Dictys

Added functionality to account for multi-TF motifs.
Exposed functionality to account for covariates in pipeline input.
Updated interfaces with external systems such as zenodo.
Bug corrections.
Improved helper scripts.
Improved documentation, tutorials, and error messages.
Minor aesthetic updates.

Added container support.
Updated CUDA support for pytorch 2.
Integrated direct & steady-state networks into the same h5 file.
Package dependency corrections.
Updated documentation.

New functionalities:
- Added option to use weighted outdegree centrality as regulatory activity for network analysis and visualization functions
- Added option to use whitelist filter when linking TFs to target genes
- Added layout templates for dynamic network animation in dictys.plot.layout

Improvements:
- Updated network file functions
- Bug corrections
- Code and interface refactoring
- Updated documentation & logging
- Added/updated tutorials
- Added continuous integration for tests, code/repo maintenance, and package release
- Added python 3.10 support

Initial release.