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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
Port details
py-MDAnalysis Python library to analyze molecular dynamics trajectories
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 View this port on Repology. pkg-fallout Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2018-05-14 00:15:59
Last Update: 2023-01-11 15:58:34
Commit Hash: 77d6847
Also Listed In: python
License: GPLv2
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}MDAnalysis>0:science/py-MDAnalysis@${PY_FLAVOR}
To install the port:
cd /usr/ports/science/py-MDAnalysis/ && make install clean
To add the package, run one of these commands:
  • pkg install science/py-MDAnalysis
  • pkg install py39-MDAnalysis
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-MDAnalysis listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-MDAnalysis
Package flavors (<flavor>: <package>)
  • py39: py39-MDAnalysis
distinfo:

Packages (timestamps in pop-ups are UTC):
py27-MDAnalysis
ABIlatestquarterly
FreeBSD:11:aarch640.18.0pkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch640.18.0pkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py36-MDAnalysis
ABIlatestquarterly
FreeBSD:11:aarch640.18.0pkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch640.18.0pkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py37-MDAnalysis
ABIlatestquarterly
FreeBSD:11:aarch64pkg-fallout0.19.2_2
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py38-MDAnalysis
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd640.19.2_20.19.2_2
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3860.19.2_20.19.2_2
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py39-MDAnalysis
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.3.0
FreeBSD:12:amd642.3.02.3.0
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch642.3.02.3.0
FreeBSD:13:amd642.3.02.3.0
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv72.3.02.3.0
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout2.3.0
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.3.0pkg-fallout
FreeBSD:14:amd642.3.0pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv72.3.0pkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-numpy>=1.16,1<1.24,1 : math/py-numpy@py39
  2. py39-packaging>=2.0 : devel/py-packaging@py39
  3. cython-3.9 : lang/cython@py39
  4. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  5. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.24,1 : math/py-numpy@py39
  2. clustalw2 : biology/clustalw
  3. rdkit>0 : science/rdkit
  4. py39-biopython>=1.71 : biology/py-biopython@py39
  5. py39-GridDataFormats>=0.4.0 : math/py-GridDataFormats@py39
  6. py39-fasteners>0 : devel/py-fasteners@py39
  7. py39-gsd>=1.9.3 : science/py-gsd@py39
  8. py39-joblib>0 : devel/py-joblib@py39
  9. py39-matplotlib>=1.5.1 : math/py-matplotlib@py39
  10. py39-mmtf-python>=1.0.0 : science/py-mmtf-python@py39
  11. py39-networkx>=2.0 : math/py-networkx@py39
  12. py39-scipy>=1.5.0 : science/py-scipy@py39
  13. py39-seaborn>0 : math/py-seaborn@py39
  14. py39-six>=1.4.0 : devel/py-six@py39
  15. py39-tqdm>=4.43.0 : misc/py-tqdm@py39
  16. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  17. python3.9 : lang/python39
This port is required by:
for Run
  1. science/py-MDAnalysisTests

Configuration Options:
Options name:

USES:

FreshPorts was unable to extract/find any pkg message

Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/M/MDAnalysis/
  2. https://pypi.org/packages/source/M/MDAnalysis/
Collapse this list.
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: 16

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.3.0
11 Jan 2023 15:58:34
commit hash:77d68471aded6907dbbcb5ef50d557e4c69db656commit hash:77d68471aded6907dbbcb5ef50d557e4c69db656commit hash:77d68471aded6907dbbcb5ef50d557e4c69db656commit hash:77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
07 Sep 2022 21:58:51
commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash:fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
2.3.0
07 Sep 2022 21:10:59
commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash:b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
2.3.0
02 Sep 2022 06:37:41
commit hash:32fed5246803bd965285fd2750522ebcdd33c2cccommit hash:32fed5246803bd965285fd2750522ebcdd33c2cccommit hash:32fed5246803bd965285fd2750522ebcdd33c2cccommit hash:32fed5246803bd965285fd2750522ebcdd33c2cc files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
science/py-MDAnalysis: Update 2.2.0 -> 2.3.0

Reported by:	portscout
2.2.0
21 Jun 2022 17:26:21
commit hash:40568cac8e3e1931ca48becdfd18e2bf0aab1061commit hash:40568cac8e3e1931ca48becdfd18e2bf0aab1061commit hash:40568cac8e3e1931ca48becdfd18e2bf0aab1061commit hash:40568cac8e3e1931ca48becdfd18e2bf0aab1061 files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
science/py-MDAnalysis*: upgrade to 2.2.0

Version 0.19.2 is too old and does not support Python-3.9.

Remark: threadpoolctl is disabled in this port. See
<https://github.com/MDAnalysis/mdanalysis/pull/2950> for the impacts on
performance.

Releases notes at <https://github.com/MDAnalysis/mdanalysis/releases>.

PR:		264716
Approved by:	yuri (maintainer)
0.19.2_2
10 May 2021 20:13:20
commit hash:1d44af58980136b882d146f21d8776943a14c5ebcommit hash:1d44af58980136b882d146f21d8776943a14c5ebcommit hash:1d44af58980136b882d146f21d8776943a14c5ebcommit hash:1d44af58980136b882d146f21d8776943a14c5eb files touched by this commit
Thierry Thomas (thierry) search for other commits by this committer
math/py-matplotlib: chase minimum Python version in dependent ports

Since the previous update changed USES=python from 3.6+ to 3.7+, all
dependent ports must have USES=python:3.7+ as well, otherwise it breaks
the @py36 flavor.

PR:		255347
Reported by:	sunpoet
0.19.2_2
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
0.19.2_2
06 Apr 2021 14:31:07
commit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344ebcommit hash:305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
0.19.2_2
13 Jun 2020 15:05:45
Revision:538676Original commit files touched by this commit
antoine search for other commits by this committer
Unbreak bulk -a
0.19.2_2
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit
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
0.19.2_1
29 Jun 2019 10:28:48
Revision:505343Original commit files touched by this commit
pkubaj search for other commits by this committer
science/py-MDAnalysis: fix build

Add USES=compiler:c++11-lang to fix:
cc1plus: error: unrecognized command line option "-std=c++11"

Approved by:	mentors (implicit approval)
0.19.2_1
12 Dec 2018 01:35:36
Revision:487272Original commit files touched by this commit
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
0.19.2
11 Nov 2018 22:33:50
Revision:484782Original commit files touched by this commit
yuri search for other commits by this committer
science/py-MDAnalysis: Update 0.19.0 -> 0.19.2

Reported by:	portscout
0.19.0
12 Oct 2018 01:15:43
Revision:481865Original commit files touched by this commit
yuri search for other commits by this committer
science/py-MDAnalysis: Update 0.18.0 -> 0.19.0

Reported by:	portscout
0.18.0
20 Jun 2018 17:05:44
Revision:472884Original commit files touched by this commit
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
0.18.0
14 May 2018 00:15:32
Revision:469841Original commit files touched by this commit
yuri search for other commits by this committer
New port: science/py-MDAnalysis: Python library to analyze molecular dynamics
trajectories

Number of commits found: 16