Improve reliability of spuriousSSM calls

.gitignore

@@ -0,0 +1,3 @@
+build/
+*.egg-info
+peppercompiler/_spuriousSSM

peppercompiler/_spuriousSSM_wrapper.py

@@ -1,8 +1,8 @@
 import sys
-import os
+import subprocess
 import pkg_resources
 
 def main():
     binary_path = pkg_resources.resource_filename(__name__,'_spuriousSSM')
 
-    os.system(binary_path + " " + " ".join(sys.argv[1:]))
+    subprocess.run([binary_path]+sys.argv[1:])

peppercompiler/design/spurious_design.py

@@ -8,6 +8,8 @@
 import string
 import subprocess
 import sys
+import pkg_resources
+import shlex
 
 from .constraint_load import Convert
 
@@ -23,7 +25,8 @@ def print_list(xs, filename, format):
     f.write(format % x)
   f.close()
 
-def design(basename, infilename, outfilename, cleanup=True, verbose=False, reuse=False, just_files=False, struct_orient=False, old_output=False, tempname=None, extra_pars="", findmfe=True, spuriousbinary="spuriousSSM"):
+def design(basename, infilename, outfilename, cleanup=True, verbose=False, reuse=False, just_files=False, struct_orient=False, 
+           old_output=False, tempname=None, extra_pars=tuple(), findmfe=True, spuriousbinary="spuriousSSM"):
 
   if not tempname:
     tempname = basename
@@ -79,12 +82,21 @@ def st_map(x):
       quiet = "quiet=TRUE"
 
     spo = open(sp_outname,'wb') 
-
-    command = "%s score=automatic template=%s wc=%s eq=%s %s %s" % (spuriousbinary, stname, wcname, eqname, extra_pars, quiet)
-    print(command)
+
+    if spuriousbinary is None:
+      sp_binary_path = pkg_resources.resource_filename(
+        "peppercompiler", "_spuriousSSM"
+        )
+    else:
+      sp_binary_path = spuriousbinary
+    if isinstance(extra_pars, str):
+        extra_pars = shlex.split(extra_pars)
+    args = [sp_binary_path, "score=automatic", f"template={stname}", f"wc={wcname}", 
+            f"eq={eqname}"] + list(extra_pars) + [quiet]
+    print(shlex.join(args))
     if just_files:
       return
-    spurious_proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE)
+    spurious_proc = subprocess.Popen(args, shell=False, stdout=subprocess.PIPE)
 
     data = spurious_proc.stdout.readline()
     while data:
@@ -162,6 +174,6 @@ def main():
     options.output = basename + ".mfe"
 
   # Collect extra arguments for spuriousSSM
-  spurious_pars = " ".join(args[1:])
+  spurious_pars = args[1:]
 
   design(basename, infilename, options.output, options.cleanup, options.verbose, options.reuse, options.just_files, options.struct_orient, options.old_output, options.tempname, spurious_pars)

setup.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 
 from setuptools import setup
-from distutils.command.build import build
+from setuptools.command.build import build
 from setuptools.command.develop import develop
 
 
@@ -31,7 +31,7 @@ def run(self):
 
 setup(
     name="peppercompiler",
-    version="0.1.3",
+    version="0.1.4",
     packages=['peppercompiler', 'peppercompiler.design'],
     install_requires=["pyparsing", "six"],
     include_package_data=True,