0.130 release

nesoni/CHANGES

@@ -1,4 +1,6 @@
 
+0.130 - grace.status returns old status, bam reader restores old status after finishing
+
 0.129 - slight tweak to error reporting
         don't require SplitsTree to be installed
 

nesoni/__init__.py

@@ -1,4 +1,4 @@
-VERSION='0.129'
+VERSION='0.130'
 #^ Note: this first line is read by the setup.py script to get the version
 
 import sys

nesoni/grace.py

@@ -81,14 +81,8 @@ def __exit__(self):
 def status(string):
     """ Display a status string. """
     from nesoni import legion
-    legion.coordinator().set_status( legion.process_identity(), string )
-    #if sys.stderr.isatty():
-    #    #Show in terminal title
-    #    sys.stderr.write('\x1b]2;'+string+'\x07')
-    #    sys.stderr.flush()
-    #    
-    #    #sys.stderr.write('\r\x1b[K\x1b[34m' + string + '\x1b[m\r')
-    #    #sys.stderr.flush()
+    return legion.coordinator().set_status( legion.process_identity(), string )
+
 
 def load(module_name):
     status('Loading')

nesoni/legion.py

@@ -287,6 +287,7 @@ def acquire_core(self):
         self.trade_cores(0,1)
 
     def set_status(self, identity, value):
+        old = self.statuses.get(identity,"")
         if value:
             self.statuses[identity] = value
         elif identity in self.statuses:
@@ -305,6 +306,8 @@ def set_status(self, identity, value):
             #Show in terminal title
             sys.stderr.write('\x1b]2;'+status+'\x07')
             sys.stderr.flush()
+
+        return old
 
     def job(self, func, *args, **kwargs):
         number = self.set_mail((func,args,kwargs))
@@ -870,11 +873,11 @@ def _make_inner(action):
         if LOCAL.abort_make and not selection.matches(LOCAL.do_selection, [action.shell_name()]):
             raise grace.Error('%s would be run. Stopping here.' % action.ident())
 
-        grace.status(action.ident())
+        old_status = grace.status(action.shell_name())
         try:
             _run_and_save_state(action, timestamp)
         finally:
-            grace.status('')
+            grace.status(old_status)
     finally:
         if cores > 1:
             coordinator().trade_cores(cores, 1)

nesoni/nesoni-r/R/nesoni_version.R

@@ -1,2 +1,2 @@
 #Autogenerated
-nesoni_version <- function() { '0.128' }
+nesoni_version <- function() { '0.129' }

nesoni/sam.py

@@ -224,6 +224,8 @@ def next(self):
 
 def bam_iter_fragments(filename, status_text='Processing'):
     reader = Bam_reader(filename)
+
+    old_status = grace.status(status_text)
 
     n = 0
     n_ambiguous = 0
@@ -280,7 +282,7 @@ def bam_iter_fragments(filename, status_text='Processing'):
 
         yield read_name, pairs + unpaired, unmapped
 
-    grace.status('')
+    grace.status(old_status)
     if n_ambiguous:
         print >> sys.stderr 
         print >> sys.stderr, 'The alignment pairing was unclear %s times, and alignments were paired arbitrarily.' % grace.pretty_number(n_ambiguous)