hubmapconsortium / portal-containers

Docker containers to pre-process data for visualization in the portal
MIT License
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[CAT-156] Handle missing H5AD files, bump travis CI env version #120

Closed NickAkhmetov closed 8 months ago

NickAkhmetov commented 8 months ago

This PR makes the scvelo_annotated.h5ad file optional by continuing iteration over the file name list if the file does not exist.

In order to fix CI, the travis config has been set to use a newer version of Ubuntu (focal), as the default (xenial) shipped with an outdated version of openssl which caused urllib3 to throw errors.

NickAkhmetov commented 8 months ago

I rolled back my previous attempt to solve CI build issues in portal-containers:

I did figure out a safer way to set marker genes without triggering pandas warnings about setting data on a copy:

 adata.obs.loc[adata.obs["leiden"] == cluster, f"marker_gene_{str(i)}"] = marker_gene

I've rolled back to before the miniconda change and will try tackling this issue without upgrading the Python version.