.hg_archival.txt

 repo: 0fdb21ec3cf53e710d679fbd7768f91510570ae7
-node: edea23ce7c21765cbd9ff601e1f91614241eae81
+node: c1fa530b9bcac13bbccacf8bfafd500536d17b7c
 branch: default
-tag: 1.1
+tag: 1.1.3

.hgignore

@@ -3,4 +3,10 @@ syntax: glob
 *.pyc
 *.DS_Store
 *.log
+examples/ade_pcopri
+examples/neisseriaceae/
+examples/caritro_fig6/
+examples/andrew_crc_cutc/
+examples/nic_erectale/
+examples/rand/
 examples/test/

.hgsubstate

-b2e0ba66718673ea28cb217c8e5dcd8e578fd033 export2graphlan
+c168a100f37e23e2c110849a8d91fac8da49f5bd export2graphlan
 eae40ebc0030c7179baed999c74de412ba696598 pyphlan

.hgtags

@@ -5,3 +5,6 @@ ba9c6f680022333b5b1bf0652748ab2db29e888a 0.9
 eaa3d2e05d74912da0f013bbfbb199764b180f05 0.9.5
 64570f7d4ae33f46ddd360101c13555396a0cab1 0.9.6
 7d483b7d34ccadb30f5c56f82b7aab19a820d1d6 1.0
+edea23ce7c21765cbd9ff601e1f91614241eae81 1.1
+17f32c8d85849d397884564680c145e5b8d28923 1.1.1
+3820c323e3c68d3d9e02bae2aefbc7d179df80bf 1.1.2

debian/changelog

+graphlan (1.1.3-1) unstable; urgency=medium
+
+  * New upstream version
+  * debhelper 11
+  * Point Vcs fields to salsa.debian.org
+  * Standards-Version: 4.2.1
+
+ -- Andreas Tille <tille@debian.org>  Wed, 26 Sep 2018 13:35:33 +0200
+
 graphlan (1.1-3) unstable; urgency=medium
 
   * Moved packaging from SVN to Git

debian/compat

-10
+11

debian/control

@@ -3,12 +3,12 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                python-all,
                dh-python
-Standards-Version: 4.1.1
-Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/graphlan.git
-Vcs-Git: https://anonscm.debian.org/git/debian-med/graphlan.git
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/graphlan
+Vcs-Git: https://salsa.debian.org/med-team/graphlan.git
 Homepage: https://bitbucket.org/nsegata/graphlan/wiki/Home
 
 Package: graphlan

examples/metaref_fams/mr1.a.txt

@@ -69,8 +69,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_shape	1	v
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_shape	1	v
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_shape	1	v
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_shape	1	v
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_shape	1	v
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_shape	1	v
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_shape	1	v
@@ -96,8 +94,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_width	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_width	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_width	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_width	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_width	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_width	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_width	1	0.6
@@ -123,8 +119,6 @@ Bacill.Bacillale.Thermoactinomycetaceae.unclassified	ring_height	1	0.6
 Bacilli.Lactobacillales.Aerococcaceae.Eremococcus	ring_height	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Carnobacterium	ring_height	1	0.6
 Bacilli.Lactobacillales.Carnobacteriaceae.Desemzia	ring_height	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Lactobacillus	ring_height	1	0.6
-Bacilli.Lactobacillales.Lactobacillaceae.Pediococcus	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Finegoldia	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Gallicola	ring_height	1	0.6
 Clostridia.Clostridiales.Incertae_Sedis_XI.Helcococcus	ring_height	1	0.6

graphlan.py

@@ -14,10 +14,16 @@
 #------------------------------------------------------------------------------
 
 __author__ = 'Nicola Segata (nsegata@hsph.harvard.edu)'
-__version__ = '0.9.7'
-__date__ = '21 July 2014'
+__version__ = '1.1.3'
+__date__ = '5 June 2018'
 
 
+import sys
+
+if sys.version_info[0] > 2:
+    raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
+                    .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
+
 from sys import argv
 from argparse import ArgumentParser
 from src.graphlan_lib import CircTree as CTree
@@ -53,6 +59,8 @@ def read_params(args):
     arg('--external_legends', default=False, action='store_true',
         help = "specify whether the two external legends should be put in separate file or keep them "
                "along with the image (default behavior)")
+    arg('--avoid_reordering', default=True, action='store_false',
+        help = "specify whether the tree will be reorder or not (default the tree will be reordered)")
     arg( '-v','--version', action='version', version="GraPhlAn version "+__version__+" ("+__date__+")",
         help="Prints the current GraPhlAn version and exit" )
     return vars(parser.parse_args())
@@ -67,4 +75,5 @@ if __name__ == "__main__":
                out_dpi=args['dpi'],
                out_size=args['size'],
                out_pad=args['pad'],
-                external_legends = args['external_legends'])
+               external_legends=args['external_legends'],
+               reorder_tree=args['avoid_reordering'])

graphlan_annotate.py

@@ -11,10 +11,16 @@
 #------------------------------------------------------------------------------
 
 __author__ = 'Nicola Segata (nsegata@hsph.harvard.edu)'
-__version__ = '0.9'
-__date__ = '22 August 2012'
+__version__ = '1.1.3'
+__date__ = '5 June 2018'
 
 
+import sys
+
+if sys.version_info[0] > 2:
+    raise Exception("GraPhlAn requires Python 2, your current Python version is {}.{}.{}"
+                    .format(sys.version_info[0], sys.version_info[1], sys.version_info[2]))
+
 from sys import argv
 from argparse import ArgumentParser
 from src.graphlan_lib import CircTree as CTree

src/pyphlan.py

@@ -171,7 +171,10 @@ class PpaTree:
         tree.root = BClade()
 
         def add_clade_rec( father, txt_tree ):
-            fl = set([t[0] for t in txt_tree])
+            fl = []
+            for c in [t[0] for t in txt_tree]:
+                if c in fl: continue
+                else: fl.append(c)
             father.clades = []
             for c in fl:
                 nclade = BClade( branch_length = 1.0,
@@ -662,25 +665,34 @@ class PpaTree:
             #self.tree.reroot_at_edge( list(longest)[-1], update_splits=True )
 
 
-    def reorder_tree( self ):
+    def reorder_tree( self, reorder_tree ):
         self._ord_terms = []
-        def reorder_tree_rec( clade ):
+
+
+        def reorder_tree_rec( clade, reorder_tree ):
             if clade.is_terminal():
                 self._ord_terms.append( clade )
                 return clade,clade
+
+            if reorder_tree:
                 clade.clades.sort(key=lambda x:len(x.get_terminals()), reverse = True)
+
             for c in clade.clades:
-                c.fc,c.lc = reorder_tree_rec( c ) 
+                c.fc,c.lc = reorder_tree_rec( c, reorder_tree )
+
             return clade.clades[0].fc,clade.clades[-1].lc
             #clade.fc, clade.lc = clade.clades[0], clade.clades[-1]
 
-        reorder_tree_rec( self.tree.root )
+
+        reorder_tree_rec( self.tree.root, reorder_tree )
         last = None # self._ord_terms[-1]
+
         for c in self._ord_terms:
             c.pc = last
             if last:
                 last.nc = c
             last = c
+
         c.nc = None
         #self._ord_terms[-1].nc = None # self._ord_terms[0]