chore(master): using black to reformat python files (reanahub#673)

Author: etlstrauss

reana_workflow_controller/config.py

@@ -321,9 +321,7 @@ def _parse_interactive_sessions_environments(env_var):
 )
 """Default image for REANA Job Controller sidecar."""
 
-REANA_JOB_CONTROLLER_SECRET  = os.getenv(
-    "REANA_JOB_CONTROLLER_SECRET"
-)
+REANA_JOB_CONTROLLER_SECRET = os.getenv("REANA_JOB_CONTROLLER_SECRET")
 """DOptional secret for REANA Job Controller sidecar."""
 
 JOB_CONTROLLER_ENV_VARS = _env_vars_dict_to_k8s_list(
@@ -475,21 +473,15 @@ def _parse_interactive_sessions_environments(env_var):
     "REANA_RUNTIME_JOBS_KUBERNETES_TOLERATIONS"
 )
 """Tolerations for jobs"""
-REANA_DATASTORE_ENABLED = os.getenv(
-    "REANA_DATASTORE_ENABLED"
-) == "true"
+REANA_DATASTORE_ENABLED = os.getenv("REANA_DATASTORE_ENABLED") == "true"
 """Set datastore (s3) sidecar for interactive sessions enabled or disabled"""
 
-if(REANA_DATASTORE_ENABLED):
-    REANA_DATASTORE_IMAGE = os.getenv(
-        "REANA_DATASTORE_IMAGE"
-    )
+if REANA_DATASTORE_ENABLED:
+    REANA_DATASTORE_IMAGE = os.getenv("REANA_DATASTORE_IMAGE")
     """Optional Image for datastore (s3) sidecar for interactive sessions"""
 
-    REANA_DATASTORE_SECRET = os.getenv(
-        "REANA_DATASTORE_SECRET"
-    )
+    REANA_DATASTORE_SECRET = os.getenv("REANA_DATASTORE_SECRET")
     """Optional secret for datastore (s3) sidecar for interactive sessions"""
 else:
     REANA_DATASTORE_IMAGE = ""
-    REANA_DATASTORE_SECRET = ""
+    REANA_DATASTORE_SECRET = ""

reana_workflow_controller/dask.py

@@ -5,6 +5,7 @@
 # under the terms of the MIT License; see LICENSE file for more details.
 
 """Dask resource manager."""
+
 import logging
 import os
 import yaml

reana_workflow_controller/k8s.py

@@ -79,19 +79,29 @@ def __init__(
         self.image = image
         self.port = port
         self.path = path
-        self.cvmfs_repos = cvmfs_repos or [],
+        self.cvmfs_repos = (cvmfs_repos or [],)
         self.image_pull_secrets = []
         metadata = client.V1ObjectMeta(
             name=deployment_name,
             labels={"reana_workflow_mode": "session"},
         )
         self._session_container = client.V1Container(
-            name=self.deployment_name, image=self.image, env=[], volume_mounts=[], ports=[client.V1ContainerPort(container_port=self.port)]
+            name=self.deployment_name,
+            image=self.image,
+            env=[],
+            volume_mounts=[],
+            ports=[client.V1ContainerPort(container_port=self.port)],
         )
         containers = [self._session_container]
-        if(REANA_DATASTORE_ENABLED):
+        if REANA_DATASTORE_ENABLED:
             self._s3_container = client.V1Container(
-                name="datastore", image=REANA_DATASTORE_IMAGE, env=[], volume_mounts=[], ports=[], image_pull_policy="Always", lifecycle=[]
+                name="datastore",
+                image=REANA_DATASTORE_IMAGE,
+                env=[],
+                volume_mounts=[],
+                ports=[],
+                image_pull_policy="Always",
+                lifecycle=[],
             )
             containers.append(self._s3_container)
 
@@ -229,55 +239,58 @@ def setup_s3_storage(self):
         volume_name = "s3-mounts"
 
         volume = client.V1Volume(
-            name=volume_name,
-            empty_dir=client.V1EmptyDirVolumeSource()
+            name=volume_name, empty_dir=client.V1EmptyDirVolumeSource()
         )
 
         volume_mount = client.V1VolumeMount(
             name=volume_name,
             mount_path="/data/s3/",
-            mount_propagation="HostToContainer"
+            mount_propagation="HostToContainer",
         )
 
         self._session_container.volume_mounts.append(volume_mount)
 
         volume_mount = client.V1VolumeMount(
-            name=volume_name,
-            mount_path="/s3-data",
-            mount_propagation="Bidirectional"
+            name=volume_name, mount_path="/s3-data", mount_propagation="Bidirectional"
         )
 
         self._s3_container.volume_mounts.append(volume_mount)
 
         self._pod_spec.volumes.append(volume)
 
     def setup_s3_sidecar(self):
-        """Add the sidecar for s3 mounts"""
+        """Add the sidecar for s3 mounts."""
         # Define the volume mount for /dev/fuse
         fuse_volume_mount = client.V1VolumeMount(
-            name="fuse-device",
-            mount_path="/dev/fuse"
+            name="fuse-device", mount_path="/dev/fuse"
         )
 
         # Define the volume for /dev/fuse
-        fuse_volume = client.V1HostPathVolumeSource(
-            path="/dev/fuse"
-        )
+        fuse_volume = client.V1HostPathVolumeSource(path="/dev/fuse")
 
         # Append the volume mount and volume to the session container and pod spec
         self._s3_container.volume_mounts.append(fuse_volume_mount)
-        self._pod_spec.volumes.append(client.V1Volume(name="fuse-device", host_path=fuse_volume))
+        self._pod_spec.volumes.append(
+            client.V1Volume(name="fuse-device", host_path=fuse_volume)
+        )
 
         security_context = client.V1SecurityContext(
-            run_as_user=0, allow_privilege_escalation=True, capabilities=client.V1Capabilities(add=["SYS_ADMIN"]), privileged=True
+            run_as_user=0,
+            allow_privilege_escalation=True,
+            capabilities=client.V1Capabilities(add=["SYS_ADMIN"]),
+            privileged=True,
         )
         self._s3_container.security_context = security_context
 
         # adding umount for correct termination
         lifecycle_dict = {
             "preStop": {
                 "exec": {
-                    "command": ["/bin/sh", "-c", "xargs umount -l < /etc/active_mounts.txt || true"]
+                    "command": [
+                        "/bin/sh",
+                        "-c",
+                        "xargs umount -l < /etc/active_mounts.txt || true",
+                    ]
                 }
             }
         }
@@ -304,9 +317,7 @@ def add_environment_variable(self, name, value):
 
     def add_run_with_root_permissions(self):
         """Run interactive session with root."""
-        security_context = client.V1SecurityContext(
-            run_as_user=0, privileged=True
-        )
+        security_context = client.V1SecurityContext(run_as_user=0, privileged=True)
         self._session_container.security_context = security_context
 
     def add_user_secrets(self):
@@ -337,7 +348,7 @@ def add_user_secrets(self):
         self._session_container.env = session_env
 
         # mount s3 secretes
-        if(REANA_DATASTORE_ENABLED):
+        if REANA_DATASTORE_ENABLED:
             self._s3_container.env = s3_env
 
     def get_deployment_objects(self):
@@ -397,7 +408,7 @@ def build_interactive_jupyter_deployment_k8s_objects(
     deployment_builder.add_command_arguments(command_args)
     deployment_builder.add_reana_shared_storage()
     deployment_builder.add_image_pull_secrets()
-    if(REANA_DATASTORE_ENABLED):
+    if REANA_DATASTORE_ENABLED:
         deployment_builder.setup_s3_sidecar()
         deployment_builder.setup_s3_storage()
     if cvmfs_repos:

reana_workflow_controller/rest/workflows_session.py

@@ -8,7 +8,6 @@
 
 """REANA Workflow Controller interactive sessions REST API."""
 
-
 from flask import Blueprint, jsonify, request
 from webargs import fields
 from webargs.flaskparser import use_kwargs
@@ -18,7 +17,6 @@
 
 from reana_workflow_controller.workflow_run_manager import KubernetesWorkflowRunManager
 
-
 blueprint = Blueprint("workflows_session", __name__)
 
 

reana_workflow_controller/workflow_run_manager.py

@@ -5,6 +5,7 @@
 # under the terms of the MIT License; see LICENSE file for more details.
 
 """Workflow run manager interface."""
+
 import base64
 import copy
 import json
@@ -876,7 +877,7 @@ def _create_job_spec(
 
         if REANA_JOB_CONTROLLER_SECRET:
             spec.template.spec.image_pull_secrets = [
-                client.V1LocalObjectReference(name= REANA_JOB_CONTROLLER_SECRET)
+                client.V1LocalObjectReference(name=REANA_JOB_CONTROLLER_SECRET)
             ]
 
         # filter out volumes with the same name

sidecars/datastore/app.py

@@ -18,11 +18,12 @@ def createFolders(aliases, base_dir):
         print(f"A error accrued during the creation of the s3-buckets: {e}")
         return False
 
+
 def getCredentials(aliases):
     aliases_credentials = []
     try:
         for alias in aliases:
-            temp_list =[alias]
+            temp_list = [alias]
             temp_list.append(os.getenv(f"S3_TO_LOCAL_{alias}_BUCKET"))
             temp_list.append(os.getenv(f"S3_TO_LOCAL_{alias}_HOST"))
             temp_list.append(os.getenv(f"S3_TO_LOCAL_{alias}_REGION"))
@@ -33,16 +34,17 @@ def getCredentials(aliases):
     except Exception as e:
         print(f"A error accrued during load of S3 credentials: {e}")
         return False
-    
+
+
 def createS3Mounts(aliases, base_dir):
-    for i in (0, len(aliases)-2):
+    for i in (0, len(aliases) - 2):
         try:
             with open(".passwd-s3fs", mode="w", encoding="utf-8") as f:
                 f.write(f"{aliases[i][4]}:{aliases[i][5]}")
             os.system("chmod 600 .passwd-s3fs")
             target_path = os.path.join(base_dir, aliases[i][0])
             target_path = os.path.join(target_path, aliases[i][1])
-            cmd=f"s3fs {aliases[i][1]} {target_path} -o passwd_file=.passwd-s3fs -o url={aliases[i][2]} -o endpoint={aliases[i][3]} -o use_path_request_style -o allow_other"
+            cmd = f"s3fs {aliases[i][1]} {target_path} -o passwd_file=.passwd-s3fs -o url={aliases[i][2]} -o endpoint={aliases[i][3]} -o use_path_request_style -o allow_other"
             rc = os.system(cmd)
             if rc != 0:
                 print(
@@ -58,23 +60,24 @@ def createS3Mounts(aliases, base_dir):
             print(f"A error accrued during the mounting of alias {aliases[i][0]}: {e}")
             return False
 
+
 def main():
     base_dir = "/s3-data"
-    
+
     # Ensure the base directory exists
     if not os.path.exists(base_dir):
         os.makedirs(base_dir)
         print(f"Base directory created: {base_dir}")
 
     # Regex pattern: S3_TO_LOCAL_<ALIAS>_ALIAS
     # The (.*) captures the <ALIAS> part
-    pattern = re.compile(r'^S3_TO_LOCAL_(.*)_ALIAS$')
+    pattern = re.compile(r"^S3_TO_LOCAL_(.*)_ALIAS$")
 
     print("Scanning environment variables for S3 aliases...")
 
     aliases = []
     for key, value in os.environ.items():
-        match = pattern.match(key)     
+        match = pattern.match(key)
         if match:
             aliases.append(value)
 
@@ -87,5 +90,6 @@ def main():
     else:
         print(f"Processed {len(aliases)} S3 alias(es).")
 
+
 if __name__ == "__main__":
     main()

tests/test_utils.py

@@ -119,7 +119,7 @@ def test_delete_workflow_with_interactive_session(
         "reana_workflow_controller.k8s",
         current_k8s_networking_api_client=mock.DEFAULT,
     ):
-        (response, http_response) = delete_workflow(workflow)
+        response, http_response = delete_workflow(workflow)
         data = json.loads(response.get_data())
         assert "Workflow successfully deleted" in data["message"]
         assert http_response == 200