Accepting request 398617 from home:ithod

Update jmol to the current stable version 14.6.0 and some minor improvements (see diff).

OBS-URL: https://build.opensuse.org/request/show/398617
OBS-URL: https://build.opensuse.org/package/show/science/jmol?expand=0&rev=7

Jmol-14.5.0_2015.11.06-binary.zip

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:39bcfc2138f631973471466f5a649639421571a65178315e3a4ab8561f9d817e
-size 60762047

_service

@@ -0,0 +1,7 @@
+<services>
+  <service name="download_url">
+    <param name="host">downloads.sf.net</param>
+    <param name="protocol">http</param>
+    <param name="path">/jmol/Jmol-14.6.0_2016.05.24-binary.zip</param>
+  </service>
+</services>

_service:download_url:Jmol-14.6.0_2016.05.24-binary.zip

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6b63fa63b45fadc82171dd651531a72905fdef6aa8b8364696ac682c53bc8f5c
+size 66473417

fsf-adress.patch

@@ -0,0 +1,13 @@
+--- /usr/share/doc/packages/jmol/COPYRIGHT.txt	2014-04-29 22:01:17.000000000 +0200
++++ COPYRIGHT.txt	2014-05-24 12:33:40.982788719 +0200
+@@ -13,8 +13,8 @@
+ 
+ You should have received a copy of the GNU Lesser General Public
+ License along with this library; if not, write to the Free Software
+-Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
+-02111-1307  USA.
++Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA
++02110-1301, USA.
+ 
+ 
+ Complete source code for the Jmol application, the Jmol applet, and

jmol.changes

@@ -1,3 +1,36 @@
+-------------------------------------------------------------------
+Sat May 28 16:18:55 UTC 2016 - thod_@gmx.de
+
+- Add manual
+- Split desktop file
+- update to version 14.6.0
+  selected new feature: 
+  * CONNECT {pair1} {pair2} ATROPISOMER
+  * C13 NMR prediction from http://www.nmrdb.org/service/jsmol13c?smiles=CCCC
+  * Jmol SMILES bond atropisomerism ^nm- and ^^nm-
+  * SMILES/nonaromatic same as SMILES/noaromatic
+  * adds SHOW SMILES/bio  and {*}.find("SMILES/bio") options:
+  * print {*}.find("SMILES/hydrogen/") adds hydrogen atoms
+  * Jmol now implements a way of indicating atropisomer chirality. 
+  * full implementation of OpenSMILES and OpenSMARTS in Jmol
+  * Polyhedra command allows for min and max radius
+  * draw POINTGROUP SPACEGROUP
+  * draw SPACEGROUP
+  * print pointgroup("spacegroup", @1)
+  * show spacegroup/xxxxx
+  * show symop 3 @3 "atom"
+  * show/draw symop @1 @2
+  * show/draw symop @1 @2 n
+  * symop() options
+  * symop(3,@3,"atom")
+  * getProperty("shapeInfo.echo") 
+  * preliminary MMTF reader 
+  * set window width height
+  * set window "xxx.png"
+  * setting DSSR on the fly
+  * show chemical xxx  where xxx is a file type
+  and many bug fixes
+
 -------------------------------------------------------------------
 Sun Mar 13 10:24:28 UTC 2016 - jengelh@inai.de
 

jmol.desktop

@@ -0,0 +1,9 @@
+[Desktop Entry]
+Name=Jmol
+Comment=An open-source Java viewer for chemical structures in 3D
+GenericName=Jmol
+Exec=jmol
+Icon=jmol
+Terminal=0
+Categories=Education;Science;Chemistry;Physics;
+Type=Application

jmol.man

@@ -0,0 +1,67 @@
+.\" Manpage for jmol.
+.\" Contact thod_@gmx.de to correct errors or typos.
+.TH man 1 "24 May 2015" "INST_VERSION" "jmol man page"
+.SH NAME
+jmol \- INST_SUMMARY
+.SH SYNOPSIS
+jmol [options]
+.SH DESCRIPTION
+Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.
+.SH OPTIONS
+ -o,--noconsole               no console -- all output to sysout
+ -c,--check                   check script syntax only - no file loading
+ -k,--kiosk                   kiosk mode -- no frame
+ -C,--checkload               check script syntax only - with file loading
+ -s,--script                  script file to execute or '-' for System.in
+ -q,--quality                 JPG image quality (1-100; default 75) or PNG
+                              image compression (0-9; default 2, maximum compression 9)
+ -g,--geometry                window width x height, e.g. -g500x500
+ -p,--printOnly               send only output from print messages to
+                              console (implies -i)
+ -x,--exit                    exit after script (implicit with -n)
+ -j,--jmolscript2             Jmol script to execute AFTER -s option
+ -J,--jmolscript1             Jmol script to execute BEFORE -s option
+ -P,--port                    port for JSON/MolecularPlayground-style
+                              communication
+ -D <property=value>          supported options are given below
+ -I,--input                   allow piping of input from System.Input
+ -L,--nosplash                start with no splash screen
+ -M,--multitouch              use multitouch interface (requires
+                              "sparshui" parameter
+ -R,--restricted              restrict local file access
+ -T,--headlessmaxtime         headless max time (sec)
+ -b,--backgroundtransparent   transparent background
+ -d,--debug                   debug
+ -h,--help                    give this help page
+ -i,--silent                  silent startup operation
+ -l,--list                    list commands during script execution
+ -m,--menu                    menu file to use
+ -n,--nodisplay               no display (and also exit when done)
+ -r,--restrictSpt             restrict local file access (allow reading of
+                              SPT files)
+ -t,--threaded                independent command thread
+ -w,--write                   CLIP or GIF|JPG|JPG64|PNG|PPM:filename
+.SH EXAMPLES
+Jmol -ions myscript.spt -w JPEG:myfile.jpg > output.txt
+
+The -D options are as follows (defaults in parenthesis) and must be called preceding '-jar Jmol.jar':
+
+  cdk.debugging=[true|false] (false)
+  cdk.debug.stdout=[true|false] (false)
+  display.speed=[fps|ms] (ms)
+  logger.debug=[true|false] (false)
+  logger.error=[true|false] (true)
+  logger.fatal=[true|false] (true)
+  logger.info=[true|false] (true)
+  logger.logLevel=[true|false] (false)
+  logger.warn=[true|false] (true)
+  plugin.dir (unset)
+  user.language=[ca|cs|de|en_GB|en_US|es|fr|hu|it|ko|nl|pt_BR|tr|zh_TW] (en_US)
+.SH SEE ALSO
+java(1)
+
+For more information, see also <http://jmol.sourceforge.net/>
+.SH BUGS
+No known bugs.
+.SH AUTHOR
+Jmol authors (jmol-developers@lists.sf.net)

jmol.spec

@@ -17,9 +17,9 @@
 
 
 Name:           jmol
-Version:        14.5.0
+Version:        14.6.0
 Release:        0
-%define date 2015.11.06
+%define date    2016.05.24
 Summary:        3D Viewer for chemical structures
 License:        LGPL-2.1
 Group:          Productivity/Scientific/Chemistry
@@ -28,57 +28,62 @@ Url:            http://jmol.sf.net/
 Source:         http://downloads.sf.net/jmol/Jmol-%{version}_%date-binary.zip
 Source2:        Jmol_icon13.png
 #Source2-Orig:  http://wiki.jmol.org/index.php/File:Jmol_icon13.png
+Source3:        %{name}.man
+Source4:        %{name}.desktop
 Patch1:         datadir.diff
+Patch2:         fsf-adress.patch
 BuildArch:      noarch
 BuildRoot:      %{_tmppath}/%{name}-%{version}-build
 BuildRequires:  dos2unix
 BuildRequires:  unzip
+BuildRequires:	desktop-file-utils 
+BuildRequires:	update-desktop-files
 Requires:       java
 
 %description
-Jmol is a Java-based viewer for chemical structures in 3D with
+Jmol is an open-source Java-based viewer for chemical structures in 3D with
 features for chemicals, crystals, materials and biomolecules.
 
 %prep
 %setup -qn %name-%{version}_%date
 %patch -P 1 -p1
+%patch -P 2 -p0
 cp %{S:2} .
 
 %build
 dos2unix CHANGES.txt COPYRIGHT.txt LICENSE.txt README.txt
 perl -i -pe 's{\@pkgdatadir\@}{%_datadir/%name}gs' jmol.sh
+# man
+cp %{S:3} .
+sed -i 's/INST_VERSION/%{version}/' jmol.man
+sed -i 's/INST_SUMMARY/%{summary}/' jmol.man
+gzip jmol.man
 
 %install
 b="%buildroot"
 # jar
 mkdir -p "$b/%_datadir/%name"
-cp -a Jmol.jar "$b/%_datadir/%name/"
+install -D -p -m 644 Jmol.jar "$b/%_datadir/%name/"
 # script
 mkdir -p "$b/%_bindir"
-cp -a jmol.sh "$b/%_bindir/jmol"
+install -D -p -m 755 jmol.sh "$b/%_bindir/jmol"
 # icon
 mkdir -p "$b/%_datadir/pixmaps"
-cp -a Jmol_icon13.png "$b/%_datadir/pixmaps/%name.png"
+install -m 644 Jmol_icon13.png "$b/%_datadir/pixmaps/%name.png"
+# manual
+mkdir -p %{buildroot}%{_mandir}/man1
+install -m 644 jmol.man.gz "$b/%_mandir/man1/jmol.1.gz"
 # .desktop
-mkdir -p "$b/%_datadir/applications"
+desktop-file-install --dir %{buildroot}%{_datadir}/applications %{S:4}
-cat >"$b/%_datadir/applications/%name.desktop" <<-EOF
+%suse_update_desktop_file %{name}
-	[Desktop Entry]
-	Name=Jmol
-	Comment=An open-source Java viewer for chemical structures in 3D
-	GenericName=Jmol
-	Exec=jmol
-	Icon=jmol
-	Terminal=0
-	Categories=Education;Science;Chemistry;Physics;
-	Type=Application
-EOF
 
 %files
 %defattr(-,root,root)
 %doc README.txt LICENSE.txt COPYRIGHT.txt CHANGES.txt
-%_bindir/jmol
+%_bindir/%name
 %_datadir/%name
 %_datadir/applications/%name.desktop
 %_datadir/pixmaps/%name.png
+%_mandir/man1/%{name}.1.gz
 
 %changelog