OME-Zarr Test Suite

This suite loops over a number of sources of OME-Zarr files, running any generation code if necessary, and then passes the URI for the fileset to all registered suites.

In pseudo-code:

for source in sources:
    for suite in suites:
        source.setup()
        try:
            suite(source)
        finally:
            source.cleanup()

so that at any one time, at most one (potentially generated) resource is active.

Each suite is expected to take all configuration values it needs from the Zarr itself. (TBD)

Sources include test files created with ome-zarr-py, local files (from data directory), remotely-hosted sample files, files generated by bioformats2raw and data served from OMERO with omero-ms-zarr. In the latter 2 cases, Docker environments are used.

The whole test suite can be run locally as shown below. NB: this will take some time as multiple Docker environments will be created. To limit the number of sources or tests, the sources.yml and suites.yml files can first be edited to exclude some items.

# this takes a while...
$ conda env create -n ome_zarr_test_suite -f environment.yml

$ conda activate ome_zarr_test_suite

# Run all tests
$ pytest