linting

bu_isciii/__main__.py

@@ -216,10 +216,10 @@ def new_service(resolution, path, no_create_folder, ask_path):
     type=click.Choice(["Service_to_scratch", "Scratch_to_service", "Remove_scratch"]),
     multiple=False,
     help=(
-            "Direction of the rsync command. Service_to_scratch "
-            "from /data/bi/service to /data/bi/scratch_tmp/bi/."
-            "Scratch_to_service: From /data/bi/scratch_tmp/bi/ to /data/bi/service"
-        ),
+        "Direction of the rsync command. Service_to_scratch "
+        "from /data/bi/service to /data/bi/scratch_tmp/bi/."
+        "Scratch_to_service: From /data/bi/scratch_tmp/bi/ to /data/bi/service"
+    ),
 )
 def scratch(resolution, path, tmp_dir, direction, ask_path):
     """

bu_isciii/archive.py

@@ -104,16 +104,17 @@ def __init__(
             sys.exit()
 
         if (
-            (date_from is not None)
-            and (date_until is not None)
-            and (service_id is not None)
-        ) or (
-            (date_from is not None)
-            and (date_until is not None)
-            and (services_file is not None)
-        ) or (
-            (services_file) is not None
-            and (service_id) is not None
+            (
+                (date_from is not None)
+                and (date_until is not None)
+                and (service_id is not None)
+            )
+            or (
+                (date_from is not None)
+                and (date_until is not None)
+                and (services_file is not None)
+            )
+            or ((services_file) is not None and (service_id) is not None)
         ):
             stderr.print(
                 "Both a date and a service ID or service list have been chosen. "
@@ -134,7 +135,12 @@ def __init__(
                 date_until = None
                 service_id = None
 
-        if (date_from is None) and (date_until is None) and (service_id is None) and (services_file is None):
+        if (
+            (date_from is None)
+            and (date_until is None)
+            and (service_id is None)
+            and (services_file is None)
+        ):
             if self.ser_type == "services_and_colaborations":
                 prompt_response = bu_isciii.utils.prompt_selection(
                     "Search services by date, or by service ID?",
@@ -187,19 +193,23 @@ def __init__(
             self.date_until = date_until
             if service_id:
                 self.services = (
-                    {service_id: {key: value for key, value in dictionary_template.items()}}
+                    {
+                        service_id: {
+                            key: value for key, value in dictionary_template.items()
+                        }
+                    }
                     if service_id is not None
                     else dict()
                 )
             elif services_file:
                 with open(services_file) as file:
                     for s_id in file:
-                        self.services[s_id] = {key: value for key, value in dictionary_template.items()}
+                        self.services[s_id] = {
+                            key: value for key, value in dictionary_template.items()
+                        }
 
         if (self.date_from is not None) and (self.date_until is not None):
-            stderr.print(
-                "Asking our trusty API about selected services"
-            )
+            stderr.print("Asking our trusty API about selected services")
             try:
                 for service in rest_api.get_request(
                     request_info="services",
@@ -266,7 +276,9 @@ def __init__(
                     )
             else:
                 self.services[service]["found_in_system"] = True
-                import pdb; pdb.set_trace()
+                import pdb
+
+                pdb.set_trace()
                 self.services[service]["archived_path"] = os.path.join(
                     bu_isciii.config_json.ConfigJson().get_configuration("global")[
                         "archived_path"

bu_isciii/new_service.py

@@ -186,7 +186,7 @@ def create_symbolic_links(self):
                 stderr.print(
                     "[red] This regex has not output any file: %s." % regex,
                     "This maybe because the project is not yet in the fastq repo"
-                    "or because some of the samples are not in the project."
+                    "or because some of the samples are not in the project.",
                 )
         stderr.print(
             "[blue] Service has %s number of selected samples in iSkyLIMS"

bu_isciii/utils.py

@@ -330,13 +330,13 @@ def ask_date(previous_date=None, posterior_date=None, initial_year=2010):
         month_list = [[num, month] for num, month in enumerate(calendar.month_name)][1:]
     else:
         month_list = [[num, month] for num, month in enumerate(calendar.month_name)][
-            1:datetime.date.today().month + 1
+            1 : datetime.date.today().month + 1
         ]
 
     # If there is a previous date
     # and year is the same as before, limit the quantity of months
     if previous_date is not None and year == previous_date.year:
-        month_list = month_list[previous_date.month - 1:]
+        month_list = month_list[previous_date.month - 1 :]
 
     chosen_month_number, chosen_month_name = (
         bu_isciii.utils.prompt_selection(
@@ -377,7 +377,7 @@ def ask_date(previous_date=None, posterior_date=None, initial_year=2010):
         and year == previous_date.year
         and chosen_month_number == previous_date.month
     ):
-        day_list = day_list[previous_date.day - 1:]
+        day_list = day_list[previous_date.day - 1 :]
 
     # from the list, get the first and last item as limits for the function
     day = bu_isciii.utils.prompt_day(