wip/py-pysam: update to version 0.16.0.1

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: wip/py-pysam: update to version 0.16.0.1
From: Brook Milligan <brook%nmsu.edu@localhost>
Date: Mon, 07 Jun 2021 23:30:26 +0000
Module Name:	pkgsrc-wip
Committed By:	Brook Milligan <brook%nmsu.edu@localhost>
Pushed By:	brook
Date:		Mon Jun 7 17:30:26 2021 -0600
Changeset:	e376678816289d306060d8dea21bce14092b52b2

Modified Files:
	py-pysam/Makefile
	py-pysam/PLIST
	py-pysam/distinfo

Log Message:
wip/py-pysam: update to version 0.16.0.1

Release 0.16.0.1

Release is identical to v0.16.0.

This release was made to be able re-upload fixed wheels of v0.16.0 to
pypi.

Release 0.16.0

This release wraps htslib/bcftools version 1.10.2 and samtools version
1.10. The following bugs reported against pysam are fixed due to this:

[#447] Writing out QNAME longer than 251 characters corrupts BAM
[#640, #734, #843] Setting VariantRecord pos or stop raises error
[#738, #919] FastxFile truncates concatenated plain gzip compressed files

Additional bugfixes:

[#840] Pileup doesn't work on python3 when index_filename is used
[#886] FastqProxy raises ValueError when instantiated from python
[#904] VariantFile.fetch() throws ValueError on files with no records
[#909] Fix incorrect quoting in VariantFile contig records
[#915, #916] Implement pileup() for unindexed files and/or SAM files

Backwards incompatible changes:

The samtools import command was removed in samtools 1.10, so pysam
no longer exports a samimport function. Use pysam.view() instead.
Many thanks to @jmarshall who has done most of the heavy lifting.

Release 0.15.4

Bugfix release. Principal reason for release is to update cython
version in order to fix pip install pysam with python 3.8.

[#879] Fix add_meta function in libcbcf.pyx, so meta-information
lines in header added with this function have double-quoting rules
in accordance to rules specified in VCF4.2 and VCF4.3 specifications
[#863] Force arg to bytes to support non-ASCII encoding
[#875] Bump minimum Cython version
[#868] Prevent segfault on Python 2.7 AlignedSegment.compare(other=None)
[#867] Fix wheel building on TravisCI
[#863] Force arg to bytes to support non-ASCII encoding
[#799] disambiguate interpretation of bcf_read return code
[#841] Fix silent truncation of FASTQ with bad q strings
[#846] Prevent segmentation fault on ID, when handling malformed records
[#829] Run configure with the correct CC/CFLAGS/LDFLAGS env va

Release 0.15.3

Bugfix release.

[#824] allow reading of UTF-8 encoded text in VCF/BCF files.
[#780] close all filehandles before opening new ones in pysam_dispatch
[#773] do not cache VariantRecord.id to avoid memory leak
[#781] default of multiple_iterators=True is changed to False for
CRAM files.
[#825] fix collections.abc import
[#825] use bcf_hdr_format instead of bcf_hdr_fmt_text, fix memcpy
bug when setting FORMAT fields.
[#804] Use HTSlib's kstring_t, which reallocates and enlarges its
memory as needed, rather than a fixed-size char buffer.
[#814] Build wheels and upload them to PyPI
[#755] Allow passing flags and arguments to index methods
[#763] Strip \0 in header check
[#761] Test Tabix index contents, not the compression

Release 0.15.2

Bugfix release.

[#746] catch pileup itorator out-of-scope segfaults
[#747] fix faixd fetch with region
[#748] increase max_pos to (1<<31)-1
[#645] Add missing macOS stub files in MANIFEST.in, @SoapZA
[#737] Fix bug in get_aligned_pairs, @bkohrn

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=e376678816289d306060d8dea21bce14092b52b2

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

diffstat:
 py-pysam/Makefile | 14 ++++++++++----
 py-pysam/PLIST    | 10 ++++------
 py-pysam/distinfo |  8 ++++----
 3 files changed, 18 insertions(+), 14 deletions(-)

diffs:
diff --git a/py-pysam/Makefile b/py-pysam/Makefile
index d62b3fb6ee..e21c0957af 100644
--- a/py-pysam/Makefile
+++ b/py-pysam/Makefile
@@ -1,17 +1,23 @@
 # $NetBSD$
 
-DISTNAME=	pysam-0.15.1
-PKGNAME=	${PYPKGPREFIX}-${DISTNAME}
+GITHUB_PROJECT=	pysam
+GITHUB_TAG=	refs/tags/v0.16.0.1
+DISTNAME=	v0.16.0.1
+PKGNAME=	${PYPKGPREFIX}-${GITHUB_PROJECT}-${DISTNAME:S,^v,,}
 CATEGORIES=	biology python
-MASTER_SITES=	${MASTER_SITE_PYPI:=p/pysam/}
+MASTER_SITES=	${MASTER_SITE_GITHUB:=pysam-developers/}
+DIST_SUBDIR=	${GITHUB_PROJECT}
 
 MAINTAINER=	bacon%NetBSD.org@localhost
-HOMEPAGE=	https://github.com/pysam-developers/pysam
+HOMEPAGE=	https://github.com/pysam-developers/pysam/
 COMMENT=	Python module for reading, manipulating and writing genomic data sets
 LICENSE=	mit
 
+WRKSRC=		${WRKDIR}/${GITHUB_PROJECT}-${PKGVERSION_NOREV}
 USE_TOOLS+=	gmake
 
+EGG_NAME=	${GITHUB_PROJECT}-${PKGVERSION_NOREV}
+
 MAKE_ENV+=	HTSLIB_MODE=external
 MAKE_ENV+=	HTSLIB_INCLUDE_DIR=${BUILDLINK_PREFIX.htslib}/include
 MAKE_ENV+=	HTSLIB_LIBRARY_DIR=${BUILDLINK_PREFIX.htslib}/lib
diff --git a/py-pysam/PLIST b/py-pysam/PLIST
index 74e5521735..3bba2177ca 100644
--- a/py-pysam/PLIST
+++ b/py-pysam/PLIST
@@ -29,11 +29,13 @@ ${PYSITELIB}/pysam/include/bcftools/bcftools.h
 ${PYSITELIB}/pysam/include/bcftools/bcftools.pysam.h
 ${PYSITELIB}/pysam/include/bcftools/bin.h
 ${PYSITELIB}/pysam/include/bcftools/call.h
+${PYSITELIB}/pysam/include/bcftools/cols.h
 ${PYSITELIB}/pysam/include/bcftools/config.h
 ${PYSITELIB}/pysam/include/bcftools/convert.h
 ${PYSITELIB}/pysam/include/bcftools/filter.h
 ${PYSITELIB}/pysam/include/bcftools/gvcf.h
 ${PYSITELIB}/pysam/include/bcftools/hclust.h
+${PYSITELIB}/pysam/include/bcftools/hex.h
 ${PYSITELIB}/pysam/include/bcftools/khash_str2str.h
 ${PYSITELIB}/pysam/include/bcftools/kheap.h
 ${PYSITELIB}/pysam/include/bcftools/kmin.h
@@ -44,9 +46,9 @@ ${PYSITELIB}/pysam/include/bcftools/rbuf.h
 ${PYSITELIB}/pysam/include/bcftools/regidx.h
 ${PYSITELIB}/pysam/include/bcftools/smpl_ilist.h
 ${PYSITELIB}/pysam/include/bcftools/tsv2vcf.h
+${PYSITELIB}/pysam/include/bcftools/variantkey.h
 ${PYSITELIB}/pysam/include/bcftools/vcfbuf.h
 ${PYSITELIB}/pysam/include/bcftools/vcmp.h
-${PYSITELIB}/pysam/include/bcftools/version.h
 ${PYSITELIB}/pysam/include/samtools/bam.h
 ${PYSITELIB}/pysam/include/samtools/bam2bcf.h
 ${PYSITELIB}/pysam/include/samtools/bam_endian.h
@@ -55,17 +57,12 @@ ${PYSITELIB}/pysam/include/samtools/bam_plbuf.h
 ${PYSITELIB}/pysam/include/samtools/bedidx.h
 ${PYSITELIB}/pysam/include/samtools/config.h
 ${PYSITELIB}/pysam/include/samtools/sam.h
-${PYSITELIB}/pysam/include/samtools/sam_header.h
 ${PYSITELIB}/pysam/include/samtools/sam_opts.h
 ${PYSITELIB}/pysam/include/samtools/sample.h
 ${PYSITELIB}/pysam/include/samtools/samtools.h
 ${PYSITELIB}/pysam/include/samtools/samtools.pysam.h
 ${PYSITELIB}/pysam/include/samtools/stats_isize.h
 ${PYSITELIB}/pysam/include/samtools/tmp_file.h
-${PYSITELIB}/pysam/include/samtools/version.h
-${PYSITELIB}/pysam/include/samtools/win32/xcurses.h
-${PYSITELIB}/pysam/include/samtools/win32/zconf.h
-${PYSITELIB}/pysam/include/samtools/win32/zlib.h
 ${PYSITELIB}/pysam/libcalignedsegment.pxd
 ${PYSITELIB}/pysam/libcalignedsegment.so
 ${PYSITELIB}/pysam/libcalignmentfile.pxd
@@ -99,6 +96,7 @@ ${PYSITELIB}/pysam/samtools.pyo
 ${PYSITELIB}/pysam/utils.py
 ${PYSITELIB}/pysam/utils.pyc
 ${PYSITELIB}/pysam/utils.pyo
+${PYSITELIB}/pysam/version.h
 ${PYSITELIB}/pysam/version.py
 ${PYSITELIB}/pysam/version.pyc
 ${PYSITELIB}/pysam/version.pyo
diff --git a/py-pysam/distinfo b/py-pysam/distinfo
index 1bf099d160..449fc0a4e9 100644
--- a/py-pysam/distinfo
+++ b/py-pysam/distinfo
@@ -1,7 +1,7 @@
 $NetBSD$
 
-SHA1 (pysam-0.15.1.tar.gz) = e44068afc7520d211f4537873a963f16a6e53a8f
-RMD160 (pysam-0.15.1.tar.gz) = f44ed399f80325bb084d254a3d16d97c6bc25f0f
-SHA512 (pysam-0.15.1.tar.gz) = 12f2b20e81554e47135a81d4d627b8130cb09645ba76bfe69826a9e1c052a4e2750eef3fc08538801b6da9e712bcf0fbdf9155700592ad25030a805b0228dda6
-Size (pysam-0.15.1.tar.gz) = 3220356 bytes
+SHA1 (pysam/v0.16.0.1.tar.gz) = 928f058c9c2df814a8698bfa88f27a9bd256748c
+RMD160 (pysam/v0.16.0.1.tar.gz) = 7a980c0bd6edac6bdd9103db0fc6f540b0db6619
+SHA512 (pysam/v0.16.0.1.tar.gz) = 5cebb9f3bc8dc6186a629e91423a3c8cb802af6529b943fcd880e056661ec6ee2a00de789cf144c9e40b9d1ef2459c0e06ce27a1b9eab8e2875d2087f275af28
+Size (pysam/v0.16.0.1.tar.gz) = 3294073 bytes
 SHA1 (patch-setup.py) = 368c4b99c1f8103d34096145f7badd9310736554
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