Unittest images #36
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Unittest images #36
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Looks through all directories for unittest.yml files. It assumes there is a Dockerfile in the directory with this file. It guesses a name for the image. Builds the Dockerfile tagging that name using docker. For each command, expected_output pair in the unittest.yml file: run the image passing the command compares the expected_output(regex) against the output from the image exits if any images failed WIP
Approach taken from apptainer/singularity#429 (comment) 1. Creates docker container using local image. 2. Create singularity image 3. export docker image | import new singularity image
Other methods didn't fully setup singularity environment.
singularity was unable to reach the image registry Adding docker registry image to the circle config. Currently using circleci `docker` machine type. The `machine` machine type might resolve this issue but > Use of machine may require additional fees in a future pricing update. https://circleci.com/docs/2.0/executor-types/
this is to work around a cached venv from docker executor type that doesn't work under machine exexutor type
Also fixes picard unittest
singularity didn't like "trimmomatic:0.32+dfsg-1" on dockerhub its trimmomatic:0.32_dfsg-1
creates tests directory to hold image testing framework renames test.py to imagecheck
Adds more print commands so it is easier to see progress in the tests
This resulted in occasional connection reset by peer errors when running `docker push`.
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Closing this for now due to the complexity and time it takes to run.
Both issues can be seen using just docker via the |
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Runs unit tests on images to make sure they will work with both docker and singularity.
test.pylook for files namedunitest.yml. These files are assumed to be in a directory with a Dockerfile. Theunittest.ymlfile will contain a list ofcommandsto run that contain acmdandexpected_outputregex pattern.TODO