Pyscenic

BugFix in command line interface: change functionality of all_modules option.

- Overall more consistent CLI.
- Possibility for the user to keep negative regulons in the analysis via the CLI.

- support for dask 0.18+
- modules_from_adjacencies: by default keep only modules in which the expression of the TFs is positively correlated with its target genes.
- Command Line Interface: support for JSON-serialized regulon output in cisTarget/prune step.

Loom export functionality (for SCope): sequence logo is now part of a regulon's metadata.

* Changed dependency: the arboretum package was renamed to arboreto. Changed the dependency requirements accordingly.
* Support for export to loom format to be able to explore cellular scatter plots and activity of regulons/gene signatures in the [SCope](https://scope.aertslab.org/#/) tool.
* Support for exporting selected regulons to Cytoscape to visualise Gene Regulatory Networks.

BugFix for NameError: free variable 'module_chunksize' referenced before assignment in enclosing scope.