[gentoo-commits] proj/sci:master commit in: sci-libs/ghmm/files/, sci-libs/ghmm/

["Andrew Ammerlaan" <andrewammerlaan@riseup.net>]

commit:     a312e72300ff482275764d9541e537a926956566
Author:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
AuthorDate: Tue Jan  5 14:59:31 2021 +0000
Commit:     Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net>
CommitDate: Tue Jan  5 18:01:30 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=a312e723

sci-libs/ghmm: drop package, py2 only latest update 2015

Package-Manager: Portage-3.0.12, Repoman-3.0.2
Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net>

 sci-libs/ghmm/files/ghmm-9999-clapack.patch       | 11 ----
 sci-libs/ghmm/files/ghmm-9999-link.patch          | 24 --------
 sci-libs/ghmm/files/ghmm-9999-obsolete.patch      | 13 -----
 sci-libs/ghmm/files/ghmm-9999-out-of-source.patch | 40 --------------
 sci-libs/ghmm/files/ghmm-9999-respect.patch       | 10 ----
 sci-libs/ghmm/ghmm-9999.ebuild                    | 67 -----------------------
 sci-libs/ghmm/metadata.xml                        | 11 ----
 7 files changed, 176 deletions(-)

diff --git a/sci-libs/ghmm/files/ghmm-9999-clapack.patch b/sci-libs/ghmm/files/ghmm-9999-clapack.patch
deleted file mode 100644
index d36cb2ab5..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-clapack.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- ghmm/matrixop.c
-+++ ghmm/matrixop.c
-@@ -45,7 +45,7 @@
- #endif
- 
- #ifdef DO_WITH_ATLAS
--#include <clapack.h>
-+#include <clapack/clapack.h>
- #endif
- 
- /*============================================================================*/

diff --git a/sci-libs/ghmm/files/ghmm-9999-link.patch b/sci-libs/ghmm/files/ghmm-9999-link.patch
deleted file mode 100644
index 9b4e919ec..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-link.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-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
deleted file mode 100644
index 2e6be54d0..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-obsolete.patch
+++ /dev/null
@@ -1,13 +0,0 @@
-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
deleted file mode 100644
index 6197d9ba1..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-out-of-source.patch
+++ /dev/null
@@ -1,40 +0,0 @@
-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
deleted file mode 100644
index cc70a0780..000000000
--- a/sci-libs/ghmm/files/ghmm-9999-respect.patch
+++ /dev/null
@@ -1,10 +0,0 @@
---- ghmmwrapper/setup.py
-+++ ghmmwrapper/setup.py
-@@ -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_bayes.i', 'wrapper_cmodel.i', 'wrapper_cseq.i',
-                                           'wrapper_dmodel.i', 'wrapper_dpmodel.i', 'wrapper_dpseq.i',
-                                           'wrapper_dseq.i', 'wrapper_xmlfile.i']

diff --git a/sci-libs/ghmm/ghmm-9999.ebuild b/sci-libs/ghmm/ghmm-9999.ebuild
deleted file mode 100644
index 012fc6499..000000000
--- a/sci-libs/ghmm/ghmm-9999.ebuild
+++ /dev/null
@@ -1,67 +0,0 @@
-# Copyright 1999-2015 Gentoo Foundation
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=5
-
-AUTOTOOLS_AUTORECONF=true
-
-PYTHON_COMPAT=( python2_7 )
-
-inherit autotools-utils distutils-r1 subversion
-
-DESCRIPTION="General Hidden Markov Model library"
-HOMEPAGE="http://ghmm.sourceforge.net/"
-SRC_URI=""
-ESVN_REPO_URI="https://ghmm.svn.sourceforge.net/svnroot/ghmm/trunk/ghmm"
-
-LICENSE="LGPL-2.1"
-SLOT="0"
-KEYWORDS=""
-IUSE="gsl lapack +python static-libs"
-
-RDEPEND="
-	dev-libs/libxml2
-	gsl? ( sci-libs/gsl )
-	lapack? (
-		sci-libs/clapack
-		virtual/lapack
-		)"
-DEPEND="${RDEPEND}"
-
-S="${WORKDIR}/${PN}"
-
-ESVN_BOOTSTRAP="autotools-utils_src_prepare"
-
-PATCHES=(
-	"${FILESDIR}"/${P}-clapack.patch
-	"${FILESDIR}"/${P}-out-of-source.patch
-	"${FILESDIR}"/${P}-link.patch
-	"${FILESDIR}"/${P}-respect.patch
-	"${FILESDIR}"/${P}-obsolete.patch
-)
-
-src_prepare() {
-	use python && AUTOTOOLS_IN_SOURCE_BUILD=1
-	autotools-utils_src_prepare
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_python_prepare
-}
-
-src_configure() {
-	local myeconfargs=(
-		--without-python
-		--disable-obsolete
-		$(use_enable gsl)
-		$(use_enable lapack atlas)
-	)
-	autotools-utils_src_configure
-}
-
-src_compile() {
-	autotools-utils_src_compile
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_compile
-}
-
-src_install() {
-	autotools-utils_src_install
-	use python && cd "${S}"/ghmmwrapper && distutils-r1_src_install
-}

diff --git a/sci-libs/ghmm/metadata.xml b/sci-libs/ghmm/metadata.xml
deleted file mode 100644
index 5fc8aa771..000000000
--- a/sci-libs/ghmm/metadata.xml
+++ /dev/null
@@ -1,11 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
-<pkgmetadata>
-	<maintainer type="project">
-		<email>sci@gentoo.org</email>
-		<name>Gentoo Science Project</name>
-	</maintainer>
-	<upstream>
-		<remote-id type="sourceforge">ghmm</remote-id>
-	</upstream>
-</pkgmetadata>