Patch few bug related to the new version of cython + intallation

problems

distutils.ext/obidistutils/command/install.py

@@ -3,8 +3,8 @@ Created on 6 oct. 2014
 
 @author: coissac
 '''
-
 from distutils.command.install import install as install_ori
+#from setuptools.command.install import install as install_ori
 
 class install(install_ori):
     

distutils.ext/obidistutils/serenity/__init__.py

@@ -108,6 +108,5 @@ def serenity_mode(package,version):
 def getVersion(source,main,version):
     path  = os.path.join(source,main,'%s.py' % version)
     spec = spec_from_file_location('version',path)
-    print(spec.loader)
     return spec.loader.load_module().version.strip()
     

distutils.ext/obidistutils/serenity/checkpackage.py

@@ -83,6 +83,8 @@ def install_requirements(requirementfile='requirements.txt'):
             log.info("  Installing requirement : %s" % x)
             pip_install_package(x)
             install_something=True
+            if x[0:3]=='pip':
+                return True
                 
     return install_something
  
@@ -134,7 +136,9 @@ def get_package_requirement(package,requirementfile='requirements.txt'):
         
 def pip_install_package(package,directory=None,upgrade=True):
 
-    log.info('installing %s in directory %s' % (package,str(directory)))
+    if directory is not None:
+        log.info('    installing %s in directory %s' % (package,str(directory)))
+        
 
     if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
         os.environ['https_proxy']=os.environ['http_proxy']
@@ -144,8 +148,8 @@ def pip_install_package(package,directory=None,upgrade=True):
     if upgrade:
         args.append('--upgrade')
     
-    if 'http_proxy' in os.environ:
-        args.append('--proxy=%s' % os.environ['http_proxy'])
+    if 'https_proxy' in os.environ:
+        args.append('--proxy=%s' % os.environ['https_proxy'])
         
     if directory is not None:
         args.append('--target=%s' % directory)

get_orgasm/get-orgasm.py

@@ -4,7 +4,7 @@ from fileinput import filename
 SOFT           = "Org.Asm"
 LIB            = "orgasm"
 PIP_MINVERSION = '1.5'
-MODE           = "svn" # or "pypi"
+MODE           = "pypi" # or "svn"
 SVNURL         = "http://www.grenoble.prabi.fr/public-svn/LECASofts/orgasm/trunk"
 
 
@@ -37280,7 +37280,7 @@ import os.path
 import shutil
 import sys
 import tempfile
-import urllib2
+import urllib.request, urllib.error, urllib.parse
 import imp
 import zipimport
 import importlib
@@ -37288,6 +37288,7 @@ import glob
 import tarfile
 import pkgutil
 import stat
+import pip
 
 from distutils.errors import DistutilsError
 from distutils.version import StrictVersion
@@ -37320,55 +37321,22 @@ def installModules():
         sys.path.insert(0,install_zip)
 
     except:
-        print >>sys.stderr,'Unable to install %s on your system' % SOFT
+        print('Unable to install %s on your system' % SOFT, file=sys.stderr)
                 
 def cleanModules():
 
     if tmpdir:
             shutil.rmtree(tmpdir[0], ignore_errors=True)
            
-def is_pip_installed(minversion=PIP_MINVERSION):
-    try:
-        import pip  # @UnresolvedImport
-        print pip.__file__
-        ok = StrictVersion(pip.__version__) >= StrictVersion(minversion)
-    except:
-        ok = False
-        
-    return ok
-
-def get_a_pip_module(minversion=PIP_MINVERSION):
-    
-    global local_pip
-        
-    tmpdir = getTmpDir()
-    
-    if not local_pip: 
-        pipmodule = importlib.import_module('pip') 
-            
-        # Prepare the CERT certificat for https download
-            
-        cert_path = os.path.join(tmpdir, "cacert.pem")
-        
-        with open(cert_path, "wb") as cert:
-            cert.write(pkgutil.get_data("pip._vendor.requests", "cacert.pem"))
-            
-        os.environ.setdefault("PIP_CERT", cert_path)
-        
-        local_pip.append(pipmodule)
-       
-    return local_pip[0]
-
-
-def pip_download_package(package,pip=None):
+def pip_download_package(package):
     tmpdir = getTmpDir()
 
-    if pip is None:
-        pip = get_a_pip_module()
-                
     args = ['install']
     
-    if 'http_proxy' in os.environ:
+    if 'http_proxy' in os.environ and 'https_proxy' not in os.environ:
+        os.environ['https_proxy']=os.environ['http_proxy']
+
+    if 'https_proxy' in os.environ:
         args.append('--proxy=%s' % os.environ['http_proxy'])
         
     args.append('--download=%s' % tmpdir)
@@ -37405,8 +37373,7 @@ def svndownload():
 def pypidownload():
     global SOFT
     
-    pip = get_a_pip_module()
-    filename=pip_download_package(SOFT,pip=pip)
+    filename=pip_download_package(SOFT)
     
     return filename
             
@@ -37439,9 +37406,9 @@ def main():
     activate = os.path.join(current,LIB)
  
     with open(activate,"w") as fp:
-        print >>fp, install_script % (virtualenvname,SOFT,SOFT)
-        print >>fp
-    
+        print(install_script % (virtualenvname,SOFT,SOFT),file=fp)
+        print(file=fp)
+        
     st = os.stat(activate)
     os.chmod(activate, st.st_mode | stat.S_IEXEC)
     

python/orgasm/assembler/_assembler.pyx

@@ -148,7 +148,7 @@ cdef bint isPalindrome(list path):
     if (lp & 1) == 1:
         return False
     
-    for i in range(lp/2):
+    for i in range(lp//2):
         if path[i]!=-path[-i-1]:
             return False
         

python/orgasm/multialign/_dynamic.pyx

@@ -66,7 +66,7 @@ cdef void reversePath(alignPath* path):
         cdef long j
         
         j=path.length
-        for i in range(path.length/2):
+        for i in range(path.length//2):
             j-=1
             path.path[i],path.path[j]=path.path[j],path.path[i]
 

python/orgasm/multialign/_multi.pyx

@@ -188,7 +188,7 @@ cdef list alignReads(readids,Index index,size_t kmer=12,int smin=10,size_t delta
     seqs = list(unique)
 #    nseq   = len(readids)
     nseq   = len(seqs)
-    nali = nseq * (nseq-1) / 2
+    nali = nseq * (nseq-1) // 2
     hashes =[hashSeq(s,kmer) for s in seqs]
     
     progressBar(1,nali,reset=True,head=bytes("Pairwise alignment %6d x %6d " % (0,0),encoding='ascii'))

python/orgasm/version.py

 major = 0
-minor = 0
+minor = '0a4'
 serial= 'alpha'
 
-version = "%2d.%02d.%s" % (major,minor,serial)
+version = "%2d.%s" % (major,minor)

requirements.txt

 --extra-index-url https://pypi.python.org/simple/
-Cython>=0.21
-Sphinx>=1.2.0
+pip>=7.1
+Cython>=0.22
+Sphinx>=1.3.1