Figure.wiggle: Reorder input parameter to 'data, x, y, z' by seisman · Pull Request #1548 · GenericMappingTools/pygmt

seisman · 2021-09-27T03:19:26Z

Description of proposed changes

Address #1479

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.

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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

pygmt/helpers/decorators.py

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

seisman · 2021-10-01T02:19:22Z

Any idea why the docs CI suddenly fails?

weiji14 · 2021-10-01T03:22:42Z

Any idea why the docs CI suddenly fails?

I don't understand either. The scheduled docs build worked 10 hours ago at https://github.com/GenericMappingTools/pygmt/actions/runs/1292065680. The logs for this PR show this error message:

ValueError: did not find a match in any of xarray's currently installed IO backends ['netcdf4', 'scipy']. Consider explicitly selecting one of the installed engines via the ``engine`` parameter, or installing additional IO dependencies, see:
http://xarray.pydata.org/en/stable/getting-started-guide/installing.html
http://xarray.pydata.org/en/stable/user-guide/io.html

but I thought we fixed that in #1264, and xarray is still on v0.19.0. Also, the Vercel docs build have failed too, so it's not a GitHub Actions thing.

I did try to build the docs locally though, and it seems that I can't download the remote data files somehow. E.g. doing gmt which -Vi @tut_bathy.nc gives me:

gmt [INFORMATION]: Downloading file http://oceania.generic-mapping-tools.org/gmt_data_server.txt ...
gmt [INFORMATION]: Unable to download file http://oceania.generic-mapping-tools.org/gmt_data_server.txt
gmt [INFORMATION]: Libcurl Error: HTTP response code said error
gmt [INFORMATION]: Failed to get remote file http://oceania.generic-mapping-tools.org/gmt_data_server.txt
gmt [INFORMATION]: Unable to obtain remote information file gmt_data_server.txt
gmt [INFORMATION]: Remote download is currently deactivated
gmt [INFORMATION]: Failed to get remote file http://oceania.generic-mapping-tools.org/gmt_hash_server.txt
gmt [INFORMATION]: Unable to obtain remote hash table gmt_hash_server.txt
gmtwhich [INFORMATION]: Writing Data Table to Standard Output stream
gmtwhich [ERROR]: File tut_bathy.nc not found!

But accessing the link at http://oceania.generic-mapping-tools.org/gmt_data_server.txt works in a browser (though it redirects to https). So not sure what's breaking 😕

maxrjones · 2021-10-01T03:44:37Z

Any idea why the docs CI suddenly fails?

I don't understand either. The scheduled docs build worked 10 hours ago at https://github.com/GenericMappingTools/pygmt/actions/runs/1292065680. The logs for this PR show this error message:
ValueError: did not find a match in any of xarray's currently installed IO backends ['netcdf4', 'scipy']. Consider explicitly selecting one of the installed engines via the ``engine`` parameter, or installing additional IO dependencies, see:
http://xarray.pydata.org/en/stable/getting-started-guide/installing.html
http://xarray.pydata.org/en/stable/user-guide/io.html
but I thought we fixed that in #1264, and xarray is still on v0.19.0. Also, the Vercel docs build have failed too, so it's not a GitHub Actions thing.

I did try to build the docs locally though, and it seems that I can't download the remote data files somehow. E.g. doing gmt which -Vi @tut_bathy.nc gives me:
gmt [INFORMATION]: Downloading file http://oceania.generic-mapping-tools.org/gmt_data_server.txt ...
gmt [INFORMATION]: Unable to download file http://oceania.generic-mapping-tools.org/gmt_data_server.txt
gmt [INFORMATION]: Libcurl Error: HTTP response code said error
gmt [INFORMATION]: Failed to get remote file http://oceania.generic-mapping-tools.org/gmt_data_server.txt
gmt [INFORMATION]: Unable to obtain remote information file gmt_data_server.txt
gmt [INFORMATION]: Remote download is currently deactivated
gmt [INFORMATION]: Failed to get remote file http://oceania.generic-mapping-tools.org/gmt_hash_server.txt
gmt [INFORMATION]: Unable to obtain remote hash table gmt_hash_server.txt
gmtwhich [INFORMATION]: Writing Data Table to Standard Output stream
gmtwhich [ERROR]: File tut_bathy.nc not found!
But accessing the link at http://oceania.generic-mapping-tools.org/gmt_data_server.txt works in a browser (though it redirects to https). So not sure what's breaking 😕

I had the same problems starting a few hours ago with the remote files. Download was successful with CLI curl. Pinging @PaulWessel as an FYI that others are encountering the same issue.

PaulWessel · 2021-10-01T03:54:49Z

I tried and got the same error. But notice that this works

curl -k -L https://oceania.generic-mapping-tools.org/gmt_data_server.txt

while this doesn't:

curl -k -L http://oceania.generic-mapping-tools.org/gmt_data_server.txt

So since we have not changed gmt from using http in these calls, presumably something happened to the server. Note I updated CentOS today which installed lots of updated libs etc, including gmt6.2. How would that break anything? It clearly works via https but not http. Perhaps SOEST RCF did something ?

weiji14 · 2021-10-01T04:10:27Z

Well, manually switching to https worked, i.e. with GMT_DATA_SERVER=https://oceania.generic-mapping-tools.org gmt which -Vi -Gc @tut_bathy.nc:

gmt [INFORMATION]: Downloading file https://oceania.generic-mapping-tools.org/gmt_data_server.txt ...
gmt [INFORMATION]: Downloading file https://oceania.generic-mapping-tools.org/gmt_hash_server.txt ...
gmtwhich [INFORMATION]: Writing Data Table to Standard Output stream
gmtwhich [INFORMATION]:   -> Download cache file: @tut_bathy.nc
gmtwhich [INFORMATION]: Downloading file https://oceania.generic-mapping-tools.org/cache/tut_bathy.nc ...
/home/username/.gmt/cache/tut_bathy.nc

seisman · 2021-10-02T00:51:34Z

@GenericMappingTools/pygmt-maintainers Please give this PR high priority, as other issues (e.g., #1546, #1547, #1479) are waiting for the fix in this PR.

…pingTools#1548) Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

Figure.wiggle: Reorder input parameter to 'data, x, y, z'

7b2ff17

seisman added this to the 0.5.0 milestone Sep 27, 2021

seisman added the deprecation Deprecating a feature label Sep 27, 2021

This was referenced Sep 27, 2021

Standardize parameter name for table data inputs #1479

Closed

Add a decorator to raise a FutureWarning when positional arguments are passed for functions that changed parameter orders #1541

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seisman force-pushed the reorder-parameters/wiggle branch from d054001 to 12799f4 Compare September 27, 2021 12:10

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Fix the check_data_input_order decorator

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seisman force-pushed the reorder-parameters/wiggle branch from 12799f4 to 95fa173 Compare September 27, 2021 12:13

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Merge branch 'main' into reorder-parameters/wiggle

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seisman commented Sep 28, 2021

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Merge branch 'main' into reorder-parameters/wiggle

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Improve the test to increase code coverage

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weiji14 reviewed Sep 30, 2021

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

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Merge branch 'main' into reorder-parameters/wiggle

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weiji14 mentioned this pull request Oct 1, 2021

Cache earth_relief_15s tile and set GMT_DATA_SERVER to use https #1553

Merged

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Merge branch 'main' into reorder-parameters/wiggle

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weiji14 approved these changes Oct 2, 2021

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seisman added the final review call This PR requires final review and approval from a second reviewer label Oct 2, 2021

michaelgrund approved these changes Oct 2, 2021

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seisman removed the final review call This PR requires final review and approval from a second reviewer label Oct 2, 2021

seisman merged commit a3cb87b into main Oct 2, 2021

seisman deleted the reorder-parameters/wiggle branch October 2, 2021 08:12

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

Figure.wiggle: Reorder input parameter to 'data, x, y, z' (GenericMap…

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…pingTools#1548) Co-authored-by: Wei Ji <23487320+weiji14@users.noreply.github.com>

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Figure.wiggle: Reorder input parameter to 'data, x, y, z'#1548

Figure.wiggle: Reorder input parameter to 'data, x, y, z'#1548
seisman merged 8 commits intomainfrom
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