Merge pull request #69 from dwhswenson/include-tests-coverage

Stop excluding tests from coverage

.coveragerc

@@ -1,6 +1,5 @@
 [report]
 omit =
-    */paths_cli/tests/*
     */paths_cli/_installed_version.py
     */paths_cli/version.py
 exclude_lines =

paths_cli/compiling/core.py

@@ -153,7 +153,7 @@ class InstanceCompilerPlugin(OPSPlugin):
     """
     SCHEMA = "http://openpathsampling.org/schemas/sim-setup/draft01.json"
     category = None
-    
+
     def __init__(self, builder, parameters, name=None, *, aliases=None,
                  description=None, requires_ops=(1, 0),
                  requires_cli=(0, 3)):

paths_cli/tests/commands/test_md.py

@@ -159,7 +159,7 @@ def test_md_main(md_fixture, inp):
             nsteps, ensembles = 5, None
         elif inp == 'ensemble':
             nsteps, ensembles = None, [ens]
-        else:
+        else:  # -no-cov-
             raise RuntimeError("pytest went crazy")
 
         traj, foo = md_main(

paths_cli/tests/commands/utils.py

@@ -1,7 +1,7 @@
 import traceback
 
 def assert_click_success(result):
-    if result.exit_code != 0:
+    if result.exit_code != 0:  # -no-cov-  (only occurs on test error)
         print(result.output)
         traceback.print_tb(result.exc_info[2])
         print(result.exc_info[0], result.exc_info[1])

paths_cli/tests/compiling/test_core.py

@@ -332,7 +332,7 @@ def _validate_obj(obj, input_type):
             assert obj == 'bar'
         elif input_type == 'dict':
             assert obj.data == 'qux'
-        else:
+        else:  # -no-cov-
             raise RuntimeError("Error in test setup")
 
     @pytest.mark.parametrize('input_type', ['str', 'dict'])

paths_cli/tests/compiling/test_volumes.py

@@ -1,6 +1,8 @@
 import pytest
 from unittest import mock
 from paths_cli.tests.compiling.utils import mock_compiler
+from paths_cli.compiling.plugins import CVCompilerPlugin
+from paths_cli.compiling.core import Parameter
 
 import yaml
 import numpy as np
@@ -23,20 +25,20 @@ def setup(self):
         }
 
         self.func = {
-            'inline': "\n  ".join(["name: foo", "type: mdtraj"]),
+            'inline': "\n  " + "\n  ".join([
+                "name: foo",
+                "type: fake_type",
+                "input_data: bar",
+            ]),
             'external': 'foo'
         }
 
-    def create_inputs(self, inline, periodic):
-        yml = "\n".join(["type: cv-volume", "cv: {func}",
-                         "lambda_min: 0", "lambda_max: 1"])
-
     def set_periodic(self, periodic):
         if periodic == 'periodic':
             self.named_objs_dict['foo']['period_max'] = 'np.pi'
             self.named_objs_dict['foo']['period_min'] = '-np.pi'
 
-    @pytest.mark.parametrize('inline', ['external', 'external'])
+    @pytest.mark.parametrize('inline', ['external', 'inline'])
     @pytest.mark.parametrize('periodic', ['periodic', 'nonperiodic'])
     def test_build_cv_volume(self, inline, periodic):
         self.set_periodic(periodic)
@@ -47,14 +49,29 @@ def test_build_cv_volume(self, inline, periodic):
         mock_cv = CoordinateFunctionCV(lambda s: s.xyz[0][0],
                                        period_min=period_min,
                                        period_max=period_max).named('foo')
+
+        patch_loc = 'paths_cli.compiling.root_compiler._COMPILERS'
+
         if inline =='external':
-            patch_loc = 'paths_cli.compiling.root_compiler._COMPILERS'
             compilers = {
                 'cv': mock_compiler('cv', named_objs={'foo': mock_cv})
             }
-            with mock.patch.dict(patch_loc, compilers):
-                vol = build_cv_volume(dct)
-        elif inline == 'internal':
+        elif inline == 'inline':
+            fake_plugin = CVCompilerPlugin(
+                name="fake_type",
+                parameters=[Parameter('input_data', str)],
+                builder=lambda input_data: mock_cv
+            )
+            compilers = {
+                'cv': mock_compiler(
+                    'cv',
+                    type_dispatch={'fake_type': fake_plugin}
+                )
+            }
+        else:  # -no-cov-
+            raise RuntimeError("Should never get here")
+
+        with mock.patch.dict(patch_loc, compilers):
             vol = build_cv_volume(dct)
 
         in_state = make_1d_traj([0.5])[0]

paths_cli/tests/test_file_copying.py

@@ -59,7 +59,8 @@ def __init__(self):
                 self.previously_seen = set([])
 
             def __call__(self, snap):
-                if snap in self.previously_seen:
+                if snap in self.previously_seen:  # -no-cov-
+                    # this is only covered if an error occurs
                     raise AssertionError("Second CV eval for " + str(snap))
                 self.previously_seen.update({snap})
                 return snap.xyz[0][0]

paths_cli/tests/test_parameters.py

@@ -103,7 +103,7 @@ def _filename(self, getter):
 
     def create_file(self, getter):
         filename = self._filename(getter)
-        if getter == "named":
+        if getter == "name":
             self.other_scheme = self.other_scheme.named("other")
             self.other_engine = self.other_engine.named("other")
 

paths_cli/tests/test_utils.py

@@ -10,7 +10,7 @@ def test_len(self):
     def test_empty(self):
         ordered = OrderedSet()
         assert len(ordered) == 0
-        for _ in ordered:
+        for _ in ordered:  # -no-cov-
             raise RuntimeError("This should not happen")
 
     def test_order(self):

paths_cli/tests/utils.py

@@ -3,13 +3,13 @@
 
 try:
     urllib.request.urlopen('https://www.google.com')
-except:
+except:  # -no-cov-
     HAS_INTERNET = False
 else:
     HAS_INTERNET = True
 
 def assert_url(url):
-    if not HAS_INTERNET:
+    if not HAS_INTERNET:  # -no-cov-
         pytest.skip("Internet connection seems faulty")
 
     # TODO: On a 404 this will raise a urllib.error.HTTPError. It would be

paths_cli/tests/wizard/mock_wizard.py

@@ -30,7 +30,9 @@ def input(self, content):
         self.input_call_count += 1
         try:
             user_input = next(self._input_iter)
-        except StopIteration as e:
+        except StopIteration as e:  # -no-cov-
+            # this only occurs on a test error and provides diagnostic
+            # information
             print(self.log_text)
             raise e
 

paths_cli/tests/wizard/test_load_from_ops.py

@@ -20,13 +20,15 @@ def __init__(self, objects):
         self._objects = objects
         self._named_objects = {obj.name: obj for obj in objects}
 
-    def __getitem__(self, key):
-        if isinstance(key, int):
-            return self._objects[key]
-        elif isinstance(key, str):
-            return self._named_objects[key]
-        else:
-            raise TypeError("Huh?")
+    # leaving this commented out... it doesn't seem to be used currently,
+    # but if it is needed in the future, this should be the implementation
+    # def __getitem__(self, key):
+    #     if isinstance(key, int):
+    #         return self._objects[key]
+    #     elif isinstance(key, str):
+    #         return self._named_objects[key]
+    #     else:  # -no-cov-
+    #         raise TypeError("Huh?")
 
     def __iter__(self):
         return iter(self._objects)

paths_cli/tests/wizard/test_parameters.py

@@ -15,16 +15,12 @@ class TestWizardParameter:
     def _reverse(string):
         return "".join(reversed(string))
 
-    @staticmethod
-    def _summarize(string):
-        return f"Here's a summary: we made {string}"
-
     def setup(self):
         self.parameter = WizardParameter(
             name='foo',
             ask="How should I {do_what}?",
             loader=self._reverse,
-            summarize=self._summarize,
+            summarize=lambda string: f"Should be unused. Input: {string}",
         )
         self.wizard = mock_wizard(["bar"])
         self.compiler_plugin = compiling.InstanceCompilerPlugin(

paths_cli/tests/wizard/test_volumes.py

@@ -16,15 +16,6 @@
 from openpathsampling.tests.test_helpers import make_1d_traj
 
 
-def _wrap(x, period_min, period_max):
-    # used in testing periodic CVs
-    while x >= period_max:
-        x -= period_max - period_min
-    while x < period_min:
-        x += period_max - period-min
-    return x
-
-
 @pytest.fixture
 def volume_setup():
     cv = CoordinateFunctionCV(lambda snap: snap.xyz[0][0]).named('x')
@@ -54,7 +45,7 @@ def test_volume_intro(as_state, has_state):
         assert "You'll need to define" in intro
     elif not as_state:
         assert intro == _VOL_DESC
-    else:
+    else:  # -no-cov-
         raise RuntimeError("WTF?")
 
 def _binary_volume_test(volume_setup, func):
@@ -120,8 +111,7 @@ def test_cv_defined_volume(periodic):
         min_ = 0.0
         max_ = 1.0
         cv = CoordinateFunctionCV(
-            lambda snap: _wrap(snap.xyz[0][0], period_min=min_,
-                               period_max=max_),
+            lambda snap: snap.xyz[0][0],
             period_min=min_, period_max=max_
         ).named('x')
         inputs = ['x', '0.75', '1.25']

paths_cli/tests/wizard/test_wizard.py

@@ -309,6 +309,7 @@ def test_save_to_file(self, toy_engine):
         assert len(storage.networks) == len(storage.schemes) == 0
         assert len(storage.engines) == 1
         assert storage.engines[toy_engine.name] == toy_engine
+        assert storage.engines[0] == toy_engine
         assert "Everything has been stored" in self.wizard.console.log_text
 
     @pytest.mark.parametrize('req,count,expected', [
@@ -382,6 +383,7 @@ def test_run_wizard(self, toy_engine):
         assert len(storage.networks) == len(storage.schemes) == 0
         assert len(storage.engines) == 1
         assert storage.engines[toy_engine.name] == toy_engine
+        assert storage.engines[0] == toy_engine
 
     def test_run_wizard_quit(self):
         console = MockConsole()