update to new lange patches
Signed-off-by: Justin Lecher <jlec@gentoo.org>
sci-chemistry/rosetta: Add patches from www.csrosetta.org

Package-Manager: portage-2.2.0_alpha179
sci-chemistry/rosetta: Fix: Ebuild calls die in a subshell

Package-Manager: portage-2.2.0_alpha179
Merge branch 'master' into jlec

* master: (120 commits)
  add missing masks for live ebuilds
  dev-python/healpy: Initial import
  dev-java/jhealpix: Initial import
  sci-astronomy/healpix_idl: Initial import
  sci-astronomy/healpix_cxx: Initial import
  sci-astronomy/chealpix: Initial import
  sci-biology/twinscan: Bump to EAPI=5 and fix license
  sci-biology/ssaha2-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/smalt-bin: Version Bump; restrict license; add QA_PREBUILT for binaries
  sci-biology/sequin: Version BUmp; restrcit license; add QA_PREBUILT for binaries; install html files into sys path
  sci-biology/quicktree: Bump to EAPI=5 and fix license
  sci-biology/gap2caf: Bump to EAPI=5 and fix license; make it build with eautoreconf
  sci-biology/erpin: Bump to EAPI=5 and respect FLAGS / AR
  sci-biology/clover: Version BUmp; fixed license; respect LDFLAGS
  sci-chemistry/shiftx2: Respect FLAGS
  Enhanced the sci-chemistry/shiftx ebuild. Still needs some love for the emake part (portage complains about LDFLAGS not respected), but should work.
  sci-chemistry/pymol-plugins-psico: Bump to EAPI=5 and distutils-r1.eclass
  sci-chemistry/smmp: Bump to EAPI=5 and python-r1.eclass
  sci-chemistry/specView: Bump to EAPI=5 and python-single-r1.eclass
  sci-chemistry/pyquante: Bump to EAPI=5 and distutils-r1.eclass
  ...
Work in progress
Signed-off-by: Justin Lecher <jlec@gentoo.org>
Merge branch 'master' into jlec

* master: (29 commits)
  sci-chemistry/shiftx: Block shiftx2 at runtime
  sci-chemistry/shiftx: Fix patch and add patch for buffer overflow fix
  The announced, but forgotten, change in sci-libs/fox-4.1.2-r2 actually done.
  The announced, but forgotten, change in sci-libs/etsf_io-1.0.3-r2 actually done.
  sci-physics/abinit/files/6.12.3-gui-makefiles.tbz put back, its deletion was a mistake.
  sci-libs/trilinos: Version bump and rewrite
  sci-libs/coinor-clp: Version bump and patch for mpi
  For sci-libs/bigdft-abi and sci-physics/bigdft, filter LDFLAGS for cuda use not to break nvcc.
  To sci-libs/bigdft-abi and sci-physics/bigdft added dev-util/gdbus-codegen among dependencies.
  Spaces in the testing snippet of fortran code in sci-libs/bigdft-abi-1.0.4.ebuild protected from reformatting.
  fixed qt4 build
  fixing manifests
  big fixes of metadata and package sub-herd re-distribution
  sci-physics/openmx upgraded to 3.7.3 with some openMP and MPI C/F90 juggling, previous sci-physics/openmx-3.6 preserved for the time being.
  sci-chemistry/talosn: drop upstream path in favour of our
  sci-chemistry/modeller: Fix broken symlink, #473680
  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.
  ...
Completly removed the directory check in the java source (we have everything under control in gentoo).
Removed the .py extension from the -system.patch to make that part working again (it's installed without extensions to /usr/bin/!).

Package-Manager: portage-2.1.12.2
Merge pull request #85 from ercpe/jlec

Changes to the patch files to make the shiftx2 package working again.
Merge branch 'master' into jlec

* master: (36 commits)
  sci-libs/msms: Version BUmp; Bump to new distutil-r1.eclass
  app-doc/root-docs: version bump
  sci-physics/root: version bump
  sys-cluster/hpl: version bump and fixes
  fixed deps
  In sci-libs/bigdft-abi-1.0.4-r1, CUDA support made compile.
  moved to gx86
  moved to gx86
  Beautify
  Beautify
  Beautify.
  Added new package: projections
  Added new package: projections
  Bashified package name mangling.
  sys-cluster/modules: Prefix keyworded. Added tests. FHS fixes. Add bunch of fedora patches
  Fixed missing use flag.
  sci-chemistry/ucsf-tools: Fix compilation with latest gcc
  sci-chemistry/modeller: Fix lib position, #474696
  sci-chemistry/pymol: Update repo uri
  sci-chemistry/pymol: Update repo uri
  ...
Merge branch 'jlec'

* jlec:
  Completly removed the directory check in the java source (we have everything under control in gentoo). Removed the .py extension from the -system.patch to make that part working again (it's installed without extensions to /usr/bin/!).
  Work in progress Signed-off-by: Justin Lecher <jlec@gentoo.org>
  sci-chemistry/rosetta: Fix: Ebuild calls die in a subshell
  sci-chemistry/rosetta: Add patches from www.csrosetta.org
  update to new lange patches Signed-off-by: Justin Lecher <jlec@gentoo.org>