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

Version 2.1.8 supports python 3

5 files changed, 65 insertions, 2 deletions

diff --git a/MOVED b/MOVED
index 565836a68a83..f5f843f86559 100644
--- a/MOVED
+++ b/MOVED
@@ -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
diff --git a/biology/Makefile b/biology/Makefile
index ae83b0bc1fb4..29616c908fff 100644
--- a/biology/Makefile
+++ b/biology/Makefile
@@ -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
diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile
new file mode 100644
index 000000000000..d81fb8a2b85a
--- /dev/null
+++ b/biology/py-biom-format/Makefile
@@ -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>
diff --git a/biology/py-biom-format/distinfo b/biology/py-biom-format/distinfo
new file mode 100644
index 000000000000..b705caff7e40
--- /dev/null
+++ b/biology/py-biom-format/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1538769748
+SHA256 (biom-format-2.1.7.tar.gz) = b47e54282ef13cddffdb00aea9183a87175a2372c91a915259086a3f444c42f4
+SIZE (biom-format-2.1.7.tar.gz) = 11820666
diff --git a/biology/py-biom-format/pkg-descr b/biology/py-biom-format/pkg-descr
new file mode 100644
index 000000000000..41a8b5b6ca30
--- /dev/null
+++ b/biology/py-biom-format/pkg-descr
@@ -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/