[packages/lal-inference] - new

Sat Feb 11 13:06:45 CET 2023

commit 534fa8ec4faa9d0ea320a803c00c75aa58d41a60
Author: Jakub Bogusz <qboosh at pld-linux.org>
Date:   Sat Feb 11 13:08:09 2023 +0100

    - new

 lal-inference.spec        | 246 ++++++++++++++++++++++++++++++++++++++++++++++
 lalinference-env.patch    |  14 +++
 lalinference-format.patch |  11 +++
 3 files changed, 271 insertions(+)
---

diff --git a/lal-inference.spec b/lal-inference.spec
new file mode 100644
index 0000000..4089ec5
--- /dev/null
+++ b/lal-inference.spec
@@ -0,0 +1,246 @@
+# TODO: MPI
+Summary:	LAL routines for Bayesian inference data analysis
+Summary(pl.UTF-8):	Procedury LAL do analizy danych wywodów bayesowskich
+Name:		lal-inference
+Version:	4.1.1
+Release:	1
+License:	GPL v2
+Group:		Libraries
+Source0:	http://software.igwn.org/lscsoft/source/lalsuite/lalinference-%{version}.tar.xz
+# Source0-md5:	9391ce2650fc47fcb34154d398b32bac
+Patch0:		lalinference-env.patch
+Patch1:		lalinference-format.patch
+URL:		https://wiki.ligo.org/Computing/LALSuite
+BuildRequires:	autoconf >= 2.63
+BuildRequires:	automake >= 1:1.11
+BuildRequires:	gsl-devel >= 1.15
+BuildRequires:	help2man
+BuildRequires:	lal-devel >= 7.2.2
+BuildRequires:	lal-burst-devel >= 1.6.0
+BuildRequires:	lal-frame-devel >= 2.0.0
+BuildRequires:	lal-inspiral-devel >= 3.0.0
+BuildRequires:	lal-metaio-devel >= 3.0.0
+BuildRequires:	lal-simulation-devel >= 4.0.0
+BuildRequires:	libgomp-devel
+BuildRequires:	libstdc++-devel
+BuildRequires:	octave-devel >= 1:3.2.0
+BuildRequires:	pkgconfig
+BuildRequires:	python3-devel >= 1:3.5
+BuildRequires:	python3-numpy-devel >= 1:1.7
+BuildRequires:	sed >= 4.0
+BuildRequires:	swig >= 4.1.0
+BuildRequires:	swig-python >= 3.0.11
+BuildRequires:	tar >= 1:1.22
+BuildRequires:	xz
+Requires:	gsl >= 1.15
+Requires:	lal >= 7.2.2
+Requires:	lal-burst >= 1.6.0
+Requires:	lal-frame >= 2.0.0
+Requires:	lal-inspiral >= 3.0.0
+Requires:	lal-metaio >= 3.0.0
+Requires:	lal-simulation >= 4.0.0
+BuildRoot:	%{tmpdir}/%{name}-%{version}-root-%(id -u -n)
+
+%description
+LAL routines for Bayesian inference data analysis.
+
+%description -l pl.UTF-8
+Procedury LAL do analizy danych wywodów bayesowskich.
+
+%package devel
+Summary:	Header files for lal-inference library
+Summary(pl.UTF-8):	Pliki nagłówkowe biblioteki lal-inference
+Group:		Development/Libraries
+Requires:	%{name} = %{version}-%{release}
+Requires:	gsl-devel >= 1.15
+Requires:	lal-devel >= 7.2.2
+Requires:	lal-burst-devel >= 1.6.0
+Requires:	lal-frame-devel >= 2.0.0
+Requires:	lal-inspiral-devel >= 3.0.0
+Requires:	lal-metaio-devel >= 3.0.0
+Requires:	lal-simulation-devel >= 4.0.0
+
+%description devel
+Header files for lal-inference library.
+
+%description devel -l pl.UTF-8
+Pliki nagłówkowe biblioteki lal-inference.
+
+%package static
+Summary:	Static lal-inference library
+Summary(pl.UTF-8):	Statyczna biblioteka lal-inference
+Group:		Development/Libraries
+Requires:	%{name}-devel = %{version}-%{release}
+
+%description static
+Static lal-inference library.
+
+%description static -l pl.UTF-8
+Statyczna biblioteka lal-inference.
+
+%package -n octave-lalinference
+Summary:	Octave interface for LAL Inference
+Summary(pl.UTF-8):	Interfejs Octave do biblioteki LAL Inference
+Group:		Applications/Math
+Requires:	%{name} = %{version}-%{release}
+Requires:	octave-lal >= 7.2.2
+
+%description -n octave-lalinference
+Octave interface for LAL Inference.
+
+%description -n octave-lalinference -l pl.UTF-8
+Interfejs Octave do biblioteki LAL Inference.
+
+%package -n python3-lalinference
+Summary:	Python bindings for LAL Inference
+Summary(pl.UTF-8):	Wiązania Pythona do biblioteki LAL Inference
+Group:		Libraries/Python
+Requires:	%{name} = %{version}-%{release}
+Requires:	python3-lal >= 7.2.2
+Requires:	python3-lalburst >= 1.6.0
+Requires:	python3-lalmetaio >= 3.0.0
+Requires:	python3-lalinspieral >= 3.0.0
+Requires:	python3-lalsimulation >= 4.0.0
+Requires:	python3-ligo-lw >= 1.7.0
+Requires:	python3-ligo-segments
+Requires:	python3-lscsoft-glue >= 1.54.1
+Requires:	python3-matplotlib >= 1.2.0
+Requires:	python3-modules >= 1:3.5
+Requires:	python3-numpy >= 1:1.7
+Requires:	python3-six
+Requires:	python3-scipy >= 0.9.0
+# TODO: healpy>=1.9.1 astropy>=1.1.1 gwdatafind gwpy h5py
+
+%description -n python3-lalinference
+Python bindings for LAL Inference.
+
+%description -n python3-lalinference -l pl.UTF-8
+Wiązania Pythona do biblioteki LAL Inference.
+
+%prep
+%setup -q -n lalinference-%{version}
+%patch0 -p1
+%patch1 -p1
+
+%{__sed} -i -e '1s,/usr/bin/env bash,/bin/bash,' bin/lalinference_mpi_wrapper
+
+%build
+%{__libtoolize}
+%{__aclocal} -I gnuscripts
+%{__autoconf}
+%{__autoheader}
+%{__automake}
+%configure \
+	--disable-silent-rules \
+	--enable-swig
+
+%{__make}
+
+%install
+rm -rf $RPM_BUILD_ROOT
+
+%{__make} install \
+	DESTDIR=$RPM_BUILD_ROOT
+
+%{__rm} $RPM_BUILD_ROOT%{py3_sitedir}/lalinference/_bayespputils.la
+# obsoleted by pkg-config
+%{__rm} $RPM_BUILD_ROOT%{_libdir}/liblalinference.la
+
+install -d $RPM_BUILD_ROOT/etc/shrc.d
+%{__mv} $RPM_BUILD_ROOT%{_sysconfdir}/*sh $RPM_BUILD_ROOT/etc/shrc.d
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%post	-p /sbin/ldconfig
+%postun	-p /sbin/ldconfig
+
+%files
+%defattr(644,root,root,755)
+%attr(755,root,root) %{_bindir}/lalinference_bench
+%attr(755,root,root) %{_bindir}/lalinference_burst
+%attr(755,root,root) %{_bindir}/lalinference_datadump
+%attr(755,root,root) %{_bindir}/lalinference_injectedlike
+%attr(755,root,root) %{_bindir}/lalinference_mpi_wrapper
+%attr(755,root,root) %{_bindir}/lalinference_nest
+%attr(755,root,root) %{_bindir}/lalinference_version
+%attr(755,root,root) %{_libdir}/liblalinference.so.*.*.*
+%attr(755,root,root) %ghost %{_libdir}/liblalinference.so.23
+/etc/shrc.d/lalinference-user-env.csh
+/etc/shrc.d/lalinference-user-env.fish
+/etc/shrc.d/lalinference-user-env.sh
+%{_datadir}/lalinference
+%{_mandir}/man1/lalinference_bench.1*
+%{_mandir}/man1/lalinference_burst.1*
+%{_mandir}/man1/lalinference_datadump.1*
+%{_mandir}/man1/lalinference_injectedlike.1*
+%{_mandir}/man1/lalinference_nest.1*
+%{_mandir}/man1/lalinference_version.1*
+
+%files devel
+%defattr(644,root,root,755)
+%attr(755,root,root) %{_libdir}/liblalinference.so
+%{_includedir}/lal/LALInference*.h
+%{_includedir}/lal/SWIGLALInferenceTest.h
+%{_includedir}/lal/SWIGLALInference*.i
+%{_includedir}/lal/cubic_interp.h
+%{_includedir}/lal/distance_integrator.h
+%{_includedir}/lal/swiglalinference.i
+%{_pkgconfigdir}/lalinference.pc
+
+%files static
+%defattr(644,root,root,755)
+%{_libdir}/liblalinference.a
+
+%files -n octave-lalinference
+%defattr(644,root,root,755)
+%attr(755,root,root) %{_libdir}/octave/*/site/oct/*/lalinference.oct
+
+%files -n python3-lalinference
+%defattr(644,root,root,755)
+%attr(755,root,root) %{_bindir}/cbcBayes*
+%attr(755,root,root) %{_bindir}/imrtgr_imr_consistency_test
+%attr(755,root,root) %{_bindir}/lalinference_burst_pp_pipe
+%attr(755,root,root) %{_bindir}/lalinference_coherence_test
+%attr(755,root,root) %{_bindir}/lalinference_compute_roq_weights
+%attr(755,root,root) %{_bindir}/lalinference_cpnest
+%attr(755,root,root) %{_bindir}/lalinference_evolve_spins_and_append_samples
+%attr(755,root,root) %{_bindir}/lalinference_merge_posteriors
+%attr(755,root,root) %{_bindir}/lalinference_multi_pipe
+%attr(755,root,root) %{_bindir}/lalinference_nest2pos
+%attr(755,root,root) %{_bindir}/lalinference_pipe
+%attr(755,root,root) %{_bindir}/lalinference_pp_pipe
+%attr(755,root,root) %{_bindir}/lalinference_review_test
+%dir %{py3_sitedir}/lalinference
+%attr(755,root,root) %{py3_sitedir}/lalinference/_bayespputils.so
+%attr(755,root,root) %{py3_sitedir}/lalinference/_lalinference.so
+%{py3_sitedir}/lalinference/*.py
+%{py3_sitedir}/lalinference/__pycache__
+%dir %{py3_sitedir}/lalinference/bayestar
+%{py3_sitedir}/lalinference/bayestar/*.py
+%{py3_sitedir}/lalinference/bayestar/__pycache__
+%dir %{py3_sitedir}/lalinference/imrtgr
+%{py3_sitedir}/lalinference/imrtgr/*.py
+%{py3_sitedir}/lalinference/imrtgr/__pycache__
+%dir %{py3_sitedir}/lalinference/io
+%{py3_sitedir}/lalinference/io/*.py
+%{py3_sitedir}/lalinference/io/__pycache__
+%dir %{py3_sitedir}/lalinference/plot
+%{py3_sitedir}/lalinference/plot/*.py
+%{py3_sitedir}/lalinference/plot/__pycache__
+%dir %{py3_sitedir}/lalinference/tiger
+%{py3_sitedir}/lalinference/tiger/*.py
+%{py3_sitedir}/lalinference/tiger/__pycache__
+%{_mandir}/man1/cbcBayes*.1*
+%{_mandir}/man1/imrtgr_imr_consistency_test.1*
+%{_mandir}/man1/lalinference_burst_pp_pipe.1*
+%{_mandir}/man1/lalinference_coherence_test.1*
+%{_mandir}/man1/lalinference_compute_roq_weights.1*
+%{_mandir}/man1/lalinference_cpnest.1*
+%{_mandir}/man1/lalinference_evolve_spins_and_append_samples.1*
+%{_mandir}/man1/lalinference_merge_posteriors.1*
+%{_mandir}/man1/lalinference_multi_pipe.1*
+%{_mandir}/man1/lalinference_nest2pos.1*
+%{_mandir}/man1/lalinference_pipe.1*
+%{_mandir}/man1/lalinference_pp_pipe.1*
+%{_mandir}/man1/lalinference_review_test.1*
diff --git a/lalinference-env.patch b/lalinference-env.patch
new file mode 100644
index 0000000..172aab9
--- /dev/null
+++ b/lalinference-env.patch
@@ -0,0 +1,14 @@
+--- lalinference-4.1.1/Makefile.am.orig	2022-05-11 00:56:41.829041103 +0200
++++ lalinference-4.1.1/Makefile.am	2023-02-11 07:56:42.424597083 +0100
+@@ -25,11 +25,6 @@ SUBDIRS = \
+ user_environment = \
+ 	set $(PACKAGE)_PREFIX $(prefix); \
+ 	set $(PACKAGE)_DATADIR $(pkgdatadir); \
+-	prepend MANPATH $(mandir); \
+-	prepend OCTAVE_PATH $(octexecdir); \
+-	prepend PATH $(bindir); \
+-	prepend PKG_CONFIG_PATH $(libdir)/pkgconfig; \
+-	prepend PYTHONPATH $(pyexecdir) $(pythondir); \
+ 	$(END_OF_LIST)
+ 
+ pkgconfigdir = $(libdir)/pkgconfig
diff --git a/lalinference-format.patch b/lalinference-format.patch
new file mode 100644
index 0000000..3c860dd
--- /dev/null
+++ b/lalinference-format.patch
@@ -0,0 +1,11 @@
+--- lalinference-4.1.1/lib/distance_integrator.c.orig	2022-09-06 10:24:18.086021797 +0200
++++ lalinference-4.1.1/lib/distance_integrator.c	2023-02-10 10:23:02.578433203 +0100
+@@ -246,7 +246,7 @@ double log_radial_integral(double r1, do
+ 			abstol*=2;
+ 			break;
+ 		case GSL_EMAXITER:
+-			fprintf(stderr,"GSL error %s, increasing n to %li\n",gsl_strerror(ret),n*=2);
++			fprintf(stderr,"GSL error %s, increasing n to %zd\n",gsl_strerror(ret),n*=2);
+ 			break;
+ 		case GSL_SUCCESS:
+ 			break;
================================================================

---- gitweb:

http://git.pld-linux.org/gitweb.cgi/packages/lal-inference.git/commitdiff/534fa8ec4faa9d0ea320a803c00c75aa58d41a60

