Change 12a43badc70bf5f4ea77b14b5044250c5ac16a76 from May 2 broke Julia

[joa-quim]

This now crashes

julia> bar(rand(15), color=:rainbow, show=1, Vd=2)
"psxy  -JX14c/9.5c -Baf -BWSen -R0.4/15.6/0/0.94 -C -i0-1,1 -Sb0.8u+b0 -P -K > C:\\TMP\\GMTjl_tmp.ps"

Very likely it's because it can't handle the -i0-1,1 anymore. The crash is indeed caused when it tries to access a 3rd column in data that has only 2 columns

[PaulWessel]

OK, so a couple of things:

1. We clearly need to improve how testing is done so that when we make any bug fixes on the API that there is either automatically or manually a run of the Julia and PyGMT tests (and of course ideally also GMT/MEX tests). Otherwise, time goes by and it is harder to get back in and rediscover what was learned. Maybe we should add a new label that can be used to flags API-related changes?
2. Remind me if you are passing this as a matrix, sets of vectors, or a GMT dataset via reference.

Thoughts on this, @seisman and @meghanrjones?

[joa-quim]

The detection problem here was that I didn't have this test in my test suites, or only tested that the GMT syntax is well generated.

The culprit was this in change in gmt_api.c/gmtapi_pick_in_col_number()

        col_pos = GMT->current.io.col[GMT_IN][col].col; /* Which data column to pick */
to
        col_pos = GMT->current.io.col[GMT_IN][col].order; /* Which data column to pick */

[seisman]

1. We clearly need to improve how testing is done so that when we make any bug fixes on the API that there is either automatically or manually a run of the Julia and PyGMT tests (and of course ideally also GMT/MEX tests).

PyGMT runs its full tests with GMT master branch nightly, so any GMT API problems should be detected by PyGMT tests (if there are covered) in a few days.

The commit reverted in #5385 comes from PR #5289.

[PaulWessel]

Please check if the revert (which was one line only) negatively affects the pyGMT examples.

[seisman]

Please check if the revert (which was one line only) negatively affects the pyGMT examples.

Yes, scripts in GenericMappingTools/pygmt#1313 now break.

[PaulWessel]

Remind me if you are passing this as a matrix, sets of vectors, or a GMT dataset via reference.

@joa-quim let me know please.

[joa-quim]

I am passing a GMTdataset. It works if I only pass the matrix.

You can reproduce it in Matlab. This crashes Matlab (if using order instead of col)

D = gmt('wrapseg', {[(1:15)' rand(15,1)]})
gmt('info -C -i0-1,1', D)

[joa-quim]

But even Matrices have problems. This should plot bars with error-bars and what is passed in is 5x3 matrix

men_means, men_std = (20, 35, 30, 35, 27), (2, 3, 4, 1, 2);
women_means, women_std = (25, 32, 34, 20, 25), (3, 5, 2, 3, 3);
x = collect(1:length(men_means));
width = 0.35;

bar(x.-width/2, collect(men_means), width=width, color=:lightblue,
    limits=(0.5,5.5,0,40), axis=:none, error_bars=(y=men_std,))
bar!(x.+width/2, collect(women_means), width=width, color=:brown,
    xaxis=(custom=(pos=1:5, label=[:G1 :G2 :G3 :G4 :G5]),), yaxis=(annot=5,label=:Scores),
    frame=(title="Scores by group and gender", axes=:WSrt), error_bars=(y=women_std,), savefig="genders.png")

The generated command is

cmd = " -R0.5/5.5/0/40 -JX14c/9.5c -Ey -C -i0-1,1,2-2 -Sb0.35u+b0"

No crash but 0-error bars

[PaulWessel]

I think I will make a test*.c example to do some more testing on -i and passing various things in.

[PaulWessel]

And @seisman, I think PyGMT uses mostly GMT_VECTOR when passing in datasets and GMT_MATRIX when passing in grids, or do you mix it up?

[seisman]

And @seisman, I think PyGMT uses mostly GMT_VECTOR when passing in datasets and GMT_MATRIX when passing in grids, or do you mix it up?

I think PyGMT doesn't use GMT_VECTOR and GMT_MATRIX together.

[PaulWessel]

I meant across all PyGMT modules you do use both methods for passing data into GMT. not mixing, but one modules may use VECTOR and another may use MATRIX.

[seisman]

one modules may use VECTOR and another may use MATRIX.

Yes.

[seisman]

one modules may use VECTOR and another may use MATRIX.

Yes.

Maybe I was wrong. For example, in PyGMT, the contour function can either pass vectors of x, y, z by calling GMT_Put_Vectors or pass a matrix of (x,y,z) by calling GMT_Put_Matrix.

[PaulWessel]

Can you check this again - should work fine after the fix. if so please close.

[joa-quim]

It's fine ... and closed.