git: ab62a2dc0745 - main - science/nifticlib: Update to 3.0.1

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From: Jason W. Bacon <jwb_at_FreeBSD.org>
Date: Sat, 05 Sep 2026 18:26:57 UTC
The branch main has been updated by jwb:

URL: https://cgit.FreeBSD.org/ports/commit/?id=ab62a2dc0745bcd7e6f85810be7c9827d78bf85a

commit ab62a2dc0745bcd7e6f85810be7c9827d78bf85a
Author:     Jason W. Bacon <jwb@FreeBSD.org>
AuthorDate: 2026-09-05 18:23:55 +0000
Commit:     Jason W. Bacon <jwb@FreeBSD.org>
CommitDate: 2026-09-05 18:23:55 +0000

    science/nifticlib: Update to 3.0.1
    
    Numerous fixes and enhancements since 2.0.0
    Changes: https://github.com/NIFTI-Imaging/nifti_clib/commits/master/
    
    No longer conflicts with science/afni
    Release to ports@
    
    Reported by:    Repology
---
 science/nifticlib/Makefile                      |  15 ++-
 science/nifticlib/distinfo                      |   5 +-
 science/nifticlib/files/patch-Makefile          | 160 +++++++-----------------
 science/nifticlib/files/patch-examples-Makefile |   8 --
 science/nifticlib/files/patch-utils-Makefile    |  10 --
 science/nifticlib/pkg-plist                     |   8 +-
 6 files changed, 58 insertions(+), 148 deletions(-)

diff --git a/science/nifticlib/Makefile b/science/nifticlib/Makefile
index dae7842e1770..458f1d532e1d 100644
--- a/science/nifticlib/Makefile
+++ b/science/nifticlib/Makefile
@@ -1,26 +1,25 @@
 PORTNAME=	nifticlib
-PORTVERSION=	2.0.0
-PORTREVISION=	2
+DISTVERSIONPREFIX=	v
+DISTVERSION=	3.0.1
 CATEGORIES=	science graphics
-MASTER_SITES=	SF/niftilib/nifticlib/nifticlib_2_0_0
 
-MAINTAINER=	jwb@FreeBSD.org
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	Neuroimaging Informatics Technology Initiative data format
 WWW=		https://nifti.nimh.nih.gov/
 
 LICENSE=	PD
 
 USES=		gmake
+USE_GITHUB=	yes
+GH_ACCOUNT=	NIFTI-Imaging
+GH_PROJECT=	nifti_clib
 
-# AFNI currently has nifti embedded in the distfile and installs the
-# nifti bins by itself.
-CONFLICTS=	afni dbh
+CONFLICTS=	dbh	# dbh.h
 
 CFLAGS+=	-fPIC
 MAKE_JOBS_UNSAFE=	yes
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/* ${STAGEDIR}${PREFIX}/bin
 	${INSTALL_DATA} ${WRKSRC}/lib/*.a ${STAGEDIR}${PREFIX}/lib
 	${INSTALL_DATA} ${WRKSRC}/include/*.h ${STAGEDIR}${PREFIX}/include
 	${INSTALL_MAN} ${FILESDIR}/nifticlib.1 ${STAGEDIR}${PREFIX}/share/man/man1
diff --git a/science/nifticlib/distinfo b/science/nifticlib/distinfo
index a1e25afaa9ce..7a7f61fe7b5b 100644
--- a/science/nifticlib/distinfo
+++ b/science/nifticlib/distinfo
@@ -1,2 +1,3 @@
-SHA256 (nifticlib-2.0.0.tar.gz) = a3e988e6a32ec57833056f6b09f940c69e79829028da121ff2c5c6f7f94a7f88
-SIZE (nifticlib-2.0.0.tar.gz) = 258491
+TIMESTAMP = 1788612382
+SHA256 (NIFTI-Imaging-nifti_clib-v3.0.1_GH0.tar.gz) = 868b611b5f8a3a73809436c9072db50db4975615905f0bd5fb7b1432e6d24b37
+SIZE (NIFTI-Imaging-nifti_clib-v3.0.1_GH0.tar.gz) = 438871
diff --git a/science/nifticlib/files/patch-Makefile b/science/nifticlib/files/patch-Makefile
index 8a3134ae00bc..80657470ca0d 100644
--- a/science/nifticlib/files/patch-Makefile
+++ b/science/nifticlib/files/patch-Makefile
@@ -1,6 +1,6 @@
---- Makefile.orig	2010-07-20 17:18:58 UTC
+--- Makefile.orig	2026-09-05 12:24:46 UTC
 +++ Makefile
-@@ -17,21 +17,21 @@ TARFILE_NAME	=	nifticlib-2.0.0
+@@ -15,21 +15,21 @@ TARFILE_NAME	=	nifticlib-2.0.0
  
  
  ## Compiler  defines
@@ -8,145 +8,73 @@
 -CC		=	gcc
 -AR		=	ar
 -RANLIB  = ranlib
--DEPENDFLAGS	=	-MM
--GNU_ANSI_FLAGS	= 	-Wall -ansi -pedantic
--ANSI_FLAGS	= 	${GNU_ANSI_FLAGS}
--CFLAGS		=	$(ANSI_FLAGS)
 +cc		?=	gcc
 +CC		?=	gcc
 +AR		?=	ar
 +RANLIB  	?=	ranlib
-+DEPENDFLAGS	?=	-MM
-+GNU_ANSI_FLAGS	?= 	-ansi -pedantic
-+ANSI_FLAGS	+= 	${GNU_ANSI_FLAGS}
+ DEPENDFLAGS	=	-MM
+ GNU_ANSI_FLAGS	= 	-Wall -ansi -pedantic
+ ANSI_FLAGS	= 	${GNU_ANSI_FLAGS}
+-CFLAGS		=	$(ANSI_FLAGS)
 +CFLAGS		+=	$(ANSI_FLAGS)
  
  ## Command defines
- ## gmake does not work on MacOSX or some versions of linux MAKE  = gmake 
+ ## gmake does not work on MacOSX or some versions of linux MAKE  = gmake
 -RM		=	rm
 -MV		=	mv
 -CP		=	cp
--TAR		=	tar
+-TAR		=	/usr/local/pkg/gnu/bin/tar
 +RM		?=	rm
 +MV		?=	mv
 +CP		?=	cp
-+TAR		?=	tar
++TAR		?=	/usr/local/pkg/gnu/bin/tar
  
  
  ## Installation
-@@ -41,9 +41,9 @@ INSTALL_INC_DIR	=	include
+@@ -39,9 +39,9 @@ INSTALL_INC_DIR	=	include
  
  
  ## Zlib defines
 -ZLIB_INC	=	-I/usr/include
 -ZLIB_PATH	=	-L/usr/lib
--ZLIB_LIBS 	= 	$(ZLIB_PATH) -lm -lz 
+-ZLIB_LIBS 	= 	$(ZLIB_PATH) -lm -lz
 +ZLIB_INC	?=	-I/usr/include
 +ZLIB_PATH	?=	-L/usr/lib
-+ZLIB_LIBS 	?= 	$(ZLIB_PATH) -lm -lz 
++ZLIB_LIBS 	?= 	$(ZLIB_PATH) -lm -lz
  
  ##############################################################
  # platform specific redefines (to use, set ARCH appropriately)
-@@ -116,33 +116,33 @@ clean_all: clean regress_clean_all insta
- 
- znz:
- 	echo "arch is $(ARCH)"
--	(cd $(ZNZ); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(ZNZ) depend lib
- 	@echo " ----------- $(ZNZ) build completed."
- 	@echo ""
- 
- nifti:	znz
--	(cd $(NIFTI); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(NIFTI) depend lib
- 	@echo " ----------- $(NIFTI) build completed."
- 	@echo ""
- 
- nifticdf:nifti
--	(cd $(NIFTICDF); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(NIFTICDF) depend lib
- 	@echo " ----------- $(NIFTICDF) build completed."
- 	@echo ""
- 
- fslio:	nifti
--	(cd $(FSLIO); $(MAKE) depend; $(MAKE) lib;)
-+	$(MAKE) -C $(FSLIO) depend lib
- 	@echo " ----------  $(FSLIO) build completed."
- 	@echo ""
- 
- example:nifti
--	(cd $(EXAMPLES); $(MAKE) all;)
-+	$(MAKE) -C $(EXAMPLES) all
- 	@echo Example programs built.
- 	@echo ""
- 
- 
- utils:  nifti nifticdf
--	(cd $(UTILS); $(MAKE) all;)
-+	$(MAKE) -C $(UTILS) all
- 	@echo Utility programs built.
- 	@echo ""
- 
-@@ -152,7 +152,7 @@ doc:
- 	@echo ""
- 
- regress_data:
--	(cd $(TESTING); $(MAKE) regress_data 'RM=$(RM)' 'TAR=$(TAR)'; )
-+	$(MAKE) -C $(TESTING) regress_data 'RM=$(RM)' 'TAR=$(TAR)'
- 	@echo ""
- 	@echo Regression testing data installed.
- 	@echo See Testing/README_regress for details.
-@@ -167,25 +167,25 @@ $(INSTALL_INC_DIR):
- $(INSTALL_LIB_DIR):
- 	mkdir -p $@
- 
--znz_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+znz_install: znz $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(ZNZ)/*.a $(INSTALL_LIB_DIR); $(CP) $(ZNZ)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(ZNZ) installed."
- 	@echo ""
- 
--nifti_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+nifti_install: nifti $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(NIFTI)/*.a $(INSTALL_LIB_DIR); $(CP) $(NIFTI)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(NIFTI) installed."
- 	@echo ""
- 
--nifticdf_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+nifticdf_install: nifticdf $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(NIFTICDF)/*.a $(INSTALL_LIB_DIR); $(CP) $(NIFTICDF)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(NIFTI) installed."
- 	@echo ""
- 
--fslio_install: $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
-+fslio_install: fslio $(INSTALL_INC_DIR) $(INSTALL_LIB_DIR)
- 	($(CP) $(FSLIO)/*.a $(INSTALL_LIB_DIR); $(CP) $(FSLIO)/*.h $(INSTALL_INC_DIR);)
- 	$(RANLIB) $(INSTALL_LIB_DIR)/*.a
- 	@echo " $(FSLIO) installed."
-@@ -212,19 +212,19 @@ fslio_clean:
- 	(cd $(FSLIO); $(RM) -f *.o *.a core; $(RM) -f depend.mk;)
- 
- examples_clean:
--	(cd $(EXAMPLES); $(MAKE) clean;)
-+	$(MAKE) -C $(EXAMPLES) clean
- 
- utils_clean:
--	(cd $(UTILS); $(MAKE) clean;)
-+	$(MAKE) -C $(UTILS) clean
- 
- doc_clean:
- 	($(RM) -fr docs/html;)
- 
- regress_clean:
--	(cd $(TESTING); $(MAKE) regress_clean; )
-+	$(MAKE) -C $(TESTING) regress_clean
+@@ -71,24 +71,24 @@ endif
+ #################################################################
+ 
+ ## ZNZ defines
+-ZNZ_INC		=	-I../$(ZNZ)
+-ZNZ_PATH	=	-L../$(ZNZ)
+-ZNZ_LIBS	=	$(ZNZ_PATH)  -lznz
++ZNZ_INC		?=	-I../$(ZNZ)
++ZNZ_PATH	?=	-L../$(ZNZ)
++ZNZ_LIBS	?=	$(ZNZ_PATH)  -lznz
+ USEZLIB         =       -DHAVE_ZLIB
+ 
+ ## NIFTI defines
+-NIFTI_INC	=	-I../$(NIFTI)
+-NIFTI_PATH	=	-L../$(NIFTI)
++NIFTI_INC	?=	-I../$(NIFTI)
++NIFTI_PATH	?=	-L../$(NIFTI)
+ NIFTI_LIBS	=	$(NIFTI_PATH) -lniftiio
+ 
+ ## NIFTICDF defines
+-NIFTICDF_INC	=	-I../$(NIFTICDF)
+-NIFTICDF_PATH	=	-L../$(NIFTICDF)
++NIFTICDF_INC	?=	-I../$(NIFTICDF)
++NIFTICDF_PATH	?=	-L../$(NIFTICDF)
+ NIFTICDF_LIBS	=	$(NIFTICDF_PATH) -lnifticdf
+ 
+ ## FSLIO defines
+-FSLIO_INC	=	-I../$(FSLIO)
+-FSLIO_PATH	=	-L../$(FSLIO)
++FSLIO_INC	?=	-I../$(FSLIO)
++FSLIO_PATH	?=	-L../$(FSLIO)
+ FSLIO_LIBS	=	$(FSLIO_PATH) -lfslio
  
- regress_clean_all:
--	(cd $(TESTING); $(MAKE) regress_clean_all; )
-+	$(MAKE) -C $(TESTING) regress_clean_all
  
- tar:
- 	(cd .. ; ln -s $(THIS_DIR) ${TARFILE_NAME} ; \
diff --git a/science/nifticlib/files/patch-examples-Makefile b/science/nifticlib/files/patch-examples-Makefile
deleted file mode 100644
index 4f85e5b8decf..000000000000
--- a/science/nifticlib/files/patch-examples-Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
---- examples/Makefile.orig	2009-04-14 14:47:16 UTC
-+++ examples/Makefile
-@@ -1,4 +1,4 @@
--CC	=	gcc
-+CC	?=	gcc
- CFLAGS	=	-ansi -pedantic
- 
- FSLIO_INCS	=	-I../include
diff --git a/science/nifticlib/files/patch-utils-Makefile b/science/nifticlib/files/patch-utils-Makefile
deleted file mode 100644
index d8177559df29..000000000000
--- a/science/nifticlib/files/patch-utils-Makefile
+++ /dev/null
@@ -1,10 +0,0 @@
---- utils/Makefile.orig	2007-05-17 20:18:44 UTC
-+++ utils/Makefile
-@@ -1,5 +1,5 @@
--CC	=	gcc
--CFLAGS	=	-ansi -pedantic
-+CC	?=	gcc
-+CFLAGS	?=	-ansi -pedantic
- 
- FSLIO_INCS	=	-I../include
- NIFTI_INCS	=	-I../include
diff --git a/science/nifticlib/pkg-plist b/science/nifticlib/pkg-plist
index f9d22c74f72b..5d1fe7bd4346 100644
--- a/science/nifticlib/pkg-plist
+++ b/science/nifticlib/pkg-plist
@@ -1,13 +1,13 @@
-@comment Generated by sysutils/genplist
-bin/nifti1_test
-bin/nifti_stats
-bin/nifti_tool
 include/dbh.h
 include/fslio.h
 include/nifti1.h
 include/nifti1_io.h
+include/nifti1_io_version.h
+include/nifti1_tool.h
 include/nifticdf.h
+include/nifticdf_version.h
 include/znzlib.h
+include/znzlib_version.h
 lib/libfslio.a
 lib/libnifticdf.a
 lib/libniftiio.a