brain-mesh-builder: Surface mesh building based on 3-dimensional images

To: pkgsrc-wip-changes%NetBSD.org@localhost
Subject: brain-mesh-builder: Surface mesh building based on 3-dimensional images
From: Jason Bacon <bacon%NetBSD.org@localhost>
Date: Fri, 11 Nov 2022 22:11:07 +0000
Module Name:	pkgsrc-wip
Committed By:	Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By:	outpaddling
Date:		Fri Nov 11 16:11:07 2022 -0600
Changeset:	f38a22d799f9cd247f61446cfb4a517263349d3e

Modified Files:
	Makefile
Added Files:
	brain-mesh-builder/DESCR
	brain-mesh-builder/Makefile
	brain-mesh-builder/PLIST
	brain-mesh-builder/distinfo
	brain-mesh-builder/patches/patch-Makefile
	brain-mesh-builder/patches/patch-inc_globals.h

Log Message:
brain-mesh-builder: Surface mesh building based on 3-dimensional images

To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=f38a22d799f9cd247f61446cfb4a517263349d3e

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

diffstat:
 Makefile                                       |  1 +
 brain-mesh-builder/DESCR                       |  2 +
 brain-mesh-builder/Makefile                    | 35 +++++++++++
 brain-mesh-builder/PLIST                       |  2 +
 brain-mesh-builder/distinfo                    |  7 +++
 brain-mesh-builder/patches/patch-Makefile      | 86 ++++++++++++++++++++++++++
 brain-mesh-builder/patches/patch-inc_globals.h | 14 +++++
 7 files changed, 147 insertions(+)

diffs:
diff --git a/Makefile b/Makefile
index 83cc938e17..24c14bcdd5 100644
--- a/Makefile
+++ b/Makefile
@@ -320,6 +320,7 @@ SUBDIR+=	bowtie
 SUBDIR+=	bowtie2
 SUBDIR+=	bpcscripts
 SUBDIR+=	bpytop
+SUBDIR+=	brain-mesh-builder
 SUBDIR+=	breakpad
 SUBDIR+=	breeze
 SUBDIR+=	breeze-gtk
diff --git a/brain-mesh-builder/DESCR b/brain-mesh-builder/DESCR
new file mode 100644
index 0000000000..8b6ebe4470
--- /dev/null
+++ b/brain-mesh-builder/DESCR
@@ -0,0 +1,2 @@
+DODRI source code files for surface mesh building based on
+3-dimensional image stacks.
diff --git a/brain-mesh-builder/Makefile b/brain-mesh-builder/Makefile
new file mode 100644
index 0000000000..3b86deadf9
--- /dev/null
+++ b/brain-mesh-builder/Makefile
@@ -0,0 +1,35 @@
+# $NetBSD$
+#
+###########################################################
+#                  Generated by fbsd2pkg                  #
+#              Fri Nov 11 12:10:09 CST 2022               #
+###########################################################
+
+# Unknown tool: USE_TOOLS=	gnome
+# Unknown tool: USE_TOOLS=	jpeg
+# Unknown tool: USE_TOOLS=	xorg
+#USE_XORG=	ice sm x11 xext
+#USE_GNOME=	libxml2
+
+DISTNAME=	brain-mesh-builder-1.0
+CATEGORIES=	biology
+MASTER_SITES=	${MASTER_SITE_GITHUB:=hwm2746/}
+GITHUB_TAG=	v.${PKGVERSION_NOREV}
+
+MAINTAINER=	bacon%NetBSD.org@localhost
+HOMEPAGE=	https://github.com/hwm2746/brain-mesh-builder
+COMMENT=	Surface mesh building based on 3-dimensional image stacks
+LICENSE=	gnu-gpl-v3
+
+USE_LANGUAGES=	c c++
+USE_TOOLS+=	gmake
+
+WRKSRC=		${WRKDIR}/${PKGBASE}-${GITHUB_TAG}
+
+post-extract:
+	${RM} ${WRKSRC}/bin/* ${WRKSRC}/obj/*.o ${WRKSRC}/obj/io/*.o
+
+.include "../../graphics/GraphicsMagick/buildlink3.mk"
+# CentOS doesn't have zlib in the base, so uncomment if needed.
+# .include "../../devel/zlib/buildlink3.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/brain-mesh-builder/PLIST b/brain-mesh-builder/PLIST
new file mode 100644
index 0000000000..1bf2238a34
--- /dev/null
+++ b/brain-mesh-builder/PLIST
@@ -0,0 +1,2 @@
+@comment $NetBSD$
+bin/dodri
diff --git a/brain-mesh-builder/distinfo b/brain-mesh-builder/distinfo
new file mode 100644
index 0000000000..a31459da9d
--- /dev/null
+++ b/brain-mesh-builder/distinfo
@@ -0,0 +1,7 @@
+$NetBSD$
+
+BLAKE2s (brain-mesh-builder-1.0.tar.gz) = 0dc3282ca814e4812bf351572a00614c626d25cdca55bfed098ec2ef0128d8a0
+SHA512 (brain-mesh-builder-1.0.tar.gz) = 3669a63047e91f0ed32ad803f48c9a94e34633af653ae84a3c652412248ff27fada7965bed7fb8ff66b4ba677bd83723fd65405f05d949e2353ec18af47b0c63
+Size (brain-mesh-builder-1.0.tar.gz) = 25799712 bytes
+SHA1 (patch-Makefile) = 45cd44b1be32ddc68b730650d457b378e982d8c5
+SHA1 (patch-inc_globals.h) = c0790ee6ea3f764a4cd034f52aee7cd5d151b064
diff --git a/brain-mesh-builder/patches/patch-Makefile b/brain-mesh-builder/patches/patch-Makefile
new file mode 100644
index 0000000000..3af3384561
--- /dev/null
+++ b/brain-mesh-builder/patches/patch-Makefile
@@ -0,0 +1,86 @@
+$NetBSD$
+
+# Support package managers
+
+--- Makefile.orig	2021-04-15 21:30:36 UTC
++++ Makefile
+@@ -1,34 +1,59 @@
++# subdirs
++SRCDIR	= src
++INCDIR	= inc
++OBJDIR	= obj
++BINDIR	= bin
++
+ # Final executable
+-TARGET=dodri
++TARGET	= $(BINDIR)/dodri
+ 
+-# subdirs
+-SRCDIR = src
+-INCDIR = inc
+-OBJDIR = obj
+-BINDIR = bin
++# Using != runs the command immediately, so the actual flags appear
++# in the compile and link commands
++GM_CPP	!= GraphicsMagick++-config --cppflags
++GM_LD	!= GraphicsMagick++-config --ldflags --libs
+ 
+ # compiler rules
+-CC = g++ #-std=c++11
+-DEBUG = -g
+-OPT = -O3 -Wall
+-IMGMGK= -fno-strict-aliasing -pthread  `GraphicsMagick++-config --cppflags --ldflags --libs`
++# -pthread appears to be unused
++# Allow user to override default compiler and optional flags using make
++# arguments or environment variables
++CXX		?= g++
++CXXFLAGS	?= -O3 -Wall -fno-strict-aliasing
+ 
+-CFLAGS=  -I$(INCDIR) $(OPT) $(IMGMGK) 
++# Add required flags
++CXXFLAGS	+= -I$(INCDIR) $(GM_CPP)
++LDFLAGS		+= $(GM_LD)
+ 
+-SOURCES := $(wildcard $(SRCDIR)/*.cpp) $(wildcard $(SRCDIR)/io/*.cpp)
+-INCLUDES := $(wildcard $(INCDIR)/*.h)
+-OBJECTS := $(SOURCES:$(SRCDIR)/%.cpp=$(OBJDIR)/%.o) 
++DEBUG	= -g
+ 
+-$(BINDIR)/$(TARGET): $(OBJECTS) $(INCLUDES)
+-	$(CC) $(OBJECTS) $(CFLAGS) -o $@
++SOURCES		:= $(wildcard $(SRCDIR)/*.cpp) $(wildcard $(SRCDIR)/io/*.cpp)
++INCLUDES	:= $(wildcard $(INCDIR)/*.h)
++OBJECTS		:= $(SOURCES:$(SRCDIR)/%.cpp=$(OBJDIR)/%.o) 
+ 
+-all: $(BINDIR)/$(TARGET) 
++# Default install tools, can be overridden by user
++MKDIR		?= mkdir
++INSTALL		?= install
++
++# Support staged installs.  Most package managers will provide
++# DESTDIR and PREFIX.
++DESTDIR		?= stagedir
++PREFIX		?= /usr/local
++
++all: $(TARGET) 
++
++$(TARGET): $(OBJECTS) $(INCLUDES)
++	$(CXX) $(OBJECTS) $(LDFLAGS) -o $@
++
+ $(OBJDIR)/%.o: $(SRCDIR)/%.cpp $(INCLUDES) 
+-	$(CC) $(CFLAGS) -c $< -o $@
++	$(CXX) $(CXXFLAGS) -c $< -o $@
+ 
+ .PHONY: 
+ clean:
+-	rm -f $(OBJECTS) $(BINDIR)/$(TARGET)
+-debug:	CFLAGS = -I$(INCDIR) $(IMGMGK) $(DEBUG) 
++	rm -f $(OBJECTS) $(TARGET)
+ 
++debug: CXXFLAGS = -I$(INCDIR) $(IMGMGK) $(DEBUG) 
++
+ debug: all 
++
++install: all
++	$(MKDIR) -p $(DESTDIR)$(PREFIX)/bin
++	$(INSTALL) -c $(TARGET) $(DESTDIR)$(PREFIX)/bin
diff --git a/brain-mesh-builder/patches/patch-inc_globals.h b/brain-mesh-builder/patches/patch-inc_globals.h
new file mode 100644
index 0000000000..9603479223
--- /dev/null
+++ b/brain-mesh-builder/patches/patch-inc_globals.h
@@ -0,0 +1,14 @@
+$NetBSD$
+
+# Fix for clang
+
+--- inc/globals.h.orig	2022-11-10 21:07:28 UTC
++++ inc/globals.h
+@@ -21,6 +21,7 @@
+ //#include <ctime>
+ //#include <list>
+ #include <map>
++#include <array>
+ #include <vector>
+ #include <numeric>
+
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