[fink:package-submissions] #4867 pymol-py.-1.8.5.0-1

Update info file change to r4166 and fix path to eMovie.py and eMovie_rigimol.inp with...

~~~
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.5
diff -u -r1.5 pymol-py.info
--- pymol-py.info	30 Aug 2016 22:37:46 -0000	1.5
+++ pymol-py.info	29 Jan 2017 01:41:35 -0000
@@ -1,13 +1,13 @@
 Info2: <<
 Package: pymol-py%type_pkg[python]
-Version: 1.8.3.2
+Version: 1.8.5.0
 Revision: 1
 UseMaxBuildJobs: false
 Maintainer: None <[email protected]>
-Type: python (2.7 3.4 3.5)
-# r4160
-Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-Source-MD5: 8c18b689d95b9a1e76e3efbfbb754816
+Type: python (2.7 3.4 3.5 3.6)
+# r4166
+Source: https://sourceforge.net/code-snapshots/svn/p/py/pymol/code/pymol-code-4166-trunk.zip
+Source-MD5: 284eb9d335b29a3581f9fdc315fab58e
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
 Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -17,10 +17,8 @@
 PatchFile2: pymol-py-gl.patch
 PatchFile2-MD5: 6e45a30ca2c47122951f6f92659da221 
 PatchFile3: pymol-py-unused.patch
-PatchFile3-MD5: d4bbf3df257a98160f4f0220e52bea93
-
-SourceRename: pymol-%v-src.tar.bz2
-SourceDirectory: pymol-%v
+PatchFile3-MD5: a75ac08e516eef4851fb1b42fdccdd60
+SourceDirectory: pymol-code-4166-trunk/pymol
 # Avoid including headers from fink before source directories
 NoSetCPPFLAGS: true
 SetCFLAGS: -Wno-c++11-extensions
@@ -53,16 +51,16 @@
 	x11-dev
 <<
 PatchScript: <<
-#! /bin/sh -ex
+#! /bin/bash -ex
 . %p/sbin/fink-buildenv-helper.sh
 sed 's|@FINKPREFIX@|%p|g' < %{PatchFile} | sed "s|@X11DIR@|$X11_BASE_DIR|g" | sed 's|python2.X|python%type_raw[python]|g' | patch -p1
 if [ $DARWIN_MAJOR_VERSION -ge 12 ] 
 	then patch -p1 < %{PatchFile2}
 fi
 patch -p0 < %{PatchFile3}
-cd ..
+pushd ../..
 perl -pi -e 's|\topen_eMovie\(\)|#\topen_eMovie\(\)|g' eMovie.py
-cd pymol-%v
+popd
 perl -pi -e 's|searchDirs.append\(os.path.join\("/opt", "local", "bin"\)\)||g' modules/pmg_tk/startup/apbs_tools.py 
 perl -pi -e "s|/usr/bin/env python|%p/bin/python%type_raw[python]|g" modules/pmg_tk/startup/apbs_tools.py
 <<
@@ -82,8 +80,8 @@
 chmod ugo+x %i/lib/pymol-py%type_pkg[python]/bin/pymol
 # skip installation of eMovie until ported to python3
 if [ "%type_raw[python]" == "2.7" ]; then
-cp ../eMovie.py %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/eMovie.py
-cp ../eMovie_rigimol.inp %i/lib/python%type_raw[python]/site-packages/pymol/eMovie_rigimol.inp
+cp ../../eMovie.py %i/lib/python%type_raw[python]/site-packages/pmg_tk/startup/eMovie.py
+cp ../../eMovie_rigimol.inp %i/lib/python%type_raw[python]/site-packages/pymol/eMovie_rigimol.inp
 fi
 rm -f %i/bin/pymol
 <<
@@ -112,9 +110,8 @@
 <<
 DescPackaging: <<
 The tarball used for this version was created in accordance to the BSD
-license of pymol using the following instructions...
-   svn -r4160 co https://svn.code.sf.net/p/pymol/code/trunk/pymol pymol-1.8.3.2
-   tar --exclude=.svn -jcvf pymol-1.8.3.2-src.tar.bz2 pymol-1.8.3.2
+license of pymol using the 'Download Snapshot' link at...
+   https://sourceforge.net/p/pymol/code/HEAD/tree/trunk/
 Added eMovie.py plug-in manually.  Commented out line that opens the window for eMovie by
 default every time pymol is started as this is annoying behavior. eMovie is activated via 
 the plugin menu.
~~~

Tested on 10.12 with 'fink -m' for python 2.7 variant.


Attachments:

- [pymol-py.info](https://sourceforge.net/p/fink/package-submissions/_discuss/thread/ab631a50/c1c0/attachment/pymol-py.info) (4.6 kB; application/octet-stream)


---

** [package-submissions:#4867] pymol-py.-1.8.5.0-1**

**Status:** open
**Group:** Awaiting_Update_from_Submitter
**Labels:** sci Updated Version of Existing 
**Created:** Tue Dec 20, 2016 01:29 PM UTC by Jack Howarth
**Last Updated:** Tue Jan 24, 2017 11:25 AM UTC
**Owner:** nobody


Update the pymol-py package to the current 1.8.5.0 release at r4165 using the Info file changes...

~~~
Index: pymol-py.info
===================================================================
RCS file: /cvsroot/fink/dists/10.9-libcxx/stable/main/finkinfo/sci/pymol-py.info,v
retrieving revision 1.5
diff -u -r1.5 pymol-py.info
--- pymol-py.info	30 Aug 2016 22:37:46 -0000	1.5
+++ pymol-py.info	20 Dec 2016 12:03:55 -0000
@@ -1,13 +1,13 @@
 Info2: <<
 Package: pymol-py%type_pkg[python]
-Version: 1.8.3.2
+Version: 1.8.5.0
 Revision: 1
 UseMaxBuildJobs: false
 Maintainer: None <[email protected]>
 Type: python (2.7 3.4 3.5)
-# r4160
+# r4165
 Source: mirror:sourceforge:fink/pymol-%v-src.tar.bz2
-Source-MD5: 8c18b689d95b9a1e76e3efbfbb754816
+Source-MD5: 2161f1a063872a57145a484fa8573971
 Source2: http://www.weizmann.ac.il/ISPC/eMovie.py
 Source2-MD5: 832252d4cee1ba88d50a35681b5ecd4b
 Source3: http://www.weizmann.ac.il/ISPC/eMovie_rigimol.inp
@@ -113,8 +113,8 @@
 DescPackaging: <<
 The tarball used for this version was created in accordance to the BSD
 license of pymol using the following instructions...
-   svn -r4160 co https://svn.code.sf.net/p/pymol/code/trunk/pymol pymol-1.8.3.2
-   tar --exclude=.svn -jcvf pymol-1.8.3.2-src.tar.bz2 pymol-1.8.3.2
+   svn -r4165 co https://svn.code.sf.net/p/pymol/code/trunk/pymol pymol-1.8.5.0
+   tar --exclude=.svn -jcvf pymol-1.8.5.0-src.tar.bz2 pymol-1.8.5.0
 Added eMovie.py plug-in manually.  Commented out line that opens the window for eMovie by
 default every time pymol is started as this is annoying behavior. eMovie is activated via 
 the plugin menu.
~~~

Tested on 10.11 with 'fink -m' and requires the fink mirrors to be populated with a source tarball generated wtih the commands...

svn -r4165 co https://svn.code.sf.net/p/pymol/code/trunk/pymol pymol-1.8.5.0
tar --exclude=.svn -jcvf pymol-1.8.5.0-src.tar.bz2 pymol-1.8.5.0

The changes since 1.8.3.2 are...

------------------------------------------------------------------------
r4165 | speleo3 | 2016-12-14 14:07:39 -0500 (Wed, 14 Dec 2016) | 7 lines

molfile plugins, fetch URLs, ...

* update molfile plugins to VMD version 1.9.3
* fetch 2fofc/fofc: update URLs, EDS will retire in 2017
* fix sf#102 pseudoatom multi-state problem
* editor.attach_amino_acid: fix PRO/N geometry

------------------------------------------------------------------------
r4164 | speleo3 | 2016-12-05 14:04:04 -0500 (Mon, 05 Dec 2016) | 18 lines

1.8.5.0 (unstable/experimental)

* avoid selection keyword name conflicts, append underscore
* load: allow format=plugin (by extension) and format=plugin:PLUGIN (with PLUGIN being a molfile plugin identifier)
* load format "vdb": VIPERdb PDB variant with retain_order=1
* load/load_traj: guess trajectory object
* fetch
    * new setting "fetch_type_default"
    * type=mmtf: fetch MMTF format
    * type=2fofc/fofc: get spacegroup from PDBe API
    * update download URLs
* new setting: editor_auto_measure
* new default: ray_transparency_oblique_power=4.0
* "update" command: support "current state" (-1)
* alter elem -> update protons and vdw
* don't allow "import cmd" (corrupts PyMOL namespace)
* support "python -m pymol" to launch PyMOL

------------------------------------------------------------------------
r4163 | speleo3 | 2016-10-18 06:37:13 -0400 (Tue, 18 Oct 2016) | 2 lines

backport C++11 features for gcc-4.5

------------------------------------------------------------------------
r4162 | speleo3 | 2016-10-05 11:23:46 -0400 (Wed, 05 Oct 2016) | 2 lines

1.8.4.0

------------------------------------------------------------------------
r4161 | speleo3 | 2016-09-26 15:49:55 -0400 (Mon, 26 Sep 2016) | 6 lines

1.8.3.3 (unstable/experimental)

* pse_export_version: legacy scenes support
* use ignore_case setting with set_name command
* setup.py: detect anaconda prefix




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