#4867 pymol-py.-1.8.5.0-1

Awaiting_Dependency
open
nobody
5
2017-01-01
2016-12-20
No

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 <fink-devel@lists.sourceforge.net>
 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

Discussion

  • Jack Howarth

    Jack Howarth - 2016-12-20

    Info file changes for pymol-py.-1.8.5.0-1

     
  • Jack Howarth

    Jack Howarth - 2016-12-20

    Revised patch for pymol-py-unused.patch

     
  • Daniel Macks

    Daniel Macks - 2016-12-22

    I got MD5=67752b321923ce89d432dfbbe097a66a for the tarball I created by that method. I don't know the details of the checkout process, if there are expected to be such variations and the MD5 in the .info needs to be set once we have a tarball.

    Do you have a place you can host the tarball yourself (which gives us a stable MD5) long enough for the master mirror to pick it up (or for us to manually transfer it)?

     
  • Daniel Macks

    Daniel Macks - 2016-12-22

    Given the upstream is sf.net SVN, isn't there a way to have that web service generate a snapshot, which we could use as a stable Source URL (if it's indeed stable) or at least to get a fix on the MD5 while we re-host it?

     
  • Daniel Macks

    Daniel Macks - 2016-12-22
    • Group: Undergoing_Validation --> Awaiting_Update_from_Submitter
     
  • Jack Howarth

    Jack Howarth - 2016-12-26

    Use 'Download Snapshot' link to auto-generate tarball and support python 3.6.

    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   26 Dec 2016 07:59:42 -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 <fink-devel@lists.sourceforge.net>
    -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)
    +# r4165
    +Source: https://sourceforge.net/code-snapshots/svn/p/py/pymol/code/pymol-code-4165-trunk.zip
    +Source-MD5: 8f0b11fed2b2e9185c66cf822fd87a82
     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-4165-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
     <<
    @@ -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 10.11 with 'fink -m'

     
  • Jack Howarth

    Jack Howarth - 2016-12-26

    Info file changes for pymol-py.-1.8.5.0-1 using 'Download Snapshot' link to auto-generate tarball and support python 3.6.

     
  • Hanspeter Niederstrasser

    • labels: --> sci, Updated Version of Existing
    • Group: Awaiting_Update_from_Submitter --> Awaiting_Dependency
     
  • Hanspeter Niederstrasser

    curl --connect-timeout 30 -f -L -A 'fink/0.41.1' -O https://sourceforge.net/code-snapshots/svn/p/py/pymol/code/pymol-code-4165-trunk.zip
      % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                     Dload  Upload   Total   Spent    Left  Speed
      0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (22) The requested URL returned error: 404 Not Found
    ### execution of curl failed, exit code 22
    Downloading the file "pymol-code-4165-trunk.zip" failed.
    
     

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