Date: Tue, 21 Apr 2026 06:39:17 +0000 From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@FreeBSD.org, dev-commits-ports-all@FreeBSD.org, dev-commits-ports-main@FreeBSD.org Subject: git: 1d496b09a024 - main - science/v_sim: update 3.9=?utf-8?Q?=2E0 =E2=86=92 3?=.9.1 Message-ID: <69e71b95.19361.69aeba12@gitrepo.freebsd.org>
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The branch main has been updated by yuri: URL: https://cgit.FreeBSD.org/ports/commit/?id=1d496b09a0244d07ad094ad6c8ea08690614f5c3 commit 1d496b09a0244d07ad094ad6c8ea08690614f5c3 Author: Yuri Victorovich <yuri@FreeBSD.org> AuthorDate: 2026-04-21 06:30:28 +0000 Commit: Yuri Victorovich <yuri@FreeBSD.org> CommitDate: 2026-04-21 06:39:05 +0000 science/v_sim: update 3.9.0 → 3.9.1 --- science/v_sim/Makefile | 12 ++-- science/v_sim/distinfo | 6 +- .../patch-Documentation_reference_Makefile.am | 6 +- science/v_sim/files/patch-configure.ac | 65 +++++++--------------- .../files/patch-lib_plug-ins_abinit_ab__symmetry.c | 59 -------------------- .../files/patch-lib_plug-ins_msym_Makefile.am | 13 +++++ .../v_sim/files/patch-src_coreTools_atoms__yaml.c | 22 -------- science/v_sim/pkg-descr | 2 +- science/v_sim/pkg-plist | 40 ++++++------- 9 files changed, 66 insertions(+), 159 deletions(-) diff --git a/science/v_sim/Makefile b/science/v_sim/Makefile index f45195c8e860..d2d99d66de77 100644 --- a/science/v_sim/Makefile +++ b/science/v_sim/Makefile @@ -1,6 +1,5 @@ PORTNAME= v_sim -DISTVERSION= 3.9.0 -PORTREVISION= 1 +DISTVERSION= 3.9.1 CATEGORIES= science MAINTAINER= thierry@FreeBSD.org @@ -15,7 +14,8 @@ 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 + bash:shells/bash \ + gtkdocize:textproc/gtk-doc LIB_DEPENDS= libgdkglext-x11-1.0.so:x11-toolkits/gtkglext \ libfontconfig.so:x11-fonts/fontconfig \ libopenbabel.so:science/openbabel \ @@ -40,7 +40,7 @@ USE_GNOME= cairo gtk30 gdkpixbuf intltool introspection pygobject3:run USE_GL= gl glu USE_GITLAB= yes GL_ACCOUNT= l_sim -GL_TAGNAME= 9dc8e5a0b2f4e7237ac50a922b87d234ff56a6e5 +GL_TAGNAME= f96c25a8aa1f4a149dd45fcb52de7216e65996a9 GNU_CONFIGURE= yes CONFIGURE_SHELL=${LOCALBASE}/bin/bash @@ -48,9 +48,11 @@ CONFIGURE_ARGS= --htmldir=${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 + --with-libxc=${LOCALBASE} --enable-python-module \ + --disable-gtk-doc GNU_CONFIGURE_MANPREFIX=${PREFIX}/share CPPFLAGS+= ${CFLAGS} +LDFLAGS+= -lm USE_LDCONFIG= yes OPTIONS_DEFINE= DOCS NLS EXAMPLES diff --git a/science/v_sim/distinfo b/science/v_sim/distinfo index 786af108bfbb..9bfeb1b8e3c2 100644 --- a/science/v_sim/distinfo +++ b/science/v_sim/distinfo @@ -1,3 +1,3 @@ -TIMESTAMP = 1665839345 -SHA256 (l_sim-v_sim-9dc8e5a0b2f4e7237ac50a922b87d234ff56a6e5_GL0.tar.gz) = 8dcdfa0ff17e9ea41f56fb498c2efef20054086fddd427a552e48f17dcee4546 -SIZE (l_sim-v_sim-9dc8e5a0b2f4e7237ac50a922b87d234ff56a6e5_GL0.tar.gz) = 6357693 +TIMESTAMP = 1776702272 +SHA256 (l_sim-v_sim-f96c25a8aa1f4a149dd45fcb52de7216e65996a9_GL0.tar.gz) = 64e948d6e1da41bafba7b7932b27c8055be4ea67ec45f57305b87ecbb5c9c357 +SIZE (l_sim-v_sim-f96c25a8aa1f4a149dd45fcb52de7216e65996a9_GL0.tar.gz) = 6272540 diff --git a/science/v_sim/files/patch-Documentation_reference_Makefile.am b/science/v_sim/files/patch-Documentation_reference_Makefile.am index 97c32ef21f78..e491eea55dad 100644 --- a/science/v_sim/files/patch-Documentation_reference_Makefile.am +++ b/science/v_sim/files/patch-Documentation_reference_Makefile.am @@ -1,7 +1,7 @@ ---- Documentation/reference/Makefile.am.orig 2020-07-07 14:26:13 UTC +--- Documentation/reference/Makefile.am.orig 2026-04-13 13:37:14 UTC +++ Documentation/reference/Makefile.am @@ -81,11 +81,11 @@ GTKDOC_LIBS= \ - @GTKS_LIBS@ @GLU_LIBS@ @EXTRA_LDFLAGS@ @EXTRA_LIBS@ + @GTKS_LIBS@ @EXTRA_LDFLAGS@ @EXTRA_LIBS@ # This includes the standard gtk-doc make rules, copied by gtkdocize. -include $(srcdir)/gtk-doc.make @@ -14,7 +14,7 @@ # Files not to distribute # for --rebuild-types in $(SCAN_OPTIONS), e.g. $(DOC_MODULE).types -@@ -93,11 +93,11 @@ EXTRA_DIST += version.in +@@ -93,11 +93,11 @@ DISTCLEANFILES = $(DOC_MODULE).types $(DOC_MODULE)-sec DISTCLEANFILES = $(DOC_MODULE).types $(DOC_MODULE)-sections.txt # Comment this out if you want your docs-status tested during 'make check' diff --git a/science/v_sim/files/patch-configure.ac b/science/v_sim/files/patch-configure.ac index b7899d16d948..99072dd30097 100644 --- a/science/v_sim/files/patch-configure.ac +++ b/science/v_sim/files/patch-configure.ac @@ -1,61 +1,34 @@ ---- configure.ac.orig 2020-07-07 14:26:13 UTC +--- configure.ac.orig 2026-04-13 13:37:14 UTC +++ configure.ac -@@ -244,7 +244,7 @@ AC_ARG_ENABLE(python-module, AS_HELP_STRING([--enable- - if test -n "$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$enable_introspection" = "xyes" ; then +@@ -327,9 +327,9 @@ if test "x$enable_introspection" = "xyes" ; then dnl Add Python support for the PythonGI plug-in. - AM_PATH_PYTHON(2.3) + AM_PATH_PYTHON(3.1) AM_CHECK_PYTHON_HEADERS(,[AC_MSG_ERROR(could not find Python headers)]) -- PYTHON_INCLUDES="`python-config --cflags`" +- PYTHON_INCLUDES="`python3-config --cflags`" + PYTHON_INCLUDES="`${PYTHON}-config --cflags`" AC_SUBST(PYTHON_INCLUDES) -- PYTHON_LIBS="`python-config --libs`" -+ PYTHON_LIBS="`${PYTHON}-config --libs`" +- PYTHON_LIBS="`python3-config --embed --ldflags`" ++ PYTHON_LIBS="`${PYTHON}-config --embed --ldflags`" AC_SUBST(PYTHON_LIBS) AC_MSG_CHECKING(for pygobject overrides directory) -@@ -434,9 +433,10 @@ if test "x$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' +@@ -354,8 +354,8 @@ if test "$GCC" = "yes" -a "$STRICT_CFLAGS" = "yes"; th + flags='Wall W' + flags_cpp='Wall W' 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' ' ++ flags_cpp=$flags_cpp'' fi for fl in $flags ; do case " $CFLAGS " in +@@ -391,7 +391,7 @@ AC_SUBST(v_simlegaldir) + AC_SUBST(v_simiconsdir) + v_simlegaldir="${docdir}" + AC_SUBST(v_simlegaldir) +-v_simexamplesdir="${docdir}/examples" ++v_simexamplesdir="/usr/local/share/examples/v_sim" + AC_SUBST(v_simexamplesdir) + v_simpluginsdir="$libdir/$PACKAGE/plug-ins" + AC_SUBST(v_simpluginsdir) diff --git a/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c b/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c deleted file mode 100644 index c467eb2e70db..000000000000 --- a/science/v_sim/files/patch-lib_plug-ins_abinit_ab__symmetry.c +++ /dev/null @@ -1,59 +0,0 @@ ---- 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); diff --git a/science/v_sim/files/patch-lib_plug-ins_msym_Makefile.am b/science/v_sim/files/patch-lib_plug-ins_msym_Makefile.am new file mode 100644 index 000000000000..7689d5ed037f --- /dev/null +++ b/science/v_sim/files/patch-lib_plug-ins_msym_Makefile.am @@ -0,0 +1,13 @@ +--- lib/plug-ins/msym/Makefile.am.orig 2026-04-20 18:38:49 UTC ++++ lib/plug-ins/msym/Makefile.am +@@ -37,8 +37,10 @@ CLEANFILES = log + + CLEANFILES = log + ++if BUILTIN_MSYM + $(srcdir)/sym.c: builtin/msym_EXPORTS.h + $(srcdir)/msym.c: builtin/msym_EXPORTS.h ++endif + + clean-local: + rm -rf builtin diff --git a/science/v_sim/files/patch-src_coreTools_atoms__yaml.c b/science/v_sim/files/patch-src_coreTools_atoms__yaml.c deleted file mode 100644 index f4e6b8d281ae..000000000000 --- a/science/v_sim/files/patch-src_coreTools_atoms__yaml.c +++ /dev/null @@ -1,22 +0,0 @@ ---- 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; diff --git a/science/v_sim/pkg-descr b/science/v_sim/pkg-descr index b733b3eabb94..99482bf609cf 100644 --- a/science/v_sim/pkg-descr +++ b/science/v_sim/pkg-descr @@ -1,5 +1,5 @@ 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 +(either in .d3 format as defined by F. Lancon, 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 diff --git a/science/v_sim/pkg-plist b/science/v_sim/pkg-plist index 1d1299811155..d7ae0dbce222 100644 --- a/science/v_sim/pkg-plist +++ b/science/v_sim/pkg-plist @@ -1,10 +1,10 @@ bin/v_sim -lib/girepository-1.0/v_sim-3.8.typelib +lib/girepository-1.0/v_sim-3.9.typelib lib/libv_sim-3.a lib/libv_sim-3.la lib/libv_sim-3.so -lib/libv_sim-3.so.8 -lib/libv_sim-3.so.8.0.0 +lib/libv_sim-3.so.9 +lib/libv_sim-3.so.9.0.0 %%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-%%PYTHON_SUFFIX%%.opt-1.pyc %%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim.cpython-%%PYTHON_SUFFIX%%.pyc %%PYTHON_SITELIBDIR%%/gi/overrides/__pycache__/v_sim%%PYTHON_TAG%%.opt-2.pyc @@ -12,43 +12,43 @@ lib/libv_sim-3.so.8.0.0 %%AB%%lib/v_sim/plug-ins/libabinit.a %%AB%%lib/v_sim/plug-ins/libabinit.la %%AB%%lib/v_sim/plug-ins/libabinit.so -%%AB%%lib/v_sim/plug-ins/libabinit.so.8 -%%AB%%lib/v_sim/plug-ins/libabinit.so.8.0.0 +%%AB%%lib/v_sim/plug-ins/libabinit.so.9 +%%AB%%lib/v_sim/plug-ins/libabinit.so.9.0.0 lib/v_sim/plug-ins/libarchives.a lib/v_sim/plug-ins/libarchives.la lib/v_sim/plug-ins/libarchives.so -lib/v_sim/plug-ins/libarchives.so.8 -lib/v_sim/plug-ins/libarchives.so.8.0.0 +lib/v_sim/plug-ins/libarchives.so.9 +lib/v_sim/plug-ins/libarchives.so.9.0.0 lib/v_sim/plug-ins/libcube.a lib/v_sim/plug-ins/libcube.la lib/v_sim/plug-ins/libcube.so -lib/v_sim/plug-ins/libcube.so.8 -lib/v_sim/plug-ins/libcube.so.8.0.0 +lib/v_sim/plug-ins/libcube.so.9 +lib/v_sim/plug-ins/libcube.so.9.0.0 lib/v_sim/plug-ins/libetsf.a lib/v_sim/plug-ins/libetsf.la lib/v_sim/plug-ins/libetsf.so -lib/v_sim/plug-ins/libetsf.so.8 -lib/v_sim/plug-ins/libetsf.so.8.0.0 +lib/v_sim/plug-ins/libetsf.so.9 +lib/v_sim/plug-ins/libetsf.so.9.0.0 lib/v_sim/plug-ins/libobloader.a lib/v_sim/plug-ins/libobloader.la lib/v_sim/plug-ins/libobloader.so -lib/v_sim/plug-ins/libobloader.so.8 -lib/v_sim/plug-ins/libobloader.so.8.0.0 +lib/v_sim/plug-ins/libobloader.so.9 +lib/v_sim/plug-ins/libobloader.so.9.0.0 lib/v_sim/plug-ins/libplugmsym.a lib/v_sim/plug-ins/libplugmsym.la lib/v_sim/plug-ins/libplugmsym.so -lib/v_sim/plug-ins/libplugmsym.so.8 -lib/v_sim/plug-ins/libplugmsym.so.8.0.0 +lib/v_sim/plug-ins/libplugmsym.so.9 +lib/v_sim/plug-ins/libplugmsym.so.9.0.0 lib/v_sim/plug-ins/libpythongi.a lib/v_sim/plug-ins/libpythongi.la lib/v_sim/plug-ins/libpythongi.so -lib/v_sim/plug-ins/libpythongi.so.8 -lib/v_sim/plug-ins/libpythongi.so.8.0.0 +lib/v_sim/plug-ins/libpythongi.so.9 +lib/v_sim/plug-ins/libpythongi.so.9.0.0 lib/v_sim/plug-ins/libxsf.a lib/v_sim/plug-ins/libxsf.la lib/v_sim/plug-ins/libxsf.so -lib/v_sim/plug-ins/libxsf.so.8 -lib/v_sim/plug-ins/libxsf.so.8.0.0 +lib/v_sim/plug-ins/libxsf.so.9 +lib/v_sim/plug-ins/libxsf.so.9.0.0 %%PORTDOCS%%%%DOCSDIR%%/ChangeLog.en %%PORTDOCS%%%%DOCSDIR%%/ChangeLog.fr %%PORTDOCS%%%%DOCSDIR%%/authors @@ -87,7 +87,7 @@ lib/v_sim/plug-ins/libxsf.so.8.0.0 %%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_isosurfaces.ascii %%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_isosurfaces.surf %%PORTEXAMPLES%%%%EXAMPLESDIR%%/values.xml -share/gir-1.0/v_sim-3.8.gir +share/gir-1.0/v_sim-3.9.gir share/icons/hicolor/16x16/apps/v_sim.png share/icons/hicolor/22x22/apps/v_sim.png share/icons/hicolor/24x24/apps/v_sim.pnghome | help
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