Add function to retrieve metadata from Nextstrain's ncov pipeline run at a specific point in time

[bsweger]

closes #20

Background

This PR addresses the issue above and also introduces a new class to simplify the interface for working with Nextstrain files: CladeTime (because we can get sequences and clade assignments at any point in time, get it?)

The only thing CladeTime currently does is instantiate with:

1. a specific as_of date for both Sars-Cov-2 sequences/sequence metadata
2. a specific as_of date for the reference tree used to assign sequences to clades

CladeTime also has an ncov_metadata attribute, because that's what we need right now to get the variant nowcast hub ready.

Review Notes

The commits are reasonably organized, so starting at the first one and reviewing commit by commit is recommended.

Demo

There's more information in the README, but to try CladeTime as a code reviewer, you'll need to install the package from this branch:

pip install "git+https://github.com/reichlab/virus-clade-utils.git@bsweger/get_nextstrain_ncov_metadata"

Then, from a Python console or script (the code below is what we'll add to get_clades_to_model.py in the variant nowcast repo, so we can save the metadata along with the clade list):

from virus_clade_utils.cladetime import CladeTime
ct = CladeTime()
ct.ncov_metadata

The above should return a Python dictionary similar to:

{
    "schema_version": "v1",
    "nextclade_version": "nextclade 3.8.2",
    "nextclade_dataset_name": "SARS-CoV-2",
    "nextclade_dataset_version": "2024-09-25--21-50-30Z",
    "nextclade_tsv_sha256sum": "fbe579554e925e4dfaf74cfb4e72b52c702e671f0f0374d896f1e30ae4fe5566",
    "metadata_tsv_sha256sum": "5a4fd84a5cd3c4ead9cf730d4df10b8734898c6c3e0cae1c8c0acf432325d22c",
}

[bsweger]

Now that we're using package functions an interactive context (in addition to using them in batch scripts), let's provide a way to make retries optional when using a requests session.

[bsweger]

See: https://httpstat.us/

[bsweger]

Nextstrain only began publishing their pipeline metadata at the beginning on 8/1/24, so we won't find it for earlier dates.