Error in plot_umap_connectivity: hammer_bundle operation requires dask and scikit-image.

[bednarsky]

Hi Stephan!

I run the RNA seq recipe without alteration on my own data (i.e., directly loading the module from GitHub with the version you specified) and the unsupervised pipeline throws this error in the rule plot_umap_connectivity:

/path/to/conda/d965d06338ed4b57fe9c14c206004e77_/lib/python3.9/site-packages/umap/plot.py:894: UserWarning: Hammer edge bundling is expensive for large graphs!
This may take a long time to compute!
  warn(
Traceback (most recent call last):
  File "/projects/proj_name/.snakemake/scripts/tmp693k2k30.plot_umap_connectivity.py", line 31, in <module>
    umap.plot.connectivity(umap_obj, edge_bundling='hammer').figure.savefig(plot_connectivity_path)
  File "/path/to/conda/d965d06338ed4b57fe9c14c206004e77_/lib/python3.9/site-packages/umap/plot.py", line 898, in
connectivity
    edges = bd.hammer_bundle(point_df, edge_df, weight="weight")
  File "/path/to/conda/d965d06338ed4b57fe9c14c206004e77_/lib/python3.9/site-packages/param/parameterized.py", lin
e 4626, in __new__
    return inst.__call__(*args,**params)
  File "/path/to/conda/d965d06338ed4b57fe9c14c206004e77_/lib/python3.9/site-packages/datashader/bundling.py", lin
e 541, in __call__
    raise ImportError("hammer_bundle operation requires dask and scikit-image. "
ImportError: hammer_bundle operation requires dask and scikit-image. Ensure you install the dependency before applying bundling.
RuleException:
CalledProcessError in file "https://raw.githubusercontent.com/epigen/unsupervised_analysis/v3.0.2/workflow/rules/visualization.smk", line 199:
Command 'source /path/to/miniconda3/bin/activate '/path/to/conda/d965d06338ed4b57fe9c1
4c206004e77_'; set -euo pipefail;  python /projects/proj_name/.snakemake/scripts/tmp693k2k30.plot_umap_connectiv
ity.py' returned non-zero exit status 1.

Do you know what this is about?

[sreichl]

My best guess is that the dependencies have changed for this function and are not included in your newly installed environment. Could you please add these two packages (dask and scikit-image) to the respective environment YAML file? Try again, and if it works, read out the respective versions, add them to the environment and create a pull request.

[bednarsky]

Yes, will do!

[sreichl]

please try now with tag="v3.0.3"

[bednarsky]

Works!