refactor: use vformat function to generate csh scripts

aria/core/cns.py

@@ -82,42 +82,42 @@ PLAN = 'plan.tbl'
 CNS_OUTPUT_PATH_NAME = 'cns'
 
 CSH_SCRIPT_REFINE = '''\
-#! %(sge_job_shell)s
+#! {sge_job_shell}
 # SGE/PBS/SLURM/LFS facility
-#$ -N %(sge_job_name)s
-#$ -S %(sge_job_shell)s
-#PBS -N %(sge_job_name)s
-#PBS -S %(sge_job_shell)s
-#BSUB -J %(sge_job_name)s
-#BSUB -L %(sge_job_shell)s
+#$ -N {sge_job_name}
+#$ -S {sge_job_shell}
+#PBS -N {sge_job_name}
+#PBS -S {sge_job_shell}
+#BSUB -J {sge_job_name}
+#BSUB -L {sge_job_shell}
 #BSUB -oo refine.lsf.out
 #BSUB -eo refine.lsf.err
 #SBATCH -o refine.%j.slurm.out
 #SBATCH -e refine.%j.slurm.err
-#SBATCH -J %(sge_job_name)s
+#SBATCH -J {sge_job_name}
 #SBATCH --ignore-pbs
 
 # results will be stored here
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
 
 # project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
 
 # individual run.cns is stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
 
 # path of ARIA2 cns protocos (for RAMA)
-setenv RAMA_DATA %(rama_data_dir)s
+setenv RAMA_DATA {rama_data_dir}
 
 # CNS working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
 
 # solves some NFS sync problems
 
-cat %(cns_input_file)s > /dev/null
+cat {cns_input_file} > /dev/null
 
 # command line
-%(cns_executable)s < %(cns_input_file)s >! %(cns_output_file)s
+{cns_executable} < {cns_input_file} >! {cns_output_file}
 
 touch done
 '''
@@ -167,20 +167,20 @@ Requirements = Arch == "X86_64" && OpSys == "LINUX" && Memory > 200
 
 CSH_SCRIPT_REFINE_CONDOR = '''\
 # results will be stored here
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
 
 # project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
 
 # individual run.cns is stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
 
 # CNS working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
 
 # solves some NFS sync problems
 
-cat %(cns_input_file)s > /dev/null
+cat {cns_input_file} > /dev/null
 
 # command line
 condor_submit condor.job
@@ -194,19 +194,19 @@ cp /dev/null done
 
 CSH_SCRIPT_ANALYSIS = """\
 # results will be stored here
-setenv ANALYSIS %(analysis_output_path)s
+setenv ANALYSIS {analysis_output_path}
 
 # results from last iteration
-setenv NEWIT %(iteration_path)s
+setenv NEWIT {iteration_path}
 
 # project path
-setenv RUN %(cns_resource_path)s
+setenv RUN {cns_resource_path}
 
 # individual run.cns and output-files are stored here
-setenv RUN_CNS %(cns_working_dir)s
+setenv RUN_CNS {cns_working_dir}
 
 # working directory
-cd %(cns_working_dir)s
+cd {cns_working_dir}
 
 # command line
 """
@@ -2017,7 +2017,8 @@ class CNS(StructureEngine):
             condor_queue = "input = %(cns_input_file)s\n" \
                            "output = %(cns_output_file)s\nqueue\n"
             self._write_condor_script(d, condor_append=condor_queue)
-            script = CSH_SCRIPT_REFINE_CONDOR % d
+            script = string.Formatter().vformat(
+                CSH_SCRIPT_REFINE_CONDOR, (), SafeFormatDict(d))
             checkscript = string.Formatter().vformat(
                 CSH_SCRIPT_CHECKPOINT, (), SafeFormatDict(d))
 
@@ -2030,7 +2031,8 @@ class CNS(StructureEngine):
             d['sge_job_shell'] = '/bin/csh -f'
             # d['sge_job_hostname'] = '%(sge_job_hostname)s'
 
-            script = CSH_SCRIPT_REFINE % d
+            script = string.Formatter().vformat(
+                CSH_SCRIPT_REFINE, (), SafeFormatDict(d))
             d['sge_checkjob_name'] = sge_job_name + "_checkpoint"
             checkscript = string.Formatter().vformat(
                 CSH_SCRIPT_CHECKPOINT, (), SafeFormatDict(d))
@@ -2466,7 +2468,8 @@ Could not create working directory for CNS analysis scripts ("%s").""" % (
                     'cns_working_dir': working_dir,
                     'cns_executable': cns_executable}
 
-        csh_script = CSH_SCRIPT_ANALYSIS % csh_dict
+        csh_script = string.Formatter().vformat(
+            CSH_SCRIPT_ANALYSIS, (), SafeFormatDict(csh_dict))
 
         condor_append = '\n'