[gentoo-commits] proj/sci:master commit in: sci-biology/erpin/, sci-biology/erpin/files/

[gentoo-commits] proj/sci:master commit in: sci-biology/erpin/, sci-biology/erpin/files/

[Jakov Smolić]

commit:     f8b429d596992ff8426674833a582610562d198e
Author:     Jakov Smolic <jakov.smolic <AT> sartura <DOT> hr>
AuthorDate: Sat Feb 20 21:17:59 2021 +0000
Commit:     Jakov Smolić <jakov.smolic <AT> sartura <DOT> hr>
CommitDate: Sat Feb 20 21:57:41 2021 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=f8b429d5

sci-biology/erpin: Port to EAPI 7

Closes: https://bugs.gentoo.org/755092
Signed-off-by: Jakov Smolic <jakov.smolic <AT> sartura.hr>

 sci-biology/erpin/erpin-5.5b.ebuild                | 14 +++---
 .../erpin/files/erpin-5.5b-fno-common.patch        | 55 ++++++++++++++++++++++
 2 files changed, 63 insertions(+), 6 deletions(-)

diff --git a/sci-biology/erpin/erpin-5.5b.ebuild b/sci-biology/erpin/erpin-5.5b.ebuild
index be821cf62..448e5d3aa 100644
--- a/sci-biology/erpin/erpin-5.5b.ebuild
+++ b/sci-biology/erpin/erpin-5.5b.ebuild
@@ -1,7 +1,7 @@
 # Copyright 1999-2021 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
-EAPI=5
+EAPI=7
 
 inherit toolchain-funcs
 
@@ -15,17 +15,19 @@ SRC_URI="
 
 LICENSE="all-rights-reserved"
 SLOT="0"
-IUSE=""
 KEYWORDS="~amd64 ~x86"
 
 DEPEND="!sys-cluster/maui" # file collision
-RDEPEND=""
+RDEPEND="${DEPEND}"
 
 S="${WORKDIR}"
 
+PATCHES=( "${FILESDIR}"/${P}-fno-common.patch )
+
 src_prepare() {
-	rm -f erpin${PV}.serv/{bin,lib}/* || die
-	rm -f ErpinBatch.${ERPIN_BATCH_V}/erpin* || die
+	default
+	rm erpin${PV}.serv/{bin,lib}/* || die
+	rm ErpinBatch.${ERPIN_BATCH_V}/erpin* || die
 	find -name '*.mk' | xargs sed -i \
 		-e 's/strip $@/echo skipping strip $@/' \
 		-e '/CFLAGS =/ d' \
@@ -44,6 +46,6 @@ src_install() {
 	insinto /usr/share/${PN}
 	doins -r erpin${PV}.serv/scripts ErpinBatch.${ERPIN_BATCH_V}
 	exeinto /usr/share/${PN}
-	newexe "${FILESDIR}/erpincommand-${PV}.pl" erpincommand
+	newexe "${FILESDIR}"/erpincommand-${PV}.pl erpincommand
 	dodoc erpin${PV}.serv/doc/doc*.pdf
 }

diff --git a/sci-biology/erpin/files/erpin-5.5b-fno-common.patch b/sci-biology/erpin/files/erpin-5.5b-fno-common.patch
new file mode 100644
index 000000000..bd38aacca
--- /dev/null
+++ b/sci-biology/erpin/files/erpin-5.5b-fno-common.patch
@@ -0,0 +1,55 @@
+--- a/erpin5.5b.serv/include/rnaIV.h
++++ b/erpin5.5b.serv/include/rnaIV.h
+@@ -178,10 +178,10 @@ typedef struct {
+   double  *vals;
+   } Histo;
+ 
+-Histo  MainMaskEvals;             /* histogramme des E-values des detections */
++extern Histo  MainMaskEvals;             /* histogramme des E-values des detections */
+                                                       /* du masque principal */
+-Histo  MainMaskDetects;    /* histogramme des detections du masque principal */
+-Map    MainMaskMap;       /* pour l'etalonnage de l'axe de 'MainMaskDetects' */
++extern Histo  MainMaskDetects;    /* histogramme des detections du masque principal */
++extern Map    MainMaskMap;       /* pour l'etalonnage de l'axe de 'MainMaskDetects' */
+ 
+ /*
+ -------------------------------------------------------------------------------
+--- a/erpin5.5b.serv/libsrc/dhisto.c
++++ b/erpin5.5b.serv/libsrc/dhisto.c
+@@ -36,6 +36,9 @@ void   AddToDetectsHisto(double x);
+ void   PrintHisto(Histo hist, char *filename);
+ Histo  ReadHisto(char *filename);
+ void   PrintScoresHisto(Context *ctxt);
++Histo MainMaskDetects;
++Histo MainMaskEvals;
++Map   MainMaskMap;
+ 
+ /*=============================================================================
+  InitDetectsHisto(): Initialise l'histogramme des detections gerees par 'ctxt'.
+@@ -44,9 +47,6 @@ void   PrintScoresHisto(Context *ctxt);
+ 
+ void InitDetectsHisto(Context *ctxt)
+ {
+-  extern Histo MainMaskDetects;
+-  extern Histo MainMaskEvals;
+-  extern Map   MainMaskMap;
+   
+   MainMaskDetects = SetupHist(ctxt->mask->threshold, MainMaskEvals.hmax,
+                               DELTA_H, 0);
+@@ -63,8 +63,6 @@ void InitDetectsHisto(Context *ctxt)
+ 
+ void AddToDetectsHisto(double x)
+ {
+-  extern Histo MainMaskDetects;
+-  extern Map   MainMaskMap;
+   int index;
+ 
+   if (x > MainMaskDetects.hmin && x < MainMaskDetects.hmax)
+@@ -132,7 +130,6 @@ Histo ReadHisto(char *filename)
+ 
+ void PrintScoresHisto(Context *ctxt)
+ {
+-  extern Histo MainMaskDetects;
+ 
+   if (ctxt->hist == ON)
+   {