[med-svn] [Git][med-team/ghmm][master] Manually merge changes by Sebastien, mention Israel in changelog for adding autopkgtest
Andreas Tille (@tille)
gitlab at salsa.debian.org
Thu Jan 18 10:21:16 GMT 2024
Andreas Tille pushed to branch master at Debian Med / ghmm
Commits:
2845f134 by Andreas Tille at 2024-01-18T11:20:21+01:00
Manually merge changes by Sebastien, mention Israel in changelog for adding autopkgtest
- - - - -
4 changed files:
- debian/changelog
- debian/control
- debian/patches/lapacke.patch
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,12 +1,19 @@
ghmm (0.9~rc3-5) UNRELEASED; urgency=medium
* Team upload.
+
+ [ Andreas Tille ]
* Standards-Version: 4.6.2 (routine-update)
* Avoid explicitly specifying -Wl,--as-needed linker flag.
* Fix: SyntaxWarning: "is" with a literal. Did you mean "=="?
* Fix clean target
Closes: #1044649
- * Port to lapacke
+
+ [ Komolehin Israel Timilehin ]
+ * Add autopkgtest
+
+ [ Sébastien Villemot ]
+ * Remove build-dependency on libatlas-base-dev
Closes: #1056673
-- Andreas Tille <tille at debian.org> Thu, 11 Jan 2024 17:06:32 +0100
=====================================
debian/control
=====================================
@@ -26,6 +26,7 @@ Depends: ${shlibs:Depends},
${python3:Depends},
python3,
libghmm1
+Recommends: libopenblas0 | libblis4
Description: General Hidden-Markov-Model library - tools
The General Hidden Markov Model Library (GHMM) is a C library with
additional Python3 bindings implementing a wide range of types of
=====================================
debian/patches/lapacke.patch
=====================================
@@ -1,61 +1,116 @@
Description: Use LAPACKE instead of ATLAS
Bug-Debian: https://bugs.debian.org/1056673
Author: Andreas Tille <tille at debian.org>
-Last-Update: Thu, 11 Jan 2024 17:06:32 +0100
-FIXME: This is not sufficient and needs more changes inside the code
-
+ Sébastien Villemot <sebastien at debian.org>
+Last-Update: 2024-01-15
--- a/configure.in
+++ b/configure.in
-@@ -226,7 +226,7 @@
+@@ -202,69 +202,30 @@ AC_ARG_ENABLE(gsl_diagonal_hack,
+ )
- dnl checking for clapack_dgetrf
- AC_MSG_CHECKING([for clapack_dgetrf in -llapack])
-- AC_TRY_COMPILE([#include <clapack.h>],
-+ AC_TRY_COMPILE([#include <lapacke.h>],
- [
- double a;
- int ipiv;
-@@ -239,7 +239,7 @@
- dnl checking for clapack_dgetri
- AC_MSG_CHECKING([for clapack_dgetri in -llapack])
-- AC_TRY_COMPILE([#include <clapack.h>],
-+ AC_TRY_COMPILE([#include <lapacke.h>],
- [
- double a;
- int ipiv;
-@@ -252,7 +252,7 @@
+-dnl check lapack functions from atlas
+-AC_ARG_ENABLE(atlas,
+- AC_HELP_STRING([--enable-atlas], [use matrix operations from atlas lapack [[default=no]]]),
++dnl check lapacke
++AC_ARG_ENABLE(lapacke,
++ AC_HELP_STRING([--enable-lapacke], [use matrix operations from lapacke [[default=no]]]),
+ [
+- if test "x$enable_lapack" != "xno" ; then
++ if test "x$enable_lapacke" != "xno" ; then
- dnl checking for clapack_dpotrf
- AC_MSG_CHECKING([for clapack_dpotrf in -llapack])
-- AC_TRY_COMPILE([#include <clapack.h>],
-+ AC_TRY_COMPILE([#include <lapacke.h>],
- [
- double a;
- int x = clapack_dpotrf(0, 0, 0, &a, 0);
-@@ -312,8 +312,9 @@
+- AC_DEFINE(DO_WITH_ATLAS,1,[use matrix operations from lapack])
++ AC_DEFINE(DO_WITH_LAPACKE,1,[use matrix operations from lapacke])
- LIBXML2_CFLAGS=`$PKGCONFIG --cflags libxml-2.0`
- LIBXML2_LIBS=`$PKGCONFIG --libs libxml-2.0`
-+LIBLAPACKE_LIBS=`$PKGCONFIG --libs lapacke`
+- echo -n "checking for lapack with pkg-config... "
+- if $PKGCONFIG --exists lapack; then
++ echo -n "checking for lapacke with pkg-config... "
++ if $PKGCONFIG --exists lapacke; then
+ AC_MSG_RESULT(yes)
+- LAPACK_CFLAGS=`$PKGCONFIG --cflags lapack`
+- LAPACK_LIBS=`$PKGCONFIG --libs lapack`
++ LAPACKE_CFLAGS=`$PKGCONFIG --cflags lapacke`
++ LAPACKE_LIBS=`$PKGCONFIG --libs lapacke`
+ else
+ AC_MSG_RESULT(no)
+- AC_MSG_NOTICE(lapack not found with pkg-config)
+- AC_MSG_NOTICE(you have to add the necessary flags to CFLAGS)
++ AC_MSG_ERROR(lapacke not found with pkg-config)
+ fi
--LIBS="$LIBS $LIBXML2_LIBS"
-+LIBS="$LIBS $LIBXML2_LIBS $LIBLAPACKE_LIBS"
- CFLAGS="$CFLAGS $LIBXML2_CFLAGS"
+- LIBS="$LIBS $LAPACK_LIBS"
+- CFLAGS="$CFLAGS $LAPACK_CFLAGS"
+-
+- dnl checking for clapack_dgetrf
+- AC_MSG_CHECKING([for clapack_dgetrf in -llapack])
+- AC_TRY_COMPILE([#include <clapack.h>],
+- [
+- double a;
+- int ipiv;
+- int x = clapack_dgetrf(0, 0, 0, &a, 0, &ipiv);
+- ],
+- AC_MSG_RESULT(yes)
+- AC_DEFINE(HAVE_CLAPACK_DGETRF,1,[clapack_dgetrf exists]),
+- AC_MSG_RESULT(no)
+- )
+-
+- dnl checking for clapack_dgetri
+- AC_MSG_CHECKING([for clapack_dgetri in -llapack])
+- AC_TRY_COMPILE([#include <clapack.h>],
+- [
+- double a;
+- int ipiv;
+- int x = clapack_dgetri(0, 0, &a, 0, &ipiv);
+- ],
+- AC_MSG_RESULT(yes)
+- AC_DEFINE(HAVE_CLAPACK_DGETRI,1,[clapack_dgetri exists]),
+- AC_MSG_RESULT(no)
+- )
+-
+- dnl checking for clapack_dpotrf
+- AC_MSG_CHECKING([for clapack_dpotrf in -llapack])
+- AC_TRY_COMPILE([#include <clapack.h>],
+- [
+- double a;
+- int x = clapack_dpotrf(0, 0, 0, &a, 0);
+- ],
+- AC_MSG_RESULT(yes)
+- AC_DEFINE(HAVE_CLAPACK_DPOTRF,1,[clapack_dpotrf exists]),
+- AC_MSG_RESULT(no)
+- )
++ LIBS="$LIBS $LAPACKE_LIBS"
++ CFLAGS="$CFLAGS $LAPACKE_CFLAGS"
+ fi
+ ],
+ [
+- AC_MSG_NOTICE("not using lapack")
++ AC_MSG_NOTICE("not using lapacke")
+ ]
+ )
- dnl final configuration
--- a/ghmm/matrixop.c
+++ b/ghmm/matrixop.c
-@@ -45,7 +45,7 @@
+@@ -44,8 +44,8 @@
+ #include <gsl/gsl_linalg.h>
#endif
- #ifdef DO_WITH_ATLAS
+-#ifdef DO_WITH_ATLAS
-#include <clapack.h>
++#ifdef DO_WITH_LAPACKE
+#include <lapacke.h>
#endif
/*============================================================================*/
-@@ -99,7 +99,7 @@
+@@ -87,7 +87,7 @@ int ighmm_invert_det(double *sigmainv, d
+ }
+
+ gsl_matrix_free(inv);
+-#elif defined HAVE_CLAPACK_DGETRF && HAVE_CLAPACK_DGETRI
++#elif defined DO_WITH_LAPACKE
+ char sign;
+ int info, i;
+ int *ipiv;
+@@ -99,7 +99,7 @@ int ighmm_invert_det(double *sigmainv, d
memcpy(sigmainv, cov, length * length * sizeof *cov);
/* perform in-place LU factorization of covariance matrix */
@@ -64,7 +119,7 @@ FIXME: This is not sufficient and needs more changes inside the code
/* determinant */
sign = 1;
-@@ -112,7 +112,7 @@
+@@ -112,7 +112,7 @@ int ighmm_invert_det(double *sigmainv, d
*det = det_tmp * sign;
/* use the LU factorization to get inverse */
@@ -73,7 +128,12 @@ FIXME: This is not sufficient and needs more changes inside the code
free(ipiv);
#else
-@@ -235,7 +235,7 @@
+@@ -231,11 +231,11 @@ int ighmm_cholesky_decomposition (double
+ }
+ gsl_matrix_free(tmp);
+
+-#elif defined HAVE_CLAPACK_DPOTRF
++#elif defined DO_WITH_LAPACKE
int info;
/* copy cov. matrix entries to result matrix, the rest is done in-place */
memcpy(sigmacd, cov, dim * dim * sizeof *cov);
=====================================
debian/rules
=====================================
@@ -10,7 +10,7 @@ export PYBUILD_NAME=HMMEd
dh $@
override_dh_auto_configure:
- dh_auto_configure --sourcedirectory=$(CURDIR) -- --enable-atlas
+ dh_auto_configure --sourcedirectory=$(CURDIR) -- --enable-lapacke
dh_auto_configure --buildsystem=pybuild --sourcedirectory=HMMEd
override_dh_auto_build:
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/2845f134775c316423398c158fc93f842709a179
--
View it on GitLab: https://salsa.debian.org/med-team/ghmm/-/commit/2845f134775c316423398c158fc93f842709a179
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