PKG-INFO

 Metadata-Version: 1.1
 Name: OBITools
-Version: 1.2.12
+Version: 1.2.13
 Summary: Scripts and library for sequence analysis
 Home-page: http://metabarcoding.org/obitools
 Author: Eric Coissac

debian/changelog

+obitools (1.2.13+dfsg-1) unstable; urgency=medium
+
+  * Team upload.
+  * New upstream version
+  * Created with routine-update script
+  * debhelper-compat 12
+  * Standards-Version: 4.4.0
+  * Build-Depends: s/python-sphinx/python3-sphinx/
+
+ -- Steffen Moeller <moeller@debian.org>  Sat, 27 Jul 2019 13:11:02 +0200
+
 obitools (1.2.12+dfsg-2) unstable; urgency=medium
 
   * Drop ecoPCR.1.gz and ecofind.1 from package

debian/compat

-12

debian/control

@@ -4,15 +4,15 @@ Uploaders: Olivier Sallou <osallou@debian.org>,
            Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~),
+Build-Depends: debhelper-compat (= 12),
                dh-python,
                python-dev,
-               python-sphinx,
+               python3-sphinx,
                cython,
                ipython,
                python-wheel,
                python-virtualenv
-Standards-Version: 4.3.0
+Standards-Version: 4.4.0
 Vcs-Browser: https://salsa.debian.org/med-team/obitools
 Vcs-Git: https://salsa.debian.org/med-team/obitools.git
 Homepage: https://pypi.python.org/pypi/OBITools

distutils.ext/obidistutils/command/build_sphinx.py

@@ -13,10 +13,6 @@ import sys
 
 try:
     from sphinx.setup_command import BuildDoc as ori_build_sphinx
-except ImportError:
-    if not is_serenity() and install_requirements():
-        log.info("Restarting installation with all dependencies ok")
-        rerun_with_anothe_python(os.path.realpath(sys.executable))
     
     class build_sphinx(ori_build_sphinx):
         '''
@@ -36,3 +32,10 @@ class build_sphinx(ori_build_sphinx):
             self.finalize_options()
             ori_build_sphinx.run(self)
 
+except ImportError:
+    if not is_serenity() and install_requirements():
+        log.info("Restarting installation with all dependencies ok")
+        rerun_with_anothe_python(os.path.realpath(sys.executable))
+        
+    
+    
\ No newline at end of file

requirements.txt

 --extra-index-url https://pypi.python.org/simple/
 Cython>=0.24
-Sphinx>=1.2.0
+Sphinx<2.0
 wheel>=0.24.0
 virtualenv>=1.11.0
 ipython<6.0

setup.py

@@ -19,7 +19,7 @@ from os import path
 
 
 PACKAGE = "OBITools"
-VERSION = "1.2.12"
+VERSION = "1.2.13"
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
 URL     = 'http://metabarcoding.org/obitools'

src/obiconvert.py

@@ -47,7 +47,7 @@ if __name__ == '__main__':
             try:
                 writer(entry)
             except:
-                print >>stderr,"Skip writing of sequence : %s" % entry.id
+                print >>stderr,"Skipping an entry"
         else:
             writer(entry)
             

src/obitaxonomy.py

@@ -331,7 +331,7 @@ if __name__ == '__main__':
         
     for t in options.newspecies:
         genus,species = t.split(" ",1)
-        parent = options.taxonomy.findTaxonByName(genus)
+        parent = options.taxonomy.findTaxonByName(genus)[0]
         taxid = options.taxonomy.addLocalTaxon(t,'species',parent[0],options.taxashift)
         taxon = options.taxonomy.findTaxonByTaxid(taxid)
         parent= options.taxonomy._taxonomy[taxon[2]]

src/obitools/format/sequence/__init__.py

@@ -14,7 +14,6 @@ def skipOnErrorIterator(seqIterator):
                 seq = si.next()
                 yield seq
             except Exception,e:
-                print >>sys.stderr,"coucou"
                 if isinstance(e,StopIteration):
                     raise e
                 else:

src/obitools/seqdb/embl/parser.py

@@ -30,19 +30,23 @@ def __emblparser(text):
         ac     = acs[0]
         acs    = acs[1:]
         
-        
         de     = _deMatcher.search(header).group()
         de     = _cleanDe.sub(' ',de).strip().strip('.')
-    except AttributeError,e:
-        print >>sys.stderr,'======================================================='
-        print >>sys.stderr,text
-        print >>sys.stderr,'======================================================='
-        raise e
+    except Exception as e:
+        print>>sys.stderr, "\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")"
+        # Do not raise any Exception if you need the possibility to resume the generator
+        # (Python generators can't resume after any exception is raised)
+        return None
     
     return (ac,seq,de,header,ft,acs)
 
+
 def emblParser(text):
-    return embl.EmblSequence(*__emblparser(text))
+    parsed_text = __emblparser(text)
+    if parsed_text is not None:
+        return embl.EmblSequence(*parsed_text)
+    else:
+        return None
     
     
 def emblIterator(file):

src/obitools/seqdb/genbank/parser.py

@@ -25,16 +25,21 @@ def __gbparser(text):
         acs    = acs[1:]
         de     = _deMatcher.search(header).group()
         de     = _cleanDe.sub(' ',de).strip().strip('.')
-    except AttributeError,e:
-        print >>sys.stderr,'======================================================='
-        print >>sys.stderr,text
-        print >>sys.stderr,'======================================================='
-        raise e
+    except Exception as e:
+        print>>sys.stderr, "\nCould not import sequence id:", text.split()[1], "(error raised:", e, ")"
+        # Do not raise any Exception if you need the possibility to resume the generator
+        # (Python generators can't resume after any exception is raised)
+        return None
     
     return (ac,seq,de,header,ft,acs)
 
+
 def genbankParser(text):
-    return gb.GbSequence(*__gbparser(text))
+    parsed_text = __gbparser(text)
+    if parsed_text is not None:
+        return gb.GbSequence(*parsed_text)
+    else:
+        return None
     
     
 def genbankIterator(file):
@@ -43,7 +48,11 @@ def genbankIterator(file):
     
     
 def genpepParser(text):
-    return gb.GpepSequence(*__gbparser(text))
+    parsed_text = __gbparser(text)
+    if parsed_text is not None:
+        return gb.GpepSequence(*parsed_text)
+    else:
+        return None
     
     
 def genpepIterator(file):

src/obitools/version.py

 major = 1
 minor = 2
-serial= '12'
+serial= '13'
 
 version = "%2d.%02d %s" % (major,minor,serial)