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biology/py-biom-format: Restore in preparation for an update to v2.1.8

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Version 2.1.8 supports python 3
This commit is contained in:
Joseph Mingrone 2020-09-24 19:31:43 +00:00
parent 381269f441
commit f244f722da
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=549943
5 changed files with 65 additions and 2 deletions
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2
MOVED
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@ -15181,7 +15181,6 @@ audio/py-openal||2020-08-15|Has expired: Uses deprecated version of python
audio/py-py-jack||2020-08-15|Has expired: Uses deprecated version of python
audio/py-xmms2||2020-08-15|Has expired: Uses deprecated version of python
audio/triceratops-lv2||2020-08-15|Has expired: Uses deprecated version of python
biology/py-biom-format||2020-08-15|Has expired: Uses deprecated version of python
comms/py-bulksms||2020-08-15|Has expired: Uses deprecated version of python
comms/py-gammu||2020-08-15|Has expired: Uses deprecated version of python
databases/py-geoalchemy||2020-08-15|Has expired: Uses deprecated version of python
@ -15534,7 +15533,6 @@ lang/julia11||2020-09-19|Has expired: Uses deprecated version of python
lang/tinypy||2020-09-19|Has expired: Uses deprecated version of python
mail/cleanup-maildir||2020-09-19|Has expired: Uses deprecated version of python
mail/courier-pythonfilter||2020-09-19|Has expired: Uses deprecated version of python
mail/getmail|mail/getmail6|2020-09-19|Has expired: Uses deprecated version of python
mail/muttils||2020-09-19|Has expired: Uses deprecated version of python
mail/nohtml||2020-09-19|Has expired: Uses deprecated version of python
mail/offlineimap||2020-09-19|Has expired: Uses deprecated version of python

1
biology/Makefile
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@ -120,6 +120,7 @@
SUBDIR += protomol
SUBDIR += psi88
SUBDIR += py-Genesis-PyAPI
SUBDIR += py-biom-format
SUBDIR += py-biopython
SUBDIR += py-bx-python
SUBDIR += py-cutadapt

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biology/py-biom-format/Makefile Normal file
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@ -0,0 +1,42 @@
# $FreeBSD$
PORTNAME= biom-format
PORTVERSION= 2.1.7
PORTREVISION= 3
CATEGORIES= biology python
MASTER_SITES= CHEESESHOP
PKGNAMEPREFIX= ${PYTHON_PKGNAMEPREFIX}
MAINTAINER= jrm@FreeBSD.org
COMMENT= Biological Observation Matrix (BIOM) Format Project
LICENSE= BSD3CLAUSE
DEPRECATED= Uses deprecated version of python
EXPIRATION_DATE= 2020-08-15
BUILD_DEPENDS= ${PYNUMPY}
RUN_DEPENDS= ${PYTHON_PKGNAMEPREFIX}click>0:devel/py-click@${PY_FLAVOR} \
${PYNUMPY} \
${PYTHON_PKGNAMEPREFIX}future>=0.16.0:devel/py-future@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}scipy>=0.13.0:science/py-scipy@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}pandas>=0.20.0:math/py-pandas@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}h5py>=2.2.0:science/py-h5py@${PY_FLAVOR} \
${PYTHON_PKGNAMEPREFIX}six>=1.10.0:devel/py-six@${PY_FLAVOR}
USES= python:-3.6
USE_PYTHON= autoplist concurrent distutils
.include <bsd.port.pre.mk>
.if ${PYTHON_REL} < 3000
RUN_DEPENDS+= ${PYTHON_PKGNAMEPREFIX}pyqi>0:devel/py-pyqi@${PY_FLAVOR}
.endif
post-extract:
${RM} -r ${WRKSRC}/tests
post-install:
${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/biom/*.so
.include <bsd.port.post.mk>

3
biology/py-biom-format/distinfo Normal file
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@ -0,0 +1,3 @@
TIMESTAMP = 1538769748
SHA256 (biom-format-2.1.7.tar.gz) = b47e54282ef13cddffdb00aea9183a87175a2372c91a915259086a3f444c42f4
SIZE (biom-format-2.1.7.tar.gz) = 11820666

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biology/py-biom-format/pkg-descr Normal file
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@ -0,0 +1,19 @@
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/