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Port details
py-pymol OpenGL-based molecular visualization system
2.4.0_3 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 View this port on Repology. pkg-fallout 2.4.0_3Version 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: 2021-06-22 18:53:08
Commit Hash: da3162c
Also Listed In: biology python
License: PyMOL
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}pymol>0:science/py-pymol@${PY_FLAVOR}
Conflicts:
CONFLICTS_INSTALL:
  • py38-chempy
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port: cd /usr/ports/science/py-pymol/ && make install clean
To add the package, run one of these commands:
  • pkg install science/py-pymol
  • pkg install py38-pymol
NOTE: This is a Python port. Instead of py38-pymol listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-pymol
Package flavors (<flavor>: <package>)
  • py38: py38-pymol
distinfo:
Packages (timestamps in pop-ups are UTC):
py27-pymol
ABIlatestquarterly
FreeBSD:11:aarch642.2.0-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch642.2.0-
FreeBSD:12:amd64--
FreeBSD:12:armv62.2.0-
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py37-pymol
ABIlatestquarterly
FreeBSD:11:aarch64-2.4.0
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64-2.4.0_2
FreeBSD:13:aarch642.4.0-
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc642.4.0_2-
 
py38-pymol
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.4.0_3
FreeBSD:12:amd642.4.0_32.4.0_3
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3862.4.0_32.4.0_3
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64-2.4.0_3
FreeBSD:13:amd642.4.0_32.4.0_3
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3862.4.0_32.4.0_3
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch642.4.0_3-
FreeBSD:14:amd642.4.0_3-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.4.0_3-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  2. glm.hpp : math/glm
  3. mmtf.hpp : science/mmtf-cpp
  4. py38-setuptools>0 : devel/py-setuptools@py38
  5. python3.8 : lang/python38
  6. xorgproto>=0 : x11/xorgproto
  7. xorgproto>=0 : x11/xorgproto
Runtime dependencies:
  1. py38-msgpack>0 : devel/py-msgpack@py38
  2. py38-Pmw>0 : x11-toolkits/py-Pmw@py38
  3. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  4. py38-setuptools>0 : devel/py-setuptools@py38
  5. python3.8 : lang/python38
  6. py38-qt5-core>=5.15.4 : devel/py-qt5-core@py38
  7. py38-qt5-gui>=5.15.4 : x11-toolkits/py-qt5-gui@py38
  8. py38-qt5-opengl>=5.15.4 : x11/py-qt5-opengl@py38
Library dependencies:
  1. libfreetype.so : print/freetype2
  2. libpng.so : graphics/png
  3. libmsgpackc.so : devel/msgpack
  4. libnetcdf.so : science/netcdf
  5. libGL.so : graphics/libglvnd
  6. libGLEW.so : graphics/glew
  7. libGLU.so : graphics/libGLU
  8. libglut.so : graphics/freeglut
  9. libxml2.so : textproc/libxml2
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/schrodinger/pymol-open-source/tar.gz/v2.4.0?dummy=/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
22 Jun 2021 18:53:08
 files touched by this commit commit hash:da3162c7c9f01912ba1940e188b253f2b5c7ba77  2.4.0_3
kbowling search for other commits by this committer
graphics/mesa-libs: Bump reverse deps for libglvnd

Per discussion with bapt on helping pkg handle the changing of these
deps and avoiding impossible upgrade senarios.

PR:		246767
Reviewed by:	manu, bapt
Approved by:	x11
Differential Revision:	https://reviews.freebsd.org/D30824
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.4.0_2
mat search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
12 Mar 2021 15:55:03
Original commit files touched by this commit Revision:568184  2.4.0_2
amdmi3 search for other commits by this committer
- Update math/glm to 0.9.9.8
26 Jan 2021 14:04:01
Original commit files touched by this commit Revision:562679  2.4.0_1
sunpoet search for other commits by this committer
Bump PORTREVISION for science/netcdf shlib change
24 Dec 2020 13:37:41
Original commit files touched by this commit Revision:559091  2.4.0
fluffy search for other commits by this committer
science/py-pymol: switch to PYTHON_EXT_SUFFIX
29 May 2020 08:42:46
Original commit files touched by this commit Revision:536956  2.4.0
antoine search for other commits by this committer
pymol fails to build with python 2.7

Reported by:	pkg-fallout
21 May 2020 07:17:55
Original commit files touched by this commit Revision:536079  2.4.0
yuri search for other commits by this committer
Add CONFLICT between science/py-chempy and science/py-pymol
21 May 2020 07:14:37
Original commit files touched by this commit Revision:536077  2.4.0
yuri search for other commits by this committer
science/py-pymol: Update 2.3.0 -> 2.4.0
23 Feb 2020 15:25:53
Original commit files touched by this commit Revision:526925  2.3.0_1
antoine search for other commits by this committer
Deprecate a few ports

With hat:	portmgr
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.3.0_1
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

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, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
16 Feb 2019 10:32:12
Original commit files touched by this commit Revision:493038  2.3.0
antoine search for other commits by this committer
Unbreak INDEX
12 Feb 2019 06:52:57
Original commit files touched by this commit Revision:492761  2.3.0
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 Revision:490472  2.2.0_3
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 Revision:487272  2.2.0_2
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 Revision:485614  2.2.0_1
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 Revision:479957  2.2.0
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 Revision:475857  2.1.0_3
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 Revision:472884  2.1.0_2
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 Revision:468048  2.1.0_2
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 Revision:465257  2.1.0_1
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 Revision:465071  2.1.0
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 Revision:456764  1.8.6.0
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 Revision:456763  1.8.6.0
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: 23