Error while running example
parashardhapola opened this issue · 1 comments
parashardhapola commented
Hi,
I tried running this: cirro launch pbmc3k.h5ad --markers markers.json
using the example data.
Got this error:
/home/parashar/miniconda3/lib/python3.7/site-packages/anndata/_core/anndata.py:21: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace.
from pandas.core.index import RangeIndex
Traceback (most recent call last):
File "/home/parashar/miniconda3/bin/cirro", line 10, in <module>
sys.exit(main())
File "/home/parashar/miniconda3/lib/python3.7/site-packages/cirrocumulus/__main__.py", line 20, in main
cmd.main(command_args)
File "/home/parashar/miniconda3/lib/python3.7/site-packages/cirrocumulus/launch.py", line 143, in main
configure(args.dataset, args.spatial, args.backed, args.markers)
File "/home/parashar/miniconda3/lib/python3.7/site-packages/cirrocumulus/launch.py", line 102, in configure
key = os.path.splitext(os.path.basename(marker_json))[0]
File "/home/parashar/miniconda3/lib/python3.7/posixpath.py", line 146, in basename
p = os.fspath(p)
TypeError: expected str, bytes or os.PathLike object, not dict
cirrocumulus version: 1.1.7
Parashar
joshua-gould commented
Thanks for reporting. This is fixed in 1.1.7.post1.