Genewalk

- A new visualization stage has been added that is run by default as part of the whole program or alone when calling `--stage visual`.
- This stage automatically generates plots of all GeneWalk results in the project/figures folder.
- The file `index.html` in the figures folder contains all visualization and allows the end user to easily browse the GeneWalk results:
- Interactive scatter plots to identify the regulator and moonlighter genes and
- Bar plots with GO annotations ranked by their global_padj for each input gene.
- Each figure is also saved as separate .png and/or .pdf file.
- Automated testing has been improved to cover the whole CLI.

- New globally adjusted p-values (`global_padj`) reported in output along with the gene-level adjusted p-values (`gene_padj`), the latter was previously called `mean_padj`.
- New CLI option for changing the dimensionality of the embeddings vectors
- GeneWalk now supports Python 3.6+ and is compatible with INDRA 1.19.0
- Automated testing is now done on GitHub Actions

- Adapt to use INDRA v18.
- Update README documentation to include all v1.2.* features.

- Replace outdated HGNC gene symbols with their current ones in Pathway Commons v12 knowledge base.
- Handle outdated HGNC gene symbols from user input list.
- Add missing documentation sections for readthedocs manual.

- Support for human Ensembl IDs in gene lists
- Support for human and mouse Entrez IDs in gene lists
- Upgrade to PathwayCommons v12
- All input genes are now present in the GeneWalk network as long as they have GO annotations, irrespective of their gene-gene connectivity (previously only genes that had other direct gene connections were included in the network).
- Fix the calculation of the 95% confidence interval around mean p-adjust (does not affect the mean value reported with prior versions).
- In case of numerical underflow for p values, a default minimum of 1e-16 is set.
- Add `--version` argument to CLI to print version
- Add `--random_seed` argument to CLI to reproduce prior results
- Compatibility updates to support networkx 2.4+
- Automated testing on TravisCI

- Improved parallelization scheme implemented in `genewalk.deepwalk`, used when `nproc` > 1
- Default number of repeats (`nreps_graph`, `nreps_null`) set to 3
- Extended README with documentation, funding and citation