Use pytest-doctestplus to skip some inline doctests (#1790)

* Use pytest-doctestplus to skip some inline doctests
* Install pytest-doctestplus in workflows
* Add the fulltest target to run all tests, including all doctests

Author: seisman

.github/workflows/ci_tests.yaml

@@ -97,7 +97,7 @@ jobs:
                         pandas xarray netCDF4 packaging \
                         ${{ matrix.optional-packages }} \
                         dvc make pytest>=6.0 \
-                        pytest-cov pytest-mpl sphinx-gallery tomli
+                        pytest-cov pytest-doctestplus pytest-mpl sphinx-gallery tomli
 
       # Show installed pkg information for postmortem diagnostic
       - name: List installed packages

.github/workflows/ci_tests_dev.yaml

@@ -93,7 +93,7 @@ jobs:
           pip install --pre --prefer-binary \
                         numpy pandas xarray netCDF4 packaging \
                         dvc ipython 'pytest>=6.0' pytest-cov \
-                        pytest-mpl sphinx-gallery tomli
+                        pytest-doctestplus pytest-mpl sphinx-gallery tomli
 
       # Pull baseline image data from dvc remote (DAGsHub)
       - name: Pull baseline image data from dvc remote

Makefile

@@ -16,7 +16,8 @@ help:
 	@echo ""
 	@echo "  install   install in editable mode"
 	@echo "  package   build source and wheel distributions"
-	@echo "  test      run the test suite (including doctests) and report coverage"
+	@echo "  test      run the test suite (including some doctests) and report coverage"
+	@echo "  fulltest  run the test suite (including all doctests) and report coverage"
 	@echo "  format    run black, blackdoc, docformatter and isort to automatically format the code"
 	@echo "  check     run code style and quality checks (black, blackdoc, docformatter, flake8 and isort)"
 	@echo "  lint      run pylint for a deeper (and slower) quality check"
@@ -31,6 +32,17 @@ package:
 	python setup.py sdist bdist_wheel
 
 test:
+	# Run a tmp folder to make sure the tests are run on the installed version
+	mkdir -p $(TESTDIR)
+	@echo ""
+	@cd $(TESTDIR); python -c "import $(PROJECT); $(PROJECT).show_versions()"
+	@echo ""
+	cd $(TESTDIR); PYGMT_USE_EXTERNAL_DISPLAY="false" pytest $(PYTEST_COV_ARGS) --doctest-plus $(PROJECT)
+	cp $(TESTDIR)/coverage.xml .
+	cp -r $(TESTDIR)/htmlcov .
+	rm -r $(TESTDIR)
+
+fulltest:
 	# Run a tmp folder to make sure the tests are run on the installed version
 	mkdir -p $(TESTDIR)
 	@echo ""

environment.yml

@@ -27,6 +27,7 @@ dependencies:
     - myst-parser
     - pylint
     - pytest-cov
+    - pytest-doctestplus
     - pytest-mpl
     - pytest>=6.0
     - sphinx

pygmt/src/grdlandmask.py

@@ -1,7 +1,6 @@
 """
 grdlandmask - Create a "wet-dry" mask grid from shoreline data base
 """
-
 from pygmt.clib import Session
 from pygmt.exceptions import GMTInvalidInput
 from pygmt.helpers import (
@@ -13,6 +12,8 @@
 )
 from pygmt.io import load_dataarray
 
+__doctest_skip__ = ["grdlandmask"]
+
 
 @fmt_docstring
 @use_alias(
@@ -95,12 +96,10 @@ def grdlandmask(**kwargs):
 
     Example
     -------
-    >>> import pygmt  # doctest: +SKIP
+    >>> import pygmt
     >>> # Create a landmask grid with an x-range of 125 to 130,
     >>> # and a y-range of 30 to 35
-    >>> landmask = pygmt.grdlandmask(
-    ...     spacing=1, region=[125, 130, 30, 35]
-    ... )  # doctest: +SKIP
+    >>> landmask = pygmt.grdlandmask(spacing=1, region=[125, 130, 30, 35])
     """
     if "I" not in kwargs or "R" not in kwargs:
         raise GMTInvalidInput("Both 'region' and 'spacing' must be specified.")