upload again

This is part of https://fedoraproject.org/wiki/Changes/SPDX_Licenses_Phase_4

create-ugene-git-bare-tarball.sh

@@ -12,7 +12,7 @@ TIME=$(date '+%H%M')
 TARNAME=${REPONAME}-free-${DATE}T${TIME}.tar.gz
 
 PWDDIR=$(pwd)
-TMPDIR=$(mktemp -d /var/tmp/${REPONAME}-XXXXXX)
+TMPDIR=$(mktemp -d $(pwd)/tmp-${REPONAME}-XXXXXX)
 pushd $TMPDIR
 
 git clone --depth 30 --no-single-branch --mirror $GITURL

sources

@@ -1 +1 @@
-SHA512 (ugene-free-46.0.tar.gz) = 755fb767b981187f5c60bd800995397c9fba4e07e72f19cd2034eafa79c77b147fb444bc8e047e64c70b377a766e88271365066285f235560c3b8510b361a53d
+SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30

ugene-40.1-libs_3rdparty-breakpad-arch-port.patch

@@ -61,7 +61,7 @@
  }  // namespace google_breakpad
 --- ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc.port	2021-11-09 11:04:57.135469882 +0900
 +++ ugene-40.1/src/libs_3rdparty/breakpad/src/client/linux/handler/exception_handler.cc	2021-11-09 12:06:47.875738562 +0900
-@@ -441,6 +441,7 @@ int ExceptionHandler::ThreadEntry(void*
+@@ -442,6 +442,7 @@ int ExceptionHandler::ThreadEntry(void*
  // This function runs in a compromised context: see the top of the file.
  // Runs on the crashing thread.
  bool ExceptionHandler::HandleSignal(int /*sig*/, siginfo_t* info, void* uc) {
@@ -69,7 +69,7 @@
    if (filter_ && !filter_(callback_context_))
      return false;
  
-@@ -482,6 +483,9 @@ bool ExceptionHandler::HandleSignal(int
+@@ -483,6 +484,9 @@ bool ExceptionHandler::HandleSignal(int
      }
    }
    return GenerateDump(&g_crash_context_);
@@ -79,7 +79,7 @@
  }
  
  // This is a public interface to HandleSignal that allows the client to
-@@ -660,6 +664,7 @@ bool ExceptionHandler::WriteMinidump(con
+@@ -661,6 +665,7 @@ bool ExceptionHandler::WriteMinidump(con
  __attribute__((optimize("no-omit-frame-pointer")))
  #endif
  bool ExceptionHandler::WriteMinidump() {
@@ -87,7 +87,7 @@
    if (!IsOutOfProcess() && !minidump_descriptor_.IsFD() &&
        !minidump_descriptor_.IsMicrodumpOnConsole()) {
      // Update the path of the minidump so that this can be called multiple times
-@@ -734,6 +739,9 @@ bool ExceptionHandler::WriteMinidump() {
+@@ -735,6 +740,9 @@ bool ExceptionHandler::WriteMinidump() {
  #endif
  
    return GenerateDump(&context);

ugene-40.1-qbswap-bigendian-workaround.patch

@@ -40,6 +40,6 @@
 +#endif
 +QT_END_NAMESPACE
 +
- namespace U2 {
- 
- static quint8 cigarOp2samtools(U2CigarOp op, U2OpStatus& os) {
+ extern "C" {
+ #include "samtools_core/htslib/cram/cram_samtools.h"
+ }

ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch

@@ -1,107 +0,0 @@
---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp.sse_2	2021-11-11 15:42:19.590500062 +0900
-+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmPlugin.cpp	2021-11-11 15:42:26.384496818 +0900
-@@ -90,13 +90,15 @@
-     swar->registerFactory(new SWTaskFactory(SW_classic), QString("Classic 2"));  // ADV search register
-     par->registerAlgorithm(new SWPairwiseAlignmentAlgorithm());
- 
-+#if defined (__SSE2__)
-     coreLog.trace("Registering SSE2 SW implementation");
-     swar->registerFactory(new SWTaskFactory(SW_sse2), QString("SSE2"));
-     par->getAlgorithm("Smith-Waterman")
-         ->addAlgorithmRealization(
-             new PairwiseAlignmentSmithWatermanTaskFactory(SW_sse2),
-             new PairwiseAlignmentSmithWatermanGUIExtensionFactory(SW_sse2),
-             "SSE2");
-+#endif
- }
- 
- QList<XMLTestFactory*> SWAlgorithmTests::createTestFactories() {
---- ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp.sse_2	2021-11-11 15:42:19.590500062 +0900
-+++ ugene-40.1/src/plugins/smith_waterman/src/SWAlgorithmTask.cpp	2021-11-11 15:46:26.960369309 +0900
-@@ -146,6 +146,7 @@
-                                                                         sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads),
-                                                                         sWatermanConfig.resultView);
-             break;
-+#ifdef __SSE2__
-         case SW_sse2:
-             neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(sWatermanConfig.ptrn,
-                                                                             sWatermanConfig.sqnc.left(c.chunkSize * c.nThreads),
-@@ -154,6 +155,7 @@
-                                                                             minScore,
-                                                                             maxScore,
-                                                                             sWatermanConfig.resultView);
-+#endif
-             break;
-         default:
-             assert(0);
-@@ -182,7 +184,12 @@
- 
-     SmithWatermanAlgorithm* sw = nullptr;
-     if (algType == SW_sse2) {
-+#if defined(__SSE2__)
-         sw = new SmithWatermanAlgorithmSSE2;
-+#else
-+        coreLog.error("SSE2 was not enabled in this build");
-+        return;
-+#endif
-     } else {
-         assert(algType == SW_classic);
-         sw = new SmithWatermanAlgorithm;
-@@ -458,7 +465,11 @@
- 
-     SmithWatermanAlgorithm* sw = nullptr;
-     if (algType == SW_sse2) {
-+#if defined(__SSE2__)
-         sw = new SmithWatermanAlgorithmSSE2;
-+#else
-+        coreLog.error("SSE2 was not enabled in this build");
-+#endif
-     } else {
-         assert(algType == SW_classic);
-         sw = new SmithWatermanAlgorithm;
-@@ -582,6 +593,7 @@
-                                                                         sqnc->left(c.chunkSize * c.nThreads),
-                                                                         SmithWatermanSettings::MULTIPLE_ALIGNMENT);
-             break;
-+#ifdef __SSE2__
-         case SW_sse2:
-             neededRam = SmithWatermanAlgorithmSSE2::estimateNeededRamAmount(*ptrn,
-                                                                             sqnc->left(c.chunkSize * c.nThreads),
-@@ -590,6 +602,7 @@
-                                                                             minScore,
-                                                                             maxScore,
-                                                                             SmithWatermanSettings::MULTIPLE_ALIGNMENT);
-+#endif
-             break;
-         default:
-             assert(0);
---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2	2021-11-11 15:42:19.591500062 +0900
-+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp	2021-11-11 15:42:26.385496818 +0900
-@@ -23,6 +23,7 @@
-  * MA 02110-1301, USA.
-  */
- 
-+#if defined(__SSE2__)
- #include <emmintrin.h>
- #include <iostream>
- 
-@@ -1214,3 +1215,4 @@
- }
- 
- }  // namespace U2
-+#endif
---- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2	2021-11-11 15:42:19.592500061 +0900
-+++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h	2021-11-11 15:42:26.385496818 +0900
-@@ -21,6 +21,7 @@
- 
- #pragma once
- 
-+#if defined(__SSE2__)
- #include <emmintrin.h>
- 
- #include "SmithWatermanAlgorithm.h"
-@@ -52,3 +53,4 @@
- };
- 
- }  // namespace U2
-+#endif

ugene-43.x-wrong-elif-SendReportDialog.patch

@@ -1,17 +0,0 @@
---- ugene-43.0/src/ugenem/src/SendReportDialog.cpp.elif	2022-08-17 15:55:45.936686547 +0900
-+++ ugene-43.0/src/ugenem/src/SendReportDialog.cpp	2022-08-17 20:56:02.123046050 +0900
-@@ -497,11 +497,11 @@
- QString ReportSender::getArchSuffix() const {
- #ifdef Q_PROCESSOR_X86_64
-     return " x64";
--#elif Q_PROCESSOR_X86_32
-+#elif defined(Q_PROCESSOR_X86_32)
-     return " x86";
--#elif Q_PROCESSOR_ARM_64
-+#elif defined(Q_PROCESSOR_ARM_64)
-     return " arm-64";
--#elif Q_PROCESSOR_ARM_32
-+#elif defined(Q_PROCESSOR_ARM_32)
-     return " arm-32";
- #else
-     return " unknown-arch";

ugene-45.1-gcc13-header-inclusion.patch

@@ -1,10 +0,0 @@
---- ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h.gcc13	2022-12-31 14:29:47.000000000 +0900
-+++ ugene-45.1/src/libs_3rdparty/breakpad/src/client/linux/handler/minidump_descriptor.h	2023-01-18 20:37:30.580774335 +0900
-@@ -34,6 +34,7 @@
- #include <sys/types.h>
- 
- #include <string>
-+#include <cstdint>
- 
- #include "client/linux/handler/microdump_extra_info.h"
- #include "common/using_std_string.h"

ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch

@@ -0,0 +1,30 @@
+--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp.sse_2	2021-11-11 15:42:19.591500062 +0900
++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.cpp	2021-11-11 15:42:26.385496818 +0900
+@@ -23,6 +23,7 @@
+  * MA 02110-1301, USA.
+  */
+ 
++#if defined(__SSE2__)
+ #include <emmintrin.h>
+ #include <iostream>
+ 
+@@ -1214,3 +1215,4 @@
+ }
+ 
+ }  // namespace U2
++#endif
+--- ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h.sse_2	2021-11-11 15:42:19.592500061 +0900
++++ ugene-40.1/src/plugins/smith_waterman/src/SmithWatermanAlgorithmSSE2.h	2021-11-11 15:42:26.385496818 +0900
+@@ -21,6 +21,7 @@
+ 
+ #pragma once
+ 
++#if defined(__SSE2__)
+ #include <emmintrin.h>
+ 
+ #include "SmithWatermanAlgorithm.h"
+@@ -52,3 +53,4 @@
+ };
+ 
+ }  // namespace U2
++#endif

ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch

@@ -2,7 +2,7 @@
 +++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/HMMSearchDialogController.cpp	2021-11-09 01:34:30.052988784 +0900
 @@ -81,7 +81,9 @@
      QWidget* w = createController->getWidget();
-     QVBoxLayout* l = qobject_cast<QVBoxLayout*>(layout());
+     auto l = qobject_cast<QVBoxLayout*>(layout());
      l->insertWidget(1, w);
 +#if defined (__SSE2__)
      algoCombo->addItem(tr("SSE optimized"), HMMSearchAlgo_SSEOptimized);
@@ -10,25 +10,6 @@
      algoCombo->addItem(tr("Conservative"), HMMSearchAlgo_Conservative);
  
      okButton = buttonBox->button(QDialogButtonBox::Ok);
---- ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp.sse	2021-10-11 15:41:23.000000000 +0900
-+++ ugene-40.1/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch.cpp	2021-11-09 01:34:30.052988784 +0900
-@@ -56,9 +56,15 @@
-     tophit_s* dhit = AllocTophits(200);  // domain hits:  200=lumpsize
- 
-     int nseq = 0;  // number of sequences searched
-+#if defined(__SSE2__)
-     if (s.alg == HMMSearchAlgo_SSEOptimized) {
-         main_loop_opt(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si, sseScoring);
--    } else if (s.alg == HMMSearchAlgo_Conservative) {
-+    }
-+#else
-+    if (0) {
-+    } 
-+#endif
-+      else if (s.alg == HMMSearchAlgo_Conservative) {
-         main_loop_serial(hmm, seq, seqLen, &thresh, do_forward, do_null2, do_xnu, histogram, ghit, dhit, &nseq, si);
-     } else {
-         assert(false && "bad hmmsearch algorithm selected");
 --- ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp.sse	2022-03-09 15:37:14.586340751 +0900
 +++ ugene-42.0/src/plugins_3rdparty/hmm2/src/u_search/uhmmsearch_sse.cpp	2022-03-09 15:47:23.559077800 +0900
 @@ -1,4 +1,5 @@

ugene-49.1-narrowing-for-unsigned-char.patch

@@ -0,0 +1,22 @@
+--- ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h.orig	2023-11-26 02:17:11.000000000 +0900
++++ ugene-49.1/src/plugins_3rdparty/ball/src/include/BALL/DATATYPE/hashGrid.h	2024-01-22 16:42:22.536722206 +0900
+@@ -37,7 +37,7 @@ namespace BALL
+ {
+ 	namespace __private
+ 	{
+-		extern const char BALL_EXPORT neighbour_table_[27][3];
++		extern const signed char BALL_EXPORT neighbour_table_[27][3];
+ 	}
+ 
+ 	template <typename Item> class HashGrid3;
+--- ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp.orig	2023-11-26 02:17:11.000000000 +0900
++++ ugene-49.1/src/plugins_3rdparty/ball/src/source/DATATYPE/hashGrid.cpp	2024-01-22 16:42:28.199724474 +0900
+@@ -9,7 +9,7 @@ namespace BALL
+ {
+ 	namespace __private
+ 	{
+-		const char neighbour_table_[27][3] =
++		const signed char neighbour_table_[27][3] =
+ 		{
+ 			{ 0,  0,  0 }, { 0,  0, -1 }, { 0,  0,  1 },
+ 			{ 0, -1, -1 }, { 0, -1,  0 }, { 0, -1,  1 },

ugene-50.x-aarch64-neon-impl-not-yet.patch

@@ -0,0 +1,26 @@
+diff --git a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
+index be907d85b..820d43cf0 100644
+--- a/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
++++ b/src/libs_3rdparty/samtools/src/samtools_core/htslib/htscodecs/htscodecs/rANS_static4x16pr.c
+@@ -1068,8 +1068,8 @@ unsigned char *(*rans_enc_func(int do_simd, int order))
+     if (do_simd) {
+         if ((rans_cpu & RANS_CPU_ENC_NEON) && have_neon())
+             return order & 1
+-                ? rans_compress_O1_32x16_neon
+-                : rans_compress_O0_32x16_neon;
++                ? rans_compress_O1_32x16
++                : rans_compress_O0_32x16;
+         else
+             return order & 1
+                 ? rans_compress_O1_32x16
+@@ -1091,8 +1091,8 @@ unsigned char *(*rans_dec_func(int do_simd, int order))
+     if (do_simd) {
+         if ((rans_cpu & RANS_CPU_DEC_NEON) && have_neon())
+             return order & 1
+-                ? rans_uncompress_O1_32x16_neon
+-                : rans_uncompress_O0_32x16_neon;
++                ? rans_uncompress_O1_32x16
++                : rans_uncompress_O0_32x16;
+         else
+             return order & 1
+                 ? rans_uncompress_O1_32x16

ugene-52.1.x-RegionSelectorController-overload.patch

@@ -0,0 +1,13 @@
+diff --git a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp
+index f052b9122..d0fdfeb0d 100644
+--- a/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp
++++ b/src/corelibs/U2Gui/src/util/RegionSelectorController.cpp
+@@ -339,7 +339,7 @@ void RegionSelectorController::connectSlots() {
+ 
+     connect(gui.startLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged);
+     connect(gui.endLineEdit, &QLineEdit::textEdited, this, &RegionSelectorController::sl_onRegionChanged);
+-    connect(gui.presetsComboBox, &QComboBox::activated, this, &RegionSelectorController::sl_onPresetChanged);
++    connect(gui.presetsComboBox, QOverload<int>::of(&QComboBox::activated), this, &RegionSelectorController::sl_onPresetChanged);
+ 
+     if (settings.selection != nullptr) {
+         connect(settings.selection, SIGNAL(si_onSelectionChanged(GSelection*)), SLOT(sl_onSelectionChanged(GSelection*)));

ugene-52.x-s390x-platform-macro.patch

@@ -0,0 +1,27 @@
+diff --git a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h
+index a4695a261..ec063f1ee 100644
+--- a/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h
++++ b/src/libs_3rdparty/qtscript/3rdparty/javascriptcore/JavaScriptCore/wtf/Platform.h
+@@ -407,6 +407,13 @@
+ #define WTF_CPU_RISCV32 1
+ #endif
+ 
++/* CPU(IBM z system) */
++#if defined(__s390x__) || defined(__s390__)
++#define WTF_CPU_S390X 1
++#define WTF_CPU_BIG_ENDIAN 1
++#endif
++
++
+ /* ==== OS() - underlying operating system; only to be used for mandated low-level services like 
+    virtual memory, not to choose a GUI toolkit ==== */
+ 
+@@ -960,6 +967,8 @@
+ #if !defined(WTF_USE_JSVALUE64) && !defined(WTF_USE_JSVALUE32) && !defined(WTF_USE_JSVALUE32_64)
+ #if (CPU(X86_64) && !CPU(X32) && (OS(UNIX) || OS(WINDOWS) || OS(SOLARIS) || OS(HPUX))) || (CPU(IA64) && !CPU(IA64_32)) || CPU(ALPHA) || CPU(AIX64) || CPU(SPARC64) || CPU(MIPS64) || CPU(AARCH64) || CPU(RISCV64)
+ #define WTF_USE_JSVALUE64 1
++#elif (CPU(S390X))
++#define WTF_USE_JSVALUE64 1
+ #elif CPU(ARM) || CPU(PPC64) || CPU(RISCV32)
+ #define WTF_USE_JSVALUE32 1
+ #elif OS(WINDOWS) && COMPILER(MINGW)

ugene.spec

@@ -2,24 +2,24 @@
 
 %if 0%{?use_release_branch} < 1
 # master
-%global	gitdate		20230214
-%global	gitcommit		15acb35b017bfa4c4c90dc14079bd52d7252c398
+%global	gitdate		20251211
+%global	gitcommit		b50ca792f254939978f0ffd3126e3d9ab770a10a
 # New git commit with non-free part removed using "git filter-branch"
-%global	gitcommit_free		16ffa2676c45f566400d78162c62fa56c5f1a15d
+%global	gitcommit_free		7e674061492924b3dfbc884c4c9503ecab9887b2
 %else
 # currently 41.0 branch
-%global	gitdate		20211117
-%global	gitcommit		2d776cc668bc5019452e25ecc330c88093e75c48
+%global	gitdate		20250313
+%global	gitcommit		c0dffab5a15e01c026f80cf0a7033b08112a355f
 # New git commit with non-free part using "git filter-branch"
-%global	gitcommit_free		f995e33068c5959c1bab249cd04ed3776e9b2d96
+%global	gitcommit_free		b0631c54cc0603a88793ed5d6ee02dec196b823e
 %endif
 
 
 %global	shortcommit	%(c=%{gitcommit}; echo ${c:0:7})
-%global	git_version	D%{gitdate}git%{shortcommit}
+%global	git_version	%{gitdate}git%{shortcommit}
 
-%global	tarballdate	20230214
-%global	tarballtime	1421
+%global	tarballdate	20251211
+%global	tarballtime	2210
 
 %global	use_release	1
 %global	use_gitbare	0
@@ -35,33 +35,34 @@
 %global	GIT	git
 %endif
 
-%global	mainrel		1
+%global	mainver		53.0
 %undefine	prever
 
 %if		0%{?use_release} >= 1
-%global	fedorarel		%{?prever:0.}%{mainrel}%{?prever:.%{prerpmver}}
+%global	fedoraver		%{mainver}%{?prever:~%{prerpmver}}
 %endif
 %if		0%{?use_gitbare} >= 1
-%global	fedorarel		%{mainrel}.%{git_version}
+%global	fedoraver		%{mainver}%{?git_version:^%{git_version}}
 %endif
 
 
 Name:		ugene
 Summary:	Integrated bioinformatics toolkit
 
-Version:	46.0
-Release:	%{fedorarel}%{?dist}
+Version:	%{fedoraver}
+Release:	1%{?dist}
 
 #The entire source code is GPLv2+ except:
 #file src/libs_3rdparty/qtbindings_core/src/qtscriptconcurrent.h which is GPLv2
 #files in src/plugins_3rdparty/script_debuger/src/qtscriptdebug/ which are GPLv2
-License:	GPLv2+ and GPLv2
+# Automatically converted from old format: GPLv2+ and GPLv2 - review is highly recommended.
+License:	GPL-2.0-or-later AND GPL-2.0-only
 URL:		http://ugene.net
 %if	0%{?use_release} >= 1
-#Source0:	https://github.com/ugeneunipro/ugene/archive/%{version}.tar.gz/#/%{name}-%{version}.tar.gz
+#Source0:	https://github.com/ugeneunipro/ugene/archive/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz
 # Removing non-free part
-Source0:	%{name}-free-%{version}.tar.gz
-# Source0 is created by # env VERSION=%%{version} source ./%{SOURCE1}
+Source0:	%{name}-free-%{mainver}.tar.gz
+# Source0 is created by # env VERSION=%%{mainver} source ./%{SOURCE1}
 %endif
 %if	0%{?use_gitbare} >= 1
 Source0:	%{name}-free-%{tarballdate}T%{tarballtime}.tar.gz
@@ -70,15 +71,17 @@ Source1:	create-ugene-free-tarball.sh
 Source2:	create-%{name}-git-bare-tarball.sh
 # This is not installed
 Source10:	ugene.wrapper
-Patch1:	ugene-45.1-gcc13-header-inclusion.patch
+Patch1:	ugene-49.1-narrowing-for-unsigned-char.patch
+Patch3:	ugene-52.1.x-RegionSelectorController-overload.patch
 # Currently distro-specific
 Patch102:	ugene-44.x-libs_3rdparty-breakpad-sys_mmap_use_system_mmap.patch
 Patch103:	ugene-40.1-libs_3rdparty-breakpad-unwind-nonsupported-arch.patch
-Patch104:	ugene-42.0-plugins_3rdparty-hmm2-nosse-arch.patch
+Patch104:	ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch
 Patch105:	ugene-40.1-libs_3rdparty-breakpad-arch-port.patch
-Patch106:	ugene-43.0-git-plgins-smith_waterman-nonsse2-arch.patch
+Patch106:	ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch
 Patch107:	ugene-40.1-qbswap-bigendian-workaround.patch
-Patch108:	ugene-43.x-wrong-elif-SendReportDialog.patch
+Patch109:	ugene-50.x-aarch64-neon-impl-not-yet.patch
+Patch110:	ugene-52.x-s390x-platform-macro.patch
 
 BuildRequires:	make
 BuildRequires:	gcc-c++
@@ -90,13 +93,16 @@ BuildRequires:	%{_bindir}/git
 
 BuildRequires:	cmake(Qt5Core)
 BuildRequires:	cmake(Qt5Gui)
+BuildRequires:	cmake(Qt5LinguistTools)
 BuildRequires:	cmake(Qt5Network)
+BuildRequires:	cmake(Qt5NetworkAuth)
 BuildRequires:	cmake(Qt5PrintSupport)
 BuildRequires:	cmake(Qt5Script)
 BuildRequires:	cmake(Qt5ScriptTools)
 BuildRequires:	cmake(Qt5Sql)
 BuildRequires:	cmake(Qt5Svg)
 BuildRequires:	cmake(Qt5Test)
+BuildRequires:	cmake(Qt5WebSockets)
 BuildRequires:	cmake(Qt5Widgets)
 BuildRequires:	cmake(Qt5Xml)
 
@@ -118,105 +124,139 @@ is a designer for custom bioinformatics workflows.
 %prep
 %if		0%{?use_release} >= 1
 %setup -q
-# Umm...
-sed -i.desktop ugene.pri -e '\@desktop@s|etc/share/|etc/shared/|'
 %endif
 
 %if		0%{?use_gitbare} >= 1
-%setup -q -c -T -a 0
+%setup -q -c -n %{name}-%{mainver}%{?git_version:-%{git_version}} -T -a 0
 git clone ./%{name}.git/
 cd %{name}
 cp -a [A-Z]* ..
 
-git checkout -b %{version}-fedora %{gitcommit_free}
+git checkout -b %{mainver}-fedora %{gitcommit_free}
 git config user.name "%{name} Fedora maintainer"
 git config user.email "%{name}-maintainers@fedoraproject.org"
 %endif
-
-%patch1 -p1 -b .gcc13 -Z
-	%GIT commit -m "add missing header file" -a
-
-%patch102 -p1 -b .sys_mmap -Z
+%patch -P1 -p1 -b .narrow
+	%GIT commit -m "Fix narrowing on arch where default char is unsigned" -a
+%patch -P3 -p1 -b .include
+	%GIT commit -m "RegionSelectorController: specify overloaded function" -a
+%patch -P102 -p1 -b .sys_mmap -Z
 	%GIT commit -m "libs_3rdparty/breakpad: use C function instead of directly using syscall assemble code" -a
-%patch103 -p1 -b .unwind -Z
+%patch -P103 -p1 -b .unwind -Z
 	%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not supporting unwind" -a
-%patch104 -p1 -b .sse -Z
+%patch -P104 -p1 -b .sse -Z
 	%GIT commit -m "plugins_3rdparty/hmm2: support architecture not supporting SSE2" -a
-%patch105 -p1 -b .port -Z
+%patch -P105 -p1 -b .port -Z
 	%GIT commit -m "libs_3rdparty/breakpad: workaround for arch not ported by the upstream" -a
-%patch106 -p1 -b .sse_2 -Z
+%patch -P106 -p1 -b .sse_2 -Z
 	%GIT	commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a
-%patch107 -p1 -b .char_bigen -Z
+%patch -P107 -p1 -b .char_bigen -Z
 	%GIT	commit -m "src/corelibs/U2Core et al.: Workaround for Qt qbswap issue on Q_BIG_ENDIAN" -a
-%patch108 -p1 -b .elif -Z
-	%GIT commit -m "ugenem/src/SendReportDialog.cpp: fix wrong elif usage" -a
+%if 1
+%patch -P109 -p1 -b .neon -Z
+	%GIT commit -m "neon impl not yet available" -a
+%endif
+%patch -P110 -p1 -b .s390x_macro -Z
+	%GIT commit -m "define s390x related macro" -a
+
+# Kill system-provided 3rd-party libs
+sed -i CMakeLists.txt \
+	-e '\@add_subdirectory.*libs_3rdparty/sqlite3@d' \
+	-e '\@add_subdirectory.*libs_3rdparty/zlib@d' \
+	%{nil}
+rm -rf src/libs_3rdparty/{sqlite3,zlib}
+rm -rf src/include/3rdparty/{sqlite3,zlib}
+	%GIT rm -r -f src/libs_3rdparty/{sqlite3,zlib} || true
+	%GIT rm -r -f src/include/3rdparty/{sqlite3,zlib} || true
+	%GIT commit -m "kill system-provided 3rd-party libs" -a
+grep -rl --exclude-dir=.git 3rdparty/zlib/zlib.h . | \
+	xargs sed -i 's|3rdparty/zlib/zlib.h|zlib.h|'
+grep -rl --exclude-dir=.git 3rdparty/sqlite3/sqlite3.h . | \
+	xargs sed -i 's|3rdparty/sqlite3/sqlite3.h|sqlite3.h|'
+find . -name CMakeLists.txt | \
+	xargs sed -i \
+		-e 's|zlib|z|' \
+		-e 's|ugenedb|sqlite3|' \
+		%{nil}
+	%GIT commit -m "fix system provided header path" -a
 
 sed -i.nonfree CMakeLists.txt -e '\@add_subdirectory.*plugins_3rdparty/psipred@d'
-sed -i.nonfree ugene.pro -e '\@plugins_3rdparty/psipred@d'
 	%GIT commit -m "remove nonfree code" -a
 
+# Remove -Werror
+sed -i CMakeLists.txt -e '\@" -Werror=@d'
+	%GIT commit -m "remove -Werror" -a
+
+# Enable some deprecated API
+sed -i CMakeLists.txt -e '\@QT_DISABLE_DEPRECATED_BEFORE=@s|0x050F00|0x050000|'
+	%GIT commit -m "enable some deprecated API" -a
+
 %build
 %if		0%{?use_gitbare} >= 1
 cd %{name}
 %endif
-%{qmake_qt5} -r \
-	PREFIX=%{_libdir}/%{name} \
-	UGENE_EXCLUDE_LIST_ENABLED=1 \
-	UGENE_USE_SYSTEM_SQLITE=1 \
-	UGENE_USE_BUNDLED_ZLIB=0 \
-	UGENE_WITHOUT_NON_FREE=1 \
-	%{nil}
 
-%make_build -k
+export QT_DIR=%{_libdir}/qt5
+export LD_LIBRARY_PATH=$(pwd)/%{_vpath_builddir}/dist
+
+%cmake \
+	-DCMAKE_SKIP_RPATH=TRUE \
+	%{nil}
+%cmake_build
 
 %install
-LIBAPPDIR=%{_libdir}/%{name}
-
 %if		0%{?use_gitbare} >= 1
 cd %{name}
 %endif
-make install \
-	INSTALL_ROOT=%{buildroot} \
-	INSTALL="install -p" \
-	%{nil}
 
-# Some needed files are not installed.....
-mkdir -p %{buildroot}$LIBAPPDIR
-cp -a src/_release/* %{buildroot}$LIBAPPDIR
-rm -f %{buildroot}$LIBAPPDIR/*.a
+%cmake_install
 
-# 1. manually move files...
-pushd %{buildroot}
-rm -f ./$LIBAPPDIR/LICENSE*
+# Install all files manually...
+# 0. Documents
+cp -a \
+	LICENSE.3rd_party.txt \
+	LICENSE.txt \
+	..
+
+pushd %_vpath_builddir
 
 # 1-0 bindir
-mkdir -p ./%{_bindir}
-install -cpm 0755 %{SOURCE10} ./%{_bindir}/%{name}
+mkdir -p %{buildroot}%{_bindir}
+install -cpm 0755 %{SOURCE10} %{buildroot}%{_bindir}/%{name}
 
-# 1-1 data files
-mkdir -p ./%{_datadir}/%{name}/
-mv ./$LIBAPPDIR/data ./%{_datadir}/%{name}
-ln -sf ../../../%{_datadir}/%{name} ./$LIBAPPDIR/data
+# 1-1 libraries
+mkdir -p %{buildroot}%{_libdir}/%{name}
+cp -a dist/* %{buildroot}%{_libdir}/%{name}/
+rm -f  %{buildroot}%{_libdir}/%{name}/*.a
 
+# Back to the top directory
+popd
+
+# 1-2 data files
+mkdir -p %{buildroot}%{_datadir}/%{name}/
+cp -a data %{buildroot}%{_datadir}/%{name}
+ln -sf ../../../%{_datadir}/%{name}/data %{buildroot}%{_libdir}/%{name}/data
+
+pushd ./etc/shared
 # 1-11 hicolor
-mkdir -p ./%{_datadir}/icons/hicolor/32x32/mimetypes/
-mv ./$LIBAPPDIR/application-x-ugene-ext.png ./%{_datadir}/icons/hicolor/32x32/mimetypes/
+mkdir -p %{buildroot}%{_datadir}/icons/hicolor/32x32/mimetypes/
+cp -p application-x-ugene-ext.png %{buildroot}/%{_datadir}/icons/hicolor/32x32/mimetypes/
 
 # 1-12 mime
-mkdir -p ./%{_datadir}/mime/packages
-mv ./$LIBAPPDIR/application-x-ugene.xml ./%{_datadir}/mime/packages
+mkdir -p %{buildroot}%{_datadir}/mime/packages
+cp -p application-x-ugene.xml %{buildroot}/%{_datadir}/mime/packages
 
 # 1-13 man file
-mkdir -p ./%{_mandir}/man1
-mv ./$LIBAPPDIR/%{name}.1* ./%{_mandir}/man1
+mkdir -p %{buildroot}%{_mandir}/man1
+cp -p %{name}.1* %{buildroot}/%{_mandir}/man1
 
 # 1-14 desktop files
-mkdir -p ./%{_datadir}/applications/
-mv ./$LIBAPPDIR/%{name}.desktop ./%{_datadir}/applications/
+mkdir -p %{buildroot}%{_datadir}/applications/
+cp -p %{name}.desktop %{buildroot}/%{_datadir}/applications/
 
 # 1-15 icons
-mkdir -p ./%{_datadir}/pixmaps
-mv ./$LIBAPPDIR/%{name}.{png,xpm} ./%{_datadir}/pixmaps
+mkdir -p %{buildroot}%{_datadir}/pixmaps
+cp -p %{name}.{png,xpm} %{buildroot}%{_datadir}/pixmaps
 popd
 
 %check
@@ -236,6 +276,8 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
 %{_libdir}/%{name}/plugins/*.plugin
 %{_libdir}/%{name}/plugins/lib*.so
 
+%{_libdir}/%{name}/transl_*.qm
+
 %{_libdir}/%{name}/%{name}
 %{_libdir}/%{name}/%{name}cl
 %{_libdir}/%{name}/%{name}m
@@ -254,6 +296,60 @@ desktop-file-validate %{buildroot}%{_datadir}/applications/%{name}.desktop
 %{_mandir}/man1/%{name}.1*
 
 %changelog
+* Sun Nov 30 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 53.0-1
+- 53.0
+
+* Fri Jul 25 2025 Fedora Release Engineering <releng@fedoraproject.org> - 52.1-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_43_Mass_Rebuild
+
+* Fri Jul 18 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.1-2
+- Fix data files symlink
+
+* Thu May 08 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.1-1
+- 52.1
+
+* Fri Jan 24 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 52.0-1
+- 52.0
+
+* Fri Jan 17 2025 Mamoru TASAKA <mtasaka@fedoraproject.org> - 51.0-2
+- Support C23 strict function prototype
+
+* Thu Sep 26 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 51.0-1
+- 51.0
+
+* Wed Aug  7 2024 Miroslav Suchý <msuchy@redhat.com> - 50.0-3
+- convert license to SPDX
+
+* Sat Jul 20 2024 Fedora Release Engineering <releng@fedoraproject.org> - 50.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_41_Mass_Rebuild
+
+* Sun Apr 14 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 50.0-1
+- 50.0
+
+* Sat Jan 27 2024 Fedora Release Engineering <releng@fedoraproject.org> - 49.1-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
+
+* Mon Jan 22 2024 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.1-2
+- Fix -Wnarrowing on non x86(-64) arch detected by gcc14
+
+* Tue Nov 28 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.1-1
+- 49.1
+
+* Thu Nov  9 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 49.0-1
+- 49.0
+
+* Tue Sep  5 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 48.1-1
+- 48.1
+
+* Thu Aug 10 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 48.0-1
+- 48.0
+
+* Sat Jul 22 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 47.0-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
+
+* Tue May 23 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 47.0-1
+- 47.0
+
 * Fri Feb 24 2023 Mamoru TASAKA <mtasaka@fedoraproject.org> - 46.0-1
 - 46.0