sci-chemistry/xcrysden: new package, add 1.6.2

Signed-off-by: Patrick Taylor <patrick.joseph.taylor@gmail.com>

sci-chemistry/xcrysden/Manifest

@@ -0,0 +1 @@
+DIST xcrysden-1.6.2.tar.gz 2460277 BLAKE2B f0b7c2c5aeff51db97b29c8052273ed44bb9c183e0df62c406eee327c4c5d86d141d8adfd05df70b97661a8cbddbf052c233c288f1f30b308e4c877539c06a84 SHA512 9ed1b7fc11674509a3f2bf6604aa11e087fd77a971afb93039ca542cb9abb62b2553c7f386b845f004df5d3d340bdf1fe673552319788f006fd031efb6a4ad67

sci-chemistry/xcrysden/files/xcrysden-1.6.2-Togl_lib.patch

@@ -0,0 +1,14 @@
+Ensures that Togl is linked properly.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..ba478fa 100644
+--- a/system/Make.sys-shared
++++ b/system/Make.sys-shared
+@@ -48,7 +48,7 @@ X_INCDIR  =
+ 
+ TCL_LIB      = -ltcl$(TCL_VER2)
+ TK_LIB       = -ltk$(TCL_VER2)
+-TOGL_LIB     = -lTogl
++TOGL_LIB     = -Wl,-rpath,"/usr/lib64/Togl2.0" -L/usr/lib64/Togl2.0 -lTogl2.0
+ GLU_LIB      = -lGLU
+ GL_LIB       = -lGL
+ FFTW3_LIB    = -lfftw3

sci-chemistry/xcrysden/files/xcrysden-1.6.2-ext-bwidget.patch

@@ -0,0 +1,14 @@
+Prevents bwidget from being automatically downloaded when it is already required as a build/run-time dependency.
+diff --git a/Makefile b/Makefile
+index cfdc14a..d0f7e6c 100644
+--- a/Makefile
++++ b/Makefile
+@@ -18,7 +18,7 @@ what:
+ 
+ all: tcl tk mesa togl fftw xcrysden
+ #  meschach 
+-xcrysden: usage bwidget bindir src-C src-F src-Tcl
++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

sci-chemistry/xcrysden/files/xcrysden-1.6.2-gcc_flags.patch

@@ -0,0 +1,14 @@
+Adds -fcommon to CFLAGS to allow compilation on more recent GCC.
+diff --git a/system/Make.sys-shared b/system/Make.sys-shared
+index 51891e7..f89f876 100644
+--- a/system/Make.sys-shared
++++ b/system/Make.sys-shared
+@@ -19,7 +19,7 @@ MAKE = make
+ # C-preprocessor flags
+ CPPFLAGS ?=
+ # C-compiler flags
+-CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall
++CFLAGS += -ffast-math -funroll-loops -fPIC -pedantic -Wall -fcommon
+ 
+ CC     = gcc 
+ #LDLIB  = -ldl

sci-chemistry/xcrysden/files/xcrysden-1.6.2-wrapper_paths.patch

@@ -0,0 +1,16 @@
+Ensures that wrapper scripts account for live filesystem merge.
+diff --git a/sys_utils/wrappers.sh b/sys_utils/wrappers.sh
+index 1fa3cc6..e078b22 100755
+--- a/sys_utils/wrappers.sh
++++ b/sys_utils/wrappers.sh
+@@ -5,8 +5,8 @@ do
+ #!/bin/sh -f
+ 
+ # simple wrapper to run $cmd
+-XCRYSDEN_TOPDIR="$prefix/share/$xcrysden"
+-XCRYSDEN_LIB_BINDIR="$prefix/lib/$xcrysden"
++XCRYSDEN_TOPDIR="/usr/share/$xcrysden"
++XCRYSDEN_LIB_BINDIR="/usr/lib/$xcrysden"
+ export XCRYSDEN_TOPDIR
+ export XCRYSDEN_LIB_BINDIR
+ 

sci-chemistry/xcrysden/files/xcrysden.desktop

@@ -0,0 +1,8 @@
+[Desktop Entry]
+Name=XCrySDen
+Type=Application
+Comment=For the visualisation of molecular and crystal structures.
+Exec=xcrysden
+TryExec=xcrysden
+Icon=/usr/share/icons/hicolor/96x96/apps/xcrysden.png
+Categories=Science;

sci-chemistry/xcrysden/xcrysden-1.6.2.ebuild

@@ -0,0 +1,67 @@
+# Copyright 1999-2022 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit desktop
+inherit xdg-utils
+
+DESCRIPTION="For the visualisation of molecular and crystal structures."
+
+HOMEPAGE="http://www.xcrysden.org/"
+
+SRC_URI="http://www.xcrysden.org/download/${P}.tar.gz"
+
+LICENSE="GPL-2+"
+
+SLOT="0"
+
+KEYWORDS="~amd64"
+
+RDEPEND=">=dev-lang/tcl-8.6.12
+	>=dev-lang/tk-8.6.12
+	>=dev-tcltk/togl-2.0-r3
+	>=dev-tcltk/bwidget-1.9.14
+	>=media-libs/mesa-22.1.3
+	>=sci-libs/fftw-3.3.10"
+
+BDEPEND="${RDEPEND}"
+
+PATCHES=(
+	"${FILESDIR}/${P}-ext-bwidget.patch"
+	"${FILESDIR}/${P}-gcc_flags.patch"
+	"${FILESDIR}/${P}-Togl_lib.patch"
+	"${FILESDIR}/${P}-wrapper_paths.patch"
+)
+
+src_prepare() {
+	default
+	cp "${S}/system/Make.sys-shared" "${S}/Make.sys" || die 'Copying Make.sys to build dir failed.'
+}
+
+src_compile() {
+	emake xcrysden
+}
+
+src_install() {
+	emake \
+		prefix="${D}"/usr \
+		install
+
+	domenu "${FILESDIR}/${PN}.desktop"
+	doicon -s 32x32 "${FILESDIR}/icons/${PN}.png"
+	docompress -x /usr/share/doc/${P}/examples/GAUSSIAN_files/ \
+		/usr/share/doc/${P}/examples/Orca_files/ \
+		/usr/share/doc/${P}/examples/XSF_Files/ \
+		/usr/share/doc/${P}/examples/Scripting/ \
+		/usr/share/doc/${P}/examples/FermiSurface \
+		/usr/share/man/
+}
+
+pkg_postinst() {
+	xdg_icon_cache_update
+}
+
+pkg_postrm() {
+	xdg_icon_cache_update
+}