Bump version, fix bin for modules

bin/param_runner

@@ -88,11 +88,16 @@ def main():
 
                 if 'gres' in p.vals:
                     gres = str(p.vals['gres'])
-                    sbatch_cmd = [ 'sbatch', '-N', nodes, '-p', partition, '-t', time_limit, '--gres', gres, '-oparam_runner_%j.out' ]
+                    sbatch_cmd = 'sbatch' + ' -N ' + nodes + ' -p ' + partition + ' -t ' + time_limit + ' --gres ' + gres + ' -oparam_runner_%j.out' 
                 else:
-                    sbatch_cmd = [ 'sbatch', '-N', nodes, '-p', partition, '-t', time_limit, '-oparam_runner_%j.out' ]
+                    sbatch_cmd = 'sbatch' + ' -N ' + nodes + ' -p ' + partition + ' -t ' + time_limit + ' -oparam_runner_%j.out' 
 
                 batch_script = "#!/bin/bash\n"
+
+                if 'modules' in p.vals.keys():
+                    for mod_name in p.vals['modules']:
+                        batch_script += "module add %s\n" % mod_name
+
                 batch_script += python_exe
                 batch_script += ' -u '
                 batch_script += this_script
@@ -101,9 +106,10 @@ def main():
                 batch_script += ' 2>&1\n'
 
                 logger.debug(sbatch_cmd)
+                logger.debug(batch_script)
 
-                sbatch_proc = subprocess.Popen( sbatch_cmd, stdin=subprocess.PIPE, stdout=subprocess.PIPE,
-                          stderr=subprocess.PIPE)
+                sbatch_proc = subprocess.Popen( sbatch_cmd, shell=True, stdin=subprocess.PIPE, stdout=subprocess.PIPE,
+                                                stderr=subprocess.PIPE, env=os.environ.copy())
 
                 stdout, stderr = sbatch_proc.communicate(batch_script)
 

setup.py

@@ -10,7 +10,7 @@ def read(fname):
 
 setup(
     name = "param_runner",
-    version = "1.0.0a2",
+    version = "1.0.0a4",
     author = "David Trudgian",
     author_email = "david.trudgian@utsouthwestern.edu",
     description = ("Parameter exploration on SLURM clusters."),