Merge pull request #1607 from fabianegli/use-pytest-raises

use pytest.raises to test for raised exception

tests/test_download.py

@@ -60,7 +60,6 @@ def test_get_release_hash_branch(self):
             == "https://github.com/nf-core/exoseq/archive/819cbac792b76cf66c840b567ed0ee9a2f620db7.zip"
         )
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_get_release_hash_non_existent_release(self):
         wfs = nf_core.list.Workflows()
         wfs.get_remote_workflows()
@@ -71,7 +70,8 @@ def test_get_release_hash_non_existent_release(self):
             download_obj.wf_revisions,
             download_obj.wf_branches,
         ) = nf_core.utils.get_repo_releases_branches(pipeline, wfs)
-        download_obj.get_revision_hash()
+        with pytest.raises(AssertionError):
+            download_obj.get_revision_hash()
 
     #
     # Tests for 'download_wf_files'
@@ -150,7 +150,6 @@ def test_matching_md5sums(self, tmpfile):
         download_obj.validate_md5(tmpfile.name, val_hash)
 
     @with_temporary_file
-    @pytest.mark.xfail(raises=IOError, strict=True)
     def test_mismatching_md5sums(self, tmpfile):
         download_obj = DownloadWorkflow(pipeline="dummy")
         test_hash = hashlib.md5()
@@ -160,7 +159,8 @@ def test_mismatching_md5sums(self, tmpfile):
         with open(tmpfile.name, "w") as f:
             f.write("test")
 
-        download_obj.validate_md5(tmpfile.name, val_hash)
+        with pytest.raises(IOError):
+            download_obj.validate_md5(tmpfile.name, val_hash)
 
     #
     # Tests for 'singularity_pull_image'

tests/test_list.py

@@ -62,12 +62,12 @@ def test_pretty_datetime(self):
         now_ts = time.mktime(now.timetuple())
         nf_core.list.pretty_date(now_ts)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_local_workflows_and_fail(self):
         """Test the local workflow class and try to get local
         Nextflow workflow information"""
         loc_wf = nf_core.list.LocalWorkflow("myWF")
-        loc_wf.get_local_nf_workflow_details()
+        with pytest.raises(AssertionError):
+            loc_wf.get_local_nf_workflow_details()
 
     def test_local_workflows_compare_and_fail_silently(self):
         """Test the workflow class and try to compare local

tests/test_schema.py

@@ -42,20 +42,18 @@ def test_load_lint_schema(self):
         self.schema_obj.get_schema_path(self.template_dir)
         self.schema_obj.load_lint_schema()
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_load_lint_schema_nofile(self):
         """Check that linting raises properly if a non-existant file is given"""
-        self.schema_obj.get_schema_path("fake_file")
-        self.schema_obj.load_lint_schema()
+        with pytest.raises(AssertionError):
+            self.schema_obj.get_schema_path("fake_file")
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_load_lint_schema_notjson(self):
         """Check that linting raises properly if a non-JSON file is given"""
         self.schema_obj.get_schema_path(os.path.join(self.template_dir, "nextflow.config"))
-        self.schema_obj.load_lint_schema()
+        with pytest.raises(AssertionError):
+            self.schema_obj.load_lint_schema()
 
     @with_temporary_file
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_load_lint_schema_noparams(self, tmp_file):
         """
         Check that linting raises properly if a JSON file is given without any params
@@ -64,7 +62,8 @@ def test_load_lint_schema_noparams(self, tmp_file):
         with open(tmp_file.name, "w") as fh:
             json.dump({"type": "fubar"}, fh)
         self.schema_obj.get_schema_path(tmp_file.name)
-        self.schema_obj.load_lint_schema()
+        with pytest.raises(AssertionError):
+            self.schema_obj.load_lint_schema()
 
     def test_get_schema_path_dir(self):
         """Get schema file from directory"""
@@ -74,22 +73,22 @@ def test_get_schema_path_path(self):
         """Get schema file from a path"""
         self.schema_obj.get_schema_path(self.template_schema)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_get_schema_path_path_notexist(self):
         """Get schema file from a path"""
-        self.schema_obj.get_schema_path("fubar", local_only=True)
+        with pytest.raises(AssertionError):
+            self.schema_obj.get_schema_path("fubar", local_only=True)
 
     def test_get_schema_path_name(self):
         """Get schema file from the name of a remote pipeline"""
         self.schema_obj.get_schema_path("atacseq")
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_get_schema_path_name_notexist(self):
         """
         Get schema file from the name of a remote pipeline
         that doesn't have a schema file
         """
-        self.schema_obj.get_schema_path("exoseq")
+        with pytest.raises(AssertionError):
+            self.schema_obj.get_schema_path("exoseq")
 
     def test_load_schema(self):
         """Try to load a schema from a file"""
@@ -135,10 +134,10 @@ def test_load_input_params_yaml(self, tmp_file):
             yaml.dump({"input": "fubar"}, fh)
         self.schema_obj.load_input_params(tmp_file.name)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_load_input_params_invalid(self):
         """Check failure when a non-existent file params file is loaded"""
-        self.schema_obj.load_input_params("fubar")
+        with pytest.raises(AssertionError):
+            self.schema_obj.load_input_params("fubar")
 
     def test_validate_params_pass(self):
         """Try validating a set of parameters against a schema"""
@@ -163,11 +162,11 @@ def test_validate_schema_pass(self):
         self.schema_obj.load_schema()
         self.schema_obj.validate_schema(self.schema_obj.schema)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_validate_schema_fail_noparams(self):
         """Check that the schema validation fails when no params described"""
         self.schema_obj.schema = {"type": "invalidthing"}
-        self.schema_obj.validate_schema(self.schema_obj.schema)
+        with pytest.raises(AssertionError):
+            self.schema_obj.validate_schema(self.schema_obj.schema)
 
     def test_validate_schema_fail_duplicate_ids(self):
         """
@@ -327,37 +326,37 @@ def test_build_schema_from_scratch(self, tmp_dir):
 
         param = self.schema_obj.build_schema(test_pipeline_dir, True, False, None)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     @mock.patch("requests.post")
     def test_launch_web_builder_timeout(self, mock_post):
         """Mock launching the web builder, but timeout on the request"""
         # Define the behaviour of the request get mock
         mock_post.side_effect = requests.exceptions.Timeout()
-        self.schema_obj.launch_web_builder()
+        with pytest.raises(AssertionError):
+            self.schema_obj.launch_web_builder()
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     @mock.patch("requests.post")
     def test_launch_web_builder_connection_error(self, mock_post):
         """Mock launching the web builder, but get a connection error"""
         # Define the behaviour of the request get mock
         mock_post.side_effect = requests.exceptions.ConnectionError()
-        self.schema_obj.launch_web_builder()
+        with pytest.raises(AssertionError):
+            self.schema_obj.launch_web_builder()
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     @mock.patch("requests.post")
     def test_get_web_builder_response_timeout(self, mock_post):
         """Mock checking for a web builder response, but timeout on the request"""
         # Define the behaviour of the request get mock
         mock_post.side_effect = requests.exceptions.Timeout()
-        self.schema_obj.launch_web_builder()
+        with pytest.raises(AssertionError):
+            self.schema_obj.launch_web_builder()
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     @mock.patch("requests.post")
     def test_get_web_builder_response_connection_error(self, mock_post):
         """Mock checking for a web builder response, but get a connection error"""
         # Define the behaviour of the request get mock
         mock_post.side_effect = requests.exceptions.ConnectionError()
-        self.schema_obj.launch_web_builder()
+        with pytest.raises(AssertionError):
+            self.schema_obj.launch_web_builder()
 
     def mocked_requests_post(**kwargs):
         """Helper function to emulate POST requests responses from the web"""

tests/test_utils.py

@@ -167,14 +167,14 @@ def test_get_repo_releases_branches_not_nf_core(self):
             raise AssertionError("MultiQC release v1.10 not found")
         assert "master" in wf_branches.keys()
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_get_repo_releases_branches_not_exists(self):
         wfs = nf_core.list.Workflows()
         wfs.get_remote_workflows()
-        pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("made_up_pipeline", wfs)
+        with pytest.raises(AssertionError):
+            nf_core.utils.get_repo_releases_branches("made_up_pipeline", wfs)
 
-    @pytest.mark.xfail(raises=AssertionError, strict=True)
     def test_get_repo_releases_branches_not_exists_slash(self):
         wfs = nf_core.list.Workflows()
         wfs.get_remote_workflows()
-        pipeline, wf_releases, wf_branches = nf_core.utils.get_repo_releases_branches("made-up/pipeline", wfs)
+        with pytest.raises(AssertionError):
+            nf_core.utils.get_repo_releases_branches("made-up/pipeline", wfs)