commit 2110091cc23ae48f8eb77d5ff652d48596d964caae0e69509d559a9fa907cc5a Author: Atri Bhattacharya Date: Sun May 31 13:11:55 2020 +0000 Accepting request 809707 from home:badshah400:GW NOTE: Depends on sr#809706 The LSC Algorithm Library Applications for gravitational wave data analysis. OBS-URL: https://build.opensuse.org/request/show/809707 OBS-URL: https://build.opensuse.org/package/show/science/lalapps?expand=0&rev=1 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-6.25.1.tar.xz b/lalapps-6.25.1.tar.xz new file mode 100644 index 0000000..a8a8610 --- /dev/null +++ b/lalapps-6.25.1.tar.xz @@ -0,0 +1,3 @@ +version https://git-lfs.github.com/spec/v1 +oid sha256:ef91dbe0c8926bd279b04ace327a61d5d88e14887b11664419edefa63e337224 +size 5002476 diff --git a/lalapps-fix-uninitialised-var.patch b/lalapps-fix-uninitialised-var.patch new file mode 100644 index 0000000..19039a2 --- /dev/null +++ b/lalapps-fix-uninitialised-var.patch @@ -0,0 +1,74 @@ +Index: lalapps-6.24.0/src/string/StringSearch.c +=================================================================== +--- lalapps-6.24.0.orig/src/string/StringSearch.c ++++ lalapps-6.24.0/src/string/StringSearch.c +@@ -203,7 +203,7 @@ 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; + MetadataTable process; +Index: lalapps-6.24.0/src/pulsar/SFTTools/SFTvalidate.c +=================================================================== +--- lalapps-6.24.0.orig/src/pulsar/SFTTools/SFTvalidate.c ++++ lalapps-6.24.0/src/pulsar/SFTTools/SFTvalidate.c +@@ -59,7 +59,7 @@ int main(int argc, char** argv) { + /* and read successive SFTs blocks from the file and validate CRC + checksums */ + for (count=0; 1; count++) { +- struct headertag2 info,lastinfo; ++ struct headertag2 info,lastinfo={}; + int err=0, swapendian, move, j; + + err=ReadSFTHeader(fp, &info, NULL, &swapendian, 1); +Index: lalapps-6.24.0/src/pulsar/SFTTools/SFTdumpheader.c +=================================================================== +--- lalapps-6.24.0.orig/src/pulsar/SFTTools/SFTdumpheader.c ++++ lalapps-6.24.0/src/pulsar/SFTTools/SFTdumpheader.c +@@ -54,7 +54,7 @@ int main(int argc, char **argv) { + /* and read successive SFTs blocks from the file and print headers */ + for (count=0; 1; count++) { + +- struct headertag2 info,lastinfo; ++ struct headertag2 info,lastinfo={}; + int err=0, swapendian, move; + char *mycomment; + +Index: lalapps-6.24.0/src/pulsar/SFTTools/SFTdumpall.c +=================================================================== +--- lalapps-6.24.0.orig/src/pulsar/SFTTools/SFTdumpall.c ++++ lalapps-6.24.0/src/pulsar/SFTTools/SFTdumpall.c +@@ -55,7 +55,7 @@ int main(int argc, char **argv) { + /* and read successive SFTs blocks from the file and print headers */ + for (count=0; 1; count++) { + +- struct headertag2 info, lastinfo; ++ struct headertag2 info, lastinfo={}; + int err=0, swapendian, move; + char *mycomment; + int whence = (int)ftell(fp); +Index: lalapps-6.24.0/src/pulsar/HoughFstat/HierarchicalSearch.c +=================================================================== +--- lalapps-6.24.0.orig/src/pulsar/HoughFstat/HierarchicalSearch.c ++++ lalapps-6.24.0/src/pulsar/HoughFstat/HierarchicalSearch.c +@@ -1270,7 +1270,7 @@ void SetUpSFTs( LALStatus *status, /** + REAL8 timebase, tObs, deltaFsft; + UINT4 k,numSFTby2; + LIGOTimeGPS tStartGPS, tEndGPS, refTimeGPS, tMidGPS; +- SFTCatalogSequence catalogSeq; ++ SFTCatalogSequence catalogSeq = {}; + + REAL8 doppWings, fMin, fMax; + REAL8 startTime_freqLo, startTime_freqHi; +@@ -1531,7 +1531,7 @@ void ComputeFstatHoughMap(LALStatus *sta + LIGOTimeGPSVector *tsMid; + REAL8Vector *timeDiffV=NULL; + UINT8Vector hist; /* histogram vector */ +- UINT8Vector histTotal; /* total histogram vector */ ++ UINT8Vector histTotal = {}; /* total histogram vector */ + HoughStats stats; /* statistics struct */ + CHAR *fileStats = NULL; + FILE *fpStats = NULL; diff --git a/lalapps.changes b/lalapps.changes new file mode 100644 index 0000000..9e8c488 --- /dev/null +++ b/lalapps.changes @@ -0,0 +1,63 @@ +------------------------------------------------------------------- +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..0f0e3e1 --- /dev/null +++ b/lalapps.spec @@ -0,0 +1,151 @@ +# +# spec file for package lalapps +# +# Copyright (c) 2019 SUSE LINUX GmbH, Nuernberg, Germany. +# +# 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 + +Name: lalapps +Version: 6.25.1 +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: http://software.ligo.org/lscsoft/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 +BuildRequires: %{python_module astropy} +BuildRequires: %{python_module devel} +BuildRequires: %{python_module glue} +BuildRequires: %{python_module lalburst >= 1.5.4} +BuildRequires: %{python_module lalframe >= 1.5.0} +BuildRequires: %{python_module lalinference >= 1.11.0} +BuildRequires: %{python_module lalmetaio >= 1.6.0} +BuildRequires: %{python_module lalpulsar >= 1.18.0} +BuildRequires: %{python_module lal >= 6.21.0} +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(gsl) +BuildRequires: pkgconfig(lal) >= 6.21.0 +BuildRequires: pkgconfig(lalburst) >= 1.5.4 +BuildRequires: pkgconfig(lalframe) >= 1.5.0 +BuildRequires: pkgconfig(lalinference) >= 1.11.0 +BuildRequires: pkgconfig(lalinspiral) >= 1.10.0 +BuildRequires: pkgconfig(lalmetaio) >= 1.6.0 +BuildRequires: pkgconfig(lalpulsar) >= 1.18.0 +BuildRequires: pkgconfig(lalsimulation) >= 1.10.0 +BuildRequires: pkgconfig(libframe) +Requires: python3-lal >= 6.21.0 +Requires: python3-lalburst >= 1.5.4 +Requires: python3-lalframe >= 1.5.0 +Requires: python3-lalinference >= 1.11.0 +Requires: python3-lalinspiral >= 1.10.0 +Requires: python3-lalmetaio >= 1.6.0 +Requires: python3-lalpulsar >= 1.18.0 +Requires: python3-lalsimulation >= 1.10.0 +Requires: python3-numpy +Requires: python3-scipy + +%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. + +%prep +%autosetup -p1 + +# FIX env-BASED HASHBANGS +sed -Ei "1{s|/usr/bin/env python|/usr/bin/python3|}" \ + src/pulsar/CrossCorr/*.py \ + src/pulsar/HeterodyneSearch/make_frame_cache + +%build +%{python_expand # Necessary to run %%configure with both py2 and py3 +export PYTHON=%{_bindir}/$python +mkdir ../$python +cp -pr ./ ../$python +pushd ../$python +%configure --enable-swig +make %{?_smp_mflags} +popd +} + +%install +%{python_expand # py2 and py3 make_install +export PYTHON=$python +pushd ../$python +%make_install +popd +} + +# 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}/ + +%files -n %{name} +%license COPYING +%{_bindir}/* +%{_datadir}/lalapps/ +%{_mandir}/man1/* +%config %{_sysconfdir}/profile.d/%{name}.* + +%files %{python_files} +%{python_sitearch}/* + +%changelog