* Trees now have names to make it easier to identify

* Clearer error messages when parsing trees
* A number of minor bug fixes
* Fixes to import and export trees
* Fixes to the mac port to allow command line interaction

Author: Jon Hill

debian/changelog

@@ -1,4 +1,14 @@
-supertree-toolkit (12) precise; urgency=low
+supertree-toolkit (2.13) precise; urgency=low
+
+  * Trees now have names to make it easier to identify
+  * Clearer error messages when parsing trees
+  * A number of minor bug fixes
+  * Fixes to import and export trees
+  * Fixes to the mac port to allow command line interaction
+
+ -- Jon Hill <[email protected]>  Wed, 03 Dec 2014 08:14:13 +0000
+
+supertree-toolkit (2.12) precise; urgency=low
 
   * Bug fixes to substitutions
   * New option on subs to match taxa at genera level

doc/gui.rst

@@ -93,8 +93,9 @@ JabRef, but your mileage with other reference managers may vary.
 Once you have a Bibtex file you can import it using the File->Import from
 bibliography and import your file. This should import all the papers in that
 bibtex file and create a source for each one (Fig. :num:`#img-stk-source`). These
-are then named in a sensible way and sorted alphabetically. You can then start
-editing your data.
+are then named in a sensible way and sorted alphabetically. The standard source
+name is the author followed by year. Once the sources are created, 
+you can then start editing your data.
 
 .. _img-stk-source:
 
@@ -122,7 +123,9 @@ button will then appear in the status bar, in the lower left of the GUI (Fig.
 
     The import tree button. Click to import a tree into a source.
 
-Once done, your tree string will appear in the data panel.
+Once done, your tree string will appear in the data panel. This will also name the tree in the STK. The names
+follow a standard pattern of "Source_name_d" where d is a number starting from 1. You can manually
+edit the tree name if you wish. 
 
 .. warning:: Avoid non-standard characters in taxa names. Your names *must* not contain commas, 
     parentheses, colons, asterisks, hyphens, slashes or percentage signs (percentage signs are allowed for non-monophyletic taxa - see later).
@@ -192,8 +195,8 @@ number of trees in the dataset, the taxa list, character list, and years (Fig.
 required. This can be used to **carefully** check the taxa list for
 user errors, for example
 
-.. note:: Incomplete data (with blue elements) may not produce a data summary.
-
+.. note:: Incomplete data (with blue elements) may not produce a sensible data summary.
+    
 .. note:: See the tutorial for more information on how nomenclature and taxonomy should be standardised.
 
 .. _img-stk-data-summary:
@@ -208,8 +211,12 @@ user errors, for example
 
 Two other functions can also be useful to check the data (and prevent errors
 when using other functions). *Clean Data* removes non-informative trees.
+
+.. warning:: Do not use Clean Data on partial datasets. It will delete empty sources
+    for example, which may not be what you wish to happen.
+
 *Standardise source names* ensures all source names are unique and will re-sort
-the sources alphabetically.
+the sources alphabetically. It will also standardise all tree names.
 
 Processing data
 ---------------
@@ -258,7 +265,10 @@ the level of overlap (default is 2), which is the number of taxa trees should
 have in common to be considered connected. The two graphic check boxes will show
 a window with the result as a graphic. There are two options; the normal graphic
 (Fig :num:`#img-stk-data-overlap-simple`) and detailed graphic (Fig
-:num:`#img-stk-data-overlap-detailed`). 
+:num:`#img-stk-data-overlap-detailed`). All graphics show each tree or group
+of trees as a circle, labelled by a number. The window also contains a list which
+maps the number to a tree name, allowing you to delete any trees that don't
+sufficiently overlap.
 
 .. _img-stk-data-overlap-gui:
 
@@ -364,7 +374,7 @@ used. This creates a number of trees per source tree, each with a different
 combination of the non-monophyletic taxa. Note that this
 produces a tree file containing the unique trees only or a matrix for each
 source tree in the dataset. The output are stored in the given format, with each
-tree permuted stored in a seperate directory, given by the tree name (e.g. 
+tree permuted stored in a separate directory, given by the tree name (e.g. 
 Hill_etal_2001_1). The filename given is used, making it easy to script the 
 creation of the mini-supertrees.
 

macosx/stk.bundle

@@ -50,16 +50,16 @@
 
   <!-- Add STK data to bundle -->
 
-  <data dest="${bundle}/Contents/share/schemata/stk/phylo_storage.rng">
+  <data dest="${bundle}/Contents/schema/phylo_storage.rng">
     ${project}/../schema/phylo_storage.rng
   </data>
-  <data dest="${bundle}/Contents/share/schemata/stk/analyses.rng">
+  <data dest="${bundle}/Contents/schema/analyses.rng">
     ${project}/../schema/analyses.rng
   </data>  
-  <data dest="${bundle}/Contents/share/schemata/stk/characters.rng">
+  <data dest="${bundle}/Contents/schema/characters.rng">
     ${project}/../schema/characters.rng
   </data>  
-  <data dest="${bundle}/Contents/Resources">
+  <data dest="${bundle}/Contents/">
     ${project}/../stk_gui/gui/gui.glade
   </data>
   <data dest="${bundle}/Contents/Resources/lib/python2.7/site-packages/plugins">

macosx/stk.sh

@@ -62,4 +62,4 @@ fi
 
 #Note that we're calling $PYTHON here to override the version in
 #pygtk-demo's shebang.
-$EXEC $PYTHON "$bundle_contents/MacOS/stk-bin"
+$EXEC $PYTHON "$bundle_contents/MacOS/stk-bin" $@

macosx/stk_cli

@@ -63,4 +63,4 @@ fi
 
 #Note that we're calling $PYTHON here to override the version in
 #pygtk-demo's shebang.
-$EXEC $PYTHON "$bundle_res/bin/stk_cli"
+$EXEC $PYTHON "$bundle_res/bin/stk_cli" $@

schema/phylo_storage.rnc

@@ -67,7 +67,7 @@ source=
     },
     ## This is a source tree and associated meta-data
     element source_tree {
-        attribute name { string }+,
+        attribute name { string },
         element tree {
             ## The tree string. This is a Newick/Nexus formatted tree string. You can import
             ## a file using the "Import tree" button below or copy 
@@ -391,7 +391,7 @@ software=
         attribute name {string},
         attribute version {string},
         comment
-    },
+    }
 )
 
 # Any value in the xml file can be accompanied by a comment

schema/phylo_storage.rng

@@ -61,7 +61,7 @@ data to the file.</a:documentation>
           <ref name="person"/>
           <optional>
             <element name="institution">
-              <data type="string" datatypeLibrary=""/>
+              <ref name="anystring"/>
             </element>
           </optional>
         </element>
@@ -77,11 +77,9 @@ to read in a bibtex file and populate all your bibliographic data</a:documentati
       <oneOrMore>
         <element name="source_tree">
           <a:documentation>This is a source tree and associated meta-data</a:documentation>
-          <oneOrMore>
-            <attribute name="name">
-              <data type="string" datatypeLibrary=""/>
-            </attribute>
-          </oneOrMore>
+          <attribute name="name">
+            <data type="string" datatypeLibrary=""/>
+          </attribute>
           <element name="tree">
             <element name="tree_string">
               <a:documentation>The tree string. This is a Newick/Nexus formatted tree string. You can import
@@ -107,7 +105,6 @@ paste a string. Tested using Meqsuite, Treeview, Dendroscope to generate trees.<
 the this tree?</a:documentation>
                 </ref>
               </oneOrMore>
-              <ref name="comment"/>
               <optional>
                 <ref name="software">
                   <a:documentation>Which software was used?</a:documentation>
@@ -215,7 +212,6 @@ If fossil and extant, which taxa are fossil taxa.</a:documentation>
               </element>
             </choice>
           </element>
-          <ref name="comment"/>
           <element name="character_data">
             <a:documentation>This stores the character data used to construct the 
 source tree(s).</a:documentation>
@@ -228,6 +224,7 @@ source tree(s).</a:documentation>
           </ref>
         </element>
       </oneOrMore>
+      <ref name="comment"/>
     </group>
   </define>
   <define name="publication">
@@ -522,8 +519,8 @@ source tree(s).</a:documentation>
       <attribute name="version">
         <data type="string" datatypeLibrary=""/>
       </attribute>
+      <ref name="comment"/>
     </element>
-    <ref name="comment"/>
   </define>
   <!--
     Any value in the xml file can be accompanied by a comment

stk/bzr_version.py

@@ -5,11 +5,11 @@
 """
 
 version_info = {'branch_nick': u'release',
- 'build_date': '2014-06-18 10:07:08 +0100',
+ 'build_date': '2014-12-03 08:18:17 +0000',
  'clean': None,
- 'date': '2014-02-27 09:36:09 +0000',
- 'revision_id': '[email protected]20140227093609-23qpyn96mjvojvk9',
- 'revno': '12'}
+ 'date': '2014-06-18 10:07:32 +0100',
+ 'revision_id': '[email protected]20140618090732-12x2gza0ljjgumxg',
+ 'revno': '13'}
 
 revisions = {}
 

stk/scripts/create_colours_itol.py

@@ -39,7 +39,7 @@ def main():
             )
     parser.add_argument(
             '--level',
-            choices=['Family','Superfamily','Infraorder','Suborder','Order'],
+            choices=['Genus','Family','Superfamily','Infraorder','Suborder','Order'],
             default='Family',
             help="Which taxonomic level to colour at. Note that not all will return data. Family and Order will always work."
             )
@@ -97,6 +97,8 @@ def main():
         index = 5
     elif (level == "Order"):
         index = 6
+    elif (level == "Genus"):
+        index = 1
 
     if (tree):
         tree_data = stk.import_tree(input_file)
@@ -110,7 +112,8 @@ def main():
     else:
         # grab taxa in dataset - ignore if tree
         fileName, fileExtension = os.path.splitext(input_file)
-        if (fileExtension == 'phyml'):
+        if (fileExtension == '.phyml'):
+            print "Parsing PHYML"            
             XML = stk.load_phyml(input_file)
             taxa = stk.get_all_taxa(XML)
         else:
@@ -151,7 +154,7 @@ def main():
             else:
                 f.write(t+",#"+output_colours[taxonomy[tt]]+","+taxonomy[tt]+"\n")
         except KeyError:
-            print "Couldn't find "+tt
+            #print "Couldn't find "+tt
             f.write(t+",#000000\n")
 
     f.close()

stk/stk

@@ -1462,8 +1462,12 @@ def convert_file(args):
                 new_trees['tree_'+str(i)] = t
                 i += 1
             output = supertree_toolkit._amalgamate_trees(new_trees,format=output_format)
+        except TreeParseError as detail:
+            print detail.msg
+            sys.exit(-1)
         except:
-            print "Error saving tree"
+            print "Error converting tree"
+            traceback.print_exc()
             sys.exit(-1)