Merge pull request populse#320 from DimitriPapadopoulos/pre-commit

Run pre-commit over latest 3.0 changes

capsul/database/redis.py

@@ -715,24 +715,23 @@ def job_json(self, engine_id, execution_id, job_uuid):
         return job
 
     def kill_jobs(self, engine_id, execution_id, job_ids):
-        """ Request killing of jobs
-        """
+        """Request killing of jobs"""
         # we just set a flag to 1 associated with the jobs to be killed.
         # Workers will poll for it while jobs are running, and react
         # accordingly.
         # TODO:
         # - atomicity: ensure jobs still exist and are running
         # - skip or error if a job is not running
-        key = f'capsul:{engine_id}:{execution_id}'
+        key = f"capsul:{engine_id}:{execution_id}"
         if job_ids is None:
-            job_ids = self.redis.hget(f'capsul:{engine_id}:{execution_id}',
-                                      'ongoing')
+            job_ids = self.redis.hget(f"capsul:{engine_id}:{execution_id}", "ongoing")
         for job_id in job_ids:
-            self.redis.hset(key, f'kill_job:{job_id}', 1)
+            self.redis.hset(key, f"kill_job:{job_id}", 1)
 
     def job_kill_requested(self, engine_id, execution_id, job_id):
-        return self.redis.hget(f'capsul:{engine_id}:{execution_id}',
-                               f'kill_job:{job_id}')
+        return self.redis.hget(
+            f"capsul:{engine_id}:{execution_id}", f"kill_job:{job_id}"
+        )
 
     def execution_report_json(self, engine_id, execution_id):
         (
@@ -781,10 +780,7 @@ def execution_report_json(self, engine_id, execution_id):
 
     def dispose(self, engine_id, execution_id, bypass_persistence=False):
         keys = [f"capsul:{engine_id}", f"capsul:{engine_id}:{execution_id}"]
-        args = [
-            execution_id,
-            int(bool(bypass_persistence))
-        ]
+        args = [execution_id, int(bool(bypass_persistence))]
         self._dispose(keys=keys, args=args)
 
     def check_shutdown(self):

capsul/engine/__init__.py

@@ -177,7 +177,7 @@ def start_workers(self):
             for i in range(start_count):
                 workers_command = self.database.workers_command(self.engine_id)
                 try:
-                    print('workers_command:', workers_command)
+                    print("workers_command:", workers_command)
                     subprocess.run(
                         workers_command,
                         capture_output=False,
@@ -344,7 +344,7 @@ def dispose(self, *args, **kwargs):
         """Remove the given execution from the database and the associated
         resources (temporary files etc.)
         """
-        print('Dispose:', self.engine_id, args, kwargs)
+        print("Dispose:", self.engine_id, args, kwargs)
         self.database.dispose(self.engine_id, *args, **kwargs)
 
     def run(self, executable, timeout=None, print_report=False, debug=False, **kwargs):

capsul/engine/builtin.py

@@ -23,7 +23,7 @@ def __init__(self, database, engine_id):
         self.current_execution = None
         self.current_job = None
         self.job_pid = None
-        self.poll_interval = 5.
+        self.poll_interval = 5.0
         self.stop_poll_interval = 0.1
 
     def run(self):
@@ -35,11 +35,11 @@ def run(self):
                 execution_id = self.current_execution
                 job_id = self.current_job
                 job_pid = self.job_pid
-            if job_id is not None and execution_id is not None \
-                    and job_pid is not None:
+            if job_id is not None and execution_id is not None and job_pid is not None:
                 # poll the database
                 kill_job = self.database.job_kill_requested(
-                    engine_id, execution_id, job_id)
+                    engine_id, execution_id, job_id
+                )
                 if kill_job:
                     os.kill(job_pid, signal.SIGTERM)
                     os.kill(job_pid, signal.SIGKILL)

capsul/run.py

@@ -14,7 +14,13 @@
 
 
 def run_job(
-    database, engine_id, execution_id, job_uuid, same_python=False, debug=False, set_pid_function=None
+    database,
+    engine_id,
+    execution_id,
+    job_uuid,
+    same_python=False,
+    debug=False,
+    set_pid_function=None,
 ):
     if same_python:
         stdout = io.StringIO()
@@ -35,8 +41,7 @@ def run_job(
             env["CAPSUL_DEBUG"] = "1"
 
         proc = subprocess.Popen(
-            [sys.executable, "-m", "capsul.run", engine_id, execution_id,
-             job_uuid],
+            [sys.executable, "-m", "capsul.run", engine_id, execution_id, job_uuid],
             env=env,
             stdout=subprocess.PIPE,
             stderr=subprocess.PIPE,