Started helper module

actions/pm-build-rawmodel

 #!/usr/bin/env ost
 
-import argparse
+import os, argparse
 from promod3 import meld
-from promod3.core import argcheck
+from promod3.core import argcheck, helper
 
 ### CHANGELOG - START
 # 2013-11-07 - created
@@ -13,6 +13,7 @@ from promod3.core import argcheck
 # 2 - template structure file has unsupported file extension
 # 3 - alignment file does not exist
 # 4 - alignment file has unsupported file extension
+# 5 - failed to write results to file
 ### EXIT STATUS - END
 
 ### SETUP - START
@@ -69,6 +70,8 @@ aln = io.LoadAlignment(opts.alignment_file)
 aln.AttachView(1, tpl.CreateFullView())
 result = meld.BuildRawModel(aln)
 io.SavePDB(result.model, opts.model_file)
+if not os.path.isfile(opts.model_file):
+  helper.MsgErrorAndExit("Failed to write model file '%s'." % opts.model_file, 5)
 ### MAIN - END
 
 

core/doc/CMakeLists.txt

 set(CORE_RST
 index.rst
 argcheck.rst
+helper.rst
 )
 
 add_doc_source(NAME core RST ${CORE_RST})

core/doc/helper.rst

+:mod:`~promod3.core.helper` - Shared functionality for the everything
+================================================================================
+
+.. currentmodule:: promod3.core.helper
+
+Introduction
+--------------------------------------------------------------------------------
+
+We collect functions here, which should be useful in many places but would make
+rather empty modules left alone.
+
+
+Messages
+--------------------------------------------------------------------------------
+
+.. testcode:: helper
+  :hide:
+
+  from promod3.core import helper
+
+  try:
+     helper.MsgErrorAndExit("Something failed!", 1)
+  except SystemExit, e:
+     if e.code == 1:
+       pass
+     else:
+       raise
+
+.. doctest:: helper
+
+  from promod3.core import helper
+
+  helper.MsgErrorAndExit("Something failed!", 1)
+
+.. autofunction:: MsgErrorAndExit
+

core/doc/index.rst

@@ -4,11 +4,14 @@
 .. module:: promod3.core
   :synopsis: Basic functionality, supporting standard tasks in your code.
   
-This module gathers functions and classes which are not devoted to homology modeling per se but cover standard programming issues.
+This module gathers functions and classes which are not devoted to homology
+modeling per se but cover standard programming issues.
 
 .. toctree:: 
   :maxdepth: 2
   
   argcheck
 
+  helper
+
 ..  LocalWords:  promod se toctree maxdepth argcheck

core/pymod/CMakeLists.txt

-set(PROMOD3_CORE_FILES __init__.py argcheck.py)
+set(PROMOD3_CORE_FILES __init__.py argcheck.py helper.py)
 pymod(NAME core PY ${PROMOD3_CORE_FILES} IN_DIR core
       __init__.py
       OUTPUT_DIR "promod3")

core/pymod/core/argcheck.py

@@ -4,10 +4,7 @@ Basic helpers for arguments.
 
 import os, sys
 import ost
-
-def _MsgErrorAndExit(msg, exit_status):
-    ost.LogError(msg)
-    sys.exit(exit_status)
+import helper
 
 def FileExists(prefix, exit_status, file):
   '''
@@ -29,7 +26,7 @@ def FileExists(prefix, exit_status, file):
             missing.
   '''
   if not os.path.exists(file):
-    _MsgErrorAndExit('%s file does not exist: %s\n' % (prefix, file),
+    helper.MsgErrorAndExit('%s file does not exist: %s\n' % (prefix, file),
                      exit_status)
 
 def FileExtension(prefix, exit_status, file, extensions, gz=False):
@@ -74,14 +71,16 @@ def FileExtension(prefix, exit_status, file, extensions, gz=False):
     filename, fileext = os.path.splitext(filename)
     if not gz:
       extension_string = ', '.join(extensions)
-      _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+      helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+                                                                        file)+
                        'Allowed extensions are: %s\n' % extension_string,
                        exit_status)
   if fileext == '':
     extension_string = ', '.join(extensions)
     if gz:
       extension_string += ', ' + '.gz, '.join(extensions) + '.gz'
-      _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+      helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+                                                                        file)+
                        'Allowed extensions are: %s\n' % extension_string,
                        exit_status)
   fileext = fileext[1:].lower()
@@ -94,7 +93,8 @@ def FileExtension(prefix, exit_status, file, extensions, gz=False):
   extension_string = ', '.join(extensions)
   if gz:
     extension_string += ', ' + '.gz, '.join(extensions) + '.gz'
-  _MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix, file)+
+  helper.MsgErrorAndExit('%s file extension not supported: %s. ' % (prefix,
+                                                                    file)+
                    'Allowed extensions are: %s\n' % extension_string,
                    exit_status)
 

core/pymod/core/helper.py

+"""
+Uncategorised functions which may come handy at several places.
+"""
+
+import sys
+import ost
+
+def MsgErrorAndExit(msg, exit_status):
+  '''
+  Send a messages to the |ost_s| :ost_docs:`error log <base/logging/>` and exit
+  the Python interpreter.
+
+  :param msg: The message.
+  :type msg: :class:`str`
+
+  :param exit_status: Exit code, ends up in ``$?`` in the shell. ``0`` is
+                      traditionally reserved to successful commands.
+  :type exit_status: :class:`int`
+
+  :returns: No return value, exits script with value ``exit_status``.
+  '''
+  ost.LogError(msg)
+  sys.exit(exit_status)
+
+__all__ = (
+  'MsgErrorAndExit',
+)

doc/conf.py.in

@@ -29,7 +29,11 @@ sys.path.insert(1, '@OST_ROOT@/@LIB_DIR@/python@PYTHON_VERSION@/site-packages')
 
 # Add any Sphinx extension module names here, as strings. They can be extensions
 # coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.extlinks']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.doctest',
+              'sphinx.ext.intersphinx', 'sphinx.ext.todo',
+              'sphinx.ext.coverage', 'sphinx.ext.pngmath',
+              'sphinx.ext.ifconfig', 'sphinx.ext.viewcode',
+              'sphinx.ext.extlinks']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -252,7 +256,9 @@ intersphinx_mapping = {'python': ('@PYTHON_DOC_URL@', None),
 
 # -- ProMod3 specific configuration --------------------------------------------
 extlinks = {'py_docs' : ('@PYTHON_DOC_URL@/%s',
-                         'Python documentation')}
+                         'Python documentation'),
+            'ost_docs' : ('@OST_DOC_URL@/%s',
+                          'OpenStructure documentation')}
 # The _nameattr is a bit ugly: we want to have __name__ formatted as Python
 # attribute but Sphinx does not go with calling :attr: inside extlinks. To keep
 # the Python url prefix, we define sth here.