fix typos in the grid defaults

attempt to fix (finally?) the joingingfile logic

binarycpython/utils/HPC.py

@@ -52,6 +52,9 @@ class HPC(condor,slurm):
             id : the job ID number, or self.HPC_jobID_tuple()[0] if None (default=None).
             overwrite : if True, overwrite an existing joiningfile (default=False)
             error_on_overwite : if True, and we try to overwrite, issue and error and exit (default=False)
+
+        Returns:
+            True if the file is made, False otherwise.
         
         """
 
@@ -69,22 +72,25 @@ class HPC(condor,slurm):
 
         # check the joiningfile doesn't exist
         if not overwrite and os.path.isfile(file):
+            # file already exists
             print("Cannot make joiningfile at {file} because it already exists.".format(file=file))
-            # perhaps cause an error if it does
+            # perhaps exit here? (e.g. for debugging)
             if error_on_overwrite:
                 self.exit(code=1)
-            
-        # write the joiningfile
-        print("Making joiningfile at {file} with range 0 to {n}".format(
-            file=file,
-            n=n
-        ))
-        with open(file,"w",encoding="utf-8") as f:
-            for i in range(0,n):
-                f.write(os.path.join(prefix,
-                                     "{i}.gz\n".format(i=i)))
-            f.close()
-        return
+            x = False
+        else:
+            # write the joiningfile
+            print("Making joiningfile at {file} with range 0 to {n}".format(
+                file=file,
+                n=n
+            ))
+            with open(file,"w",encoding="utf-8") as f:
+                for i in range(0,n):
+                    f.write(os.path.join(prefix,
+                                         "{i}.gz\n".format(i=i)))
+                    f.close()
+            x = True
+        return x
                     
     def HPC_joinfiles(self,joinlist=None):
         """

binarycpython/utils/grid_options_defaults.py

@@ -201,7 +201,7 @@ class grid_options_defaults():
             ########################################
             "condor": 0,  # 1 to use condor, 0 otherwise
             "condor_dir": "",  # working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all)
-            "condor_njobs": "",  # number of scripts/jobs that CONDOR will run in total
+            "condor_njobs": 0,  # number of scripts/jobs that CONDOR will run in total
             "condor_ClusterID": None,  # condor cluster id, equivalent to Slurm's jobid
             "condor_Process": None,  # condor process, equivalent to Slurm's jobarrayindex
             "condor_postpone_submit": 0,  # if 1, the condor script is not submitted (useful for debugging). Default 0.
@@ -281,7 +281,7 @@ class grid_options_defaults():
             ############################################################
             # Condor
             "condor": "Integer flag used to control HTCondor (referred to as Condor here) jobs. Default is 0 which means no Condor. 1 means launch Condor jobs. Do not manually set this to 2 (run Condor jobs) or 3 (join Condor job data) unless you know what you are doing, this is usually done for you.",
-            "condor_dir": "String. Working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all jobs). This directory should not exist when you launch the Condor jobs."
+            "condor_dir": "String. Working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all jobs). This directory should not exist when you launch the Condor jobs.",
             "condor_njobs": "Integer. Number of jobs that Condor will run",
             "condor_ClusterID": "Integer. Condor ClusterID variable, equivalent to Slurm's jobid. Jobs are numbered <ClusterID>.<Process>",
             "condor_Process": "Integer. Condor Process variable, equivalent to Slurm's jobarrayindex. Jobs are numbered <ClusterID>.<Process>",
@@ -296,7 +296,7 @@ class grid_options_defaults():
             'condor_stream_error':"Boolean. If True, we activate Condor's stderr stream. If False, this data is copied at the end of the job.",
             'condor_should_transfer_files' : "Integer. Condor's option to transfer files at the end of the job. You should set this to \"YES\"",
             'condor_when_to_transfer_output' : "Integer. Condor's option to decide when output files are transferred. You should usually set this to \"ON_EXIT_OR_EVICT\"",
-            'condor_requirements':'', "String. Condor job requirements. These are passed to Condor directly, you should read the HTCondor manual to learn about this. If no requirements exist, leave as an string.",
+            'condor_requirements': "String. Condor job requirements. These are passed to Condor directly, you should read the HTCondor manual to learn about this. If no requirements exist, leave as an string.",
             'condor_env' : "String. Points the location of the \"env\" command, e.g. /usr/bin/env or /bin/env, that is used in Condor launch scripts. This is set automatically on the submit machine, so if it is different on the nodes, you should set it manually.",
             'condor_bash' : "String. Points the location of the \"bash\" command, e.g. /bin/bash, that is used in Condor launch scripts. This is set automatically on the submit machine, so if it is different on the nodes, you should set it manually.",
             'condor_pwd' : "String. Points the location of the \"pwd\" command, e.g. /bin/pwd, that is used in Condor launch scripts. This is set automatically on the submit machine, so if it is different on the nodes, you should set it manually.",
@@ -312,7 +312,7 @@ class grid_options_defaults():
             ############################################################
             "slurm": "Integer flag used to control Slurm jobs. Default is 0 which means no Slurm. 1 means launch Slurm jobs. Do not manually set this to 2 (run Slurm jobs) or 3 (join Slurm job data) unless you know what you are doing, this is usually done for you.",
             "slurm_dir": "String. Working directory containing e.g. scripts, output, logs (e.g. should be NFS available to all jobs). This directory should not exist when you launch the Slurm jobs.",
-            "slurm_ntasks": "Integer. Number of CPUs required per array job: usually only need this to be 1 (the default)."
+            "slurm_ntasks": "Integer. Number of CPUs required per array job: usually only need this to be 1 (the default).",
             "slurm_njobs": "Integer. Number of Slurm jobs to be launched.",
             "slurm_jobid": "Integer. Slurm job id. Each job is numbered <slurm_jobid>.<slurm_jobarrayindex>.",
             "slurm_jobarrayindex": "Integer. Slurm job array index. Each job is numbered <slurm_jobid>.<slurm_jobarrayindex>.",