Refactor functions that use run_shell_cmd() function in test_sourmash.py and test_sourmash_compute.py per #987

[erikyoung85]

This PR removes all references to the old run_shell_cmd function and replaces it making use of the @utils.in_tempdir decorator
Fixes #987

• Is it mergeable?
• make test Did it pass the tests?
• make coverage Is the new code covered?
• Did it change the command-line interface? Only additions are allowed
  without a major version increment. Changing file formats also requires a
  major version number increment.
• Was a spellchecker run on the source code and documentation after
  changes were made?

[codecov]

Codecov Report

Merging #1032 into master will increase coverage by 0.05%.
The diff coverage is n/a.

@@            Coverage Diff             @@
##           master    #1032      +/-   ##
==========================================
+ Coverage   92.37%   92.42%   +0.05%     
==========================================
  Files          72       72              
  Lines        5454     5454              
==========================================
+ Hits         5038     5041       +3     
+ Misses        416      413       -3     

Impacted Files	Coverage Δ
sourmash/commands.py	86.78% <0.00%> (+0.52%)	⬆️

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[ctb]

Looks good!

Could you edit the PR description (not title, but the textbox with the checklist in it) to reference #987? If you put in "Fixes #987" on the start of a new line, when we merge this PR it will automatically close it.

As I noted in a comment, this PR is built off of the refactor_test branch in #1020, and while that's probably OK right now, it would be better if it were not :). If you want to learn some more git, read on! The only difference between this PR and #1020 is commit 0ecd740, so you could try "fixing it" like so --

# start fro updated master branch.
git checkout master
git pull origin master
# make new branch based off of latest master
git checkout -b remove_run_shell_cmd_2
# pick off _just_ the commit that made the run_shell_cmd changes
git cherry-pick 0ecd740d
# forcibly overwrite (with a force-push) the `remove_run_shell_cmd` branch on master
git push -f origin remove_run_shell_cmd_2:remove_run_shell_cmd
# remove your local (old) run_shell_cmd branch
git branch -D remove_run_shell_cmd
# make a new one based off of this
git checkout -b remove_run_shell_cmd

and that should work. An alternative would be to close this PR and make a new one with a new branch based off of master, with that same cherry-pick.

[erikyoung85]

Yes, I was worried that I accidentally had made this PR built off of the refactor_test branch. I'll try fixing it with the git code you provided maybe learn some stuff along the way too :)

[ctb]

LGTM! Thanks!

Can you push the "update from latest master" button, and then, assuming the tests pass, go ahead and squash & merge it? Bump me if you can't do something, I'm not 100% sure you have merge permissions :)

[erikyoung85]

it says "You're not authorized to merge this pull request."

also, is there a specific spell checker I should be using to check my code?

[ctb]

ok, I'll figure out permissions later! re spell checker, most editors have them in some form. If you're not writing docs or adding substantial new code it's probably fine not to worry about it, and I will catch most misspellings in my review too.

Congrats on your second merge!