Date: Wednesday, October 24, 2018 @ 21:41:13 Author: arcanis Revision: 398888
archrelease: copy trunk to community-x86_64 Added: pymol/repos/community-x86_64/ChangeLog (from rev 398887, pymol/trunk/ChangeLog) pymol/repos/community-x86_64/PKGBUILD (from rev 398887, pymol/trunk/PKGBUILD) pymol/repos/community-x86_64/apbstools_tcltk8.6.patch (from rev 398887, pymol/trunk/apbstools_tcltk8.6.patch) Deleted: pymol/repos/community-x86_64/ChangeLog pymol/repos/community-x86_64/PKGBUILD pymol/repos/community-x86_64/apbstools_tcltk8.6.patch --------------------------+ ChangeLog | 116 ++++++++++++------------ PKGBUILD | 104 ++++++++++------------ apbstools_tcltk8.6.patch | 212 ++++++++++++++++++++++----------------------- 3 files changed, 217 insertions(+), 215 deletions(-) Deleted: ChangeLog =================================================================== --- ChangeLog 2018-10-24 21:40:53 UTC (rev 398887) +++ ChangeLog 2018-10-24 21:41:13 UTC (rev 398888) @@ -1,56 +0,0 @@ -2.1.0-1: -* upstream update -* use python3 instead of python2 -* move pmw to optdep list - -1.8.6.2-1: -upstream update - -1.8.6.0-2: -rollback to python2 (see FS#53654) - -1.8.6.0-1: -* upstream update -* use python3 instead of python2 - -1.8.4.0-1: -upstream update - -1.8.2.1-2 -glew-2.0 rebuild - -1.8.2.1-1: -upstream update - -1.8.2.0-2: -drop install file, use pacman hooks instead - -1.8.2.0-1: -upstream update - -1.8.0.0.r4144-1: -upstream update - -1.8.0.0-1: -upstream update - -1.7.6.0-1: -upstream update - -1.7.4.0-2: -glew rebuild - -1.7.4.0-1: -upstream update - -1.7.2.1-2: -fix dep list - -1.7.2.1-1: -upstream update - -1.7.2.0-2: -glew rebuild - -1.7.2.0-1: -upstream update Copied: pymol/repos/community-x86_64/ChangeLog (from rev 398887, pymol/trunk/ChangeLog) =================================================================== --- ChangeLog (rev 0) +++ ChangeLog 2018-10-24 21:41:13 UTC (rev 398888) @@ -0,0 +1,60 @@ +2.2.0-1: +* upstream update +* use github sources + +2.1.0-1: +* upstream update +* use python3 instead of python2 +* move pmw to optdep list + +1.8.6.2-1: +upstream update + +1.8.6.0-2: +rollback to python2 (see FS#53654) + +1.8.6.0-1: +* upstream update +* use python3 instead of python2 + +1.8.4.0-1: +upstream update + +1.8.2.1-2 +glew-2.0 rebuild + +1.8.2.1-1: +upstream update + +1.8.2.0-2: +drop install file, use pacman hooks instead + +1.8.2.0-1: +upstream update + +1.8.0.0.r4144-1: +upstream update + +1.8.0.0-1: +upstream update + +1.7.6.0-1: +upstream update + +1.7.4.0-2: +glew rebuild + +1.7.4.0-1: +upstream update + +1.7.2.1-2: +fix dep list + +1.7.2.1-1: +upstream update + +1.7.2.0-2: +glew rebuild + +1.7.2.0-1: +upstream update Deleted: PKGBUILD =================================================================== --- PKGBUILD 2018-10-24 21:40:53 UTC (rev 398887) +++ PKGBUILD 2018-10-24 21:41:13 UTC (rev 398888) @@ -1,53 +0,0 @@ -# $Id$ -# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org> -# Contributor: graysky -# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com> - -pkgname=pymol -pkgver=2.1.0 -_majorver=2 -pkgrel=4 -pkgdesc="Molecular visualization system on an Open Source foundation" -arch=('x86_64') -url="http://pymol.org/" -license=('custom') -depends=('freetype2' 'glew' 'glut' 'python-numpy' 'tcsh') -makedepends=('desktop-file-utils' 'gendesk' 'msgpack-c') -optdepends=('python-pmw: pmw based UI' - 'python-pyqt5: Qt5 based UI') -source=("https://downloads.sourceforge.net/project/pymol/pymol/${_majorver}/pymol-v${pkgver}.tar.bz2" - ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon" - "apbstools_tcltk8.6.patch") -sha512sums=('67175c0668a13826febcb73f7c62a43cfa03a7f86bb80113d52fb337e7d29008684c03163fc06338c4d68edd9246ffcf63aec1ee3110ae91c8a71ef24ab7b605' - '39917c1dc80cd6a59e8f6b3ea49a59491eaf23d14e32ac264f6d71f33007f686deb6a66e50e7f20ef9df5337038e3572b018633c361460d5ee0c1d8f0a8259d1' - '90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c') -changelog=ChangeLog - -prepare() { - # create desktop file - gendesk -f -n --pkgname "${pkgname}" --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}/pymol/setup.py" - # fix FS#39526 - cd "${srcdir}/${pkgname}" - patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch" -} - -build() { - cd "${srcdir}/${pkgname}" - python setup.py build -} - -package() { - cd "${srcdir}/${pkgname}" - python setup.py install --prefix=/usr --root="${pkgdir}" - 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" -} - -# vim:set ts=2 sw=2 et: - Copied: pymol/repos/community-x86_64/PKGBUILD (from rev 398887, pymol/trunk/PKGBUILD) =================================================================== --- PKGBUILD (rev 0) +++ PKGBUILD 2018-10-24 21:41:13 UTC (rev 398888) @@ -0,0 +1,51 @@ +# Maintainer: Evgeniy Alekseev <arcanis at archlinux dot org> +# Contributor: graysky +# Contributor: Tomasz Żok <tomasz dot zok at gmail dot com> + +pkgname=pymol +pkgver=2.2.0 +pkgrel=1 +pkgdesc="Molecular visualization system on an Open Source foundation" +arch=('x86_64') +url="http://pymol.org/" +license=('custom') +depends=('freetype2' 'glew' 'glm' 'glut' 'python-numpy' 'tcsh') +makedepends=('desktop-file-utils' 'gendesk' 'msgpack-c') +optdepends=('python-pmw: pmw based UI' + 'python-pyqt5: Qt5 based UI') +source=("https://github.com/schrodinger/pymol-open-source/archive/v${pkgver}.tar.gz" + ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon" + "apbstools_tcltk8.6.patch") +sha512sums=('56776586276208d42cc4bd4c3cb7d6b9a08e7239186b8f398c75cb57f85e05ebf51aaa8cdec5672e56beeda26f1cd9d14c6de7fba1a741f9c8ec22c1292b9c63' + '39917c1dc80cd6a59e8f6b3ea49a59491eaf23d14e32ac264f6d71f33007f686deb6a66e50e7f20ef9df5337038e3572b018633c361460d5ee0c1d8f0a8259d1' + '90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c') +changelog=ChangeLog + +prepare() { + # create desktop file + gendesk -f -n --pkgname "${pkgname}" --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}/${pkgname}-open-source-${pkgver}/setup.py" + # fix FS#39526 + cd "${srcdir}/${pkgname}-open-source-${pkgver}" + patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch" +} + +build() { + cd "${srcdir}/${pkgname}-open-source-${pkgver}" + python setup.py build +} + +package() { + cd "${srcdir}/${pkgname}-open-source-${pkgver}" + python setup.py install --prefix=/usr --root="${pkgdir}" + install -Dm644 "LICENSE" "${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" +} + +# vim:set ts=2 sw=2 et: + Deleted: apbstools_tcltk8.6.patch =================================================================== --- apbstools_tcltk8.6.patch 2018-10-24 21:40:53 UTC (rev 398887) +++ apbstools_tcltk8.6.patch 2018-10-24 21:41:13 UTC (rev 398888) @@ -1,106 +0,0 @@ ---- 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)) - - - Copied: pymol/repos/community-x86_64/apbstools_tcltk8.6.patch (from rev 398887, pymol/trunk/apbstools_tcltk8.6.patch) =================================================================== --- apbstools_tcltk8.6.patch (rev 0) +++ apbstools_tcltk8.6.patch 2018-10-24 21:41:13 UTC (rev 398888) @@ -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)) + + +