Remove python package

CMakeLists.txt

@@ -25,7 +25,6 @@ dune_enable_all_packages()
  # Always activate tests for now
  set(DUNE_COPASI_TESTS ON)
 
-add_subdirectory(python)
 add_subdirectory(src)
 add_subdirectory(dune)
 add_subdirectory(doc)

python/CMakeLists.txt

-configure_file("dune/copasi/cli/cmake_variables.py.in" 
-               "${CMAKE_CURRENT_SOURCE_DIR}/dune/copasi/cli/cmake_variables.py")
-
-dune_python_install_package(PATH .)
\ No newline at end of file

python/dune/copasi/cli/cmake_variables.py.in

-# environmental variables when package is setup with CMake
-
-DUNE_COPASI_EXEC = "@CMAKE_BINARY_DIR@/src/dune-copasi-exec"
\ No newline at end of file

python/dune/copasi/cli/parser.py

-import os
-import argparse
-
-try:
-  from .cmake_variables import DUNE_COPASI_EXEC
-except:
-  pass
-
-from .run import run
-from .preprocess import preprocess_config
-
-def get_parser():
-
-  parser = argparse.ArgumentParser()
-
-  subparsers = parser.add_subparsers(title="Commands", dest="command")
-  subparsers.required = True
-
-  parser_run = subparsers.add_parser('run',
-      help="Run the dune-copasi main routine.",
-      description="Run the dune-copasi main routine.")
-  parser_run.add_argument('config',
-                          help="Configuration file.")
-
-  try:
-    executable = os.environ['DUNE_COPASI_EXEC']
-  except Exception as e:
-    try:
-      executable = DUNE_COPASI_EXEC
-    except Exception as e:
-      raise IOError("dune-copasi executable not found")
-
-  parser_run.add_argument('--exec',
-                           default=executable,
-                           help="dune-copasi c++ executable.")
-  
-  parser_run.set_defaults(func=run)
-
-
-  parser_preprocess = subparsers.add_parser('preprocess',
-      help="Preprocess the config file.",
-      description="Preprocess the config file.")
-  parser_preprocess.add_argument('config',
-                          help="Configuration file.")
-
-  parser_preprocess.add_argument('new_config',
-                          help="Preprocessed configuration file.")
-
-  parser_preprocess.set_defaults(func=preprocess_config)
-
-  return parser
\ No newline at end of file

python/dune/copasi/cli/preprocess.py

-import os
-import configparser
-import sympy
-from sympy.parsing.sympy_parser import parse_expr
-
-def inject_jacobian(section,config):
-  jac_section = section+'.jacobian'
-
-  jac_ditc = {}
-  for vari_str in config[section]:
-    func_str = config[section][vari_str].replace('^','**')
-    func_symb = parse_expr(func_str)
-
-    for varj_str in config[section]:
-      jac_key = 'd({})/d({})'.format(vari_str,varj_str)
-
-      has_jac = False
-      if config.has_section(jac_section):
-        if jac_key in config[jac_section]:
-          jac_str = str(config[jac_section][jac_key])
-          has_jac = True
-      
-      if not has_jac:
-        varj_symb = sympy.Symbol(varj_str)
-        jac_symb = sympy.diff(func_symb,varj_symb)
-        jac_str = str(jac_symb).replace('**','^')
-
-      jac_ditc[jac_key] = jac_str
-  config[jac_section] = jac_ditc
-  return config
-
-def preprocess_compartement(compartement,config):
-  reaction_key = 'model.'+compartement+'.reaction'
-  config = inject_jacobian(reaction_key,config)
-  return config
-
-def preprocess_config(args):
-
-  if not os.path.isfile(args["config"]):
-    raise IOError("Configuration file {} not found".format(args["config"]))
-
-  config = configparser.ConfigParser()
-  config.read(args['config'])
-  
-
-  for compartement in config['model.compartements']:
-    preprocess_compartement(compartement, config)
-  
-  with open(args['new_config'], 'w') as configfile:
-    config.write(configfile)
\ No newline at end of file

python/dune/copasi/cli/run.py

-import os
-import sys
-import subprocess
-
-def run(args):
-    if not os.path.isfile(args["config"]):
-        raise IOError("Configuration file {} not found".format(args["config"]))
-    try:
-        subprocess.check_call([args["exec"], args["config"]])
-    except subprocess.CalledProcessError:
-        print("Error while running dune-copasi")
-        sys.exit(1)
\ No newline at end of file

python/scripts/dune-copasi

-#!/usr/bin/env python3
-
-import sys
-import warnings
-
-from dune.copasi.cli.parser import get_parser
-
-if __name__ == "__main__": # parse command line and call command handler
-    try:
-        with warnings.catch_warnings(record=True) as warn:
-            try:
-                parser = get_parser()
-                args = parser.parse_args()
-            except SystemExit:
-                sys.exit(1)
-            args.func(vars(args))
-    except Exception as e:
-        print("dune-copasi failed with ({0}) warning(s) and ({1}) error(s)".format(len(warn),1))
-        raise

python/setup.py

-#!/usr/bin/env python
-
-import sys
-from setuptools import setup
-
-
-def dune_copasi_scripts():
-    return ['./scripts/dune-copasi']
-
-setup(name='dune.copasi',
-      version='0.0.0',
-      namespace_packages=['dune'],
-      description='Biochemical System Simulator COPASI in DUNE',
-      author='Santiago Ospina De Los Ríos <santiago.ospina@iwr.uni-heidelberg.de>',
-      author_email='no_mailinglist_yet@dune-copasi.de',
-      url='http://copasi.org',
-      packages=['dune.copasi',
-                'dune.copasi.cli',
-                ],
-      install_requires=['sympy',
-                        'configparser',
-                        'argparse'],
-      scripts=dune_copasi_scripts())