Add a new option --chronumental_add_inferred_date

[AngieHinrichs]

This adds the new option --chronumental_add_inferred_date <column_name> that I suggested in #607. Feel free to bounce it back if there is anything big or small that you'd like me to change / rename / reword / etc.

An example usage is

usher_to_taxonium -i my_tree.pb -m my_tree.metadata.tsv -o my_tree.jsonl.gz \
    --chronumental --chronumental_steps 300 \
    --chronumental_add_inferred_date chronumental_date

After running chronumental, it reads the date output file(*) and adds a new metadata 'column' (in this example, chronumental_date) whose value for each node is the date inferred by chronumental for that node. When viewing the resulting my_tree.jsonl.gz in taxonium, the inferred date is displayed for each node when hovering over or clicking on the node, appearing as an extra metadata item. When the node is clicked on, the label for the inferred date is "Chronumental date" in this example (derived the usual way from chronumental_date).

(*) The date output file is either the filename specified with --chronumental_date_output if given, or the default name which currently is derived from the metadata file name (chronumental_dates_metadata_file.tsv). If --chronumental_date_output is not given and the expected metadata-derived date output file does not exist, then it quits with a suggestion to add --chronumental_date_output.

I have tested it with and without --chronumental_date_output and with a relative and absolute path for the metadata file from which the default date output file name is derived, and it seems to work.

Thanks as always for taxonium, don't know what I'd do without it! 🙂

[vercel]

@AngieHinrichs is attempting to deploy a commit to the theosanderson's projects Team on Vercel.

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[theosanderson]

Thank you for an amazing PR. This looks fantastic. Huge thanks for taking it on. There's one inconsequential typo, which I guess we might as well fix.

Thanks so much again

[theosanderson]

@allcontributors if you're still active please add @AngieHinrichs for code

[allcontributors]

@theosanderson

I've put up a pull request to add @AngieHinrichs! 🎉

[AngieHinrichs]

lococation

Ha! It's, uh, a California thing, yeah. 😆 Thanks Theo!