--no commit message

distutils.ext/obidistutils/command/build.py

@@ -5,6 +5,7 @@ Created on 20 oct. 2012
 '''
 
 from distutils.command.build import build as ori_build
+from obidistutils.serenity.checksystem import is_mac_system
 
 
 class build(ori_build):
@@ -24,7 +25,11 @@ class build(ori_build):
     def has_littlebigman(self):
         return True
     
+    def has_pidname(self):
+        return is_mac_system()
+    
     sub_commands = [('littlebigman', has_littlebigman),
+                    ('pidname',has_pidname)
                     ('build_ctools', has_ctools),
                     ('build_files', has_files),
                     ('build_cexe', has_executables),

distutils.ext/obidistutils/command/pidname.py

+'''
+Created on 20 oct. 2012
+
+@author: coissac
+'''
+
+import os
+
+from obidistutils.command.build_exe import build_exe
+from obidistutils.serenity.checksystem import is_mac_system
+
+
+class pidname(build_exe):
+    
+    description = "build the pidname executable returning the executable path from a PID on a mac"
+
+
+    def initialize_options(self):
+        build_exe.initialize_options(self)
+
+        self.pidname = False
+
+
+    def finalize_options(self):
+        # This might be confusing: both build-cexe and build-temp default
+        # to build-temp as defined by the "build" command.  This is because
+        # I think that C libraries are really just temporary build
+        # by-products, at least from the point of view of building Python
+        # extensions -- but I want to keep my options open.
+        
+        build_exe.finalize_options(self)
+        
+        self.set_undefined_options('build',
+                                   ('build_scripts', 'build_cexe'))
+
+        # self.ctools = self.distribution.ctools
+        
+        if os.path.isfile("src/pidname.c"):
+            self.executables = [('pidname',{"sources":["src/pidname.c"]})]
+            self.check_executable_list(self.executables)
+        else:
+            self.executables = []
+
+
+    def run(self):
+        if is_mac_system():
+            build_exe.run(self)
+            self.pidname=True
+        else:
+            self.pidname=False
+        
\ No newline at end of file

distutils.ext/obidistutils/core.py

@@ -29,6 +29,7 @@ from obidistutils.command.build_files import build_files
 from obidistutils.command.build_scripts import build_scripts
 from obidistutils.command.install_scripts import install_scripts
 from obidistutils.command.install import install
+from obidistutils.command.pidname import pidname
 
 from obidistutils.dist import Distribution
 
@@ -118,6 +119,7 @@ def rootname(x):
 
 COMMANDS = {'build':build,
             'littlebigman':littlebigman,
+            'pidname':pidname,
             'build_ctools':build_ctools, 
             'build_files':build_files,
             'build_cexe':build_cexe, 

distutils.ext/src/littlebigman.c

+/*
+ * littlebigman.c
+ *
+ *  Created on: 11 juil. 2012
+ *      Author: coissac
+ */
+
+#include<stdio.h>
+
+int main(int argc, char *argv[])
+{
+    union { int entier;
+            char caractere[4] ;
+    } test;
+
+    test.entier=0x01020304;
+
+    if (test.caractere[3] == 1)
+       printf("-DLITTLE_END");
+    else
+        printf("-DBIG_END");
+
+	return 0;
+}

distutils.ext/src/pidname.c

+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
+#include <errno.h>
+#include <libproc.h>
+
+int main (int argc, char* argv[])
+{
+	pid_t pid; int ret;
+	char pathbuf[PROC_PIDPATHINFO_MAXSIZE];
+
+	if ( argc > 1 ) {
+		pid = (pid_t) atoi(argv[1]);
+		ret = proc_pidpath (pid, pathbuf, sizeof(pathbuf));
+		if ( ret <= 0 ) {
+			fprintf(stderr, "PID %d: proc_pidpath ();\n", pid);
+			fprintf(stderr,	"    %s\n", strerror(errno));
+		} else {
+			printf("proc %d: %s\n", pid, pathbuf);
+		}
+	}
+
+	return 0;
+}

get_obitools/get_obitools.py

@@ -4142,6 +4142,7 @@ import zipimport
 import importlib
 import glob
 import tarfile
+import stat
 
 from distutils.version import LooseVersion
 
@@ -4277,6 +4278,25 @@ def main():
     
     os.system(command)
     
+    activate = os.path.join(current,'obitools')
+    binpath  = os.path.join(virtualenvname,'bin')
+    python   = os.path.join(binpath,'python') 
+ 
+    with open(activate,"w") as fp:
+        print >>fp,"#!%s" % python
+        print >>fp 
+        print >>fp,"import os"
+        print >>fp,"ppid = os.getppid()"
+        print >>fp,"if os.path.islink('/proc/%d/exe' % ppid):"
+        print >>fp,'    shell = os.path.realpath("/proc/%d/exe" % ppid)'
+        print >>fp,"else:"
+        print >>fp,"os.environ['PATH']='%s:%s' % (binpath,os.environ['PATH'])"
+        print >>fp,"os.execlp(shell,shell)"
+        print >>fp
+    
+    st = os.stat(activate)
+    os.chmod(activate, st.st_mode | stat.S_IEXEC)
+    
     cleanModules()
     
      

src/obitools/utils/bioseq.py

@@ -68,7 +68,7 @@ def uniqSequence(seqIterator,taxonomy=None,mergedKey=None,mergeIds=False,categor
                         s["taxid_dist"][seq.id]=seq['taxid']
                         
                 mkey = "merged_%s" % key 
-                #cas ou on met  jour les merged_keys mais il n'y a pas de merged_keys dans la sequence qui arrive
+                #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
                 #cas ou merged_keys existe deja