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

Stop excluding tests from coverage

Author: dwhswenson

.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