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Port details
py-biom-format Biological Observation Matrix (BIOM) Format Project
2.1.10 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 2.1.10Version of this port present on the latest quarterly branch.
Maintainer: jrm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2016-05-09 16:37:53
Last Update: 2021-04-07 08:09:01
Commit Hash: cf118cc
Also Listed In: python
License: BSD3CLAUSE
Description:
SVNWeb : git : Homepage
pkg-plist: as obtained via: make generate-plist
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}biom-format>0:biology/py-biom-format@${PY_FLAVOR}
To install the port:
cd /usr/ports/biology/py-biom-format/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/py-biom-format
  • pkg install py38-biom-format
NOTE: This is a Python port. Instead of py38-biom-format listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py38-biom-format
Package flavors (<flavor>: <package>)
  • py38: py38-biom-format
distinfo:
Packages (timestamps in pop-ups are UTC):
py27-biom-format
ABIlatestquarterly
FreeBSD:11:aarch642.1.6_22.1.7_3
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch642.1.6_2-
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py36-biom-format
ABIlatestquarterly
FreeBSD:11:aarch642.1.6_2-
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch642.1.6_2-
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 
py37-biom-format
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd64--
FreeBSD:11:armv6--
FreeBSD:11:i386--
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64--
FreeBSD:12:amd64--
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i386--
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch64--
FreeBSD:13:amd64--
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i386--
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch64--
FreeBSD:14:amd64--
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i386--
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc642.1.10-
 
py38-biom-format
ABIlatestquarterly
FreeBSD:11:aarch64--
FreeBSD:11:amd642.1.102.1.10
FreeBSD:11:armv6--
FreeBSD:11:i3862.1.102.1.10
FreeBSD:11:mips--
FreeBSD:11:mips64--
FreeBSD:12:aarch64-2.1.10
FreeBSD:12:amd642.1.102.1.10
FreeBSD:12:armv6--
FreeBSD:12:armv7--
FreeBSD:12:i3862.1.102.1.10
FreeBSD:12:mips--
FreeBSD:12:mips64--
FreeBSD:12:powerpc64--
FreeBSD:13:aarch642.1.102.1.10
FreeBSD:13:amd642.1.102.1.10
FreeBSD:13:armv6--
FreeBSD:13:armv7-2.1.10
FreeBSD:13:i3862.1.102.1.10
FreeBSD:13:mips--
FreeBSD:13:mips64--
FreeBSD:13:powerpc64--
FreeBSD:14:aarch642.1.10-
FreeBSD:14:amd642.1.10-
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3862.1.10-
FreeBSD:14:mips--
FreeBSD:14:mips64--
FreeBSD:14:powerpc64--
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  2. cython-3.8 : lang/cython@py38
  3. py38-setuptools>0 : devel/py-setuptools@py38
  4. python3.8 : lang/python38
Runtime dependencies:
  1. py38-click>0 : devel/py-click@py38
  2. py38-numpy>=1.16,1<1.20,1 : math/py-numpy@py38
  3. py38-future>=0.16.0 : devel/py-future@py38
  4. py38-scipy>=1 : science/py-scipy@py38
  5. py38-pandas>=0.20.0 : math/py-pandas@py38
  6. py38-h5py>=2.2.0 : science/py-h5py@py38
  7. py38-six>=1.10.0 : devel/py-six@py38
  8. py38-setuptools>0 : devel/py-setuptools@py38
  9. python3.8 : lang/python38
There are no ports dependent upon this port

Configuration Options:
Options name:

USES:

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/biom-format/
  2. https://pypi.org/packages/source/b/biom-format/
Collapse this list.

Number of commits found: 23

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
07 Apr 2021 08:09:01
 files touched by this commit commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c  2.1.10
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
06 Apr 2021 14:31:07
 files touched by this commit commit hash:305f148f482daf30dcf728039d03d019f88344eb  2.1.10
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
30 Jan 2021 13:29:58
Original commit files touched by this commit Revision:563407  2.1.10
sunpoet search for other commits by this committer
Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+

PR:		250103
11 Jan 2021 05:28:11
Original commit files touched by this commit Revision:561187  2.1.10
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.10

https://github.com/biocore/biom-format/releases/tag/2.1.10
26 Sep 2020 09:10:38
Original commit files touched by this commit Revision:550141  2.1.8
jrm search for other commits by this committer
biology/py-biom-format: Fix fetch and relax scipy requirement

- The broken fetch was due to a commit error.

- The relaxing of the scipy constraint is temporary until scipy can be
  updated.
25 Sep 2020 01:03:03
Original commit files touched by this commit Revision:549977  2.1.8
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.8

Upstream changes:
https://github.com/biocore/biom-format/releases/tag/2.1.8
24 Sep 2020 19:31:44
Original commit files touched by this commit Revision:549943  2.1.7_3
jrm search for other commits by this committer
biology/py-biom-format: Restore in preparation for an update to v2.1.8

Version 2.1.8 supports python 3
15 Aug 2020 10:50:59
Original commit files touched by this commit Revision:544927  2.1.7_3
rene search for other commits by this committer
Remove deprecated ports:

2020-08-15 archivers/py-backports.lzma: Uses deprecated version of python
2020-08-15 archivers/py-bup: Uses deprecated version of python
2020-08-15 archivers/py-librtfcomp: Uses deprecated version of python
2020-08-15 audio/blop-lv2: Uses deprecated version of python
2020-08-15 audio/bs2b-lv2: Uses deprecated version of python
2020-08-15 audio/py-gmusicproxy: Uses deprecated version of python
2020-08-15 audio/py-karaoke: Uses deprecated version of python
2020-08-15 audio/py-openal: Uses deprecated version of python
2020-08-15 audio/py-py-jack: Uses deprecated version of python
2020-08-15 audio/py-xmms2: Uses deprecated version of python
2020-08-15 audio/triceratops-lv2: Uses deprecated version of python
2020-08-15 biology/py-biom-format: Uses deprecated version of python
2020-08-15 comms/py-bulksms: Uses deprecated version of python
(Only the first 15 lines of the commit message are shown above View all of this commit message)
23 Feb 2020 15:25:53
Original commit files touched by this commit Revision:526925  2.1.7_3
antoine search for other commits by this committer
Deprecate a few ports

With hat:	portmgr
08 Nov 2019 12:12:42
Original commit files touched by this commit Revision:517051  2.1.7_3
amdmi3 search for other commits by this committer
- Limit python version (does not build with 3.7+)

Approved by:	portmgr blanket
26 Jul 2019 20:46:57
Original commit files touched by this commit Revision:507372  2.1.7_3
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
10 Apr 2019 06:18:32
Original commit files touched by this commit Revision:498530  2.1.7_2
antoine search for other commits by this committer
Bump a few PORTREVISIONs after r498529

With hat:	portmgr
12 Dec 2018 01:35:36
Original commit files touched by this commit Revision:487272  2.1.7_1
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
06 Oct 2018 15:28:02
Original commit files touched by this commit Revision:481369  2.1.7
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.7

Reported by:	portscout
20 Jun 2018 17:05:44
Original commit files touched by this commit Revision:472884  2.1.6_2
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
10 Mar 2018 17:46:06
Original commit files touched by this commit Revision:464084  2.1.6_2
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).
10 Dec 2017 03:33:04
Original commit files touched by this commit Revision:455879  2.1.6_1
jrm search for other commits by this committer
biology/py-biom-format: Add required dependency on math/py-pandas and do
not install tests.
30 Nov 2017 15:50:34
Original commit files touched by this commit Revision:455210  2.1.6  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)
29 Apr 2017 13:59:15
Original commit files touched by this commit Revision:439751  2.1.6
jrm search for other commits by this committer
biology/py-biom-format: Update to version 2.1.6

Upstream changes: https://github.com/biocore/biom-format/releases/tag/2.1.6

Approved by:	swills (mentor, implicit)
23 Sep 2016 21:42:02
Original commit files touched by this commit Revision:422697  2.1.5_1
jrm search for other commits by this committer
Update email address to jrm@FreeBSD.org for ports that I maintain

Reviewed by:	mat, swills (mentor)
Approved by:	swills (mentor)
Differential Revision:	https://reviews.freebsd.org/D7995
11 Jun 2016 09:25:04
Original commit files touched by this commit Revision:416710  2.1.5_1
olivierd search for other commits by this committer
- Fix run-time dependency issues
- Bump PORTREVISION

PR:		209767
Submitted by:	Joseph Mingrone (maintainer)
09 May 2016 16:42:17
Original commit files touched by this commit Revision:414866  2.1.5
olivierd search for other commits by this committer
Add final slash in WWW entry
09 May 2016 16:37:44
Original commit files touched by this commit Revision:414865  2.1.5
olivierd search for other commits by this committer
The BIOM file format (canonically pronounced biome) is designed to be a
general-use format for representing biological sample by observation contingency
tables. BIOM is a recognized standard for the Earth Microbiome Project and is a
Genomics Standards Consortium supported project.

The BIOM format is designed for general use in broad areas of comparative
-omics. For example, in marker-gene surveys, the primary use of this format is
to represent OTU tables: the observations in this case are OTUs and the matrix
contains counts corresponding to the number of times each OTU is observed in
each sample. With respect to metagenome data, this format would be used to
represent metagenome tables: the observations in this case might correspond to
SEED subsystems, and the matrix would contain counts corresponding to the number
of times each subsystem is observed in each metagenome. Similarly, with respect
to genome data, this format may be used to represent a set of genomes: the
observations in this case again might correspond to SEED subsystems, and the
counts would correspond to the number of times each subsystem is observed in
each genome.

WWW: http://biom-format.org/

PR:		209193
Submitted by:	Joseph Mingrone

Number of commits found: 23