updated package

3 files changed, 133 insertions, 22 deletions

diff --git a/.SRCINFO b/.SRCINFO
index eb18f8c33f16..dda875fc40f1 100644
--- a/.SRCINFO
+++ b/.SRCINFO
@@ -1,6 +1,6 @@
 pkgbase = pymol-git
 	pkgdesc = Molecular visualization system on an Open Source foundation
-	pkgver = r4593.4948dd0f
+	pkgver = r4707.7b4e2af9
 	pkgrel = 1
 	url = https://pymol.org/
 	arch = x86_64
@@ -9,6 +9,7 @@ pkgbase = pymol-git
 	makedepends = gendesk
 	makedepends = libmmtf
 	makedepends = msgpack-c
+	makedepends = netcdf
 	makedepends = git
 	depends = freetype2
 	depends = glew
@@ -21,11 +22,10 @@ pkgbase = pymol-git
 	optdepends = ffmpeg
 	provides = pymol
 	conflicts = pymol
-	source = git+https://github.com/schrodinger/pymol-open-source.git
+	source = pymol::git+https://github.com/schrodinger/pymol-open-source.git
 	source = pymol.png::https://c.fsdn.com/allura/p/pymol/icon
+    source = apbstools_tcltk8.6.patch
 	sha512sums = SKIP
-	sha512sums = SKIP
-
+	sha512sums = 39917c1dc80cd6a59e8f6b3ea49a59491eaf23d14e32ac264f6d71f33007f686deb6a66e50e7f20ef9df5337038e3572b018633c361460d5ee0c1d8f0a8259d1
+   	sha512sums = 90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c
 pkgname = pymol-git
-
-
diff --git a/PKGBUILD b/PKGBUILD
index b088da09ae73..876a113b3e7b 100644
--- a/PKGBUILD
+++ b/PKGBUILD
@@ -1,50 +1,55 @@
 # Maintainer: Lorenzo Gaifas <brisvag at gmail dot com>
 
-pkgname=pymol-git
-_pkgname=pymol
-pkgver=r4593.4948dd0f
+_name=pymol
+pkgname="${_name}-git"
+pkgver=r4707.7b4e2af9
 pkgrel=1
 pkgdesc="Molecular visualization system on an Open Source foundation"
 arch=('x86_64')
 url="https://pymol.org/"
 license=('custom')
 depends=('freetype2' 'glew' 'glm' 'glut' 'python-numpy' 'tcsh')
-makedepends=('desktop-file-utils' 'gendesk' 'libmmtf' 'msgpack-c' 'git')
+makedepends=('desktop-file-utils' 'gendesk' 'libmmtf' 'msgpack-c' 'netcdf' 'git')
 optdepends=('python-pmw: pmw based UI'
             'python-pyqt5: Qt5 based UI'
 			'ffmpeg: MPEG encoding')
 conflicts=('pymol')
-provides=('pymol')
-source=(${pkgname}::'git+https://github.com/schrodinger/pymol-open-source.git'
-		${_pkgname}.png::'https://c.fsdn.com/allura/p/pymol/icon')
+provides=("${_name}=${pkgver}")
+source=(${_name}::"git+https://github.com/schrodinger/pymol-open-source.git"
+		${_name}.png::"https://c.fsdn.com/allura/p/pymol/icon"
+        "apbstools_tcltk8.6.patch")
 md5sums=('SKIP'
-		 'SKIP')
+         'a6b62ae41658a772f75b3b123a8e5c0b'
+         '138550367b74fd62a7c7bc48d339eb2d')
 
 pkgver() {
-  cd "${srcdir}/${pkgname}"
-  printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
+    cd "${srcdir}/${_name}"
+    printf "r%s.%s" "$(git rev-list --count HEAD)" "$(git rev-parse --short HEAD)"
 }
 
 prepare() {
   # create desktop file
-  gendesk -f -n --pkgname "${_pkgname}" --pkgdesc "${pkgdesc}" \
+  gendesk -f -n --pkgname "${_name}" --pkgdesc "${pkgdesc}" \
           --name="PyMOL Molecular Graphics System" \
           --categories="Science;Chemistry"
 
   # suppress non-zero exit code that breaks makepkg
-  sed -i '/sys.exit/ s,2,0,' "${srcdir}/${pkgname}/setup.py"
+  sed -i '/sys.exit/ s,2,0,' "${srcdir}/${_name}/setup.py"
+
+  # fix FS#39526
+  cd "${srcdir}/${_name}"
+  patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch"
 }
 
 build() {
-  cd "${srcdir}/${pkgname}"
+  cd "${srcdir}/${_name}"
   python setup.py build
 }
 
 package() {
-  cd "${srcdir}/${pkgname}"
+  cd "${srcdir}/${_name}"
   python setup.py install --prefix=/usr --root="${pkgdir}"
-  install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${_pkgname}/LICENSE"
+  install -Dm644 "LICENSE" "${pkgdir}/usr/share/licenses/${pkgname}/LICENSE"
   install -Dm644 "${srcdir}/pymol.desktop" "${pkgdir}/usr/share/applications/pymol.desktop"
   install -Dm644 "${srcdir}/pymol.png" "${pkgdir}/usr/share/pixmaps/pymol.png"
 }
-
diff --git a/apbstools_tcltk8.6.patch b/apbstools_tcltk8.6.patch
new file mode 100644
index 000000000000..f60b5c78a69a
--- /dev/null
+++ b/apbstools_tcltk8.6.patch
@@ -0,0 +1,106 @@
+--- 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))
+         self.selection = Pmw.EntryField(group.interior(),
+                                         labelpos='w',
+                                         label_text='Selection to use: ',
+@@ -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))
+         def quickFileValidation(s):
+             if s == '': return Pmw.PARTIAL
+             elif os.path.isfile(s): return Pmw.OK
+@@ -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))
+         self.pymol_generated_pqr_filename = Pmw.EntryField(group.interior(),
+                                                            labelpos = 'w',
+                                                            label_pyclass = FileDialogButtonClassFactory.get(self.setPymolGeneratedPqrFilename),
+@@ -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))
+
+         page = self.notebook.add('Visualization (2)')
+         group = VisualizationGroup(page,tag_text='Visualization',visgroup_num=2)
+         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))
+
+         # Create a couple of other empty pages
+         page = self.notebook.add('About')
+         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))
+         text = """This plugin integrates PyMOL (http://PyMOL.org/) with APBS (http://www.poissonboltzmann.org/apbs/).
+
+ Documentation may be found at
+@@ -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.ms_group = Pmw.Group(self.interior(),tag_text='Molecular Surface')
+             self.ms_buttonbox = Pmw.ButtonBox(self.ms_group.interior(), padx=0)
+@@ -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.fl_group = Pmw.Group(self.interior(),tag_text='Field Lines')
+             self.fl_buttonbox = Pmw.ButtonBox(self.fl_group.interior(), padx=0)
+@@ -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.pi_group = Pmw.Group(self.interior(),tag_text='Positive Isosurface')
+             self.pi_buttonbox = Pmw.ButtonBox(self.pi_group.interior(), padx=0)
+@@ -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.ni_group = Pmw.Group(self.interior(),tag_text='Negative Isosurface')
+             self.ni_buttonbox = Pmw.ButtonBox(self.ni_group.interior(), padx=0)
+@@ -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))
+
+
+