Version Bump

Package-Manager: portage-2.2_rc67/cvs/Linux x86_64

diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog
index 2501a7b31b6b3ed1ee5eac0ed1d5f7ffa1611ca9..48e64b6093fdd948c8332f8f17c4af899b1277bb 100644 (file)
--- a/sci-chemistry/coot/ChangeLog
+++ b/sci-chemistry/coot/ChangeLog
@@ -1,6 +1,12 @@
 # ChangeLog for sci-chemistry/coot
 # Copyright 1999-2010 Gentoo Foundation; Distributed under the GPL v2
-# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.23 2010/04/25 11:37:01 jlec Exp $
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/ChangeLog,v 1.24 2010/05/17 10:30:52 jlec Exp $
+
+*coot-0.6.1 (17 May 2010)
+
+  17 May 2010; Justin Lecher <jlec@gentoo.org> +files/0.6.1-libpng14.patch,
+  +coot-0.6.1.ebuild:
+  Version Bump
 
   22 Apr 2010; Justin Lecher <jlec@gentoo.org> coot-0.6.ebuild:
   Fixes for Python ABIs

diff --git a/sci-chemistry/coot/Manifest b/sci-chemistry/coot/Manifest
index 552f6cf069a0f929d42eb9b59d32128779f03388..e5dda7e121431c0113ea7f4e3f0ef6ef1f8423f8 100644 (file)
--- a/sci-chemistry/coot/Manifest
+++ b/sci-chemistry/coot/Manifest
@@ -9,17 +9,21 @@ AUX 0.3.3-link-against-guile-gtk-properly.patch 785 RMD160 7c98e6510b484baa6a47c
 AUX 0.4_pre2-as-needed.patch 19258 RMD160 a9ad8cbc84f9c2a35edb9ea7ec8926c3c4eb9491 SHA1 b49cee7d3cb03e1c4ac4c7c65e71cde99b9fa19d SHA256 a3c3bc4ac1ba9c2f7c6bed75b99f777f568989fc39253f352000f012949e87ab
 AUX 0.4_pre2-link-against-guile-gtk-properly.patch 800 RMD160 e4a9931de152385d552542e11d9a74a548810964 SHA1 74264270682a9135af92bf40a030c008876252e4 SHA256 c7271c82bb6e9e1ba89096ef0a7416609a81b455a1633637b84952db686d5080
 AUX 0.4_pre2-r549-fix-namespace-error.patch 1081 RMD160 ebecd51b87c39dc2c37e565f18fc88b7aa837d05 SHA1 f732df5f4795e728bdf217aac9c9f53952e2890c SHA256 fd271dd22eec5725fcbd20c68b57008eed0f435d1e0ac212fbfd389a0a970beb
+AUX 0.6.1-libpng14.patch 950 RMD160 c2d1c298ada419272d79d49972b13e414a234cd3 SHA1 bfd4828ab8e05863ce197c59865901ce3186fb66 SHA256 7b121a0bccd49da0c459003512a2c61368eeab41b33a6726525ace501eb03559
 AUX glib.m4 8444 RMD160 f3f4b2987796f16d17758f2af3459279351d6f2c SHA1 201eb58c2b3f3c5395dacd3913a4fb9d950d3276 SHA256 ada4a0a46bd00eda39afe77f675b721f60cd20c0080170848f4d7e92b4ba4dc8
 AUX gtk.m4 8516 RMD160 3860fe211902d5b9290f0a70e7d75ebec6b0ec67 SHA1 98b93b820423a52ebd80e3f1822a8f2bd4b3f15d SHA256 4eb6e0bb2c6863139d1fb4ca2d1d0f0ef07e3a85fdbb5ba98d03373f610f0c37
+DIST coot-0.6.1.tar.gz 12229005 RMD160 76cbf28320ff52f02b40164eea00e7ec8a6b6c2c SHA1 cdd74e394e07dc17b99f56fce7cf180a177d53d7 SHA256 7897eb62e1add5f8deddd16d24ffd9b4c763e784714cd47fa9777beb79f56066
 DIST coot-0.6.tar.gz 11929700 RMD160 6485a56f1d17b103e69b07b5fc128d266e83aa27 SHA1 ec3d486eda514e36bdbc99e8796484e584e4f851 SHA256 7700e7e758934ee5b4177c7bb8e1d7d564b838966dd3c77919fa08778627353b
+DIST greg-data-0.6.1.tar.gz 7930213 RMD160 e9a17d1ef2d3f15b3792ea5c7204901e0105b76b SHA1 f4158fa440406b88d0bb72880cdee9a3653c4233 SHA256 658a557b85ee6b90fc446cb3c605556586a2a5a0575ddd11b42265e019eb74a0
 DIST greg-data-0.6.tar.gz 7929638 RMD160 d152fb3703eec8c4b3df37b24a1fa2a80a4a9d9f SHA1 5dda8e7e393e3602aa51b2ae830287f93534312f SHA256 032f223f86c0ac504ace427ac84a2bf31f9adaf4da581207526b198f4bb2d76d
+EBUILD coot-0.6.1.ebuild 3587 RMD160 d1412dcdc2c4013357dc74f7d2a14357b2b23919 SHA1 1b537217d8502623272e54248e423b90cd79285d SHA256 ea0c6f041c247b373577ff455402d4e1293514256ba1a3480170531a3779e567
 EBUILD coot-0.6.ebuild 3617 RMD160 60b4b74c57d7bf740a07a5fa815b9d5b6d5c28be SHA1 b61021525370819f4a0a0e8df5a0e608f4eca924 SHA256 96272f82f4e5b5dfebee4ae96bcbd859a84399d7d860d1cfece0c18ac665fa4a
-MISC ChangeLog 3996 RMD160 119c7857eccaa99b9eb699afcd704b9eec71ba53 SHA1 5df76598ba99f34e1dc81f3bc35279b09164430b SHA256 da8c290880ee78b3ec5b9b70ba3f435d4de7910cd39d73aa0f1a0e04e8417ac6
+MISC ChangeLog 4137 RMD160 4c99efda548db3b99c7e1446fc334f0766e4408e SHA1 2b4dd9fe0e96dcf83af01f1ccb750152253fabdb SHA256 4e119f23c9f31afe6d15f07faae80d12c0572cb71fc5b1abff0313867b450ed1
 MISC metadata.xml 166 RMD160 4452298fd03e7c9395d1182bfe69d60a14144af6 SHA1 cb0b513473c0348f4f6f6cd9a132e4884155fddb SHA256 84c92b49702daf95eace8d2765215cbd8650da4ef776f9f700b5ce3785dec852
 -----BEGIN PGP SIGNATURE-----
 Version: GnuPG v2.0.14 (GNU/Linux)
 
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-nLkAoMSqurUwrnZzAfPozQGy0S/nXsGq
-=VY1d
+iEYEARECAAYFAkvxGuIACgkQgAnW8HDreRbIzgCfY0DgKypv4JpiG0LJpMKWM/Cr
+vl8An2SUi02TcVkp5LVnarphlcyXo/Yc
+=Y0TK
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diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild
new file mode 100644 (file)
index 0000000..d1c572c
--- /dev/null
+++ b/sci-chemistry/coot/coot-0.6.1.ebuild
@@ -0,0 +1,146 @@
+# Copyright 1999-2010 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/coot/coot-0.6.1.ebuild,v 1.1 2010/05/17 10:30:52 jlec Exp $
+
+EAPI="3"
+
+PYTHON_DEPEND="2"
+
+inherit autotools base eutils python versionator
+
+MY_S2_PV=$(replace_version_separator 2 - ${PV})
+MY_S2_P=${PN}-${MY_S2_PV/pre1/pre-1}
+MY_S_P=${MY_S2_P}-${PR/r/revision-}
+MY_PV=${PV}
+MY_P=${PN}-${MY_PV}
+
+DESCRIPTION="Crystallographic Object-Oriented Toolkit for model building, completion and validation"
+HOMEPAGE="http://www.biop.ox.ac.uk/coot/"
+SRC_URI="
+       http://www.biop.ox.ac.uk/coot/software/source/releases/${MY_P}.tar.gz
+       test? ( mirror://gentoo/greg-data-${PV}.tar.gz  )"
+
+SLOT="0"
+LICENSE="GPL-3"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+
+SCIDEPS="
+       >=sci-libs/ccp4-libs-6.1
+       >=sci-libs/clipper-20090520
+       >=sci-libs/coot-data-2
+       >=sci-libs/gsl-1.3
+       sci-libs/mmdb
+       sci-chemistry/reduce
+       sci-chemistry/refmac
+       sci-chemistry/probe"
+
+XDEPS="
+       gnome-base/libgnomecanvas
+       gnome-base/librsvg
+       media-libs/libpng
+       virtual/glut
+       >=x11-libs/gtk+-2.2
+       x11-libs/gtkglext"
+
+SCHEMEDEPS="
+       dev-scheme/net-http
+       dev-scheme/guile-gui
+       >=dev-scheme/guile-lib-0.1.6
+       dev-scheme/guile-www
+       =x11-libs/guile-gtk-2.1"
+
+RDEPEND="
+       ${SCIDEPS}
+       ${XDEPS}
+       ${SCHEMEDEPS}
+       dev-python/pygtk
+       >=dev-libs/gmp-4.2.2-r2
+       >=net-misc/curl-7.19.6"
+DEPEND="${RDEPEND}
+       dev-lang/swig
+       test? ( dev-scheme/greg )"
+
+S="${WORKDIR}/${MY_P}"
+#S="${WORKDIR}/${MY_S2_P}"
+
+pkg_setup() {
+       python_set_active_version 2
+}
+
+src_prepare() {
+       base_src_prepare
+
+       # Link against single-precision fftw
+       sed -i \
+               -e "s:lfftw:lsfftw:g" \
+               -e "s:lrfftw:lsrfftw:g" \
+               "${S}"/macros/clipper.m4
+
+       epatch "${FILESDIR}"/${PV}-libpng14.patch
+
+       eautoreconf
+}
+
+src_configure() {
+       # All the --with's are used to activate various parts.
+       # Yes, this is broken behavior.
+       econf \
+               --includedir='${prefix}/include/coot' \
+               --with-gtkcanvas-prefix="${EPREFIX}"/usr \
+               --with-clipper-prefix="${EPREFIX}"/usr \
+               --with-mmdb-prefix="${EPREFIX}"/usr \
+               --with-ssmlib-prefix="${EPREFIX}"/usr \
+               --with-gtkgl-prefix="${EPREFIX}"/usr \
+               --with-guile \
+               --with-python="${EPREFIX}"/usr \
+               --with-guile-gtk \
+               --with-gtk2 \
+               --with-pygtk
+}
+
+src_compile() {
+       emake || die "emake failed"
+       python_convert_shebangs $(python_get_version) src/coot_gtk2.py
+       cp "${S}"/src/coot_gtk2.py python/coot.py || die
+}
+
+src_test() {
+       mkdir "${T}"/coot_test
+
+       export COOT_STANDARD_RESIDUES="${S}/standard-residues.pdb"
+       export COOT_SCHEME_DIR="${S}/scheme/"
+       export COOT_RESOURCES_FILE="${S}/cootrc"
+       export COOT_PIXMAPS_DIR="${S}/pixmaps"
+       export COOT_DATA_DIR="${S}"
+       export COOT_PYTHON_DIR="${S}/python"
+       export PYTHONPATH="${COOT_PYTHON_DIR}:${PYTHONPATH}"
+       export PYTHONHOME="${EPREFIX}"/usr
+       export CCP4_SCR="${T}"/coot_test
+
+       export COOT_TEST_DATA_DIR="${WORKDIR}"/data/greg-data
+
+       cat > command-line-greg.scm <<- EOF
+       (use-modules (ice-9 greg))
+               (set! greg-tools (list "greg-tests"))
+                       (set! greg-debug #t)
+                       (set! greg-verbose 5)
+                       (let ((r (greg-test-run)))
+                               (if r
+                               (coot-real-exit 0)
+                               (coot-real-exit 1)))
+       EOF
+
+       einfo "Running test with following paths ..."
+       einfo "COOT_STANDARD_RESIDUES $COOT_STANDARD_RESIDUES"
+       einfo "COOT_SCHEME_DIR $COOT_SCHEME_DIR"
+       einfo "COOT_RESOURCES_FILE $COOT_RESOURCES_FILE"
+       einfo "COOT_PIXMAPS_DIR $COOT_PIXMAPS_DIR"
+       einfo "COOT_DATA_DIR $COOT_DATA_DIR"
+       einfo "COOT_PYTHON_DIR $COOT_PYTHON_DIR"
+       einfo "PYTHONPATH $PYTHONPATH"
+       einfo "PYTHONHOME $PYTHONHOME"
+       einfo "CCP4_SCR ${CCP4_SCR}"
+
+       "${S}"/src/coot-real --no-graphics --script command-line-greg.scm || die
+}

diff --git a/sci-chemistry/coot/files/0.6.1-libpng14.patch b/sci-chemistry/coot/files/0.6.1-libpng14.patch
new file mode 100644 (file)
index 0000000..cb09759
--- /dev/null
+++ b/sci-chemistry/coot/files/0.6.1-libpng14.patch
@@ -0,0 +1,17 @@
+http://code.google.com/p/coot/source/diff?spec=svn2956&old=2307&r=2907&format=unidiff&path=%2Ftrunk%2Fccp4mg-utils%2Fppmutil.cc
+diff --git a/ccp4mg-utils/ppmutil.cc b/ccp4mg-utils/ppmutil.cc
+index 4f0fb5e..20b1d0d 100644
+--- a/ccp4mg-utils/ppmutil.cc
++++ b/ccp4mg-utils/ppmutil.cc
+@@ -2501,7 +2501,11 @@ void image_info::readpng(const char *filename){
+         pixels[i*width*colourspace+j*colourspace+1] = png_ptr->palette[row_pointers[i][j]].green;
+         pixels[i*width*colourspace+j*colourspace+2] = png_ptr->palette[row_pointers[i][j]].blue;
+         if(row_pointers[i][j]<png_ptr->num_trans){
++#if PNG_LIBPNG_VER_MAJOR >= 1 && PNG_LIBPNG_VER_MINOR >=4
++         pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans_alpha[row_pointers[i][j]];
++#else
+          pixels[i*width*colourspace+j*colourspace+3] = png_ptr->trans[row_pointers[i][j]];
++#endif
+         }else
+          pixels[i*width*colourspace+j*colourspace+3] = 255;
+       }