[hg] galaxy 3497: Update psycopg2 to 2.0.13/postgresql 8.4.2 - galaxy-dev

11 Mar 2010

details:   http://www.bx.psu.edu/hg/galaxy/rev/a719c6971613
changeset: 3497:a719c6971613
user:      Nate Coraor nate@bx.psu.edu
date:      Tue Mar 09 14:13:05 2010 -0500
description:
Update psycopg2 to 2.0.13/postgresql 8.4.2
diffstat:
dist-eggs.ini                                |   2 +-
 eggs.ini                                     |   6 +-
 scripts/scramble/scripts/psycopg2-linux.py   |   1 +
 scripts/scramble/scripts/psycopg2-macosx.py  |  85 ++++++++++++++++++++++++++++
 scripts/scramble/scripts/psycopg2-solaris.py |   1 +
 scripts/scramble/scripts/psycopg2.py         |   1 +
 6 files changed, 92 insertions(+), 4 deletions(-)
diffs (162 lines):
diff -r 5f7ace3195b7 -r a719c6971613 dist-eggs.ini

--- a/dist-eggs.ini	Tue Mar 09 13:54:30 2010 -0500
+++ b/dist-eggs.ini	Tue Mar 09 14:13:05 2010 -0500
@@ -22,7 +22,7 @@
 py2.4-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.4
 py2.5-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.5
 py2.6-macosx-10.3-fat-ucs2 = medeski.bx.psu.edu /usr/local/bin/python2.6
-py2.6-macosx-10.6-universal-ucs2 = lion.bx.psu.edu /usr/bin/python2.6
+py2.6-macosx-10.6-universal-ucs2 = bach.bx.psu.edu /usr/bin/python2.6
 py2.4-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.4
 py2.5-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.5
 py2.6-solaris-2.10-i86pc_32-ucs2 = thumper.bx.psu.edu /afs/bx.psu.edu/project/pythons/solaris-2.10-i86pc_32-ucs2/bin/python2.6
diff -r 5f7ace3195b7 -r a719c6971613 eggs.ini
--- a/eggs.ini	Tue Mar 09 13:54:30 2010 -0500
+++ b/eggs.ini	Tue Mar 09 14:13:05 2010 -0500
@@ -17,7 +17,7 @@
 DRMAA_python = 0.2
 MySQL_python = 1.2.3c1
 pbs_python = 2.9.4
-psycopg2 = 2.0.6
+psycopg2 = 2.0.13
 pycrypto = 2.0.1
 pysam = 0.1.1
 pysqlite = 2.5.6
@@ -56,7 +56,7 @@
; extra version information
 [tags]
-psycopg2 = _8.2.6_static
+psycopg2 = _8.4.2_static
 pysqlite = _3.6.17_static
 MySQL_python = _5.1.41_static
 bx_python = _dev_3b9d30e47619
@@ -68,5 +68,5 @@
 ; the wiki page above
 [source]
 MySQL_python = mysql-5.1.41
-psycopg2 = postgresql-8.2.6
+psycopg2 = postgresql-8.4.2
 pysqlite = sqlite-amalgamation-3_6_17
diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-linux.py
--- a/scripts/scramble/scripts/psycopg2-linux.py	Tue Mar 09 13:54:30 2010 -0500
+++ b/scripts/scramble/scripts/psycopg2-linux.py	Tue Mar 09 14:13:05 2010 -0500
@@ -20,6 +20,7 @@
         "Configuring postgres (./configure)" )
# compile
+    run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" )
     run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" )
     run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" )
diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-macosx.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/scripts/scramble/scripts/psycopg2-macosx.py	Tue Mar 09 14:13:05 2010 -0500
@@ -0,0 +1,85 @@
+import os, sys, shutil
+from distutils.sysconfig import get_config_var
+
+def prep_postgres( prepped, args ):
+
+    pg_version = args['version']
+    pg_srcdir = os.path.join( os.getcwd(), "postgresql-%s" % pg_version )
+
+    # set up environment
+    os.environ['CC'] = get_config_var('CC')
+    os.environ['CFLAGS'] = get_config_var('CFLAGS')
+    os.environ['LDFLAGS'] = get_config_var('LDFLAGS')
+
+    if '-fPIC' not in os.environ['CFLAGS']:
+        os.environ['CFLAGS'] += ' -fPIC'
+
+    # run configure
+    run( "./configure --prefix=%s/postgres --disable-dependency-tracking --enable-static --disable-shared --without-readline --with-thread-safety" % os.getcwd(),
+        os.path.join( os.getcwd(), "postgresql-%s" % pg_version ),
+        "Configuring postgres (./configure)" )
+
+    # compile
+    run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" )
+    run( "make all-static-lib", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" )
+    run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" )
+
+    # install
+    run( "make install-lib-static", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make install)" )
+    run( "make install", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make install)" )
+    run( "make install", os.path.join( pg_srcdir, 'src', 'include' ), "Compiling pg_config (cd src/include; make install)" )
+
+    # manually install some headers
+    run( "cp libpq-fe.h %s" % os.path.join( os.getcwd(), 'postgres', 'include' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" )
+    run( "cp libpq-events.h %s" % os.path.join( os.getcwd(), 'postgres', 'include' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" )
+    run( "cp libpq-int.h %s" % os.path.join( os.getcwd(), 'postgres', 'include', 'internal' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" )
+    run( "cp pqexpbuffer.h %s" % os.path.join( os.getcwd(), 'postgres', 'include', 'internal' ), os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Installing libpq-fe.h" )
+
+    # create prepped archive
+    print "%s(): Creating prepped archive for future builds at:" % sys._getframe().f_code.co_name
+    print " ", prepped
+    compress( prepped,
+           'postgres/bin',
+           'postgres/include',
+           'postgres/lib' )
+
+if __name__ == '__main__':
+
+    # change back to the build dir
+    if os.path.dirname( sys.argv[0] ) != "":
+        os.chdir( os.path.dirname( sys.argv[0] ) )
+
+    # find setuptools
+    sys.path.append( os.path.abspath( os.path.join( '..', '..', '..', 'lib' ) ) )
+    from scramble_lib import *
+
+    tag = get_tag()
+
+    pg_version = ( tag.split( "_" ) )[1]
+    pg_archive_base = os.path.join( archives, "postgresql-%s" % pg_version )
+    pg_archive = get_archive( pg_archive_base )
+    pg_archive_prepped = os.path.join( archives, "postgresql-%s-%s.tar.gz" % ( pg_version, platform_noucs ) )
+
+    # clean up any existing stuff (could happen if you run scramble.py by hand)
+    clean( [ 'postgresql-%s' % pg_version ] )
+
+    # unpack postgres
+    unpack_dep( pg_archive, pg_archive_prepped, prep_postgres, dict( version=pg_version ) )
+
+    # localize setup.cfg
+    if not os.path.exists( 'setup.cfg.orig' ):
+        shutil.copy( 'setup.cfg', 'setup.cfg.orig' )
+        f = open( 'setup.cfg', 'a' )
+        f.write( '\npg_config=postgres/bin/pg_config\n' )
+        f.close()
+
+    # tag
+    me = sys.argv[0]
+    sys.argv = [ me ]
+    if tag is not None:
+        sys.argv.append( "egg_info" )
+        sys.argv.append( "--tag-build=%s" %tag )
+    sys.argv.append( "bdist_egg" )
+
+    # go
+    execfile( "setup.py", globals(), locals() )
diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2-solaris.py
--- a/scripts/scramble/scripts/psycopg2-solaris.py	Tue Mar 09 13:54:30 2010 -0500
+++ b/scripts/scramble/scripts/psycopg2-solaris.py	Tue Mar 09 14:13:05 2010 -0500
@@ -23,6 +23,7 @@
         "Configuring postgres (./configure)" )
# compile
+    run( "gmake ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; gmake ../../src/include/utils/fmgroids.h)" )
     run( "gmake", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; gmake)" )
     run( "gmake", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; gmake)" )
diff -r 5f7ace3195b7 -r a719c6971613 scripts/scramble/scripts/psycopg2.py
--- a/scripts/scramble/scripts/psycopg2.py	Tue Mar 09 13:54:30 2010 -0500
+++ b/scripts/scramble/scripts/psycopg2.py	Tue Mar 09 14:13:05 2010 -0500
@@ -20,6 +20,7 @@
         "Configuring postgres (./configure)" )
# compile
+    run( "make ../../src/include/utils/fmgroids.h", os.path.join( pg_srcdir, 'src', 'backend' ), "Compiling fmgroids.h (cd src/backend; make ../../src/include/utils/fmgroids.h)" )
     run( "make", os.path.join( pg_srcdir, 'src', 'interfaces', 'libpq' ), "Compiling libpq (cd src/interfaces/libpq; make)" )
     run( "make", os.path.join( pg_srcdir, 'src', 'bin', 'pg_config' ), "Compiling pg_config (cd src/bin/pg_config; make)" )

    