Merge remote-tracking branch 'origin/public/tests/pytest_wrong_test_m…

…ethods' into public/tests/pytest_sage_files

src/bin/sage-coverage

@@ -130,6 +130,11 @@ class CoverageResults:
         if not docstring:
             self.no_doc.append(fullname)
             return
+
+        if "pytest" in docstring:
+            self.good.append(fullname)
+            return
+
         if "sage: " not in docstring:
             self.no_test.append(fullname)
             return
@@ -276,6 +281,10 @@ def go(filename):
             or filename.endswith('.sage')):
         return
 
+    # Filter pytest files which are not supposed to have doctests
+    if filename.endswith('_test.py'):
+        return
+
     with open(filename, 'r') as f:
         cr = CoverageResults(filename).check_file(f)
     bad = cr.no_doc or cr.no_test or cr.possibly_wrong

src/conftest.py

@@ -15,16 +15,38 @@
 from importlib.machinery import ModuleSpec
 from importlib.util import spec_from_loader
 from pathlib import Path
-from typing import Any, Sequence
+from typing import Any, List, Sequence
 
 import pytest
 
-# Ignore a few test files that are (not yet) using pytest
-collect_ignore = [
-    "sage/misc/nested_class_test.py",
-    "sage/repl/rich_output/backend_test.py",
-    "sage/tests/deprecation_test.py"
-]
+
+def pytest_collection_modifyitems(
+    session: pytest.Session, config: pytest.Config, items: List[pytest.Item]
+):
+    """
+    This hook is called after collection has been performed, and can be used to
+    modify the list of items that will be run.
+
+    See `pytest documentation <https://docs.pytest.org/en/latest/reference/reference.html#std-hook-pytest_collection_modifyitems>`_.
+    """
+    skip_as_false_positive = pytest.mark.skip(
+        reason="Skipping this because its not a pytest test but an ordinary"
+        + "method that happens to start with 'test_'"
+    )
+    for item in items:
+        # Add a mark to all tests that should be skipped
+        if item.name in [
+            "test_relation_maxima",
+            "test_b2_local",
+            "test_b2_global",
+            "test_a1a3_local",
+            "test_a1a3_global",
+            "test_rst_global",
+            "test_comparison",
+            "test_signed_infinity",
+            "test_pickle",
+        ]:
+            item.add_marker(skip_as_false_positive)
 
 
 def pytest_collect_file(parent: pytest.Collector, file_path: Path):

src/doc/en/developer/coding_basics.rst

@@ -509,6 +509,12 @@ information. You can use the existing functions of Sage as templates.
     However, lines only containing double colons `::` do not
     end "TESTS" blocks.
 
+  Sometimes (but rarely) one has private or protected methods that don't need a
+  proper ``EXAMPLES`` doctest. In these cases, one can either write traditional
+  doctest using the ``TESTS`` block or use pytest to test the method.
+  In the latter case, one has to add ``TESTS: pytest`` to the docstring, so that
+  the method is explicitly marked as tested.
+
 Note about Sphinx directives vs. other blocks
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

src/doc/en/reference/misc/index.rst

@@ -290,7 +290,7 @@ Testing
 
    sage/misc/sage_unittest
    sage/misc/random_testing
-   sage/misc/nested_class_test
+   sage/misc/test_nested_class
 
 Benchmarking and Profiling
 ~~~~~~~~~~~~~~~~~~~~~~~~~~

src/doc/en/reference/repl/index.rst

@@ -77,7 +77,7 @@ Display Backend Infrastructure
    sage/repl/rich_output/output_catalog
 
    sage/repl/rich_output/backend_base
-   sage/repl/rich_output/backend_test
+   sage/repl/rich_output/test_backend
    sage/repl/rich_output/backend_doctest
    sage/repl/rich_output/backend_ipython
 

src/sage/categories/primer.py

@@ -1152,7 +1152,7 @@ class ElementMethods:
     reveal some glitches in their implementation, in particular around
     class naming and introspection. Sage currently works around the
     more annoying ones but some remain visible. See
-    e.g. :mod:`sage.misc.nested_class_test`.
+    e.g. :mod:`sage.misc.test_nested_class`.
 
 
 Let us now look at the categories of ``C``::

src/sage/crypto/mq/sr.py

@@ -3339,7 +3339,7 @@ def __exit__(self, typ, value, tb):
         """
         self.sr._allow_zero_inversions = self.allow_zero_inversions
 
-def test_consistency(max_n=2, **kwargs):
+def _test_consistency(max_n=2, **kwargs):
     r"""
     Test all combinations of ``r``, ``c``, ``e`` and ``n`` in ``(1,
     2)`` for consistency of random encryptions and their polynomial
@@ -3358,8 +3358,8 @@ def test_consistency(max_n=2, **kwargs):
     on machines with "only" 2GB of RAM, we test ``max_n`` = 1, which
     has a more reasonable memory usage. ::
 
-        sage: from sage.crypto.mq.sr import test_consistency
-        sage: test_consistency(1)  # long time (65s on sage.math, 2012)
+        sage: from sage.crypto.mq.sr import _test_consistency
+        sage: _test_consistency(1)  # long time (65s on sage.math, 2012)
         True
     """
     consistent = True

src/sage/docs/conf.py

@@ -623,7 +623,7 @@ def process_docstring_module_title(app, what, name, obj, options, docstringlines
             break
 
 skip_picklability_check_modules = [
-    #'sage.misc.nested_class_test', # for test only
+    #'sage.misc.test_nested_class', # for test only
     'sage.misc.latex',
     'sage.misc.explain_pickle',
     '__builtin__',

src/sage/graphs/graph_decompositions/modular_decomposition.py

@@ -299,7 +299,7 @@ def modular_decomposition(graph):
 
     The Icosahedral graph is Prime::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import modular_decomposition, print_md_tree, _test_modular_decomposition
         sage: print_md_tree(modular_decomposition(graphs.IcosahedralGraph()))
         PRIME
          5
@@ -376,7 +376,7 @@ def modular_decomposition(graph):
         ....:       11:[12,1], 12:[11,1], 13:[14,16,17,1], 14:[13,17,1],
         ....:       16:[13,17,1], 17:[13,14,16,18,1], 18:[17], 24:[5,4,3,1]}
         sage: g = Graph(d)
-        sage: test_modular_decomposition(modular_decomposition(g), g)
+        sage: _test_modular_decomposition(modular_decomposition(g), g)
         True
 
     Graph from the :wikipedia:`Modular_decomposition`::
@@ -386,7 +386,7 @@ def modular_decomposition(graph):
         ....:       7:[2,3,4,5,8,9,10,11], 8:[6,7,9,10,11], 9:[6,7,8,10,11],
         ....:       10:[6,7,8,9], 11:[6,7,8,9]}
         sage: g = Graph(d2)
-        sage: test_modular_decomposition(modular_decomposition(g), g)
+        sage: _test_modular_decomposition(modular_decomposition(g), g)
         True
     """
     if graph.is_directed():
@@ -2488,8 +2488,8 @@ def gamma_classes(graph):
 
     Ensure that the returned vertex sets from some random graphs are modules::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import test_gamma_modules
-        sage: test_gamma_modules(2, 10, 0.5)
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import _test_gamma_modules
+        sage: _test_gamma_modules(2, 10, 0.5)
     """
     from itertools import chain
     from sage.sets.disjoint_set import DisjointSet
@@ -2538,7 +2538,8 @@ def habib_maurer_algorithm(graph, g_classes=None):
 
     The Icosahedral graph is Prime::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import (
+        ....:    modular_decomposition, habib_maurer_algorithm, print_md_tree, _test_modular_decomposition)
         sage: print_md_tree(habib_maurer_algorithm(graphs.IcosahedralGraph()))
         PRIME
          1
@@ -2599,7 +2600,7 @@ def habib_maurer_algorithm(graph, g_classes=None):
         ....:       11:[12,1], 12:[11,1], 13:[14,16,17,1], 14:[13,17,1],
         ....:       16:[13,17,1], 17:[13,14,16,18,1], 18:[17], 24:[5,4,3,1]}
         sage: g = Graph(d)
-        sage: test_modular_decomposition(habib_maurer_algorithm(g), g)
+        sage: _test_modular_decomposition(habib_maurer_algorithm(g), g)
         True
 
     Graph from the :wikipedia:`Modular_decomposition`::
@@ -2609,7 +2610,7 @@ def habib_maurer_algorithm(graph, g_classes=None):
         ....:       7:[2,3,4,5,8,9,10,11], 8:[6,7,9,10,11], 9:[6,7,8,10,11],
         ....:       10:[6,7,8,9], 11:[6,7,8,9]}
         sage: g = Graph(d2)
-        sage: test_modular_decomposition(habib_maurer_algorithm(g), g)
+        sage: _test_modular_decomposition(habib_maurer_algorithm(g), g)
         True
 
     Tetrahedral Graph is Series::
@@ -2705,7 +2706,7 @@ def habib_maurer_algorithm(graph, g_classes=None):
 #=============================================================================
 
 # Function implemented for testing
-def test_modular_decomposition(tree_root, graph):
+def _test_modular_decomposition(tree_root, graph):
     """
     Test the input modular decomposition tree using recursion.
 
@@ -2721,30 +2722,32 @@ def test_modular_decomposition(tree_root, graph):
 
     EXAMPLES::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import (
+        ....:    modular_decomposition, _test_modular_decomposition)
         sage: g = graphs.HexahedralGraph()
-        sage: test_modular_decomposition(modular_decomposition(g), g)
+        sage: _test_modular_decomposition(modular_decomposition(g), g)
         True
     """
     if tree_root.node_type != NodeType.NORMAL:
         for module in tree_root.children:
-            if not test_module(module, graph):
+            if not _test_module(module, graph):
                 # test whether modules pass the defining
                 # characteristics of modules
                 return False
-            if not test_modular_decomposition(module,
-                                              graph.subgraph(get_vertices(module))):
+            if not _test_modular_decomposition(
+                module, graph.subgraph(get_vertices(module))
+            ):
                 # recursively test the modular decomposition subtrees
                 return False
 
-        if not test_maximal_modules(tree_root, graph):
+        if not _test_maximal_modules(tree_root, graph):
             # test whether the mdoules are maximal in nature
             return False
 
     return True
 
 # Function implemented for testing
-def test_maximal_modules(tree_root, graph):
+def _test_maximal_modules(tree_root, graph):
     r"""
     Test the maximal nature of modules in a modular decomposition tree.
 
@@ -2770,9 +2773,10 @@ def test_maximal_modules(tree_root, graph):
 
     EXAMPLES::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import (
+        ....:    modular_decomposition, _test_maximal_modules)
         sage: g = graphs.HexahedralGraph()
-        sage: test_maximal_modules(modular_decomposition(g), g)
+        sage: _test_maximal_modules(modular_decomposition(g), g)
         True
     """
     if tree_root.node_type != NodeType.NORMAL:
@@ -2903,7 +2907,7 @@ def form_module(index, other_index, tree_root, graph):
                     break
 
 # Function implemented for testing
-def test_module(module, graph):
+def _test_module(module, graph):
     """
     Test whether input module is actually a module
 
@@ -2919,12 +2923,13 @@ def test_module(module, graph):
 
     EXAMPLES::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import (
+        ....:    modular_decomposition, _test_module)
         sage: g = graphs.HexahedralGraph()
         sage: tree_root = modular_decomposition(g)
-        sage: test_module(tree_root, g)
+        sage: _test_module(tree_root, g)
         True
-        sage: test_module(tree_root.children[0], g)
+        sage: _test_module(tree_root.children[0], g)
         True
     """
     # A single vertex is a module
@@ -3212,7 +3217,7 @@ def relabel_tree(root, perm):
 
 from sage.misc.random_testing import random_testing
 @random_testing
-def test_gamma_modules(trials, vertices, prob, verbose=False):
+def _test_gamma_modules(trials, vertices, prob, verbose=False):
     r"""
     Verify that the vertices of each gamma class of a random graph are modules
     of that graph.
@@ -3230,8 +3235,8 @@ def test_gamma_modules(trials, vertices, prob, verbose=False):
 
     EXAMPLES::
 
-        sage: from sage.graphs.graph_decompositions.modular_decomposition import *
-        sage: test_gamma_modules(3, 7, 0.5)
+        sage: from sage.graphs.graph_decompositions.modular_decomposition import _test_gamma_modules
+        sage: _test_gamma_modules(3, 7, 0.5)
     """
     from sage.graphs.generators.random import RandomGNP
     for _ in range(trials):
@@ -3272,8 +3277,8 @@ def permute_decomposition(trials, algorithm, vertices, prob, verbose=False):
             print(random_perm)
         t1 = algorithm(g1)
         t2 = algorithm(g2)
-        assert(test_modular_decomposition(t1, g1))
-        assert(test_modular_decomposition(t2, g2))
+        assert _test_modular_decomposition(t1, g1)
+        assert _test_modular_decomposition(t2, g2)
         t1p = relabel_tree(t1, random_perm)
         assert(equivalent_trees(t1p, t2))
         if verbose:

src/sage/homology/tests.py

@@ -6,15 +6,15 @@
 
 TESTS::
 
-    sage: from sage.homology.tests import test_random_chain_complex
-    sage: test_random_chain_complex(trials=20)  # optional - CHomP
-    sage: test_random_chain_complex(level=2, trials=20)  # optional - CHomP
-    sage: test_random_chain_complex(level=3, trials=20)  # long time # optional - CHomP
-
-    sage: from sage.homology.tests import test_random_simplicial_complex
-    sage: test_random_simplicial_complex(level=1, trials=20)  # optional - CHomP
-    sage: test_random_simplicial_complex(level=2, trials=20)  # optional - CHomP
-    sage: test_random_simplicial_complex(level=5/2, trials=10)  # long time # optional - CHomP
+    sage: from sage.homology.tests import _test_random_chain_complex
+    sage: _test_random_chain_complex(trials=20)  # optional - CHomP
+    sage: _test_random_chain_complex(level=2, trials=20)  # optional - CHomP
+    sage: _test_random_chain_complex(level=3, trials=20)  # long time # optional - CHomP
+
+    sage: from sage.homology.tests import _test_random_simplicial_complex
+    sage: _test_random_simplicial_complex(level=1, trials=20)  # optional - CHomP
+    sage: _test_random_simplicial_complex(level=2, trials=20)  # optional - CHomP
+    sage: _test_random_simplicial_complex(level=5/2, trials=10)  # long time # optional - CHomP
 """
 
 from sage.misc.random_testing import random_testing
@@ -56,7 +56,7 @@ def random_chain_complex(level=1):
     return ChainComplex({dim: mat}, degree = deg)
 
 @random_testing
-def test_random_chain_complex(level=1, trials=1, verbose=False):
+def _test_random_chain_complex(level=1, trials=1, verbose=False):
     """
     Compute the homology of a random chain complex with and without
     CHomP, and compare the results.  If they are not the same, raise
@@ -72,8 +72,8 @@ def test_random_chain_complex(level=1, trials=1, verbose=False):
 
     EXAMPLES::
 
-        sage: from sage.homology.tests import test_random_chain_complex
-        sage: test_random_chain_complex(trials=2)  # optional - CHomP
+        sage: from sage.homology.tests import _test_random_chain_complex
+        sage: _test_random_chain_complex(trials=2)  # optional - CHomP
     """
     for i in range(trials):
         C = random_chain_complex(level=level)
@@ -111,7 +111,7 @@ def random_simplicial_complex(level=1, p=0.5):
     return RandomComplex(n, dim, p)
 
 @random_testing
-def test_random_simplicial_complex(level=1, trials=1, verbose=False):
+def _test_random_simplicial_complex(level=1, trials=1, verbose=False):
     """
     Compute the homology of a random simplicial complex with and
     without CHomP, and compare the results.  If they are not the same,
@@ -129,8 +129,8 @@ def test_random_simplicial_complex(level=1, trials=1, verbose=False):
 
     EXAMPLES::
 
-        sage: from sage.homology.tests import test_random_simplicial_complex
-        sage: test_random_simplicial_complex(trials=2)  # optional - CHomP
+        sage: from sage.homology.tests import _test_random_simplicial_complex
+        sage: _test_random_simplicial_complex(trials=2)  # optional - CHomP
     """
     for i in range(trials):
         X = random_simplicial_complex(level=level)