ci: added flake8 linter

addresses reanahub/reana#456

.flake8

@@ -0,0 +1,20 @@
+[flake8]
+max-line-length = 89
+
+exclude =
+    build
+    modules
+    dist
+    docs
+    coverage.xml
+    reana_job_controller.egg-info
+    .*/
+    env/
+    .git
+    __pycache__
+
+ignore = E203, E231, E266, E501, W503, F403, F401
+
+max-complexity = 18
+
+select = B,C,E,F,W,T4,B9

.github/workflows/ci.yml

@@ -36,6 +36,23 @@ jobs:
           pip install black==19.10b0
           ./run-tests.sh --check-black
 
+  lint-flake8:
+    runs-on: ubuntu-20.04
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Setup Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Check compliance with pep8, pyflakes and circular complexity
+        run: |
+          pip install --upgrade pip
+          pip install flake8
+          ./run-tests.sh --check-flake8
+
   lint-pydocstyle:
     runs-on: ubuntu-20.04
     steps:
@@ -94,7 +111,7 @@ jobs:
         run: ./run-tests.sh --check-sphinx
 
   python-tests:
-    runs-on: ubuntu-18.04
+    runs-on: ubuntu-20.04
     strategy:
       matrix:
         python-version: [2.7, 3.6, 3.7, 3.8]

MANIFEST.in

@@ -10,6 +10,7 @@ include *.rst
 include *.sh
 include *.yaml
 include *.yml
+include .flake8
 include pytest.ini
 prune docs/_build
 recursive-include reana_commons *.py

reana_commons/errors.py

@@ -21,8 +21,9 @@ def __init__(self, missing_secrets_list=None):
 
     def __str__(self):
         """Represent REANA secret does not exist exception as a string."""
-        return "Operation cancelled. Secrets {} "
-        "do not exist.".format(self.missing_secrets_list)
+        return "Operation cancelled. Secrets {} do not exist.".format(
+            self.missing_secrets_list
+        )
 
 
 class REANASecretAlreadyExists(Exception):

reana_commons/k8s/secrets.py

@@ -50,7 +50,7 @@ def _initialise_user_secrets_store(self):
                 REANA_RUNTIME_KUBERNETES_NAMESPACE, empty_k8s_secret
             )
             return empty_k8s_secret
-        except ApiException as api_e:
+        except ApiException:
             log.error(
                 "Something went wrong while creating "
                 "Kubernetes secret for user {0}.".format(
@@ -113,12 +113,12 @@ def _load_json_annotation_from_k8s_object(self, k8s_object, annotation_key):
         """Load string annotations from Kubernetes object."""
         try:
             return json.loads(k8s_object.metadata.annotations[annotation_key])
-        except ValueError as e:
+        except ValueError:
             log.error(
                 "Annotations for user {} secret store could not be"
                 "loaded as json.".format(annotation_key)
             )
-        except KeyError as e:
+        except KeyError:
             log.error(
                 "Annotation key {annotation_key} does not exist for"
                 " user {user} secret store, so it can not be loaded".format(

reana_commons/utils.py

@@ -323,7 +323,7 @@ def check_htcondor_max_runtime(specification):
         htcondor_max_runtime = step["htcondor_max_runtime"]
         if (
             not str.isdigit(htcondor_max_runtime)
-            and not htcondor_max_runtime in HTCONDOR_JOB_FLAVOURS
+            and htcondor_max_runtime not in HTCONDOR_JOB_FLAVOURS
         ):
             check_pass = False
             click.secho(

run-tests.sh

@@ -20,6 +20,10 @@ check_black () {
     black --check .
 }
 
+check_flake8 () {
+    flake8 .
+}
+
 check_pydocstyle () {
     pydocstyle reana_commons
 }
@@ -39,6 +43,7 @@ check_pytest () {
 check_all () {
     check_script
     check_black
+    check_flake8
     check_pydocstyle
     check_manifest
     check_sphinx
@@ -55,6 +60,7 @@ do
     case $arg in
         --check-shellscript) check_script;;
         --check-black) check_black;;
+        --check-flake8) check_flake8;;
         --check-pydocstyle) check_pydocstyle;;
         --check-manifest) check_manifest;;
         --check-sphinx) check_sphinx;;

setup.py

@@ -55,7 +55,7 @@
 
 # Get the version string. Cannot be done with import!
 with open(os.path.join("reana_commons", "version.py"), "rt") as f:
-    version = re.search('__version__\s*=\s*"(?P<version>.*)"\n', f.read()).group(
+    version = re.search(r'__version__\s*=\s*"(?P<version>.*)"\n', f.read()).group(
         "version"
     )
 

tests/test_secrets_store.py

@@ -42,7 +42,7 @@ def test_create_existing_secrets_fail(
     ) as api_client:
         secrets_store = REANAUserSecretsStore(no_db_user)
         with pytest.raises(REANASecretAlreadyExists):
-            secrets_list = secrets_store.add_secrets(user_secrets)
+            secrets_store.add_secrets(user_secrets)
         api_client.replace_namespaced_secret.assert_not_called()
 
 
@@ -55,7 +55,7 @@ def test_overwrite_secret(
         corev1_api_client_with_user_secrets(user_secrets),
     ) as api_client:
         secrets_store = REANAUserSecretsStore(no_db_user.id_)
-        secrets_list = secrets_store.add_secrets(user_secrets, overwrite=True)
+        secrets_store.add_secrets(user_secrets, overwrite=True)
         api_client.replace_namespaced_secret.assert_called()
 
 

tests/test_utils.py

@@ -61,7 +61,7 @@ def test_click_table_printer_filter_wrong_header(capsys):
     assert out == "\n\n\n"
 
 
-def test_calculate_hash_of_dir(sample_workflow_workspace):
+def test_calculate_hash_of_dir(sample_workflow_workspace):  # noqa: F811
     """Test calculate_hash_of_dir."""
     non_existing_dir_hash = calculate_hash_of_dir("a/b/c")
     assert non_existing_dir_hash == -1
@@ -90,7 +90,7 @@ def test_calculate_job_input_hash():
     ) == calculate_job_input_hash(job_spec_2, workflow_json)
 
 
-def test_calculate_file_access_time(sample_workflow_workspace):
+def test_calculate_file_access_time(sample_workflow_workspace):  # noqa: F811
     """Test calculate_file_access_time."""
     sample_workflow_workspace_path = next(sample_workflow_workspace("sample"))
     access_times = calculate_file_access_time(sample_workflow_workspace_path)