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We just rebooted with several updates: * new HMTLify code * no port maintainer is now highly visible (e.g. https://freshports.org/security/sssd/) * fixed search logic error when using plain/ text details at https://github.com/FreshPorts/freshports/releases/tag/2.2.34
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 Version 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: 2023-01-11 15:58:34
Commit Hash: 77d6847
Also Listed In: python
License: BSD3CLAUSE
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb
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 py39-biom-format
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-biom-format listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-biom-format
Package flavors (<flavor>: <package>)
  • py39: py39-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:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch642.1.6_2pkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py36-biom-format
ABIlatestquarterly
FreeBSD:11:aarch642.1.6_2pkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch642.1.6_2pkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py38-biom-format
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd642.1.102.1.10
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i3862.1.102.1.10
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-falloutpkg-fallout
FreeBSD:12:amd64pkg-falloutpkg-fallout
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i386pkg-falloutpkg-fallout
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch64pkg-falloutpkg-fallout
FreeBSD:13:amd64pkg-falloutpkg-fallout
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv7pkg-falloutpkg-fallout
FreeBSD:13:i386pkg-falloutpkg-fallout
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch64pkg-falloutpkg-fallout
FreeBSD:14:amd64pkg-falloutpkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv7pkg-falloutpkg-fallout
FreeBSD:14:i386pkg-falloutpkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
py39-biom-format
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd64pkg-falloutpkg-fallout
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i386pkg-falloutpkg-fallout
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout2.1.10
FreeBSD:12:amd642.1.102.1.10
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i3862.1.102.1.10
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch642.1.102.1.10
FreeBSD:13:amd642.1.102.1.10
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv72.1.102.1.10
FreeBSD:13:i3862.1.102.1.10
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-fallout2.1.10
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch642.1.10pkg-fallout
FreeBSD:14:amd642.1.10pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv72.1.10pkg-fallout
FreeBSD:14:i3862.1.10pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-numpy>=1.16,1<1.24,1 : 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-click>0 : devel/py-click@py39
  2. py39-numpy>=1.16,1<1.24,1 : math/py-numpy@py39
  3. py39-future>=0.16.0 : devel/py-future@py39
  4. py39-scipy>=1 : science/py-scipy@py39
  5. py39-pandas>=0.20.0 : math/py-pandas@py39
  6. py39-h5py>=2.2.0 : science/py-h5py@py39
  7. py39-six>=1.10.0 : devel/py-six@py39
  8. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  9. python3.9 : lang/python39
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.
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 26

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.1.10
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)
2.1.10
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)
2.1.10
07 Apr 2021 08:09:01
commit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash:cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
2.1.10
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.
2.1.10
30 Jan 2021 13:29:58
Revision:563407Original commit files touched by this commit
sunpoet search for other commits by this committer
Update USES=python: math/py-pandas 1.2.0 requires Python 3.7+

PR:		250103
2.1.10
11 Jan 2021 05:28:11
Revision:561187Original commit files touched by this commit
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
2.1.8
26 Sep 2020 09:10:38
Revision:550141Original commit files touched by this commit
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.
2.1.8
25 Sep 2020 01:03:03
Revision:549977Original commit files touched by this commit
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
2.1.7_3
24 Sep 2020 19:31:44
Revision:549943Original commit files touched by this commit
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
2.1.7_3
15 Aug 2020 10:50:59
Revision:544927Original commit files touched by this commit
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)
2.1.7_3
23 Feb 2020 15:25:53
Revision:526925Original commit files touched by this commit
antoine search for other commits by this committer
Deprecate a few ports

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

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

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

Reported by:	portscout
2.1.6_2
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
2.1.6_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).
2.1.6_1
10 Dec 2017 03:33:04
Revision:455879Original commit files touched by this commit
jrm search for other commits by this committer
biology/py-biom-format: Add required dependency on math/py-pandas and do
not install tests.
2.1.6
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)
2.1.6
29 Apr 2017 13:59:15
Revision:439751Original commit files touched by this commit
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)
2.1.5_1
23 Sep 2016 21:42:02
Revision:422697Original commit files touched by this commit
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
2.1.5_1
11 Jun 2016 09:25:04
Revision:416710Original commit files touched by this commit
olivierd search for other commits by this committer
- Fix run-time dependency issues
- Bump PORTREVISION

PR:		209767
Submitted by:	Joseph Mingrone (maintainer)
2.1.5
09 May 2016 16:42:17
Revision:414866Original commit files touched by this commit
olivierd search for other commits by this committer
Add final slash in WWW entry
2.1.5
09 May 2016 16:37:44
Revision:414865Original commit files touched by this commit
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: 26