Incorporate review feedback

docker-wrappers/SPRAS/snakemake_long.py

@@ -20,45 +20,50 @@
 need different arguments. The "top" mode is for submitting the HTCondor wrapper, and the "long" mode
 is for running the Snakemake command itself.
 """
-def parseArgs(isLocal=False):
+def parse_args(isLocal=False):
     parser = argparse.ArgumentParser(description="A tool for long-running Snakemake jobs with HTCondor.")
-    # We add a special command to trigger allowing this script to execute the long-running Snakemake command.
     if isLocal:
+        # We add a special command that allows this singular executable to serve two purposes. The executable
+        # is first run by the user with their args to submit the local universe job. Then, the local universe
+        # job runs `snakemake_long.py long <user args>` to indicate to the script that it's time to submit the
+        # long-running Snakemake process instead of submitting another local universe job.
         parser.add_argument("command", help="Helper command to run", choices=["long"])
-    parser.add_argument("--snakefile", help="The Snakefile to run.", required=False)
+    parser.add_argument("--snakefile", help="The Snakefile to run. If omitted, the Snakefile is assumed to be in the current directory.", required=False)
     parser.add_argument("--profile", help="A path to a directory containing the desired Snakemake profile.", required=True)
     # I'd love to change this to "logdir", but using the same name as Snakemake for consistency of feeling between this script
     # and Snakemake proper.
-    parser.add_argument("--htcondor-jobdir", help="The directory Snakemake will write logs to.", required=False)
+    parser.add_argument("--htcondor-jobdir", help="The directory Snakemake will write logs to. If omitted, a 'logs` directory will be created in the current directory", required=False)
     return parser.parse_args()
 
 """
 Given a Snakefile, profile, and HTCondor job directory, submit a local universe job that runs
 Snakemake from the context of the submission directory.
 """
-def submitLocal(snakefile, profile, htcondor_jobdir):
+def submit_local(snakefile, profile, htcondor_jobdir):
     # Get the location of this script, which also serves as the executable for the condor job.
     script_location = pathlib.Path(__file__).resolve()
 
     submit_description = htcondor.Submit({
         "executable":              script_location,
+        # We use the "long" command to indicate to the script that it should run the Snakemake command instead of submitting another job.
+        # See comment in parse_args for more information.
         "arguments":               f"long --snakefile {snakefile} --profile {profile} --htcondor-jobdir {htcondor_jobdir}",
         "universe":                "local",
         "request_disk":            "512MB",
         "request_cpus":            1,
         "request_memory":          512,
 
         # Set up logging
-        "log":                     f"{htcondor_jobdir}/snakemake-long.log",
-        "output":                  f"{htcondor_jobdir}/snakemake-long.out",
-        "error":                   f"{htcondor_jobdir}/snakemake-long.err",
+        "log":                     f"{htcondor_jobdir}/snakemake.log",
+        "output":                  f"{htcondor_jobdir}/snakemake.out",
+        "error":                   f"{htcondor_jobdir}/snakemake.err",
 
         # Specify `getenv` so that our script uses the appropriate environment
         # when it runs in local universe. This allows the job to access
         # modules we've installed in the submission environment (notably spras).
         "getenv":                  "true",
 
-        "JobBatchName":            f"spras-long-{time.strftime('%Y%m%d-%H%M%S')}",
+        "JobBatchName":            f"spras-{time.strftime('%Y%m%d-%H%M%S')}",
     })
 
     schedd = htcondor.Schedd()
@@ -70,8 +75,8 @@ def submitLocal(snakefile, profile, htcondor_jobdir):
 The top level function for the script that handles file creation/validation and triggers submission of the
 wrapper job.
 """
-def topMain():
-    args = parseArgs()
+def top_main():
+    args = parse_args()
 
     # Check if the snakefile is provided. If not, assume it's in the current directory.
     if args.snakefile is None:
@@ -97,19 +102,18 @@ def topMain():
             os.makedirs(args.htcondor_jobdir)
 
 
-    submitLocal(args.snakefile, args.profile, args.htcondor_jobdir)
+    submit_local(args.snakefile, args.profile, args.htcondor_jobdir)
     return 0
 
 """
-
+Command to activate conda environment and run Snakemake. This is run by the local universe job, not the user.
 """
-def longMain():
-    args = parseArgs(True)
+def long_main():
+    args = parse_args(True)
 
-    # Command to activate conda environment and run Snakemake. Note that we need to unset APPTAINER_CACHEDIR
-    # in this case but not in the local terminal case because the wrapper HTCondor job has a different environment
-    # and populating this value causes Snakemake to fail when it tries to write to spool (a read-only filesystem from
-    # the perspective of the EP job).
+    # Note that we need to unset APPTAINER_CACHEDIR in this case but not in the local terminal case because the wrapper
+    # HTCondor job has a different environment and populating this value causes Snakemake to fail when it tries to write
+    # to spool (a read-only filesystem from the perspective of the EP job).
     command = f"""
     source $(conda info --base)/etc/profile.d/conda.sh && \
     conda activate spras && \
@@ -126,9 +130,9 @@ def longMain():
 def main():
     if len(sys.argv) > 1:
         if sys.argv[1] in ["long"]:
-            return longMain()
+            return long_main()
 
-    return topMain()
+    return top_main()
 
 if __name__ == '__main__':
     sys.exit(main())