update

Author: William Majoros

ConfigFile.py

@@ -16,6 +16,7 @@
 #   configFile=ConfigFile(filename)
 #   value=configFile.lookup(key)
 #   value=configFile.lookupOrDie(key)
+#   list=configFile.lookupList(key,sep=", ")
 # Private methods:
 #   self.load(filename)
 ######################################################################
@@ -28,6 +29,11 @@ def __init__(self,filename):
         self.hash={}
         self.load(filename)
 
+    def lookupList(self,key,sep=", "):
+        value=self.lookup(key)
+        if(value is None): return value
+        return value.split(sep)
+        
     def lookup(self,key):
         return self.hash[key]
 

MatrixMarket.py

@@ -23,7 +23,7 @@
 #    nextLine : string
 # Instance Methods:
 #    MatrixMarket(filename)
-#    nextGroup(self,colIndex)
+#    nextGroup(self,colIndex) # returns array of records
 #    getHeader()
 # Class Methods:
 #    allGroups=loadFile(filename,colIndex)
@@ -65,7 +65,8 @@ def nextGroup(self,colIndex):
             if(len(fields)==0): return None
             if(prevID is None): prevID=int(fields[colIndex])
             if(colIndex>len(fields)-1):
-                raise Exception("colIndex=",colIndex,"len(fields)=",len(fields))
+                raise Exception("colIndex=",colIndex,"len(fields)=",
+                                len(fields))
             thisID=int(fields[colIndex])
             if(thisID!=prevID):
                 self.nextLine=line

Pipe.py

@@ -12,20 +12,25 @@
 
 #=========================================================================
 # Attributes:
-#   iter
+#   iter = iterator for the subprocess lines
+#   p = subprocess
 # Instance Methods:
 #   pipe=Pipe(command)
 #   line=pipe.readline()
+#   close()
 # Class Methods:
 #   output=Pipe.run(command)
 #=========================================================================
 class Pipe:
     """Pipe reads output from a shell command"""
     def __init__(self,cmd):
-        p=subprocess.Popen(cmd,stdout=subprocess.PIPE,shell=True,
+        self.p=subprocess.Popen(cmd,stdout=subprocess.PIPE,shell=True,
                            stderr=subprocess.STDOUT)
-        self.iter=iter(p.stdout.readline, b'')
+        self.iter=iter(self.p.stdout.readline, b'')
 
+    def close(self):
+        self.p.terminate()
+        
     def readline(self):
         line=next(self.iter,None)
         if(line is None): return None

SlurmWriter.py

@@ -88,7 +88,6 @@ def writeArrayScript(self,slurmDir,jobName,maxParallel,moreSBATCH=""):
                      "#",
                      "#SBATCH --get-user-env",
                      "#SBATCH -J "+jobName,
-                     "#SBATCH -A "+jobName,
                      "#SBATCH -o "+slurmDir+"/outputs/%a.output",
                      "#SBATCH -e "+slurmDir+"/outputs/%a.output",
                      "#SBATCH --array=1-"+str(numJobs)+"%"+str(maxParallel),
@@ -115,7 +114,6 @@ def writeScript(self,slurmFile,outFile,jobName,command,moreSBATCH=""):
                      "#",
                      "#SBATCH --get-user-env",
                      "#SBATCH -J "+jobName,
-                     "#SBATCH -A "+jobName,
                      "#SBATCH -o "+outFile,
                      "#SBATCH -e "+outFile,
                      queue+moreSBATCH+"#",

template.py

@@ -1,6 +1,8 @@
 #!/usr/bin/env python
 #=========================================================================
-# Copyright (C)William H. Majoros (bmajoros@alumni.duke.edu)
+# This is OPEN SOURCE SOFTWARE governed by the Gnu General Public
+# License (GPL) version 3, as described at www.opensource.org.
+# Copyright (C)2021 William H. Majoros <bmajoros@alumni.duke.edu>
 #=========================================================================
 from __future__ import (absolute_import, division, print_function, 
    unicode_literals, generators, nested_scopes, with_statement)