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pygmt.which: Fix the bug when passing multiple files #2726

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Merged
merged 3 commits into from
Oct 15, 2023
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pygmt.which: Fix the bug when passing multiple files #2726

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pygmt.which: Fix the bug when passing multiple files
seisman Oct 9, 2023
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Apply suggestions from code review
seisman Oct 15, 2023
436eec8
Merge branch 'main' into which
seisman Oct 15, 2023
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6 changes: 4 additions & 2 deletions pygmt/src/which.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,13 @@
GMTTempFile,
build_arg_string,
fmt_docstring,
kwargs_to_strings,
is_nonstr_iter,
use_alias,
)


@fmt_docstring
@use_alias(G="download", V="verbose")
@kwargs_to_strings(fname="sequence_space")
def which(fname, **kwargs):
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Reading up on https://peps.python.org/pep-0570/#positional-or-keyword-arguments and https://stackoverflow.com/questions/9450656/positional-argument-vs-keyword-argument (see also Max's previous comment at #731 (comment)), should we explicitly mark fname as positional_or_keyword like this (unsure if syntax is ok)?

Suggested change
def which(fname, **kwargs):
def which(/, fname, *, **kwargs):

Or just stick with the current one (which works also I think).

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Better to open a separate issue so that we can have more discussions about the behavior and also have consistent function definitions in the whole project.

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@weiji14 weiji14 Oct 15, 2023 •
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On second thought, maybe we should enforce using keyword-only arguments like so:

Suggested change
def which(fname, **kwargs):
def which(*, fname, **kwargs):

Then the gmtwhich [ERROR] you mentioned at #2361 (comment) would turn into a slightly more useful error:

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
Cell In[4], line 1
----> 1 cached_files = which([f"@{fname}" for fname in filenames], download="c")

File ~/pygmt/pygmt/helpers/decorators.py:598, in use_alias.<locals>.alias_decorator.<locals>.new_module(*args, **kwargs)
    591     msg = (
    592         "Parameters 'Y' and 'yshift' are deprecated since v0.8.0. "
    593         "and will be removed in v0.12.0. "
    594         "Use Figure.shift_origin(yshift=...) instead."
    595     )
    596     warnings.warn(msg, category=SyntaxWarning, stacklevel=2)
--> 598 return module_func(*args, **kwargs)

TypeError: which() takes 0 positional arguments but 1 was given

Well, actually not that useful (it doesn't say that the fname keyword should be used. But something to consider - if we want to allow 1) positional_or_keyword (current), or 2) only keyword.

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Instead, I prefer to def which(fname, *, **kwargs). It allows which("file.txt") which is much simpler than which(fname="file.txt").

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Ok, let's go with that. I'll approve this PR, but you can apply the change afterwards.

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def which(fname, *, **kwargs)

gives a syntax error:

'named arguments must follow bare *

See https://stackoverflow.com/questions/14301967/what-does-a-bare-asterisk-do-in-a-parameter-list-what-are-keyword-only-parame.

I'll leave the function definition as it is now.

r"""
Find the full path to specified files.
Expand Down Expand Up @@ -63,6 +62,9 @@ def which(fname, **kwargs):
FileNotFoundError
If the file is not found.
"""
if is_nonstr_iter(fname): # Got a list of files
fname = " ".join(fname)

with GMTTempFile() as tmpfile:
with Session() as lib:
lib.call_module(
Expand Down
14 changes: 7 additions & 7 deletions pygmt/tests/test_which.py
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
"""
Test pygmt.which.
"""
import os
from pathlib import Path

import pytest
from pygmt import which
Expand All @@ -13,20 +13,20 @@ def test_which():
Make sure `which` returns file paths for @files correctly without errors.
"""
for fname in ["tut_quakes.ngdc", "tut_bathy.nc"]:
cached_file = which(f"@{fname}", download="c")
assert os.path.exists(cached_file)
assert os.path.basename(cached_file) == fname
cached_file = which(fname=f"@{fname}", download="c")
assert Path(cached_file).exists()
assert Path(cached_file).name == fname


def test_which_multiple():
"""
Make sure `which` returns file paths for multiple @files correctly.
"""
filenames = ["ridge.txt", "tut_ship.xyz"]
cached_files = which(fname=[f"@{fname}" for fname in filenames], download="c")
cached_files = which([f"@{fname}" for fname in filenames], download="c")
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Now we can pass a list of files without having to use fname=

for cached_file in cached_files:
assert os.path.exists(cached_file)
assert os.path.basename(cached_file) in filenames
assert Path(cached_file).exists()
assert Path(cached_file).name in filenames


def test_which_fails():
Expand Down