Index: head/science/v_sim/Makefile =================================================================== --- head/science/v_sim/Makefile (revision 561486) +++ head/science/v_sim/Makefile (revision 561487) @@ -1,87 +1,94 @@ # Created by: Thierry Thomas # $FreeBSD$ PORTNAME= v_sim -PORTVERSION= 3.7.2 -PORTREVISION= 12 +PORTVERSION= 3.8.0 CATEGORIES= science -MASTER_SITES= http://inac.cea.fr/sp2m/L_Sim/V_Sim/download/ +MASTER_SITES= https://gitlab.com/l_sim/${PORTNAME}/-/archive/${PORTVERSION}/ MAINTAINER= thierry@FreeBSD.org COMMENT= Visualization of atomic structures LICENSE= CeCILL LICENSE_NAME= CeCILL LICENSE_FILE= ${WRKSRC}/COPYING LICENSE_PERMS= dist-mirror dist-sell pkg-mirror pkg-sell auto-accept +BUILD_DEPENDS= p5-XML-LibXML>0:textproc/p5-XML-LibXML \ + libarchive>0:archivers/libarchive \ + xcrysden:science/xcrysden \ + bash:shells/bash LIB_DEPENDS= libfontconfig.so:x11-fonts/fontconfig \ + libopenbabel.so:science/openbabel \ libfreetype.so:print/freetype2 \ - libftgl.so:graphics/ftgl + libyaml.so:textproc/libyaml \ + libnetcdf.so:science/netcdf \ + libmsym.so:science/libmsym \ + libftgl.so:graphics/ftgl \ + libxc.so:science/libxc +RUN_DEPENDS= ${PYNUMPY} \ + xcrysden:science/xcrysden \ + libarchive>0:archivers/libarchive \ + ${PYTHON_PKGNAMEPREFIX}gobject3>0:devel/py-gobject3@${PY_FLAVOR} \ + ${PYTHON_PKGNAMEPREFIX}matplotlib>0:math/py-matplotlib@${PY_FLAVOR} -USES= compiler:c11 fortran gl gmake gnome libtool localbase:ldflags \ - pkgconfig tar:bzip2 xorg +USES= autoreconf blaslapack compiler:c11 fortran gl gmake gnome \ + libtool:keepla localbase:ldflags pkgconfig python:3.6+ \ + shebangfix tar:bzip2 xorg +SHEBANG_GLOB= *.py USE_XORG= x11 -USE_GNOME= gtk20 intltool cairo +USE_GNOME= cairo gtk30 intltool introspection USE_GL= gl glu GNU_CONFIGURE= yes -CONFIGURE_ARGS= --disable-gtk-doc --with-html-dir=${PREFIX}/share/doc --disable-python-module +CONFIGURE_SHELL=${LOCALBASE}/bin/bash +CONFIGURE_ARGS= --htmldir=${PREFIX}/share/doc --with-openbabel \ + --with-netcdf=${LOCALBASE} --with-etsf-file-format \ + --with-xsf --with-cube --with-msym=${LOCALBASE} \ + --with-msym-inc=-I${LOCALBASE}/include/libmsym \ + --with-libxc=${LOCALBASE} --enable-python-module CPPFLAGS+= ${CFLAGS} USE_LDCONFIG= yes INSTALLS_ICONS= yes -INSTALL_TARGET= install-strip OPTIONS_DEFINE= DOCS NLS EXAMPLES +.if defined(WITH_DEBUG) +CONFIGURE_ARGS+=--enable-debug-messages +.endif + .include +.if ${ARCH:Mamd64*} +BUILD_DEPENDS+= abinit:science/abinit +RUN_DEPENDS+= abinit:science/abinit +CONFIGURE_ARGS+=--with-abinit +.endif + .if ${PORT_OPTIONS:MNLS} USES+= gettext PLIST_SUB+= NLS="" .else USES+= gettext-tools PLIST_SUB+= NLS="@comment " .endif -.if !defined(WITHOUT_CDF) -LIB_DEPENDS+= libnetcdf.so:science/netcdf -CONFIGURE_ARGS+=--with-netcdf=${LOCALBASE} -PLIST_SUB+= CDF="" -.else -CONFIGURE_ARGS+=--without-netcdf -PLIST_SUB+= CDF="@comment " -.endif - -.if !defined(WITHOUT_BABEL) -LIB_DEPENDS+= libopenbabel.so:science/openbabel -CONFIGURE_ARGS+=--with-openbabel -PLIST_SUB+= BABEL="" -.else -CONFIGURE_ARGS+=--without-openbabel -PLIST_SUB+= BABEL="@comment " -.endif - pre-configure: - @${REINPLACE_CMD} -e 's|$$datadir/doc/$$PACKAGE/examples|${EXAMPLESDIR}|' \ - -e 's| CFLAGS="-O2"|#CFLAGS="-O2"|;s|Werror ansi pedantic-errors||' \ - -e 's| FCFLAGS="-O2"|FCFLAGS=${FFLAGS}|;s|$${docdir}/examples|${EXAMPLESDIR}|' \ - ${WRKSRC}/${CONFIGURE_SCRIPT} + ${REINPLACE_CMD} -e 's|$${docdir}/examples|${EXAMPLESDIR}|' \ + ${WRKSRC}/configure.ac + ${REINPLACE_CMD} -e 's|print sys.prefix|print (sys.prefix)|' \ + -e 's|print sys.exec_prefix|print (sys.exec_prefix)|' \ + ${WRKSRC}/m4/python.m4 pre-configure-NLS-off: - @${REINPLACE_CMD} -e '/^ po /d' \ - ${WRKSRC}/Makefile.in + ${REINPLACE_CMD} -e '/^ po /d' ${WRKSRC}/Makefile.am pre-configure-DOCS-off: - @${REINPLACE_CMD} -e '/^ Documentation/d' \ - ${WRKSRC}/Makefile.in + ${REINPLACE_CMD} -e '/^ Documentation/d' ${WRKSRC}/Makefile.am pre-configure-EXAMPLES-off: - @${REINPLACE_CMD} -e '/^ examples/d' \ - ${WRKSRC}/Makefile.in - @${FIND} ${WRKSRC}/lib/plug-ins -name Makefile.in | ${XARGS} \ - ${REINPLACE_CMD} -e \ - 's|install-v_simexamplesDATA install-v_simpixmapsDATA|install-v_simpixmapsDATA|' - @${REINPLACE_CMD} -e 's|: install-v_simexamplesDATA|:|' \ - ${WRKSRC}/lib/python/Makefile.in + ${REINPLACE_CMD} -e '/^ examples/d' \ + ${WRKSRC}/Makefile.am + ${REINPLACE_CMD} -e 's|: install-v_simexamplesDATA|:|' \ + ${WRKSRC}/lib/python/Makefile.am .include Index: head/science/v_sim/distinfo =================================================================== --- head/science/v_sim/distinfo (revision 561486) +++ head/science/v_sim/distinfo (revision 561487) @@ -1,2 +1,3 @@ -SHA256 (v_sim-3.7.2.tar.bz2) = 9212e6321d8ad8188529b9fab543268489e2f37d96e3ae55fa90d47d8ba4e70c -SIZE (v_sim-3.7.2.tar.bz2) = 3103269 +TIMESTAMP = 1608928526 +SHA256 (v_sim-3.8.0.tar.bz2) = af23f0eac641017d0ce52d92f83a8bca8f07776c4fac40b1970f073d88096f1f +SIZE (v_sim-3.8.0.tar.bz2) = 5957293 Index: head/science/v_sim/files/patch-lib_plug-ins_Makefile.in =================================================================== --- head/science/v_sim/files/patch-lib_plug-ins_Makefile.in (revision 561486) +++ head/science/v_sim/files/patch-lib_plug-ins_Makefile.in (nonexistent) @@ -1,10 +0,0 @@ ---- lib/plug-ins/Makefile.in.orig 2014-04-09 09:37:31.000000000 +0200 -+++ lib/plug-ins/Makefile.in 2014-04-24 23:23:33.000000000 +0200 -@@ -341,7 +341,6 @@ - xsf \ - cube \ - abinit \ -- python-gi \ - archives \ - bigdft - Property changes on: head/science/v_sim/files/patch-lib_plug-ins_Makefile.in ___________________________________________________________________ Deleted: fbsd:nokeywords ## -1 +0,0 ## -yes \ No newline at end of property Deleted: svn:eol-style ## -1 +0,0 ## -native \ No newline at end of property Deleted: svn:mime-type ## -1 +0,0 ## -text/plain \ No newline at end of property Index: head/science/v_sim/files/patch-Documentation_reference_Makefile.am =================================================================== --- head/science/v_sim/files/patch-Documentation_reference_Makefile.am (nonexistent) +++ head/science/v_sim/files/patch-Documentation_reference_Makefile.am (revision 561487) @@ -0,0 +1,34 @@ +--- Documentation/reference/Makefile.am.orig 2020-07-07 14:26:13 UTC ++++ Documentation/reference/Makefile.am +@@ -81,11 +81,11 @@ GTKDOC_LIBS= \ + @GTKS_LIBS@ @GLU_LIBS@ @EXTRA_LDFLAGS@ @EXTRA_LIBS@ + + # This includes the standard gtk-doc make rules, copied by gtkdocize. +-include $(srcdir)/gtk-doc.make ++#include $(srcdir)/gtk-doc.make + + # Other files to distribute + # e.g. EXTRA_DIST += version.xml.in +-EXTRA_DIST += version.in ++EXTRA_DIST = version.in + + # Files not to distribute + # for --rebuild-types in $(SCAN_OPTIONS), e.g. $(DOC_MODULE).types +@@ -93,11 +93,11 @@ EXTRA_DIST += version.in + DISTCLEANFILES = $(DOC_MODULE).types $(DOC_MODULE)-sections.txt + + # Comment this out if you want your docs-status tested during 'make check' +-if ENABLE_GTK_DOC +-TESTS_ENVIRONMENT = \ +- DOC_MODULE=$(DOC_MODULE) DOC_MAIN_SGML_FILE=$(DOC_MAIN_SGML_FILE) \ +- SRCDIR=$(abs_srcdir) BUILDDIR=$(abs_builddir) +-TESTS = $(GTKDOC_CHECK) +-endif ++#if ENABLE_GTK_DOC ++#TESTS_ENVIRONMENT = \ ++# DOC_MODULE=$(DOC_MODULE) DOC_MAIN_SGML_FILE=$(DOC_MAIN_SGML_FILE) \ ++# SRCDIR=$(abs_srcdir) BUILDDIR=$(abs_builddir) ++#TESTS = $(GTKDOC_CHECK) ++#endif + + #-include $(top_srcdir)/git.mk Property changes on: head/science/v_sim/files/patch-Documentation_reference_Makefile.am ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/v_sim/files/patch-configure.ac =================================================================== --- head/science/v_sim/files/patch-configure.ac (nonexistent) +++ head/science/v_sim/files/patch-configure.ac (revision 561487) @@ -0,0 +1,61 @@ +--- configure.ac.orig 2020-07-07 14:26:13 UTC ++++ configure.ac +@@ -244,7 +244,7 @@ AC_ARG_ENABLE(python-module, AS_HELP_STRING([--enable- + if test -n "$enable_python" -a "$enable_python" != "no" ; then + AM_PATH_PYTHON(2.3.5) + AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR(could not find Python headers)]) +- py_prefix=`$PYTHON -c "import sys; print sys.prefix"` ++ py_prefix=`$PYTHON -c "import sys; print (sys.prefix)"` + PYTHON_INCLUDES="-I${py_prefix}/include/python${PYTHON_VERSION}" + + PKG_CHECK_MODULES(PYGTK, pygobject-2.0 pygtk-2.0, [have_pygtk=yes], [have_pygtk=no]) +@@ -269,7 +269,6 @@ if test "$with_debug_messages" = "yes" ; then + fi + + dnl Building the doc +-GTK_DOC_CHECK([1.3]) + + + dnl Test for plug-ins compilation +@@ -423,9 +422,9 @@ if test "x$enable_introspection" = "xyes" ; then + dnl Add Python support for the PythonGI plug-in. + AM_PATH_PYTHON(2.3) + AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR(could not find Python headers)]) +- PYTHON_INCLUDES="`python-config --cflags`" ++ PYTHON_INCLUDES="`${PYTHON}-config --cflags`" + AC_SUBST(PYTHON_INCLUDES) +- PYTHON_LIBS="`python-config --libs`" ++ PYTHON_LIBS="`${PYTHON}-config --libs`" + AC_SUBST(PYTHON_LIBS) + + AC_MSG_CHECKING(for pygobject overrides directory) +@@ -434,9 +433,10 @@ if test "x$enable_introspection" = "xyes" ; then + if test "x$overrides_dir" = "x" ; then + overrides_dir="${pyexecdir}/gi/overrides" + fi +- if ! test -w $overrides_dir ; then +- overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides +- fi ++ # Do not test -w $overrides_dir to allow build as non-root ++ #if ! test -w $overrides_dir ; then ++ # overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides ++ #fi + AC_MSG_RESULT($overrides_dir) + else + overrides_dir=${libdir}/python$PYTHON_VERSION/dist-packages/gi/overrides +@@ -446,12 +446,12 @@ AM_CONDITIONAL([WITH_GOBJECT_INTROSPECTION], [test "x$ + dnl AC_PROG_CC set the CC variable and detect if we use the GNU compiler + dnl We now append some various CFLAGS depending on platform and choice + dnl of the user. +-AC_ARG_WITH(strict-cflags, AS_HELP_STRING([--with-strict-cflags], [if set or absent some correctness cflags are appended to the CFLAGS variable. Appended values dependent on the platform and code branch (default on Unix for development is Wall Wno-unused W Werror ansi pedantic-errors).]), [STRICT_CFLAGS=$withval], [STRICT_CFLAGS="no"]) ++AC_ARG_WITH(strict-cflags, AS_HELP_STRING([--with-strict-cflags], [if set or absent some correctness cflags are appended to the CFLAGS variable. Appended values dependent on the platform and code branch (default on Unix for development is Wall Wno-unused W ansi ).]), [STRICT_CFLAGS=$withval], [STRICT_CFLAGS="no"]) + flags='Wall W ansi' + flags_cpp='Wall W ansi' + if test "$GCC" = "yes" -a "$STRICT_CFLAGS" = "yes"; then +- flags=$flags' Werror Wpedantic std=c99' +- flags_cpp=$flags_cpp' Werror Wpedantic' ++ flags=$flags' std=c99' ++ flags_cpp=$flags_cpp' ' + fi + for fl in $flags ; do + case " $CFLAGS " in Property changes on: head/science/v_sim/files/patch-configure.ac ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c =================================================================== --- head/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c (nonexistent) +++ head/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c (revision 561487) @@ -0,0 +1,59 @@ +--- lib/plug-ins/abinit/ab_symmetry.c.orig 2020-07-07 14:26:13 UTC ++++ lib/plug-ins/abinit/ab_symmetry.c +@@ -458,7 +458,7 @@ gpointer startThreadSymmetry(gpointer data _U_) + char *spGrp; + double box[3][3], genAfm[3], *xred; + int i, *typat, grpId, grpMagnId; +- AbError errno; ++ AbError error; + VisuNodeArrayIter iter; + + AbinitData *dt; +@@ -492,13 +492,13 @@ gpointer startThreadSymmetry(gpointer data _U_) + /* Ask for the calculation of the symmetries. */ + DBG_fprintf(stderr, "AB symmetry(%p): Ready to get symmetries from ABINIT.\n", + (gpointer)g_thread_self()); +- errno = ab_symmetry_get_group(dt->sym, &spGrp, &grpId, ++ error = ab_symmetry_get_group(dt->sym, &spGrp, &grpId, + &grpMagnId, genAfm); + DBG_fprintf(stderr, "AB symmetry(%p): return from ABINIT (%d).\n", +- (gpointer)g_thread_self(), errno); +- if (errno == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED) ++ (gpointer)g_thread_self(), error); ++ if (error == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED) + g_free(spGrp); +- else if (errno != AB_ERROR_SYM_NOT_PRIMITIVE) ++ else if (error != AB_ERROR_SYM_NOT_PRIMITIVE) + dt->error = g_error_new(TOOL_FILE_FORMAT_ERROR, TOOL_FILE_FORMAT_ERROR_METHOD, + "An error occured in ABINIT plug-in."); + abinit_mutexUnlock(); +@@ -517,7 +517,7 @@ static void updateSymmetries(VisuData *dataObj, gdoubl + gchar *bravais[7] = {"triclinic", "monoclinic", "orthorhombic", + "tetragonal", "trigonal", "hexagonal", "cubic"}; + gchar *center[7] = {"F", "F", "I", "P", "A", "B", "C"}; +- AbError errno; ++ AbError error; + #ifdef G_THREADS_ENABLED + GThread *ld_thread; + #endif +@@ -571,9 +571,9 @@ static void updateSymmetries(VisuData *dataObj, gdoubl + + /* We get then the space group. */ + DBG_fprintf(stderr, "AB symmetry: get group.\n"); +- errno = ab_symmetry_get_group(sym, &spGrp, &grpId, ++ error = ab_symmetry_get_group(sym, &spGrp, &grpId, + &grpMagnId, genAfm); +- if (errno == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED) ++ if (error == AB_NO_ERROR || errno == AB_ERROR_SYM_BRAVAIS_XRED) + { + str = g_strdup_printf("%s (#%d)", spGrp, grpId); + gtk_label_set_text(GTK_LABEL(lblSymId), str); +@@ -629,7 +629,7 @@ static void updateSymmetries(VisuData *dataObj, gdoubl + + /* If the bravais lattice doesn't match with the xred bravais + lattice, we print a message. */ +- if (errno == AB_ERROR_SYM_BRAVAIS_XRED) ++ if (error == AB_ERROR_SYM_BRAVAIS_XRED) + gtk_widget_show(lblSymWarning); + else + gtk_widget_hide(lblSymWarning); Property changes on: head/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/v_sim/files/patch-m4_libxc.m4 =================================================================== --- head/science/v_sim/files/patch-m4_libxc.m4 (nonexistent) +++ head/science/v_sim/files/patch-m4_libxc.m4 (revision 561487) @@ -0,0 +1,22 @@ +--- m4/libxc.m4.orig 2020-07-07 14:26:13 UTC ++++ m4/libxc.m4 +@@ -57,17 +57,13 @@ AC_DEFUN([AC_CHECK_LIBXC], + + LIBS="$LIBS -lxc" + AC_MSG_CHECKING([for LIBXC library]) +- AC_LINK_IFELSE([[ +-program main +- +- call xc_f90_family_from_id() +-end]], ac_libxc_ok=yes, ac_libxc_ok=no) ++ ac_libxc_ok=yes + AC_MSG_RESULT([$ac_libxc_ok]) + LIBS="$LIBS_SVG" + LDFLAGS="$LDFLAGS_SVG" + FCFLAGS="$FCFLAGS_SVG" + if test "$ac_libxc_ok" = "yes"; then +- LIBXC_LIBS="-lxc" ++ LIBXC_LIBS="-lxc -lxcf90" + AS_IF([test -n "$LIBXC_PATH_LIBDIR"], [LIBXC_LIBS="-L$LIBXC_PATH_LIBDIR $LIBXC_LIBS"]) + AC_SUBST([LIBXC_LIBS]) + fi Property changes on: head/science/v_sim/files/patch-m4_libxc.m4 ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/v_sim/files/patch-src_coreTools_atoms__yaml.c =================================================================== --- head/science/v_sim/files/patch-src_coreTools_atoms__yaml.c (nonexistent) +++ head/science/v_sim/files/patch-src_coreTools_atoms__yaml.c (revision 561487) @@ -0,0 +1,22 @@ +--- src/coreTools/atoms_yaml.c.orig 2020-07-07 14:26:13 UTC ++++ src/coreTools/atoms_yaml.c +@@ -1270,19 +1270,7 @@ static int posinp_yaml_forces(yaml_parser_t *parser, P + + return done; + } +-#if SYSTEM_X11 == 1 +-static char* strdup(const char *src) +-{ +- char *dest; +- size_t ln; + +- ln = strlen(src); +- dest = malloc(sizeof(char) * (ln + 1)); +- memcpy(dest, src, sizeof(char) * ln); +- dest[ln] = '\0'; +- return dest; +-} +-#endif + static int posinp_yaml_external_potential(const PosinpDict *dict, PosinpAtoms *atoms, char **message) + { + int done; Property changes on: head/science/v_sim/files/patch-src_coreTools_atoms__yaml.c ___________________________________________________________________ Added: fbsd:nokeywords ## -0,0 +1 ## +yes \ No newline at end of property Added: svn:eol-style ## -0,0 +1 ## +native \ No newline at end of property Added: svn:mime-type ## -0,0 +1 ## +text/plain \ No newline at end of property Index: head/science/v_sim/pkg-descr =================================================================== --- head/science/v_sim/pkg-descr (revision 561486) +++ head/science/v_sim/pkg-descr (revision 561487) @@ -1,9 +1,9 @@ V_Sim visualizes atomic structures such as crystals, grain boundaries and so on (either in .d3 format as defined by F. Lançon, or in plain text format as described in the sample page). The rendering is done in pseudo-3D with colored sphere to represent the atoms. The user can interact through many functions to choose the view, the size of the atoms, their color, the background color, the type of fog... Much of it is detailled in the user guide. Moreover V_Sim allows to export the view as image in GIF, PS or more formats. -WWW: http://inac.cea.fr/L_Sim/V_Sim/ +WWW: https://gitlab.com/l_sim/v_sim Index: head/science/v_sim/pkg-plist =================================================================== --- head/science/v_sim/pkg-plist (revision 561486) +++ head/science/v_sim/pkg-plist (revision 561487) @@ -1,237 +1,153 @@ bin/v_sim +lib/girepository-1.0/v_sim-3.8.typelib lib/libv_sim-3.a +lib/libv_sim-3.la lib/libv_sim-3.so -lib/libv_sim-3.so.7 -lib/libv_sim-3.so.7.0.0 -%%BABEL%%lib/v_sim/plug-ins/libobloader.a -%%BABEL%%lib/v_sim/plug-ins/libobloader.so -%%BABEL%%lib/v_sim/plug-ins/libobloader.so.7 -%%BABEL%%lib/v_sim/plug-ins/libobloader.so.7.0.0 -%%PORTDOCS%%man/man1/v_sim.1.gz +lib/libv_sim-3.so.8 +lib/libv_sim-3.so.8.0.0 +%%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-37.opt-1.pyc +%%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-37.pyc +%%PYTHON_SITELIBDIR%%/gi/overrides/v_sim.py 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