Cleaned up warnings

maouw · Sep 20, 2023 · 3961481 · 3961481
1 parent 7bbf3d0
commit 3961481
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Showing 3 changed files with 20 additions and 20 deletions.
diff --git a/hyakvnc/__main__.py b/hyakvnc/__main__.py
@@ -40,7 +40,7 @@ def get_apptainer_vnc_instances(read_apptainer_config: bool = False):
     for p, name_meta in running_hyakvnc_json_files.items():
         with open(p, 'r') as f:
             d = json.load(f)
-            assert needed_keys <= d.keys(), f"Missing keys {needed_keys - d.keys()} in {jf}"
+            assert needed_keys <= d.keys(), f"Missing keys {needed_keys - d.keys()} in {d}"
 
             logOutPath = Path(d['logOutPath']).expanduser()
             if not logOutPath.exists():
@@ -51,19 +51,18 @@ def get_apptainer_vnc_instances(read_apptainer_config: bool = False):
             else:
                 d['config'] = json.loads(base64.b64decode(d['config']).decode('utf-8'))
 
-            d['slurm_compute_node'] = slurm_compute_node = p.relative_to(app_dir).parts[0]
             d['slurm_job_id'] = name_meta['jobid']
 
-            with open(logOutPath, 'r') as f:
-                logOutFile_contents = f.read()
+            with open(logOutPath, 'r') as lf:
+                logOutFile_contents = lf.read()
                 rfbports = re.findall(r'\s+-rfbport\s+(?P<rfbport>\d+)\b', logOutFile_contents)
                 if not rfbports:
                     continue
 
                 vnc_port = rfbports[-1]
 
                 vnc_log_file_paths = re.findall(
-                    rf'(?m)Log file is\s*(?P<logfilepath>.*[/]{d["slurm_compute_node"]}.*:{vnc_port}\.log)$',
+                    rf'(?m)Log file is\s*(?P<logfilepath>.*/{d["slurm_compute_node"]}.*:{vnc_port}\.log)$',
                     logOutFile_contents)
                 if not vnc_log_file_paths:
                     continue
@@ -125,7 +124,7 @@ def cmd_create(container_path):
     # needs to match rf'(?P<prefix>{app_config.apptainer_instance_prefix})(?P<jobid>\d+)-(?P<appinstance>.*)'):
     apptainer_instance_name = rf"{app_config.apptainer_instance_prefix}-\$SLURM_JOB_ID-{container_name}"
 
-    apptainer_cmd = apptainer_env_vars_string + rf"apptainer instance start {container_path} {container_name}"
+    apptainer_cmd = apptainer_env_vars_string + rf"apptainer instance start {container_path} {apptainer_instance_name}"
     apptainer_cmd_with_rest = rf"{apptainer_cmd} && while true; do sleep 10; done"
 
     cmds += ["--wrap", apptainer_cmd_with_rest]
@@ -148,7 +147,7 @@ def cmd_create(container_path):
     logging.info("Waiting for job to start running")
 
     try:
-        state = wait_for_job_status(job_id, states={"RUNNING"}, timeout=app_config.sbatch_post_timeout,
+        wait_for_job_status(job_id, states=["RUNNING"], timeout=app_config.sbatch_post_timeout,
                                     poll_interval=app_config.sbatch_post_poll_interval)
     except TimeoutError:
         raise TimeoutError(f"Job {job_id} did not start running within {app_config.sbatch_post_timeout} seconds")
@@ -200,8 +199,7 @@ def create_arg_parser():
     parser_create.add_argument('-c', '--cpus', dest='cpus', metavar='<num_cpus>', help='Subnode cpu count', default=1,
                                type=int)
     parser_create.add_argument('-G', '--gpus', dest='gpus', metavar='[type:]<num_gpus>', help='Subnode gpu count',
-                               default="0"
-    type = str)
+                               default="0", type = str)
     parser_create.add_argument('--mem', dest='mem', metavar='<NUM[K|M|G|T]>', help='Subnode memory amount with units',
                                type=str)
     parser_create.add_argument('--container', dest='container', metavar='<path_to_container.sif>',
@@ -223,7 +221,7 @@ def create_arg_parser():
 
 
 arg_parser = create_arg_parser()
-args = (arg_parser).parse_args()
+args = arg_parser.parse_args()
 
 if args.debug:
     os.environ["HYAKVNC_LOG_LEVEL"] = "DEBUG"

diff --git a/hyakvnc/config.py b/hyakvnc/config.py
@@ -1,5 +1,4 @@
 import json
-import json
 import logging
 import os
 from dataclasses import dataclass, asdict
@@ -50,7 +49,6 @@ class HyakVncConfig:
     ssh_host = "klone.hyak.uw.edu"  # intermediate host address between local machine and compute node
 
     # slurm attributes
-    ## sbatch environment variables
     account: Optional[str] = None  # account to use for sbatch jobs | -A, --account, SBATCH_ACCOUNT
     partition: Optional[str] = None  # partition to use for sbatch jobs | -p, --partition, SBATCH_PARTITION
     cluster: Optional[str] = None  # cluster to use for sbatch jobs |  --clusters, SBATCH_CLUSTERS
@@ -88,7 +86,7 @@ def __post_init__(self) -> None:
             self.apptainer_env_vars["APPTAINER_WRITABLE_TMPFS"] = "1" if self.apptainer_use_writable_tmpfs else "0"
 
         if self.apptainer_cleanenv is not None:
-            self.apptainer_env_vars[["APPTAINER_CLEANENV"] = "1" if self.apptainer_cleanenv else "0"
+            self.apptainer_env_vars["APPTAINER_CLEANENV"] = "1" if self.apptainer_cleanenv else "0"
 
             if self.apptainer_set_bind_paths is not None:
                 self.apptainer_env_vars["APPTAINER_BINDPATH"] = self.apptainer_set_bind_paths

diff --git a/hyakvnc/slurmutil.py b/hyakvnc/slurmutil.py
@@ -40,8 +40,9 @@ def get_default_account(user: Optional[str] = None, cluster: Optional[str] = Non
     raise LookupError(f"Could not find default account for user '{user}' on cluster '{cluster}'")
 
 
-def get_partitions(user: Optional[str] = None, account: Optional[str] = None, cluster: Optional[str] = None) -> set[
-    str]:
+def get_partitions(user: Optional[str] = None,
+                   account: Optional[str] = None,
+                   cluster: Optional[str] = None) -> set[str]:
     """
     Gets the SLURM partitions for the specified user and account on the specified cluster.
 
@@ -89,7 +90,7 @@ def node_range_to_list(s: str) -> list[str]:
     :return: list of SLURM nodes
     :raises ValueError: if the node range could not be converted to a list of nodes
     """
-    output = subproces.run(f"scontrol show hostnames {s}", stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
+    output = subprocess.run(f"scontrol show hostnames {s}", stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)
     if output.returncode != 0:
         raise ValueError(f"Could not convert node range '{s}' to list of nodes:\n{output.stderr}")
     return output.stdout.rstrip().splitlines()
@@ -150,9 +151,11 @@ def from_squeue_line(line: str, field_order=None) -> "SlurmJob":
         return SlurmJob(**field_dict)
 
 
-def get_job(user: Optional[str] = os.getlogin(), jobs: Optional[Union[int, list[int]]] = None,
-            cluster: Optional[str] = None, field_names: Optional[Container[str]] = None) -> Union[
-    SlurmJob, list[SlurmJob], None]:
+def get_job(jobs: Optional[Union[int, list[int]]] = None,
+            user: Optional[str] = os.getlogin(),
+            cluster: Optional[str] = None,
+            field_names: Optional[Container[str]] = None
+            ) -> Union[SlurmJob, list[SlurmJob], None]:
     """
     Gets the specified slurm job(s).
     :param user: User to get jobs for
@@ -177,7 +180,8 @@ def get_job(user: Optional[str] = os.getlogin(), jobs: Optional[Union[int, list[
         cmds += ['--jobs', jobs]
 
     slurm_job_fields = [f for f in fields(SlurmJob) if f.name in field_names]
-    squeue_format_fields = [f.metadata.get("squeue_field", "") for f in slurm_job_fields].join()
+    assert len(slurm_job_fields) > 0, "Must specify at least one field to get for slurm jobs"
+    squeue_format_fields = ",".join([f.metadata.get("squeue_field", "") for f in slurm_job_fields])
 
     cmds += ['--Format', squeue_format_fields]
     res = subprocess.run(cmds, stdout=subprocess.PIPE, stderr=subprocess.PIPE, text=True)