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Port details
pyfasta Fast, memory-efficient, pythonic access to fasta sequence files
0.5.2_5 biology 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 0.5.2_5Version of this port present on the latest quarterly branch.
Maintainer: wen@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-11-18 05:53:48
Last Update: 2023-06-27 19:34:34
Commit Hash: 3d9a815
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.
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:
  • ${PYTHON_PKGNAMEPREFIX}pyfasta>0:biology/pyfasta@${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>)
  • py39: py39-pyfasta
distinfo:
SHA256 (pyfasta-0.5.2.tar.gz) = ab08d75fa90253bc91933d10567d5d9cca2718f4796ef3bdc36b68df0e45b258 SIZE (pyfasta-0.5.2.tar.gz) = 19072

Packages (timestamps in pop-ups are UTC):
py39-pyfasta
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.5.2_50.5.2_5-0.5.2_50.5.2_5---
FreeBSD:13:quarterly0.5.2_50.5.2_5--0.5.2_5-0.5.2_5-
FreeBSD:14:latest0.5.2_50.5.2_5-0.5.2_50.5.2_5---
FreeBSD:14:quarterly0.5.2_50.5.2_5--0.5.2_5-0.5.2_5-
FreeBSD:15:latest0.5.2_50.5.2_5n/a0.5.2_5n/a-0.5.2_50.5.2_5
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. 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:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/p/pyfasta/
  2. https://pypi.org/packages/source/p/pyfasta/
Collapse this list.

Number of commits found: 37

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.5.2_5
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>
0.5.2_5
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
0.5.2_4
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)
0.5.2_4
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)
0.5.2_4
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
0.5.2_4
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.
0.5.2_4
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
0.5.2_4
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
0.5.2_3
07 Feb 2019 09:30:41
Revision:492353Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Update WWW

Approved by:	portmgr blanket
0.5.2_3
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
0.5.2_2
10 Mar 2018 17:46:06
Revision:464084Original commit files touched by this commit
gerald search for other commits by this committer
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
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)
0.5.2_1
19 May 2016 10:21:25
Revision:415498Original commit files touched by this commit
amdmi3 search for other commits by this committer
- Fix trailing whitespace in pkg-descrs, categories [a-f]*

Approved by:	portmgr blanket
0.5.2_1
19 Oct 2014 07:38:12
Revision:371171Original commit files touched by this commit
mva search for other commits by this committer
- Convert ports from benchmarks/ and biology/ to new USES=python

Approved by:	portmgr (implicit)
0.5.2_1
10 Sep 2014 20:50:37
Revision:367888Original commit files touched by this commit
gerald search for other commits by this committer
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
Revision:350289Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.5.2
- Add LICENSE
0.5.1_3
10 Mar 2014 20:55:22
Revision:347809Original commit files touched by this commit
gerald search for other commits by this committer
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
Revision:341984Original commit files touched by this commit
miwi search for other commits by this committer
- Convert to PYDISTUTILS_AUTOPLIST
- Stage support
- Bump PORTREV
0.5.1_1
13 Jan 2014 21:00:04
Revision:339634Original commit files touched by this commit
rene search for other commits by this committer
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
Revision:331644Original commit files touched by this commit
gerald search for other commits by this committer
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 View all of this commit message)
0.5.1
04 Oct 2013 08:09:02
Revision:329270Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.5.1
0.4.5
20 Sep 2013 15:55:44
Revision:327709Original 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:
biology)
0.4.5
01 Jun 2013 14:22:36
Revision:319570Original commit files touched by this commit
wen search for other commits by this committer
- Trim Makefile headers
0.4.5
23 Feb 2012 13:43:25
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4.5
0.4.4
13 Oct 2011 06:27:34
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.44
0.4.3
02 Jun 2011 01:38:55
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4.3
0.4.2
13 Apr 2011 09:11:20
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4.2
0.4.1
02 Dec 2010 13:42:09
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4.1
0.4.0
26 Oct 2010 00:34:36
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.4.0
0.3.9
18 Aug 2010 14:09:35
Original commit files touched by this commit
glarkin search for other commits by this committer
- 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
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.3.9
0.3.7
24 Dec 2009 03:14:34
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.3.7
0.3.5
21 Dec 2009 03:29:55
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.3.5
0.3.4
16 Dec 2009 12:48:04
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.3.4
0.3.3
06 Dec 2009 08:47:36
Original commit files touched by this commit
wen search for other commits by this committer
- Update to 0.3.3
0.3.1
18 Nov 2009 05:53:17
Original commit files touched by this commit
wen search for other commits by this committer
pyfasta is a python module for fast, memory-efficient, pythonic
access to fasta sequence files.

WWW:    http://bitbucket.org/brentp/biostuff/src/

Number of commits found: 37