pymol-py stable port information

Info2: <<
Package: pymol-py%type_pkg[python]
Version: 1.5
Revision: 6
UseMaxBuildJobs: false
Maintainer: W. G. Scott
Type: python (2.6 2.7)
# r3983
#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
Source: http://diablo.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
Source-MD5: 7ec7f1eb4302672d65bbe4de9ffc01e5
Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
Source3-MD5: 7f61fc224103aa24a92f1a03f985ce49
Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
PatchFile: pymol-py.patch
PatchFile-MD5: 04fd2893af1db8924f6da71cd3afc03e
PatchFile2: pymol-py-rest.patch
PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
SourceDirectory: pymol-%v
Depends: python%type_pkg[python], libpng15-shlibs, scipy-py%type_pkg[python], tcltk, pmw-py%type_pkg[python] (>= 1.3.2-1000), freeglut-shlibs, glew-shlibs, blt-shlibs, meschach-shlibs, freetype219-shlibs
BuildDepends: libpng15, freeglut, glew, readline5, gdbm3, tcltk-dev, blt, x11-dev, swig, meschach, freetype219, fink (>= 0.30.0)
Conflicts: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, pymol-py27
Replaces: pymol, pymol-py22, pymol-py23, pymol-py24, pymol-py25, pymol-py26, pymol-py27
PatchScript: <<
#! /bin/sh -ex
sed 's|@FINKPREFIX@|%p|g' < %{PatchFile} | sed 's|python2.X|python%type_raw[python]|g' | patch -p1
cd ..
sed 's|@FINKPREFIX@|%p|g' < %{PatchFile2} | sed 's|python2.X|python%type_raw[python]|g' | sed 's|pymol-py2X|pymol-py%type_pkg[python]|g' | patch -p1
cd pymol-%v
perl -pi -e 's|self.dialog.activate|\#self.dialog.activate|g' modules/pmg_tk/startup/apbs_tools.py
perl -pi -e 's/lglew/lGLEW/g' setup.py
perl -pi -e 's|searchDirs.append\(os.path.join\("/opt", "local", "bin"\)\)||g' modules/pmg_tk/startup/apbs_tools.py
<<
CompileScript: <<
#! /bin/sh -ex
cd %b/../pynmr_0.37f_src/pmg_tk/startup/pynmr
perl -pi -e 's|Numeric import|numpy.oldnumeric import|g' *.py
perl -pi -e 's|LinearAlgebra import|numpy.oldnumeric.linear_algebra import|g' *.py
perl -pi -e 's|import MLab|import numpy.oldnumeric.mlab as MLab|g' *.py
./run.macos
<<
InstallScript: <<
#! /bin/sh -ex
%p/bin/python%type_raw[python] setup.py install --root %d
# setup2.py currently mishandles the creation of the pymol_path symlink
# and the placement of the associated subdirectories.
#%p/bin/python%type_raw[python] setup2.py install --root %d
ln -s %p/lib/python%type_raw[python]/site-packages/pymol %i/lib/python%type_raw[python]/site-packages/pymol/pymol_path
cp -r data modules examples test scripts %i/lib/python%type_raw[python]/site-packages/pymol
mkdir -p %i/lib/pymol-py%type_pkg[python]/bin
cp pymol.cmd %i/lib/pymol-py%type_pkg[python]/bin/pymol
chmod ugo+x %i/lib/pymol-py%type_pkg[python]/bin/pymol
cp ../eMovie.py %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/eMovie.py
cp ../eMovie_rigimol.inp %i/lib/python%type_raw[python]/site-packages/pymol/eMovie_rigimol.inp
mkdir %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr
cd ../pynmr_0.37f_src/pmg_tk/startup
cp plug_nmr.py %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup
cd pynmr
cp -r Crmsd.so *.py BIOPYTHON_LICENSE LICENSE README help images test_data %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr
rm %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/pynmr/test_data/.noe.tbl.swp
<<
DocFiles: DEVELOPERS LICENSE README
PostInstScript: <<
update-alternatives --install %p/bin/pymol pymol %p/lib/pymol-py%type_pkg[python]/bin/pymol %type_pkg[python]
<<
PreRmScript: <<
if [ $1 != "upgrade" ]; then
update-alternatives --remove pymol %p/lib/pymol-py%type_pkg[python]/bin/pymol
fi
<<
Description: Molecular graphics system
DescDetail: <<
Launch with command "pymol"
Lauch with command "pymol -M" to avoid flickering artifacts on some ATI
graphics cards.
Launch with command "pymol -S -t 6" for Zalman stereo.
PyMOL is a molecular graphics system with an embedded Python interpreter
designed for real-time visualization and rapid generation of high-quality
molecular graphics images and animations.
<<
DescPort: <<
Versions prior to 0.97-1 were ported and maintained by Matt Stephenson

<<
DescPackaging: <<
The tarball used for this version was created in accordance to the BSD
license of pymol using the following instructions...
svn -r3983 co https://pymol.svn.sourceforge.net/svnroot/pymol/trunk/pymol pymol-1.5
tar --exclude=.svn -jcvf pymol-1.5-src.tar.bz2 pymol-1.5
Added eMovie.py plug-in manually. Commented out line that opens the window for eMovie by
default every time pymol is started as this is annoying behavior. eMovie is activated via
the plugin menu.
Added -d "_ set stereo_double_pump_mono,quiet=1" to exec on pymol to limit video
artifacts on drivers that do not properly support hardware stereo yet such as those for the
HD 2600 XT.
Added pynmr plugin.
<<
DescUsage: Just type 'pymol' at the command prompt inside an X environment.
License: OSI-Approved
Homepage: http://pymol.sourceforge.net
<<

pymol-py stable port .patch

--- pymol-1.5/setup.py.orig 2012-02-18 13:25:51.000000000 -0500
+++ pymol-1.5/setup.py 2012-02-18 13:29:45.000000000 -0500
@@ -43,7 +43,7 @@
ext_link_args=[]
#============================================================================
elif sys.platform=='darwin':
- using_fink = "'/sw/" in str(sys.path)
+ using_fink = "'@FINKPREFIX@/" in str(sys.path)
if using_fink:
# under Fink, with the following packages installed:
#
@@ -84,9 +84,9 @@
inc_dirs=["ov/src",
"layer0","layer1","layer2",
"layer3","layer4","layer5",
- "/sw/include/freetype2/freetype",
- "/sw/include/freetype2",
- "/sw/include",
+ "@FINKPREFIX@/include/freetype2/freetype",
+ "@FINKPREFIX@/include/freetype2",
+ "@FINKPREFIX@/include",
"/usr/X11/include",
"modules/cealign/src",
"modules/cealign/src/tnt",
@@ -113,12 +113,12 @@
]
ext_comp_args=[]
ext_link_args=[
- "-L/sw/lib", "-lpng",
+ "-L@FINKPREFIX@/lib", "-lpng",
"/usr/X11/lib/libGL.dylib",
"/usr/X11/lib/libGLU.dylib",
"-lfreeglut",
"-lglew",
- "-L/sw/lib/freetype219/lib", "-lfreetype"
+ "-L@FINKPREFIX@/lib/freetype219/lib", "-lfreetype"
]
else:
# Not using Fink -- building as if we are on Linux/X11 with
--- /dev/null 2012-02-14 20:24:44.000000000 -0500
+++ pymol-1.5.0.1/pymol.cmd 2012-02-14 19:31:08.000000000 -0500
@@ -0,0 +1,16 @@
+#!/bin/sh
+#
+# PyMOL startup script
+#
+# ==============================================================
+# Set PYMOL_PATH to point at the correct location on your system
+#
+PYMOL_PATH=@FINKPREFIX@/lib/python2.X/site-packages/pymol
+export PYMOL_PATH
+#
+# ==============================================================
+# (no changes usually required below here)
+#
+# python modules
+#
+exec @FINKPREFIX@/bin/python2.X @FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set stereo_double_pump_mono,quiet=1" "$@"
--- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py.orig 2012-02-18 14:50:35.000000000 -0500
+++ pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-02-18 14:51:33.000000000 -0500
@@ -141,7 +141,7 @@
# APBS_BINARY_LOCATION = '/opt/bin/apbs'
#
APBS_BINARY_LOCATION = None
-APBS_PSIZE_LOCATION = None
+APBS_PSIZE_LOCATION = '@FINKPREFIX@/share/apbs/tools/manip'
APBS_PDB2PQR_LOCATION = None
TEMPORARY_FILE_DIR = None

--- pymol-1.5/modules/pmg_tk/PMGApp.py.orig 2012-02-18 13:31:34.000000000 -0500
+++ pymol-1.5/modules/pmg_tk/PMGApp.py 2012-02-18 13:32:15.000000000 -0500
@@ -219,7 +219,7 @@


def my_show(self,win,center=1):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
win.show()
else: # autocenter, deiconify, and run mainloop
# this is a workaround for a bug in the
@@ -237,7 +237,7 @@
win.deiconify()

def my_withdraw(self,win):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') or (sys.platform!='darwin'):
win.withdraw()
else:
win.destroy()
--- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py.orig 2012-02-18 13:31:47.000000000 -0500
+++ pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 2012-02-18 13:32:15.000000000 -0500
@@ -250,7 +250,7 @@
self.buttonArea.destroy()

def my_show(self,win,center=1):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
win.show()
else: # autocenter, deiconify, and run mainloop
# this is a workaround for a bug in the
@@ -269,13 +269,13 @@
# win.show()

def my_withdraw(self,win):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') or (sys.platform!='darwin'):
win.withdraw()
else:
win.destroy()

def my_activate(self,win,center=1,focus=None):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') and (sys.platform!='darwin'):
win.activate()
else: # autocenter, deiconify, and run mainloop
# this is a workaround for a bug in the
@@ -296,7 +296,7 @@
win.mainloop()

def my_deactivate(self,win):
- if sys.platform!='linux2':
+ if (sys.platform!='linux2') or (sys.platform!='darwin'):
win.deactivate()
else: # autocenter, deiconify, and run mainloop
win.destroy()

pymol-py _unstable_ port .patch