debian/changelog

@@ -3,9 +3,15 @@ elastix (4.9.0-1) UNRELEASED; urgency=medium
   [ Andreas Tille ]
   * Team upload.
   * Fix watch file
-  * debhelper 11
+  * debhelper 12
   * Point Vcs fields to salsa.debian.org
-  * Standards-Version: 4.2.1
+  * Standards-Version: 4.3.0
+  * Suppress dh_dwz due to: 'dwz: Too few files for multifile optimization'
+  * Fix EPOCH_DATE
+  * Set "Rules-Requires-Root: no" to avoid issues with fakeroot
+  * Fix generation of docs using doxygen and move all code under one target
+  * Install Apache NOTICE file
+  * Remove unused lintian-override
 
   [ Jelmer Vernooij ]
   * Trim trailing whitespace.

debian/compat

-11
+12

debian/control

@@ -4,7 +4,7 @@ Uploaders: Steve M. Robbins <smr@debian.org>,
            Gert Wollny <gewo@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper (>= 12~),
                cmake,
                libinsighttoolkit4-dev,
                libdcmtk-dev,
@@ -21,7 +21,8 @@ Build-Depends-Indep: doxygen,
                      texlive-fonts-recommended,
                      texlive-publishers,
                      ghostscript
-Standards-Version: 4.2.1
+Standards-Version: 4.3.0
+Rules-Requires-Root: no
 Vcs-Browser: https://salsa.debian.org/med-team/elastix
 Vcs-Git: https://salsa.debian.org/med-team/elastix.git
 Homepage: http://elastix.isi.uu.nl/

debian/copyright

@@ -22,7 +22,7 @@ License: Apache-2.0
  On Debian systems this license may be found in file
  /usr/share/common-licenses/Apache-2.0.  
 
-Files: src/Common/KNN/ann_1.1/*
+Files: Components/Metrics/KNNGraphAlphaMutualInformation/KNN/ann_1.1/*
 Copyright: 1997-2005 University of Maryland and Sunil Arya and David Mount
 License: LGPL-2.1
  This program is free software; you can redistribute it and/or modify it

debian/elastix-doc.doc-base

@@ -13,4 +13,4 @@ Abstract: toolbox for rigid and nonrigid registration of images
 Section: Science/Biology
 
 Format: pdf
-Files: /usr/share/doc/elastix-doc/manual.pdf.gz
+Files: /usr/share/doc/elastix/manual.pdf.gz

debian/elastix-doc.docs

 dox/manual/manual.pdf
-help
+*/help

debian/elastix-doc.lintian-overrides

-# The embedded jquery.js is generated by Doxygen and can not be replaced 
-# by the one provided by libjs-jquery.  
-# For a racionale please see src::Doxygen/debian/README.jquery. 
-
-elastix-doc binary: embedded-javascript-library

debian/elastix.docs

+NOTICE

debian/patches/doxygen_cleanup.patch

@@ -5,7 +5,7 @@ Forwarded: no
 Cleanup of the doxygen documentation:
  [dox/doxygen/doxyfile.in]
  * use svg instead of png for graphics to save space
- * supress timestamps created by Doxygen
+ * suppress timestamps created by Doxygen
  * Enable HTML_DYNAMIC_SECTIONS because otherwise the required
    dynsections.js is not added 
 .

debian/patches/no_include_install.patch

+Author: Gert Wollny
+Last-Update: 2018-12-23 20:44:27 +0100
+Description: Do not install all header files
+Comment by Andreas Tille: Why?
+
 --- a/Core/CMakeLists.txt
 +++ b/Core/CMakeLists.txt
 @@ -231,21 +231,6 @@

debian/patches/static_libann.patch

+Author: Gert Wollny
+Last-Update: 2018-12-23 19:03:44 +0100
+Description: Force static linking of libann
+Comment by Andreas Tille: Why?
+
 --- a/Components/Metrics/KNNGraphAlphaMutualInformation/KNN/ann_1.1/CMakeLists.txt
 +++ b/Components/Metrics/KNNGraphAlphaMutualInformation/KNN/ann_1.1/CMakeLists.txt
 @@ -40,18 +40,4 @@

debian/rules

@@ -6,17 +6,11 @@ export DEB_CXXFLAGS_MAINT_APPEND  = -fvisibility=hidden
 
 export DEB_LDFLAGS_MAINT_APPEND=-lniftiio
 
-EPOCH_DATE:=$(shell date -u -d ${SOURCE_DATE_EPOCH} +%d.%m.%Y)
+EPOCH_DATE:=$(shell TZ=UTC LC_ALL=C date --utc --date=@${SOURCE_DATE_EPOCH} +%d.%m.%Y)
 
 %:
 	dh $@
 
-binary: binary-arch binary-indep
-
-binary-indep: doc-stamp
-	dh $@
-
-
 # Need -DUSE_KNNGraphAlphaMutualInformationMetric:BOOL=ON, otherwise
 # KNN is not built, and link of elastix fails.
 #
@@ -33,27 +27,23 @@ override_dh_auto_configure:
 	dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS)
 
 override_dh_installdocs-indep:
+	# create help files using doxygen
+	set -x ; \
+	DOXDIR=`find . -name help -type d | sed 's?/help??'` ; \
+	cd $${DOXDIR} ; \
+	doxygen help/doxyfile.out ; \
+	find help -name "*.md5" -delete
+	sed -ie 's/^%\\date{/\\date{'"$(EPOCH_DATE)"'/' dox/manual/manual.tex 
+	sed -ie 's/\\today/'"$(EPOCH_DATE)"'/' dox/manual/manual.tex 
+	cd dox/manual && latex manual && bibtex manual && latex manual && latex manual && latex manual && dvipdf manual
 	dh_installdocs -i
 	# avoid privacy breach by using local logo
-	sed -i 's#http://elastix.isi.uu.nl/images/##' debian/elastix-doc/usr/share/doc/elastix-doc/help/html/*.html
-	sed -i 's#http://elastix.isi.uu.nl/images/#html/#' debian/elastix-doc/usr/share/doc/elastix-doc/help/*.html
-	cp -a dox/art/elastix_logo_full.gif debian/elastix-doc/usr/share/doc/elastix-doc/help/html/elastixLogo.gif
-
-doc: doc-stamp
-
-doc-stamp: help/html/index.html dox/manual/manual.pdf
-	touch $@
+	sed -i 's#http://elastix.isi.uu.nl/images/##' debian/elastix-doc/usr/share/doc/elastix/help/html/*.html
+	sed -i 's#http://elastix.isi.uu.nl/images/#html/#' debian/elastix-doc/usr/share/doc/elastix/help/*.html
+	cp -a dox/art/elastix_logo_full.gif debian/elastix-doc/usr/share/doc/elastix/help/html/elastixLogo.gif
 
 override_dh_auto_test:
         LD_LIBRARY_PATH=`pwd`/obj-*/bin dh_auto_test
 
-# build-deps: doxygen, latex, dot
-help/html/index.html: help/doxyfile.out
-	doxygen $<
-	rm help/html/*.md5
-
-dox/manual/manual.pdf: dox/manual/manual.tex
-	sed -ie 's/^%\\date{/\\date{'"$(EPOCH_DATE)"'/' dox/manual/manual.tex 
-	sed -ie 's/\\today/'"$(EPOCH_DATE)"'/' dox/manual/manual.tex 
-	cd dox/manual && latex manual && bibtex manual && latex manual && latex manual && latex manual && dvipdf manual
-
+override_dh_dwz:
+	echo "Suppress dh_dwz due to: 'dwz: Too few files for multifile optimization'"