angelolab / ark-analysis / 5297

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Remove intermediate `_clustered`/`_consensus` directories/files from pixel and cell clustering pipeline (#586)

* Remove pixel_mat_clustered and pixel_mat_consensus directories

* Update cell clustering to not have duplicate cluster and consensus files

* First pass of updating tests

* Final pass updating tests to account for one home directory for pixel clustering and one home file for cell clustering

* Remove unused argument from docstring of cell_consensus_cluster

* Same docfix needed for pixel_consensus_cluster

* Update notebook tests to account for new directory structure

* Commit updated cell clustering pipeline

* Reset cell_cluster_prefix back to None

* Remove old commented code in example_cell_clustering.ipynb

* Fix merge conflict (pre_dir to data_dir)

* Remove extraneous string formatter for norm vals name

35 of 35 new or added lines in 2 files covered. (100.0%)

2574 of 2707 relevant lines covered (95.09%)

0.95 hits per line