biology/migrate: Update to 5.0.5

- Switch to DISTVERSION
- Add license
- Pet portlint, portclippy and portfmt
- Take maintainership

ChangeLog: https://peterbeerli.com/programs/migrate/distribution_4.x/HISTORY

3 files changed, 27 insertions, 31 deletions

diff --git a/biology/migrate/Makefile b/biology/migrate/Makefile
index 6d17d8438450..1f04a5ee0923 100644
--- a/biology/migrate/Makefile
+++ b/biology/migrate/Makefile
@@ -1,30 +1,32 @@
 PORTNAME=	migrate
-PORTVERSION=	3.6.11
-PORTREVISION=	1
+DISTVERSION=	5.0.5
 CATEGORIES=	biology
-MASTER_SITES=	http://popgen.sc.fsu.edu/currentversions/
+MASTER_SITES=	https://peterbeerli.com/migrate-html5/download_version4/
 DISTNAME=	${PORTNAME}-${PORTVERSION}.src
 
-MAINTAINER=	ports@FreeBSD.org
+MAINTAINER=	eduardo@FreeBSD.org
 COMMENT=	Program to estimate population sizes and migration rates
 WWW=		https://popgen.sc.fsu.edu/Migrate/Migrate-n.html
 
-BROKEN_armv6=		fails to build: make[2]: cannot open makefile
-BROKEN_armv7=		fails to build: make[2]: cannot open makefile
-BROKEN_mips=		fails to build: make[2]: cannot open makefile
-BROKEN_riscv64=		fails to build: make[2]: cannot open makefile
+LICENSE=	MIT
+LICENSE_FILE=	${WRKSRC}/../README
 
-WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
-EXTRACT_AFTER_ARGS=--exclude zlib
+# Waiting on build reports, 2024-03-27
+#BROKEN_armv6=	fails to build: make[2]: cannot open makefile
+#BROKEN_armv7=	fails to build: make[2]: cannot open makefile
+#BROKEN_mips=	fails to build: make[2]: cannot open makefile
+#BROKEN_riscv64=	fails to build: make[2]: cannot open makefile
 
 GNU_CONFIGURE=	yes
 CONFIGURE_ENV=	ac_cv_prog_GMAKE="${MAKE}"
-MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu \
-		-DPRETTY -lstdc++"
+MAKE_ARGS=	PRETTYCFLAGS="${CFLAGS} -DNOJPEG -DNOZLIB -DNOPNG -Iharu -DPRETTY -lstdc++"
 
 CONFLICTS_INSTALL=	py*-sqlalchemy-migrate # bin/migrate
 
-PORTDOCS=	HISTORY README README_PARALLEL_GENERAL ${PORTNAME}.html
+EXTRACT_AFTER_ARGS=	--exclude zlib
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}/src
+
+PORTDOCS=	${PORTNAME}.html HISTORY README README_PARALLEL_GENERAL
 PORTEXAMPLES=	*
 
 OPTIONS_DEFINE=		DOCS EXAMPLES THREAD
@@ -33,7 +35,7 @@ THREAD_ALL_TARGET=	thread
 
 post-patch:
 	@${REINPLACE_CMD} -e 's|="-O "|="$$CFLAGS"|g' ${WRKSRC}/configure
-	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/definitions.h
+	@${REINPLACE_CMD} -e '/PRETTY$$/d' ${WRKSRC}/src/definitions.h
 	@${REINPLACE_CMD} -e 's|-O3||g' ${WRKSRC}/haru/makefile.gcc
 
 do-install:
diff --git a/biology/migrate/distinfo b/biology/migrate/distinfo
index 6d0ec05f83bb..498a5f72dd3d 100644
--- a/biology/migrate/distinfo
+++ b/biology/migrate/distinfo
@@ -1,2 +1,3 @@
-SHA256 (migrate-3.6.11.src.tar.gz) = a9ba06a4e995a45b8d04037f5f2da23e1fe64a2f3565189bdd50c62c6fe01fb8
-SIZE (migrate-3.6.11.src.tar.gz) = 27809896
+TIMESTAMP = 1711535851
+SHA256 (migrate-5.0.5.src.tar.gz) = 43d456f2432c0ec77ad33877f184d3b4b36f61e416f8fffa51077768df91ea51
+SIZE (migrate-5.0.5.src.tar.gz) = 4746835
diff --git a/biology/migrate/files/patch-Makefile.in b/biology/migrate/files/patch-Makefile.in
index 814875b4b1a8..0119cb51c758 100644
--- a/biology/migrate/files/patch-Makefile.in
+++ b/biology/migrate/files/patch-Makefile.in
@@ -1,18 +1,11 @@
---- Makefile.in.orig	2015-06-24 02:57:05 UTC
+--- Makefile.in.orig	2024-03-27 11:13:06 UTC
 +++ Makefile.in
-@@ -89,7 +89,7 @@ PAPERFORMAT       = @PAPERFORMAT@
- # -DINTEGRATEDLIKE may be used to get a marginal likelihood different to the current thermodynamic integr and harmonic mean [does not work]
- # -UEP calculates unique event polymorphism [not checked in a long time -- most likely does not work]
- NEWSTUFF          =  -DNEXUSTREE
--COMMONFLAGS       = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
-+COMMONFLAGS       = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
+@@ -94,7 +94,7 @@ NEWSTUFF          = 
+ # -DTHERMOCHECK prints heated likelihood into mixfile (needs to be added the parmfile)
+ #NEWSTUFF          = -DNEWVERSION
+ NEWSTUFF          = 
+-COMMONFLAGS       = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DNEXUSTREE -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
++COMMONFLAGS       = $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DNEXUSTREE -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT) $(HARDWARECFLAGS)
+ VALGRINDCOMMONFLAGS       = $(ARCH) $(MACOSVERSION) $(NEWSTUFF) $(HAVE_ZNZ) -DHIGHBITS -DHAVE_CONFIG_H -DHAVE_MALLOCWRAP $(CFLAGS_MT)
  #
  # combine the common flags with the version number and subversion number
- COMMONVFLAGS      =  $(COMMONFLAGS)  -DMIGRATESUBVERSION=\"\\\"$(MIGRATESUBVERSION)\\\"\" 
-@@ -544,4 +544,4 @@ parallel_short_test::
- #----------------------------------------------------------------
- # BEAGLE
- beagle:
--	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"
-\ No newline at end of file
-+	$(MAKE) $(NAME) "CFLAGS = $(DEBUGCFLAGS)  $(BEAGLEFLAGS) $(PRETTYCFLAGS)" "LIBS = $(PDFLIB) $(LIBS)"  "LDFLAGS =$(LDFLAGS) $(EXCEPTIONS) `pkg-config /Users/beerli/src/beagle-lib/hmsbeagle-1.0.pc --cflags --libs` -framework OpenCL"