Add support for passing pathlib.Path objects as filenames by aitorres · Pull Request #1382 · GenericMappingTools/pygmt

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

yieldarg

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).

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

 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
ifisinstance(data, (str, pathlib.Path)):
ifisinstance(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.

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 <seisman.info@gmail.com> Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

Add support for passing pathlib.Path into pygmt modules
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vercelBottemporarily deployed to Preview July 10, 2021 21:23 Inactive

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

weiji14 assigned aitorres Jul 13, 2021

Handle pathlib.Path as string file paths for virtual files
32654d3

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Update docstring to mention support for pathlib.Path
2cea6da

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Fix length of docstring
3bfdb56

weiji14 reviewed Jul 19, 2021
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Comment threadpygmt/clib/session.py Outdated

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Remove unused import
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weiji14 approved these changes Jul 19, 2021
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weiji14 added the final review call This PR requires final review and approval from a second reviewer label Jul 19, 2021

seisman reviewed Jul 19, 2021
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weiji14 removed the final review call This PR requires final review and approval from a second reviewer label Jul 31, 2021

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
367d6e9

Expand tests to support Windows and POSIX Path classes
9dc3fb7

seisman reviewed Aug 23, 2021
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Comment threadpygmt/tests/test_info.py Outdated
Comment threadpygmt/tests/test_info.py Outdated
Comment threadpygmt/tests/test_info.py Outdated
Comment threadpygmt/tests/test_info.py

Apply suggestions from code review
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seisman added the final review call This PR requires final review and approval from a second reviewer label Sep 10, 2021

Merge branch 'main' into feature/pathlib-support
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weiji14 approved these changes Sep 12, 2021
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michaelgrund approved these changes Sep 12, 2021
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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 filenamesSep 13, 2021

seisman merged commit 7f53b9d into GenericMappingTools:mainSep 13, 2021

weiji14 removed the final review call This PR requires final review and approval from a second reviewer label Sep 18, 2021

seisman mentioned this pull request Mar 19, 2022
Add a tutorial explaining the generally accepted input types #1268
Open

seisman mentioned this pull request Oct 16, 2024
clib.Session.virtualfile_in: Refactor if-else statements into match-case statements #3521
Merged

	ifisinstance(data, (str, pathlib.Path)):
	ifisinstance(data, (str, pathlib.PurePath)):

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