sci-biology/bfast: Port to EAPI 7

Closes: https://bugs.gentoo.org/625490
Package-Manager: Portage-3.0.17, Repoman-3.0.2
Signed-off-by: David Seifert <soap@gentoo.org>

4 files changed, 207 insertions, 26 deletions

diff --git a/sci-biology/bfast/bfast-0.7.0a.ebuild b/sci-biology/bfast/bfast-0.7.0a.ebuild
index 97282d2244a4..6a48785022f4 100644
--- a/sci-biology/bfast/bfast-0.7.0a.ebuild
+++ b/sci-biology/bfast/bfast-0.7.0a.ebuild
@@ -1,11 +1,9 @@
-# Copyright 1999-2019 Gentoo Authors
+# Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
-AUTOTOOLS_AUTORECONF=true
-
-inherit autotools-utils flag-o-matic
+inherit autotools
 
 DESCRIPTION="Blat-like Fast Accurate Search Tool"
 HOMEPAGE="https://sourceforge.net/projects/bfast/"
@@ -13,30 +11,19 @@ SRC_URI="mirror://sourceforge/${PN}/${P}.tar.gz"
 
 LICENSE="GPL-2"
 SLOT="0"
-IUSE="test"
-RESTRICT="!test? ( test )"
 KEYWORDS="~amd64 ~x86"
+IUSE="test"
+RESTRICT="test" # tests broken, upstream unresponsive
 
-DEPEND=""
 RDEPEND="dev-perl/XML-Simple"
 
-src_prepare() {
-	sed \
-		-e 's/-m64//' \
-		-e 's/CFLAGS="${default_CFLAGS} ${extended_CFLAGS}"/CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}"/' \
-		-e 's:-g -O2::g' \
-		-i configure.ac || die
-	sed \
-		-e 's:. test.definitions.sh:. ./test.definitions.sh:g' \
-		-i tests/*sh || die
-
-	sed \
-		-e '/docdir/d' \
-		-i Makefile.am || die
-
-	use test && AUTOTOOLS_IN_SOURCE_BUILD=1
+PATCHES=(
+	"${FILESDIR}"/${P}-autotools.patch
+	"${FILESDIR}"/${P}-test-sourcing.patch
+	"${FILESDIR}"/${P}-C99-inline.patch
+)
 
-	append-flags -fgnu89-inline
-
-	autotools-utils_src_prepare
+src_prepare() {
+	default
+	eautoreconf
 }
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch
new file mode 100644
index 000000000000..86450c96048a
--- /dev/null
+++ b/sci-biology/bfast/files/bfast-0.7.0a-C99-inline.patch
@@ -0,0 +1,74 @@
+--- a/bfast/AlignNTSpace.c
++++ b/bfast/AlignNTSpace.c
+@@ -478,7 +478,7 @@
+ 	}
+ }
+ 
+-inline void AlignNTSpaceFillInCell(char *read,
++void AlignNTSpaceFillInCell(char *read,
+ 		int32_t readLength,
+ 		char *reference,
+ 		int32_t referenceLength,
+--- a/bfast/AlignNTSpace.h
++++ b/bfast/AlignNTSpace.h
+@@ -10,5 +10,5 @@
+ void AlignNTSpaceRecoverAlignmentFromMatrix(AlignedEntry*, AlignMatrix*, char*, int, char*, int, int32_t, int32_t, int, int32_t, char, int);
+ void AlignNTSpaceInitializeAtStart(AlignMatrix*, ScoringMatrix*, int32_t, int32_t);
+ void AlignNTSpaceInitializeToExtend(AlignMatrix*, ScoringMatrix*, int32_t, int32_t, int32_t, int32_t);
+-inline void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
++void AlignNTSpaceFillInCell(char*, int32_t, char*, int32_t, ScoringMatrix*, AlignMatrix*, int32_t, int32_t, int32_t, int32_t);
+ #endif
+--- a/bfast/BLib.c
++++ b/bfast/BLib.c
+@@ -90,7 +90,7 @@
+ }
+ 
+ /* TODO */
+-inline char ToUpper(char a)
++char ToUpper(char a)
+ {
+   if(97 <= a && a < 122) return (char)(a - 32);
+   return a;
+--- a/bfast/BLib.h
++++ b/bfast/BLib.h
+@@ -16,7 +16,7 @@
+ int ParseFastaHeaderLine(char*);
+ char ToLower(char);
+ void ToLowerRead(char*, int);
+-inline char ToUpper(char);
++char ToUpper(char);
+ void ToUpperRead(char*, int);
+ void ReverseRead(char*, char*, int);
+ void ReverseReadFourBit(int8_t*, int8_t*, int);
+--- a/bfast/ScoringMatrix.c
++++ b/bfast/ScoringMatrix.c
+@@ -98,14 +98,14 @@
+ 	return 1;
+ }
+ 
+-inline int32_t ScoringMatrixGetNTScore(char a,
++int32_t ScoringMatrixGetNTScore(char a,
+ 		char b,
+ 		ScoringMatrix *sm)
+ {
+ 	return (ToUpper(a) == ToUpper(b)) ? sm->ntMatch : sm->ntMismatch;
+ }
+ 
+-inline int32_t ScoringMatrixGetColorScore(char a, 
++int32_t ScoringMatrixGetColorScore(char a, 
+ 		char b, 
+ 		ScoringMatrix *sm) 
+ {
+--- a/bfast/ScoringMatrix.h
++++ b/bfast/ScoringMatrix.h
+@@ -3,8 +3,8 @@
+ 
+ #include "BLibDefinitions.h"
+ 
+-inline int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
+-inline int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
++int32_t ScoringMatrixGetNTScore(char, char, ScoringMatrix*);
++int32_t ScoringMatrixGetColorScore(char, char, ScoringMatrix*);
+ 
+ int ScoringMatrixRead(char*, ScoringMatrix*, int);
+ void ScoringMatrixInitialize(ScoringMatrix*);
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch
new file mode 100644
index 000000000000..993f6a554662
--- /dev/null
+++ b/sci-biology/bfast/files/bfast-0.7.0a-autotools.patch
@@ -0,0 +1,41 @@
+--- a/configure.ac
++++ b/configure.ac
+@@ -8,7 +8,7 @@
+ AC_INIT([bfast],[0.7.0a],[bfast-help@lists.sourceforge.net],[bfast])
+ AC_COPYRIGHT([See LICENSE for copyright information.])
+ AC_CONFIG_AUX_DIR(config)
+-AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects])
++AM_INIT_AUTOMAKE([dist-bzip2 subdir-objects serial-tests])
+ AC_CONFIG_SRCDIR([config.h.in])
+ AC_CONFIG_HEADERS([config.h])
+ 
+@@ -21,10 +21,10 @@
+ 
+ AC_PROG_INSTALL
+ AC_GNU_SOURCE
++AC_SYS_LARGEFILE
+ 
+ # set CFLAGS and CXXFLAGS
+-default_CFLAGS="-Wall -g -O2 -pthread";
+-extended_CFLAGS="";# "-m64 -D_FILE_OFFSET_BITS=64";
++default_CFLAGS="-Wall -pthread"
+ 
+ # Define some variables
+ GITREV="Revision: undefined$";
+@@ -42,7 +42,7 @@
+ 					AC_DEFINE(HAVE_LIBBZ2, 1, [Define to 1 if you have the <bzlib.h> header file.])], 
+ 					AC_MSG_ERROR("could not find the bzlib library.  Please use --disable-bzlib if you wish to disable bzlib support."))])
+ 
+-CFLAGS="${default_CFLAGS} ${extended_CFLAGS}";
++CFLAGS="${CFLAGS} ${default_CFLAGS} ${extended_CFLAGS}";
+ 
+ # Enable large file support; disable with --disable-largefile
+ AC_SYS_LARGEFILE
+--- a/Makefile.am
++++ b/Makefile.am
+@@ -16,5 +16,4 @@
+ 
+ SUBDIRS = bfast butil scripts tests
+ 
+-docdir = ${datadir}/doc/${PACKAGE}
+ dist_doc_DATA = LICENSE manual/bfast-book.pdf
diff --git a/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch
new file mode 100644
index 000000000000..f4dd64e75cac
--- /dev/null
+++ b/sci-biology/bfast/files/bfast-0.7.0a-test-sourcing.patch
@@ -0,0 +1,79 @@
+--- a/tests/test.cleanup.sh
++++ b/tests/test.cleanup.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Cleaning up files.";
+ 
+--- a/tests/test.diff.sh
++++ b/tests/test.diff.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ #error()
+ #{
+--- a/tests/test.fasta2brg.sh
++++ b/tests/test.fasta2brg.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ TMP_DIR="tmp/";
+ 
+ echo "      Building a reference genome.";
+--- a/tests/test.index.sh
++++ b/tests/test.index.sh
+@@ -1,5 +1,5 @@
+ #!/bin/sh 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Building an index.";
+ 
+--- a/tests/test.initialize.sh
++++ b/tests/test.initialize.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Initializing data for tests.";
+ 
+--- a/tests/test.localalign.sh
++++ b/tests/test.localalign.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Running local alignment.";
+ 
+--- a/tests/test.match.sh
++++ b/tests/test.match.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Finding matches.";
+ 
+--- a/tests/test.postprocess.sh
++++ b/tests/test.postprocess.sh
+@@ -1,6 +1,6 @@
+ #!/bin/sh
+ 
+-. test.definitions.sh
++. ./test.definitions.sh
+ 
+ echo "      Running postprocessing.";
+