sci-libs/ghmm: Drop obsolete tools, #163; correctly support python modules; add optional support for gsl and lapack

Package-Manager: portage-2.2.7

4 files changed, 89 insertions, 0 deletions

diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch
new file mode 100644
index 000000000..9b4e919ec
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-link.patch
@@ -0,0 +1,24 @@
+Index: tools/Makefile.am
+===================================================================
+--- tools/Makefile.am	(revision 2332)
++++ tools/Makefile.am	(working copy)
+@@ -23,5 +23,5 @@
+ smix_hmm_SOURCES = smix_hmm.c
+ smo2xml_SOURCES = smo2xml.c
+ 
+-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
++LDADD = $(top_builddir)/ghmm/libghmm.la
+ bin_SCRIPTS = ghmm-config
+Index: tests/Makefile.am
+===================================================================
+--- tests/Makefile.am	(revision 2332)
++++ tests/Makefile.am	(working copy)
+@@ -34,7 +34,7 @@
+ 		  read_fa \
+                   mcmc
+ 
+-LDADD = $(top_builddir)/ghmm/.libs/libghmm.a
++LDADD = $(top_builddir)/ghmm/libghmm.la
+ 
+ TESTS_ENVIRONMENT = GHMM_SILENT_TESTS
+ TESTS =           root_finder_test \
diff --git a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
new file mode 100644
index 000000000..2e6be54d0
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
@@ -0,0 +1,13 @@
+Index: configure.in
+===================================================================
+--- configure.in	(revision 2332)
++++ configure.in	(working copy)
+@@ -293,7 +293,7 @@
+ CFLAGS="$CFLAGS $LIBXML2_CFLAGS"
+ 
+ dnl final configuration
+-SUBDIRS="ghmm tools tests"
++SUBDIRS="ghmm"
+ 
+ dnl python wrapper can be switched on or off
+ AC_ARG_WITH(python,
diff --git a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
new file mode 100644
index 000000000..6197d9ba1
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
@@ -0,0 +1,40 @@
+Index: tools/Makefile.am
+===================================================================
+--- tools/Makefile.am	(revision 2332)
++++ tools/Makefile.am	(working copy)
+@@ -12,7 +12,7 @@
+ MAINTAINERCLEANFILES = Makefile.in
+ 
+ BUILT_SOURCES = 
+-INCLUDES = -I$(top_srcdir)
++INCLUDES = -I$(top_srcdir) -I$(top_builddir)/ghmm
+ 
+ bin_PROGRAMS = probdist cluster scluster smix_hmm $(OBSOLETE_TOOLS)
+ EXTRA_PROGRAMS = smo2xml
+Index: tests/Makefile.am
+===================================================================
+--- tests/Makefile.am	(revision 2332)
++++ tests/Makefile.am	(working copy)
+@@ -15,7 +15,7 @@
+ MAINTAINERCLEANFILES = Makefile.in
+ # stuff from dejagnu
+ 
+-INCLUDES=-I$(top_srcdir)
++INCLUDES=-I$(top_srcdir) -I$(top_builddir)/ghmm
+ 
+ #these tests will not be installed
+ # in progress: test_sdfoba nullmodel ciscreen test_sdmodel 
+Index: ghmmwrapper/Makefile.am
+===================================================================
+--- ghmmwrapper/Makefile.am	(revision 2332)
++++ ghmmwrapper/Makefile.am	(working copy)
+@@ -47,7 +47,9 @@
+                  testdata/model_label.xml \
+                  testdata/tiny.txt.sqd
+ 
++INCLUDES=-I$(top_builddir)
+ 
++
+ EXTRA_DIST = ${SWIG_INTERFACE_FILES} ${EXTENSION_C_FILES} ${PYTHON_FILES} ${PYTHON_GATO_FILES} ${TESTDATA_FILES}
+ 
+ all: setup.py ghmm.py ${SWIG_INTERFACE_FILES}
diff --git a/sci-libs/ghmm/files/ghmm-9999-respect.patch b/sci-libs/ghmm/files/ghmm-9999-respect.patch
new file mode 100644
index 000000000..09c8721c9
--- /dev/null
+++ b/sci-libs/ghmm/files/ghmm-9999-respect.patch
@@ -0,0 +1,12 @@
+Index: ghmmwrapper/setup.py
+===================================================================
+--- ghmmwrapper/setup.py	(revision 2332)
++++ ghmmwrapper/setup.py	(working copy)
+@@ -48,7 +48,6 @@
+                                include_dirs = ['..'],
+                                library_dirs = ['../ghmm/.libs'],
+                                libraries = ['ghmm', 'm', 'pthread', 'xml2', 'z'],
+-                               extra_compile_args = ["-O2", "-pipe", "-Wall"], # -g might help debugging
+                                depends = ['wrapper_alphabet.i', 'wrapper_cmodel.i', 'wrapper_cseq.i',
+                                           'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i',
+                                           'wrapper_dseq.i', 'wrapper_xmlfile.i']