Merge remote-tracking branch 'origin/master' into feature/6677_wikima…

…ker_win_debug. Refs #6677

Wouldn't usually merge from master but these conflicts were quite involved
to solve.

Conflicts:
	Code/Mantid/Build/wiki_maker.py
	Code/Mantid/Framework/PythonInterface/mantid/simpleapi.py

Code/Mantid/Build/CMake/CPackLinuxSetup.cmake

@@ -45,7 +45,7 @@ if ( ${UNIX_DIST} MATCHES "Ubuntu" )
 endif ( ${UNIX_DIST} MATCHES "Ubuntu" )
 
 #RedHatEnterpriseClient RedHatEnterpriseWorkstation
-if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora")
+if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
   find_program ( RPMBUILD_CMD rpmbuild )
   if ( RPMBUILD_CMD )
     set ( CPACK_GENERATOR "RPM" )
@@ -61,6 +61,10 @@ if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora")
       set ( CPACK_RPM_PACKAGE_RELEASE "${CPACK_RPM_PACKAGE_RELEASE}.fc15" )
     elseif ( ${UNIX_CODENAME} MATCHES "Verne" )
       set ( CPACK_RPM_PACKAGE_RELEASE "${CPACK_RPM_PACKAGE_RELEASE}.fc16" )
+    elseif ( ${UNIX_CODENAME} MATCHES "BeefyMiracle" )
+      set ( CPACK_RPM_PACKAGE_RELEASE "${CPACK_RPM_PACKAGE_RELEASE}.fc17" )
+    elseif ( ${UNIX_CODENAME} MATCHES "SphericalCow" )
+      set ( CPACK_RPM_PACKAGE_RELEASE "${CPACK_RPM_PACKAGE_RELEASE}.fc18" )
     endif ( ${UNIX_CODENAME} MATCHES "Tikanga" )
 
     # If CPACK_SET_DESTDIR is ON then the Prefix doesn't get put in the spec file
@@ -73,4 +77,5 @@ if ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora")
     set ( CPACK_PACKAGE_FILE_NAME
       "${CPACK_PACKAGE_NAME}-${CPACK_PACKAGE_VERSION}-${CPACK_RPM_PACKAGE_RELEASE}.${CPACK_RPM_PACKAGE_ARCHITECTURE}" )
   endif ( RPMBUILD_CMD)
-endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora")
+endif ( ${UNIX_DIST} MATCHES "RedHatEnterprise" OR ${UNIX_DIST} MATCHES "Fedora" OR ${UNIX_DIST} MATCHES "SUSE LINUX" )
+

Code/Mantid/Build/wiki_maker.py

@@ -16,12 +16,14 @@
 reporter = WikiReporter()
 
 #======================================================================
-def confirm(prompt=None, resp=False):
+def confirm(prompt=None, resp=False, continueconfirm=False):
     """prompts for yes or no response from the user. Returns True for yes and
     False for no.
 
     'resp' should be set to the default value assumed by the caller when
     user simply types ENTER.
+    
+    if 'continueconfirm', then skip the confirmation, using No (false) as the choice.
 
     >>> confirm(prompt='Create Directory?', resp=True)
     Create Directory? [y]|n: 
@@ -35,6 +37,11 @@ def confirm(prompt=None, resp=False):
 
     """
 
+    # Early exit. 
+    if continueconfirm:
+        print 'Skip confirmation, changes have not been accepted.'
+        return False
+
     if prompt is None:
         prompt = 'Confirm'
 
@@ -84,9 +91,13 @@ def last_page_editor(page):
 def wiki_maker_page(page):
     """
     returns True if the wikimaker was the last editor.
+    determines if there is a bot comment, which implies that the wikimaker was used to create the page last.
     """
-    return ("WikiMaker" == last_page_editor(page))
-
+    #Get the last editor of the page.
+    revisions = page.revisions()
+    for rev in revisions: 
+        return re.search("^Bot", rev['comment'])
+
 #======================================================================
 def do_algorithm(args, algo, version):
     """ Do the wiki page
@@ -139,25 +150,27 @@ def do_algorithm(args, algo, version):
         print
 
         wiki_maker_edited_last = wiki_maker_page(page)
-
+        last_modifier = last_page_editor(page);
         if not wiki_maker_edited_last:
-            print "The last editor was NOT the WIKIMAKER"
-            last_modifier = last_page_editor(page);
-            print "The last page editor was ", last_modifier
+            print "The last edit was manual. Last edit NOT done by WIKIMAKER script."
             if not last_modifier == None:
                 # Report a failure test case
                 reporter.addFailureTestCase(algo, version, last_modifier, ''.join(diff_list))
+        else:
+            print "The last edit was automatic via a script. Last edit was done by WIKIMAKER script."
+        print "Last change by ", last_modifier
 
         if args.dryrun:
             print "Dry run of saving page to http://www.mantidproject.org/%s" % wiki_page_name
-        elif wiki_maker_edited_last or args.force or confirm("Do you want to replace the website wiki page?", True):
+        elif wiki_maker_edited_last or args.force or confirm("Do you want to replace the website wiki page?", True, args.continueconfirm):
             print "Saving page to http://www.mantidproject.org/%s" % wiki_page_name
             page.save(new_contents, summary = 'Bot: replaced contents using the wiki_maker.py script.' )
 
     saved_text = open(wiki_page_name+'.txt', 'w')
     saved_text.write(new_contents)
     saved_text.close()
 
+
 #======================================================================
 if __name__ == "__main__":
 
@@ -195,16 +208,19 @@ def do_algorithm(args, algo, version):
                         help="Force overwriting the wiki page on the website if different (don't ask the user)")
 
     parser.add_option('--alg-version', dest='algversion', default=noversion, 
-                        help='Algorithm version to create the wiki for.')
+                        help='Algorithm version to create the wiki for. Latest version if absent.')
 
     parser.add_option('--report', dest='wikimakerreport', default=False, action='store_const', const=True,
                         help="Record authors and corresponding algorithm wiki-pages that have not been generated with the wiki-maker")
 
     parser.add_option('--cache-config', dest='cacheconfig', default=False, action='store_const', const=True,
-                        help="If true, the creditials of the executor will be cached for the next run.")
+                        help="If set, the creditials of the executor will be cached for the next run.")
 
     parser.add_option('--dry-run', dest='dryrun', default=False, action='store_const', const=True,
-                        help="If false, then the utility will work exactly the same, but no changes will actually be pushed to the wiki.")
+                        help="If set, then the utility will work exactly the same, but no changes will actually be pushed to the wiki.")
+
+    parser.add_option('--continue-confirm', dest='continueconfirm', default=False, action='store_const', const=True,
+                        help="If set, then any user-required confirmation will be skipped, without applying the change.")
 
 
     (args, algos) = parser.parse_args()

Code/Mantid/Build/wiki_tools.py

@@ -15,6 +15,12 @@
 python_d_exe = None
 # no version identier
 noversion = -1
+# Direction
+InputDirection = "Input"
+OutputDirection = "Output"
+InOutDirection = "InOut"
+NoDirection = "None"
+direction_string = [InputDirection, OutputDirection, InOutDirection, NoDirection]
 
 # Holds on to location of sources
 file_search_done=False
@@ -106,6 +112,61 @@ def get_wiki_description(algo, version):
         print "Getting algorithm description from source."
         return desc
 
+#======================================================================
+def create_function_signature(alg, algo_name):
+    """
+    create the function signature for the algorithm.
+    """
+    from mantid.simpleapi import _get_function_spec
+    import mantid.simpleapi
+    _alg = getattr(mantid.simpleapi, algo_name)
+    prototype =  algo_name + _get_function_spec(_alg)
+
+    # Replace every nth column with a newline.
+    nth = 4
+    commacount = 0
+    prototype_reformated = ""
+    for char in prototype:
+        if char == ',':
+            commacount += 1
+            if (commacount % nth == 0):
+                prototype_reformated += ",\n  "
+            else:
+                prototype_reformated += char
+        else: 
+           prototype_reformated += char
+
+    # Strip out the version.
+    prototype_reformated = prototype_reformated.replace(",[Version]", "")
+
+    # Add the output properties
+    props = alg.getProperties()
+    allreturns = []
+    workspacereturn = None
+    # Loop through all the properties looking for output properties
+    for prop in props:
+        if (direction_string[prop.direction] == OutputDirection):
+            allreturns.append(prop.name)
+            # Cache the last workspace property seen.
+            if isinstance(prop, IWorkspaceProperty): 
+                workspacereturn = prop.name
+
+    lhs = ""
+    comments = ""
+    if not allreturns:
+        pass
+    elif (len(allreturns) == 1) and (workspacereturn is not None): 
+        lhs =   workspacereturn + " = "
+    else :
+        lhs = "result = "
+        comments = "\n "
+        comments += "\n # -------------------------------------------------- \n"
+        comments += " # result is a tuple containing\n"
+        comments += " # (" + ",".join(allreturns ) + ")\n"
+        comments += " # To access individual outputs use result[i], where i is the index of the required output.\n"
+
+    return lhs + prototype_reformated + comments
+
 #======================================================================
 def intialize_files():
     """ Get path to every header file """
@@ -415,13 +476,19 @@ def make_wiki(algo_name, version, latest_version):
             raise RuntimeError("Error in processing output from subprocess. Most likely a bug in wiki_tools")
     return output
 
+#======================================================================
 def do_make_wiki(algo_name, version, latest_version):
     """ Return wiki text for a given algorithm
     @param algo_name :: name of the algorithm (bare)
     @param version :: version requested
     @param latest_version :: the latest algorithm 
     """ 
-    out = ""
+
+    external_image = "http://download.mantidproject.org/algorithm_screenshots/ScreenShotImages/%s_dlg.png" % algo_name  
+    out = "<anchor url='%s'><img width=400px align='right' src='%s' style='position:relative; z-index:1000;'></anchor>\n\n" % (external_image, external_image)  
+
+    # Deprecated algorithms: Simply return the deprecation message
+    print "Creating... ", algo_name, version
     import mantid
     from mantid.api import AlgorithmManager,DeprecatedAlgorithmChecker
     # Deprecated algorithms: Simply returnd the deprecation message
@@ -435,10 +502,10 @@ def do_make_wiki(algo_name, version, latest_version):
         deprecstr = deprecstr.replace(" instead.", "]] instead.")
         out += deprecstr 
         out += "\n\n"
-
+    
     alg = AlgorithmManager.createUnmanaged(algo_name, version)
     alg.initialize()
-
+    
     if (latest_version > 1):
         if (version < latest_version):
             out += "Note: This page refers to version %d of %s. The latest version is %d - see [[%s v.%d]].\n\n" % (version, algo_name, latest_version, algo_name, latest_version)
@@ -455,6 +522,10 @@ def do_make_wiki(algo_name, version, latest_version):
 
     out += "== Summary ==\n\n"
     out += alg.getWikiSummary().replace("\n", " ") + "\n\n"
+
+    out += "\n\n== Usage ==\n\n"
+    out += " " + create_function_signature(alg, algo_name) + "\n\n" 
+    out += "<br clear=all>\n\n" 
     out += "== Properties ==\n\n"
 
     out += """{| border="1" cellpadding="5" cellspacing="0" 
@@ -513,7 +584,7 @@ def do_make_wiki(algo_name, version, latest_version):
         out +=  "{{AlgorithmLinks|%s}}\n" % (algo_name)
 
     return out
-    
+
 #======================================================================
 def make_property_table_line(propnum, p):
     """ Make one line of the property table
@@ -523,20 +594,15 @@ def make_property_table_line(propnum, p):
         p :: Property object
     Returns:
         string to add to the wiki
-    """
+    """    
     from mantid.api import IWorkspaceProperty
 
     out = ""
     # The property number
     out += "|" + str(propnum) + "\n"
     # Name of the property
     out += "|" + p.name + "\n"
-    # Direction
-    InputDirection = "Intput"
-    OutputDirection = "Output"
-    InOutDirection = "InOut"
-    NoDirection = "None"
-    direction_string = [InputDirection, OutputDirection, InOutDirection, NoDirection]
+
     out += "|" + direction_string[p.direction] + "\n"
     # Type (as string) wrap an IWorkspaceProperty in a link.
     if isinstance(p, IWorkspaceProperty): 
@@ -557,6 +623,7 @@ def make_property_table_line(propnum, p):
     # End of table line
     out += "|-\n"
     return out
+
 
 #======================================================================
 def make_group_header_line(group):

Code/Mantid/Framework/API/inc/MantidAPI/Axis.h

@@ -50,9 +50,9 @@ class MANTID_API_DLL Axis
   virtual ~Axis();
 
   /// Virtual constructor
-  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace = NULL) = 0;
+  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace) = 0;
   /// Virtual constructor for axis of different length
-  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace = NULL) = 0;
+  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace) = 0;
 
   const std::string& title() const;
   std::string& title();
@@ -84,8 +84,8 @@ class MANTID_API_DLL Axis
   /// @param index :: The index
   /// @param value :: The new value
   virtual void setValue(const std::size_t& index, const double& value) = 0;
-  /// Get a non-mutable spectrum index
-  virtual const specid_t& spectraNo(const std::size_t& index) const;
+  /// Get the spectrum index
+  virtual specid_t spectraNo(const std::size_t& index) const;
 
   /// Get the length of the axis
   virtual std::size_t length() const = 0;

Code/Mantid/Framework/API/inc/MantidAPI/NumericAxis.h

@@ -51,8 +51,8 @@ class MANTID_API_DLL NumericAxis: public Axis
 public:
   NumericAxis(const std::size_t& length);
   virtual ~NumericAxis(){}
-  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace = NULL);
-  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace = NULL);
+  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace);
+  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace);
   ///Is the axis numeric - always true for this class
   virtual bool isNumeric() const{return true;}
   virtual std::size_t length() const{return m_values.size();}

Code/Mantid/Framework/API/inc/MantidAPI/SpectraAxis.h

@@ -58,35 +58,35 @@ class MatrixWorkspace;
 class MANTID_API_DLL SpectraAxis: public Axis
 {
 public:
-  explicit SpectraAxis(const std::size_t& length, const bool initWithDefaults = true);
-  explicit SpectraAxis(const std::size_t length, const Geometry::ISpectraDetectorMap & spectramap);
+  explicit SpectraAxis(const MatrixWorkspace* const parentWorkspace);
   virtual ~SpectraAxis(){}
-  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace = NULL);
-  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace = NULL);
-  virtual std::size_t length() const{return m_values.size();}
+  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace);
+  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace);
+  virtual std::size_t length() const;
   /// If this is a spectra Axis - always true for this class
   virtual bool isSpectra() const{return true;}
   virtual double operator()(const std::size_t& index, const std::size_t& verticalIndex = 0) const;
   virtual void setValue(const std::size_t& index, const double& value);
   virtual bool operator==(const Axis&) const;
   std::string label(const std::size_t& index)const;
 
-  const specid_t& spectraNo(const std::size_t& index) const;
+  specid_t spectraNo(const std::size_t& index) const;
   // Get a map that contains the spectra index as the key and the index in the array as teh value
   void getSpectraIndexMap(spec2index_map&) const;
   void getIndexSpectraMap(index2spec_map& map) const;
 
-  /// returns min value defined on axis
-  double getMin()const{return double(m_values.front()) ; }
-   /// returns max value defined on axis
-  double getMax()const{return double(m_values.back()); }
+  double getMin() const;
+  double getMax() const;
+
 private:
   /// Default constructor
   SpectraAxis();
+  /// Private, undefined copy constructor
+  SpectraAxis(const SpectraAxis&);
   /// Private, undefined copy assignment operator
   const SpectraAxis& operator=(const SpectraAxis&);
-  /// A vector holding the axis values for the axis.
-  std::vector<specid_t> m_values;
+  /// A pointer to the workspace holding the axis
+  const MatrixWorkspace* const m_parentWS;
 };
 
 } // namespace API

Code/Mantid/Framework/API/inc/MantidAPI/TextAxis.h

@@ -52,8 +52,8 @@ class MANTID_API_DLL TextAxis: public Axis
 public:
   TextAxis(const std::size_t& length);
   virtual ~TextAxis(){}
-  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace = NULL);
-  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace = NULL);
+  virtual Axis* clone(const MatrixWorkspace* const parentWorkspace);
+  virtual Axis* clone(const std::size_t length, const MatrixWorkspace* const parentWorkspace);
   virtual std::size_t length() const{return m_values.size();}
   /// If this is a TextAxis, always return true for this class
   virtual bool isText() const{return true;}

Code/Mantid/Framework/API/src/Axis.cpp

@@ -83,7 +83,7 @@ double Axis::getValue(const std::size_t& index, const std::size_t& verticalIndex
  *  @return The spectrum number as an int
  *  @throw  domain_error If this method is called on a numeric axis
  */
-const specid_t& Axis::spectraNo(const std::size_t& index) const
+specid_t Axis::spectraNo(const std::size_t& index) const
 {
   UNUSED_ARG(index)
   throw std::domain_error("Cannot call spectraNo() on a non-spectra axis.");