Add CX2 conversion functionality

[pkalita-lbl]

Fixes #3

These changes add a new package (gocam.translation.cx2) with one main function (model_to_cx2) responsible for converting a GO-CAM Model instance to CX2 format. This functionality is also exposed through a new convert CLI subcommand. The CLI also has some very basic functionality for uploading to NDEx.

Details

• The new dependency on the ndex2 package is used to facilitate both CX2 generation and interacting with the NDEx API.
• src/gocam/translation/cx2/main.py is the crux of the conversion logic. Some style-related constants are defined in src/gocam/translation/cx2/style.py. The edge style mappings are designed to be aligned with the GO-CAM visualization widget.
• A new convert subcommand is added to the CLI in src/gocam/cli.py. For now the only supported output format is CX2, but I assume we will have more in the future. If not, we could consider having this be a dedicated CX2 subcommand.

Examples

Using the CLI to convert an example Model file to CX2 (printed to stdout):

gocam convert --output-format cx2 src/data/examples/Model-663d668500002178.yaml 

Using the CLI to fetch a GO-CAM model and then convert it to CX2:

gocam fetch 663d668500002178 | gocam convert --input-format yaml --output-format cx2

[github-actions]

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on branch gh-pages at 2024-08-08 00:00 UTC