Code cleanup

Author: ksuderman

abm/lib/common.py

@@ -456,7 +456,6 @@ def find_dataset(gi, history_id, name_or_id):
     # return datasets[0]['id']
 
 
-
 def find_config(name: str) -> str:
     if os.path.exists(".abm"):
         if os.path.exists(f".abm/{name}"):

abm/lib/config.py

@@ -2,16 +2,8 @@
 from pathlib import Path
 
 import yaml
-from common import (
-    Context,
-    find_config,
-    get_yaml_parser,
-    load_profiles,
-    print_json,
-    print_yaml,
-    save_config,
-    save_profiles,
-)
+from common import (Context, find_config, get_yaml_parser, load_profiles,
+                    print_json, print_yaml, save_config, save_profiles)
 
 
 def do_list(context: Context, args: list):

abm/lib/dataset.py

@@ -133,6 +133,7 @@ def upload(context: Context, args: list):
         result = gi.tools.upload_file(url, history, file_name=name)
         print(result)
 
+
 def collection(context: Context, args: list):
     type = 'list:paired'
     collection_name = 'collection'

abm/lib/experiment.py

@@ -235,7 +235,11 @@ def summarize(context: Context, args: list):
             # cpu = '' if len(row[11]) == 0 else f"{float(row[11])/10**9:4.1f}"
             memory_cell = 13
             # memory_cell = 11
-            memory = '' if len(row[memory_cell]) == 0 else f"{float(row[memory_cell])/GB:4.3f}"
+            memory = (
+                ''
+                if len(row[memory_cell]) == 0
+                else f"{float(row[memory_cell])/GB:4.3f}"
+            )
             # memory = '' if len(row[memory_cell]) == 0 else f"{float(row[memory_cell])}"
             # memory = float(row[13]) / GB
             print(
@@ -259,13 +263,14 @@ def summarize(context: Context, args: list):
     'galaxy_slots',
     'galaxy_memory_mb',
     'runtime_seconds',
-    'cpuacct.usage', # Shouldn't this be cpu.stat.usage_usec?
+    'cpuacct.usage',  # Shouldn't this be cpu.stat.usage_usec?
     'memory.limit_in_bytes',
     'memory.peak',
 ]  # ,'memory.soft_limit_in_bytes']
 
 accept_metrics = accept_metrics_v2
 
+
 def make_table_row(data: dict):
     row = [
         str(data[key])

abm/lib/job.py

@@ -12,7 +12,9 @@
 def do_list(context: Context, args: list):
     parser = argparse.ArgumentParser()
     parser.add_argument('-s', '--state', help='list jobs in this state', required=False)
-    parser.add_argument('--history', help='show jobs in the given history', required=False)
+    parser.add_argument(
+        '--history', help='show jobs in the given history', required=False
+    )
     parser.add_argument('-u', '--user', help='show jobs for this user', required=False)
     argv = parser.parse_args(args)
 
@@ -28,7 +30,9 @@ def do_list(context: Context, args: list):
         if history_id is None:
             print("ERROR: No such history")
             return
-    job_list = gi.jobs.get_jobs(state=argv.state, history_id=argv.history, user_id=argv.user)
+    job_list = gi.jobs.get_jobs(
+        state=argv.state, history_id=argv.history, user_id=argv.user
+    )
     log.debug(f"Iterating over job list with {len(job_list)} items")
     for job in job_list:
         print(f"{job['id']}\t{job['state']}\t{job['update_time']}\t{job['tool_id']}")