Attachment 221157 Details for Bug 252221 – Patch produced by `diff -urN'

[patch] Patch produced by `diff -urN'

science_abinit-regular.diff (text/plain), 9.67 KB, created by Thierry Thomas on 2021-01-01 11:39:50 UTC

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Creator: Thierry Thomas

Created: 2021-01-01 11:39:50 UTC

Size: 9.67 KB

patch

obsolete

>diff -urN science/abinit.orig/Makefile science/abinit/Makefile
>--- science/abinit.orig/Makefile	2020-06-01 12:21:54.999661000 +0200
>+++ science/abinit/Makefile	2020-12-27 17:18:48.025991000 +0100
>@@ -2,10 +2,8 @@
> # $FreeBSD: head/science/abinit/Makefile 536951 2020-05-29 08:38:54Z antoine $
> 
> PORTNAME=	abinit
>-DISTVERSION=	8.10.3
>-PORTREVISION=	6
>+DISTVERSION=	9.2.2
> CATEGORIES=	science
>-MASTER_SITES=	LOCAL/yuri/ # https://www.abinit.org/sites/default/files/packages/ has the updated 8.10.3 tarball that doesn't compile
> 
> MAINTAINER=	yuri@FreeBSD.org
> COMMENT=	Full-featured atomic-scale first-principles simulation software
>@@ -13,33 +11,80 @@
> LICENSE=	GPLv3
> LICENSE_FILE=	${WRKSRC}/COPYING
> 
>-ONLY_FOR_ARCHS=	amd64 i386
>-BROKEN=		fails to build
>-BROKEN_i386=	Type mismatch in argument 'block_displ', see https://github.com/abinit/abinit/issues/19
>+ONLY_FOR_ARCHS=	amd64
> 
>-LIB_DEPENDS=	liblapack.so:math/lapack \
>-		libblas.so:math/blas
>+BUILD_DEPENDS=	gm4:devel/m4	\
>+		${PYNUMPY}	\
>+		${PY_PYGMENTS}	\
>+		${PYTHON_PKGNAMEPREFIX}pandas>0:math/py-pandas@${PY_FLAVOR} \
>+		${PYTHON_PKGNAMEPREFIX}graphviz>0:graphics/py-graphviz@${PY_FLAVOR}
>+LIB_DEPENDS=	libelpa.so:math/elpa		\
>+		libsz.so:science/szip		\
>+		libelpa.so:math/elpa		\
>+		libxc.so:science/libxc		\
>+		libfftw3.so:math/fftw3		\
>+		libhdf5.so:science/hdf5		\
>+		libxml2.so:textproc/libxml2	\
>+		libnetcdf.so:science/netcdf	\
>+		libxmlf90.so:textproc/xmlf90	\
>+		libwannier90.so:science/wannier90	\
>+		libnetcdff.so:science/netcdf-fortran
> RUN_DEPENDS=	atompaw:science/atompaw
>+TEST_DEPENDS=	${PYNUMPY}	\
>+		libyaml>0:textproc/libyaml
> 
>-USES=		fortran gmake localbase:ldflags
>-GNU_CONFIGURE=	yes
>+USE_GITHUB=	yes
> 
>-CONFIGURE_ENV=	CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}"
>-CONFIGURE_ARGS=	--enable-shared --disable-static
>+USES=		autoreconf:build blaslapack:netlib fortran gmake gnome localbase:ldflags	\
>+		python:3.6+ shebangfix
>+USE_GNOME=	libxml2
>+SHEBANG_FILES=	config/scripts/* doc/tutorial/paral_gspw_assets/abinit.sub.*
>+SHEBANG_GLOB=	*.py
>+GNU_CONFIGURE=	yes
>+CONFIGURE_ENV=	CC_LDFLAGS="${LDFLAGS}" CXX_LDFLAGS="${LDFLAGS}" FC_LDFLAGS="${LDFLAGS}"	\
>+		LINALG_FCFLAGS="-I${LOCALBASE}/include/elpa-2019.05.002/modules"	\
>+		LINALG_LIBS="${BLASLIB}  ${LAPACKLIB} -lelpa"	\
>+		NETCDF_FORTRAN_FCFLAGS=-I${LOCALBASE}/include	\
>+		XMLF90_FCFLAGS=-I${LOCALBASE}/include	\
>+		WANNIER90_LIBS="${BLASLIB}  ${LAPACKLIB} -lwannier90"
>+CONFIGURE_ARGS=	--with-fft --with-libxc --with-libxml2 --with-netcdf	\
>+		--with-netcdf-fortran --with-wannier90 --with-xmlf90
> FCFLAGS+=	-ffree-line-length-none
>+TEST_TARGET=	tests_abirules tests_buildsys
>+TEST_WRKSRC=	${WRKSRC}/abichecks
>+PORTDOCS=	*
> 
>-OPTIONS_DEFINE=			OPENMP MPI
>+OPTIONS_DEFINE=			DOCS OPENMP MPI
> OPTIONS_DEFAULT=		OPENMP MPI
> 
> OPENMP_CONFIGURE_ENABLE=	openmp
> OPENMP_LDFLAGS=			-lomp
> 
>-MPI_CONFIGURE_ENABLE=		mpi
>-MPI_VARS=			FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include
>-MPI_LDFLAGS=			${LOCALBASE}/lib/libmpich.so ${LOCALBASE}/lib/libmpicxx.so ${LOCALBASE}/lib/libmpifort.so
>+MPI_CONFIGURE_WITH=		mpi=yes
>+# fftw3 not enabled because libfftw3_mpi is required but not packaged
>+MPI_VARS=			FFLAGS+=-I${LOCALBASE}/include FCFLAGS+=-I${LOCALBASE}/include	\
>+				CONFIGURE_ENV+=MPI_LIBS="`pkg-config --libs mpich` -lmpifort"	\
>+				CONFIGURE_ENV+MPI_LDFLAGS="`pkg-config --libs mpich` -lmpifort"
> MPI_LIB_DEPENDS=		libmpi.so:net/mpich
> 
>-do-test:
>-	@cd ${WRKSRC}/tests && ./configure && ${GMAKE} check
>+.if defined(WITH_LEVMAR)
>+# --with-levmar seems deprecated
>+LIB_DEPENDS+=	liblevmar.so:math/levmar
>+CONFIGURE_ENV+=	LEVMAR_LIBS="-llevmar ${BLASLIB} ${LAPACKLIB}"
>+CONFIGURE_ARGS+=	--with-levmar
>+.endif
>+
>+pre-configure:
>+	(cd ${WRKSRC} && ./autogen.sh)
>+
>+post-install-DOCS-on:
>+	${REINPLACE_CMD} -e 's|/usr/bin/env  python|${PYTHON_CMD}|'	\
>+		${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py
>+	${RM} ${WRKSRC}/doc/tutorial/paral_moldyn_assets/diag_moldyn.py.bak
>+	@${MKDIR} ${STAGEDIR}${DOCSDIR}
>+	${CP} -R ${WRKSRC}/doc/tutorial ${STAGEDIR}${DOCSDIR}
>+
>+pre-test:
>+	${TOUCH} ${TEST_WRKSRC}/make.log
> 
> .include <bsd.port.mk>
>diff -urN science/abinit.orig/distinfo science/abinit/distinfo
>--- science/abinit.orig/distinfo	2020-05-24 11:21:32.649216000 +0200
>+++ science/abinit/distinfo	2020-12-26 18:27:17.000000000 +0100
>@@ -1,3 +1,3 @@
>-TIMESTAMP = 1550812825
>-SHA256 (abinit-8.10.3.tar.gz) = 922e38edab95e1763c4d504a927f7ea4e19da3143e5b33c5d6e4b41210bf5a9d
>-SIZE (abinit-8.10.3.tar.gz) = 88310400
>+TIMESTAMP = 1608996405
>+SHA256 (abinit-abinit-9.2.2_GH0.tar.gz) = 29511bbc4f4e318cf3676aafdfea48ce2beb8ab6bd64062bd38d516fc02a8543
>+SIZE (abinit-abinit-9.2.2_GH0.tar.gz) = 98949530
>diff -urN science/abinit.orig/files/patch-Makefile.in science/abinit/files/patch-Makefile.in
>--- science/abinit.orig/files/patch-Makefile.in	2020-05-24 11:21:32.673007000 +0200
>+++ science/abinit/files/patch-Makefile.in	1970-01-01 01:00:00.000000000 +0100
>@@ -1,11 +0,0 @@
>---- Makefile.in.orig	2018-06-14 05:16:42 UTC
>-+++ Makefile.in
>-@@ -876,7 +876,7 @@ AM_DISTCHECK_CONFIGURE_FLAGS = \
>-   @abi_ac_distcheck@ \
>-   PYFLAGS="@PYFLAGS@ -B"
>- 
>--SUBDIRS = fallbacks src abichecks tests
>-+SUBDIRS = fallbacks src abichecks
>- 
>- # Additional files to clean
>- CLEANFILES = config.optim config.fc_info.tmp
>diff -urN science/abinit.orig/files/patch-config_m4_sd__levmar.m4 science/abinit/files/patch-config_m4_sd__levmar.m4
>--- science/abinit.orig/files/patch-config_m4_sd__levmar.m4	1970-01-01 01:00:00.000000000 +0100
>+++ science/abinit/files/patch-config_m4_sd__levmar.m4	2020-12-26 21:08:45.000000000 +0100
>@@ -0,0 +1,10 @@
>+--- config/m4/sd_levmar.m4.orig	2020-11-10 12:21:53 UTC
>++++ config/m4/sd_levmar.m4
>+@@ -239,6 +239,7 @@ AC_DEFUN([_SD_LEVMAR_CHECK_USE], [
>+   AC_LANG_PUSH([C])
>+   AC_LINK_IFELSE([AC_LANG_PROGRAM(
>+     [[
>++#     include <stddef.h>
>+ #     include <levmar.h>
>+ 
>+       void dfit_function(double *p, double *y, int m, int n, void *adata)
>diff -urN science/abinit.orig/files/patch-config_scripts_makemake science/abinit/files/patch-config_scripts_makemake
>--- science/abinit.orig/files/patch-config_scripts_makemake	1970-01-01 01:00:00.000000000 +0100
>+++ science/abinit/files/patch-config_scripts_makemake	2020-12-26 18:28:09.000000000 +0100
>@@ -0,0 +1,11 @@
>+--- config/scripts/makemake.orig	2020-12-26 16:36:41 UTC
>++++ config/scripts/makemake
>+@@ -408,7 +408,7 @@ if ( opts.run_clean ):
>+   sys.exit(0)
>+ 
>+ # Get Autotools versions
>+-(m4_ret, m4_version) = getstatusoutput("m4 --version | sed 's/o/ /g' ")
>++(m4_ret, m4_version) = getstatusoutput("gm4 --version | sed 's/o/ /g' ")
>+ (ac_ret, ac_version) = getstatusoutput("autoconf --version")
>+ (am_ret, am_version) = getstatusoutput("automake --version")
>+ (lt_ret, lt_version) = getstatusoutput("libtool  --version")
>diff -urN science/abinit.orig/files/patch-shared__common__src__02_clib__md5.c science/abinit/files/patch-shared__common__src__02_clib__md5.c
>--- science/abinit.orig/files/patch-shared__common__src__02_clib__md5.c	1970-01-01 01:00:00.000000000 +0100
>+++ science/abinit/files/patch-shared__common__src__02_clib__md5.c	2020-12-26 18:36:57.000000000 +0100
>@@ -0,0 +1,11 @@
>+--- shared/common/src/02_clib/md5.c.orig	2017-02-28 12:02:53 UTC
>++++ shared/common/src/02_clib/md5.c
>+@@ -47,7 +47,7 @@
>+ #ifdef HAVE_MALLOC_MALLOC_H
>+ #  include <malloc/malloc.h>
>+ #else
>+-#  include <malloc.h>
>++#  include <stdlib.h>
>+ #endif
>+ 
>+ #include "md5.h"
>diff -urN science/abinit.orig/files/patch-shared_common_src_02__clib_calling__levmar.c science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c
>--- science/abinit.orig/files/patch-shared_common_src_02__clib_calling__levmar.c	1970-01-01 01:00:00.000000000 +0100
>+++ science/abinit/files/patch-shared_common_src_02__clib_calling__levmar.c	2020-12-27 12:50:52.000000000 +0100
>@@ -0,0 +1,20 @@
>+--- shared/common/src/02_clib/calling_levmar.c.orig	2020-11-10 12:21:53 UTC
>++++ shared/common/src/02_clib/calling_levmar.c
>+@@ -150,7 +150,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
>+       /* invoke the optimisation function with box boundaries*/
>+       ret=dlevmar_bc_dif(dim_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
>+            lower_bounds, upper_bounds, 3000, opts, info, NULL, NULL, \
>+-           (void *)&adata); // Box boundary conditions without Jacobian
>++           NULL, (void *)&adata); // Box boundary conditions without Jacobian
>+     //}
>+   //}
>+   
>+@@ -220,7 +220,7 @@ double opts[LM_OPTS_SZ], info[LM_INFO_SZ];
>+       /* invoke the optimisation function with box boundaries*/
>+       ret=dlevmar_bc_dif(dre_and_im_screening, coeffs, yvals, c_ncoeffs, c_nvals, \
>+            lower_bounds, upper_bounds, 1000, opts, info, NULL, NULL, \
>+-           (void *)&adata); // Box boundary conditions without Jacobian
>++           NULL, (void *)&adata); // Box boundary conditions without Jacobian
>+     //}
>+   //}
>+   
>diff -urN science/abinit.orig/files/patch-src_02__clib_md5.c science/abinit/files/patch-src_02__clib_md5.c
>--- science/abinit.orig/files/patch-src_02__clib_md5.c	2020-05-24 11:21:32.707465000 +0200
>+++ science/abinit/files/patch-src_02__clib_md5.c	1970-01-01 01:00:00.000000000 +0100
>@@ -1,11 +0,0 @@
>---- src/02_clib/md5.c.orig	2017-02-28 12:02:53 UTC
>-+++ src/02_clib/md5.c
>-@@ -47,7 +47,7 @@
>- #ifdef HAVE_MALLOC_MALLOC_H
>- #  include <malloc/malloc.h>
>- #else
>--#  include <malloc.h>
>-+#  include <stdlib.h>
>- #endif
>- 
>- #include "md5.h"
>diff -urN science/abinit.orig/pkg-plist science/abinit/pkg-plist
>--- science/abinit.orig/pkg-plist	2020-05-24 11:21:32.727574000 +0200
>+++ science/abinit/pkg-plist	2020-12-27 10:37:54.000000000 +0100
>@@ -1,8 +1,9 @@
> bin/abinit
>+bin/abitk
> bin/aim
> bin/anaddb
>+bin/atdep
> bin/band2eps
>-bin/bsepostproc
> bin/conducti
> bin/cut3d
> bin/dummy_tests
>@@ -17,7 +18,7 @@
> bin/mrgscr
> bin/multibinit
> bin/optic
>-bin/tdep
>+bin/testtransposer
> bin/ujdet
> bin/vdw_kernelgen
> libdata/pkgconfig/abinit.pc

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Attachments on bug 252221: 221028 | 221157