git: 04a6a89cf6ea - main - science/afni: update to 24.0.09
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Date: Sun, 03 Mar 2024 17:09:45 UTC
The branch main has been updated by fernape:
URL: https://cgit.FreeBSD.org/ports/commit/?id=04a6a89cf6ea0a1c3a54996a049ef6a489b866a5
commit 04a6a89cf6ea0a1c3a54996a049ef6a489b866a5
Author: Fernando Apesteguía <fernape@FreeBSD.org>
AuthorDate: 2024-02-29 08:14:46 +0000
Commit: Fernando Apesteguía <fernape@FreeBSD.org>
CommitDate: 2024-03-03 17:08:15 +0000
science/afni: update to 24.0.09
---
science/afni/Makefile | 2 +-
science/afni/distinfo | 6 +++---
science/afni/files/patch-Makefile.INCLUDE | 14 +++++++-------
.../afni/files/patch-crorden_dcm2niix__console_makefile | 12 ++++++------
science/afni/pkg-plist | 1 +
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