[gentoo-commits] proj/sci:ccp4 commit in: /

["Justin Lecher" <jlec@gentoo.org>]

commit:     1c75b2410a7dce9cc1762cb8c434cbabc12fe3ef
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Tue Jun 18 09:12:35 2013 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Tue Jun 18 09:12:35 2013 +0000
URL:        http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=commit;h=1c75b241

Merge branch 'master' into ccp4

* master:
  sci-chemistry/mics: New package
  sci-chemistry/talosn: New package
  Abinit & friends upgraded to sci-physics/abinit-7.2.2. BigDFT moved from sci-libs to sci-physics, sci-physics/abinit uses sci-libs/bigdft-abi instead. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as mostly used upstream. Old files cleaned up.
  Version of bigdft bumped to 1.7_pre24, moved from sci-libs to sci-physics. No longer used as a library by sci-physics/abinit. Usage of LIBDIR/finclude abandoned in favour of /usr/include, as used upstream.
  Don't let openmpi override malloc, works around sandbox issue in #462602
  Fixed bug in jabref ebuild.
  Renamed ebuild to conform with Gentoo Ebuild Naming Convention (TM).
  media-gfx/librecad: Cleanup and apply patch from bug #473388
  Mangling of the sources of sci-chemistry/freeon reduced, both for 2012.05.03, and for 9999.
  [sci-chemistry/nMOLDYN] Update deps
  [sci-chemistry/nMOLDYN] Add to overlay


 app-text/jabref/ChangeLog                          |  10 +
 ...jabref-2.10b.ebuild => jabref-2.10_beta.ebuild} |   8 +-
 media-gfx/librecad/ChangeLog                       |   6 +
 media-gfx/librecad/Manifest                        |   4 +-
 media-gfx/librecad/files/1.0.0_rc2-gcc4.6.patch    |  38 ---
 .../files/librecad-1.0.0_rc2-version.patch         |  11 -
 media-gfx/librecad/librecad-1.0.2.ebuild           |  45 ---
 media-gfx/librecad/librecad-2.0.0_beta5.ebuild     |  48 ---
 media-gfx/librecad/librecad-2.0.0_rc1.ebuild       |  27 +-
 media-gfx/librecad/metadata.xml                    |  23 +-
 sci-chemistry/freeon/ChangeLog                     |   9 +
 ...ch => freeon-2012.05.03-no_internal_hdf5.patch} |  32 +-
 .../files/freeon-9999-no_internal_hdf5.patch       |  25 ++
 .../files/freeon-9999-no_internal_libs.patch       |  47 ---
 sci-chemistry/mics/ChangeLog                       |  10 +
 sci-chemistry/mics/Manifest                        |   1 +
 .../{mgltools-autodocktools => mics}/metadata.xml  |   0
 sci-chemistry/mics/mics-1.00.2011.327.12.00.ebuild |  51 +++
 sci-chemistry/nMOLDYN/ChangeLog                    |  12 +
 sci-chemistry/nMOLDYN/Manifest                     |   1 +
 sci-chemistry/{trajng => nMOLDYN}/metadata.xml     |   0
 sci-chemistry/nMOLDYN/nMOLDYN-3.0.10.ebuild        |  24 ++
 sci-chemistry/talosn/ChangeLog                     |  10 +
 sci-chemistry/talosn/Manifest                      |   1 +
 .../metadata.xml                                   |   0
 .../talosn/talosn-4.01.2013.148.15.55.ebuild       |  59 ++++
 sci-libs/bigdft-abi/ChangeLog                      |  12 +
 sci-libs/bigdft-abi/Manifest                       |   3 +
 .../bigdft-abi-1.0.4.ebuild}                       |  79 +++--
 .../files/bigdft-abi-1.0.4-tests.tar.bz2           | Bin 0 -> 402968 bytes
 sci-libs/etsf_io/ChangeLog                         |   9 +-
 ..._io-1.0.3-r1.ebuild => etsf_io-1.0.3-r2.ebuild} |   0
 sci-libs/fox/ChangeLog                             |  10 +-
 ...patch => 4.1.2-r2-install-customizations.patch} |   0
 .../{fox-4.1.2-r1.ebuild => fox-4.1.2-r2.ebuild}   |  10 +-
 sci-libs/libxc/ChangeLog                           |  11 +-
 ...libxc-1.1.0-r1.ebuild => libxc-1.2.0-r1.ebuild} |  26 +-
 .../{libxc-1.2.0.ebuild => libxc-2.0.1.ebuild}     |  27 +-
 sci-libs/mumps/ChangeLog                           |   5 +-
 sci-libs/mumps/mumps-4.10.0-r2.ebuild              |   5 +-
 sci-libs/wannier90/ChangeLog                       |   7 +
 ...annier90-1.2.ebuild => wannier90-1.2-r1.ebuild} |   0
 sci-physics/abinit/ChangeLog                       |   9 +
 sci-physics/abinit/abinit-7.0.5.ebuild             | 356 ---------------------
 .../{abinit-7.0.4.ebuild => abinit-7.2.2.ebuild}   |  75 +++--
 sci-physics/abinit/files/6.0.3-fftw.patch          |  14 -
 .../abinit/files/6.12.1-libabinit_options.patch    |  57 ----
 sci-physics/abinit/files/6.12.3-gui-makefiles.tbz  | Bin 14600 -> 0 bytes
 sci-physics/atompaw/ChangeLog                      |   7 +
 ...aw-3.0.1.9.ebuild => atompaw-3.0.1.9-r1.ebuild} |  11 +-
 {sci-libs => sci-physics}/bigdft/ChangeLog         |  10 +-
 .../bigdft/bigdft-1.7_pre24.ebuild                 |  35 +-
 .../files/bigdft-1.7-dev.24-nolib_mods.patch       |  14 +-
 53 files changed, 497 insertions(+), 797 deletions(-)