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Port details
py-pymol OpenGL-based molecular visualization system
2.3.0 science on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port
2.3.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-12-19 19:49:25
Last Update: 2019-02-16 10:32:12
SVN Revision: 493038
Also Listed In: biology python
License: PyMOL
PyMOL is a Python-enhanced molecular graphics tool. It excels at
3D visualization of proteins, small molecules, density, surfaces,
and trajectories. It also includes molecular editing, ray tracing,
and movies. Open Source PyMOL is free to everyone!

This version represents the community-supported open source distribution
of the closed source commercial product PyMOL.

WWW: https://pymol.org/2/
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py27-pymol>0:science/py-pymol

To install the port: cd /usr/ports/science/py-pymol/ && make install clean
To add the package: pkg install py27-pymol

PKGNAME: py27-pymol

Package flavors (<flavor>: <package>)
  • py27: py27-pymol

distinfo:

TIMESTAMP = 1549950556
SHA256 (schrodinger-pymol-open-source-v2.3.0_GH0.tar.gz) = 62aa21fafd1db805c876f89466e47513809f8198395e1f00a5f5cc40d6f40ed0
SIZE (schrodinger-pymol-open-source-v2.3.0_GH0.tar.gz) = 10448674


NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.

Build dependencies:
  1. py27-numpy>0 : math/py-numpy@py27
  2. glm.hpp : math/glm
  3. mmtf.hpp : science/mmtf-cpp
  4. py27-setuptools>0 : devel/py-setuptools@py27
  5. python2.7 : lang/python27
  6. xorgproto>=0 : x11/xorgproto
  7. xorgproto>=0 : x11/xorgproto
Runtime dependencies:
  1. py27-msgpack>0 : devel/py-msgpack@py27
  2. py27-Pmw>0 : x11-toolkits/py-Pmw@py27
  3. py27-numpy>0 : math/py-numpy@py27
  4. py27-setuptools>0 : devel/py-setuptools@py27
  5. python2.7 : lang/python27
  6. py27-qt5-core>=5.11.3 : devel/py-qt5-core@py27
  7. py27-qt5-gui>=5.11.3 : x11-toolkits/py-qt5-gui@py27
  8. py27-qt5-opengl>=5.11.3 : x11/py-qt5-opengl@py27
Library dependencies:
  1. libfreetype.so : print/freetype2
  2. libpng.so : graphics/png
  3. libmsgpackc.so : devel/msgpack
  4. libGL.so : graphics/mesa-libs
  5. libGLEW.so : graphics/glew
  6. libGLU.so : graphics/libGLU
  7. libglut.so : graphics/freeglut
  8. libxml2.so : textproc/libxml2
There are no ports dependent upon this port

Configuration Options
===> The following configuration options are available for py27-pymol-2.3.0:
====> GUI (Graphical User Interface) support: you have to select exactly one of them
     QT5=on: Qt 5 toolkit support
     TK=off: Tk GUI toolkit support
===> Use 'make config' to modify these settings

USES:
compiler:c++11-lang gl gnome python:2.7 shebangfix tar:bz2 pyqt:5

Master Sites:
  1. https://codeload.github.com/schrodinger/pymol-open-source/tar.gz/v2.3.0?dummy=/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 13

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
16 Feb 2019 10:32:12
Original commit files touched by this commit  2.3.0
Revision:493038
antoine search for other commits by this committer
Unbreak INDEX
12 Feb 2019 06:52:57
Original commit files touched by this commit  2.3.0
Revision:492761
yuri search for other commits by this committer
science/py-pymol: Update 2.2.0 -> 2.3.0

Reported by:	portscout
16 Jan 2019 11:13:45
Original commit files touched by this commit  2.2.0_3
Revision:490472
tijl search for other commits by this committer
Fix Qt5 symbol version scripts to put the catch-all clause first.  When
a symbol matches multiple clauses the last one takes precedence.  If the
catch-all is last it captures everything.  In the case of Qt5 libraries
this caused all symbols to have a Qt_5 label while some should have
Qt_5_PRIVATE_API.  This only affects lld because GNU ld always gives the
catch-all lowest priority.

Older versions of Qt5Webengine exported some memory allocation symbols from
the bundled Chromium.  Version 5.9 stopped exporting these [1] but the
symbols were kept as weak wrappers for the standard allocation functions to
maintain binary compatibility. [2][3]  The problem is that the call to the
standard function in these weak wrappers is only resolved to the standard
function if there's a call to this standard function in other parts of
Qt5Webengine, because only then is there a non-weak symbol that takes
precedence over the weak one.  If there's no such non-weak symbol the call
(Only the first 15 lines of the commit message are shown above View all of this commit message)
12 Dec 2018 01:35:36
Original commit files touched by this commit  2.2.0_2
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
22 Nov 2018 20:18:37
Original commit files touched by this commit  2.2.0_1
Revision:485614
tcberner search for other commits by this committer
pyqt: Change install directories for Python flavor support

* PyQt could not be installed for multiple Python versions at
  the same time, as there were conflicting files.

  This patch creates Python-version versioned directories for
  all these, and further installs binaries with a version number.

* Note, there might be some hickups for software that depends on
  on of the .so's provided by PyQt5, which might not be found
  anymore autmotically, and maybe need some LD-flaggery.

* Update PyQt5 to 5.10.1

* Mark www/py-qt5-webengine broken. It is unforuntately no longer
  compatible with the old qt5-webengine-5.9.4 we ship.

PR:		232745
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D8714
17 Sep 2018 20:48:45
Original commit files touched by this commit  2.2.0
Revision:479957
yuri search for other commits by this committer
science/py-pymol: Update 2.1.0 -> 2.2.0

Moved to GitHub.
Also update WWW.
29 Jul 2018 22:18:46
Original commit files touched by this commit  2.1.0_3
Revision:475857
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
in the ports tree (via Mk/bsd.default-versions.mk and lang/gcc) which
has now moved from GCC 6 to GCC 7 by default.

This includes ports
 - featuring USE_GCC=yes or USE_GCC=any,
 - featuring USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and those
 - with USES=compiler specifying one of openmp, nestedfct, c11, c++0x,
   c++11-lib, c++11-lang, c++14-lang, c++17-lang, or gcc-c++11-lib.

PR:		222542
20 Jun 2018 17:05:44
Original commit files touched by this commit  2.1.0_2
Revision:472884
mat search for other commits by this committer
Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
22 Apr 2018 18:29:51
Original commit files touched by this commit  2.1.0_2
Revision:468048
sunpoet search for other commits by this committer
Move devel/py-msgpack-python to devel/py-msgpack

- Update to 0.5.6
- Update pkg-descr
- Update WWW

Changes:	https://github.com/msgpack/msgpack-python/blob/master/ChangeLog.rst
22 Mar 2018 05:48:25
Original commit files touched by this commit  2.1.0_1
Revision:465257
yuri search for other commits by this committer
science/py-pymol: Add GUI options QT5 and TK; Add missing dependency NUMPY

Now QT5 is the default, while Tk is still available as a second choice.
20 Mar 2018 07:53:14
Original commit files touched by this commit  2.1.0
Revision:465071
yuri search for other commits by this committer
science/py-pymol: Update to 2.1.0

Release notes:
https://pymol.org/dokuwiki/?id=media:new21

Port changes:
* Fixed shebang in bin/pymol
* Misc minor changes

Reported by:	portscout
19 Dec 2017 20:06:09
Original commit files touched by this commit  1.8.6.0
Revision:456764
antoine search for other commits by this committer
- Canonicalize LIB_DEPENDS
- Limit to python 2.7, the dependencies and the plist are not compatible
  with python3
- Cleanup plist

With hat:	portmgr (poudriere bulk -a broken)
19 Dec 2017 19:49:17
Original commit files touched by this commit  1.8.6.0
Revision:456763
yuri search for other commits by this committer
Re-added port: science/py-pymol: OpenGL based molecular visualization system
(existed 2002/08/13-2014/09/01, deleted in r366862)

Approved by:	adamw (mentor)
Differential Revision:	https://reviews.freebsd.org/D12902

Number of commits found: 13

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