[MRG] update default db to rs207 reps

[taylorreiter]

Addresses #212 by updating to the GTDB rs207 reps database by default. Notes of potential importance:

1. downloads the full gtdb rs207 lineage file, not reps. Other than taking up space, this doesn't change how charcoal runs.
2. changes scaled value from 1000 -> 2000, which is the scaled value reps is built at. May cause some short contigs to be missed that previously were detectable, but I think the benefit is outweighed having the larger database.

[taylorreiter]

Interesting -- fails with

    raise ValueError(f"empty or improperly formatted pickfile '{pickfile}'")
ValueError: empty or improperly formatted pickfile '/tmp/charcoal_testr532yde4/stage1/TOBG_NAT-167.fna.gz.matches.csv'
Traceback (most recent call last):
  File "/usr/share/miniconda/lib/python3.9/runpy.py", line 197, in _run_module_as_main
    return _run_code(code, main_globals, None,
  File "/usr/share/miniconda/lib/python3.9/runpy.py", line 87, in _run_code
    exec(code, run_globals)
  File "/home/runner/work/charcoal/charcoal/charcoal/contigs_search_taxonomy.py", line 151, in <module>
    returncode = cmdline(sys.argv[1:])
  File "/home/runner/work/charcoal/charcoal/charcoal/contigs_search_taxonomy.py", line 146, in cmdline
    return main(args)
  File "/home/runner/work/charcoal/charcoal/charcoal/contigs_search_taxonomy.py", line 36, in main
    picklist.load(args.matches_csv, picklist.column_name)
  File "/usr/share/miniconda/lib/python3.9/site-packages/sourmash/picklist.py", line 163, in load
    raise ValueError(f"empty or improperly formatted pickfile '{pickfile}'")
ValueError: empty or improperly formatted pickfile '/tmp/charcoal_testr532yde4/stage1/GCF_000005845-subset.fa.gz.matches.csv'

[taylorreiter]

I'm pretty sure these are failing bc of missing dependencies lxml, plotly, and interval. @ctb, I'm not sure how to handle this within tests. I think tests is taking the environment from environmentl.yml, but snakemake installs these in their own env when it runs these scripts. Should i make a test_environment.yml and change the github actions?

[taylorreiter]

hmm no, they were failing locally bc of missing dependencies, but now that I have those installed, i'm getting the same

File "/home/tereiter/miniconda3/envs/charcoal/lib/python3.9/site-packages/sourmash/picklist.py", line 163, in load
    raise ValueError(f"empty or improperly formatted pickfile '{pickfile}'")

and not totally sure why updating the databases would do that. wondering if it's on the sourmash side?

[mr-eyes]

Is the Python version that created the pickle file the same as the one reading it?

[mr-eyes]

Oh sorry, it's pickfile not pickle.

[taylorreiter]

Ok! so downgrading to sourmash 4.2.3 from 4.4.0 fixed the failed tests. I'll post an issue on sourmash repo, not sure what's causing the problem exactly, but this PR is ready for review and merge @ctb!