Issue #402: Fix tests that fail as a result of running pytest with no flags

[baileythegreen]

CLI parsing in pyani_script.py and some test files made the implicit assumption that they were dealing with a pyani command; however, these files also parse the command line when a pytest command is issued. When:

$ pytest

is run on its own (with no flags), this therefore caused things to fail.

Closes #402.

Type of change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality not to work as expected)
• This change requires a documentation update
• This is a documentation update

Action Checklist

• Work on a single issue/concept (if there are multiple separate issues to address, please use a separate pull request for each)
• Fork the pyani repository under your own account (please allow write access for repository maintainers)
• Set up an appropriate development environment (please see CONTRIBUTING.md)
• Create a new branch with a short, descriptive name
• Work on this branch
  • style guidelines have been followed
  • new code is commented, especially in hard-to-understand areas
  • corresponding changes to documentation have been made
  • tests for the change have been added that demonstrate the fix or feature works
• Test locally with pytest -v non-passing code will not be merged
• Rebase against origin/master
• Check changes with flake8 and black before submission
• Commit branch
• Submit pull request, describing the content and intent of the pull request
• Request a code review
• Continue the discussion at Pull requests section in the pyani repository

[codecov]

Codecov Report

Merging #404 (5676e63) into master (62949c4) will decrease coverage by 0.00%.
The diff coverage is 80.00%.

@@            Coverage Diff             @@
##           master     #404      +/-   ##
==========================================
- Coverage   75.82%   75.81%   -0.01%     
==========================================
  Files          55       55              
  Lines        3747     3750       +3     
==========================================
+ Hits         2841     2843       +2     
- Misses        906      907       +1     

[widdowquinn]

I don't understand why endswith() is used in preference to ==. What is your thinking, here?

Also, the pyani command would not executeaverage_nucleotide_identity.py - the command for this is average_nucleotide_identity.py (see this line), so should this not be testing for average_nucleotide_identity.py rather than pyani?

[baileythegreen]

For the == part, see my response below.

Also, the pyani command would not execute average_nucleotide_identity.py

Yes, you're right; that was a mistake on my part.

[widdowquinn]

So long as you make the change such that v0.2 tests for average_nucleotide_identity.py this part of the conversation can be resolved.

[widdowquinn]

I don't understand why endswith() is used in preference to ==. What is your thinking, here?

[baileythegreen]

Because sys.argv[0] in this case is not pyani, but:

/Users/baileythegreen/Software/miniconda3/envs/pyani_dev/bin/pyani.

The same goes for pytest above. I tried == first, and it failed.

[widdowquinn]

I see. It would be more robust to either (i) treat sys.argv[0] as a Path object and test for equality using the .name attribute, or (ii) .split("/") the passed path and test the last element in the resulting collection. Using .endswith() does give a True value with the case you want, but also in cases where the executable is not simply pyani (or pytest, in the case where you'r echecking for that):

>>> from pathlib import Path
>>> pyani_path = "/my/path/to/pyani"
>>> notpyani_path = "/my/path/to/notpyani"
>>> Path(pyani_path).name
'pyani'
>>> Path(notpyani_path).name
'notpyani'
>>> pyani_path.split("/")[-1]
'pyani'
>>> notpyani_path.split("/")[-1]
'notpyani'
>>> pyani_path.endswith("pyani")
True
>>> notpyani_path.endswith("pyani")
True

[baileythegreen]

I mentioned in our last meeting that I'd thought of a better way to do it, and I think I said that was using a Path() object; you said you thought not testing for pytest specifically would be better—and I thought part of the implication there was you didn't want Path() used.

I must have misunderstood; I can of course use Path() and test for whether the program is pyani, or not.

[baileythegreen]

Sorry, I missed there were comments on this the other day; I only saw the email about codecov.