Update seqspec check so we can run it directly in python script

[mingjiecn]

Previously, we need those two parameters beside seqspec file path to run check function: schema: Draft4Validator, spec: Assay. I updated the function so those two parameters are no longer needed. Only seqspec file path is needed to run check function in python script.

[sbooeshaghi]

Thank you for the PR! To be consistent with other functionality, can you modify the code slightly so that the already loaded spec is passed to the check function? So that way run_check takes in the spec_fn, loads the spec, and then passes it to the check function (like how index works

seqspec/seqspec/seqspec_index.py

Line 149 in e3a6dea

def run_index(

)

[mingjiecn]

If we do so, how to run check in python script when only seqspec file name provided? The purpose of this PR is to remove the schema and the spec parameters out of function check so we can run check directly with only spec file name parameter since seqspec file is the only info we have before, for example: errors = check(seqpec_file_path). Let me know if you can enable check using python script without running it in terminal in some other ways. Thanks!

[sbooeshaghi]

I agree that removing the schema (making it a param that doesn't need to be passed) is a good idea. The way that you can run check in a python script with only the seqspec file name provided is the following

from seqspec.utils import load_spec
from seqspec.seqspec_check import check

spec = load_spec(spec_fn)
errors = check(spec)

This requires making the changes that I suggested (which has the benefit of making the code consistent across seqspec functionality).

[mingjiecn]

Got it. Will do! Thanks!

[mingjiecn]

OK, I put spec back in function check parameters. I can't remove spec_fn since it is used inside check function. Let me know if this is OK. Thank you! @sbooeshaghi

[sbooeshaghi]

Looks great! Thank you. Will merge.