haplohseq: Update to 0.1.2.3

[Jason Bacon (via pkgsrc-wip) <commit-notify%pkgsrc.org@localhost>]

Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Tue May 20 14:25:13 2025 -0500
Changeset:	9a5ff9533c7f854ad06e62f09153f1a4ad590d2f

Modified Files:
	haplohseq/Makefile
	haplohseq/distinfo
Removed Files:
	haplohseq/patches/patch-src_HaplohSeq.cpp

Log Message:
haplohseq: Update to 0.1.2.3

Patch for boost 1.87+

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=9a5ff9533c7f854ad06e62f09153f1a4ad590d2f

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

diffstat:
 haplohseq/Makefile                        |  9 ++---
 haplohseq/distinfo                        |  9 ++---
 haplohseq/patches/patch-src_HaplohSeq.cpp | 61 -------------------------------
 3 files changed, 8 insertions(+), 71 deletions(-)

diffs:
diff --git a/haplohseq/Makefile b/haplohseq/Makefile
index d38916d05d..1199fff7ee 100644
--- a/haplohseq/Makefile
+++ b/haplohseq/Makefile
@@ -1,13 +1,12 @@
-# $NetBSD: Makefile,v 1.3 2024/12/29 15:09:39 adam Exp $
+# $NetBSD: Makefile,v 1.5 2025/03/06 01:19:04 bacon Exp $
 
-DISTNAME=	haplohseq-0.1.2.2
-PKGREVISION=	2
+DISTNAME=	haplohseq-0.1.2.3
 CATEGORIES=	biology
 MASTER_SITES=	${MASTER_SITE_GITHUB:=outpaddling/}
 GITHUB_PROJECT=	haplohseq
-GITHUB_TAG=	e4892945eced075a5bb98f208786cdf85eb3d82a
+GITHUB_TAG=	feb9267e6a0aaa224eba2485dc64729837863464
 
-OWNER=		bacon%NetBSD.org@localhost
+MAINTAINER=	bacon%NetBSD.org@localhost
 HOMEPAGE=	https://sites.google.com/site/integrativecancergenomics/software/haplohseq
 COMMENT=	Identify regions of allelic imbalance
 LICENSE=	mit
diff --git a/haplohseq/distinfo b/haplohseq/distinfo
index b505fd8d4c..8bf098a2ea 100644
--- a/haplohseq/distinfo
+++ b/haplohseq/distinfo
@@ -1,6 +1,5 @@
-$NetBSD: distinfo,v 1.1 2024/10/12 12:19:51 bacon Exp $
+$NetBSD$
 
-BLAKE2s (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = dbd48a3854197dbf71189a56bdd0075ce8e6a78bca92b58673ae2770eae3daa6
-SHA512 (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 8de2c75d4e443eab79f520d43bd2e0c238dca798bf53cc7821d6fe8bdf94f3d3ae3b9319b9b21aae10dab6b52e5c1e81380380c456a240bfcfa8863b83c5feff
-Size (haplohseq-0.1.2.2-e4892945eced075a5bb98f208786cdf85eb3d82a.tar.gz) = 12085199 bytes
-SHA1 (patch-src_HaplohSeq.cpp) = 7aa7d525b573f18b711b698c5509b5038911ad9a
+BLAKE2s (haplohseq-0.1.2.3-feb9267e6a0aaa224eba2485dc64729837863464.tar.gz) = 0250597977abf2c74619a0b636bd36319d0badc9843b4e33bd0325b50a07692b
+SHA512 (haplohseq-0.1.2.3-feb9267e6a0aaa224eba2485dc64729837863464.tar.gz) = 5a2448c5250c761fbc543fe90077fdc91a6f104e255148d27cada546f1015d9da37845ea35e1add70c27d8463b4357988e869444030fbc46edbac24880032bbe
+Size (haplohseq-0.1.2.3-feb9267e6a0aaa224eba2485dc64729837863464.tar.gz) = 12085198 bytes
diff --git a/haplohseq/patches/patch-src_HaplohSeq.cpp b/haplohseq/patches/patch-src_HaplohSeq.cpp
deleted file mode 100644
index 15aa93ced1..0000000000
--- a/haplohseq/patches/patch-src_HaplohSeq.cpp
+++ /dev/null
@@ -1,61 +0,0 @@
-$NetBSD$
-
---- src/HaplohSeq.cpp.orig	2021-01-23 22:44:43.000000000 +0000
-+++ src/HaplohSeq.cpp
-@@ -195,14 +195,14 @@ void HaplohSeq::runBafHaplohseq(	std::st
- 	for (unsigned int i = 0; i < numParamEventStarts; i++) {
- 
- 		// Create thread pool
--		boost::asio::io_service ioService;
--	//	boost::asio::io_service::work work(ioService);
--		boost::shared_ptr<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
-+		boost::asio::io_context ioContext;
-+	//	boost::asio::io_context::work work(ioContext);
-+		boost::shared_ptr<boost::asio::io_context::work> work(new boost::asio::io_context::work(ioContext));
- 		boost::thread_group threadPool;
- 
- 		// Spawn worker threads
- 		for (std::size_t t = 0; t < numThreads; t++) {
--			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
-+			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_context::*)())&boost::asio::io_context::run, &ioContext));
- 		}
- 
- 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
-@@ -220,7 +220,7 @@ void HaplohSeq::runBafHaplohseq(	std::st
- 
- 			std::cout << "Posting job to thread pool for chromosome " << chr << "\n";
- 			// IMPORTANT: do not pass shared_ptr by reference because the shared_ptr expects a new pointer to the object
--			ioService.post(boost::bind(&HaplohSeq::runBafHaplohseqChr, this,
-+			ioContext.post(boost::bind(&HaplohSeq::runBafHaplohseqChr, this,
- 													chr,
- 													boost::ref(chrHmms),
- 													boost::ref(fp),
-@@ -413,14 +413,14 @@ void HaplohSeq::runVcfHaplohseq(	std::st
- 	for (unsigned int i = 0; i < numParamEventStarts; i++) {
- 
- 		// Create thread pool
--		boost::asio::io_service ioService;
--	//	boost::asio::io_service::work work(ioService);
--		boost::shared_ptr<boost::asio::io_service::work> work(new boost::asio::io_service::work(ioService));
-+		boost::asio::io_context ioContext;
-+	//	boost::asio::io_context::work work(ioContext);
-+		boost::shared_ptr<boost::asio::io_context::work> work(new boost::asio::io_context::work(ioContext));
- 		boost::thread_group threadPool;
- 
- 		// Spawn worker threads
- 		for (std::size_t t = 0; t < numThreads; t++) {
--			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_service::*)())&boost::asio::io_service::run, &ioService));
-+			threadPool.create_thread(boost::bind((boost::asio::io_context::count_type (boost::asio::io_context::*)())&boost::asio::io_context::run, &ioContext));
- 		}
- 
- 		std::map<std::string, boost::shared_ptr<Hmm> > chrHmms;
-@@ -438,7 +438,8 @@ void HaplohSeq::runVcfHaplohseq(	std::st
- 
- //			std::cout << "Posting job to thread pool for chromosome " << chr << "\n";
- 			// IMPORTANT: do not pass shared_ptr by reference because the shared_ptr expects a new pointer to the object
--			ioService.post(boost::bind(&HaplohSeq::runVcfHaplohseqChr, this,
-+			// https://github.com/boostorg/asio/issues/110
-+			ioContext.get_executor().post(boost::bind(&HaplohSeq::runVcfHaplohseqChr, this,
- 													chr,
- 													boost::ref(chrHmms),
- 													boost::ref(fp),