Merge pull request #802 from glotzerlab/fix/doctests-pytest

Fix doctests to work with pytest.

ChangeLog.md

@@ -11,6 +11,7 @@ and this project adheres to
 
 ### Fixed
 * Added error checking for `r_min`, `r_max` arguments in `freud.density.RDF` and `freud.locality.NeighborList`.
+* Doctests are now run with pytest.
 
 ## v2.7.0 -- 2021-10-01
 

doc/source/reference/credits.rst

@@ -123,6 +123,7 @@ Bradley Dice - **Lead developer**
 * Contributed code, design, documentation, and testing for ``StaticStructureFactorDebye`` class.
 * Fixed ``Box.contains`` to run in linear time, ``O(num_points)``.
 * Contributed code, design, documentation, and testing for ``StaticStructureFactorDirect`` class.
+* Fixed doctests to run with pytest.
 
 Eric Harper, University of Michigan - **Former lead developer**
 

freud/diffraction.pyx

@@ -184,14 +184,22 @@ cdef class StaticStructureFactorDebye(_StaticStructureFactor):
 
         Example for a single component system::
 
+            >>> box, points = freud.data.make_random_system(10, 100, seed=0)
             >>> sf = freud.diffraction.StaticStructureFactorDebye(
             ...     bins=100, k_max=10, k_min=0
             ... )
             >>> sf.compute((box, points))
+            freud.diffraction.StaticStructureFactorDebye(...)
 
         Example for partial mixed structure factor for a multiple component
         system with types A and B::
 
+            >>> N_particles = 100
+            >>> box, points = freud.data.make_random_system(
+            ...     10, N_particles, seed=0
+            ... )
+            >>> A_points = points[:N_particles//2]
+            >>> B_points = points[N_particles//2:]
             >>> sf = freud.diffraction.StaticStructureFactorDebye(
             ...     bins=100, k_max=10, k_min=0
             ... )
@@ -200,6 +208,7 @@ cdef class StaticStructureFactorDebye(_StaticStructureFactor):
             ...     query_points=B_points,
             ...     N_total=N_particles
             ... )
+            freud.diffraction.StaticStructureFactorDebye(...)
 
         Args:
             system:
@@ -352,21 +361,31 @@ cdef class StaticStructureFactorDirect(_StaticStructureFactor):
 
         Example for a single component system::
 
+            >>> box, points = freud.data.make_random_system(10, 100, seed=0)
             >>> sf = freud.diffraction.StaticStructureFactorDirect(
             ...     bins=100, k_max=10, k_min=0
             ... )
             >>> sf.compute((box, points))
+            freud.diffraction.StaticStructureFactorDirect(...)
 
         Example for partial mixed structure factor for multiple component
-        system AB::
+        system with types A and B::
 
+            >>> N_particles = 100
+            >>> box, points = freud.data.make_random_system(
+            ...     10, N_particles, seed=0
+            ... )
+            >>> A_points = points[:N_particles//2]
+            >>> B_points = points[N_particles//2:]
             >>> sf = freud.diffraction.StaticStructureFactorDirect(
             ...     bins=100, k_max=10, k_min=0
             ... )
             >>> sf.compute(
             ...     (box, A_points),
-            ...     query_points=B_points, N_total=N_particles
+            ...     query_points=B_points,
+            ...     N_total=N_particles
             ... )
+            freud.diffraction.StaticStructureFactorDirect(...)
 
         Args:
             system:

requirements/requirements-test.txt

@@ -1,17 +1,17 @@
 ase==3.22.0
 cmake==3.21.3
 codecov==2.1.12
-coverage==5.5
+coverage==6.1
 cython==0.29.24
-dynasor==1.1b0; platform_system != "Windows"
+dynasor==1.1.1; platform_system != "Windows"
 garnett==0.7.1
 GitPython==3.1.24
 gsd==2.4.2
 matplotlib>=3.0.0
 numpy==1.21.2
 pillow==8.3.2
 pytest==6.2.5
-pytest-cov==2.12.1
+pytest-cov==3.0.0
 rowan==1.3.0.post1
 scikit-build==0.12.0
 scipy==1.7.1

tests/test_doctests.py

@@ -1,12 +1,28 @@
 import doctest
 import inspect
 
+import pytest
+
 import freud
 
 
-def load_tests(loader, tests, ignore):
-    optionflags = doctest.ELLIPSIS | doctest.NORMALIZE_WHITESPACE
+def fetch_doctests():
+    finder = doctest.DocTestFinder()
     for name, member in inspect.getmembers(freud):
         if inspect.ismodule(member):
-            tests.addTests(doctest.DocTestSuite(member, optionflags=optionflags))
-    return tests
+            for docstring in finder.find(member):
+                if docstring.examples:
+                    yield docstring
+
+
+class TestDoctests:
+    @pytest.mark.parametrize(
+        "docstring", fetch_doctests(), ids=lambda docstring: docstring.name
+    )
+    def test_docstring(self, docstring):
+        optionflags = doctest.ELLIPSIS | doctest.NORMALIZE_WHITESPACE
+        runner = doctest.DocTestRunner(optionflags=optionflags)
+        runner.run(docstring)
+        results = runner.summarize()
+        if results.failed:
+            raise AssertionError(results)