Genewalk

- Bugfix to ensure same gene ordering in `genewalk_results.csv` as input gene list

- GeneWalk can be installed using conda.
- Require GeneWalk gensim version >= 4.0 This reduces GeneWalk's run time.
- Make GeneWalk compatible with pandas version >= 1.3.0.
- Support for Python v3.8+, no longer v3.6 and 3.7.

- Update to make GeneWalk compatible with latest human GO annotations release 2.2. This affects GeneWalk with all options except `--network_source sif_annot` or `sif_full`: if no earlier annotation file is present in the resources folder, this latest `human_goa.gaf` file will be downloaded and used.

- Require to use version gensim<4. This is a temporary fix to maintain compatibility of GeneWalk with gensim 3.x . In the future GeneWalk will be updated to become compatible with gensim 4.
- Added CLI smoketest for `--network_source sif_annot` to automated testing.

- Minor bug fix that affected only the custom input network options `sif_annot` and `sif_full`: added them to the `--network_source` input argument choice list.

- Increased support for alternative organisms:
- Rat as an organism is now fully automated, similar to GeneWalk for mouse. We allow rat gene identifiers as input gene list with `--id_type rgd_id`. Rat gene ids are then automatically mapped to human ortholog genes with subsequent automated network assembly.
- For organisms other than human, mouse and rat, we now allow custom gene ids with `--id_type custom`: these gene ids are not attempted to be mapped to human orthologs. So the columns hgnc_symbol and hgnc_id are not applicable in the genewalk_results.csv output file and thus not included with `--id_type custom`. When genewalk is run with this option, it requires as additional input a user-provided network file specified with `--network_file` and `--network_source`.
- More options and support for `--network_source`: `edge_list, sif, sif_annot`, or `sif_full` to enable full network assembly when the end user either provides a gene network, gene + GO annotation networks or a full GeneWalk network (gene-gene interactions, GO annotations + GO ontology relations) as input network file in SIF or edge list format. See the README section Custom input networks for full details and which to options to use for other organisms.
- Bug fix: we now include in the genewalk_results.csv output genes without GO annotations. By default, this results file contains all (properly recognized) input genes. See the perform_statistics.GeneWalk class description for the reasons on the fringe cases that input genes could not be included in the results file.
- Download resource files only when needed, instead of previously all in advance.
- Remove INDRA as a default install dependency: INDRA can be separately installed when it is needed in case of using option `--network_source indra`
- Automated gene mapping is now done within genewalk through a stand alone GeneMapper instead of previous INDRA hgnc_client calling.
- Added automated testing for the run options that require a specified `--network_file` and `--id_type rgd_id` or `custom`.