[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-20 Thread Justin Lecher 
commit: 5f7b312a1fa336fc5f4b98909502579ce5557155
Author: Justin Lecher  gentoo  org>
AuthorDate: Mon Oct 20 18:00:45 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Mon Oct 20 18:01:10 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=5f7b312a

sci-chemistry/pymol: Fix broken plugin listing

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog  |  4 
 sci-chemistry/pymol/files/pymol--listing.patch | 17 +
 sci-chemistry/pymol/pymol-.ebuild  |  1 +
 3 files changed, 22 insertions(+)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 2cce805..0364715 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -3,6 +3,10 @@
 # $Header: $
 
   20 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--listing.patch:
+  Fix broken plugin listing
+
+  20 Oct 2014; Justin Lecher  pymol-.ebuild,
   +files/pymol--options.patch:
   Fix upstream buildsystem
 

diff --git a/sci-chemistry/pymol/files/pymol--listing.patch 
b/sci-chemistry/pymol/files/pymol--listing.patch
new file mode 100644
index 000..1b4039c
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--listing.patch
@@ -0,0 +1,17 @@
+ pymol/modules/pymol/plugins/repository.py | 3 ++-
+ 1 file changed, 2 insertions(+), 1 deletion(-)
+
+diff --git a/pymol/modules/pymol/plugins/repository.py 
b/pymol/modules/pymol/plugins/repository.py
+index 9697f68..9820fac 100644
+--- a/pymol/modules/pymol/plugins/repository.py
 b/pymol/modules/pymol/plugins/repository.py
+@@ -182,7 +182,8 @@ class GithubRepository(HttpRepository):
+ 
+ def fetchjson(self, url):
+ handle = urlopen('https://api.github.com' + url)
+-return eval(handle.read())
++ret = handle.read().replace("false", "False")
++return eval(ret)
+ 
+ class LocalRepository(Repository):
+ def __init__(self, url):

diff --git a/sci-chemistry/pymol/pymol-.ebuild 
b/sci-chemistry/pymol/pymol-.ebuild
index a811e69..cbc6a4b 100644
--- a/sci-chemistry/pymol/pymol-.ebuild
+++ b/sci-chemistry/pymol/pymol-.ebuild
@@ -39,6 +39,7 @@ RDEPEND="${DEPEND}"
 
 PATCHES=(
"${FILESDIR}"/${P}-options.patch
+   "${FILESDIR}"/${P}-listing.patch
 )
 
 src_unpack() {

[gentoo-commits] proj/sci:master commit in: sci-chemistry/pymol/, sci-chemistry/pymol/files/

2014-10-30 Thread Justin Lecher 
commit: ecb0dc0854f860d87e7ebd237d3c83ef8f815444
Author: Justin Lecher  gentoo  org>
AuthorDate: Thu Oct 30 13:48:47 2014 +
Commit: Justin Lecher  gentoo  org>
CommitDate: Thu Oct 30 13:48:47 2014 +
URL:http://sources.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=ecb0dc08

sci-chemistry/pymol: Make it really multi py ABI ready; use internal apbs plugin

Package-Manager: portage-2.2.14

---
 sci-chemistry/pymol/ChangeLog|   4 +
 sci-chemistry/pymol/files/pymol--tk8.6.patch | 163 +++
 sci-chemistry/pymol/pymol-.ebuild|  21 ++-
 3 files changed, 183 insertions(+), 5 deletions(-)

diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog
index 67954f0..15af521 100644
--- a/sci-chemistry/pymol/ChangeLog
+++ b/sci-chemistry/pymol/ChangeLog
@@ -2,6 +2,10 @@
 # Copyright 1999-2014 Gentoo Foundation; Distributed under the GPL v2
 # $Header: $
 
+  30 Oct 2014; Justin Lecher  pymol-.ebuild,
+  +files/pymol--tk8.6.patch:
+  Make it really multi py ABI ready; use internal apbs plugin
+
   27 Oct 2014; Justin Lecher  pymol-.ebuild:
   Add missing PYTHON_USEDEP
 

diff --git a/sci-chemistry/pymol/files/pymol--tk8.6.patch 
b/sci-chemistry/pymol/files/pymol--tk8.6.patch
new file mode 100644
index 000..c4fa209
--- /dev/null
+++ b/sci-chemistry/pymol/files/pymol--tk8.6.patch
@@ -0,0 +1,163 @@
+ pymol/modules/pmg_tk/startup/apbs_tools.py | 36 +++---
+ 1 file changed, 18 insertions(+), 18 deletions(-)
+
+diff --git a/pymol/modules/pmg_tk/startup/apbs_tools.py 
b/pymol/modules/pmg_tk/startup/apbs_tools.py
+index 9b76070..ad82df3 100644
+--- a/pymol/modules/pmg_tk/startup/apbs_tools.py
 b/pymol/modules/pmg_tk/startup/apbs_tools.py
+@@ -612,7 +612,7 @@ class APBSTools2:
+ # 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.grid(padx = 10, pady = 5, sticky=(N, S, E, W))
+ self.selection = Pmw.EntryField(group.interior(),
+ labelpos='w',
+ label_text='Selection to use: ',
+@@ -658,7 +658,7 @@ class APBSTools2:
+ page = self.notebook.add('Configuration')
+ 
+ group = Pmw.Group(page,tag_text='Dielectric Constants')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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:',
+@@ -677,7 +677,7 @@ class APBSTools2:
+ #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.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):',
+@@ -735,7 +735,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text='Ions')
+-group.pack(fill='both',expand=1, padx=4, pady=5)
++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',
+@@ -794,7 +794,7 @@ class APBSTools2:
+ 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.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(),
+@@ -809,7 +809,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Fine Mesh Length')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(),
+@@ -824,7 +824,7 @@ class APBSTools2:
+ 
+ 
+ group = Pmw.Group(page,tag_text = 'Grid Center')
+-group.pack(fill = 'both', expand = 1, padx = 4, pady = 5)
++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(