Update of /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci
In directory sfp-cvs-1.v30.ch3.sourceforge.com:/tmp/cvs-serv20804
Modified Files:
pymol-py.info pymol-py.patch
Log Message:
pymol update from upstream svn changes
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.10
retrieving revision 1.11
diff -u -d -r1.10 -r1.11
--- pymol-py.info 6 Oct 2012 17:51:51 -0000 1.10
+++ pymol-py.info 26 Feb 2013 03:29:05 -0000 1.11
@@ -1,14 +1,14 @@
Info2: <<
Package: pymol-py%type_pkg[python]
Version: 1.5
-Revision: 7
+Revision: 8
UseMaxBuildJobs: false
Maintainer: W. G. Scott <wgsc...@users.sourceforge.net>
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
+# r4023
+#Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
+Source: http://scottlab.ucsc.edu/~wgscott/pymol/pymol-%v-src.tar.bz2
+Source-MD5: 7f7c377c4f6e04dfba4a842543144a35
Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -16,7 +16,7 @@
Source4: http://diablo.ucsc.edu/~wgscott/pymol/pynmr_0.37f_src.tar.bz2
Source4-MD5: cb4a3906766681ce9230ef5515e1aa1c
PatchFile: pymol-py.patch
-PatchFile-MD5: f812def4c13c0542e3830f187ac00523
+PatchFile-MD5: 2e287d04ecb51af1eeee3767e658ef5d
PatchFile2: pymol-py-rest.patch
PatchFile2-MD5: 2df10a5a2d66b16082317a823878bde0
SourceDirectory: pymol-%v
@@ -61,6 +61,7 @@
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
+rm -f %i/bin/pymol
<<
DocFiles: DEVELOPERS LICENSE README
PostInstScript: <<
@@ -88,7 +89,7 @@
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
+ svn -r4023 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
Index: pymol-py.patch
===================================================================
RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/sci/pymol-py.patch,v
retrieving revision 1.5
retrieving revision 1.6
diff -u -d -r1.5 -r1.6
--- pymol-py.patch 6 Oct 2012 17:51:51 -0000 1.5
+++ pymol-py.patch 26 Feb 2013 03:29:05 -0000 1.6
@@ -1,76 +1,8 @@
---- 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
-+HasRadeon=($(system_profiler SPDisplaysDataType | grep Radeon ))
-+# ==============================================================
-+if [[ -z "$HasRadeon" ]];then
-+ exec @FINKPREFIX@/bin/python2.X
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set
stereo_double_pump_mono,quiet=1" "$@"
-+else
-+ exec @FINKPREFIX@/bin/python2.X
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set
stereo_double_pump_mono,quiet=1" -M "$@"
-+fi
---- 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 @@
-
+diff -uNr pymol-1.5/modules/pmg_tk/PMGApp.py
pymol-1.5.fink/modules/pmg_tk/PMGApp.py
+--- pymol-1.5/modules/pmg_tk/PMGApp.py 2012-05-16 21:39:13.000000000 -0400
++++ pymol-1.5.fink/modules/pmg_tk/PMGApp.py 2013-02-25 21:01:06.000000000
-0500
+@@ -184,7 +184,7 @@
+ self.fifo.put(cmmd)
def my_show(self,win,center=1):
- if sys.platform!='linux2':
@@ -78,7 +10,7 @@
win.show()
else: # autocenter, deiconify, and run mainloop
# this is a workaround for a bug in the
-@@ -237,7 +237,7 @@
+@@ -202,7 +202,7 @@
win.deiconify()
def my_withdraw(self,win):
@@ -87,8 +19,9 @@
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
+diff -uNr pymol-1.5/modules/pmg_tk/skins/normal/__init__.py
pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py
+--- pymol-1.5/modules/pmg_tk/skins/normal/__init__.py 2013-02-25
20:51:28.000000000 -0500
++++ pymol-1.5.fink/modules/pmg_tk/skins/normal/__init__.py 2013-02-25
21:01:06.000000000 -0500
@@ -250,7 +250,7 @@
self.buttonArea.destroy()
@@ -123,3 +56,47 @@
win.deactivate()
else: # autocenter, deiconify, and run mainloop
win.destroy()
+diff -uNr pymol-1.5/modules/pmg_tk/startup/apbs_tools.py
pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py
+--- pymol-1.5/modules/pmg_tk/startup/apbs_tools.py 2012-04-28
12:45:52.000000000 -0400
++++ pymol-1.5.fink/modules/pmg_tk/startup/apbs_tools.py 2013-02-25
21:01:06.000000000 -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
+
+diff -uNr pymol-1.5/pymol.cmd pymol-1.5.fink/pymol.cmd
+--- pymol-1.5/pymol.cmd 1969-12-31 19:00:00.000000000 -0500
++++ pymol-1.5.fink/pymol.cmd 2013-02-25 21:01:06.000000000 -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
++HasRadeon=($(system_profiler SPDisplaysDataType | grep Radeon ))
++# ==============================================================
++if [[ -z "$HasRadeon" ]];then
++ exec @FINKPREFIX@/bin/python2.X
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set
stereo_double_pump_mono,quiet=1" "$@"
++else
++ exec @FINKPREFIX@/bin/python2.X
@FINKPREFIX@/lib/python2.X/site-packages/pymol/__init__.py -d "_ set
stereo_double_pump_mono,quiet=1" -M "$@"
++fi
+diff -uNr pymol-1.5/setup.py pymol-1.5.fink/setup.py
+--- pymol-1.5/setup.py 2013-02-25 20:51:33.000000000 -0500
++++ pymol-1.5.fink/setup.py 2013-02-25 21:05:43.000000000 -0500
+@@ -216,7 +216,7 @@
+
+ libs += ["png", "freetype"]
+
+- for prefix in ["/usr", "/usr/X11", "/opt/local", "/sw"]:
++ for prefix in ["@FINKPREFIX@", "/usr", "/usr/X11"]:
+ inc_dirs += filter(os.path.isdir, [prefix + s for s in ["/include",
"/include/freetype2"]])
+ lib_dirs += filter(os.path.isdir, [prefix + s for s in ["/lib"]])
+
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