From a3a97ec41d0aea2d985e4d12daf2a98f6d009e63 Mon Sep 17 00:00:00 2001 From: Justin Lecher Date: Thu, 2 Jun 2011 08:39:41 +0000 Subject: Fix collision with dev-python/webpy, #368947 (Portage version: 2.2.0_alpha37/cvs/Linux x86_64) --- sci-chemistry/pymol/ChangeLog | 432 +----------------------------- sci-chemistry/pymol/files/1.4.1-web.patch | 19 ++ sci-chemistry/pymol/metadata.xml | 1 + sci-chemistry/pymol/pymol-1.4.1.ebuild | 9 +- 4 files changed, 30 insertions(+), 431 deletions(-) create mode 100644 sci-chemistry/pymol/files/1.4.1-web.patch (limited to 'sci-chemistry/pymol') diff --git a/sci-chemistry/pymol/ChangeLog b/sci-chemistry/pymol/ChangeLog index e1c81953d04a..adab98470532 100644 --- a/sci-chemistry/pymol/ChangeLog +++ b/sci-chemistry/pymol/ChangeLog @@ -1,432 +1,8 @@ # ChangeLog for sci-chemistry/pymol # Copyright 1999-2011 Gentoo Foundation; Distributed under the GPL v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.80 2011/05/24 18:44:14 phajdan.jr Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/ChangeLog,v 1.81 2011/06/02 08:39:41 jlec Exp $ - 24 May 2011; Pawel Hajdan jr - pymol-1.3.1_pre3925-r1.ebuild: - x86 stable wrt bug #366229 + 02 Jun 2011; Justin Lecher +files/1.4.1-web.patch, + pymol-1.4.1.ebuild, metadata.xml: + Fix collision with dev-python/webpy, #368947 - 11 May 2011; Christoph Mende - pymol-1.3.1_pre3925-r1.ebuild: - Stable on amd64 wrt bug #366229 - -*pymol-1.4.1 (06 May 2011) - - 06 May 2011; Justin Lecher +files/1.4.1-data-path.patch, - -pymol-1.3.0.ebuild, -pymol-1.3.1_pre3924.ebuild, -pymol-1.4_beta1.ebuild, - +pymol-1.4.1.ebuild, +files/1.4.1-shaders.patch: - Version Bump, notified by euscan; cleaned old - - 05 Apr 2011; Justin Lecher pymol-1.4_beta1.ebuild: - Cleaned unneeded SRC_URI entries - -*pymol-1.4_beta1 (04 Apr 2011) - - 04 Apr 2011; Justin Lecher +files/1.4-shaders.patch, - +files/1.4-vmd.patch, +pymol-1.4_beta1.ebuild: - Version Bump - -*pymol-1.3.1_pre3925-r1 (12 Nov 2010) - - 12 Nov 2010; Justin Lecher -pymol-1.3.1_pre3925.ebuild, - +pymol-1.3.1_pre3925-r1.ebuild: - Fixed digests, #345151 - -*pymol-1.3.1_pre3925 (11 Nov 2010) - - 11 Nov 2010; Justin Lecher +pymol-1.3.1_pre3925.ebuild: - Version Bump, Python byte-compilation fix - -*pymol-1.3.1_pre3924 (22 Oct 2010) - - 22 Oct 2010; Justin Lecher -pymol-1.3.1_pre3923.ebuild, - +pymol-1.3.1_pre3924.ebuild: - Version Bump - - 15 Oct 2010; Justin Lecher pymol-1.3.1_pre3923.ebuild: - Mirroring the tarball on request of dberkholz - -*pymol-1.3.1_pre3923 (13 Oct 2010) - - 13 Oct 2010; Justin Lecher +pymol-1.3.1_pre3923.ebuild: - Version Bump to pre release - - 19 Sep 2010; Justin Lecher pymol-1.2.3-r1.ebuild, - pymol-1.3.0.ebuild: - rekeyworded for ~ppc, fixes #309007 - - 19 Sep 2010; Justin Lecher -pymol-0.99_rc10.ebuild, - pymol-1.2.3-r1.ebuild, pymol-1.3.0.ebuild: - Dropped ppc, #309007; dropped old version which doesn't work with recent - python - - 16 Sep 2010; Tomáš Chvátal - pymol-0.99_rc10.ebuild, pymol-1.2.3-r1.ebuild, pymol-1.3.0.ebuild: - virtual/glut -> media-libs/glut - - 29 Jun 2010; Justin Lecher -pymol-1.2.1.ebuild: - Removed unneeded version - - 24 Jun 2010; Christoph Mende pymol-1.2.3-r1.ebuild: - Stable on amd64 wrt bug #309007 - - 15 Jun 2010; Arfrever Frehtes Taifersar Arahesis - pymol-0.99_rc10.ebuild, pymol-1.2.1.ebuild: - Delete deprecation warnings. - -*pymol-1.3.0 (09 Jun 2010) - - 09 Jun 2010; Justin Lecher +files/1.3.0-vmd.patch, - pymol-1.2.3-r1.ebuild, +pymol-1.3.0.ebuild: - Version Bump, fixes for usage of python.eclass - - 09 Jun 2010; Justin Lecher -pymol-1.0-r1.ebuild, - -files/pymol-1.0-r1-data-path.patch, -pymol-1.2.2.ebuild, - -pymol-1.2.2-r2.ebuild, -pymol-1.2.2-r4.ebuild, - -files/nosplash-gentoo.patch: - removed old version which having problems with PYTHON ABIs stuff - - 16 May 2010; Justin Lecher pymol-1.2.2-r4.ebuild, - pymol-1.2.3-r1.ebuild: - RESTRICT PY ABI 2.5 - - 23 Mar 2010; Christian Faulhammer - pymol-1.2.3-r1.ebuild: - stable x86, bug 309007 - - 11 Mar 2010; Joseph Jezak pymol-1.2.2-r4.ebuild, - pymol-1.2.3-r1.ebuild: - Marked ~ppc for bug #299014. - -*pymol-1.2.3-r1 (22 Feb 2010) - - 22 Feb 2010; Justin Lecher - -pymol-1.2.3.ebuild, +pymol-1.2.3-r1.ebuild: - Fix the actual revision of version 1.2.3 - -*pymol-1.2.3 (20 Feb 2010) - - 20 Feb 2010; Justin Lecher +pymol-1.2.3.ebuild: - Version Bump - -*pymol-1.2.2-r4 (19 Feb 2010) - - 19 Feb 2010; Justin Lecher - -pymol-1.2.2-r1.ebuild, -pymol-1.2.2-r3.ebuild, +pymol-1.2.2-r4.ebuild: - Cleaned old revisions, fixed usage of distutils.eclass at EAPI=3, multiple - python version support - -*pymol-1.2.2-r3 (18 Feb 2010) - - 18 Feb 2010; Justin Lecher - +files/1.2.2-prefix.patch, +pymol-1.2.2-r3.ebuild: - Fixed usage of pathon eclass, EAPI=3 and PREFIX ready fixes, keyworded for - amd64-linux & x86-linux - -*pymol-1.2.2-r2 (10 Feb 2010) - - 10 Feb 2010; Justin Lecher - +files/1.2.2-data-path.patch, +pymol-1.2.2-r2.ebuild: - Fixing PYMOL_DATA again per 304259 - - 06 Feb 2010; Peter Volkov pymol-1.2.1.ebuild, - pymol-1.2.2.ebuild, pymol-1.2.2-r1.ebuild: - added missed inherit eutils, bug #303693, thank Christian Becke for - report. - -*pymol-1.2.2-r1 (01 Feb 2010) - - 01 Feb 2010; Justin Lecher - +pymol-1.2.2-r1.ebuild, +files/pymol-1.2.2-vmd.patch, metadata.xml: - vmd and numpy added to IUSE - apbs plugin support now depends on sci-chemistry/pymol-apbs-plugin - - 01 Feb 2010; Justin Lecher pymol-1.2.1.ebuild, - pymol-1.2.2.ebuild: - We don't install the splash window until we have a gentoo community - contribution, fixes bug 299020 - - 31 Jan 2010; Justin Lecher - -files/1.1/pymol-1.1-r2-data-path.patch, - -files/1.1/pymol-1.1-r2-shaders.patch, -files/1.1/apbs-070604.patch.bz2, - -files/1.1/nosplash-gentoo.patch: - Cleanup of forgotten files, fixes bug 274865 - Added myself as maintainer - - 31 Jan 2010; Justin Lecher pymol-1.2.1.ebuild, - pymol-1.2.2.ebuild, metadata.xml: - Needs media-libs/freetype:2, fixes bug 299019 - - 13 Jan 2010; Diego E. Pettenò pymol-1.2.2.ebuild: - Fix path to patch, bug #300399, thanks to Priit Laes for reporting and - jlec for warning me. - -*pymol-1.2.2 (30 Dec 2009) - - 30 Dec 2009; Diego E. Pettenò pymol-1.2.1.ebuild, - +pymol-1.2.2.ebuild, +files/pymol-1.2.2-shaders.patch: - Make 1.2.1 not use live subversion, bump to version 1.2.2. Thanks to - Justin Lecher who provided the updated ebuilds. Closes bug #282503. - - 03 Oct 2009; Petteri Räty -pymol-1.1-r2.ebuild: - Remove old version with built_with_use. Fixes bug #285463. - - 09 Sep 2009; Markus Meier pymol-1.2.1.ebuild: - amd64/x86 stable, bug #283639 - - 02 Aug 2009; Jeff Gardner - +files/1.2.1/nosplash-gentoo.patch, pymol-1.2.1.ebuild: - Fix nosplash patch - -*pymol-1.2.1 (02 Aug 2009) - - 02 Aug 2009; Jeff Gardner +pymol-1.2.1.ebuild, - +files/1.2.1/pymol-1.2.1-data-path.patch, - +files/1.2.1/pymol-1.2.1-shaders.patch: - New version, works with python 2.6, closes bug #269119. Many thanks to - Justin Lecher for doing the work, and fauli for a kick in the pants :) - - 06 May 2009; Markus Meier pymol-1.1-r2.ebuild: - amd64/x86 stable, bug #250903 - - 16 Apr 2009; Sébastien Fabbro - pymol-0.99_rc10.ebuild, pymol-1.1-r2.ebuild: - Proxying for jlec: removing numeric dependencies - - 19 Dec 2008; Jeff Gardner ChangeLog: - Rename patches - -*pymol-1.1-r2 (19 Dec 2008) - - 19 Dec 2008; Jeff Gardner -pymol-1.1-r1.ebuild, - +pymol-1.1-r2.ebuild: - Bump to fix compilation and use moved svn repository. Thanks to jlec on - IRC. - - 17 Aug 2008; Jeff Gardner - files/1.1/apbs-070604.patch.bz2: - Fix patch - -*pymol-1.1-r1 (13 Aug 2008) - - 13 Aug 2008; Jeff Gardner - +files/1.1/pymol-1.1-r1-shaders.patch, +files/1.1/nosplash-gentoo.patch, - +files/1.1/pymol-1.1-r1-data-path.patch, +files/1.1/apbs-070604.patch.bz2, - +pymol-1.1-r1.ebuild: - Version bump, thanks to jschmitz and hodak for the kick in the pants :) - - 02 Aug 2007; Jeff Gardner pymol-0.99_rc10.ebuild: - Fix ESVN_REPO_URI wrt bug #187462. Thanks to Michael Mysinger. - - 11 Jul 2007; Jeff Gardner pymol-1.0-r1.ebuild: - Fix svn path wrt bug 184948. Thanks to Rene Meier. - - 04 Jul 2007; Jeff Gardner ChangeLog: - Updating Manifest. - - 04 Jul 2007; Jeff Gardner - -files/pymol-0.99_rc6-data-path.patch, -pymol-0.99_rc6-r2.ebuild: - Removing unneeded files. - - 04 Jul 2007; Christoph Mende pymol-0.99_rc10.ebuild: - Stable on amd64 wrt bug #183879 - - 03 Jul 2007; Jeff Gardner - -files/pymol-0.99_rc8-data-path.patch: - Removed unneeded file. - -*pymol-1.0-r1 (03 Jul 2007) - - 03 Jul 2007; Jeff Gardner - +files/pymol-1.0-r1-data-path.patch, -files/header_order.patch, - -files/pymol-gentoo.diff, -files/setup.py-gentoo.patch, - -files/setup2.py-gentoo.patch, -pymol-0.98.ebuild, -pymol-0.99_rc8.ebuild, - pymol-0.99_rc10.ebuild, +pymol-1.0-r1.ebuild: - Adding 1.0 release, changed LICENCE to pymol for the last 2 releases, and - cleaned up old files. - - 02 Jul 2007; Christian Faulhammer - pymol-0.99_rc10.ebuild: - stable x86, bug 183879 - - 02 Jul 2007; Lars Weiler pymol-0.99_rc10.ebuild: - Stable on ppc; bug #183879. - - 14 Jun 2007; Jeff Gardner pymol-0.99_rc10.ebuild: - Removing dev-python/numeric dependency wrt bug #181653. - -*pymol-0.99_rc10 (06 Jun 2007) - - 06 Jun 2007; Jeff Gardner - +files/pymol-0.99_rc10-data-path.patch, +pymol-0.99_rc10.ebuild: - Adding pymol-0.99_rc10 which now depends on virtual/glut instead of - media-libs/glut. - - 01 Jun 2007; nixnut pymol-0.99_rc6-r2.ebuild: - Stable on ppc wrt bug 176831 - - 16 May 2007; Steve Dibb pymol-0.99_rc6-r2.ebuild: - amd64 stable, bug 176831 - - 07 May 2007; Raúl Porcel pymol-0.99_rc6-r2.ebuild: - x86 stable wrt #176831 - - 04 May 2007; Jeff Gardner - +files/pymol-0.99_rc8-data-path.patch: - Adding the forgotten pymol-0.99_rc8-data-path.patch. - -*pymol-0.99_rc8 (02 May 2007) - - 02 May 2007; Jeff Gardner +pymol-0.99_rc8.ebuild: - Version bump to pymol-0.99_rc8, big thanks to hodak at ncsu. - - 10 Feb 2007; Steve Dibb pymol-0.98.ebuild: - amd64 stable, bug 165712 - - 07 Jan 2007; Danny van Dyk -pymol-0.97.ebuild, - -pymol-0.99_rc6.ebuild, -pymol-0.99_rc6-r1.ebuild: - QA: Removed unused versions. - - 22 Oct 2006; Olivier Fisette pymol-0.98.ebuild: - Backporting Tkinter fix to the stable branch. - - 22 Oct 2006; Olivier Fisette - pymol-0.99_rc6-r2.ebuild: - Added build-time Python Tkinter dependency check. - - 20 Sep 2006; Donnie Berkholz ; metadata.xml: - (#148281) Change herd to sci-chemistry from sci. - - 19 Sep 2006; Donnie Berkholz ; pymol-0.98.ebuild, - pymol-0.99_rc6.ebuild, pymol-0.99_rc6-r1.ebuild, pymol-0.99_rc6-r2.ebuild: - Switch dep back to media-libs/glut from virtual/glut, pymol works really - poorly with freeglut. You get messages about being unable to acquire a - direct rendering context (i.e., no accelerated 3D). - -*pymol-0.99_rc6-r2 (26 May 2006) - - 26 May 2006; Olivier Fisette - +pymol-0.99_rc6-r2.ebuild: - Moved path variable declarations from the wrapper to an env.d file - (necessary for Python scripting). - -*pymol-0.99_rc6-r1 (16 Mar 2006) - - 16 Mar 2006; Olivier Fisette - +files/pymol-0.99_rc6-data-path.patch, pymol-0.99_rc6.ebuild, - +pymol-0.99_rc6-r1.ebuild: - Put the 0.99 series back in the testing branch. This has not been tested for - 30 days, and is buggy. (It was commited straight to stable.) Fixed - references to shared data in the mutagenesis wizard and other modules - (0.99_rc6-r1) (thanks to Pierres-Yves Savard for - reporting). - -*pymol-0.99_rc6 (07 Mar 2006) - - 07 Mar 2006; Donnie Berkholz ; - +pymol-0.99_rc6.ebuild, -pymol-0.99.ebuild: - (#124994) Upstream doesn't understand how to tell people when an actual - version is released, instead they silently push out a series of release - candidates and call them all 0.99. - -*pymol-0.99 (03 Mar 2006) - - 03 Mar 2006; Donnie Berkholz ; +pymol-0.99.ebuild: - (#124611) New version. Based on ebuild from hodak@nemo.physics.ncsu.edu, - with changes to locations as suggested by upstream. - - 19 Dec 2005; Donnie Berkholz ; pymol-0.98.ebuild: - virtual/glut, not media-libs/glut. - - 13 Aug 2005; Michael Hanselmann pymol-0.98.ebuild: - Stable on ppc. - - 25 Jun 2005; Olivier Fisette -pymol-0.88.ebuild, - pymol-0.98.ebuild: - Added to x86. Removed obsolete version. - - 17 Jun 2005; Michael Hanselmann pymol-0.97.ebuild: - Stable on ppc. - -*pymol-0.98 (18 May 2005) - - 18 May 2005; Olivier Fisette -pymol-0.90.ebuild, - -pymol-0.95.ebuild, +pymol-0.98.ebuild: - New version: 0.98. Removed obsolete versions. - - 13 May 2005; Olivier Fisette pymol-0.97.ebuild: - Fixed multilib issue (bug #92103). - - 04 May 2005; David Holm pymol-0.97.ebuild: - Readded to ~ppc. Please don't remove it without filing a proper bug report. - - 06 Feb 2005; Simon Stelling pymol-0.97.ebuild: - added ~amd64 - -*pymol-0.97 (24 Dec 2004) - - 24 Dec 2004; Olivier Fisette +metadata.xml, - +files/header_order.patch, +files/nosplash-gentoo.patch, - +files/pymol-gentoo.diff, +files/setup.py-gentoo.patch, - +files/setup2.py-gentoo.patch, +pymol-0.88.ebuild, +pymol-0.90.ebuild, - +pymol-0.95.ebuild, +pymol-0.97.ebuild: - Moved from app-sci/pymol to sci-chemistry/pymol. - - 31 Oct 2004; Olivier Fisette pymol-0.97.ebuild: - Added to x86. - -*pymol-0.97 (26 Jul 2004) - - 26 Jul 2004; Olivier Fisette pymol-0.97.ebuild: - Version bump suggested by Stéphane Gagné (bug #58097). - Removed header order patch since it is no longer needed. - -*pymol-0.95 (20 Apr 2004) - - 20 Apr 2004; Patrick Kursawe pymol-0.95.ebuild, - files/header_order.patch: - Version bump. Needed a little patch and a change to the setup2.py call (if it - does not find the modules, it will create no python.com) - - 19 Apr 2004; Patrick Kursawe pymol-0.82.ebuild, - pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild: - Adding IUSE, cleanup - - 03 Mar 2004; Peter Bienstman pymol-0.90: - marked stable on x86 - - 02 Sep 2003; Alastair Tse pymol-0.82.ebuild, - pymol-0.86.ebuild, pymol-0.88.ebuild, pymol-0.90.ebuild: - moved dev-python/Numeric to dev-python/numeric - -*pymol-0.90 (23 Jul 2003) - - 23 Jul 2003; George Shapovalov pymol-0.90, files/setup.py-gentoo.patch : - new version + fix for setup.py, (#24967) - thanks to Ben Cornett for the update - -*pymol-0.88 (29 Jun 2003) - - 19 Jun 2003; George Shapovalov pymol-0.88.ebuild, files/{digest-pymol-0.88,nosplash-gentoo.patch,setup2.py-gentoo.patch} : - new version (#22235) - now uses distutils for python - thanks to Todd Geders for update notification - and Ben Cornett for "distutilized" ebuild submission - -*pymol-0.86 (05 Feb 2003) - - 05 Feb 2003; George Shapovalov pymol-0.86.ebuild, files/digest-pymol-0.86 : - new version, (#13531) - removed -funroll-loops from CFLAGS - -*pymol-0.82 (17 Jul 2002) - - 19 Oct 2002; Daniel Ahlberg pymol-0.82.ebuild : - Updated to mirror://sourceforge in SRC_URI. - - 17 Jul 2002; George Shapovalov pymol-0.82.ebuild, files/digest-pymol-0.82, ChangeLog : - - Inital release, - molecular visualization package - - ebuild submitted by Ben Cornett diff --git a/sci-chemistry/pymol/files/1.4.1-web.patch b/sci-chemistry/pymol/files/1.4.1-web.patch new file mode 100644 index 000000000000..2d6957df594d --- /dev/null +++ b/sci-chemistry/pymol/files/1.4.1-web.patch @@ -0,0 +1,19 @@ + setup.py | 5 +---- + 1 files changed, 1 insertions(+), 4 deletions(-) + +diff --git a/setup.py b/setup.py +index b0f4dad..94d292d 100644 +--- a/setup.py ++++ b/setup.py +@@ -180,10 +180,7 @@ setup ( # Distribution meta-data + 'pymol/opengl/gl', + 'pymol/opengl/glu', + 'pymol/opengl/glut', +- 'pymol/wizard', +- 'web', +- 'web/examples', +- 'web/javascript', ], ++ 'pymol/wizard', ], + ext_modules = [ + Extension("pymol._cmd", [ + "modules/cealign/src/ccealignmodule.cpp", diff --git a/sci-chemistry/pymol/metadata.xml b/sci-chemistry/pymol/metadata.xml index 4a1b6bfe8bb6..bf11e08cfb39 100644 --- a/sci-chemistry/pymol/metadata.xml +++ b/sci-chemistry/pymol/metadata.xml @@ -10,5 +10,6 @@ Compile numpy support Build with Shaders support - good for high-end 3D video cards. Enable vmd module for trajectories + Install Pymodule needed for web app support diff --git a/sci-chemistry/pymol/pymol-1.4.1.ebuild b/sci-chemistry/pymol/pymol-1.4.1.ebuild index c2a37b37235d..e52f29d26142 100644 --- a/sci-chemistry/pymol/pymol-1.4.1.ebuild +++ b/sci-chemistry/pymol/pymol-1.4.1.ebuild @@ -1,6 +1,6 @@ # Copyright 1999-2011 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 -# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4.1.ebuild,v 1.1 2011/05/06 07:59:31 jlec Exp $ +# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/pymol/pymol-1.4.1.ebuild,v 1.2 2011/06/02 08:39:41 jlec Exp $ EAPI="3" @@ -19,7 +19,7 @@ SRC_URI="http://dev.gentoo.org/~jlec/distfiles/${P}.tar.xz" LICENSE="PSF-2.2" SLOT="0" KEYWORDS="~amd64 ~ppc ~x86 ~amd64-linux ~x86-linux" -IUSE="apbs numpy vmd" +IUSE="apbs numpy vmd web" DEPEND=" dev-python/numpy @@ -35,7 +35,8 @@ DEPEND=" sci-chemistry/apbs sci-chemistry/pdb2pqr sci-chemistry/pymol-apbs-plugin - )" + ) + web? ( !dev-python/webpy )" RDEPEND="${DEPEND}" src_prepare() { @@ -43,6 +44,8 @@ src_prepare() { "${FILESDIR}"/${PV}-data-path.patch \ "${FILESDIR}"/${PV}-shaders.patch + use web || epatch "${FILESDIR}"/${PV}-web.patch + epatch "${FILESDIR}"/1.2.2-prefix.patch && \ eprefixify setup.py -- cgit v1.2.3-65-gdbad