Improving the virtual python environment script, updating the pygeos package (#396)

Author: cssherman

pygeos_package/pygeos/__main__.py

@@ -0,0 +1,27 @@
+
+import argparse
+from pygeos import preprocessGEOSXML
+
+
+def main():
+  # Parse the user arguments
+  parser = argparse.ArgumentParser()
+  parser.add_argument('input', type=str, help='Input file name')
+  parser.add_argument('-o', '--output', type=str, help='Output file name (otherwise, it is randomly genrated)', default='')
+  parser.add_argument('-s', '--schema', type=str, help='GEOSX schema to use for validation', default='')
+  parser.add_argument('-v', '--verbose', type=int, help='Verbosity of outputs', default=0)
+  args = parser.parse_args()
+
+  # Process the xml file
+  output_name = preprocessGEOSXML(args.input,
+                                  outputFile=args.output,
+                                  schema=args.schema,
+                                  verbose=args.verbose)
+
+  print(output_name)
+
+
+if __name__ == "__main__":
+  main()
+
+

pygeos_package/pygeos/example/compile_xml

@@ -1,15 +1,27 @@
-#!/usr/gapps/GEOS/python/anaconda2/bin/python
-import os
-import sys
-import pygeos
 
-# Note: This script will compile an input xml file into one that can be run by GEOS.
-#       Usage:  compile_xml input.xml output.xml
+import argparse
+from pygeos import preprocessGEOSXML
+
+
+def main():
+  # Parse the user arguments
+  parser = argparse.ArgumentParser()
+  parser.add_argument('input', type=str, help='Input file name')
+  parser.add_argument('-o', '--output', type=str, help='Output file name (otherwise, it is randomly genrated)', default='')
+  parser.add_argument('-s', '--schema', type=str, help='GEOSX schema to use for validation', default='')
+  parser.add_argument('-v', '--verbose', type=int, help='Verbosity of outputs', default=0)
+  args = parser.parse_args()
+
+  # Process the xml file
+  output_name = preprocessGEOSXML(args.input,
+                                  outputFile=args.output,
+                                  schema=args.schema,
+                                  verbose=args.verbose)
+
+  print(output_name)
+
+
+if __name__ == "__main__":
+  main()
 
-if (len(sys.argv) == 3):
-  newFile = pygeos.preprocessGEOSXML(sys.argv[1], schema='/usr/gapps/GEOS/schema/gpac_new.xsd')
-  pygeos.format_xml_file(newFile, sys.argv[2])
-  os.system('rm %s' % (newFile))
 
-else:
-  print('Usage: preprocess_xml inputFile outputFile')

pygeos_package/pygeos/xml_processor.py

@@ -109,12 +109,13 @@ def generateRandomName(prefix='', suffix='.xml'):
   from time import time
   from os import getpid
 
-  return '%s%s%s' % (prefix, md5(str(time())+str(getpid())).hexdigest(), suffix)
+  tmp = str(time()) + str(getpid())
+  return '%s%s%s' % (prefix, md5(tmp.encode('utf-8')).hexdigest(), suffix)
 
 
-def preprocessGEOSXML(inputFile, schema='/g/g17/sherman/GEOS/geosx/src/components/core/src/schema/gpac_new.xsd', verbose=1):
+def preprocessGEOSXML(inputFile, outputFile='', schema='', verbose=0):
 
-  if (verbose > 0):
+  if verbose:
     print('\nReading input xml parameters and parsing symbolic math...')
 
   # Expand the input path
@@ -146,31 +147,38 @@ def preprocessGEOSXML(inputFile, schema='/g/g17/sherman/GEOS/geosx/src/component
       Pmap[p.get('name')] = p.get('value')
   parameterHandler.target = Pmap
 
-  # Apply regexes and write the new file
+  # Process the xml
   applyRegexToNode(root)
-  recordName = generateRandomName(prefix='prep_')
-  tree.write(recordName, pretty_print=True)
+
+  # Generate a random output name if not specified
+  if not outputFile:
+    outputFile = generateRandomName(prefix='prep_')
+
+  # Write the output file
+  tree.write(outputFile, pretty_print=True)
 
   # Check for un-matched special characters
-  with open(recordName, 'r') as ofile:
+  with open(outputFile, 'r') as ofile:
     for line in ofile:
       if any([sc in line for sc in ['$', '[', ']', '{', '}']]):
         raise Exception('Found un-matched special characters in the pre-processed input file on line:\n%s\n Check your input xml for errors!' % (line))
 
-  if (verbose > 0):
-    print('Preprocessed xml file stored in %s' % (recordName))
-    validateXML(recordName, schema)
+  if verbose:
+    print('Preprocessed xml file stored in %s' % (outputFile))
+
+  if schema:
+    validateXML(outputFile, schema, verbose)
 
-  return recordName
+  return outputFile
 
 
-def validateXML(fname, schema):
-  print('Validating the xml against the schema...')
+def validateXML(fname, schema, verbose):
+  if verbose:
+    print('Validating the xml against the schema...')
   try:
     ofile = ElementTree.parse(fname)
     sfile = ElementTree.XMLSchema(ElementTree.parse(os.path.expanduser(schema)))
     sfile.assertValid(ofile)
-    print('Done!')
   except ElementTree.DocumentInvalid as err:
     print(err)
     print('\nWarning: input XML contains potentially invalid input parameters:')
@@ -179,4 +187,6 @@ def validateXML(fname, schema):
     print('\n'+'-'*20)
     print('(Total schema warnings: %i)\n' % (len(sfile.error_log)))
 
+  if verbose:
+    print('Done!')
 

pygeos_package/setup.py

@@ -5,5 +5,6 @@
       description='GEOS front-end preprocessing package',
       author='Chris Sherman',
       author_email='[email protected]',
-      packages=['pygeos', 'pygeos.tests'])
+      packages=['pygeos', 'pygeos.tests'],
+      entry_points={'console_scripts': ['pygeos = pygeos.__main__:main']})