version to 0.11.1

Changelog.txt

@@ -1,3 +1,28 @@
+Moa 0.11.1 / 2012-10-14
+==========================
+
+  * lots of (pep8) cleanup
+  * git repositories as templates
+  * reworked templates/providers
+  * new moa.cli for all CLI code
+  * allowing a default title
+  * fixed a few unittests
+  * started using pelican for static website generation - in progress
+  * reworked changelogs & blog messages - now stored in ./doc/*
+  * better openlava actor
+  * Not using os.getcwd - prevent dereferencing of symlinks
+  * uses TTYtter to send tweets
+  * better autogenerated changelog messages
+  * writes exec scripts to ./.moa/tmp now - easier to track
+  * retains title when running moa new
+  * better plugin structure - distinguish between job & system plugins
+  * start drawing images of moa workflows
+  * track versioning
+  * moved `fileset` code to the core
+  * moa mv now works
+  * new argparse structure - better command line interface
+  * remoteLogger logs to mysql
+
 Moa 0.10.15 / 2012-01-30
 ==========================
 
@@ -87,7 +112,7 @@ Moa 0.10.10 / 2011-05-10
 ==========================
 
   * jinja2 version of the ncbi template
-  * recursively defined variables are adapted if they appear to be 
+  * recursively defined variables are adapted if they appear to be
     a relative path
   * rearranged plugin management
   * many small fixes improving recursive & multithreaded operation
@@ -125,7 +150,7 @@ Moa 0.10.7 / 2011-04-27
 
   * fixed a bug confusing the ~/.moa config dir with a proper moa job
 
-Moa 0.10.6 / 2011-04-27 
+Moa 0.10.6 / 2011-04-27
 =======================
 
   * debian pacakaging is deprecated

VERSION

@@ -1 +1 @@
-0.11.0
+0.11.1

bin/moa_template_setup

@@ -62,7 +62,8 @@ def process_dir():
     else:
         print "README.md exists - use '-f' to overwrite"
 
-    os.system('git add README.md COPYING')
+    os.system('git add -f README.md COPYING')
+    os.system('git add -f template *.jinja2')
 
     print "possible commands that might need to be executed"
     print "writing README.md"

lib/python/Yaco/__init__.py

@@ -33,7 +33,7 @@
     >>> x = Yaco()
     >>> x.a.b.c.d = 1
     >>> assert(x.a.b.c.d == 1)
-    
+
 works - `a`, `b` and `c` are assumed to be `Yaco` dictionaries and d
 is give value `1`. This makes populating data structures easy.
 
@@ -67,6 +67,7 @@
 import yaml
 import pprint
 
+
 class Yaco(dict):
     """
     Rather loosely based on http://code.activestate.com/recipes/473786/ (r1)
@@ -78,13 +79,13 @@ class Yaco(dict):
     >>> v= Yaco({'a':1})
     >>> assert(v.a == 1)
     >>> assert(v['a'] == 1)
-    
+
     """
-    
+
     def __init__(self, data={}):
         """
         Constructor
-        
+
         :param data: data to initialize the Yaco structure with
         :type data: dict
         """
@@ -96,7 +97,7 @@ def __init__(self, data={}):
     def __str__(self):
         """
         Map the structure to a string
-        
+
         >>> v= Yaco({'a':1})
         >>> assert(str(v.a) == '1')
         """
@@ -105,7 +106,7 @@ def __str__(self):
     def __setattr__(self, key, value):
         """
         Set the value of a key
-        
+
         >>> v= Yaco()
         >>> v.a = 18
         >>> assert(v.a == 18)
@@ -114,7 +115,7 @@ def __setattr__(self, key, value):
         >>> assert(v.a == 72)
 
         >>> v.a = {'b' : 5}
-        >>> assert(v.a.b == 5)        
+        >>> assert(v.a.b == 5)
 
         >>> v.a = {'c' : {'d' : 19}}
         >>> assert(v.a.b == 5)
@@ -152,15 +153,15 @@ def __setattr__(self, key, value):
             super(Yaco, self).__setitem__(key, new_value)
         else:
             super(Yaco, self).__setitem__(key, value)
-     
+
     def has_key(self, key):
         rv = super(Yaco, self).has_key(key)
         return rv
 
     def __getattr__(self, key):
         """
         >>> v= Yaco()
-        >>> v.a = 18       
+        >>> v.a = 18
         >>> assert(v.a == 18)
         >>> assert(isinstance(v.a, int))
         """
@@ -173,7 +174,7 @@ def __getattr__(self, key):
             rv = Yaco()
             super(Yaco, self).__setitem__(key, rv)
             return rv
-        
+
     def __delitem__(self, name):
         return super(Yaco, self).__delitem__(name)
 
@@ -182,7 +183,7 @@ def simple(self):
         """
         return a simplified representation of this
         Yaco struct - remove Yaco from the equation - and
-        all object reference. Leave only bool, float, str, 
+        all object reference. Leave only bool, float, str,
         lists, tuples and dicts
 
         >>> x = Yaco()
@@ -208,7 +209,7 @@ def _returnSimple(item):
                 return str(item)
 
         return _returnSimple(self)
-            
+
     def _list_parser(self, old_list):
         """
         Recursively parse a list & replace all dicts with Yaco objects
@@ -231,7 +232,7 @@ def update(self, data):
         >>> assert(v.a[3][1].b == 12)
 
         """
-        if not data: return 
+        if not data: return
         for key, value in data.items():
             #if isinstance(value, Yaco):
             #    raise Exception("Wow - updating with a Yaco - "+
@@ -244,7 +245,7 @@ def update(self, data):
                 else:
                     super(Yaco, self).__setitem__(key, Yaco(value))
             elif isinstance(value, list):
-                #parse the list to see if there are dicts - which need to be translated to Yaco objects                
+                #parse the list to see if there are dicts - which need to be translated to Yaco objects
                 new_value = self._list_parser(value)
                 super(Yaco, self).__setitem__(key, new_value)
             else:
@@ -256,7 +257,7 @@ def update(self, data):
     def copy(self):
         ch = Yaco(self)
         return ch
-    
+
     def load(self, from_file):
         """
         Load this dict from_file
@@ -280,7 +281,7 @@ def pretty(self):
         Return data as a pprint.pformatted string
         """
         return pprint.pformat(self.get_data())
-    
+
     def get_data(self):
         """
         Prepare & parse data for export
@@ -299,7 +300,7 @@ def get_data(self):
         >>> assert(d.has_key('a') == True)
         >>> assert(d.has_key('b') == False)
         >>> assert(d.has_key('_c') == False)
-        
+
         """
         data = {}
         _priv = self.get('_private', [])
@@ -313,17 +314,17 @@ def get_data(self):
                 val = val.get_data()
             data[k] = val
         return data
-                 
+
     def save(self, to_file, doNotSave=[]):
         """
-        
-        """        
+
+        """
         with open(to_file, 'w') as F:
             data = self.get_data()
             for k in data.keys():
                 if k in doNotSave:
                     del data[k]
-            
+
             F.write(yaml.dump(data, default_flow_style=False))
 
 if __name__ == "__main__":

lib/python/moa/resources.py

@@ -1,11 +1,11 @@
 #!/usr/bin/env python
 # Copyright 2009-2011 Mark Fiers
 # The New Zealand Institute for Plant & Food Research
-# 
+#
 # This file is part of Moa - http://github.com/mfiers/Moa
-# 
+#
 # Licensed under the GPL license (see 'COPYING')
-# 
+#
 """
 moa.resources
 -------------
@@ -25,8 +25,9 @@ def resourceExists(what):
         __name__, os.path.join('..', what)) \
         or \
         pkg_resources.resource_exists(
-        __name__, os.path.join('..', '..', '..', what))
-
+            __name__, os.path.join('..', '..', '..', what))
+
+
 def getResource(what):
     """
     Gets a data file from the moa package.
@@ -35,20 +36,21 @@ def getResource(what):
     either three dirs up, or only one. This depends on if this a
     pypi (one dir up) package or the git package (three dirs up)
     """
-    
+
     try:
         res = pkg_resources.resource_string(__name__, os.path.join('..', what))
     except IOError:
-        #this is the git-package structure - bit inconvenient really
+        #this seems to be the package structure - bit inconvenient really
         res = pkg_resources.resource_string(
             __name__, os.path.join('..','..','..', what))
     return res
 
+
 def listResource(what):
     """
     List a directory
     """
-    
+
     if pkg_resources.resource_isdir(__name__, os.path.join('..', what)):
         what = os.path.join('..', what)
     else:

lib/python/moa/sysConf.py

@@ -1,10 +1,10 @@
 # Copyright 2009-2011 Mark Fiers
 # The New Zealand Institute for Plant & Food Research
-# 
+#
 # This file is part of Moa - http://github.com/mfiers/Moa
-# 
+#
 # Licensed under the GPL license (see 'COPYING')
-# 
+#
 """
 moa.sysConf
 -----------
@@ -16,42 +16,46 @@
 import os
 
 import Yaco
- 
+
 import moa.logger as l
 import moa.resources
 import moa.plugin
 
 sysConf = None
 
 USERCONFIGFILE = os.path.join(os.path.expanduser('~'),
-                          '.config', 'moa', 'config')
+                              '.config', 'moa', 'config')
+
 
 class SysConf(Yaco.Yaco):
 
-
     def __init__(self):
-
-        super(SysConf, self).__init__(moa.resources.getResource('etc/config'))
+
+        if os.path.exists('/etc/moa/config'):
+            with open('/etc/moa/config') as F:
+                super(SysConf, self).__init__(F.read())
+        else:
+            #try the local package
+            super(SysConf, self).__init__(
+                moa.resources.getResource('etc/config'))
 
         l.debug("Loading system config: %s" % USERCONFIGFILE)
         if os.path.exists(USERCONFIGFILE):
             self.load(USERCONFIGFILE)
-            
+
         #assign a runId
         runid = '.moa/last_run_id'
         if os.path.exists(runid):
             lri = open(runid).read().strip()
         else:
             lri = 1
-
 
-
     def getVersion(self):
         """
         Return the version number of this Moa instance
         """
         return moa.resources.getResource('VERSION').strip()
-
 
-if sysConf == None:
+
+if sysConf is None:
     sysConf = SysConf()