upload again

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

sources

@@ -1 +1 @@
-SHA512 (ugene-free-48.1.tar.gz) = dca7746e78dfa64f6557c17b0c2e0d1edf7bab50bba6c4dc245ba976b854b86d77c3594f8b59bf5d8a541df73f8f806217947ce90dc96dc29f95d353aabee5d9
+SHA512 (ugene-free-53.0.tar.gz) = 233c857d9a0ea42005efaa53e5ba5162e76a149f01d7406a73bd9215b96c096b3c379cc3b14c7d7b83c61df5ea2435412f6d43c71aef84b23d1d683d5a172b30

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-47.x-has-sse-i686.patch

@@ -1,10 +0,0 @@
---- ugene-47.x/src/ugene_globals.pri.i386	2023-07-20 19:37:10.106204731 +0900
-+++ ugene-47.x/src/ugene_globals.pri	2023-07-20 22:31:43.266627766 +0900
-@@ -168,6 +168,7 @@ defineTest( target_platform_has_sse ) {
-     contains(QMAKE_TARGET.arch, x86_64) : return (true)
-     # This check works on Linux & Mac.
-     contains(QMAKE_HOST.arch, x86_64) : return (true)
-+    contains(QMAKE_HOST.arch, i686) : return (true)
-     return (false)
- }
- 

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		20230903
-%global	gitcommit		3dd4779ff42843fd7c653643840c8ae23c784646
+%global	gitdate		20251211
+%global	gitcommit		b50ca792f254939978f0ffd3126e3d9ab770a10a
 # New git commit with non-free part removed using "git filter-branch"
-%global	gitcommit_free		5b1c13afdeac24ae9af8f7d93da33ee183270879
+%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	%{gitdate}git%{shortcommit}
 
-%global	tarballdate	20230904
-%global	tarballtime	1053
+%global	tarballdate	20251211
+%global	tarballtime	2210
 
 %global	use_release	1
 %global	use_gitbare	0
@@ -35,7 +35,7 @@
 %global	GIT	git
 %endif
 
-%global	mainver		48.1
+%global	mainver		53.0
 %undefine	prever
 
 %if		0%{?use_release} >= 1
@@ -55,7 +55,8 @@ 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/%{mainver}.tar.gz/#/%{name}-%{mainver}.tar.gz
@@ -70,6 +71,8 @@ Source1:	create-ugene-free-tarball.sh
 Source2:	create-%{name}-git-bare-tarball.sh
 # This is not installed
 Source10:	ugene.wrapper
+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
@@ -77,7 +80,8 @@ Patch104:	ugene-47.x-plugins_3rdparty-hmm2-nosse-arch.patch
 Patch105:	ugene-40.1-libs_3rdparty-breakpad-arch-port.patch
 Patch106:	ugene-47.x-git-plgins-smith_waterman-nonsse2-arch.patch
 Patch107:	ugene-40.1-qbswap-bigendian-workaround.patch
-Patch108:	ugene-47.x-has-sse-i686.patch
+Patch109:	ugene-50.x-aarch64-neon-impl-not-yet.patch
+Patch110:	ugene-52.x-s390x-platform-macro.patch
 
 BuildRequires:	make
 BuildRequires:	gcc-c++
@@ -89,13 +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)
 
@@ -117,8 +124,6 @@ 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
@@ -131,7 +136,10 @@ git checkout -b %{mainver}-fedora %{gitcommit_free}
 git config user.name "%{name} Fedora maintainer"
 git config user.email "%{name}-maintainers@fedoraproject.org"
 %endif
-
+%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
 %patch -P103 -p1 -b .unwind -Z
@@ -144,75 +152,111 @@ git config user.email "%{name}-maintainers@fedoraproject.org"
 	%GIT	commit -m "plugins/smith_waterman: support architecture not supporting SSE2" -a
 %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
-%patch -P108 -p1 -b .sse_i686 -Z
-	%GIT commit -m "ugene_globals.pri: tell sse2 available also on i686" -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
@@ -232,6 +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
@@ -250,6 +296,48 @@ 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