[arch-commits] Commit in pymol/trunk (PKGBUILD apbstools_tcltk8.6.patch)
Evgeniy Alekseev
arcanis at nymeria.archlinux.org
Tue May 13 21:32:08 UTC 2014
Date: Tuesday, May 13, 2014 @ 23:32:07
Author: arcanis
Revision: 111106
upgpkg: pymol 1.7.1.3-1
Modified:
pymol/trunk/PKGBUILD
pymol/trunk/apbstools_tcltk8.6.patch
--------------------------+
PKGBUILD | 14 +++-----
apbstools_tcltk8.6.patch | 72 ++++++++++++++++++++++-----------------------
2 files changed, 42 insertions(+), 44 deletions(-)
Modified: PKGBUILD
===================================================================
--- PKGBUILD 2014-05-13 21:19:52 UTC (rev 111105)
+++ PKGBUILD 2014-05-13 21:32:07 UTC (rev 111106)
@@ -4,8 +4,8 @@
# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com>
pkgname=pymol
-pkgver=1.7.0.0
-pkgrel=3
+pkgver=1.7.1.3
+pkgrel=1
pkgdesc="Molecular visualization system on an Open Source foundation"
arch=('i686' 'x86_64')
url="http://pymol.org/"
@@ -16,14 +16,14 @@
"${pkgname}-38899.patch"
"apbstools_tcltk8.6.patch")
install="${pkgname}.install"
-md5sums=('36fc735f6104e59802f109d0d25b6676'
+md5sums=('414e57a76d8e6e58540b743c1c2fb5ee'
'1f8152c4604ba2939b24e25a022937ca'
- 'a3c1544017762613bebc3f5763a434a9')
+ 'c48bf253e59ff97c14114cd285a4f1e1')
prepare() {
# create desktop file
gendesk -f --pkgname "${pkgname}" --pkgdesc "${pkgdesc}" --name="PyMOL" --categories="Science;Chemistry"
-
+
# suppress non-zero exit code that breaks makepkg
sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py"
# change python to python2
@@ -31,14 +31,12 @@
sed -i "s|python|python2|g" "${srcdir}/pymol/test/run"
sed -i "s|python|python2|g" "${srcdir}/pymol/test/show"
sed -i "s|python|python2|g" "${srcdir}/pymol/modules/pmg_tk/startup/apbs_tools.py"
-
# fix FS#38899
patch -p0 -i "${pkgname}-38899.patch"
mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb"
-
# fix FS#39526
cd "${srcdir}/${pkgname}"
- patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
+ #patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
}
build() {
Modified: apbstools_tcltk8.6.patch
===================================================================
--- apbstools_tcltk8.6.patch 2014-05-13 21:19:52 UTC (rev 111105)
+++ apbstools_tcltk8.6.patch 2014-05-13 21:32:07 UTC (rev 111106)
@@ -1,112 +1,112 @@
---- modules/pmg_tk/startup/apbs_tools.py.orig 2013-08-16 20:29:27.000000000 -0400
-+++ modules/pmg_tk/startup/apbs_tools.py 2013-08-16 20:31:35.000000000 -0400
-@@ -560,7 +560,8 @@
+--- modules/pmg_tk/startup/apbs_tools.py.orig 2014-05-14 01:07:32.000000000 +0400
++++ modules/pmg_tk/startup/apbs_tools.py 2014-05-14 01:15:35.090032827 +0400
+@@ -612,7 +612,8 @@
# Set up the Main page
page = self.notebook.add('Main')
group = Pmw.Group(page,tag_text='Main options')
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
self.selection = Pmw.EntryField(group.interior(),
labelpos='w',
label_text='Selection to use: ',
-@@ -606,7 +607,8 @@
+@@ -658,7 +659,8 @@
page = self.notebook.add('Configuration')
group = Pmw.Group(page,tag_text='Dielectric Constants')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column=0, row=0)
self.interior_dielectric = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Protein Dielectric:',
-@@ -625,7 +627,8 @@
+@@ -677,7 +679,8 @@
#entry.pack(side='left',fill='both',expand=1,padx=4) # side-by-side
entry.pack(fill='x',expand=1,padx=4,pady=1) # vertical
group = Pmw.Group(page,tag_text='Other')
- group.pack(fill='both',expand=1, padx=4, pady=5)
+ #group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
++ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
group.grid(column=1, row=1,columnspan=4)
self.max_mem_allowed = Pmw.EntryField(group.interior(),labelpos='w',
label_text = 'Maximum Memory Allowed (MB):',
-@@ -683,7 +686,8 @@
+@@ -735,7 +738,8 @@
group = Pmw.Group(page,tag_text='Ions')
- group.pack(fill='both',expand=1, padx=4, pady=5)
+ #group.pack(fill='both',expand=1, padx=4, pady=5)
-+ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
++ group.grid(padx=4, pady=5, sticky=(N, S, E, W))
group.grid(column=0, row=1, )
self.ion_plus_one_conc = Pmw.EntryField(group.interior(),
labelpos='w',
-@@ -742,7 +746,8 @@
+@@ -794,7 +798,8 @@
entry.pack(fill='x',expand=1,padx=4)
group = Pmw.Group(page,tag_text = 'Coarse Mesh Length')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 1, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_coarse_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -757,7 +762,8 @@
+@@ -809,7 +814,8 @@
group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 2, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_fine_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -772,7 +778,8 @@
+@@ -824,7 +830,8 @@
group = Pmw.Group(page,tag_text = 'Grid Center')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 3, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_center_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -786,7 +793,8 @@
+@@ -838,7 +845,8 @@
getattr(self,'grid_center_%s'%coord).pack(fill='x', expand=1, padx=4, pady=1)
group = Pmw.Group(page,tag_text = 'Grid Points')
- group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
-+ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
group.grid(column = 4, row = 0)
for coord in 'x y z'.split():
setattr(self,'grid_points_%s'%coord,Pmw.EntryField(group.interior(),
-@@ -804,7 +812,8 @@
+@@ -856,7 +864,8 @@
page.grid_columnconfigure(5,weight=1)
page = self.notebook.add('Program Locations')
group = Pmw.Group(page,tag_text='Locations')
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
def quickFileValidation(s):
if s == '': return Pmw.PARTIAL
elif os.path.isfile(s): return Pmw.OK
-@@ -867,7 +876,8 @@
+@@ -955,7 +964,8 @@
page = self.notebook.add('Temp File Locations')
group = Pmw.Group(page,tag_text='Locations')
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
labelpos = 'w',
label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
-@@ -915,17 +925,20 @@
+@@ -1003,17 +1013,20 @@
page = self.notebook.add('Visualization (1)')
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=1)
self.visualization_group_1 = group
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
page = self.notebook.add('Visualization (2)')
group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
@@ -113,7 +113,7 @@
self.visualization_group_2 = group
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
# Create a couple of other empty pages
page = self.notebook.add('About')
@@ -120,57 +120,57 @@
group = Pmw.Group(page, tag_text='About PyMOL APBS Tools')
- group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
+ #group.pack(fill = 'both', expand = 1, padx = 10, pady = 5)
-+ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
++ group.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
Documentation may be found at
-@@ -2158,7 +2171,8 @@
+@@ -2271,7 +2284,8 @@
self.update_buttonbox = Pmw.ButtonBox(self.mm_group.interior(), padx=0)
self.update_buttonbox.pack(side=LEFT)
self.update_buttonbox.add('Update',command=self.refresh)
- self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
+ #self.mm_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ self.mm_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
self.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
-@@ -2209,7 +2223,8 @@
+@@ -2322,7 +2336,8 @@
bars = (self.mol_surf_low,self.mol_surf_middle,self.mol_surf_high)
Pmw.alignlabels(bars)
for bar in bars: bar.pack(side=LEFT)
- self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
+ #self.ms_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ self.ms_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
self.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
-@@ -2224,7 +2239,8 @@
+@@ -2337,7 +2352,8 @@
text = """Follows same coloring as surface.""",
)
label.pack()
- self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
+ #self.fl_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=TOP)
-+ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ self.fl_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
self.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
-@@ -2243,7 +2259,8 @@
+@@ -2356,7 +2372,8 @@
entryfield_validate = {'validator' : 'real', 'min':0}
)
self.pos_surf_val.pack(side=LEFT)
- self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
+ #self.pi_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ self.pi_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
self.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
-@@ -2262,7 +2279,8 @@
+@@ -2375,7 +2392,8 @@
entryfield_validate = {'validator' : 'real', 'max':0}
)
self.neg_surf_val.pack(side=LEFT)
- self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
+ #self.ni_group.pack(fill = 'both', expand = 1, padx = 4, pady = 5, side=LEFT)
-+ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
++ self.ni_group.grid(padx = 4, pady = 5, sticky=(N, S, E, W))
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