commit: e0b38273977b99aad7dd94c460f5783c98bb46a9 Author: Reinis Danne <rei4dan <AT> gmail <DOT> com> AuthorDate: Fri Jan 22 13:16:08 2016 +0000 Commit: Justin Lecher <jlec <AT> gentoo <DOT> org> CommitDate: Fri Feb 19 12:55:38 2016 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=e0b38273
sci-chemistry/ambertools: Bump to EAPI=6, cleanup - Remove unused eclass imports - Fix symlink creation - Declare loop variable local - Use proper functions for library installation sci-chemistry/ambertools/ambertools-15_p6.ebuild | 56 ++++++++++++++++------ .../ambertools/files/ambertools-15-gentoo.patch | 31 ++++-------- 2 files changed, 50 insertions(+), 37 deletions(-) diff --git a/sci-chemistry/ambertools/ambertools-15_p6.ebuild b/sci-chemistry/ambertools/ambertools-15_p6.ebuild index c3a46c5..a80390c 100644 --- a/sci-chemistry/ambertools/ambertools-15_p6.ebuild +++ b/sci-chemistry/ambertools/ambertools-15_p6.ebuild @@ -2,11 +2,11 @@ # Distributed under the terms of the GNU General Public License v2 # $Id$ -EAPI=5 +EAPI=6 PYTHON_COMPAT=( python2_7 ) -inherit eutils fortran-2 multilib python-r1 toolchain-funcs +inherit fortran-2 python-r1 toolchain-funcs DESCRIPTION="A suite for carrying out complete molecular mechanics investigations" HOMEPAGE="http://ambermd.org/#AmberTools"; @@ -49,11 +49,12 @@ pkg_setup() { } src_prepare() { - epatch \ - "${FILESDIR}"/${PN}-15-gentoo.patch \ + eapply \ + "${FILESDIR}"/${PN}-15-gentoo.patch + eapply -p0 \ "${FILESDIR}"/${PN}-15-update.{1..6}.patch - epatch_user + eapply_user cd "${S}"/AmberTools/src || die rm -r \ @@ -116,19 +117,20 @@ src_configure() { gnu || die } -src_test() { - source ${AMBERHOME}/amber.sh - - emake test -} - src_compile() { emake \ CC=$(tc-getCC) \ FC=$(tc-getFC) } +src_test() { + source ${AMBERHOME}/amber.sh + + emake test +} + src_install() { + local x for x in bin/* do [ ! -d ${x} ] && dobin ${x} @@ -143,16 +145,40 @@ src_install() { dodir /usr/share/${PN}/bin cd "${ED}/usr/bin" || die for x in * - do dosym /usr/bin/${x} ../share/${PN}/bin/${x} + do + dosym ../../../bin/${x} /usr/share/${PN}/bin/${x} done cd "${S}" || die dodoc doc/Amber15.pdf - dolib.a lib/*{.a,.so} - insinto /usr/$(get_libdir) - doins -r lib/python2.7 + + dolib.a lib/*.a + dolib.so lib/*.so + + local m=( + chemistry + compat24.py + cpinutils + fortranformat + interface + mcpb + mdoutanalyzer + MMPBSA_mods + ParmedTools + pymsmtexp.py + pymsmtlib + pymsmtmol + sander + sanderles + ) + for x in ${m[@]} + do + python_domodule lib/${EPYTHON}/site-packages/${x} + done + insinto /usr/include/${PN} doins include/* + insinto /usr/share/${PN} doins -r dat cd AmberTools || die diff --git a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch index f949a49..76be4f8 100644 --- a/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch +++ b/sci-chemistry/ambertools/files/ambertools-15-gentoo.patch @@ -1,5 +1,5 @@ diff --git a/AmberTools/src/Makefile b/AmberTools/src/Makefile -index 3d69773..c2a5045 100644 +index 3d69773..71c794c 100644 --- a/AmberTools/src/Makefile +++ b/AmberTools/src/Makefile @@ -15,12 +15,6 @@ install: $(INSTALLTYPE) @@ -36,26 +36,26 @@ index 3d69773..c2a5045 100644 (cd pbsa && $(MAKE) libinstall ) (cd rism && $(MAKE) $(RISM) ) (cd cifparse && $(MAKE) install ) -@@ -144,12 +131,6 @@ parallel: configured_parallel THIRDPARTY +@@ -144,12 +131,7 @@ parallel: configured_parallel THIRDPARTY # (cd pbsa && $(MAKE) clean && $(MAKE) install.parallel ) (cd pbsa && $(MAKE) libinstall ) $(MAKE) cpptraj - (cd byacc && $(MAKE) install ) - (cd ucpp-1.3 && $(MAKE) $(UCPP) ) -- (cd cifparse && $(MAKE) install ) + (cd cifparse && $(MAKE) install ) - (cd arpack && $(MAKE) install ); - (cd lapack && $(MAKE) $(LAPACK) ) - (cd blas && $(MAKE) $(BLAS) ) (cd mdgx && $(MAKE) $(MDGX) ) (if [ "$(RISM)" = "yes" ]; then \ cd rism && $(MAKE) install_mpi ; \ -@@ -215,18 +196,11 @@ netcdf_uninstall: +@@ -215,18 +197,12 @@ netcdf_uninstall: -/bin/rm -f netcdf_config.log ../lib/libnetcdf* ../include/netcdf.* clean:: - -(cd ucpp-1.3 && $(MAKE) clean ) - -(cd byacc && $(MAKE) clean ) -- -(cd cifparse && $(MAKE) clean ) + -(cd cifparse && $(MAKE) clean ) -(cd nab && $(MAKE) clean ) -(cd sff && $(MAKE) clean ) -(cd nss && $(MAKE) clean ) @@ -68,7 +68,7 @@ index 3d69773..c2a5045 100644 -(cd etc && $(MAKE) clean ) -(cd chamber && $(MAKE) clean ) -(cd pbsa && $(MAKE) clean ) -@@ -236,15 +210,12 @@ clean:: +@@ -236,15 +212,12 @@ clean:: -(cd lib && $(MAKE) clean ) -(cd ptraj && $(MAKE) clean ) -(cd cpptraj && $(MAKE) clean) @@ -84,7 +84,7 @@ index 3d69773..c2a5045 100644 -(cd mmpbsa_py && /bin/rm -fr MMPBSA.py.MPI build/ mpi4py-1.2.2/) -(cd mm_pbsa && $(MAKE) clean ) -(cd FEW && $(MAKE) clean ) -@@ -315,7 +286,7 @@ $(LIBDIR)/libxblas-amb.a: +@@ -315,7 +288,7 @@ $(LIBDIR)/libxblas-amb.a: $(LIBDIR)/libfftw3.a $(LIBDIR)/libfftw3_mpi.a: cd fftw-3.3 && $(MAKE) && $(MAKE) -j 1 install; @@ -447,19 +447,6 @@ index 12acf35..4f26593 100644 $(FC) $(FPPFLAGS) $(FFLAGS) $(AMBERFFLAGS) -o quasih$(SFX) \ quasih.o fileio.o thermo.o mexit.o \ $(LIBOBJ) binpos.o ../lib/sys.a -L$(LIBDIR) $(FLIBSF) \ -diff --git a/AmberTools/src/parmed/chemistry/unit/unit.py b/AmberTools/src/parmed/chemistry/unit/unit.py -index 7767f39..a8d8a47 100644 ---- a/AmberTools/src/parmed/chemistry/unit/unit.py -+++ b/AmberTools/src/parmed/chemistry/unit/unit.py -@@ -612,7 +612,7 @@ class UnitSystem(object): - to_base_units[m][n] = power - try: - self.from_base_units = ~to_base_units -- except ArithmeticError, e: -+ except ArithmeticError as e: - raise ArithmeticError("UnitSystem is not a valid basis set. " + str(e)) - - def __iter__(self): diff --git a/AmberTools/src/pbsa/Makefile b/AmberTools/src/pbsa/Makefile index 1b2c09a..6dc65a6 100644 --- a/AmberTools/src/pbsa/Makefile @@ -517,7 +504,7 @@ index df789e8..48227d5 100644 netlib: cd ../lapack && $(MAKE) $(LAPACK) diff --git a/AmberTools/src/sander/Makefile b/AmberTools/src/sander/Makefile -index 9b9488c..67fe45a 100644 +index 9b9488c..de25fc7 100644 --- a/AmberTools/src/sander/Makefile +++ b/AmberTools/src/sander/Makefile @@ -90,7 +90,7 @@ APBSOBJ= \ @@ -651,7 +638,7 @@ index 9b9488c..67fe45a 100644 -o rand2.o ../sff/rand2.c +dsarpack.o: ../sff/dsarpack.f -+ $(CC) -c -DSQM $(CNOOPTFLAGS) $(CFLAGS) $(AMBERCFLAGS) \ ++ $(FC) -c $(FPPFLAGS) $(CFLAGS) $(AMBERFFLAGS) \ + -o dsarpack.o ../sff/dsarpack.f + lmodC.o: ../sff/lmodC.c
