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
  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

9 files changed, 15 insertions, 17 deletions

diff --git a/biology/libsbml/Makefile b/biology/libsbml/Makefile
index 6ae00f67c805..4ef28a036795 100644
--- a/biology/libsbml/Makefile
+++ b/biology/libsbml/Makefile
@@ -27,7 +27,7 @@ OPTIONS_SUB=	yes
 PLIST_SUB+=	PORTVERSION=${PORTVERSION}
 
 PYTHON_BUILD_DEPENDS=	swig2.0:devel/swig20
-PYTHON_USES=		python
+PYTHON_USES=		python:2.7
 PYTHON_CMAKE_ON=	-DWITH_PYTHON:BOOL=ON \
 			-DPYTHON_INCLUDE_DIR:STRING="${PYTHON_INCLUDEDIR}" \
 			-DPYTHON_LIBRARY:STRING="${PYTHONBASE}/lib/lib${PYTHON_VERSION}.so" \
diff --git a/biology/py-biom-format/Makefile b/biology/py-biom-format/Makefile
index 03b3d210cc32..0c7c567cdafe 100644
--- a/biology/py-biom-format/Makefile
+++ b/biology/py-biom-format/Makefile
@@ -13,10 +13,10 @@ LICENSE=	BSD3CLAUSE
 
 BUILD_DEPENDS=	${PYNUMPY}
 RUN_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}h5py>=2.6.0:science/py-h5py    \
-		${PYTHON_PKGNAMEPREFIX}click>=6.6:devel/py-click      \
-		${PYTHON_PKGNAMEPREFIX}future>=0.15.2:devel/py-future \
-		${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy
+		${PYTHON_PKGNAMEPREFIX}h5py>=2.6.0:science/py-h5py@${FLAVOR}    \
+		${PYTHON_PKGNAMEPREFIX}click>=6.6:devel/py-click@${FLAVOR}      \
+		${PYTHON_PKGNAMEPREFIX}future>=0.15.2:devel/py-future@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}scipy>=0.16.1:science/py-scipy@${FLAVOR}
 
 USE_GITHUB=	yes
 GH_ACCOUNT=	biocore
@@ -27,7 +27,7 @@ USE_PYTHON=	autoplist distutils
 .include <bsd.port.pre.mk>
 
 .if ${PYTHON_REL} < 3000
-RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}pyqi>=0.2.0:devel/py-pyqi
+RUN_DEPENDS+=	${PYTHON_PKGNAMEPREFIX}pyqi>=0.2.0:devel/py-pyqi@${FLAVOR}
 .endif
 
 post-install:
diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index c893687ef364..edc8c7a1e2ef 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -20,6 +20,6 @@ OPTIONS_DEFINE=	REPORTLAB
 OPTIONS_DEFAULT=	REPORTLAB
 
 REPORTLAB_DESC=	PDF support in Bio.Graphics module
-REPORTLAB_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1
+REPORTLAB_RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}reportlab1>0:print/py-reportlab1@${FLAVOR}
 
 .include <bsd.port.mk>
diff --git a/biology/py-bx-python/Makefile b/biology/py-bx-python/Makefile
index 89ccb9749a3e..0a11dd8824da 100644
--- a/biology/py-bx-python/Makefile
+++ b/biology/py-bx-python/Makefile
@@ -14,7 +14,7 @@ LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/LICENSE
 
 BUILD_DEPENDS=	${PYNUMPY} \
-		${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo
+		${PYTHON_PKGNAMEPREFIX}python-lzo>0:archivers/py-python-lzo@${FLAVOR}
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USE_GITHUB=	yes
diff --git a/biology/py-cutadapt/Makefile b/biology/py-cutadapt/Makefile
index 0d215ac15be5..863a1ee70ab2 100644
--- a/biology/py-cutadapt/Makefile
+++ b/biology/py-cutadapt/Makefile
@@ -12,7 +12,7 @@ COMMENT=	Finds and removes adapter sequences, primers, poly-A tails, etc
 
 LICENSE=	MIT
 
-RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen
+RUN_DEPENDS=	${PYTHON_PKGNAMEPREFIX}xopen>0:archivers/py-xopen@${FLAVOR}
 
 USES=		python
 USE_PYTHON=	distutils
diff --git a/biology/py-pysam/Makefile b/biology/py-pysam/Makefile
index 6bcbc6e2584e..afec069f8422 100644
--- a/biology/py-pysam/Makefile
+++ b/biology/py-pysam/Makefile
@@ -12,11 +12,8 @@ COMMENT=	Python module for reading, manipulating and writing genomic data sets
 LICENSE=	MIT
 LICENSE_FILE=	${WRKSRC}/COPYING
 
-BUILD_DEPENDS=	cython:lang/cython
-RUN_DEPENDS=	cython:lang/cython
-
 USES=		gmake python
-USE_PYTHON=	autoplist distutils
+USE_PYTHON=	autoplist distutils cython cython_run
 
 post-install:
 	${STRIP_CMD} ${STAGEDIR}${PYTHONPREFIX_SITELIBDIR}/pysam/*.so
diff --git a/biology/pycogent/Makefile b/biology/pycogent/Makefile
index f0725592332c..a70e2e31f00c 100644
--- a/biology/pycogent/Makefile
+++ b/biology/pycogent/Makefile
@@ -11,13 +11,12 @@ COMMENT=	Toolkit for statistical analysis of biological sequences
 LICENSE=	GPLv2
 
 BUILD_DEPENDS=	${PYNUMPY} \
-		${LOCALBASE}/bin/cython:lang/cython \
-		${LOCALBASE}/bin/sphinx-build:textproc/py-sphinx \
-		${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=1.0.13:databases/py-sqlalchemy10
+		${LOCALBASE}/bin/sphinx-build:textproc/py-sphinx@${FLAVOR} \
+		${PYTHON_PKGNAMEPREFIX}sqlalchemy10>=1.0.13:databases/py-sqlalchemy10@${FLAVOR}
 RUN_DEPENDS:=	${BUILD_DEPENDS}
 
 USES=		python:-2.7
 USE_GITHUB=	yes
-USE_PYTHON=	distutils autoplist
+USE_PYTHON=	distutils autoplist cython
 
 .include <bsd.port.mk>
diff --git a/biology/pyfasta/Makefile b/biology/pyfasta/Makefile
index 2c7d49cd2532..c06752787757 100644
--- a/biology/pyfasta/Makefile
+++ b/biology/pyfasta/Makefile
@@ -6,6 +6,7 @@ PORTVERSION=	0.5.2
 PORTREVISION=	1
 CATEGORIES=	biology python
 MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Fast, memory-efficient, pythonic access to fasta sequence files
diff --git a/biology/python-nexus/Makefile b/biology/python-nexus/Makefile
index c55243d5e23a..bf0cb8d97943 100644
--- a/biology/python-nexus/Makefile
+++ b/biology/python-nexus/Makefile
@@ -5,6 +5,7 @@ PORTNAME=	python-nexus
 PORTVERSION=	1.53
 CATEGORIES=	biology python
 MASTER_SITES=	CHEESESHOP
+PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
 MAINTAINER=	wen@FreeBSD.org
 COMMENT=	Generic nexus file format reader for python