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MANIFEST.in

@@ -2,6 +2,7 @@ include setup.py
 recursive-include distutils.ext *.py *.c *.pem
 recursive-include src *.pyx *.pxd *.c *.h *.cfiles
 recursive-include doc/sphinx/source *.txt *.rst *.py
+recursive-include doc/sphinx/sphinxext *.py
 include doc/sphinx/make.bat
 include doc/sphinx/Makefile
 include README.txt

distutils.ext/obidistutils/command/sdist.py

+'''
+Created on 10 mars 2015
+
+@author: coissac
+'''
+
+import os.path
+
+from distutils.command.sdist import sdist as orig_sdist
+from distutils import dir_util
+
+class sdist(orig_sdist):
+
+    def make_distribution(self):
+        """Create the source distribution(s).  First, we create the release
+        tree with 'make_release_tree()'; then, we create all required
+        archive files (according to 'self.formats') from the release tree.
+        Finally, we clean up by blowing away the release tree (unless
+        'self.keep_temp' is true).  The list of archive files created is
+        stored so it can be retrieved later by 'get_archive_files()'.
+        """
+        # Don't warn about missing meta-data here -- should be (and is!)
+        # done elsewhere.
+        base_dir = self.distribution.get_fullname()
+        base_name = os.path.join(self.dist_dir,base_dir)
+
+        self.make_release_tree(os.path.join('tmp',base_dir), self.filelist.files)
+        archive_files = []              # remember names of files we create
+        # tar archive must be created last to avoid overwrite and remove
+        if 'tar' in self.formats:
+            self.formats.append(self.formats.pop(self.formats.index('tar')))
+
+        for fmt in self.formats:
+            file = self.make_archive(base_name, fmt, root_dir='tmp',base_dir=base_dir,
+                                     owner=self.owner, group=self.group)
+            archive_files.append(file)
+            self.distribution.dist_files.append(('sdist', '', file))
+
+        self.archive_files = archive_files
+
+        if not self.keep_temp:
+            dir_util.remove_tree(os.path.join('tmp',base_dir), dry_run=self.dry_run)

distutils.ext/obidistutils/core.py

@@ -8,6 +8,7 @@ from os import path
 import os.path
 import glob
 import sys
+from obidistutils.command.sdist import sdist
 
 
 try:
@@ -127,7 +128,8 @@ COMMANDS = {'build':build,
             'build_sphinx':build_sphinx, 
             'install_scripts':install_scripts,
             'install_sphinx':install_sphinx,
-            'install':install}
+            'install':install,
+            'sdist':sdist}
 
 CTOOLS =[]
 CEXES  =[]

setup.py

@@ -19,7 +19,7 @@ from os import path
 
 
 PACKAGE = "OBITools"
-VERSION = "1.1.3"
+VERSION = "1.1.4"
 AUTHOR  = 'Eric Coissac'
 EMAIL   = 'eric@coissac.eu'
 URL     = 'metabarcoding.org/obitools'

src/obitools/utils/bioseq.py

@@ -58,6 +58,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
                 s['count']+=seq['count']
             else:
                 s['count']+=1
+                seq['count']=1
 #            if taxonomy is not None and 'taxid' in seq:
 #                s['merged_taxid'][seq['taxid']]=
             for key in mergedKey:
@@ -70,7 +71,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
                 mkey = "merged_%s" % key 
                 #cas ou on met a jour les merged_keys mais il n'y a pas de merged_keys dans la sequence qui arrive
                 if key in seq:
-                    s[mkey][seq[key]]=s[mkey].get(seq[key],0)+1
+                    s[mkey][seq[key]]=s[mkey].get(seq[key],0)+seq['count']
                 #cas ou merged_keys existe deja
                 else:
                     if mkey in seq:
@@ -98,7 +99,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
                 if mkey not in seq:
                     seq[mkey]={}
                 if key in seq:
-                    seq[mkey][seq[key]]=seq[mkey].get(seq[key],0)+1
+                    seq[mkey][seq[key]]=seq[mkey].get(seq[key],0)+seq['count']
                     del(seq[key])
 
             if 'count' not in seq:

src/obitools/version.py

 major = 1
 minor = 1
-serial= '3'
+serial= '4'
 
 version = "%2d.%02d %s" % (major,minor,serial)