| Port details |
- py-DendroPy Phylogenetic computing library
- 4.6.1 science
 =0      4.6.1Version of this port present on the latest quarterly branch. - Maintainer: wen@FreeBSD.org
- Port Added: 2010-01-09 12:20:30
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- 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.
  ¦  ¦  ¦  ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}DendroPy>0:science/py-DendroPy@${PY_FLAVOR}
- 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 py39-DendroPy
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-DendroPy listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-DendroPy
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1686639965
SHA256 (DendroPy-4.6.1.tar.gz) = 26fcbe1cb5831301e8f1f2e15a0563620f0b8e29e6d409dd6a2a7c957dd64c16
SIZE (DendroPy-4.6.1.tar.gz) = 15200462
Packages (timestamps in pop-ups are UTC):
- Dependencies
- NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
- Build dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- This port is required by:
- for Run
-
- 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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
4.6.1
27 Jun 2023 19:34:34
 |
Rene Ladan (rene) |
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
|
Wen Heping (wen) |
science/py-DendroPy: Update to 4.6.1 |
4.6.0
03 Jun 2023 23:14:18
|
Wen Heping (wen) |
science/py-DendroPy: Update to 4.6.0
Take maintainership |
4.5.2
03 Jun 2023 19:02:51
|
Carlo Strub (cs) |
science/py-DendroPy: Back to @ports |
4.5.2
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
4.5.2
20 Jul 2022 14:22:51
|
Tobias C. Berner (tcberner) |
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 ) |
4.5.2
05 Jun 2022 07:43:08
|
Wen Heping (wen) |
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
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
4.4.0
28 Dec 2020 23:02:15
 |
antoine |
Drop python 2.7 support from a few ports
With hat: portmgr |
4.4.0
14 Aug 2019 12:16:13
|
mat |
Convert to UCL & cleanup pkg-message (categories s) |
4.4.0
12 Oct 2018 14:58:58
|
antoine |
Fix packaging with python 3.x
Reported by: pkg-fallout |
4.4.0
09 Oct 2018 21:04:29
|
cs |
Update to 4.4.0 |
4.3.0
28 Jan 2018 22:26:46
|
antoine |
%%PYTHON_PYOEXTENSION%% is harmful in python2 style plists
Pointy hat: cs@ |
4.3.0
27 Jan 2018 19:16:04
|
cs |
Update to 4.3.0 |
4.2.0
20 Jan 2018 20:08:15
|
antoine |
Fix packaging with python 3 by using py3kplist |
4.2.0
30 Nov 2017 15:50:34
 |
mat |
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 ) |
4.2.0
29 Mar 2017 21:16:07
|
cs |
Update to 4.2.0 |
4.1.0
23 May 2016 18:36:52
|
amdmi3 |
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
|
cs |
Update to 4.1.0 |
4.0.3
25 Dec 2015 12:30:50
|
cs |
Update to 4.0.3 |
3.12.0_1
27 May 2015 00:15:05
|
amdmi3 |
- Don't cat pkg-message from Makefiles
Approved by: portmgr blanket |
3.12.0_1
12 Nov 2014 18:48:53
|
antoine |
Cleanup plist |
3.12.0_1
24 Oct 2014 16:50:43
|
mva |
- Convert ports of science/ and security to new USES=python
Approved by: portmgr (implicit) |
3.12.0_1
01 Jun 2014 21:30:41
|
cs |
- Support staging
- Minor edits |
3.12.0
20 Sep 2013 22:48:31
|
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
science) |
3.12.0
18 Jul 2012 06:21:15
|
cs |
Update to 3.12.0 |
3.11.0
14 Apr 2012 18:41:27
|
cs |
Update to 3.11.0 |
3.10.1
31 Jan 2012 23:23:38
|
cs |
Update to 3.10.1
Approved by: glarkin@ (mentor, implicit) |
3.9.0
15 Sep 2011 12:33:27
|
cs |
Change maintainer address to my FreeBSD address
Approved by: wen@ (mentor) |
3.9.0
24 Aug 2011 18:15:24
|
glarkin |
- 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
|
wen |
- Update to 3.8.1 |
3.7.1
21 Oct 2010 01:45:15
|
wen |
- Update to 3.7.1 |
3.7.0
08 Oct 2010 17:24:54
|
glarkin |
- 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
|
wen |
- Update to 3.6.1 |
3.5.0
22 Aug 2010 18:09:23
|
lwhsu |
- Update to 3.5.0 |
3.4.1
08 Aug 2010 09:22:03
|
lwhsu |
- 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
|
wen |
- Update to 3.4.0
Feature safe: yes |
3.3.0
13 May 2010 06:08:26
|
wen |
- Update to 3.3.0
- Reset maintainer |
3.2.0
30 Mar 2010 01:24:46
|
wen |
- Update to 3.2.0 |
3.1.3
25 Feb 2010 07:18:49
|
wen |
- Update to 3.1.3
Feature safe: yes |
3.1.2
02 Feb 2010 05:55:43
|
wen |
- Update to 3.1.2 |
3.0.7
21 Jan 2010 08:09:16
|
wen |
- Update to 3.0.7 |
3.0.5
15 Jan 2010 06:21:10
|
wen |
- Update to 3.0.5 |
3.0.2
09 Jan 2010 12:19:58
|
wen |
py-DendroPy is a python library for phylogenetic scripting,
simulation, data processing and manipulation.
WWW: http://packages.python.org/DendroPy/ |
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