibabel dependency. Also updates MRtrix3 to version 3.0.1.
These are now included in the MRtrix3 installation.
Exceeded 10 minutes with no output in build 79.
- Use apt-get rather than apt throughout. - Use correct version of tzdata for Singularity. - Force ants version in Singularity.
Missing changes from 8fb0fa3.
CircleCI job 286 failed with "write /dev/stdout: no space left on device"
- Don't attempt to call "docker builder prune", since it appears to not be supported on the CircleCI version of Docker. - Don't make any attempt to load cache in the build job.
Testing to see whether this prevents a "permission denied" error when attempting to extract the downloaded test data.
Separate test data for "preproc" and "participant" uploaded to OSF. Will also try to run separate jobs for testing "preproc" and "participant" analysis levels.
- Fix N=1 intensity normalisation factor using undefined variable due to having been duplicated from another area of code. - Defer calculation of voxel volume from the SessionPaths class constructor to later in execution, so that the scratch directory will have already been constructed, and therefore the Image.Header constructor will write the corresponding temporary JSON to the scratch directory, avoiding a filesystem write access issue in some circumstances.
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Second attempt at moving to CircleCI 2.0. My first attempts a long time ago were unsuccessful, but thanks to bids-apps/example#27 I now have a working example to go off.
Even if the CI is configured correctly up-front, it likely won't work the first time because I need to generate new test data to conform to the expectations of version
0.5.0. In the process of making that change I'll hopefully include a wider breadth of tests, including BIDS raw data for different acquisition designs, to satisfy #76.