Expand table-like input options for sphdistance by willschlitzer · Pull Request #1491 · GenericMappingTools/pygmt

willschlitzer · 2021-09-11T00:11:58Z

This pull request adds data to the parameter list in the docstring and moves the sphdistance function to the tabular data section in the index.

Fixes #

Reminders

Run make format and make check to make sure the code follows the style guide.
Add tests for new features or tests that would have caught the bug that you're fixing.
Add new public functions/methods/classes to doc/api/index.rst.
Write detailed docstrings for all functions/methods.
If adding new functionality, add an example to docstrings or tutorials.

Slash Commands

You can write slash commands (/command) in the first line of a comment to perform
specific operations. Supported slash commands are:

/format: automatically format and lint the code
/test-gmt-dev: run full tests on the latest GMT development version

weiji14

Could you also:

Rename table to data at L25, L61, and also in pygmt/tests/test_sphdistance.py
At L52: Insert blank line between:

 Return type depends on whether the ``outgrid`` parameter is set:
- :class:`xarray.DataArray` if ``outgrid`` is not set

to prevent a Sphinx warning pygmt/pygmt/src/sphdistance.py:docstring of pygmt.src.sphdistance.sphdistance:67: WARNING: Unexpected indentation

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

seisman · 2021-09-23T09:53:02Z

Do you want to add "xyz" input support (like #1531) in this PR or a separate PR?

willschlitzer · 2021-09-23T12:23:31Z

Do you want to add "xyz" input support (like #1531) in this PR or a separate PR?

I can give it a try.

Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

willschlitzer · 2021-09-26T07:10:08Z

@seisman Doesn't sphdistance only require lat-long inputs? I don't think there should be z inputs.

seisman · 2021-09-26T07:23:24Z

@seisman Doesn't sphdistance only require lat-long inputs? I don't think there should be z inputs.

I've never used sphdistance, but reading the sphdistance manpage, I think only x and y are required.

willschlitzer · 2021-09-26T07:50:12Z

@seisman Doesn't sphdistance only require lat-long inputs? I don't think there should be z inputs.
I've never used sphdistance, but reading the sphdistance manpage, I think only x and y are required.

So should I then remove z from the parameters? I'm getting this error when I run the tests: pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns

seisman · 2021-09-26T08:00:29Z

@seisman Doesn't sphdistance only require lat-long inputs? I don't think there should be z inputs.
I've never used sphdistance, but reading the sphdistance manpage, I think only x and y are required.
So should I then remove z from the parameters? I'm getting this error when I run the tests: pygmt.exceptions.GMTInvalidInput: data must provide x, y, and z columns

Yes, please. Sorry for misleading you.

Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

weiji14

The docstring description reads: sphdistance reads one or more ASCII [or binary] files (or standard input), but 'standard input' (stdin) doesn't make sense in the Python world, suggest rewording it to use just 'table', similar to #1418 (comment).

weiji14 · 2021-09-27T22:02:30Z

-def sphdistance(table, **kwargs):
+def sphdistance(data=None, x=None, y=None, **kwargs):
 r"""
 Create Voroni polygons from lat/lon coordinates.


Typo here. Also, just noticed that this summary doesn't seem correct. It seems to suggest Voronoi polygons are created, but the output is a raster grid, not a vector polygon. Maybe follow https://docs.generic-mapping-tools.org/6.2/sphdistance.html.
Suggested change
CreateVoronipolygonsfromlat/loncoordinates.
CreateVoronoipolygonsfromlat/loncoordinates.

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

seisman · 2021-09-28T08:23:22Z

@willschlitzer The tests fail because the Windows server cannot download the cache file EGM96_to_36.txt, which was added in #1434, but not cached.

Please trigger the cache_data.yml workflow manually to update the caches.

willschlitzer · 2021-09-28T14:07:11Z

Please trigger the cache_data.yml workflow manually to update the caches.

@seisman How do I do this?

seisman · 2021-09-28T14:12:53Z

Please trigger the cache_data.yml workflow manually to update the caches.
@seisman How do I do this?

You need to uncomment the following line (removing the leading #), commit the changes, and wait for the finish of the workflow. After that, you need to revert that commit:

pygmt/.github/workflows/cache_data.yaml

Line 6 in 0926206

# pull_request:

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

…1491) *Add parameter and tests for x/y inputs *Rename "table" parameter to "data" *Improve docstring for new parameters Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com> Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

willschlitzer added 2 commits September 10, 2021 19:59

Add table docstring to parameters list
de206a3

move sphdistance to tabular data section
0e41a09

willschlitzer added the enhancement Improving an existing feature label Sep 11, 2021

willschlitzer added this to the 0.5.0 milestone Sep 11, 2021

willschlitzer self-assigned this Sep 11, 2021

weiji14 reviewed Sep 11, 2021
View reviewed changes

Comment threadpygmt/src/sphdistance.py Outdated

maxrjones mentioned this pull request Sep 11, 2021
Standardize parameter name for table data inputs #1479
Closed

weiji14 reviewed Sep 17, 2021
View reviewed changes

Comment threadpygmt/src/sphdistance.py Outdated

weiji14 added the skip-changelog Skip adding Pull Request to changelog label Sep 17, 2021

Merge branch 'main' into sphdistance-fixes
8dc55b6

vercelBottemporarily deployed to Preview September 23, 2021 07:25 Inactive

willschlitzerand others added 4 commits September 23, 2021 08:26

Update pygmt/src/sphdistance.py
68fcb68
Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

change "table" to "data"
9422b51

add blank line to prevent Sphinx error
10a1aee

run make format
663805f

vercelBottemporarily deployed to Preview September 23, 2021 07:41 Inactive

willschlitzer added 2 commits September 25, 2021 07:23

add parameters for xy input
b1d573f

add test for xy inputs
d434195

vercelBottemporarily deployed to Preview September 25, 2021 06:23 Inactive

seisman reviewed Sep 26, 2021
View reviewed changes

Comment threadpygmt/src/sphdistance.py Outdated
Comment threadpygmt/src/sphdistance.py Outdated
Comment threadpygmt/src/sphdistance.py Outdated

Apply suggestions from code review
24a3c2a
Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

vercelBottemporarily deployed to Preview September 26, 2021 07:08 Inactive

seisman changed the title ~~Make suggested fixes for sphdistance~~Expand table-like input options for sphdistanceSep 26, 2021

remove z parameter
7db2128

seisman approved these changes Sep 27, 2021
View reviewed changes

Apply suggestions from code review
b9591f8
Co-authored-by: Dongdong Tian <seisman.info@gmail.com>

vercelBottemporarily deployed to Preview September 27, 2021 06:51 Inactive

Merge branch 'main' into sphdistance-fixes
9243a90

vercelBottemporarily deployed to Preview September 27, 2021 07:01 Inactive

weiji14 reviewed Sep 27, 2021
View reviewed changes

willschlitzer added 2 commits September 28, 2021 07:53

add reference to GMT docs
c6113a9

update table docstring
b3ad116

vercelBottemporarily deployed to Preview September 28, 2021 07:18 Inactive

willschlitzerand others added 2 commits September 28, 2021 08:19

Update pygmt/src/sphdistance.py
a314688
Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

Merge branch 'main' into sphdistance-fixes
6f3956d

vercelBottemporarily deployed to Preview September 28, 2021 07:27 Inactive

update cache list
97108f2

vercelBottemporarily deployed to Preview September 28, 2021 20:42 Inactive

weiji14 reviewed Sep 28, 2021
View reviewed changes

Comment thread.github/workflows/cache_data.yaml Outdated
Comment threadpygmt/src/sphdistance.py Outdated

comment out line for data caching
b836da2

vercelBottemporarily deployed to Preview September 29, 2021 06:20 Inactive

willschlitzerand others added 2 commits September 29, 2021 07:21

Update pygmt/src/sphdistance.py
b59620c
Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

Merge branch 'main' into sphdistance-fixes
aacfc71

vercelBottemporarily deployed to Preview September 29, 2021 06:30 Inactive

weiji14 approved these changes Sep 30, 2021
View reviewed changes

Merge branch 'main' into sphdistance-fixes
14b1dd7

vercelBottemporarily deployed to Preview September 30, 2021 12:20 Inactive

willschlitzer merged commit e10df16 into mainSep 30, 2021

willschlitzer deleted the sphdistance-fixes branch September 30, 2021 17:32

weiji14 removed the final review call This PR requires final review and approval from a second reviewer label Oct 21, 2021

	CreateVoronipolygonsfromlat/loncoordinates.
	CreateVoronoipolygonsfromlat/loncoordinates.

Uh oh!

Conversation

willschlitzer commented Sep 11, 2021• edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Uh oh!

Uh oh!

weiji14 left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

seisman commented Sep 23, 2021

Uh oh!

willschlitzer commented Sep 23, 2021

Uh oh!

Uh oh!

Uh oh!

Uh oh!

willschlitzer commented Sep 26, 2021

Uh oh!

seisman commented Sep 26, 2021

Uh oh!

willschlitzer commented Sep 26, 2021

Uh oh!

seisman commented Sep 26, 2021

Uh oh!

weiji14 left a comment

Choose a reason for hiding this comment

Uh oh!

weiji14Sep 27, 2021• edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Choose a reason for hiding this comment

Uh oh!

Uh oh!

seisman commented Sep 28, 2021

Uh oh!

willschlitzer commented Sep 28, 2021

Uh oh!

seisman commented Sep 28, 2021

Uh oh!

Uh oh!

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

willschlitzer commented Sep 11, 2021•
edited
Loading

weiji14Sep 27, 2021•
edited
Loading