Update failing doctests with upstream dataset changes #2988

seisman · 2024-01-11T10:34:30Z

Description of proposed changes

.github/workflows/ci_tests.yaml

seisman · 2024-01-11T10:43:25Z

There are still two failures:

=================================== FAILURES ===================================
_______________ [doctest] pygmt.datasets.tile_map.load_tile_map ________________
105     Raises
106     ------
107     ImportError
108         If ``contextily`` is not installed or can't be imported. Follow
109         :doc:`install instructions for contextily <contextily:index>`, (e.g.
110         via ``python -m pip install contextily``) before using this function.
111 
112     Examples
113     --------
114     >>> import contextily
UNEXPECTED EXCEPTION: ModuleNotFoundError("No module named 'contextily'")
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/pygmt/lib/python3.9/doctest.py", line 1334, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest pygmt.datasets.tile_map.load_tile_map[0]>", line 1, in <module>
ModuleNotFoundError: No module named 'contextily'
/home/runner/work/pygmt/pygmt/pygmt/datasets/tile_map.py:114: UnexpectedException
__________________ [doctest] pygmt.src.grdproject.grdproject ___________________
179 >>> import pygmt
180 >>> # Load a grid of @earth_relief_30m data, with a longitude range of
181 >>> # 10° E to 30° E, and a latitude range of 15° N to 25° N
182 >>> grid = pygmt.datasets.load_earth_relief(
183 ...     resolution="30m", region=[10, 30, 15, 25]
184 ... )
185 >>> # Create a new grid from the input grid, set the projection to
186 >>> # Mercator, and set inverse to "True" to change from "geographic"
187 >>> # to "rectangular"
188 >>> new_grid = pygmt.grdproject(grid=grid, projection="M10c", inverse=True)
Error: TED EXCEPTION: GMTCLibError("Module 'grdproject' failed with status code 72:\ngrdproject [ERROR]: Option -J: If map width is given you must also specify a region with -R")
Traceback (most recent call last):
  File "/home/runner/micromamba/envs/pygmt/lib/python3.9/doctest.py", line 1334, in __run
    exec(compile(example.source, filename, "single",
  File "<doctest pygmt.src.grdproject.grdproject[2]>", line 1, in <module>
  File "/home/runner/work/pygmt/pygmt/pygmt/helpers/decorators.py", line 603, in new_module
    return module_func(*args, **kwargs)
  File "/home/runner/work/pygmt/pygmt/pygmt/helpers/decorators.py", line 776, in new_module
    return module_func(*bound.args, **bound.kwargs)
  File "/home/runner/work/pygmt/pygmt/pygmt/src/grdproject.py", line 122, in grdproject
    lib.call_module(
  File "/home/runner/work/pygmt/pygmt/pygmt/clib/session.py", line 624, in call_module
    raise GMTCLibError(
pygmt.exceptions.GMTCLibError: Module 'grdproject' failed with status code 72:
Error: ect [ERROR]: Option -J: If map width is given you must also specify a region with -R
/home/runner/work/pygmt/pygmt/pygmt/src/grdproject.py:188: UnexpectedException
----------------------------- Captured stderr call -----------------------------
Error: ect [ERROR]: Option -J: If map width is given you must also specify a region with -R

seisman · 2024-01-11T13:16:23Z

The pygmt.datasets.tile_map.load_tile_map failure is because contextily is an optional dependency and is not installed in the Python 3.9 job run. It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

The pygmt.src.grdproject.grdproject is likely an upstream bug, reported in GenericMappingTools/gmt#8273.

weiji14 · 2024-01-15T03:20:27Z

The pygmt.datasets.tile_map.load_tile_map failure is because contextily is an optional dependency and is not installed in the Python 3.9 job run. It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

This doctest should be skipped with the __doctest_requires__ = {("load_tile_map"): ["contextily"]} line (see https://github.com/scientific-python/pytest-doctestplus/tree/v1.1.0#doctest-dependencies and #2125 (comment)). I thought we had pytest-doctestplus installed here:

pygmt/.github/workflows/ci_doctests.yaml

Line 68 in 2d61b54

pytest-doctestplus

Is that doctest still being run somehow?

seisman · 2024-01-15T04:02:59Z

The pygmt.datasets.tile_map.load_tile_map failure is because contextily is an optional dependency and is not installed in the Python 3.9 job run. It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

This doctest should be skipped with the __doctest_requires__ = {("load_tile_map"): ["contextily"]} line (see https://github.com/scientific-python/pytest-doctestplus/tree/v1.1.0#doctest-dependencies and #2125 (comment)). I thought we had pytest-doctestplus installed here:

pygmt/.github/workflows/ci_doctests.yaml

Line 68 in 2d61b54

pytest-doctestplus

Is that doctest still being run somehow?

The doctest will be skipped only if the --doctest-plus option is given. So, the doctest is skipped for make test but will be run for make fulltest (see

pygmt/Makefile

Line 45 in 621d6da

test: PYTEST_ARGS=--doctest-plus $(PYTEST_COV_ARGS) ${PYTEST_EXTRA}

).

weiji14 · 2024-01-15T04:23:05Z

The doctest will be skipped only if the --doctest-plus option is given. So, the doctest is skipped for make test but will be run for make fulltest (see

pygmt/Makefile

Line 45 in 621d6da

test: PYTEST_ARGS=--doctest-plus $(PYTEST_COV_ARGS) ${PYTEST_EXTRA}

Hmm, you mentioned at #1790 (comment) that we were using --doctest-modules --doctest-plus for make fulltest, but looking at the code, it looks like only --doctest-modules is applied (from pyproject.toml).

It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

Do we need to run the full tests on GMT Legacy/Dev? The ci_doctests.yaml should cover the doctests, and ci_tests.yaml should cover the non-doctest tests already right?

seisman · 2024-01-15T04:33:59Z

The doctest will be skipped only if the --doctest-plus option is given. So, the doctest is skipped for make test but will be run for make fulltest (see

pygmt/Makefile

Line 45 in 621d6da

test: PYTEST_ARGS=--doctest-plus $(PYTEST_COV_ARGS) ${PYTEST_EXTRA}

Hmm, you mentioned at #1790 (comment) that we were using --doctest-modules --doctest-plus for make fulltest, but looking at the code, it looks like only --doctest-modules is applied (from pyproject.toml).

Hmm, I think the description in #1790 (comment) is incorrect. make test uses --doctest-modules --doctest-plus and make fulltest uses --doctest-modules. I've updated the comment.

It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

Do we need to run the full tests on GMT Legacy/Dev? The ci_doctests.yaml should cover the doctests, and ci_tests.yaml should cover the non-doctest tests already right?

You're right, I almost forgot this workflow. I was looking at the checklist at #2843, which only mentions "GMT Legacy" and "GMT Tests" but not "Doctests".

I think we should mention the "DocTests" workflow in both checklists (#2843 and #2961).

weiji14 · 2024-01-15T04:44:22Z

It also means we can't run full tests in the Tests workflow, but fortunately we can still run them in GMT Legacy Tests and Dev Tests.

Do we need to run the full tests on GMT Legacy/Dev? The ci_doctests.yaml should cover the doctests, and ci_tests.yaml should cover the non-doctest tests already right?

You're right, I almost forgot this workflow. I was looking at the checklist at #2843, which only mentions "GMT Legacy" and "GMT Tests" but not "Doctests".

Yeah, could you trigger the "Doctests" workflow in this PR? I did try it locally and it seems to work fine without contextily if you add --doctest-plus here:

pygmt/Makefile

Lines 52 to 54 in 621d6da

    
           # run doctests only 
        
           doctest: PYTEST_ARGS=--ignore=../pygmt/tests ${PYTEST_EXTRA} 
        
           doctest: _runtest

I think we should mention the "DocTests" workflow in both checklists (#2843 and #2961).

Sounds good.

weiji14 · 2024-01-15T04:49:57Z

Yeah, could you trigger the "Doctests" workflow in this PR? I did try it locally and it seems to work fine without contextily if you add --doctest-plus here:

Owh, but using --doctest-plus only runs 34 tests, compared to 74 doctests if using only --doctest-modules. Maybe don't add that --doctest-plus line to make doctest then, as we agreed on in #1790 (comment).

weiji14 · 2024-01-15T04:55:04Z

pygmt/src/grdproject.py

-    >>> # Create a new grid from the input grid, set the projection to
-    >>> # Mercator, and set inverse to "True" to change from "geographic"
-    >>> # to "rectangular"
-    >>> new_grid = pygmt.grdproject(grid=grid, projection="M10c", inverse=True)
+    >>> region = [10, 30, 15, 25]
+    >>> grid = pygmt.datasets.load_earth_relief(resolution="30m", region=region)
+    >>> # Project the geographic gridded data onto a rectangular grid
+    >>> new_grid = pygmt.grdproject(grid=grid, projection="M10c", region=region)


Oh wow, did we write the wrong description before. Default (when inverse=False) should have been "geographic" to "rectangular" 😅

.github/workflows/ci_doctests.yaml

seisman added 2 commits January 11, 2024 18:34

Fix failing inline doctests

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Temporarily enable full tests in this PR

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seisman commented Jan 11, 2024

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Fix the grdproject doctest

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seisman changed the title ~~Fix failing inline doctests~~ Update failing doctests with upstream dataset changes Jan 11, 2024

Improve the docstrings

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seisman marked this pull request as ready for review January 11, 2024 14:15

seisman added maintenance Boring but important stuff for the core devs skip-changelog Skip adding Pull Request to changelog labels Jan 11, 2024

seisman added this to the 0.11.0 milestone Jan 11, 2024

Update .github/workflows/ci_tests.yaml

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seisman added the needs review This PR has higher priority and needs review. label Jan 14, 2024

Merge branch 'main' into inline-doctests

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weiji14 approved these changes Jan 15, 2024

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seisman added 2 commits January 15, 2024 13:15

Merge branch 'main' into inline-doctests

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Temporarily trigger docstest in PR

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seisman mentioned this pull request Jan 15, 2024

doc: Add 'Doctests workflow' to release checklist and GMT bumping checklist #3001

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seisman merged commit ec75e7b into main Jan 15, 2024
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Update failing doctests with upstream dataset changes #2988

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Update failing doctests with upstream dataset changes #2988

Update failing doctests with upstream dataset changes #2988

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