Port details |
- pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
- 0.5.2_5 biology
=2 0.5.2_5Version of this port present on the latest quarterly branch. - Maintainer: wen@FreeBSD.org
 - Port Added: 2009-11-18 05:53:48
- Last Update: 2023-06-27 19:34:34
- Commit Hash: 3d9a815
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- Also Listed In: python
- License: MIT
- WWW:
- https://bitbucket.org/brentp/biostuff/src/
- Description:
- pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.
¦ ¦ ¦ ¦ 
- 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:
-
- ${PYTHON_PKGNAMEPREFIX}pyfasta>0:biology/pyfasta@${PY_FLAVOR}
- To install the port:
- cd /usr/ports/biology/pyfasta/ && make install clean
- To add the package, run one of these commands:
- pkg install biology/pyfasta
- pkg install py39-pyfasta
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-pyfasta listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py39-pyfasta
- Package flavors (<flavor>: <package>)
- distinfo:
- SHA256 (pyfasta-0.5.2.tar.gz) = ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258
SIZE (pyfasta-0.5.2.tar.gz) = 19072
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-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- Test dependencies:
-
- python3.9 : lang/python39
- Runtime dependencies:
-
- py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
- py39-setuptools>=63.1.0 : devel/py-setuptools@py39
- python3.9 : lang/python39
- There are no ports dependent upon this port
Configuration Options:
- No options to configure
- Options name:
- biology_pyfasta
- USES:
- python
- FreshPorts was unable to extract/find any pkg message
- Master Sites:
|
Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
Commit | Credits | Log message |
0.5.2_5 27 Jun 2023 19:34:34
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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> |
0.5.2_5 23 Apr 2023 09:09:58
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Gerald Pfeifer (gerald)  |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
0.5.2_4 11 Jan 2023 15:58:34
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Dmitry Marakasov (amdmi3)  |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
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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) |
0.5.2_4 07 Sep 2022 21:10:59
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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 ) |
0.5.2_4 20 Jul 2022 14:20:57
    |
Tobias C. Berner (tcberner)  |
biology: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Aaron Dalton <aaron@FreeBSD.org>
* Akinori MUSHA aka knu <knu@idaemons.org>
* Andrey Zakhvatov
* Bob Zimmermann <rpz@cse.wustl.edu>
* Camson Huynh <chuynh@biolateral.com.au>
* Dan Siercks <dsiercks@uwm.edu>
* Fernan Aguero <fernan@iib.unsam.edu.ar>
* Hannes Hauswedell <h2+fbsdports@fsfe.org>
* J. Bacon <jwb@FreeBSD.org>
* Jason Bacon <jwb@FreeBSD.org>
* Jeremy <karlj000@unbc.ca> (Only the first 15 lines of the commit message are shown above ) |
0.5.2_4 06 Apr 2021 14:31:07
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Mathieu Arnold (mat)  |
Remove # $FreeBSD$ from Makefiles. |
0.5.2_4 28 Dec 2020 23:02:15
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antoine  |
Drop python 2.7 support from a few ports
With hat: portmgr |
0.5.2_4 26 Jul 2019 20:46:57
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gerald  |
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 |
0.5.2_3 07 Feb 2019 09:30:41
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amdmi3  |
- Update WWW
Approved by: portmgr blanket |
0.5.2_3 12 Dec 2018 01:35:36
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gerald  |
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 |
0.5.2_2 10 Mar 2018 17:46:06
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gerald  |
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079). |
0.5.2_1 30 Nov 2017 15:50:34
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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 ) |
0.5.2_1 19 May 2016 10:21:25
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amdmi3  |
- Fix trailing whitespace in pkg-descrs, categories [a-f]*
Approved by: portmgr blanket |
0.5.2_1 19 Oct 2014 07:38:12
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mva  |
- Convert ports from benchmarks/ and biology/ to new USES=python
Approved by: portmgr (implicit) |
0.5.2_1 10 Sep 2014 20:50:37
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gerald  |
Update the default version of GCC in the Ports Collection from GCC 4.7.4
to GCC 4.8.3.
Part II, Bump PORTREVISIONs.
PR: 192025
Tested by: antoine (-exp runs)
Approved by: portmgr (implicit) |
0.5.2 06 Apr 2014 04:05:43
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wen  |
- Update to 0.5.2
- Add LICENSE |
0.5.1_3 10 Mar 2014 20:55:22
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gerald  |
Update the default version of GCC used in the Ports Collection from
GCC 4.6.4 to GCC 4.7.3. This entails updating the lang/gcc port as
well as changing the default in Mk/bsd.default-versions.mk.
Part II, Bump PORTREVISIONs.
PR: 182136
Supported by: Christoph Moench-Tegeder <cmt@burggraben.net> (fixing many ports)
Tested by: bdrewery (two -exp runs) |
0.5.1_2 31 Jan 2014 12:31:24
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miwi  |
- Convert to PYDISTUTILS_AUTOPLIST
- Stage support
- Bump PORTREV |
0.5.1_1 13 Jan 2014 21:00:04
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rene  |
Python cleanup:
- USE_PYTHON* = 2.X -> USE_PYTHON* = 2
- USE_PYTHON* = 2.X+ -> USE_PYTHON* = yes
Reviewed by: python (mva, rm)
Approved by: portmgr-lurkers (mat) |
0.5.1_1 26 Oct 2013 00:52:36
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gerald  |
Update to libmpc version 1.0.1 which brings the following fixes:
- Switched to automake 1.11.6, see CVE-2012-3386.
- #14669: Fixed extraction of CC from gmp.h.
- Fixed case of intermediate zero real or imaginary part in mpc_fma,
found by hydra with GMP_CHECK_RANDOMIZE=1346362345.
This is on top of the following changes from version 1.0
- Licence change towards LGPLv3+ for the code and GFDLv1.3+ (with no
invariant sections) for the documentation.
- 100% of all lines are covered by tests
- Renamed functions
. mpc_mul_2exp to mpc_mul_2ui
. mpc_div_2exp to mpc_div_2ui (Only the first 15 lines of the commit message are shown above ) |
0.5.1 04 Oct 2013 08:09:02
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wen  |
- Update to 0.5.1 |
0.4.5 20 Sep 2013 15:55:44
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bapt  |
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology) |
0.4.5 01 Jun 2013 14:22:36
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wen  |
- Trim Makefile headers |
0.4.5 23 Feb 2012 13:43:25
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wen  |
- Update to 0.4.5 |
0.4.4 13 Oct 2011 06:27:34
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wen  |
- Update to 0.44 |
0.4.3 02 Jun 2011 01:38:55
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wen  |
- Update to 0.4.3 |
0.4.2 13 Apr 2011 09:11:20
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wen  |
- Update to 0.4.2 |
0.4.1 02 Dec 2010 13:42:09
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wen  |
- Update to 0.4.1 |
0.4.0 26 Oct 2010 00:34:36
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wen  |
- Update to 0.4.0 |
0.3.9 18 Aug 2010 14:09:35
 |
glarkin  |
- Update USE_PYTHON in Makefile to reflect upstream Python
dependency version requirement
PR: ports/149251
Submitted by: glarkin
Approved by: wen (via email) |
0.3.9 19 Mar 2010 08:32:48
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wen  |
- Update to 0.3.9 |
0.3.7 24 Dec 2009 03:14:34
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wen  |
- Update to 0.3.7 |
0.3.5 21 Dec 2009 03:29:55
 |
wen  |
- Update to 0.3.5 |
0.3.4 16 Dec 2009 12:48:04
 |
wen  |
- Update to 0.3.4 |
0.3.3 06 Dec 2009 08:47:36
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wen  |
- Update to 0.3.3 |
0.3.1 18 Nov 2009 05:53:17
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wen  |
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.
WWW: http://bitbucket.org/brentp/biostuff/src/ |