Pyscenic

Updates:
* Fix bug in motif url construction (158)
* Integrate arboreto multiprocessing script into pySCENIC CLI
* cisTarget step: Check for modules with zero db overlap and skip them (158, 177, 132, 85)
* Bugfix in TF-gene correlation calculation. Quit with error if there is a mismatch between the genes present in the GRN and the expression matrix (103, 149)
* Error message when regulons file is empty (133)

Updates:
- Bugfix for CLI grn step

Updates:
* CLI: file compression (optionally) enabled for intermediate files for the major steps: grn (adjacencies matrix), ctx (regulons), and aucell (auc matrix). Compression is used when the file name argument has a `.gz` ending.
* Restrict packages (pyarrow, pandas) for compatibility.

Updates:
- Added a helper script scripts/arboreto_with_multiprocessing.py that runs the Arboreto GRN algorithms (GRNBoost2, GENIE3) without Dask for compatibility.
- Initial support for the use of sparse expression matrices (applies only to the GRN step in the CLI currently). Using sparse matrices with the GRN step requires a patch to Arboreto (tmoerman/arboreto20)
- AUCell uses a random sampling of the expression matrix to break ties in the ranking step. The CLI parameter --seed or aucell function parameter seed uses a fixed seed for this step. The regulon thresholds also depend on random sampling in the binarization step (bimodality test: np.random.uniform), and the seed parameters apply here as well.
- Fixed typo in regulon threshold labeling
- Security patch: Bump bleach from 3.1.0 to 3.1.1.

-BugFixes: 100 and 51.

In the modules_from_adjacencies function, the default value of rho_mask_dropouts is changed to False. This now matches the behavior of the R version of SCENIC. Since this is likely to change the final output regulons slightly, warnings have been added to the logging system. The cli version has an additional option to turn dropout masking back on (--mask_dropouts).