Merge pull request #895 from psafont/no-unittest

Remove unittest dependency

Author: mr-c

setup.py

@@ -74,7 +74,7 @@
       python_requires='>=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4',
       setup_requires=[] + pytest_runner,
       test_suite='tests',
-      tests_require=['pytest', 'mock >= 2.0.0', 'arcp >= 0.2.0', 'rdflib-jsonld >= 0.4.0'],
+      tests_require=['pytest', 'mock >= 2.0.0', 'pytest-mock >= 1.10.0', 'arcp >= 0.2.0', 'rdflib-jsonld >= 0.4.0'],
       entry_points={
           'console_scripts': ["cwltool=cwltool.main:run"]
       },

test-requirements.txt

@@ -1,4 +1,5 @@
 pytest
 mock >= 2.0.0
+pytest-mock >= 1.10.0
 arcp >= 0.2.0
 rdflib-jsonld >= 0.4.0

tests/test_check.py

@@ -1,15 +1,17 @@
-from __future__ import absolute_import
-
-import unittest
+import pytest
 
 from cwltool.main import main
 
 from .util import get_data, needs_docker
 
 
-class TestCheck(unittest.TestCase):
-    @needs_docker
-    def test_output_checking(self):
-        self.assertEquals(main([get_data('tests/wf/badout1.cwl')]), 1)
-        self.assertEquals(main([get_data('tests/wf/badout2.cwl')]), 1)
-        self.assertEquals(main([get_data('tests/wf/badout3.cwl')]), 1)
+bad_flows = [
+    'tests/wf/badout1.cwl',
+    'tests/wf/badout2.cwl',
+    'tests/wf/badout3.cwl'
+]
+
+@needs_docker
+@pytest.mark.parametrize('bad_flow', bad_flows)
+def test_output_checking(bad_flow):
+    assert main([get_data(bad_flow)]) == 1

tests/test_cwl_version.py

@@ -1,16 +1,12 @@
-from __future__ import absolute_import
-
-import unittest
-
 from cwltool.main import main
 
 from .util import get_data
 
 
-class CWLVersionChecks(unittest.TestCase):
-    def test_missing_cwl_version(self):
-        """no cwlVersion in the workflow"""
-        self.assertEqual(main([get_data('tests/wf/missing_cwlVersion.cwl')]), 1)
-    def test_incorrect_cwl_version(self):
-        """using cwlVersion: v0.1 in the workflow"""
-        self.assertEqual(main([get_data('tests/wf/wrong_cwlVersion.cwl')]), 1)
+def test_missing_cwl_version():
+    """no cwlVersion in the workflow"""
+    assert main([get_data('tests/wf/missing_cwlVersion.cwl')]) == 1
+
+def test_incorrect_cwl_version():
+    """using cwlVersion: v0.1 in the workflow"""
+    assert main([get_data('tests/wf/wrong_cwlVersion.cwl')]) == 1

tests/test_default_path.py

@@ -1,19 +1,16 @@
-import unittest
-
 from schema_salad.ref_resolver import Loader
 
 from cwltool.load_tool import fetch_document, validate_document
 
 from .util import get_data
 
 
-class TestDefaultPath(unittest.TestCase):
-    def test_default_path(self):
-        """Testing that error is not raised when default path is not present"""
-        document_loader, workflowobj, uri = fetch_document(
-            get_data("tests/wf/default_path.cwl"))
-        document_loader, avsc_names, processobj, metadata, uri = validate_document(
-            document_loader, workflowobj, uri)
+def test_default_path():
+    """Testing that error is not raised when default path is not present"""
+    document_loader, workflowobj, uri = fetch_document(
+        get_data("tests/wf/default_path.cwl"))
+    document_loader, _, processobj, _, uri = validate_document(
+        document_loader, workflowobj, uri)
 
-        self.assertIsInstance(document_loader,Loader)
-        self.assertIn("cwlVersion",processobj)
+    assert isinstance(document_loader, Loader)
+    assert "cwlVersion" in processobj

tests/test_dependencies.py

@@ -1,41 +1,33 @@
-from __future__ import absolute_import
+import pytest
 
 import pytest
 
 from cwltool.utils import onWindows
 
-from .test_examples import TestCmdLine
-from .util import get_data, needs_docker
+from .util import get_data, get_main_output, needs_docker
+
 
 try:
-    from galaxy.tools.deps.requirements import ToolRequirement, ToolRequirements
     from galaxy.tools import deps
 except ImportError:
     deps = None
 
-class TestBetaDependenciesResolver(TestCmdLine):
-
-    @needs_docker
-    def test_biocontainers(self):
-        if not deps:
-            pytest.skip("galaxy-lib is not installed.")
-        wflow = get_data("tests/seqtk_seq.cwl")
-        job = get_data("tests/seqtk_seq_job.json")
-        error_code, stdout, stderr = self.get_main_output(
-            ["--beta-use-biocontainers", wflow, job])
-        print(stderr)
-        print(stdout)
-        assert error_code is 0
-
-    def test_bioconda(self):
-        if onWindows() or not deps:
-            pytest.skip("bioconda currently not working on MS Windows.")
-        elif not deps:
-            pytest.skip("galaxy-lib is not installed.")
-        wflow = get_data("tests/seqtk_seq.cwl")
-        job = get_data("tests/seqtk_seq_job.json")
-        error_code, stdout, stderr = self.get_main_output(
-            ["--beta-conda-dependencies", "--debug", wflow, job])
-        print(stderr)
-        print(stdout)
-        assert error_code is 0
+@needs_docker
+@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
+def test_biocontainers():
+    wflow = get_data("tests/seqtk_seq.cwl")
+    job = get_data("tests/seqtk_seq_job.json")
+    error_code, _, _ = get_main_output(
+        ["--beta-use-biocontainers", wflow, job])
+
+    assert error_code == 0
+
+@pytest.mark.skipif(onWindows(), reason="bioconda currently not working on MS Windows")
+@pytest.mark.skipif(not deps, reason="galaxy-lib is not installed")
+def test_bioconda():
+    wflow = get_data("tests/seqtk_seq.cwl")
+    job = get_data("tests/seqtk_seq_job.json")
+    error_code, _, stderr = get_main_output(
+        ["--beta-conda-dependencies", "--debug", wflow, job])
+
+    assert error_code == 0, stderr

tests/test_docker_warning.py

@@ -1,30 +1,26 @@
-from __future__ import absolute_import
-
-import unittest
-
-from mock import mock
-
-from cwltool.command_line_tool import DEFAULT_CONTAINER_MSG, CommandLineTool
-from cwltool.context import RuntimeContext
+from cwltool import command_line_tool
 from cwltool.utils import windows_default_container_id
+from cwltool.context import RuntimeContext
 
 
-class TestDefaultDockerWarning(unittest.TestCase):
+# Test to check warning when default docker Container is used on Windows
+def test_default_docker_warning(mocker):
+    mocker.patch("cwltool.command_line_tool.onWindows", return_value=True)
+    mocker.patch("cwltool.command_line_tool._logger")
 
-    # Test to check warning when default docker Container is used on Windows
-    @mock.patch("cwltool.command_line_tool.onWindows",return_value = True)
-    @mock.patch("cwltool.command_line_tool._logger")
-    def test_default_docker_warning(self,mock_logger,mock_windows):
+    class TestCommandLineTool(command_line_tool.CommandLineTool):
+        def __init__(self, **kwargs):
+            self.requirements = []
+            self.hints = []
 
-        class TestCommandLineTool(CommandLineTool):
-            def __init__(self, **kwargs):
-                self.requirements=[]
-                self.hints=[]
+        def find_default_container(self, args, builder):
+            return windows_default_container_id
 
-            def find_default_container(self, args, builder):
-                return windows_default_container_id
+    tool = TestCommandLineTool()
+    tool.make_job_runner(RuntimeContext({
+        "find_default_container": lambda x: "frolvlad/alpine-bash"}))
 
-        TestObject = TestCommandLineTool()
-        TestObject.make_job_runner(RuntimeContext({
-            "find_default_container": lambda x: "frolvlad/alpine-bash"}))
-        mock_logger.warning.assert_called_with(DEFAULT_CONTAINER_MSG, windows_default_container_id, windows_default_container_id)
+    command_line_tool._logger.warning.assert_called_with(
+        command_line_tool.DEFAULT_CONTAINER_MSG,
+        windows_default_container_id,
+        windows_default_container_id)