From ddc335e8d24b9c47f6eccda618f4c0e8372819327f56025ff6f6ed10b29ee8ca Mon Sep 17 00:00:00 2001 From: Atri Bhattacharya Date: Wed, 24 Jul 2024 07:56:25 +0000 Subject: [PATCH] Update lalapps to 10.0.0. OBS-URL: https://build.opensuse.org/package/show/science/lalapps?expand=0&rev=21 --- .gitattributes | 23 +++ .gitignore | 1 + lalapps-10.0.0.tar.xz | 3 + lalapps-9.2.2.tar.xz | 3 + ...pps-disable-testWeave-for-non-x86_64.patch | 18 ++ lalapps-fix-uninitialised-var.patch | 13 ++ lalapps.changes | 170 ++++++++++++++++ lalapps.spec | 187 ++++++++++++++++++ 8 files changed, 418 insertions(+) create mode 100644 .gitattributes create mode 100644 .gitignore create mode 100644 lalapps-10.0.0.tar.xz create mode 100644 lalapps-9.2.2.tar.xz create mode 100644 lalapps-disable-testWeave-for-non-x86_64.patch create mode 100644 lalapps-fix-uninitialised-var.patch create mode 100644 lalapps.changes create mode 100644 lalapps.spec diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..9b03811 --- /dev/null +++ b/.gitattributes @@ -0,0 +1,23 @@ +## Default LFS +*.7z filter=lfs diff=lfs merge=lfs -text +*.bsp filter=lfs diff=lfs merge=lfs -text +*.bz2 filter=lfs diff=lfs merge=lfs -text +*.gem filter=lfs diff=lfs merge=lfs -text +*.gz filter=lfs diff=lfs merge=lfs -text +*.jar filter=lfs diff=lfs merge=lfs -text +*.lz filter=lfs diff=lfs merge=lfs -text +*.lzma filter=lfs diff=lfs merge=lfs -text +*.obscpio filter=lfs diff=lfs merge=lfs -text +*.oxt filter=lfs diff=lfs merge=lfs -text +*.pdf filter=lfs diff=lfs merge=lfs -text +*.png filter=lfs diff=lfs merge=lfs -text +*.rpm filter=lfs diff=lfs merge=lfs -text +*.tbz filter=lfs diff=lfs merge=lfs -text +*.tbz2 filter=lfs diff=lfs merge=lfs -text +*.tgz filter=lfs diff=lfs merge=lfs -text +*.ttf filter=lfs diff=lfs merge=lfs -text +*.txz filter=lfs diff=lfs merge=lfs -text +*.whl filter=lfs diff=lfs merge=lfs -text +*.xz filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.zst filter=lfs diff=lfs merge=lfs -text diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..57affb6 --- /dev/null +++ b/.gitignore @@ -0,0 +1 @@ +.osc diff --git a/lalapps-10.0.0.tar.xz b/lalapps-10.0.0.tar.xz new file mode 100644 index 0000000..652cd0d --- /dev/null +++ b/lalapps-10.0.0.tar.xz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:1d677956daafc00def55f88cefd8c99a3ce2514af98f8af28b3e36d86bab714e +size 2269020 diff --git a/lalapps-9.2.2.tar.xz b/lalapps-9.2.2.tar.xz new file mode 100644 index 0000000..137c0a5 --- /dev/null +++ b/lalapps-9.2.2.tar.xz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:f64ced5a18756178afbf6e3c271b1501915683b428f08f9ff8714cb0e5c051a5 +size 2281872 diff --git a/lalapps-disable-testWeave-for-non-x86_64.patch b/lalapps-disable-testWeave-for-non-x86_64.patch new file mode 100644 index 0000000..14817fb --- /dev/null +++ b/lalapps-disable-testWeave-for-non-x86_64.patch @@ -0,0 +1,18 @@ +Index: lalapps-9.2.1/configure.ac +=================================================================== +--- lalapps-9.2.1.orig/configure.ac ++++ lalapps-9.2.1/configure.ac +@@ -268,6 +268,13 @@ AM_CPPFLAGS="-I\$(top_srcdir)/src ${AM_C + # RedHat-derived systems. + AC_SUBST([pkgpythondir], ["\${pkgpyexecdir}"]) + ++# testWeave_* results have tolerance issues that show up in some archs, use only for x86_64 ++# See https://git.ligo.org/lscsoft/lalsuite/-/issues/105 ++AC_MSG_CHECKING([if arch is non-x86_64 so weave tests should be disabled]) ++AC_DEFINE([SKIP_WEAVE_TESTS], [0], [Set to 1 for non-x86_64 architectures]) ++AS_IF([test x"$(arch)" != "xx86_64"], AC_MSG_RESULT([yes]), AC_MSG_RESULT([no])) ++AM_CONDITIONAL([SKIP_WEAVE_TESTS], [test x"$(arch)" != "xx86_64"]) ++ + # output + AC_OUTPUT + AC_MSG_NOTICE([ diff --git a/lalapps-fix-uninitialised-var.patch b/lalapps-fix-uninitialised-var.patch new file mode 100644 index 0000000..a4a8f6a --- /dev/null +++ b/lalapps-fix-uninitialised-var.patch @@ -0,0 +1,13 @@ +Index: lalapps-9.2.1/src/string/StringSearch.c +=================================================================== +--- lalapps-9.2.1.orig/src/string/StringSearch.c ++++ lalapps-9.2.1/src/string/StringSearch.c +@@ -200,7 +200,7 @@ int main(int argc,char *argv[]) + unsigned seg_length; + StringTemplate strtemplate[MAXTEMPLATES]; + int NTemplates; +- int NTemplates_fix; /* number of template given by the template bank file */ ++ int NTemplates_fix = 0; /* number of template given by the template bank file */ + REAL8 fcutoff_fix[MAXTEMPLATES]; /* high frequency cutoffs given by the template bank file */ + SnglBurst *events=NULL; + ProcessTable *process; diff --git a/lalapps.changes b/lalapps.changes new file mode 100644 index 0000000..29afd66 --- /dev/null +++ b/lalapps.changes @@ -0,0 +1,170 @@ +------------------------------------------------------------------- +Sat Jul 20 03:50:36 UTC 2024 - Atri Bhattacharya + +- Update to version 10.0.0: + * No release notes. + +------------------------------------------------------------------- +Mon Jan 22 08:20:01 UTC 2024 - Atri Bhattacharya + +- Update to version 9.2.2: + * No release notes. + +------------------------------------------------------------------- +Tue May 23 12:06:57 UTC 2023 - Atri Bhattacharya + +- Update to version 9.2.1: + * No release notes. +- Update versions of lal related packages in (Build)Requires. + +------------------------------------------------------------------- +Sat Aug 20 02:48:16 UTC 2022 - Atri Bhattacharya + +- Update to version 9.0.0: + * No release notes. +- Update source URL. + +------------------------------------------------------------------- +Mon Jan 3 00:52:11 UTC 2022 - Atri Bhattacharya + +- Update to version 7.4.0: + * No release notes. +- Drop lalapps-gcc11-array-bounds-decl.patch: upstreamed. + +------------------------------------------------------------------- +Wed Sep 15 09:20:02 UTC 2021 - Atri Bhattacharya + +- Do not pass "-Wno-enum-conversion" to CFLAGS as XLALERROR + issues have been fixed (probably with version 7.1.0). + +------------------------------------------------------------------- +Mon Sep 13 13:58:08 UTC 2021 - Atri Bhattacharya + +- Add lalapps-disable-testWeave-for-non-x86_64.patch: Disable + Weave related tests on all but x86_64 where tolerance errors + show up, see https://git.ligo.org/lscsoft/lalsuite/-/issues/105, + boo#1189928; introduces BuildRequires: libtool and requires + running autoreconf before configure. + +------------------------------------------------------------------- +Tue Jun 8 20:51:27 UTC 2021 - Atri Bhattacharya + +- Add lalapps-gcc11-array-bounds-decl.patch: Fix building with gcc + 11 by correcting array bounds declaration; patch part of + upstream merge request + [https://git.ligo.org/lscsoft/lalsuite/-/merge_requests/1605]. + +------------------------------------------------------------------- +Tue Apr 20 13:53:56 UTC 2021 - Ben Greiner + +- Fix runtime requirement for python-lal 7.1.0 + +------------------------------------------------------------------- +Sat Feb 27 00:02:59 UTC 2021 - Atri Bhattacharya + +- Update to version 7.2.0 (no release notes). + +------------------------------------------------------------------- +Fri Feb 12 21:51:42 UTC 2021 - Ben Greiner + +- Update to version 7.1.0 + * no public changelog +- Skip python36 build. Due to NEP 29, astropy, numpy, scipy and co. + do not have a python36 flavored package in TW +- Refresh lalapps-fix-uninitialised-var.patch +- Enable test suite +- Fix the python subpackage setup + +------------------------------------------------------------------- +Mon Nov 2 10:49:34 UTC 2020 - Atri Bhattacharya + +- Replace BuildRequires: libframe-devel by framel-devel: the + former is superseded by the latter. +- Specfile cleanups using spec-cleaner. + +------------------------------------------------------------------- +Mon Aug 31 06:10:58 UTC 2020 - Atri Bhattacharya + +- Update to version 6.26.1: + * No release notes. + +------------------------------------------------------------------- +Tue Jul 7 02:34:22 UTC 2020 - Atri Bhattacharya + +- Update to version 6.26.0: + * No release notes. +- Minor refresh of lalapps-fix-uninitialised-var.patch with + upstream file naming and other changes. +- Disable 32-bit builds: no longer supported upstream. +- Fix an env based hashbang. + +------------------------------------------------------------------- +Wed Jul 1 01:21:52 UTC 2020 - Atri Bhattacharya + +- Pass "-Wno-enum-conversion" to CFLAGS to workaround build errors + because XLAL_ERROR implictly converts to different function + return types. + +------------------------------------------------------------------- +Wed May 27 22:34:40 UTC 2020 - Atri Bhattacharya + +- Fix package description. + +------------------------------------------------------------------- +Mon Feb 3 01:32:43 UTC 2020 - Atri Bhattacharya + +- Update to version 6.25.1 + * MakeSFTs.c: fix incorrect XLAL error checks +- Changes from version 6.25.0: + * O3b release +- Update version numbers in BuildRequires and Requires in keeping + with upstream. + +------------------------------------------------------------------- +Mon Jan 20 22:45:54 UTC 2020 - Atri Bhattacharya + +- Disable python2 builds to prepare for removal of py2 support; + switch Requires to python3 modules. + +------------------------------------------------------------------- +Tue Oct 1 14:13:06 UTC 2019 - Atri Bhattacharya + +- Build packages for both python2 and python3. + +------------------------------------------------------------------- +Mon Jul 22 15:46:41 UTC 2019 - Atri Bhattacharya + +- Add lalapps-fix-uninitialised-var.patch: Fix usage of + uninitialised variables. + +------------------------------------------------------------------- +Mon Jul 22 14:40:08 UTC 2019 - Atri Bhattacharya + +- Update to version 6.24.0: + * O3 release. +- Drop patches incorporated upstream: + * lalapps-gcc8-format-overflow-errors.patch + * lalapps-truncation-errors-with-gcc82.patch + * lalapps-drop-abandoned-code.patch. + +------------------------------------------------------------------- +Fri Feb 8 13:32:21 UTC 2019 - badshah400@gmail.com + +- Switch builds to python2. +- Switch installable package name to use python{2,3}- naming + scheme. + +------------------------------------------------------------------- +Fri Feb 8 13:01:54 UTC 2019 - badshah400@gmail.com + +- Explicitly use python3- for Requires. + +------------------------------------------------------------------- +Thu Feb 7 14:59:25 UTC 2019 - badshah400@gmail.com + +- Update Requires for %{name}. + +------------------------------------------------------------------- +Thu Feb 7 14:07:00 UTC 2019 - badshah400@gmail.com + +- Initial package diff --git a/lalapps.spec b/lalapps.spec new file mode 100644 index 0000000..e5126da --- /dev/null +++ b/lalapps.spec @@ -0,0 +1,187 @@ +# +# spec file for package lalapps +# +# Copyright (c) 2024 SUSE LLC +# +# All modifications and additions to the file contributed by third parties +# remain the property of their copyright owners, unless otherwise agreed +# upon. The license for this file, and modifications and additions to the +# file, is the same license as for the pristine package itself (unless the +# license for the pristine package is not an Open Source License, in which +# case the license is the MIT License). An "Open Source License" is a +# license that conforms to the Open Source Definition (Version 1.9) +# published by the Open Source Initiative. + +# Please submit bugfixes or comments via https://bugs.opensuse.org/ +# + + +%define skip_python2 1 +# NEP 29: astropy, numpy, scipy do not have a python36 flavor package in TW +%define skip_python36 1 +Name: lalapps +Version: 10.0.0 +Release: 0 +Summary: LSC Algorithm Library Applications +License: GPL-2.0-or-later +Group: Productivity/Scientific/Physics +URL: https://wiki.ligo.org/Computing/DASWG/LALSuite +Source: https://software.igwn.org/sources/source/lalsuite/%{name}-%{version}.tar.xz +# PATCH-FIX-UPSTREAM lalapps-fix-uninitialised-var.patch badshah400@gmail.com -- Fix usage of uninitialised variable +Patch0: lalapps-fix-uninitialised-var.patch +# PATCH-FIX-UPSTREAM lalapps-disable-testWeave-for-non-x86_64.patch badshah400@gmail.com -- Disable Weave related tests on all but x86_64 where tolerance errors show up, see https://git.ligo.org/lscsoft/lalsuite/-/issues/105 +Patch2: lalapps-disable-testWeave-for-non-x86_64.patch +BuildRequires: %{python_module astropy} +BuildRequires: %{python_module devel} +BuildRequires: %{python_module glue} +BuildRequires: %{python_module lal >= 7.3.0} +BuildRequires: %{python_module lalburst >= 2.0.1} +BuildRequires: %{python_module lalframe >= 3.0.1} +BuildRequires: %{python_module lalinference >= 4.1.3} +BuildRequires: %{python_module lalmetaio >= 4.0.1} +BuildRequires: %{python_module lalpulsar >= 6.0.1} +BuildRequires: %{python_module matplotlib} +BuildRequires: %{python_module numpy-devel} +BuildRequires: %{python_module numpy} +BuildRequires: %{python_module scipy} +BuildRequires: cfitsio-devel +BuildRequires: fdupes +BuildRequires: openmpi-devel +BuildRequires: pkgconfig +BuildRequires: python-rpm-macros +BuildRequires: swig +BuildRequires: pkgconfig(fftw3) +BuildRequires: pkgconfig(framel) >= 8.39.2 +BuildRequires: pkgconfig(gsl) +BuildRequires: pkgconfig(lal) >= 7.3.0 +BuildRequires: pkgconfig(lalburst) >= 2.0.1 +BuildRequires: pkgconfig(lalframe) >= 3.0.1 +BuildRequires: pkgconfig(lalinference) >= 4.1.3 +BuildRequires: pkgconfig(lalinspiral) >= 4.0.2 +BuildRequires: pkgconfig(lalmetaio) >= 4.0.1 +BuildRequires: pkgconfig(lalpulsar) >= 6.0.1 +BuildRequires: pkgconfig(lalsimulation) >= 5.2.0 +# SECTION For tests +BuildRequires: %{python_module pytest} +BuildRequires: bc +BuildRequires: lalpulsar-data +Requires: python3-%{name} = %{version} +# /SECTION +# SECTION Required for Patch2 +BuildRequires: libtool +# /SECTION +# 32-bit no longer supported upstream +ExcludeArch: %{ix86} +%define python_subpackage_only 1 +%python_subpackages + +%description +The LSC Algorithm Library Applications for gravitational wave data analysis. +This package contains applications that are built on tools in the LSC +Algorithm Library. + +%package -n python-%{name} +Summary: LSC Algorithm Library Applications +Group: Productivity/Scientific/Physics +Requires: python-h5py +Requires: python-lal >= 7.3.0 +Requires: python-lalburst >= 2.0.1 +Requires: python-lalframe >= 3.0.1 +Requires: python-lalinference >= 4.1.3 +Requires: python-lalmetaio >= 4.0.1 +Requires: python-lalpulsar >= 6.0.1 +Requires: python-ligo-lw +Requires: python-ligo-segments +Requires: python-matplotlib +Requires: python-numpy +Requires: python-scipy + +%description -n python-%{name} +The LSC Algorithm Library Applications for gravitational wave data analysis. +This package contains applications that are built on tools in the LSC +Algorithm Library. + +This package contains the python files + +%prep +%autosetup -p1 + +%build +# Patch2 touches autotool files +autoreconf -fvi +%{python_expand # Necessary to run %%configure for all active python flavors +export PYTHON=%{_bindir}/$python +mkdir ../$python +cp -pr ./ ../$python +pushd ../$python +%configure --enable-swig +%make_build +popd +} + +%install +%{python_expand # install for all active python flavors +export PYTHON=$python +pushd ../$python +%make_install +popd +} + +# env-based hashbang /usr/bin/env tclsh => /usr/bin/tclsh +sed -Ei "1{s/env //}" %{buildroot}%{_bindir}/lalapps_CopySFTs + +# SECTION EXPORT LAL SPECIFIC ENV VARIABLES +# We do not use upstream's env files because they also set more generic +# variables (e.g. PATH) which may ruin setups + +# NUKE UPSTREAM ENV SCRIPTS +rm %{buildroot}%{_sysconfdir}/%{name}-user-env.* + +cat << EOF >> %{name}.sh +export LALAPPS_PREFIX=%{_prefix} +export LALAPPS_DATADIR=%{_datadir}/%{name} +EOF + +cat << EOF >> %{name}.csh +setenv LALAPPS_PREFIX "%{_prefix}" +setenv LALAPPS_DATADIR "%{_datadir}/%{name}" +EOF + +cat << EOF >> %{name}.fish +set LALAPPS_PREFIX (echo "%{_prefix}" | %{_bindir}/sed -e 's| |:|g;') +set LALAPPS_DATADIR (echo "%{_datadir}/%{name}" | %{_bindir}/sed -e 's| |:|g;') +EOF + +install -D -m0644 %{name}.sh %{buildroot}%{_sysconfdir}/profile.d/%{name}.sh +install -D -m0644 %{name}.csh %{buildroot}%{_sysconfdir}/profile.d/%{name}.csh +install -D -m0644 %{name}.fish %{buildroot}%{_sysconfdir}/profile.d/%{name}.fish + +# /SECTION + +# SECTION REMOVE STATIC LIB AND LIBTOOL ARCHIVE +find %{buildroot}%{_libdir}/ -name "*.a" -delete -print +find %{buildroot} -type f -name "*.la" -delete -print +# /SECTION + +%python_expand %fdupes %{buildroot}%{$python_sitearch}/%{name}/ +%fdupes %{buildroot}/%{_datadir}/%{name}/ + +%check +%{python_expand # +export PYTHON=$python +pushd ../$python +%make_build check +popd +} + +%files -n %{name} +%license COPYING +%{_bindir}/* +%{_datadir}/lalapps/ +%{_mandir}/man1/* +%config %{_sysconfdir}/profile.d/%{name}.* + +%files %{python_files %{name}} +%{python_sitearch}/* + +%changelog