science/afni: update to 24.0.09

5 files changed, 18 insertions, 17 deletions

diff --git a/science/afni/Makefile b/science/afni/Makefile
index 3cf61a264707..1ec4d0fe1f08 100644
--- a/science/afni/Makefile
+++ b/science/afni/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=		afni
 DISTVERSIONPREFIX=	AFNI_
-DISTVERSION=		24.0.08
+DISTVERSION=		24.0.09
 CATEGORIES=		science biology graphics perl5 python
 
 MAINTAINER=	fernape@FreeBSD.org
diff --git a/science/afni/distinfo b/science/afni/distinfo
index 507cf615a19f..bcabddda8027 100644
--- a/science/afni/distinfo
+++ b/science/afni/distinfo
@@ -1,3 +1,3 @@
-TIMESTAMP = 1708694522
-SHA256 (afni-afni-AFNI_24.0.08_GH0.tar.gz) = e71066f7a1539e01e17004b2bbd09e82b241e7044b3aa82ab1f77cfb8c591f26
-SIZE (afni-afni-AFNI_24.0.08_GH0.tar.gz) = 52917832
+TIMESTAMP = 1709194473
+SHA256 (afni-afni-AFNI_24.0.09_GH0.tar.gz) = 0ea8350ef4ef49563c29f761e3d7594d7685a9851267d7f6a0d76d9d591a1acc
+SIZE (afni-afni-AFNI_24.0.09_GH0.tar.gz) = 52934713
diff --git a/science/afni/files/patch-Makefile.INCLUDE b/science/afni/files/patch-Makefile.INCLUDE
index de01b18022f6..a892005530a3 100644
--- a/science/afni/files/patch-Makefile.INCLUDE
+++ b/science/afni/files/patch-Makefile.INCLUDE
@@ -1,6 +1,6 @@
---- Makefile.INCLUDE.orig	2021-09-01 13:56:01 UTC
+--- Makefile.INCLUDE.orig	2024-02-29 01:05:45 UTC
 +++ Makefile.INCLUDE
-@@ -99,7 +99,7 @@ MISC    = AFNI_atlas_spaces.niml AFNI.Xdefaults AFNI.a
+@@ -105,7 +105,7 @@ MISC    = $(MISC_TEXT) 3d*.lib
  ## AFNI package, but included because they are useful.  Some of
  ## them are Open Source programs, not from the AFNI group at all.
  
@@ -9,7 +9,7 @@
  
  # mpegtoppm in above list
  
-@@ -112,7 +112,7 @@ EXTRAS   = cjpeg djpeg whirlgif myget rmz aiv mycat qu
+@@ -118,7 +118,7 @@ PROGS_1  = afni to3d from3d 3dclust nsize 3dinfo 3dmer
  PROGS_1  = afni to3d from3d 3dclust nsize 3dinfo 3dmerge count                \
             sfim tfim imrotate imreg imstat 3dnvals                            \
             fim2 imand immask imdump imaver 3dhistog 3daxialize                \
@@ -18,7 +18,7 @@
             waver 3dnewid 3dcalc ccalc imcalc 1dmatcalc 3drefit 3dbucket       \
             3dNLfim 3dTSgen plugout_tt plugout_ijk                             \
             3dMannWhitney 3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna       \
-@@ -125,7 +125,7 @@ PROGS_2  = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
+@@ -131,7 +131,7 @@ PROGS_2  = 3dTshift 3dDetrend 1dfft 1dcat 3drename 1dn
             3dfim+ imcutup imcat 3dWinsor 3dZeropad 3dTagalign                 \
             3dMean 3dAttribute cat_matvec 3dOverlap 3dClipLevel 3dZregrid      \
             3dEntropy 3ddelay 3dRowFillin 1dgrayplot 3dToutcount 1dsum         \
@@ -27,7 +27,7 @@
             3dGetrow 3dTcorrelate 3dcopy Vecwarp 3dCM fdrval                   \
             3dAFNItoANALYZE 3dAFNItoNIFTI                                      \
             3dAutoTcorrelate 3dFDR rtfeedme 3dAutomask 3dBrickStat             \
-@@ -148,7 +148,7 @@ PROGS_3  = 3dAnhist 3dAFNIto3D 3dWarp nicat           
+@@ -154,7 +154,7 @@ PROGS_4  = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPer
  PROGS_4  = 3dBlurInMask 3dRank 3dFFT 1dgenARMA11 3dPeriodogram 1dAstrip       \
             3dLocalPV 3dBandpass 3dSetupGroupInCorr 3dGroupInCorr 3dTcorr1D    \
             3dClustSim 3dRetinoPhase 3dMaskToASCII 3dttest++ 3dDTtoDWI         \
@@ -36,7 +36,7 @@
             1dCorrelate 3dNwarpCalc dicom_hinfo apsearch 1dBport               \
             3dNormalityTest 3dmask_tool FIRdesign help_format 2perm            \
             3dClustCount column_cat 3dUnifize 3dNwarpCat 3dQwarp 3dLocalHistog \
-@@ -175,7 +175,7 @@ PROGRAMS = $(PROGS_1) $(PROGS_2) $(PROGS_3) $(PROGS_4)
+@@ -182,7 +182,7 @@ PROGRAMS_NOPLUG =                                     
  PROGRAMS_NOPLUG =                                                             \
          afni to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate      \
          imreg imstat count fim2 imand immask imdump imaver 3dhistog imupsam   \
@@ -45,7 +45,7 @@
          3dcalc ccalc imcalc 2dImReg 3dmaskave adwarp fdrval 3dMannWhitney     \
          3dWilcoxon 3dKruskalWallis 3dFriedman 3dRegAna imstack byteorder      \
          3dDeconvolve 3dTcat 3drotate 3dvolreg 1dplot 24swap 3dTsmooth RSFgen  \
-@@ -213,7 +213,7 @@ PROGRAMS_NOPLUG =                                     
+@@ -221,7 +221,7 @@ PROGRAMS_EXE =                                        
  PROGRAMS_EXE =                                                                \
          afni.exe to3d from3d 3dclust nsize 3dinfo 3dmerge sfim tfim imrotate  \
          imreg imstat 3dnvals count fim2 imand immask imdump imaver 3dhistog   \
diff --git a/science/afni/files/patch-crorden_dcm2niix__console_makefile b/science/afni/files/patch-crorden_dcm2niix__console_makefile
index 284366c03452..ad2ce657740c 100644
--- a/science/afni/files/patch-crorden_dcm2niix__console_makefile
+++ b/science/afni/files/patch-crorden_dcm2niix__console_makefile
@@ -1,4 +1,4 @@
---- crorden/dcm2niix_console/makefile.orig	2023-08-17 23:49:49 UTC
+--- crorden/dcm2niix_console/makefile.orig	2024-02-29 01:05:45 UTC
 +++ crorden/dcm2niix_console/makefile
 @@ -1,5 +1,5 @@
  # Regular use
@@ -7,16 +7,16 @@
  
  # Debugging
  #CFLAGS=-g
-@@ -35,7 +35,7 @@ ifneq ($(OS),Windows_NT)
- 		#CFLAGS= -O3
+@@ -34,7 +34,7 @@ ifneq ($(OS),Windows_NT)
+ 		#CFLAGS=-dead_strip -O3
  		# ponder -sectcreate later [rickr]
  		# CFLAGS=-O3 -sectcreate __TEXT __info_plist Info.plist
--		CFLAGS=-O3
-+		CXXFLAGS=-O3
+-		CFLAGS= -O3
++		CXXFLAGS= -O3
  		#Apple notarization requires a Info.plist
  		# For .app bundles, the Info.plist is a separate file, for executables it is appended as a section
  		#you can check that the Info.plist section has been inserted with either of these commands
-@@ -46,4 +46,4 @@ ifneq ($(OS),Windows_NT)
+@@ -45,4 +45,4 @@ all:
  	endif
  endif
  all:
diff --git a/science/afni/pkg-plist b/science/afni/pkg-plist
index 9638c0d23c3f..38a698402448 100644
--- a/science/afni/pkg-plist
+++ b/science/afni/pkg-plist
@@ -837,6 +837,7 @@ lib/afni/plug_zeropad.so
 %%PYTHON_SITELIBDIR%%/afnipy/lib_apqc_stats_dset.py
 %%PYTHON_SITELIBDIR%%/afnipy/lib_apqc_tcsh.py
 %%PYTHON_SITELIBDIR%%/afnipy/lib_b0_corr.py
+%%PYTHON_SITELIBDIR%%/afnipy/lib_cbar_pbar.py
 %%PYTHON_SITELIBDIR%%/afnipy/lib_cdiflist.py
 %%PYTHON_SITELIBDIR%%/afnipy/lib_csv.py
 %%PYTHON_SITELIBDIR%%/afnipy/lib_decay_timing.py