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authorReinis Danne <rei4dan@gmail.com>2016-01-22 15:16:08 +0200
committerJustin Lecher <jlec@gentoo.org>2016-02-19 13:55:38 +0100
commite0b38273977b99aad7dd94c460f5783c98bb46a9 (patch)
tree53922a4c2bc52dd4384e786b568579fa19ba3e7d /sci-chemistry
parentsci-chemistry/ambertools: Version bump to 15 (diff)
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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
Diffstat (limited to 'sci-chemistry')
-rw-r--r--sci-chemistry/ambertools/ambertools-15_p6.ebuild56
-rw-r--r--sci-chemistry/ambertools/files/ambertools-15-gentoo.patch31
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 c3a46c561..a80390cdc 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 f949a4945..76be4f8af 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