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Port details
py-bx-python Python module for reading, manipulating and writing genomic data sets
0.11.0 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 0.11.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:28:34
Last Update: 2024-02-12 23:07:35
Commit Hash: 3fad843
Also Listed In: python
License: MIT
WWW:
https://github.com/bxlab/bx-python
Description:
bx-python is a python library and associated set of scripts to allow for rapid implementation of genome scale analyses. The library contains a variety of useful modules, but the particular strengths are: Classes for reading and working with genome-scale multiple local alignments (in MAF, AXT, and LAV formats). Generic data structure for indexing on disk files that contain blocks of data associated with intervals on various sequences (used, for example, to provide random access to individual alignments in huge files; optomized for use over network filesystems). Data structures for working with intervals on sequences: * "Binned bitsets" which act just like chromosome sized bit arrays, but lazily allocate regions and allow large blocks of all set or all unset bits to be stored compactly * "Intersecter" for performing fast intersection tests that preserve both query and target intervals and associated annotation
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:
  • ${PYTHON_PKGNAMEPREFIX}bx-python>0:biology/py-bx-python@${PY_FLAVOR}
To install the port:
cd /usr/ports/biology/py-bx-python/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-bx-python
  • pkg install py39-bx-python
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-bx-python listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-bx-python
Package flavors (<flavor>: <package>)
  • py39: py39-bx-python
distinfo:
TIMESTAMP = 1707725546 SHA256 (bx-python-0.11.0.tar.gz) = 2cf8872572817e0d36145cc2711889df5729987ffed4e51280da1e3c2ccb9429 SIZE (bx-python-0.11.0.tar.gz) = 1935085

Packages (timestamps in pop-ups are UTC):
py39-bx-python
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest0.11.00.11.0-0.11.00.11.0---
FreeBSD:13:quarterly0.11.00.11.0-0.11.00.11.0-0.8.13_1-
FreeBSD:14:latest0.11.00.11.0-0.11.00.11.0---
FreeBSD:14:quarterly0.11.00.11.0-0.11.00.11.0-0.8.13_1-
FreeBSD:15:latest0.11.00.11.0n/a-n/a-0.10.00.11.0
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
  2. cython-3.9 : lang/cython@py39
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.26,1 : math/py-numpy@py39
  2. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  3. python3.9 : lang/python39
This port is required by:
for Run
  1. biology/py-crossmap

Configuration Options:
No options to configure
Options name:
biology_py-bx-python
USES:
compiler 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/b/bx-python/
  2. https://pypi.org/packages/source/b/bx-python/
Collapse this list.

Number of commits found: 25

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
0.11.0
12 Feb 2024 23:07:35
commit hash: 3fad843b18c920fec85d5c5fbf75234ffb614414commit hash: 3fad843b18c920fec85d5c5fbf75234ffb614414commit hash: 3fad843b18c920fec85d5c5fbf75234ffb614414commit hash: 3fad843b18c920fec85d5c5fbf75234ffb614414 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-bx-python: update 0.10.0 → 0.11.0

Reported by:	portscout
0.10.0
28 Jan 2024 22:08:29
commit hash: 3dae35c0aadfc7f9077bbef5e427c04c9d38e64acommit hash: 3dae35c0aadfc7f9077bbef5e427c04c9d38e64acommit hash: 3dae35c0aadfc7f9077bbef5e427c04c9d38e64acommit hash: 3dae35c0aadfc7f9077bbef5e427c04c9d38e64a files touched by this commit
Ruslan Makhmatkhanov (rm) search for other commits by this committer
biology/py-bx-python: update to 0.10.0

Update to 0.10.0. This release adds support for python 3.11

Changes: https://github.com/bxlab/bx-python/releases/tag/v0.10.0

PR:		276683
PR:     275494
Approved by:	yuri (maintainer)
0.8.13_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>
0.8.13_1
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
0.8.13
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)
0.8.13
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)
0.8.13
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)
0.8.13
21 Dec 2021 09:03:57
commit hash: 7697bf311c29556133514387d5037fcdc0df1d65commit hash: 7697bf311c29556133514387d5037fcdc0df1d65commit hash: 7697bf311c29556133514387d5037fcdc0df1d65commit hash: 7697bf311c29556133514387d5037fcdc0df1d65 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-bx-python: Update 0.8.11-6 -> 0.8.13

Reported by:	portscout
0.8.11.6
17 Aug 2021 19:10:45
commit hash: 640855add1423c3ab2f9bec57f84514b260702c9commit hash: 640855add1423c3ab2f9bec57f84514b260702c9commit hash: 640855add1423c3ab2f9bec57f84514b260702c9commit hash: 640855add1423c3ab2f9bec57f84514b260702c9 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/py-bx-python: Update 0.8.10 -> 0.8.11-6
0.8.10
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.
0.8.10
27 Feb 2021 03:55:36
Revision:566662Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.9 -> 0.8.10
0.8.9
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
0.8.9
26 Jun 2020 04:17:12
Revision:540420Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.8 -> 0.8.9

Reported by:	portscout
0.8.8
15 Feb 2020 20:08:30
Revision:526239Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.6 -> 0.8.8

Reported by:	portscout
0.8.6
23 Nov 2019 05:53:50
Revision:518184Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.4 -> 0.8.6

Reported by:	portscout
0.8.4_1
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
0.8.4
19 Jun 2019 08:08:31
Revision:504521Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.2 -> 0.8.4

Reported by:	pirtscout
0.8.2_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
0.8.2
26 Aug 2018 09:50:41
Revision:478115Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.1 -> 0.8.2

Reported by:	portscout
0.8.1_1
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
0.8.1_1
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).
0.8.1
10 Feb 2018 00:09:57
Revision:461348Original commit files touched by this commit
yuri search for other commits by this committer
biology/py-bx-python: Update to 0.8.1

Additional port changes:
* Changed to DISTVERSION.
* Added USE_PYTHON=cython.
* Added stripping.
* Updated maintainer e-mail.

Reported compiler warnings to the upstream.

Reported by:	portscout
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14283
0.7.4
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)
0.7.4
06 May 2017 06:07:04
Revision:440232Original commit files touched by this commit
miwi search for other commits by this committer
bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

Number of commits found: 25