beeflow:useContainer support for SquashFS

[arhall0]

Closes #967

Enables the use of SquashFS format for the DockerRequirement beeflow:useContainer.

I tested this by modifying the clamr example's clamr_wf.cwl file and changed the two DockerRequirements to be:

        DockerRequirement:
            beeflow:useContainer: "$WORKDIR_PATH/clamr-ffmpeg.sqfs"

Where clamr-ffmpeg.sqfs was made using the Dockerfile included with the example.

[arhall0]

I'm currently not checking if SquashFS is installed. So an error would be thrown from the job by Charliecloud and end up in the archive. I don't have a good way to check this situation.

We could throw an error earlier with something like if shutil.which('fusermount3') is None then error based on https://hpc.github.io/charliecloud/ch-run.html#image-format

[pagrubel]

I'm currently not checking if SquashFS is installed. So an error would be thrown from the job by Charliecloud and end up in the archive. I don't have a good way to check this situation.

We could throw an error earlier with something like if shutil.which('fusermount3') is None then error based on https://hpc.github.io/charliecloud/ch-run.html#image-format

Could this be tested in our github ci, I don't think we have Squash fuse installed.

[arhall0]

Could this be tested in our github ci, I don't think we have Squash fuse installed.

I made a debug test to run in CI to see if fusermount3 is available and it seems like it is:

 =================================== FAILURES ===================================
_________________________ test_debug_check_fusermount3 _________________________

    def test_debug_check_fusermount3():
        """Debug check if system has `fusermount3`."""
>       assert shutil.which('fusermount3') is None
E       AssertionError: assert '/usr/bin/fusermount3' is None
E        +  where '/usr/bin/fusermount3' = <function which at 0x7f5cc7b41990>('fusermount3')
E        +    where <function which at 0x7f5cc7b41990> = shutil.which

beeflow/tests/test_charliecloud_driver.py:76: AssertionError

I believe fusermount3 is all that Charliecloud needs to use SquashFS for ch-run, although I could be mistaken.

[arhall0]

Note: Unit tests failure in the CI right now seems to be when its trying to update the coverage badge. This branch is a bit out of date with develop and that seems to break that process until you merge/rebase.

[pagrubel]

I think we can let Charliecloud handle what happens if the requirement for sqfs doesn't exist. I just had an error. It did it fairly well when I tried the .sqfs conatiner using the develop branch. The clamr task failed and the workflow failed due to that. I was able to find the errors in the stderr file.

[pagrubel]

This looks good, can you get the unit tests cleared up?

[pagrubel]

This works well and looks great. Thanks for adding the test.