sci-biology/eugene: update EAPI 6 -> 8

Closes: https://bugs.gentoo.org/829816
Signed-off-by: David Seifert <soap@gentoo.org>

3 files changed, 114 insertions, 31 deletions

diff --git a/sci-biology/eugene/eugene-4.1d.ebuild b/sci-biology/eugene/eugene-4.1d-r1.ebuild
index dbf8139e9e20..b1d9f409c096 100644
--- a/sci-biology/eugene/eugene-4.1d.ebuild
+++ b/sci-biology/eugene/eugene-4.1d-r1.ebuild
@@ -1,7 +1,7 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2022 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=6
+EAPI=8
 
 inherit autotools
 
@@ -12,16 +12,13 @@ SRC_URI="https://mulcyber.toulouse.inra.fr/frs/download.php/1359/${P}.tar.gz"
 LICENSE="Artistic"
 SLOT="0"
 KEYWORDS="amd64 x86"
-IUSE=""
+RESTRICT="test"
 
 DEPEND="
 	media-libs/gd[png]
-	media-libs/libpng:0=
-	"
+	media-libs/libpng:="
 RDEPEND="${DEPEND}"
 
-RESTRICT="test"
-
 PATCHES=(
 	# https://mulcyber.toulouse.inra.fr/tracker/index.php?func=detail&aid=1170
 	"${FILESDIR}"/${PN}-3.6-overflow.patch
@@ -29,6 +26,7 @@ PATCHES=(
 	"${FILESDIR}"/${PN}-4.1-format-security.patch
 	"${FILESDIR}"/${PN}-4.1d-fix-c++14.patch
 	"${FILESDIR}"/${PN}-4.1d-Wformat.patch
+	"${FILESDIR}"/${PN}-4.1d-portable-getopt.patch
 )
 
 src_prepare() {
@@ -37,5 +35,6 @@ src_prepare() {
 		-e '/SUBDIRS/ s/doc//' \
 		-e '/INSTALL.*doc/ s/\(.*\)//' \
 		-i Makefile.am || die
+	rm src/getopt.h || die
 	eautoreconf
 }
diff --git a/sci-biology/eugene/files/eugene-3.6-plugins.patch b/sci-biology/eugene/files/eugene-3.6-plugins.patch
index 1e910a13d5b1..e7424f73fc63 100644
--- a/sci-biology/eugene/files/eugene-3.6-plugins.patch
+++ b/sci-biology/eugene/files/eugene-3.6-plugins.patch
@@ -1,7 +1,36 @@
-http://bugs.gentoo.org/show_bug.cgi?id=297536
+https://bugs.gentoo.org/297536
 
---- eugene-3.6/src/Makefile.am
-+++ eugene-3.6/src/Makefile.am
+--- a/configure.ac
++++ b/configure.ac
+@@ -28,6 +28,7 @@
+ AC_PROG_CC
+ AC_PROG_AWK
+ AC_PROG_LN_S 
++AM_PROG_AR
+ AC_PROG_RANLIB
+ 
+ 
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -137,7 +137,7 @@
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
+-	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
++	$(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
+ 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
+@@ -160,6 +160,6 @@
+ 	$(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
+ 	$(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
+ 	$(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
+-	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(pkgdatadir)/plugins
++	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(libdir)/eugene/plugins
+ 	$(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
+ 	$(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
+--- a/src/Makefile.am
++++ b/src/Makefile.am
 @@ -20,7 +20,7 @@
  
  SUBDIRS = Parametrization GDIF . SensorPlugins
@@ -11,8 +40,8 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536
  AM_CFLAGS = 
  
  bin_PROGRAMS = eugene
---- eugene-3.6/src/MSensor.cc
-+++ eugene-3.6/src/MSensor.cc
+--- a/src/MSensor.cc
++++ b/src/MSensor.cc
 @@ -97,7 +97,7 @@
    std::string use_name;
  
@@ -22,22 +51,3 @@ http://bugs.gentoo.org/show_bug.cgi?id=297536
  
      // On récupère les couples nom de sensor/priorité du .par
      PAR.ResetIter();
---- eugene-3.6/Makefile.am
-+++ eugene-3.6/Makefile.am
-@@ -125,7 +125,7 @@
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Style
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Javascripts
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/web/Images
--	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) -d $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models
- 	$(INSTALL) -d $(DESTDIR)/$(pkgdatadir)/models/WAM
-@@ -144,6 +144,6 @@
- 	$(INSTALL) -m 644 $(srcdir)/web/Images/*jpg $(DESTDIR)/$(pkgdatadir)/web/Images
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.obo $(DESTDIR)/$(pkgdatadir)/cfg
- 	$(INSTALL) -m 644 $(srcdir)/cfg/*.par $(DESTDIR)/$(pkgdatadir)/cfg
--	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(pkgdatadir)/plugins
-+	$(INSTALL) src/SensorPlugins/*/*.so  $(DESTDIR)/$(libdir)/eugene/plugins
- 	$(INSTALL) $(srcdir)/Procedures/Eval/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Eval
- 	$(INSTALL) $(srcdir)/Procedures/Get/egn_* $(DESTDIR)/$(pkgdatadir)/Procedures/Get
diff --git a/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch
new file mode 100644
index 000000000000..156cb4bbdfac
--- /dev/null
+++ b/sci-biology/eugene/files/eugene-4.1d-portable-getopt.patch
@@ -0,0 +1,74 @@
+--- a/src/Param.h
++++ b/src/Param.h
+@@ -28,26 +28,14 @@
+ #include <vector>
+ #include <string>
+ #include <string.h>
++#include <unistd.h>
+ #ifdef HAVE_STRINGS_H
+ #include <strings.h>
+ #endif
+-// MacOS-X has getopt() defined is stdlib and the library in the libSystem
+-#ifndef __APPLE__
+-#ifdef HAVE_GETOPT_H
+-#include <getopt.h>
+-#else
+-#ifndef HAVE_GETOPT
+-#include "getopt.h"
+-#endif
+-#endif
+-#endif
+ 
+ #include "Const.h"
+ #include "System.h"
+ 
+-extern char   *optarg;   
+-extern int     optind;
+-
+ 
+ class ltstr
+ {
+--- a/src/SensorPlugins/MarkovIMM/GetData/CEM.cc
++++ b/src/SensorPlugins/MarkovIMM/GetData/CEM.cc
+@@ -22,18 +22,11 @@
+ #include "../../../../config.h"
+ #endif
+ 
+-#ifdef HAVE_GETOPT_H
+-#include <getopt.h>
+-#else
+-#ifndef HAVE_GETOPT
+-#include "../../../getopt.h"
+-#endif
+-#endif
+-
+ #include "../../../System.cc"
+ #include "../../../Const.h"
+ #include "../../0_SensorTk/EndianConv.h"
+ #include "strarray.h"
++#include "unistd.h"
+ #include <vector>
+ 
+ // Constantes
+--- a/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc
++++ b/src/SensorPlugins/MarkovIMM/GetData/TrainIMM.cc
+@@ -22,18 +22,11 @@
+ #include "../../../../config.h"
+ #endif
+ 
+-#ifdef HAVE_GETOPT_H
+-#include <getopt.h>
+-#else
+-#ifndef HAVE_GETOPT
+-#include "../../../getopt.h"
+-#endif
+-#endif
+-
+ #include "../../../System.cc"
+ #include "../../../Const.h"
+ #include "../../0_SensorTk/EndianConv.h"
+ #include "strarray.h"
++#include "unistd.h"
+ 
+ 
+ // Constantes