[med-svn] [Git][med-team/graphlan][master] 5 commits: Use 2to3 to port to Python3
Andreas Tille
gitlab at salsa.debian.org
Fri Nov 8 12:59:49 GMT 2019
Andreas Tille pushed to branch master at Debian Med / graphlan
Commits:
ebbe13dd by Andreas Tille at 2019-11-08T12:38:47Z
Use 2to3 to port to Python3
- - - - -
c8113616 by Andreas Tille at 2019-11-08T12:39:06Z
debhelper-compat 12
- - - - -
313a3899 by Andreas Tille at 2019-11-08T12:39:11Z
Standards-Version: 4.4.1
- - - - -
38ff1c9a by Andreas Tille at 2019-11-08T12:48:18Z
Supress check that explicitly enforces Python2
- - - - -
43c74efa by Andreas Tille at 2019-11-08T12:49:08Z
Python3 in packaging
- - - - -
6 changed files:
- debian/changelog
- − debian/compat
- debian/control
- + debian/patches/2to3.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+graphlan (1.1.3-2) UNRELEASED; urgency=medium
+
+ * Use 2to3 to port to Python3
+ Closes: #936652
+ * debhelper-compat 12
+ * Standards-Version: 4.4.1
+
+ -- Andreas Tille <tille at debian.org> Fri, 08 Nov 2019 13:37:28 +0100
+
graphlan (1.1.3-1) unstable; urgency=medium
* New upstream version
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -3,21 +3,21 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.
Uploaders: Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
- python-all,
+Build-Depends: debhelper-compat (= 12),
+ python3-all,
dh-python
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
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
Architecture: all
-Depends: ${python:Depends},
+Depends: ${python3:Depends},
${misc:Depends},
- python-biopython,
- python-numpy,
- python-matplotlib
+ python3-biopython,
+ python3-numpy,
+ python3-matplotlib
Description: circular representations of taxonomic and phylogenetic trees
GraPhlAn is a software tool for producing high-quality circular
representations of taxonomic and phylogenetic trees. It focuses on
=====================================
debian/patches/2to3.patch
=====================================
@@ -0,0 +1,233 @@
+Description: Use 2to3 to port to Python3
+Bug-Debian: https://bugs.debian.org/936652
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Fri, 08 Nov 2019 13:37:28 +0100
+
+--- a/examples/hmp_metahit_functional/merge-humann.py
++++ b/examples/hmp_metahit_functional/merge-humann.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ from sys import argv
+
+@@ -13,8 +13,8 @@ if __name__ == "__main__":
+ argv[5]
+ argv[6]
+ except:
+- print "Usage error!"
+- print "$ python merge_humann.py <in_hmp> <skip_rows_hmp> <in_metahit> <skip_rows_metahit> <metahit_map> <out_file>"
++ print("Usage error!")
++ print("$ python3 merge_humann.py <in_hmp> <skip_rows_hmp> <in_metahit> <skip_rows_metahit> <metahit_map> <out_file>")
+ exit(1)
+
+ infile1 = str(argv[1])
+--- a/graphlan.py
++++ b/graphlan.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #------------------------------------------------------------------------------
+ # NAME: graphlan.py
+@@ -20,9 +20,9 @@ __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]))
++#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
+--- a/graphlan_annotate.py
++++ b/graphlan_annotate.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+
+ #------------------------------------------------------------------------------
+ # NAME: graphlan_annotate.py
+@@ -17,9 +17,9 @@ __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]))
++#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
+--- a/src/graphlan_lib.py
++++ b/src/graphlan_lib.py
+@@ -1,8 +1,8 @@
+ 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]))
++#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 Bio import Phylo
+ from Bio.Phylo import PhyloXML
+@@ -25,7 +25,7 @@ import matplotlib
+ matplotlib.use('Agg')
+ matplotlib.rcParams['svg.fonttype'] = 'none'
+ from pylab import *
+-from pyphlan import PpaTree
++from .pyphlan import PpaTree
+
+
+ clade_attr = ( ( 'clade_marker_size', float, 20.0 ),
+@@ -255,17 +255,17 @@ class CircTree(PpaTree):
+ clade.properties = []
+
+ if 'class' in props[n]:
+- for k,v in classes[props[n]['class']].items():
++ for k,v in list(classes[props[n]['class']].items()):
+ lprop[k] = v
+- for k,v in props[n].items():
++ for k,v in list(props[n].items()):
+ if type(v) == dict:
+- for kk,vv in v.items():
++ for kk,vv in list(v.items()):
+ lprop["__".join(['ext',str(kk),k])] = vv
+ else:
+ lprop[k] = v
+
+ cp = []
+- for k,v in lprop.items():
++ for k,v in list(lprop.items()):
+ value = v
+ if k == 'annotation':
+ if v.count(":"):
+@@ -278,7 +278,7 @@ class CircTree(PpaTree):
+
+ if kkk == '*':
+ if fn is None:
+- kkk = rkeys_gen.next()
++ kkk = next(rkeys_gen)
+ else:
+ kkk = fn
+ fn = kkk
+@@ -297,7 +297,7 @@ class CircTree(PpaTree):
+ _rec_annotate_( c, rkeys_gen, npath )
+
+ all_keys = set()
+- for p in props.values():
++ for p in list(props.values()):
+ if 'annotation' in p and p['annotation'].count(":"):
+ all_keys.add( p['annotation'].split(":")[0] )
+ rkeys = random_keys(all_keys)
+@@ -305,9 +305,9 @@ class CircTree(PpaTree):
+
+ _rec_annotate_( self.tree.root, rkeys, "" )
+ tgprop = []
+- for k,v in gprops.items():
++ for k,v in list(gprops.items()):
+ if type(v) == dict:
+- for kk,vv in v.items():
++ for kk,vv in list(v.items()):
+ if k in int_attr_d:
+ pn = "__".join(['int',str(kk),k])
+ else:
+@@ -320,7 +320,7 @@ class CircTree(PpaTree):
+ ref='A:1', applies_to='phylogeny',
+ datatype='xsd:string' )]
+
+- ckeys = sorted([c for c in classes.keys()
++ ckeys = sorted([c for c in list(classes.keys())
+ if not ('label' in classes[c] and classes[c]['label'] in ['none','None'])])
+ if ckeys:
+ newidrefs = ['leg_keys']
+@@ -619,7 +619,7 @@ class CircTree(PpaTree):
+ if not l in self.int_levs:
+ self.int_levs[l] = {}
+ self.int_levs[l][k] = v
+- for k,v in self.ext_levs.items():
++ for k,v in list(self.ext_levs.items()):
+ for att,typ,default in ext_attr:
+ if att in v:
+ self.ext_levs[k][att] = typ(self.ext_levs[k][att])
+@@ -645,7 +645,7 @@ class CircTree(PpaTree):
+
+ self._ext_max_height = {}
+ if 'ring_height' in gprops:
+- for i,v in gprops['ring_height'].items():
++ for i,v in list(gprops['ring_height'].items()):
+ self._ext_max_height[i] = float(v) if float(v) >= 0.0 else 0.0
+ for lev,attr,val in eggrops:
+ if attr == 'ring_height':
+@@ -902,7 +902,7 @@ class CircTree(PpaTree):
+
+ def _init_attr( self ):
+ self._depths = dict([(c.name,dist) for c,dist in
+- self.tree.depths(self.ignore_branch_len).items()])
++ list(self.tree.depths(self.ignore_branch_len).items())])
+ self._max_depth = max(self._depths.values())
+ if not self._max_depth:
+ self._max_depth = 1.0
+@@ -993,7 +993,7 @@ class CircTree(PpaTree):
+
+ wbar = ax.bar(self._wing_thetas, self._wing_radii, width=self._wing_widths, bottom=self._wing_bottoms, alpha=self.annotation_background_alpha, color=self._wing_colors, edgecolor=self._wing_colors, align='edge')
+
+- for lev,d in self.int_levs.items():
++ for lev,d in list(self.int_levs.items()):
+ if 'internal_label' in d:
+ start_rot = ( self.internal_labels_rotation
+ if self.internal_labels_rotation
+@@ -1057,11 +1057,11 @@ class CircTree(PpaTree):
+ # ax.add_line(l)
+
+ offset = self._wing_tot_offset + self.annotation_background_offset
+- for l,v in self.ext_levs.items():
++ for l,v in list(self.ext_levs.items()):
+ for p in ['ring_internal_separator_thickness','ring_external_separator_thickness']:
+ if p in v and float(v[p]) > 0.0:
+- if l not in self._ext_bottoms.keys():
+- print('[e] External ring #'+str(l), 'defined, but not used. Please check your annotations file')
++ if l not in list(self._ext_bottoms.keys()):
++ print(('[e] External ring #'+str(l), 'defined, but not used. Please check your annotations file'))
+ continue
+
+ bot = offset + self._ext_bottoms[l]
+--- a/src/pyphlan.py
++++ b/src/pyphlan.py
+@@ -421,9 +421,9 @@ class PpaTree:
+ if markerness < markerness_th:
+ continue
+ cl2markers[gid].append( line )
+- for k,v in cl2markers.items():
++ for k,v in list(cl2markers.items()):
+ cl2markers[k] = sorted(v,key=lambda x:float(x[2]),reverse=True)[:max_markers]
+- return cl2markers.values()
++ return list(cl2markers.values())
+
+ def get_c2t( self ):
+ tc2t = {}
+@@ -503,7 +503,7 @@ class PpaTree:
+ def tax_precision( self, c2t_f, strategy = 'lca' ):
+ c2t = self.read_tax_clades( c2t_f )
+ res = []
+- for c,terms in c2t.items():
++ for c,terms in list(c2t.items()):
+ lca = self.lca( terms )
+ num = partial_branch_length(lca,terms)
+ den = lca.total_branch_length()
+@@ -514,7 +514,7 @@ class PpaTree:
+ def tax_recall( self, c2t_f ):
+ c2t = self.read_tax_clades( c2t_f )
+ res = []
+- for c,terms in c2t.items():
++ for c,terms in list(c2t.items()):
+ lca = self.lca( terms )
+ ltcs = self.ltcs( terms )
+ lca_terms = set(lca.get_terminals())
=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+2to3.patch
=====================================
debian/rules
=====================================
@@ -5,7 +5,7 @@ export LC_ALL=C.UTF-8
%:
- dh $@ --with python2
+ dh $@ --with python3
override_dh_installexamples:
dh_installexamples
View it on GitLab: https://salsa.debian.org/med-team/graphlan/compare/bc2c069e756fb55189f1197be1e763fcdd377d7b...43c74efa7c2b660e514d234f98bc585805877148
--
View it on GitLab: https://salsa.debian.org/med-team/graphlan/compare/bc2c069e756fb55189f1197be1e763fcdd377d7b...43c74efa7c2b660e514d234f98bc585805877148
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