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Issue #402: Fix tests that fail as a result of running pytest with no flags #404

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Issue #402: Fix tests that fail as a result of running pytest with no flags #404

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c0ab9c9
Add CLI parsing check to ignore some checks if the program isn't pyani
baileythegreen Jun 15, 2022
5676e63
Make CLI check for program name more robust
baileythegreen Jun 21, 2022
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3 changes: 2 additions & 1 deletion pyani/scripts/average_nucleotide_identity.py
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Original file line number Diff line number Diff line change
Expand Up @@ -871,7 +871,8 @@ def process_arguments(args: Optional[Namespace]) -> Namespace:
shows the version and exits.
"""
# Catch execution with no arguments
if len(sys.argv) == 1:
# But only for the `pyani` executable (`pytest` was also being caught here)
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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?

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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.

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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.

if len(sys.argv) == 1 and sys.argv[0].endswith("pyani"):
sys.stderr.write("pyani version: {0}\n".format(__version__))
raise SystemExit(0)

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4 changes: 4 additions & 0 deletions pyani/scripts/pyani_script.py
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Expand Up @@ -103,6 +103,10 @@ def run_main(argv: Optional[List[str]] = None) -> int:
sys.stderr.write(f"{VERSION_INFO}\n")
return 0

# If the command run is not pyani (e.g., `pytest`, then we
# don't want to apply pyani-specific checks)
if len(sys.argv) == 1 and not sys.argv[0].endswith("pyani"):
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I don't understand why endswith() is used in preference to ==. What is your thinking, here?

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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.

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@widdowquinn widdowquinn Jun 20, 2022 •
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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

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@baileythegreen baileythegreen Jun 20, 2022 •
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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.

pass
# Catch requests for citation and version information
if sys.argv[1].startswith("-"):
if args.citation:
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