Add support for passing pathlib.Path objects as filenames #1382

aitorres · 2021-07-10T21:23:23Z

Description of proposed changes

This PR addresses and fixes issue #1381. By adding support to pathlib.Path values that represent file paths to the data_kind helper function, it can be used interchangeably with file name strings on pygmt modules.

Fixes #1381

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welcome · 2021-07-10T21:23:25Z

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weiji14 · 2021-07-13T23:00:29Z

Hmm, supporting pathlib.Path might not be as simple as I thought. We'll need to convert the pathlib.Path object into a str in order for the GMT C API to understand it (the new test_info_path unit test is currently failing at https://github.com/GenericMappingTools/pygmt/pull/1382/checks?check_run_id=3040356636#step:11:589). Do you want to walk through the virtualfile_from_data function at https://github.com/GenericMappingTools/pygmt/blob/master/pygmt/clib/session.py and see if you can find a good place to do the pathlib.Path->str conversion? Or we could change the line at

pygmt/pygmt/helpers/utils.py

Line 106 in 60a92b3

yield arg

to say yield str(arg) perhaps?

aitorres · 2021-07-19T00:56:53Z

I'm sorry for the delay! I've examined the virtualfile_from_data function and modified the conditional statement to cast data to str in presence of "file" data kind, instead of modifying the dummy_context function.

I've pushed my changes to my branch already, and will keep an eye on the tests in case something fails again. Thanks for your help!

weiji14

I'm sorry for the delay! I've examined the virtualfile_from_data function and modified the conditional statement to cast data to str in presence of "file" data kind, instead of modifying the dummy_context function.

Nice one, that's a much better solution! Will see if the tests pass on all platforms (Linux/macOS/Windows).

pygmt/clib/session.py

weiji14

Thanks @aitorres, looks good. I'll merge in 24hrs unless any of the other devs have something to add.

Edit: Please resolve #1382 (comment) before we can proceed.

seisman · 2021-07-19T14:57:08Z

pygmt/helpers/utils.py

@@ -66,7 +71,7 @@ def data_kind(data, x=None, y=None, z=None):
    if data is None and (x is None or y is None):
        raise GMTInvalidInput("Must provided both x and y.")

-    if isinstance(data, str):
+    if isinstance(data, (str, pathlib.Path)):


What will happen if people use pathlib.PurePath or path.PurePosixPath?

The answer at https://stackoverflow.com/questions/58647584/how-to-test-if-object-is-a-pathlib-path/58966089#58966089 suggests using isinstance(pathlib.PurePath). @aitorres, could you perhaps see if this works?

Suggested change

if isinstance(data, (str, pathlib.Path)):

if isinstance(data, (str, pathlib.PurePath)):

Also, it might be a good idea to test that PureWindowsPath and PurePosixPath objects work on Windows and macOS/Linux respectively. Let us know if you're able to update the unit test to do that. If not, we can also just ignore it.

Gentle ping @aitorres to see if you're still available to finish up this PR! If not, we can get one of the maintainers to finish this up in the next week or so.

Really sorry for the delay! I've just added and pushed the changes to use PurePath, and added two tests that specifically use PureWindowsPath and PurePosixPath.

pygmt/tests/test_info.py

seisman · 2021-08-29T21:50:07Z

Ping @aitorres to finalize this PR if you have time. Otherwise, I'll take over this PR and make edits to this branch.

weiji14

Should be ok to merge after tests all pass, but prefer to have a second approval.

welcome · 2021-09-13T00:09:07Z

🎉🎉🎉 Congrats on merging your first pull request and welcome to the team! 🎉🎉🎉

Please open a new pull request to add yourself to the AUTHORS.md file. We hope that this was a good experience for you. Let us know if there is any way that the contributing process could be improved.

…pingTools#1382) Co-authored-by: Dongdong Tian <[email protected]> Co-authored-by: Wei Ji <[email protected]>

Add support for passing pathlib.Path into pygmt modules

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weiji14 added the enhancement Improving an existing feature label Jul 13, 2021

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Handle pathlib.Path as string file paths for virtual files

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Update docstring to mention support for pathlib.Path

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Fix length of docstring

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Remove unused import

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weiji14 added this to the 0.5.0 milestone Aug 11, 2021

aitorres added 2 commits August 22, 2021 18:10

Check for to cover all possible cases of across OSes

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Expand tests to support Windows and POSIX Path classes

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Merge branch 'main' into feature/pathlib-support

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seisman changed the title ~~Add support for passing pathlib.Path into pygmt modules~~ Add support for passing pathlib.Path objects as filenames Sep 13, 2021

seisman merged commit 7f53b9d into GenericMappingTools:main Sep 13, 2021

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seisman mentioned this pull request Mar 19, 2022

Add a tutorial explaining the generally accepted input types #1268

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sixy6e pushed a commit to sixy6e/pygmt that referenced this pull request Dec 21, 2022

Add support for passing pathlib.Path objects as filenames (GenericMap…

3c630f6

…pingTools#1382) Co-authored-by: Dongdong Tian <[email protected]> Co-authored-by: Wei Ji <[email protected]>

seisman mentioned this pull request Oct 16, 2024

clib.Session.virtualfile_in: Refactor if-else statements into match-case statements #3521

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Add support for passing pathlib.Path objects as filenames #1382

Add support for passing pathlib.Path objects as filenames #1382

aitorres commented Jul 10, 2021 •

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	if isinstance(data, (str, pathlib.Path)):
	if isinstance(data, (str, pathlib.PurePath)):

Add support for passing pathlib.Path objects as filenames #1382

Add support for passing pathlib.Path objects as filenames #1382

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