Initial commit after restructuring Stork repo

Makefile.app → Makefile

@@ -26,7 +26,7 @@ include $(MOOSE_DIR)/modules/modules.mk
 
 # dep apps
 APPLICATION_DIR    := $(CURDIR)
-APPLICATION_NAME   := stork
+APPLICATION_NAME   := MOON
 BUILD_EXEC         := yes
 DEP_APPS           := $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
 include            $(FRAMEWORK_DIR)/app.mk

Makefile.module

-###############################################################################
-################### MOOSE Application Standard Makefile #######################
-###############################################################################
-#
-# Optional Environment variables
-# MOOSE_DIR        - Root directory of the MOOSE project 
-# HERD_TRUNK_DIR   - Location of the HERD repository
-# FRAMEWORK_DIR    - Location of the MOOSE framework
-#
-###############################################################################
-MODULE_DIR         ?= $(shell dirname `pwd`)
-MOOSE_DIR          ?= $(shell dirname $(MODULE_DIR))
-FRAMEWORK_DIR      ?= $(MOOSE_DIR)/framework
-###############################################################################
-
-# framework
-include $(FRAMEWORK_DIR)/build.mk
-include $(FRAMEWORK_DIR)/moose.mk
-
-# dep apps
-APPLICATION_DIR    := $(MODULE_DIR)/stork
-APPLICATION_NAME   := stork
-BUILD_EXEC         := yes
-DEP_APPS           := $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
-include            $(FRAMEWORK_DIR)/app.mk
-
-###############################################################################
-# Additional special case targets should be added here

README.md

-Stork
+Moon
 =====
 
-"Fork Stork" to create a new MOOSE-based application.
+"Fork Moon" to create a new MOOSE-based application.
 
 For more information see: [http://mooseframework.org/create-an-app/](http://mooseframework.org/create-an-app/)

doc/doxygen/Doxyfile

@@ -4,7 +4,7 @@
 # Project related configuration options
 #---------------------------------------------------------------------------
 DOXYFILE_ENCODING      = UTF-8
-PROJECT_NAME           = "stork"
+PROJECT_NAME           = "MOON"
 PROJECT_NUMBER         =
 PROJECT_BRIEF          =
 PROJECT_LOGO           =

include/base/StorkApp.h → include/base/MoonApp.h

-#ifndef STORKAPP_H
-#define STORKAPP_H
+#ifndef MOONAPP_H
+#define MOONAPP_H
 
 #include "MooseApp.h"
 
-class StorkApp;
+class MoonApp;
 
 template<>
-InputParameters validParams<StorkApp>();
+InputParameters validParams<MoonApp>();
 
-class StorkApp : public MooseApp
+class MoonApp : public MooseApp
 {
 public:
-  StorkApp(InputParameters parameters);
-  virtual ~StorkApp();
+  MoonApp(InputParameters parameters);
+  virtual ~MoonApp();
 
   static void registerApps();
   static void registerObjects(Factory & factory);
   static void associateSyntax(Syntax & syntax, ActionFactory & action_factory);
 };
 
-#endif /* STORKAPP_H */
+#endif /* MOONAPP_H */

make_new_application.py

-#!/usr/bin/env python
-
-# This script is for creating a new herd animal.  Just run this script
-# from the "stork" directory supplying a new animal name and it should
-# create a complete application template built with support for both
-# MOOSE and ELK.  Enjoy!
-
-import os, sys, string, re, subprocess
-from optparse import OptionParser
-from shutil import copytree, ignore_patterns
-
-# DO NOT MODIFY
-# This value should be set to true if this stork is within the svn herd repository
-global_in_herd = False
-global_ignores = ['.svn', '.git']
-global_app_name = ''
-global_rename_suffix = 'app'
-
-def renameFiles(app_path):
-  rename_pattern = re.compile(r'(stork)(.*)', re.I)
-  suffix_pattern = re.compile(r'(.*)\.' + global_rename_suffix + '$')
-
-  for dirpath, dirnames, filenames in os.walk(app_path):
-    # Don't traverse into ignored directories
-    for ignore in global_ignores:
-      if ignore in dirnames:
-        dirnames.remove(ignore)
-
-    for file in filenames:
-      match = rename_pattern.match(file)
-
-      # Replace 'stork' in the contents
-      replaceNameInContents(dirpath + '/' + file)
-
-      # See if the file needs to be renamed and rename
-      if match != None:
-        replace_string = replacementFunction(match)
-        os.rename(dirpath + '/' + file, dirpath + '/' + replace_string + match.group(2))
-        # update the file
-        file = replace_string + match.group(2)
-
-      # If there are files with .app suffixes drop the suffix
-      match = suffix_pattern.search(file)
-      if match != None:
-        os.rename(dirpath + '/' + file, dirpath + '/' + match.group(1))
-
-def replaceNameInContents(filename):
-  f = open(filename)
-  text = f.read()
-  f.close()
-
-  # Replace all instances of the word stork with the right case
-  pattern = re.compile(r'(stork)', re.I)
-  text = pattern.sub(replacementFunction, text)
-
-  # Retrieve original file attribute to be applied later
-  mode = os.stat(filename).st_mode
-
-  # Now write the file back out
-  f = open(filename + '~tmp', 'w')
-  f.write(text)
-  f.close()
-  os.chmod(filename + '~tmp', mode)
-  os.rename(filename + '~tmp', filename)
-
-def replacementFunction(match):
-  # There are 3 "case" cases
-  # Case 1: all lower case
-  if match.group(1) == 'stork':
-    return global_app_name
-
-  # Case 2: all upper case
-  if match.group(1) == 'STORK':
-    return string.upper(global_app_name)
-
-  # Case 3: First letter is capitalized
-  if match.group(1) == 'Stork':
-    name = global_app_name.replace("_", " ")
-    name = name.title()
-    name = name.replace(" ", "")
-    return name
-
-  print match.group(0) + "\nBad Case Detected!"
-  sys.exit(1)
-
-if __name__ == '__main__':
-  parser = OptionParser()
-  (global_options, args) = parser.parse_args()
-
-  # Get the animal name
-  if global_in_herd:
-    if len(args) != 1:
-      print 'Usage: ./make_new_application.py <animal name>'
-      sys.exit()
-    global_app_name = string.lower(args[0])
-  else:
-    if len(args) != 0:
-      print 'Usage: ./make_new_application.py'
-      sys.exit()
-    global_app_name = os.path.basename(os.path.dirname(os.path.realpath(__file__)))
-
-  # Make the new application
-  if global_in_herd:
-    copytree('.', '../' + global_app_name, ignore=ignore_patterns('.svn', '.git', '*.module', 'make_new*', 'LICENSE'))
-    renameFiles('../' + global_app_name)
-
-    print 'Your application should be ready!\nAdd the directory ../' + global_app_name + ' to your checkout and commit.'
-  else:
-    # We are in a git clone
-    renameFiles('.')
-    try:
-      os.remove('Makefile.module')
-      os.remove('run_tests.module')
-      os.remove(os.path.join('src', 'base', 'StorkApp.C.module'))
-      os.remove('make_new_application.py')
-      os.remove('make_new_module.py')
-    except:
-      pass
-
-    # Add the newly created untracked files and delete the removed ones
-    subprocess.check_output("git rm -f *.py Makefile.* run_tests.*", shell=True)
-    subprocess.call("git add --all *", shell=True)
-
-    print 'Your application should be ready!\nCommit this directory to your local repository and push.'

make_new_module.py

-#!/usr/bin/env python
-
-# This script is for creating a new herd animal.  Just run this script
-# from the "stork" directory supplying a new animal name and it should
-# create a complete application template built with support for both
-# MOOSE and ELK.  Enjoy!
-
-import os, sys, string, re, subprocess
-from optparse import OptionParser
-from shutil import copytree, ignore_patterns
-
-global_ignores = ['.svn', '.git']
-global_app_name = ''
-global_app_name_stripped = ''
-global_rename_suffix = 'module'
-
-def renameFiles(app_path):
-  rename_pattern = re.compile(r'(stork)(.*)', re.I)
-  suffix_pattern = re.compile(r'(.*)\.' + global_rename_suffix + '$')
-
-  for dirpath, dirnames, filenames in os.walk(app_path):
-    # Don't traverse into ignored directories
-    for ignore in global_ignores:
-      if ignore in dirnames:
-        dirnames.remove(ignore)
-
-    for file in filenames:
-      match = rename_pattern.match(file)
-
-      # Replace 'stork' in the contents
-      replaceNameInContents(dirpath + '/' + file)
-
-      # See if the file needs to be renamed and rename
-      if match != None:
-        replace_string = replacementFunction(match)
-        os.rename(dirpath + '/' + file, dirpath + '/' + replace_string + match.group(2))
-        # update the file
-        file = replace_string + match.group(2)
-
-      # If there are files with .app suffixes drop the suffix
-      match = suffix_pattern.search(file)
-      if match != None:
-        os.rename(dirpath + '/' + file, dirpath + '/' + match.group(1))
-
-
-def replaceNameInContents(filename):
-  f = open(filename)
-  text = f.read()
-  f.close()
-
-  # Replace all instances of the word stork with the right case
-  pattern = re.compile(r'(stork)', re.I)
-  text = pattern.sub(replacementFunction, text)
-
-  # Retrieve original file attribute to be applied later
-  mode = os.stat(filename).st_mode
-
-  # Now write the file back out
-  f = open(filename + '~tmp', 'w')
-  f.write(text)
-  f.close()
-  os.chmod(filename + '~tmp', mode)
-  os.rename(filename + '~tmp', filename)
-
-def replacementFunction(match):
-  # There are 3 "case" cases
-  # Case 1: all lower case
-  if match.group(1) == 'stork':
-    return global_app_name_stripped
-
-  # Case 2: all upper case
-  if match.group(1) == 'STORK':
-    return string.upper(global_app_name_stripped)
-
-  # Case 3: First letter is capitalized
-  if match.group(1) == 'Stork':
-    name = global_app_name_stripped.replace("_", " ")
-    name = name.title()
-    name = name.replace(" ", "")
-    return name
-  
-  print match.group(0) + "\nBad Case Detected!"
-  sys.exit(1)
-
-def printUsage():
-  print './make_new_module.py <module name> <moose dir>'
-  sys.exit()
-
-if __name__ == '__main__':
-  parser = OptionParser()
-  (global_options, args) = parser.parse_args()
-
-  # Make sure an animal name was supplied (args[0])
-  if len(args) != 2:
-    printUsage()
-
-  modules_dir = args[1] + '/modules/'
-  if not os.path.exists(modules_dir):
-    print "Unable to access ", modules_dir
-    sys.exit()
-
-  global_app_name = string.lower(args[0])
-  global_app_name_stripped = global_app_name
-  m = re.search(r'(\D*)', global_app_name)
-  if m != None:
-    global_app_name_stripped = m.group(1)
-
-  # Copy the directory
-  copytree('.', modules_dir + global_app_name, ignore=ignore_patterns('.svn', '.git', '*.app', 'make_new*', 'LICENSE'))
-
-  renameFiles(modules_dir + global_app_name)
-
-  print 'Your new module should be ready!\nYou need to edit the following files to include your new module into MOOSE:'
-  print  modules_dir + 'modules.mk'
-  print  modules_dir + 'combined/src/base/ModulesApp.C'

run_tests.app → run_tests

@@ -5,7 +5,7 @@ import sys, os, inspect
 os.chdir(os.path.abspath(os.path.dirname(sys.argv[0])))
 
 #### Set the name of the application here and moose directory relative to the application
-app_name = 'stork'
+app_name = 'MOON'
 
 MOOSE_DIR = os.path.abspath(os.path.join('..', 'moose'))
 #### See if a submodule is available

run_tests.module

-#!/usr/bin/env python
-import sys, os
-
-# Set the current working directory to the directory where this script is located
-os.chdir(os.path.abspath(os.path.dirname(sys.argv[0])))
-
-#### Set the name of the application here and moose directory relative to the application
-app_name = 'stork'
-
-MODULE_DIR = os.path.abspath('..')
-MOOSE_DIR = os.path.abspath(os.path.join(MODULE_DIR, '..'))
-#### See if MOOSE_DIR is already in the environment instead
-if os.environ.has_key("MOOSE_DIR"):
-  MOOSE_DIR = os.environ['MOOSE_DIR']
-
-sys.path.append(os.path.join(MOOSE_DIR, 'python'))
-import path_tool
-path_tool.activate_module('TestHarness')
-
-from TestHarness import TestHarness
-# Run the tests!
-TestHarness.buildAndRun(sys.argv, app_name, MOOSE_DIR)

src/base/StorkApp.C.app → src/base/MoonApp.C

-#include "StorkApp.h"
+#include "MoonApp.h"
 #include "Moose.h"
 #include "AppFactory.h"
 #include "ModulesApp.h"
 #include "MooseSyntax.h"
 
 template<>
-InputParameters validParams<StorkApp>()
+InputParameters validParams<MoonApp>()
 {
   InputParameters params = validParams<MooseApp>();
 
@@ -16,40 +16,40 @@ InputParameters validParams<StorkApp>()
   return params;
 }
 
-StorkApp::StorkApp(InputParameters parameters) :
+MoonApp::MoonApp(InputParameters parameters) :
     MooseApp(parameters)
 {
   Moose::registerObjects(_factory);
   ModulesApp::registerObjects(_factory);
-  StorkApp::registerObjects(_factory);
+  MoonApp::registerObjects(_factory);
 
   Moose::associateSyntax(_syntax, _action_factory);
   ModulesApp::associateSyntax(_syntax, _action_factory);
-  StorkApp::associateSyntax(_syntax, _action_factory);
+  MoonApp::associateSyntax(_syntax, _action_factory);
 }
 
-StorkApp::~StorkApp()
+MoonApp::~MoonApp()
 {
 }
 
 // External entry point for dynamic application loading
-extern "C" void StorkApp__registerApps() { StorkApp::registerApps(); }
+extern "C" void MoonApp__registerApps() { MoonApp::registerApps(); }
 void
-StorkApp::registerApps()
+MoonApp::registerApps()
 {
-  registerApp(StorkApp);
+  registerApp(MoonApp);
 }
 
 // External entry point for dynamic object registration
-extern "C" void StorkApp__registerObjects(Factory & factory) { StorkApp::registerObjects(factory); }
+extern "C" void MoonApp__registerObjects(Factory & factory) { MoonApp::registerObjects(factory); }
 void
-StorkApp::registerObjects(Factory & factory)
+MoonApp::registerObjects(Factory & factory)
 {
 }
 
 // External entry point for dynamic syntax association
-extern "C" void StorkApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { StorkApp::associateSyntax(syntax, action_factory); }
+extern "C" void MoonApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { MoonApp::associateSyntax(syntax, action_factory); }
 void
-StorkApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
+MoonApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
 {
 }

src/base/StorkApp.C.module → src/base/MoonApp.C.module

-#include "StorkApp.h"
+#include "MoonApp.h"
 #include "Moose.h"
 #include "AppFactory.h"
 #include "MooseSyntax.h"
 
 template<>
-InputParameters validParams<StorkApp>()
+InputParameters validParams<MoonApp>()
 {
   InputParameters params = validParams<MooseApp>();
 
@@ -15,38 +15,38 @@ InputParameters validParams<StorkApp>()
   return params;
 }
 
-StorkApp::StorkApp(InputParameters parameters) :
+MoonApp::MoonApp(InputParameters parameters) :
     MooseApp(parameters)
 {
   Moose::registerObjects(_factory);
-  StorkApp::registerObjects(_factory);
+  MoonApp::registerObjects(_factory);
 
   Moose::associateSyntax(_syntax, _action_factory);
-  StorkApp::associateSyntax(_syntax, _action_factory);
+  MoonApp::associateSyntax(_syntax, _action_factory);
 }
 
-StorkApp::~StorkApp()
+MoonApp::~MoonApp()
 {
 }
 
 // External entry point for dynamic application loading
-extern "C" void StorkApp__registerApps() { StorkApp::registerApps(); }
+extern "C" void MoonApp__registerApps() { MoonApp::registerApps(); }
 void
-StorkApp::registerApps()
+MoonApp::registerApps()
 {
-  registerApp(StorkApp);
+  registerApp(MoonApp);
 }
 
 // External entry point for dynamic object registration
-extern "C" void StorkApp__registerObjects(Factory & factory) { StorkApp::registerObjects(factory); }
+extern "C" void MoonApp__registerObjects(Factory & factory) { MoonApp::registerObjects(factory); }
 void
-StorkApp::registerObjects(Factory & factory)
+MoonApp::registerObjects(Factory & factory)
 {
 }
 
 // External entry point for dynamic syntax association
-extern "C" void StorkApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { StorkApp::associateSyntax(syntax, action_factory); }
+extern "C" void MoonApp__associateSyntax(Syntax & syntax, ActionFactory & action_factory) { MoonApp::associateSyntax(syntax, action_factory); }
 void
-StorkApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
+MoonApp::associateSyntax(Syntax & /*syntax*/, ActionFactory & /*action_factory*/)
 {
 }

src/main.C

-#include "StorkApp.h"
+#include "MoonApp.h"
 #include "MooseInit.h"
 #include "Moose.h"
 #include "MooseApp.h"
 #include "AppFactory.h"
 
 // Create a performance log
-PerfLog Moose::perf_log("Stork");
+PerfLog Moose::perf_log("Moon");
 
 // Begin the main program.
 int main(int argc, char *argv[])
@@ -14,10 +14,10 @@ int main(int argc, char *argv[])
   MooseInit init(argc, argv);
 
   // Register this application's MooseApp and any it depends on
-  StorkApp::registerApps();
+  MoonApp::registerApps();
 
   // This creates dynamic memory that we're responsible for deleting
-  MooseApp * app = AppFactory::createApp("StorkApp", argc, argv);
+  MooseApp * app = AppFactory::createApp("MoonApp", argc, argv);
 
   // Execute the application
   app->run();

unit/Makefile

@@ -31,19 +31,19 @@ ADDITIONAL_LIBS 	:= -L$(CPPUNIT_DIR)/lib -lcppunit
 
 # dep apps
 APPLICATION_DIR    := $(CURRENT_DIR)/..
-APPLICATION_NAME   := stork
+APPLICATION_NAME   := MOON
 include            $(FRAMEWORK_DIR)/app.mk
 
 APPLICATION_DIR    := $(CURRENT_DIR)
-APPLICATION_NAME   := stork-unit
+APPLICATION_NAME   := MOON-unit
 BUILD_EXEC         := yes
 DEP_APPS    ?= $(shell $(FRAMEWORK_DIR)/scripts/find_dep_apps.py $(APPLICATION_NAME))
 include $(FRAMEWORK_DIR)/app.mk
 
-# Find all the STORK unit test source files and include their dependencies.
-stork-unit_srcfiles := $(shell find $(CURRENT_DIR) -name "*.C")
-stork-unit_deps := $(patsubst %.C, %.$(obj-suffix).d, $(stork-unit_srcfiles))
--include $(stork-unit_deps)
+# Find all the MOON unit test source files and include their dependencies.
+MOON-unit_srcfiles := $(shell find $(CURRENT_DIR) -name "*.C")
+MOON-unit_deps := $(patsubst %.C, %.$(obj-suffix).d, $(MOON-unit_srcfiles))
+-include $(MOON-unit_deps)
 
 ###############################################################################
 # Additional special case targets should be added here

unit/run_tests

 #!/bin/bash
 
-APPLICATION_NAME=stork
+APPLICATION_NAME=MOON
 # If $METHOD is not set, use opt
 if [ -z $METHOD ]; then
   export METHOD=opt

unit/src/main.C

@@ -24,7 +24,7 @@
 
 #include "Factory.h"
 #include "AppFactory.h"
-#include "StorkApp.h"
+#include "MoonApp.h"
 
 #include <fstream>
 #include <string>
@@ -35,7 +35,7 @@ int main(int argc, char **argv)
 {
   MooseInit init(argc, argv);
 
-  registerApp(StorkApp);
+  registerApp(MoonApp);
 
   CppUnit::Test *suite = CppUnit::TestFactoryRegistry::getRegistry().makeTest();