py-htseq: Begin work on update to 2.0.3

[Jason W. Bacon <bacon%NetBSD.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason W. Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Thu Jul 27 18:50:06 2023 -0500
Changeset:	1cd386d3429febf9efeafb0d5cae0fe5d731a0d3

Modified Files:
	py-htseq/DESCR
	py-htseq/Makefile
	py-htseq/PLIST
	py-htseq/distinfo
Removed Files:
	py-htseq/TODO
	py-htseq/buildlink3.mk

Log Message:
py-htseq: Begin work on update to 2.0.3

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=1cd386d3429febf9efeafb0d5cae0fe5d731a0d3

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 py-htseq/DESCR         |  8 ++++----
 py-htseq/Makefile      | 37 ++++++++++++++++++++++++++++---------
 py-htseq/PLIST         | 29 -----------------------------
 py-htseq/TODO          |  1 -
 py-htseq/buildlink3.mk | 12 ------------
 py-htseq/distinfo      |  6 +++---
 6 files changed, 35 insertions(+), 58 deletions(-)

diffs:
diff --git a/py-htseq/DESCR b/py-htseq/DESCR
index efe1c0efce..afafda9c12 100644
--- a/py-htseq/DESCR
+++ b/py-htseq/DESCR
@@ -1,4 +1,4 @@
-HTSeq is a Python package that provides infrastructure to process data from
-high-throughput sequencing assays.
-
-WWW: http://pypi.python.org/pypi/HTSeq
+HTSeq is a Python library to facilitate programmatic analysis of data
+from high-throughput sequencing (HTS) experiments. A popular component
+of HTSeq is htseq-count, a script to quantify gene expression in bulk
+and single-cell RNA-Seq and similar experiments.
diff --git a/py-htseq/Makefile b/py-htseq/Makefile
index 80f688b88f..f2cb06c116 100644
--- a/py-htseq/Makefile
+++ b/py-htseq/Makefile
@@ -1,21 +1,40 @@
 # $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Thu Jul 27 18:40:57 CDT 2023               #
+###########################################################
 
-DISTNAME=	HTSeq-${PORTVERSION}
-PKGNAME=	${PYPKGPREFIX}-htseq-${PORTVERSION}
-CATEGORIES=	biology python
+###########################################################
+# Unconverted and partially converted FreeBSD port syntax:
+
+#post-install:
+#	${STRIP} ${DESTDIR}${PYTHON_SITELIBDIR}/HTSeq/_StepVector.cpython-39.so
+#	${STRIP} ${DESTDIR}${PYTHON_SITELIBDIR}/HTSeq/_HTSeq.cpython-39.so
+
+DISTNAME=	HTSeq-2.0.3
+PKGNAME=	${PYPKGPREFIX}-HTSeq-2.0.3
+CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_PYPI:=H/HTSeq/}
 
-MAINTAINER=	bacon%NetBSD.org@localhost
-COMMENT=	Framework to analyze data from high-throughput sequencing assays
+OWNER=		bacon%NetBSD.org@localhost
+HOMEPAGE=	https://pypi.python.org/project/htseq/
+COMMENT=	Python library to facilitate programmatic analysis of sequence data
 LICENSE=	gnu-gpl-v3
 
-DEPENDS+=	${PYPKGPREFIX}-matplotlib-[0-9]*:../../graphics/py-matplotlib
+DEPENDS=	${PYPKGPREFIX}-pysam>0:../../wip/py-pysam \
+		${PKGNAMEPREFIX}matplotlib>=1.4.3:../../graphics/py-matplotlib
+
+TEST_DEPENDS=	${PYTHON_PKGNAMEPREFIX}scipy>1.5.0:../../math/py-scipy \
+		${PYPKGPREFIX}-pandas>=1.1.0:../../math/py-pandas \
+		${PYPKGPREFIX}-matplotlib>=1.4:../../graphics/py-matplotlib
 
 # Just assuming C and C++: Adjust this!
 USE_LANGUAGES=	c c++
 
-PORTVERSION=	0.6.1p1
-
-.include "../../wip/python/distutils.mk"
+# Verify that we shouldn't use distutils.mk or extensions.mk instead.
+.include "../../lang/python/egg.mk"
 .include "../../math/py-numpy/buildlink3.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
 .include "../../mk/bsd.pkg.mk"
diff --git a/py-htseq/PLIST b/py-htseq/PLIST
index b4d73e9f57..48d96a5493 100644
--- a/py-htseq/PLIST
+++ b/py-htseq/PLIST
@@ -1,30 +1 @@
 @comment $NetBSD$
-bin/htseq-count
-bin/htseq-qa
-${PYSITELIB}/${EGG_FILE}/dependency_links.txt
-${PYSITELIB}/${EGG_FILE}/PKG-INFO
-${PYSITELIB}/${EGG_FILE}/SOURCES.txt
-${PYSITELIB}/${EGG_FILE}/top_level.txt
-${PYSITELIB}/HTSeq/_HTSeq_internal.py
-${PYSITELIB}/HTSeq/_HTSeq_internal.pyc
-${PYSITELIB}/HTSeq/_HTSeq_internal.pyo
-${PYSITELIB}/HTSeq/_HTSeq.so
-${PYSITELIB}/HTSeq/__init__.py
-${PYSITELIB}/HTSeq/__init__.pyc
-${PYSITELIB}/HTSeq/__init__.pyo
-${PYSITELIB}/HTSeq/scripts/count.py
-${PYSITELIB}/HTSeq/scripts/count.pyc
-${PYSITELIB}/HTSeq/scripts/count.pyo
-${PYSITELIB}/HTSeq/scripts/__init__.py
-${PYSITELIB}/HTSeq/scripts/__init__.pyc
-${PYSITELIB}/HTSeq/scripts/__init__.pyo
-${PYSITELIB}/HTSeq/scripts/qa.py
-${PYSITELIB}/HTSeq/scripts/qa.pyc
-${PYSITELIB}/HTSeq/scripts/qa.pyo
-${PYSITELIB}/HTSeq/StepVector.py
-${PYSITELIB}/HTSeq/StepVector.pyc
-${PYSITELIB}/HTSeq/StepVector.pyo
-${PYSITELIB}/HTSeq/_StepVector.so
-${PYSITELIB}/HTSeq/_version.py
-${PYSITELIB}/HTSeq/_version.pyc
-${PYSITELIB}/HTSeq/_version.pyo
diff --git a/py-htseq/TODO b/py-htseq/TODO
deleted file mode 100644
index b687356e6b..0000000000
--- a/py-htseq/TODO
+++ /dev/null
@@ -1 +0,0 @@
-Clean up and test
diff --git a/py-htseq/buildlink3.mk b/py-htseq/buildlink3.mk
deleted file mode 100644
index 5afb30403b..0000000000
--- a/py-htseq/buildlink3.mk
+++ /dev/null
@@ -1,12 +0,0 @@
-# $NetBSD$
-
-BUILDLINK_TREE+=	HTSeq
-
-.if !defined(HTSEQ_BUILDLINK3_MK)
-HTSEQ_BUILDLINK3_MK:=
-
-BUILDLINK_API_DEPENDS.HTSeq+=	HTSeq>=0.6.1p1
-BUILDLINK_PKGSRCDIR.HTSeq?=	../../wip/py-htseq
-.endif	# HTSEQ_BUILDLINK3_MK
-
-BUILDLINK_TREE+=	-HTSeq
diff --git a/py-htseq/distinfo b/py-htseq/distinfo
index 1d5de0d1bc..60170ba187 100644
--- a/py-htseq/distinfo
+++ b/py-htseq/distinfo
@@ -1,5 +1,5 @@
 $NetBSD$
 
-RMD160 (HTSeq-0.6.1p1.tar.gz) = c4d1b8cb687c51ad95264d4fc109715502808f32
-SHA512 (HTSeq-0.6.1p1.tar.gz) = d71aead88eba7630636330376aebb91084fae1596215597845872b0ae79799d1eb48b1faba7d22e1d3dd7361f3ad9de4448b17e1d743326d94039119902ad89c
-Size (HTSeq-0.6.1p1.tar.gz) = 226234 bytes
+BLAKE2s (HTSeq-2.0.3.tar.gz) = 0ae11b333ffa57f09437b207b32facd85a29262e4745b8f7e986d834c12acfed
+SHA512 (HTSeq-2.0.3.tar.gz) = 8e7f2e47146083b111ae007d406ceab49252e35b6049b95b0626dd98b9ee100a0535e85f11572d2fc63688d4c75c187cba144cc169f77e4ea0c117a29dfa2469
+Size (HTSeq-2.0.3.tar.gz) = 394178 bytes