[140738] trunk/dports/science

1 Oct 2015

Revision: 140738
          https://trac.macports.org/changeset/140738
Author:   dstrubbe@macports.org
Date:     2015-10-01 12:52:13 -0700 (Thu, 01 Oct 2015)
Log Message:
-----------
xcrysden: new port. Closes ticket #41320.

Added Paths:
-----------
    trunk/dports/science/xcrysden/
    trunk/dports/science/xcrysden/Portfile
    trunk/dports/science/xcrysden/files/
    trunk/dports/science/xcrysden/files/patch-Makefile.diff
    trunk/dports/science/xcrysden/files/patch-Tcl-Viewer.tcl.diff
    trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Main.tcl.diff
    trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Multi.tcl.diff
    trunk/dports/science/xcrysden/files/patch-Tcl-wnOpen.tcl.diff
    trunk/dports/science/xcrysden/files/patch-tests-crystals.tcl.diff

Added: trunk/dports/science/xcrysden/Portfile
===================================================================

--- trunk/dports/science/xcrysden/Portfile	                        (rev 0)
+++ trunk/dports/science/xcrysden/Portfile	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,121 @@
+# -*- coding: utf-8; mode: tcl; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4 -*- vim:fenc=utf-8:ft=tcl:et:sw=4:ts=4:sts=4
+# $Id$
+
+PortSystem          1.0
+PortGroup           active_variants 1.1
+PortGroup           compilers 1.0
+
+name                xcrysden
+version             1.5.60
+categories          science
+platforms           darwin
+license             GPL-2+
+maintainers         dstrubbe
+
+description         X-windows CRYstalline Structures and DENsities
+
+long_description    XCrySDen is a crystalline and molecular structure visualisation program aiming at display of \
+                    isosurfaces and contours, which can be superimposed on crystalline structures and interactively \
+                    rotated and manipulated.
+
+homepage            http://www.xcrysden.org/
+master_sites        ${homepage}/download
+
+checksums           rmd160  2473752e074b2877df890b232cdc7bd02580a9e5 \
+                    sha1    388cf837aa757e612f36a12eb7fb592c36cfd6f3
+
+compilers.choose    fc
+compilers.setup     require_fortran
+
+require_active_variants tk x11
+
+depends_lib         port:fftw-3 port:mesa port:tcl port:tk \
+                    port:xorg-libXmu port:xorg-libX11 port:xorg-libXext
+depends_run         port:BWidget
+
+set prefix_share ${prefix}/share/${distname}
+notes               "You can test this installation via the command:" \
+                    "XCRYSDEN_TOPDIR=${prefix_share} XCRYSDEN_SCRATCH=/tmp ${prefix_share}/tests/run_test.sh structures" \
+                    "Additional functionality can be enabled by installing any of these ports, detected at runtime:" \
+                    "netpbm (for ppmtompeg), openbabel, whirlgif, imagemagick, mplayer (for mencoder), gifsicle."
+
+# Package ImageMagick's convert: /opt/local/bin/convert
+# Package ImageMagick's import: /opt/local/bin/import
+# Package Gifsicle: /opt/local/bin/gifsicle
+# Package Whirlgif: /opt/local/bin/whirlgif
+# Package Mencoder: /opt/local/bin/mencoder
+# Package Ppmtompeg: /opt/local/bin/ppmtompeg
+# Package Babel: /opt/local/bin/babel
+# Package Xwd: /opt/X11/bin/xwd
+
+# Patched issues:
+# Makefile did not respect DESTDIR, or install tests, or allow use of external BWidget
+# CRYSTAL tests should only be run if CRYSTAL package is available
+# WIEN2K conversion (str2xcr) wrote into working directory not scratch
+# last 3 are to fix this error that would happen with Mesa versions later than 7.0.2:
+#   X Error of failed request: BadWindow (invalid Window parameter)
+#       Major opcode of failed request: 3
+#       ResourceID in failed request: 0xffffffff
+#       Serial number of failed request: 567
+#   X Error of failed request: BadWindow (invalid Window parameter)
+#       Major opcode of failed request: 3
+#       ResourceID in failed request: 0xffffffff
+#       Serial number of failed request: 569
+
+patchfiles          patch-Makefile.diff \
+                    patch-tests-crystals.tcl.diff \
+                    patch-Tcl-wnOpen.tcl.diff \
+                    patch-Tcl-Viewer.tcl.diff \
+                    patch-Tcl-fs-FS_Main.tcl.diff \
+                    patch-Tcl-fs-FS_Multi.tcl.diff
+
+configure {
+    system -W ${worksrcpath} "echo '
+CC=${configure.cc}
+CFLAGS=-O3 -DUSE_INTERP_RESULT
+FC=${configure.fc}
+FFLAGS=-O3
+COMPILE_TCLTK=no
+COMPILE_MESA=no
+COMPILE_FFTW=no
+FFTW3_LIB=${prefix}/lib/libfftw3.dylib
+X_LIB=${prefix}/lib/libXmu.dylib ${prefix}/lib/libX11.dylib ${prefix}/lib/libXext.dylib
+TK_LIB=${prefix}/lib/libtk.dylib
+TCL_LIB=${prefix}/lib/libtcl.dylib
+GL_LIB=${prefix}/lib/libGL.dylib
+GLU_LIB=${prefix}/lib/libGLU.dylib
+GL_INCDIR=-I${prefix}/include/mesa
+FFTW3_INCDIR=-I${prefix}/include' > Make.sys"
+}
+
+test {
+   ui_error "The normal test infrastructure cannot be used because tests for this port need to use X11."
+   ui_error "You can test this installation by hand via the command:"
+   ui_error "XCRYSDEN_TOPDIR=${prefix_share} XCRYSDEN_SCRATCH=/tmp ${prefix_share}/tests/run_test.sh structures"
+   return -code error "Test can only be run by hand."
+}
+
+use_parallel_build  yes
+universal_variant   no
+
+build.target xcrysden
+
+destroot.env prefix=${prefix}
+
+# replace path to where XCrySDen would install BWidget itself
+post-build {
+    reinplace -W ${worksrcpath}/Tcl "s|\$system(TOPDIR)/external/lib/bwidget-\*|${prefix}/lib/BWidget|" xcInit.tcl
+}
+
+# Doesn't work to run test, I guess X11 display cannot be used in that. Error message:
+# cannot application-specific initialization failed: couldn't connect to display "/tmp/launch-TfisC0/org.macosforge.xquartz:0"
+# See way to run by hand in notes above.
+
+#test {
+#    xinstall -W ${worksrcpath} C/xcrys bin/xcrys
+#    system -W ${worksrcpath}/tests "sh run_test.sh structures"
+#}
+
+livecheck.type      regex
+livecheck.url       [lindex ${master_sites} 0]
+livecheck.regex     xcrysden-(\[0-9.\]+)${extract.suffix}


Property changes on: trunk/dports/science/xcrysden/Portfile
___________________________________________________________________
Added: svn:keywords
   + Id
Added: svn:eol-style
   + native

Added: trunk/dports/science/xcrysden/files/patch-Makefile.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-Makefile.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-Makefile.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,65 @@
+--- Makefile.orig	2015-10-01 14:38:39.000000000 -0400
++++ Makefile	2015-10-01 14:45:53.000000000 -0400
+@@ -16,8 +16,8 @@
+ 
+ # some varibales ...
+ 
+-all: tcl tk mesa fftw meschach xcrysden 
+-xcrysden: usage bwidget bindir src-C src-F src-Tcl
++all: tcl tk mesa fftw meschach bwidget xcrysden 
++xcrysden: usage bindir src-C src-F src-Tcl
+ 
+ usage: $(TOPDIR)/docs/xcrysden.1
+ 	man $(TOPDIR)/docs/xcrysden.1 | awk 'BEGIN {lprint=0; print "## do not edit changes will be lost (file automatically generated)\n"; } /SYNOPSIS/ { lprint=1; } /SEE ALSO/ { lprint=0; } /a*/ { if (lprint) print; }' > usage
+@@ -230,35 +230,37 @@
+ version  := $(shell cat version)
+ xcrysden  = xcrysden-$(version)
+ 
++dprefix=$(DESTDIR)/$(prefix)
++
+ install: xcrysden
+ 	@echo
+ 	@echo "#-----"
+ 	@echo "#                          "
+-	@echo "#   Installing XCRYSDEN to: $(prefix)"
++	@echo "#   Installing XCRYSDEN to: $(dprefix)"
+ 	@echo "#                          "
+ 	@echo "#-----"
+ 	@echo	
+-	install -m755 -d $(prefix)/share/$(xcrysden)
+-	cp -a $(IRON_ITEMS) $(prefix)/share/$(xcrysden)
++	install -m755 -d $(dprefix)/share/$(xcrysden)
++	cp -a $(IRON_ITEMS) $(dprefix)/share/$(xcrysden)
+ 	\
+-	for subdir in Awk examples $(EXTERNAL_LIB_BWIDGET) images scripts Tcl util; do \
++	for subdir in Awk examples images scripts Tcl util tests; do \
+ 		if test -d $$subdir; then \
+-			install -m755 -d $(prefix)/share/$(xcrysden)/$$subdir; \
+-			cp -a   $$subdir/* $(prefix)/share/$(xcrysden)/$$subdir; \
++			install -m755 -d $(dprefix)/share/$(xcrysden)/$$subdir; \
++			cp -a   $$subdir/* $(dprefix)/share/$(xcrysden)/$$subdir; \
+ 		fi; \
+ 	done
+ 	\
+-	install -m755 -d $(prefix)/share/man/man1
+-	install -m644 $(MAN_FILES) $(prefix)/share/man/man1/
+-	gzip -f $(addprefix $(prefix)/share/man/man1/,$(MAN_PAGES))
++	install -m755 -d $(dprefix)/share/man/man1
++	install -m644 $(MAN_FILES) $(dprefix)/share/man/man1/
++	gzip -f $(addprefix $(dprefix)/share/man/man1/,$(MAN_PAGES))
+ 	\
+-	install -m755 -d $(prefix)/lib/$(xcrysden)
+-	install -m755 bin/*  $(prefix)/lib/$(xcrysden)/
++	install -m755 -d $(dprefix)/lib/$(xcrysden)
++	install -m755 bin/*  $(dprefix)/lib/$(xcrysden)/
+ 	\
+-	prefix=$(prefix) xcrysden=$(xcrysden) sh sys_utils/wrappers.sh
+-	if test ! -d $(prefix)/bin; then install -m755 -d $(prefix)/bin; fi
++	prefix=$(dprefix) xcrysden=$(xcrysden) sh sys_utils/wrappers.sh
++	if test ! -d $(dprefix)/bin; then install -m755 -d $(dprefix)/bin; fi
+ 	for prog in $(PROGS); do \
+-		install -m755 $$prog.wrapper   $(prefix)/bin/$$prog; \
++		install -m755 $$prog.wrapper   $(dprefix)/bin/$$prog; \
+ 	done
+ 
+ 

Added: trunk/dports/science/xcrysden/files/patch-Tcl-Viewer.tcl.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-Tcl-Viewer.tcl.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-Tcl-Viewer.tcl.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,11 @@
+--- Tcl/Viewer.tcl.orig	2015-10-01 13:46:22.000000000 -0400
++++ Tcl/Viewer.tcl	2015-10-01 13:47:26.000000000 -0400
+@@ -480,7 +480,7 @@
+ 			 -double         true  \
+ 			 -depth          true  \
+ 			 -depthsize      1     \
+-			 -accum          true  \
++			 -accum          false  \
+ 			 -accumredsize   1     \
+ 			 -accumgreensize 1     \
+ 			 -accumbluesize  1     \

Added: trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Main.tcl.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Main.tcl.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Main.tcl.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,18 @@
+--- Tcl/fs/FS_Main.tcl.orig	2015-10-01 13:47:51.000000000 -0400
++++ Tcl/fs/FS_Main.tcl	2015-10-01 13:48:10.000000000 -0400
+@@ -111,7 +111,7 @@
+ 		    -double         true  \
+ 		    -depth          true  \
+ 		    -depthsize      1     \
+-		    -accum          true  \
++		    -accum          false  \
+ 		    -accumredsize   1     \
+ 		    -accumgreensize 1     \
+ 		    -accumbluesize  1     \
+@@ -1356,4 +1356,4 @@
+ 	    FS_fsConfig $i $spin	    
+ 	}
+     }
+-}
+\ No newline at end of file
++}

Added: trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Multi.tcl.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Multi.tcl.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-Tcl-fs-FS_Multi.tcl.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,11 @@
+--- Tcl/fs/FS_Multi.tcl.orig	2015-10-01 13:48:01.000000000 -0400
++++ Tcl/fs/FS_Multi.tcl	2015-10-01 13:48:21.000000000 -0400
+@@ -57,7 +57,7 @@
+ 			       -double         true  \
+ 			       -depth          true  \
+ 			       -depthsize      1     \
+-			       -accum          true  \
++			       -accum          false  \
+ 			       -accumredsize   1     \
+ 			       -accumgreensize 1     \
+ 			       -accumbluesize  1     \

Added: trunk/dports/science/xcrysden/files/patch-Tcl-wnOpen.tcl.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-Tcl-wnOpen.tcl.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-Tcl-wnOpen.tcl.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,23 @@
+--- Tcl/wnOpen.tcl.orig	2013-11-10 23:19:33.000000000 -0500
++++ Tcl/wnOpen.tcl	2013-11-10 23:54:15.000000000 -0500
+@@ -76,14 +76,16 @@
+     #########################################################
+     # get the filehead out of filename (case.struct --> case)
+     set pwd [pwd]
+-    cd [file dirname $file]
++    file copy $file $system(SCRDIR)
++    cd $system(SCRDIR)
+     set filehead [file tail [FileHead $file]]
+     if { [catch {exec $system(FORDIR)/str2xcr $filehead}] } {
+-	ErrorDialog "error while executing \"str2xcr\" program"
++	set mypwd [pwd]
++	ErrorDialog "error while executing $system(FORDIR)/str2xcr $filehead in $mypwd"
+ 	return
+     }
+-    # now copy $filehead.xcr to $system(SCRDIR)/xc_str2xcr.$$
+-    file rename -force ${filehead}.xcr $system(SCRDIR)/xc_str2xcr.$system(PID)
++    # now copy $filehead.xcr to xc_str2xcr.$$
++    file rename -force ${filehead}.xcr xc_str2xcr.$system(PID)
+     cd $pwd
+ 
+     #

Added: trunk/dports/science/xcrysden/files/patch-tests-crystals.tcl.diff
===================================================================
--- trunk/dports/science/xcrysden/files/patch-tests-crystals.tcl.diff	                        (rev 0)
+++ trunk/dports/science/xcrysden/files/patch-tests-crystals.tcl.diff	2015-10-01 19:52:13 UTC (rev 140738)
@@ -0,0 +1,30 @@
+--- tests/crystals.tcl.orig	2013-11-11 00:23:27.000000000 -0500
++++ tests/crystals.tcl	2013-11-11 00:17:15.000000000 -0500
+@@ -6,10 +6,6 @@
+ 	
+ 	{scripting::filter::pwscfOutput -oc $env(XCRYSDEN_TOPDIR)/examples/PWSCF_files/EthAl001-2x2.out 2 {1 13   2 6   3 1}}
+ 	
+-	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/argonite.r1}
+-	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/Pt322.r1}
+-	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/polymer.r1}
+-
+ 	{scripting::filter::fhiInpini $env(XCRYSDEN_TOPDIR)/examples/FHI98MD_files/GaAs_inp.ini 3 {Gallium 31   Arsenic 33}}
+ 	{scripting::filter::fhiCoord  $env(XCRYSDEN_TOPDIR)/examples/FHI98MD_files/GaAsSurface_coord.out 2 {
+ 	    Gallium 31	    Arsenic 33	    hy_1.25 1	    hy_0.75 1}
+@@ -21,6 +17,16 @@
+     } {
+ 	eval scripting::exec $job
+     }
++
++    if { $system(c95_exist) != 0 } {
++        foreach job {
++    	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/argonite.r1}
++    	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/Pt322.r1}
++    	{scripting::filter::crystalInput $env(XCRYSDEN_TOPDIR)/examples/CRYSTALxx_input_files/polymer.r1}
++        } {
++    	eval scripting::exec $job
++        }
++    }
+ } {
+ 
+     #if { [xcIsActive c95] } {

    

dstrubbe＠macports.org

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