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
current python flavor. It can be used in dependency lines when the
port itself is not python flavored. For example, deskutils/calibre.
By default, all the flavors are generated. To only generate flavors
for the versions in PYTHON2_DEFAULT and PYTHON3_DEFAULT, define
BUILD_DEFAULT_PYTHON_FLAVORS in your make.conf.
In all the ports with Python dependencies, the *_DEPENDS entries MUST
end with the flavor so that the framework knows which to build/use.
This is done by appending '@${PY_FLAVOR}' after the origin (or
@${FLAVOR} if in a Python module with Python flavors, as the content
will be the same). For example:
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}six>0:devel/py-six@${PY_FLAVOR}
PR: 223071
Reviewed by: portmgr, python
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D12464
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
