Add splines figure and script #6656

Esteban82 · 2022-05-02T12:13:03Z

This PR is related to issue #6643. It add a new figure and script to better explain the splines in the docs.

Here I add the script. Let me know if it is ok.

In what part of the docs should the figure go? At the end of -F argument?

This PR is related to issue #6643. It add a new figure and script to better explain the splines in the docs. Here I add the script. Let me know if it is ok. In what part of the docs should the figure go? At the end of -F argument?

PaulWessel

Looks good but may I ask for a few improvements:

add a tab in front of all commands inside the gmt begin/end block
Add "show" to gmt end [the tests and doc builds turns that off anyway but it is handy when debugging and testing]

If you plan to add the PostScript file and update the sample1d.rst file perhaps do that as part of the same PR? If you follow the guidelines you will see that once you get the PS file and is happy with it and place it in the image directory then it needs to be added to git (so there will be another file showing up here) plus of course using dvc to add it to taht repo as well. Only after that would we be able to test this branch and build the doc, for instan.ce

Updated script following Paul's suggestions.

Changed name and format of the output file.

Esteban82 · 2022-05-02T12:35:15Z

Thanks Paul.

Yes, my idea is to edit the rst file and add the figure. I let you know if I need help.

Esteban82 · 2022-05-03T12:30:30Z

I am bit confused on how to proceed. Where should I add the ps file?

PaulWessel · 2022-05-03T12:36:40Z

Follow the instructions for adding a new test or doc script on https://docs.generic-mapping-tools.org/dev/devdocs/contributing.html#contributing-documentation

Basically:
Run the full tests
Copy the new PS file to doc/scripts/images
run dvc diff etc etc as it shows above. This assumes you have set up dvc which I got the impression you had.

maxrjones · 2022-05-03T13:07:20Z

This is the specific section with instructions for adding the figure to doc/scripts/images. Please let me know if you think any part of the instructions needs improvement.

Esteban82 · 2022-05-03T13:45:00Z

I think I have a problem with running the test. I do it as indicated in docs.

1038/1044 Test #1036: test/time/time_testing_6.sh ..................   Passed    1.32 sec
          Start 1042: test/triangulate/nnn.sh
1039/1044 Test #1040: test/trend1d/trend1.sh .......................   Passed    1.26 sec
          Start 1043: test/triangulate/trivor.sh
1040/1044 Test #1042: test/triangulate/nnn.sh ......................   Passed    1.31 sec
          Start 1044: test/xyz2grd/gridrange.sh
1041/1044 Test #1044: test/xyz2grd/gridrange.sh ....................   Passed    0.21 sec
1042/1044 Test #1041: test/trend2d/trend.sh ........................   Passed    1.61 sec
1043/1044 Test #1043: test/triangulate/trivor.sh ...................   Passed    0.95 sec

## It runs until here where it stops for several minutes and I cancel it (Ctrl+c).

^Cmake[3]: *** [CMakeFiles/check.dir/build.make:57: CMakeFiles/check] Interrupción
make[2]: *** [CMakeFiles/Makefile2:660: CMakeFiles/check.dir/all] Interrupción
make[1]: *** [CMakeFiles/Makefile2:667: CMakeFiles/check.dir/rule] Interrupción
make: *** [Makefile:223: check] Interrupción

maxrjones · 2022-05-03T14:18:46Z

I think I have a problem with running the test. I do it as indicated in docs.

1038/1044 Test #1036: test/time/time_testing_6.sh ..................   Passed    1.32 sec
          Start 1042: test/triangulate/nnn.sh
1039/1044 Test #1040: test/trend1d/trend1.sh .......................   Passed    1.26 sec
          Start 1043: test/triangulate/trivor.sh
1040/1044 Test #1042: test/triangulate/nnn.sh ......................   Passed    1.31 sec
          Start 1044: test/xyz2grd/gridrange.sh
1041/1044 Test #1044: test/xyz2grd/gridrange.sh ....................   Passed    0.21 sec
1042/1044 Test #1041: test/trend2d/trend.sh ........................   Passed    1.61 sec
1043/1044 Test #1043: test/triangulate/trivor.sh ...................   Passed    0.95 sec

## It runs until here where it stops for several minutes and I cancel it (Ctrl+c).

^Cmake[3]: *** [CMakeFiles/check.dir/build.make:57: CMakeFiles/check] Interrupción
make[2]: *** [CMakeFiles/Makefile2:660: CMakeFiles/check.dir/all] Interrupción
make[1]: *** [CMakeFiles/Makefile2:667: CMakeFiles/check.dir/rule] Interrupción
make: *** [Makefile:223: check] Interrupción

Could you try running the tests without any parallelization to find out which test is hanging? I.e., cd build; ctest without any -j args.

joa-quim · 2022-05-03T14:25:03Z

I have the same problem since 1 or 2 years.

Esteban82 · 2022-05-04T16:19:50Z

Could you try running the tests without any parallelization to find out which test is hanging? I.e., cd build; ctest without any -j args.

When I run Ctest it finished and I got this message:

1042/1044 Test #1042: test/triangulate/nnn.sh ......................***Failed    0.06 sec
          Start 1043: test/triangulate/trivor.sh
1043/1044 Test #1043: test/triangulate/trivor.sh ...................***Failed    0.06 sec
          Start 1044: test/xyz2grd/gridrange.sh
1044/1044 Test #1044: test/xyz2grd/gridrange.sh ....................***Failed    0.05 sec

20% tests passed, 839 tests failed out of 1044

Total Test time (real) = 327.40 sec

The following tests FAILED:
CMake Error: Cannot open file for write: /home/federico/Software/gmt/test/Testing/Temporary/LastTestsFailed.log.tmp
CMake Error: : System Error: Permission denied
Problem opening file: /home/federico/Software/gmt/test/Testing/Temporary/LastTestsFailed.log
Cannot create log file: LastTestsFailed.log

When I run sudo Ctest it stops at test 842.

 841/1044 Test  #841: test/psxy/cartsegmentize.sh ..................   Passed    1.77 sec
          Start  842: test/psxy/cartvec.sh
 842/1044 Test  #842: test/psxy/cartvec.sh .........................   Passed    0.95 sec
          Start  843: test/psxy/categorical.sh

seisman · 2022-05-04T16:40:31Z

@Esteban82 You don't have run the full tests. You can simply run ctest -R GMT_splines.sh to run a single test.

joa-quim · 2022-05-04T18:19:10Z

So this may also happen on Linux. I though it was only a problem on Windows. The issue in not in the tests themselves but ... somewhere else. Running them individually works but the whole suite hangs before the last two.

ctest -R gridrange
Test project C:/v/build
    Start 1044: test/xyz2grd/gridrange.sh
1/1 Test #1044: test/xyz2grd/gridrange.sh ........   Passed    1.17 sec

100% tests passed, 0 tests failed out of 1

PaulWessel · 2022-05-05T08:43:14Z

Script did not have executable permission set.

PaulWessel · 2022-05-06T08:03:38Z

Hi @Esteban82, are you ready to try to upload the PS to dvc and add the lines to sample1d.rst to include the figure and caption? The plot looks good to me.

Esteban82 · 2022-05-06T10:43:14Z

Hi Paul.

Not really. I am still a bit lost. I think it would be better if someone else do it.

PaulWessel · 2022-05-06T10:46:44Z

OK, I can do the next bit and sort of show u the steps in the process. Paul Wessel Professor, Department of Earth Sciences (808) 956-4778 | ***@***.*** http:https://www.soest.hawaii.edu/earthsciences On May 6, 2022 at 11:43:26 AM, Federico Esteban ***@***.***) wrote: Hi Paul. Not really. I am still a bit lost. I think it would be better if someone else do it. — Reply to this email directly, view it on GitHub <#6656 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AGJ7IXYGM7ZXMKAF3TFM3KDVITZU3ANCNFSM5U3ZXICA> . You are receiving this because you commented.Message ID: ***@***.***>

PaulWessel · 2022-05-06T10:58:31Z

OK, so I checked out this branch, built it and ran all the test. I am getting this failure because the orig PS is not yet in the system:

157 - doc/scripts/GMT_splines.sh (Failed)

I follow the Contribution guide on test failures and first check that the plot is OK and then copy it to where DVC expects it:

cp rbuild/doc/scripts/GMT_splines/GMT_splines.ps doc/scripts/images

Now I can check with dvc:

dvc diff
Added:                                                                                                                                           
    doc/scripts/images/GMT_splines.ps

Modified:
    doc/scripts/images/

Loos good so I add it to the database:

dvc add doc/scripts/images
100% Adding...|█████████████████████████████████████████████████████████████████████████████████████████████████████████|1/1 [00:00,  4.96file/s]
                                                                                                                                                 
To track the changes with git, run:                                                                                                              

    git add doc/scripts/images.dvc

To enable auto staging, run:

	dvc config core.autostage true

After that, git tells me that a new file has been staged:

--- a/doc/scripts/images.dvc

So I commit my changes to git.

PaulWessel · 2022-05-06T10:58:59Z

OK, had not added the figure and caption to sample1d.rst yet so doing that now.

PaulWessel · 2022-05-06T11:02:22Z

Alright, now I need to upload the PS file to dvc:

dvc push
2 files pushed

PaulWessel · 2022-05-06T11:03:17Z

I am now building the whole branch again and will run the tests to verify we pass and then I will build the documentation to ensure the sample1d man page is OK. This will take some minutes...

PaulWessel · 2022-05-06T11:10:16Z

Good, the tests pass and I built the documentation. Here is a screenshot from the relevant new section:

Looks good I think - I will remove the WIP tag.

PaulWessel · 2022-05-06T11:10:47Z

Now it is good and ready to be reviewed by all.

doc/scripts/GMT_splines.sh

seisman · 2022-05-06T11:43:46Z

@PaulWessel When you merged the master branch into this branch, you probably reverted the changes to the dvc file.

Fix whiespace

…ppingTools/gmt into add_gmt_splines_figure

PaulWessel · 2022-05-06T11:54:10Z

Yes, something did not got exactly as planned. I am not sure why but I got a conflict on the dvc file.
I can fix the script to be clean - done.
ANy idea why the dvc file had a conflict and if we need to do anything to fix?

seisman · 2022-05-06T11:58:17Z

Yes, something did not got exactly as planned. I am not sure why but I got a conflict on the dvc file.

It's because PR #6673 also updated the dvc file.

seisman · 2022-05-06T12:00:05Z

if we need to do anything to fix?

I think you need to run dvc add doc/scripts/images and dvc push again.

PaulWessel · 2022-05-06T12:32:14Z

OK done

seisman · 2022-05-06T12:48:32Z

Did you run git add doc/scripts/images.dvc again?

PaulWessel · 2022-05-06T12:53:30Z

Just 10 seconds ago. Should be OK now.

Esteban82 · 2022-05-06T13:13:27Z

Many thanks Paui!! I will look into detail this for the next time.

Esteban82 · 2022-05-06T13:27:27Z

I was thinking that the script could go to gmt-examples.
What do you think?

BTW, for gmt-examples, I wonder if would be possible to create like a list of scripts and figure to add on it.

Add files via upload

911c223

This PR is related to issue #6643. It add a new figure and script to better explain the splines in the docs. Here I add the script. Let me know if it is ok. In what part of the docs should the figure go? At the end of -F argument?

Esteban82 changed the title ~~Add files via upload~~ Add splines figure and script May 2, 2022

PaulWessel reviewed May 2, 2022

View reviewed changes

Esteban82 added 2 commits May 2, 2022 09:29

Update GMT_splines.sh

cef2c77

Updated script following Paul's suggestions.

Update GMT_splines.sh

dd97a15

Changed name and format of the output file.

Esteban82 changed the title ~~Add splines figure and script~~ WIP Add splines figure and script May 2, 2022

Set executable permissionm

743ea39

Update images.dvc

6dcf105

Update sample1d.rst

55f7b53

PaulWessel changed the title ~~WIP Add splines figure and script~~ Add splines figure and script May 6, 2022

Merge branch 'master' into add_gmt_splines_figure

9b4327b

seisman reviewed May 6, 2022

View reviewed changes

doc/scripts/GMT_splines.sh Outdated Show resolved Hide resolved

PaulWessel added 2 commits May 6, 2022 12:53

Update GMT_splines.sh

6461f3e

Fix whiespace

Merge branch 'add_gmt_splines_figure' of https://github.com/GenericMa…

d0d1d5f

…ppingTools/gmt into add_gmt_splines_figure

Update images.dvc

b4cae20

seisman approved these changes May 6, 2022

View reviewed changes

PaulWessel merged commit 5c8cc24 into master May 6, 2022

PaulWessel deleted the add_gmt_splines_figure branch May 6, 2022 13:10

maxrjones added the documentation Improve documentation label Jun 1, 2022

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Add splines figure and script #6656

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