Date: Monday, March 19, 2018 @ 13:39:26 Author: arcanis Revision: 309158
upgpkg: pymol 2.1.0-1 Modified: pymol/trunk/ChangeLog pymol/trunk/PKGBUILD Deleted: pymol/trunk/pymol-38899.patch -------------------+ ChangeLog | 8 + PKGBUILD | 35 ++----- pymol-38899.patch | 251 ---------------------------------------------------- 3 files changed, 22 insertions(+), 272 deletions(-) Modified: ChangeLog =================================================================== --- ChangeLog 2018-03-19 10:19:59 UTC (rev 309157) +++ ChangeLog 2018-03-19 13:39:26 UTC (rev 309158) @@ -1,3 +1,11 @@ +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) Modified: PKGBUILD =================================================================== --- PKGBUILD 2018-03-19 10:19:59 UTC (rev 309157) +++ PKGBUILD 2018-03-19 13:39:26 UTC (rev 309158) @@ -4,22 +4,24 @@ # Contributor: Tomasz Żok <tomasz dot zok at gmail dot com> pkgname=pymol -pkgver=1.8.6.0 -pkgrel=3 +pkgver=2.1.0 +_majorver=2 +pkgrel=1 pkgdesc="Molecular visualization system on an Open Source foundation" arch=('x86_64') url="http://pymol.org/" license=('custom') -depends=('glew' 'glut' 'libgl' 'libxml2' 'python2-numpy' 'python2-pmw' 'tcsh') +depends=('freetype2' 'glew' 'glut' 'python-numpy' 'tcsh') makedepends=('desktop-file-utils' 'gendesk' 'msgpack-c') -source=("http://downloads.sourceforge.net/project/pymol/pymol/1.8/pymol-v${pkgver}.tar.bz2" +optdepends=('python-pmw: pmw based UI' + 'python-pyqt4: Qt4 based UI' + 'python-pyqt5: Qt5 based UI') +source=("https://downloads.sourceforge.net/project/pymol/pymol/${_majorver}/pymol-v${pkgver}.tar.bz2" ${pkgname}.png::"https://c.fsdn.com/allura/p/pymol/icon" - "${pkgname}-38899.patch" "apbstools_tcltk8.6.patch") -md5sums=('dc317a4046d653417ac6d4a984176e26' - '0e9df23150d39cbcb8f79c38ce2a52e5' - '1f8152c4604ba2939b24e25a022937ca' - '138550367b74fd62a7c7bc48d339eb2d') +sha512sums=('67175c0668a13826febcb73f7c62a43cfa03a7f86bb80113d52fb337e7d29008684c03163fc06338c4d68edd9246ffcf63aec1ee3110ae91c8a71ef24ab7b605' + '4ceb8123b21becac7f2f1e7c3521b8fbaa22038d76b4749d07d286eed1646025dccd1962e58c0923357261006deb589aaf1fe4f6f53fd2327475d8db3adca5c4' + '90fce6d3c4364cd775b44bdd9013a08f26392339bec40ecd749220b3d11391381f5b159734bdb2e2ac675fbc016a6a1b9c4cec2fa8c9c0226609a5f09b610b9c') changelog=ChangeLog prepare() { @@ -30,14 +32,6 @@ # suppress non-zero exit code that breaks makepkg sed -i '/sys.exit/ s,2,0,' "${srcdir}/pymol/setup.py" - # change python to python2 - find "${pkgname}" -name '*.py' -type f -exec \ - sed -i 's|env python|env python2|g' {} \; - find "${pkgname}/test" -type f -exec \ - sed -i 's|bin/python|bin/python2|g' {} \; - # fix FS#38899 - patch -p0 -i "${pkgname}-38899.patch" - mv "${srcdir}/${pkgname}/modules/web" "${srcdir}/${pkgname}/modules/pymolweb" # fix FS#39526 cd "${srcdir}/${pkgname}" patch -p0 -i "${srcdir}/apbstools_tcltk8.6.patch" @@ -45,14 +39,12 @@ build() { cd "${srcdir}/${pkgname}" - # required c++11 - export CPPFLAGS="$CPPFLAGS -std=c++11" - python2 setup.py build + python setup.py build } package() { cd "${srcdir}/${pkgname}" - python2 setup.py install --prefix=/usr --root="${pkgdir}" + python setup.py install --prefix=/usr --root="${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" @@ -59,3 +51,4 @@ } # vim:set ts=2 sw=2 et: + Deleted: pymol-38899.patch =================================================================== --- pymol-38899.patch 2018-03-19 10:19:59 UTC (rev 309157) +++ pymol-38899.patch 2018-03-19 13:39:26 UTC (rev 309158) @@ -1,251 +0,0 @@ -diff -ruN pymol.orig/modules/pymol/importing.py pymol/modules/pymol/importing.py ---- pymol.orig/modules/pymol/importing.py 2014-01-15 00:02:55.000000000 +0400 -+++ pymol/modules/pymol/importing.py 2014-02-14 10:19:11.275591741 +0400 -@@ -473,7 +473,7 @@ - def _processPWG(fname,_self=cmd): - r = DEFAULT_ERROR - try: -- from web.pymolhttpd import PymolHttpd -+ from pymolweb.pymolhttpd import PymolHttpd - browser_flag = 0 - launch_flag = 0 - report_url = None -diff -ruN pymol.orig/modules/web/examples/content/SOP.html pymol/modules/web/examples/content/SOP.html ---- pymol.orig/modules/web/examples/content/SOP.html 2014-01-15 00:02:58.000000000 +0400 -+++ pymol/modules/web/examples/content/SOP.html 2014-02-14 10:19:11.275591741 +0400 -@@ -49,7 +49,7 @@ - The first seven - <a href="../index.html#sample01" target="_blank"> sample applications</a> - are implemented like this, residing in folders at --<code>$PYMOL_PATH/modules/web/examples/sample[0-7]</code> There -+<code>$PYMOL_PATH/modules/pymolweb/examples/sample[0-7]</code> There - may be future PyMOL web applications delivered with new versions of - PyMOL. Of course, you are free to write your own PyMOL web - applications and store them on each user's machine, or perhaps on a -diff -ruN pymol.orig/modules/web/examples/content/pwg.html pymol/modules/web/examples/content/pwg.html ---- pymol.orig/modules/web/examples/content/pwg.html 2014-01-15 00:02:58.000000000 +0400 -+++ pymol/modules/web/examples/content/pwg.html 2014-02-14 10:19:11.275591741 +0400 -@@ -58,13 +58,13 @@ - - <p>In contrast, the PWG file which launches the Sample 01 application is:</p> - <pre> --root $PYMOL_PATH/modules/web/examples/sample01/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs - browser - </pre> - - <p>which tells PyMOL to (1) launch its internal web server on a - dynamically assigned port with a root content directory of --$PYMOL_PATH/modules/web/examples/sample01/htdocs and (2) open -+$PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs and (2) open - up a local browser window pointing at that server instance. The - assumption in this scenario is that this newly-opened web page will be - responsible for sending requests to the PyMOL server (and thus, will -diff -ruN pymol.orig/modules/web/examples/content/running.html pymol/modules/web/examples/content/running.html ---- pymol.orig/modules/web/examples/content/running.html 2014-01-15 00:02:58.000000000 +0400 -+++ pymol/modules/web/examples/content/running.html 2014-02-14 10:19:11.278925074 +0400 -@@ -36,7 +36,7 @@ - - <p>The main index file with sample application links is located at</p> - --<pre>./modules/web/examples/index.html</pre> -+<pre>./modules/pymolweb/examples/index.html</pre> - - <p>If you are reading this file from within a browser, then you may - <a href="../index.html">return to it now</a> in order to try the sample -@@ -55,7 +55,7 @@ - - <pre># from within the PyMOL folder - --cd ./modules/web/examples -+cd ./modules/pymolweb/examples - - # then - -diff -ruN pymol.orig/modules/web/examples/content/server.html pymol/modules/web/examples/content/server.html ---- pymol.orig/modules/web/examples/content/server.html 2014-01-15 00:02:58.000000000 +0400 -+++ pymol/modules/web/examples/content/server.html 2014-02-14 10:19:11.278925074 +0400 -@@ -18,7 +18,7 @@ - browser window).</p> - - <p>The source code is located at --<code>$PYMOL_PATH/modules/web/pymolhttpd.py</code>, -+<code>$PYMOL_PATH/modules/pymolweb/pymolhttpd.py</code>, - and this file serves as a python module that can be imported by any - python script running inside of PyMOL. </p> - -@@ -33,7 +33,7 @@ - <p>Alternatively, pymolhttpd.py can be used as the start-up script - when you launch PyMOL.</p> - --<pre>pymol $PYMOL_PATH/modules/web/pymolhttpd.py</pre> -+<pre>pymol $PYMOL_PATH/modules/pymolweb/pymolhttpd.py</pre> - - <p>This will cause PyMOL to start serving requests on the default port - (8080, assuming of course that the port is not already claimed by -@@ -44,7 +44,7 @@ - <p> - The PyMOL web server module can be imported into and launched using code like this. - <pre> --from web import pymolhttpd -+from pymolweb import pymolhttpd - httpd = pymolhttpd.PymolHttpd("htdocs", 8080) - httpd.start() - </pre> -diff -ruN pymol.orig/modules/web/examples/index.html pymol/modules/web/examples/index.html ---- pymol.orig/modules/web/examples/index.html 2014-01-15 00:02:58.000000000 +0400 -+++ pymol/modules/web/examples/index.html 2014-02-14 10:19:11.288925075 +0400 -@@ -156,7 +156,7 @@ - services interface!</p> - - <p>The code for the applications above is located inside a series of folders located at: --<pre>$PYMOL_PATH/modules/web/examples/sample*</pre></p> -+<pre>$PYMOL_PATH/modules/pymolweb/examples/sample*</pre></p> - - </body> - </html> -diff -ruN pymol.orig/modules/web/examples/sample01/htdocs/api.html pymol/modules/web/examples/sample01/htdocs/api.html ---- pymol.orig/modules/web/examples/sample01/htdocs/api.html 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample01/htdocs/api.html 2014-02-14 10:19:11.288925075 +0400 -@@ -9,9 +9,9 @@ - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>load</b></font> --<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<i>filename, object, state, format, finish, discrete, quiet, multiplex, zoom, partial</i><pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre> - - </p></li> - <li><p><font face="Courier" size="2"><b>enable</b></font> -@@ -38,7 +38,7 @@ - </p></li> - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>color</b></font> - <i>color, selection, quiet, flags</i><pre><a target="result" href="/apply/pymol.cmd.color?color=yellow&selection=elem c">/apply/pymol.cmd.color?color=yellow&selection=elem c</a></pre> -@@ -118,9 +118,9 @@ - </p></li> - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/map.ccp4</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/map.ccp4</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>isomesh</b></font> - <i>name, map, level, selection, buffer, state, carve, source_state, quiet</i><pre><a target="result" href="/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0">/apply/pymol.cmd.isomesh?name=mesh&map=map&level=1.0</a></pre> -@@ -142,7 +142,7 @@ - </p></li> - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>show</b></font> - <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show?representation=sticks">/apply/pymol.cmd.show?representation=sticks</a></pre> -@@ -174,7 +174,7 @@ - </p></li> - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>show_as</b></font> - <i>representation, selection</i><pre><a target="result" href="/apply/pymol.cmd.show_as?representation=spheres">/apply/pymol.cmd.show_as?representation=spheres</a></pre> -@@ -224,7 +224,7 @@ - </p></li> - </ul><hr><p>Please click the link(s) below before testing methods in this section (in order).</p><pre><a target="result" href="/apply/pymol.cmd.reinitialize">/apply/pymol.cmd.reinitialize</a></pre> - --<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/web/examples/data/ref.pdb</a></pre> -+<pre><a target="result" href="/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb">/apply/pymol.cmd.load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/ref.pdb</a></pre> - - <ul><li><p><font face="Courier" size="2"><b>super</b></font> - <i>mobile, target, cutoff, cycles, gap, extend, max_gap, object, matrix, mobile_state, target_state, quiet, max_skip, transform, reset, seq, radius, scale, base, coord, expect, window, ante</i><pre><a target="result" href="/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/">/apply/pymol.cmd.create?name=helix1&selection=polymer and 5-17/</a></pre> -diff -ruN pymol.orig/modules/web/examples/sample01/start.pwg pymol/modules/web/examples/sample01/start.pwg ---- pymol.orig/modules/web/examples/sample01/start.pwg 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample01/start.pwg 2014-02-14 10:19:11.288925075 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample01/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample01/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample02/start.pwg pymol/modules/web/examples/sample02/start.pwg ---- pymol.orig/modules/web/examples/sample02/start.pwg 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample02/start.pwg 2014-02-14 10:19:11.292258408 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample02/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample02/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample03/start.pwg pymol/modules/web/examples/sample03/start.pwg ---- pymol.orig/modules/web/examples/sample03/start.pwg 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample03/start.pwg 2014-02-14 10:19:11.292258408 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample03/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample03/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js pymol/modules/web/examples/sample04/htdocs/pdbshow.js ---- pymol.orig/modules/web/examples/sample04/htdocs/pdbshow.js 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample04/htdocs/pdbshow.js 2014-02-14 10:19:11.292258408 +0400 -@@ -12,7 +12,7 @@ - function get_protein(a) { - // load protein, unless already loaded - if (load_state[a] == undefined) { -- load = "load?filename=$PYMOL_PATH/modules/web/examples/data/" + a + ".pdb.gz" + zoom; -+ load = "load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/" + a + ".pdb.gz" + zoom; - cmd(load); - zoom = "&zoom=0"; // subsequent loads shold not zoom - cmd("orient?selection=bymol organic and elem n&animate=2"); -diff -ruN pymol.orig/modules/web/examples/sample04/start.pwg pymol/modules/web/examples/sample04/start.pwg ---- pymol.orig/modules/web/examples/sample04/start.pwg 2014-01-15 00:02:56.000000000 +0400 -+++ pymol/modules/web/examples/sample04/start.pwg 2014-02-14 10:19:11.292258408 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample04/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample04/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample05/htdocs/index.html pymol/modules/web/examples/sample05/htdocs/index.html ---- pymol.orig/modules/web/examples/sample05/htdocs/index.html 2014-01-15 00:02:57.000000000 +0400 -+++ pymol/modules/web/examples/sample05/htdocs/index.html 2014-02-14 10:19:11.292258408 +0400 -@@ -108,7 +108,7 @@ - - function loadPDB(code) - { -- return cmd('load?filename=$PYMOL_PATH/modules/web/examples/data/'+code+'.pdb'); -+ return cmd('load?filename=$PYMOL_PATH/modules/pymolweb/examples/data/'+code+'.pdb'); - } - - </script> -diff -ruN pymol.orig/modules/web/examples/sample05/start.pwg pymol/modules/web/examples/sample05/start.pwg ---- pymol.orig/modules/web/examples/sample05/start.pwg 2014-01-15 00:02:57.000000000 +0400 -+++ pymol/modules/web/examples/sample05/start.pwg 2014-02-14 10:19:11.292258408 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample05/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample05/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample06/start.pwg pymol/modules/web/examples/sample06/start.pwg ---- pymol.orig/modules/web/examples/sample06/start.pwg 2014-01-15 00:02:57.000000000 +0400 -+++ pymol/modules/web/examples/sample06/start.pwg 2014-02-14 10:19:11.292258408 +0400 -@@ -1,3 +1,3 @@ --root $PYMOL_PATH/modules/web/examples/sample06/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample06/htdocs - browser - logging 0 -diff -ruN pymol.orig/modules/web/examples/sample07/start.pwg pymol/modules/web/examples/sample07/start.pwg ---- pymol.orig/modules/web/examples/sample07/start.pwg 2014-01-15 00:02:57.000000000 +0400 -+++ pymol/modules/web/examples/sample07/start.pwg 2014-02-14 10:19:11.295591741 +0400 -@@ -1,2 +1,2 @@ --root $PYMOL_PATH/modules/web/examples/sample07/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample07/htdocs - browser -diff -ruN pymol.orig/modules/web/examples/sample08/start.pwg pymol/modules/web/examples/sample08/start.pwg ---- pymol.orig/modules/web/examples/sample08/start.pwg 2014-01-15 00:02:57.000000000 +0400 -+++ pymol/modules/web/examples/sample08/start.pwg 2014-02-14 10:19:11.295591741 +0400 -@@ -1,3 +1,3 @@ --root $PYMOL_PATH/modules/web/examples/sample08/htdocs -+root $PYMOL_PATH/modules/pymolweb/examples/sample08/htdocs - browser - logging 0 \ No newline at end of file