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Port details
py-DendroPy Phylogenetic computing library
5.0.1 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 4.6.1Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2010-01-09 12:20:30
Last Update: 2024-06-03 07:29:16
Commit Hash: e3bf124
Also Listed In: python
License: BSD3CLAUSE
WWW:
http://packages.python.org/DendroPy/
Description:
py-DendroPy is a python library for phylogenetic scripting, simulation, data processing and manipulation.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • py311-DendroPy>0:science/py-DendroPy
To install the port:
cd /usr/ports/science/py-DendroPy/ && make install clean
To add the package, run one of these commands:
  • pkg install science/py-DendroPy
  • pkg install py311-DendroPy
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: py311-DendroPy
Package flavors (<flavor>: <package>)
  • py311: py311-DendroPy
distinfo:
TIMESTAMP = 1717397726 SHA256 (DendroPy-5.0.1.tar.gz) = f2815e7649a6fe2924ff3fdf00a660c948dc6f3316e303b8b022f74cc75ca42e SIZE (DendroPy-5.0.1.tar.gz) = 395057

Packages (timestamps in pop-ups are UTC):
py311-DendroPy
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest5.0.15.0.1-5.0.15.0.1---
FreeBSD:13:quarterly-5.0.1--5.0.1---
FreeBSD:14:latest5.0.15.0.1-5.0.15.0.1---
FreeBSD:14:quarterly-5.0.1--5.0.1---
FreeBSD:15:latest5.0.15.0.1n/a-n/a---
 
py37-DendroPy
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--4.4.0---4.4.0-
FreeBSD:13:quarterly--------
FreeBSD:14:latest--------
FreeBSD:14:quarterly--------
FreeBSD:15:latest--n/a-n/a---
 
py39-DendroPy
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest4.6.1--4.6.1----
FreeBSD:13:quarterly4.6.1-4.6.14.6.1-4.6.14.6.14.6.1
FreeBSD:14:latest--4.5.2--4.6.1-4.6.1
FreeBSD:14:quarterly4.6.1--4.6.1-4.6.14.6.14.6.1
FreeBSD:15:latest--n/a4.6.1n/a4.6.14.6.14.6.1
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py311-pip>0 : devel/py-pip@py311
  2. py311-wheel>=0 : devel/py-wheel@py311
  3. py311-pytest-runner>0 : devel/py-pytest-runner@py311
  4. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  5. python3.11 : lang/python311
Test dependencies:
  1. python3.11 : lang/python311
Runtime dependencies:
  1. py311-setuptools>=63.1.0 : devel/py-setuptools@py311
  2. python3.11 : lang/python311
This port is required by:
for Run
  1. biology/checkm

Configuration Options:
No options to configure
Options name:
science_py-DendroPy
USES:
python
pkg-message:
For install:
If you use this library either in whole or in part in your analysis, or use any code derived from it, please cite it as: Sukumaran, J. and Mark T. Holder. 2010. DendroPy: A Python library for phylogenetic computing. Bioinformatics 26: 1569-1571.
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/D/DendroPy/
  2. https://pypi.org/packages/source/D/DendroPy/
Collapse this list.

Number of commits found: 48

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
5.0.1
03 Jun 2024 07:29:16
commit hash: e3bf124b2c0d35b395d2704220612949a32c17cdcommit hash: e3bf124b2c0d35b395d2704220612949a32c17cdcommit hash: e3bf124b2c0d35b395d2704220612949a32c17cdcommit hash: e3bf124b2c0d35b395d2704220612949a32c17cd files touched by this commit
Wen Heping (wen) search for other commits by this committer
science/py-DendroPy: Update to 5.0.1
5.0.0
29 May 2024 23:45:44
commit hash: d002af2079655510de749be04e1d1bf5290cdcaecommit hash: d002af2079655510de749be04e1d1bf5290cdcaecommit hash: d002af2079655510de749be04e1d1bf5290cdcaecommit hash: d002af2079655510de749be04e1d1bf5290cdcae files touched by this commit
Wen Heping (wen) search for other commits by this committer
science/py-DendroPy: Update to 5.0.0
4.6.1
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
4.6.1
13 Jun 2023 07:30:02
commit hash: aee1d4c081eceebe06701dff6beb961346c82b01commit hash: aee1d4c081eceebe06701dff6beb961346c82b01commit hash: aee1d4c081eceebe06701dff6beb961346c82b01commit hash: aee1d4c081eceebe06701dff6beb961346c82b01 files touched by this commit
Wen Heping (wen) search for other commits by this committer
science/py-DendroPy: Update to 4.6.1
4.6.0
03 Jun 2023 23:14:18
commit hash: e9a7d03356d791eb390c0ac9ee35a3d9bf9a07c6commit hash: e9a7d03356d791eb390c0ac9ee35a3d9bf9a07c6commit hash: e9a7d03356d791eb390c0ac9ee35a3d9bf9a07c6commit hash: e9a7d03356d791eb390c0ac9ee35a3d9bf9a07c6 files touched by this commit
Wen Heping (wen) search for other commits by this committer
science/py-DendroPy: Update to 4.6.0

Take maintainership
4.5.2
03 Jun 2023 19:02:51
commit hash: 93913bf49228a0280513d8cdd640c77c4312708bcommit hash: 93913bf49228a0280513d8cdd640c77c4312708bcommit hash: 93913bf49228a0280513d8cdd640c77c4312708bcommit hash: 93913bf49228a0280513d8cdd640c77c4312708b files touched by this commit
Carlo Strub (cs) search for other commits by this committer
science/py-DendroPy: Back to @ports
4.5.2
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)
4.5.2
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)
4.5.2
20 Jul 2022 14:22:51
commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
science: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Andreas Fehlner <fehlner@gmx.de>
  *  Brad Huntting <huntting@glarp.com>
  *  Chao Shin <quakelee@cn.FreeBSD.org>
  *  Cheng-Lung Sung <clsung@FreeBSD.org>
  *  Chia-Hsing Yu <me@davidyu.org>
  *  Chris Rees <utisoft@gmail.com>
  *  David Naylor <dbn@FreeBSD.org>
  *  Dmitry Sivachenko <demon@FreeBSD.org>
  *  Ed Schouten <ed@FreeBSD.org>
  *  Eric Freeman <freebsdports@chillibear.com>
  *  Erik B Knudsen
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.5.2
05 Jun 2022 07:43:08
commit hash: 472faa276e363f720e69c93aed06a207d94ce7bccommit hash: 472faa276e363f720e69c93aed06a207d94ce7bccommit hash: 472faa276e363f720e69c93aed06a207d94ce7bccommit hash: 472faa276e363f720e69c93aed06a207d94ce7bc files touched by this commit
Wen Heping (wen) search for other commits by this committer
science/py-DendroPy: Update to 4.5.2

PR:		263706
Reported by:	yuri@
Approved by:	maintainer(timeout, >1 month)
4.4.0
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.
4.4.0
28 Dec 2020 23:02:15
Revision:559531Original commit files touched by this commit
antoine search for other commits by this committer
Drop python 2.7 support from a few ports

With hat:	portmgr
4.4.0
14 Aug 2019 12:16:13
Revision:508909Original commit files touched by this commit
mat search for other commits by this committer
Convert to UCL & cleanup pkg-message (categories s)
4.4.0
12 Oct 2018 14:58:58
Revision:481907Original commit files touched by this commit
antoine search for other commits by this committer
Fix packaging with python 3.x

Reported by:	pkg-fallout
4.4.0
09 Oct 2018 21:04:29
Revision:481669Original commit files touched by this commit
cs search for other commits by this committer
Update to 4.4.0
4.3.0
28 Jan 2018 22:26:46
Revision:460232Original commit files touched by this commit
antoine search for other commits by this committer
%%PYTHON_PYOEXTENSION%% is harmful in python2 style plists

Pointy hat:	cs@
4.3.0
27 Jan 2018 19:16:04
Revision:460143Original commit files touched by this commit
cs search for other commits by this committer
Update to 4.3.0
4.2.0
20 Jan 2018 20:08:15
Revision:459546Original commit files touched by this commit
antoine search for other commits by this committer
Fix packaging with python 3 by using py3kplist
4.2.0
30 Nov 2017 15:50:34
Revision:455210Original commit files touched by this commit Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
4.2.0
29 Mar 2017 21:16:07
Revision:437243Original commit files touched by this commit
cs search for other commits by this committer
Update to 4.2.0
4.1.0
23 May 2016 18:36:52
Revision:415738Original commit files touched by this commit
amdmi3 search for other commits by this committer
Convert tab after WWW: in pkg-descrs to single space as per PHB

Approved by:	portmgr blanket
4.1.0
07 Apr 2016 20:30:12
Revision:412694Original commit files touched by this commit
cs search for other commits by this committer
Update to 4.1.0
4.0.3
25 Dec 2015 12:30:50
Revision:404418Original commit files touched by this commit
cs search for other commits by this committer
Update to 4.0.3
3.12.0_1
27 May 2015 00:15:05
Revision:387529Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Don't cat pkg-message from Makefiles

Approved by:	portmgr blanket
3.12.0_1
12 Nov 2014 18:48:53
Revision:372500Original commit files touched by this commit
antoine search for other commits by this committer
Cleanup plist
3.12.0_1
24 Oct 2014 16:50:43
Revision:371453Original commit files touched by this commit
mva search for other commits by this committer
- Convert ports of science/ and security to new USES=python

Approved by:	portmgr (implicit)
3.12.0_1
01 Jun 2014 21:30:41
Revision:356177Original commit files touched by this commit
cs search for other commits by this committer
- Support staging
- Minor edits
3.12.0
20 Sep 2013 22:48:31
Revision:327767Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
science)
3.12.0
18 Jul 2012 06:21:15
Original commit files touched by this commit Sanity Test Failure
cs search for other commits by this committer
Update to 3.12.0
3.11.0
14 Apr 2012 18:41:27
Original commit files touched by this commit
cs search for other commits by this committer
Update to 3.11.0
3.10.1
31 Jan 2012 23:23:38
Original commit files touched by this commit
cs search for other commits by this committer
Update to 3.10.1

Approved by:    glarkin@ (mentor, implicit)
3.9.0
15 Sep 2011 12:33:27
Original commit files touched by this commit
cs search for other commits by this committer
Change maintainer address to my FreeBSD address

Approved by:    wen@ (mentor)
3.9.0
24 Aug 2011 18:15:24
Original commit files touched by this commit
glarkin search for other commits by this committer
- Updated to 3.9.0
  ChangeLog: http://packages.python.org/DendroPy/changes.html

PR:             ports/159157
Submitted by:   C-S <c-s@c-s.li> (maintainer)
3.8.1
16 Jun 2011 08:07:58
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.8.1
3.7.1
21 Oct 2010 01:45:15
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.7.1
3.7.0
08 Oct 2010 17:24:54
Original commit files touched by this commit
glarkin search for other commits by this committer
- Updated to 3.7.0
- Passed maintainership to submitter
- Switched to BSD license to adhere to upstream package

PR:             ports/151178
Submitted by:   Carlo Strub <c-s at c-s dot li>
3.6.1
03 Sep 2010 10:46:39
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.6.1
3.5.0
22 Aug 2010 18:09:23
Original commit files touched by this commit
lwhsu search for other commits by this committer
- Update to 3.5.0
3.4.1
08 Aug 2010 09:22:03
Original commit files touched by this commit
lwhsu search for other commits by this committer
- Update to 3.4.1

PR:             ports/149415
Submitted by:   Frederic Culot <frederic AT culot.org>
3.4.0
06 Jul 2010 01:45:21
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.4.0

Feature safe:   yes
3.3.0
13 May 2010 06:08:26
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.3.0
- Reset maintainer
3.2.0
30 Mar 2010 01:24:46
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.2.0
3.1.3
25 Feb 2010 07:18:49
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.1.3

Feature safe:   yes
3.1.2
02 Feb 2010 05:55:43
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.1.2
3.0.7
21 Jan 2010 08:09:16
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.0.7
3.0.5
15 Jan 2010 06:21:10
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 3.0.5
3.0.2
09 Jan 2010 12:19:58
Original commit files touched by this commit
wen search for other commits by this committer
py-DendroPy is a python library for phylogenetic scripting,
simulation, data processing and manipulation.

WWW:    http://packages.python.org/DendroPy/

Number of commits found: 48