diff options
-rw-r--r-- | sci-chemistry/coot/ChangeLog | 8 | ||||
-rw-r--r-- | sci-chemistry/coot/Manifest | 12 | ||||
-rw-r--r-- | sci-chemistry/coot/coot-0.6.1.ebuild | 146 | ||||
-rw-r--r-- | sci-chemistry/coot/files/0.6.1-libpng14.patch | 17 |
4 files changed, 178 insertions, 5 deletions
diff --git a/sci-chemistry/coot/ChangeLog b/sci-chemistry/coot/ChangeLog index 2501a7b31b6b..48e64b6093fd 100644 --- 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 552f6cf069a0..e5dda7e12143 100644 --- 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) -iEYEARECAAYFAkvUKWMACgkQgAnW8HDreRbQ6ACfeQIQzD4lqWAUQvXc9BhZCp6X -nLkAoMSqurUwrnZzAfPozQGy0S/nXsGq -=VY1d +iEYEARECAAYFAkvxGuIACgkQgAnW8HDreRbIzgCfY0DgKypv4JpiG0LJpMKWM/Cr +vl8An2SUi02TcVkp5LVnarphlcyXo/Yc +=Y0TK -----END PGP SIGNATURE----- diff --git a/sci-chemistry/coot/coot-0.6.1.ebuild b/sci-chemistry/coot/coot-0.6.1.ebuild new file mode 100644 index 000000000000..d1c572cdc20c --- /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 index 000000000000..cb09759ed1a2 --- /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; + } |