rest of changes fram lab

documentation/users/manual.bib

@@ -42,11 +42,12 @@ @article{Nylander:2008p471
 	Pmid = {1263122639890197121},
 	Rating = {0},
 	Read = {Yes},
-	Title = {AWTY(are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian {\ldots}},
+	Title = {{AWTY} (are we there yet?): a system for graphical exploration of {MCMC} convergence in {Bayesian} phylogenetics},
 	Uri = {papers://599A4529-B910-4F83-B5ED-A165D6176425/Paper/p1936},
 	Url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/581},
 	Volume = {24},
-	Year = {2008}}
+	Year = {2008},
+	Bdsk-Url-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/24/4/581}}
 
 @article{XieLewisFanKuoChen2010,
 	Author = {Wangang Xie and Paul O. Lewis and Yu Fan and Lynn Kuo and Ming-Hui Chen},

installer/mac/iterm/makeDMG.sh

@@ -30,24 +30,15 @@ then
 	ditto -rsrc "$PHYCAS_ROOT/LICENSE" "phycasimg/LICENSE" || exit
 	ditto -rsrc "README" "phycasimg/README" || exit
 	ditto -rsrc "$PHYCAS_ROOT/documentation/users/manual.pdf" "phycasimg/manual.pdf" || exit
-	ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/basic.py" "phycasimg/tutorial/basic.py" || exit
-	ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/summarize.py" "phycasimg/tutorial/summarize.py" || exit
-	ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/partition.py" "phycasimg/tutorial/partition.py" || exit
-	ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/steppingstone.py" "phycasimg/tutorial/steppingstone.py" || exit
-	ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/polytomy.py" "phycasimg/tutorial/polytomy.py" || exit
-	# mkdir "phycasimg/PhycasTutorial"
-	# mkdir "phycasimg/PhycasTutorial/scripts"
-	# for f in $PHYCAS_ROOT/phycas/Examples/Tutorial/PhycasWHExamples/*nex
-	# do 
-	# 	ditto -rsrc "$f" "phycasimg/PhycasTutorial" || exit
-	# done
-	# for f in $PHYCAS_ROOT/phycas/Examples/Tutorial/PhycasWHExamples/scripts/*py
-	# do 
-	# 	ditto -rsrc "$f" "phycasimg/PhycasTutorial/scripts/" || exit
-	# 	ditto -rsrc "$f" "phycasimg/PhycasTutorial/" || exit
-	# done
-	# ditto -rsrc "$PHYCAS_ROOT/phycas/Examples/Tutorial/phycas_woods_hole_08.pdf" "phycasimg/PhycasTutorial/PhycasTutorial.pdf" || exit
-
+	mkdir "phycasimg/tutorial"
+	mkdir "phycasimg/tutorial/ex1basic"
+	mkdir "phycasimg/tutorial/ex2steppingstone"
+	mkdir "phycasimg/tutorial/ex3-4polytomyPriors"
+	for f in ex1basic/basic.py ex1basic/green.nex ex2steppingstone/murphy29.rag1rag2.nex ex2steppingstone/setUpByCodonPosPartition.py ex2steppingstone/setUpByGeneAndCodonPosPartition.py ex2steppingstone/steppingstone1.py ex2steppingstone/steppingstone2.py ex2steppingstone/steppingstone3.py ex2steppingstone/steppingstoneDoMCMC.py ex2steppingstone/steppingstoneReadData.py ex3-4polytomyPriors/IntExtPrior.py ex3-4polytomyPriors/NoPolytomy.py ex3-4polytomyPriors/Polytomy.py ex3-4polytomyPriors/ShoupLewis.nex
+	do
+		ditto -rsrc "$PHYCAS_ROOT/documentation/users/tutorial/$i" "phycasimg/tutorial/$i" || exit
+	done
+
 	hdiutil create -srcfolder phycasimg $MASTER_DMG
 else
 	echo "PHYCAS_ROOT is not defined as a directory"

installer/mac/iterm/refill_phycas_gui_app.sh

@@ -33,10 +33,28 @@ if test -d Frameworks
 then
 	cp -r Frameworks Phycas.app/Contents/Frameworks
 fi
+if test -z "$TARGETTED_PYTHON_VERSION"
+then
+	echo "TARGETTED_PYTHON_VERSION must be defined to major.minor"
+	exit 1
+fi 
 cp -r "$PHYCAS_ROOT/phycas" Phycas.app/Contents/Resources/ || exit 2
 cp -r ./active_phycas_env.sh Phycas.app/Contents/Resources/ || exit 2
 cp -r ./run_phycas.sh Phycas.app/Contents/Resources/ || exit 2
+
+cat run_phycas.sh | sed -e "s/PYTHONINTERPRETER=python/PYTHONINTERPRETER=python${TARGETTED_PYTHON_VERSION}/" > Phycas.app/Contents/Resources/run_phycas.sh || exit 2
+
 cp  ./startup.py Phycas.app/Contents/Resources/ || exit 2
+
+if test -z $PY_PACKAGES_TO_BUNDLE
+then
+	echo not bundling python extras because PY_PACKAGES_TO_BUNDLE is not set!
+else
+	cp -r $PY_PACKAGES_TO_BUNDLE/setuptools-0.6c11-py2.5.egg Phycas.app/Contents/Resources/ || exit 1
+	cp -r $PY_PACKAGES_TO_BUNDLE/IPython Phycas.app/Contents/Resources/ || exit 1
+fi
+
+
 find  Phycas.app/Contents/Resources/phycas -name .svn -exec rm -rf {} \;
 cat Phycas.app/Contents/Resources/phycas/__init__.py  | sed "s/PHYCAS_SVN_REVISION_NUMBER_HERE/$sv/g" > t
 mv t Phycas.app/Contents/Resources/phycas/__init__.py

phycas/Phycas/MCMCImpl.py

@@ -1197,13 +1197,13 @@ def run(self):
 					# if using working prior with steppingstone sampling, it is now time to 
 					# parameterize the working prior for all updaters so that this working prior
 					# can be used in the sequel
-					self.output('\nWorking prior details:')
+					self.output('\nReference distribution details:')
 					all_updaters = cold_chain.chain_manager.getAllUpdaters() 
 					for u in all_updaters:		# good candidate for moving into C++
 						if not u.isFixed():
 							u.setUseWorkingPrior(True)
 							if u.computesUnivariatePrior() or u.computesMultivariatePrior():
-								self.output('  Finalizing working prior for %s...' % u.getName())
+								self.output('  Finalizing reference distribution for %s...' % u.getName())
 								u.finalizeWorkingPrior()
 								self.output('  %s --> %s' % (u.getName(), u.getWorkingPriorDescr()))
 					self.output()

phycas/Phycas/Partition.py

@@ -132,7 +132,7 @@ def addSubset(self, sites, model_for_sites, name = None):
 		
 		model.type = 'hky'
 		hky = model()
-		partition.addSubset(range(1,100,3), hky, 'first')
+		partition.addSubset(subset(1,100,3), hky, 'first')
 		
 		"""
 		# the index of the new subset is simply the length of self.subset

phycas/Phycas/SS.py

@@ -9,7 +9,7 @@ def __init__(self):
 				   ("xcycles", 0, "The number of extra cycles (above and beyond mcmc.ncycles) that will be spent exploring the posterior (additional posterior cycles help stepping stone analyses formulate an effective reference distribution).", IntArgValidate(min=0)),
 				   ("maxbeta", 1.0, "The first beta value that will be sampled.", FloatArgValidate(min=0.0, max=1.0)),
 				   ("minbeta", 0.0, "The last beta value that will be sampled.", FloatArgValidate(min=0.0, max=1.0)),
-				   ("minsample", 10, "Minimum sample size needed to create a split-specific edge length working prior.", IntArgValidate(min=0)),
+				   ("minsample", 10, "Minimum sample size needed to create a split-specific edge length reference distribution.", IntArgValidate(min=0)),
 				   ("shape1", 1.0, "The first shape parameter of the distribution used to determine the beta values to be sampled. This distribution is, confusingly, a Beta distribution. Thus, if both shape1 and shape2 are set to 1, beta values will be chosen at uniform intervals from minbeta to maxbeta.", FloatArgValidate(greaterthan=0.0)),
 				   ("shape2", 1.0, "The second shape parameter of the distribution used to determine the beta values to be sampled. This distribution is, confusingly, a Beta distribution. Thus, if both shape1 and shape2 are set to 1, beta values will be chosen at uniform intervals from minbeta to maxbeta.", FloatArgValidate(greaterthan=0.0)),
 				)

phycas/Phycas/SumPImpl.py

@@ -662,7 +662,7 @@ def handleFile(self, fn):
 			if headers[1] == 'beta':
 				try:
 					self.marginal_likelihood(headers, lines, burnin)
-				except InvalidNumberOfColumnsError as e:
+				except InvalidNumberOfColumnsError, e:
 					print e
 			else:
 				self.std_summary(headers, lines, burnin)

phycas/Utilities/PhycasCommand.py

@@ -1084,6 +1084,7 @@ def explain(self):
         a = [self.cmd_name]
         a.extend(PhycasTablePrinter._text_wrapper.wrap(self.cmd_descrip))
         o = opts._help_str_list()
+        o.sort()
         h = PhycasTablePrinter.format_help("Attribute", "Explanation")
         if len(o) > 0:
             a.extend(["\nAvailable input options:", h, d])
@@ -1103,6 +1104,7 @@ def current(self):
         d = PhycasTablePrinter.get_help_divider()
         h = PhycasTablePrinter.format_help("Attribute", "Current Value")
         o = opts._current_str_list()
+        o.sort()
         if len(o) > 0:
             a.extend(["\nCurrent %s input settings:" % self.cmd_name , h, d])
             a.extend(o)