debian/README.Debian

+MRtrix for Debian
+-----------------
+
+Packaging is based on the original one for mrtrix package, but now resides as
+a branch on top of the upstream Git repository.
+
+All MRtrix programs are installed in /usr/lib/mrtrix/bin (due to too generic
+names of some of them, e.g. 'average'). You either have to call them with their
+full path, or extend the search path by this directory. The MRtrix documentation
+has information on how to do that for a number of popular environments. Please
+note that it is not necessary to modify LD_LIBRARY_PATH -- despite the advice
+in the MRtrix manual.
+
+For convenience, 'mrview' and other 'mr*' tools are directly avialable in
+/usr/bin and 'mrview' is also listed in Desktop environment menus.
+
+Note: conflicts known so far were discovered by
+
+  $> for f in *; do echo "---- $f"; dlocate bin/$f; done
+  ---- dirsplit
+  genisoimage: /usr/bin/dirsplit
+
+
+ -- Yaroslav Halchenko <debian@onerussian.com>, Thu, 30 Aug 2018 09:32:03 -0400

debian/README.source

+Debian source package
+---------------------
+
+Debian source packages for new (possibly snapshot) releases are
+generated using gbp buildpackage directly from Git repository, while
+relying on settings within provided `debian/gbp.conf`.  It is done so
+to incorporate content of the test data which is provided within git
+submodule under `testing/data`.
+
+pristine-tar is not used to store generated tarballs because of it not
+supporting git submodules (yet) and thus resulting in large binary
+deltas, ruining its utility.
+
+ -- Yaroslav Halchenko <debian@onerussian.com>, Fri,  7 Sep 2018 16:25:08 -0400

debian/changelog

+mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-4) UNRELEASED; urgency=medium
+
+  * Team upload.
+  * s/libqt4-opengl-dev/libqt5opengl5-dev/
+
+ -- Andreas Tille <tille@debian.org>  Mon, 20 Jan 2020 21:42:52 +0100
+
+mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-3) unstable; urgency=medium
+
+  * Clean up *.py? files upon install
+  * debian/control, debian/patches/up_blend_python - just ask/use default
+    Python (currently python2)
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Tue, 22 Jan 2019 14:49:00 -0500
+
+mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-2) neurodebian; urgency=medium
+
+  * Picked up two commits from upstream's origin/simplify_gl_core_header
+    to resolve i386 build failure
+  * Fix symlinks for the manpages to point to mrtrix3.1.gz
+    not the absent mrtrix.1.gz (Closes: #916775)
+  * Ship Python mrtrix3 module for internal use:
+    - Many tools rely on Python (2) support module, which was omitted
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Mon, 21 Jan 2019 23:32:15 -0500
+
+mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-1) UNRELEASED; urgency=medium
+
+  * Fresh upstream snapshot
+    - potentially fixes FTBFS on some non-x32 platforms where failure was
+      due to the absent SSE support and xmmintrin.h
+  * debian/gbp.conf
+    - adjusted to relfect used branches layout, where debian branch is based on
+      (original) upstream's master branch.
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Thu, 13 Dec 2018 17:28:22 -0500
+
+mrtrix3 (3.0~rc3+git86-g4b523b413-2) neurodebian; urgency=medium
+
+  * Need to disable PIE on older systems
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Wed, 21 Nov 2018 23:08:01 -0500
+
+mrtrix3 (3.0~rc3+git86-g4b523b413-1) unstable; urgency=medium
+
+  * Initial packaging based on mrtrix package (Closes: #907978)
+  * Initial packaging for mrtrix3 as a separate source package to
+    allow retaining (although with installation conflict) of both
+    2 and 3 series
+
+ -- Yaroslav Halchenko <debian@onerussian.com>  Wed, 05 Sep 2018 10:07:15 -0400

debian/compat

+9

debian/control

+Source: mrtrix3
+Maintainer: Debian Med Packaging Team <debian-med-packaging@alioth-lists.debian.net>
+Uploaders: Michael Hanke <mih@debian.org>,
+           Yaroslav Halchenko <debian@onerussian.com>
+Section: science
+Priority: optional
+Build-Depends: debhelper (>= 9~),
+               liboctave-dev,
+               libgsl-dev | libgsl0-dev,
+               libeigen3-dev,
+               libqt5opengl5-dev,
+               qtbase5-dev-tools,
+               libqt5svg5-dev,
+               python,
+               pkg-config,
+               libgtkmm-2.4-dev,
+               libgtkglext1-dev,
+               imagemagick,
+               libtiff-dev,
+               matlab-support-dev,
+               bc,
+Standards-Version: 4.2.1
+Vcs-Browser: https://salsa.debian.org/med-team/mrtrix3
+Vcs-Git: https://salsa.debian.org/med-team/mrtrix3.git
+Homepage: http://www.mrtrix.org
+
+Package: mrtrix3
+Architecture: any
+Section: science
+Depends: ${shlibs:Depends},
+         ${misc:Depends},
+         python,
+Recommends: python-numpy
+Conflicts: mrtrix
+Suggests: mrtrix3-doc,
+          octave,
+          matlab-support
+Description: diffusion-weighted MRI white matter tractography
+ Set of tools to perform diffusion-weighted MRI white matter tractography of the
+ brain in the presence of crossing fibres, using Constrained Spherical
+ Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance
+ images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.
+
+Package: mrtrix3-doc
+Architecture: all
+Section: doc
+Conflicts: mrtrix-doc
+Depends: ${misc:Depends}
+Description: documentation for mrtrix3
+ Set of tools to perform diffusion-weighted MRI white matter tractography of the
+ brain in the presence of crossing fibres, using Constrained Spherical
+ Deconvolution, and a probabilisitic streamlines algorithm. Magnetic resonance
+ images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.
+ .
+ This package provides the documentation in HTML format.

debian/copyright

+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MRtrix3
+Upstream-Contact: Donald Tournier <jdtournier@gmail.com>
+Source: http://github.com/MRtrix3/mrtrix3
+
+
+Files: *
+Copyright: 2008-2018 the MRtrix3 contributors
+License: MPL-2.0
+
+Files: core/file/json.h
+Copyright: 2013-2017 Niels Lohmann <http://nlohmann.me>
+License: MIT
+  Permission is hereby  granted, free of charge, to any  person obtaining a copy
+  of this software and associated  documentation files (the "Software"), to deal
+  in the Software  without restriction, including without  limitation the rights
+  to  use, copy,  modify, merge,  publish, distribute,  sublicense, and/or  sell
+  copies  of  the Software,  and  to  permit persons  to  whom  the Software  is
+  furnished to do so, subject to the following conditions:
+  .
+  The above copyright notice and this permission notice shall be included in all
+  copies or substantial portions of the Software.
+  .
+  THE SOFTWARE  IS PROVIDED "AS  IS", WITHOUT WARRANTY  OF ANY KIND,  EXPRESS OR
+  IMPLIED,  INCLUDING BUT  NOT  LIMITED TO  THE  WARRANTIES OF  MERCHANTABILITY,
+  FITNESS FOR  A PARTICULAR PURPOSE AND  NONINFRINGEMENT. IN NO EVENT  SHALL THE
+  AUTHORS  OR COPYRIGHT  HOLDERS  BE  LIABLE FOR  ANY  CLAIM,  DAMAGES OR  OTHER
+  LIABILITY, WHETHER IN AN ACTION OF  CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+  OUT OF OR IN CONNECTION WITH THE SOFTWARE  OR THE USE OR OTHER DEALINGS IN THE
+  SOFTWARE.
+
+Files: debian/*
+Copyright: 2010-2014, Michael Hanke <michael.hanke@gmail.com>
+           2018, Yaroslav Halchenko <debian@onerussian.com>
+License: MPL-2.0
+
+
+License: MPL-2.0
+  On Debian systems the full text of the Mozilla Public License can be found
+  in the `/usr/share/common-licenses/MPL-2.0' file.

debian/gbp.conf

+[DEFAULT]
+submodules = True
+debian-tag = debian/%(version)s
+upstream-tag = %(version)s
+upstream-branch = master
+debian-branch = debian
+
+
+

debian/mrtrix3-doc.install

+src/doc/* usr/share/doc/mrtrix3-doc/html

debian/mrtrix3.1

+.TH MRTRIX "1" "April 2010" "MRtrix" "User Commands"
+.SH NAME
+MRtrix3 \- diffusion-weighted MRI white matter tractography
+.SH DESCRIPTION
+MRtrix is a set of tools to perform diffusion-weighted MRI white matter
+tractography of the brain in the presence of crossing fibres, using Constrained
+Spherical Deconvolution, and a probabilisitic streamlines algorithm. Magnetic
+resonance images in DICOM, ANALYZE, or uncompressed NIfTI format are supported.
+.SH "DEBIAN"
+All MRtrix programs are installed in /usr/lib/mrtrix/bin.  You either have to
+call them with their full path, or extend the search path by this directory.
+The MRtrix documentation has information on how to do that for a number of
+popular environments. Please note that it is not necessary to modify
+LD_LIBRARY_PATH -- despite the advice in the MRtrix manual.
+.SH "AUTHOR"
+MRtrix has been written by J\-Donald Tournier (d.tournier@brain.org.au)
+.PP
+This manual page was written by Michael Hanke <michael.hanke@gmail.com>,
+for the Debian project (but may be used by others).
+.SH "SEE ALSO"
+The full MRtrix user manual is provided by the mrtrix-doc package.
+.TP
+\fBMRtrix Homepage:\fR http://www.mrtrix.org

debian/mrtrix3.desktop

+[Desktop Entry]
+Encoding=UTF-8
+GenericName=MRI Tractography View
+Name=MRview
+Exec=mrview %F
+TryExec=mrview
+Type=Application
+Terminal=false
+Categories=Education;Graphics;Science;DataVisualization;MedicalSoftware;GTK;Viewer;
+Icon=mrtrix

debian/mrtrix3.install

+bin/* usr/lib/mrtrix3/bin
+lib/*.so usr/lib/mrtrix3/lib
+lib/mrtrix3 usr/lib/mrtrix3/lib/
+icons usr/lib/mrtrix3
+icons/mrtrix.png usr/share/pixmaps
+debian/*.desktop usr/share/applications
+matlab usr/share/mrtrix3

debian/mrtrix3.links

+usr/lib/mrtrix3/bin/mraverageheader usr/bin/mraverageheader
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mraverageheader.1.gz
+usr/lib/mrtrix3/bin/mrcalc usr/bin/mrcalc
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcalc.1.gz
+usr/lib/mrtrix3/bin/mrcat usr/bin/mrcat
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcat.1.gz
+usr/lib/mrtrix3/bin/mrcheckerboardmask usr/bin/mrcheckerboardmask
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcheckerboardmask.1.gz
+usr/lib/mrtrix3/bin/mrclusterstats usr/bin/mrclusterstats
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrclusterstats.1.gz
+usr/lib/mrtrix3/bin/mrconvert usr/bin/mrconvert
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrconvert.1.gz
+usr/lib/mrtrix3/bin/mrcrop usr/bin/mrcrop
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrcrop.1.gz
+usr/lib/mrtrix3/bin/mrdegibbs usr/bin/mrdegibbs
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrdegibbs.1.gz
+usr/lib/mrtrix3/bin/mrdump usr/bin/mrdump
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrdump.1.gz
+usr/lib/mrtrix3/bin/mredit usr/bin/mredit
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mredit.1.gz
+usr/lib/mrtrix3/bin/mrfilter usr/bin/mrfilter
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrfilter.1.gz
+usr/lib/mrtrix3/bin/mrhistmatch usr/bin/mrhistmatch
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrhistmatch.1.gz
+usr/lib/mrtrix3/bin/mrhistogram usr/bin/mrhistogram
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrhistogram.1.gz
+usr/lib/mrtrix3/bin/mrinfo usr/bin/mrinfo
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrinfo.1.gz
+usr/lib/mrtrix3/bin/mrmath usr/bin/mrmath
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrmath.1.gz
+usr/lib/mrtrix3/bin/mrmetric usr/bin/mrmetric
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrmetric.1.gz
+usr/lib/mrtrix3/bin/mrpad usr/bin/mrpad
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrpad.1.gz
+usr/lib/mrtrix3/bin/mrregister usr/bin/mrregister
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrregister.1.gz
+usr/lib/mrtrix3/bin/mrresize usr/bin/mrresize
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrresize.1.gz
+usr/lib/mrtrix3/bin/mrstats usr/bin/mrstats
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrstats.1.gz
+usr/lib/mrtrix3/bin/mrthreshold usr/bin/mrthreshold
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrthreshold.1.gz
+usr/lib/mrtrix3/bin/mrtransform usr/bin/mrtransform
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrtransform.1.gz
+usr/lib/mrtrix3/bin/mrview usr/bin/mrview
+/usr/share/man/man1/mrtrix3.1.gz /usr/share/man/man1/mrview.1.gz
+/usr/share/mrtrix3/matlab /usr/share/matlab/site/m/mrtrix
+/usr/share/mrtrix3/matlab /usr/share/octave/site/m/mrtrix

debian/mrtrix3.manpages

+debian/mrtrix3.1

debian/patches/changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff

+From: J-Donald Tournier <jdtournier@gmail.com>
+Subject: gl_core_3_3.h: fix missing semicolon
+
+--- a/src/gui/opengl/gl_core_3_3.h
++++ b/src/gui/opengl/gl_core_3_3.h
+@@ -105,7 +105,7 @@ using GLchar = char;
+ using GLcharARB = char;
+ 
+ #ifdef _WIN64
+-using GLintptr = signed long long int
++using GLintptr = signed long long int;
+ #else
+ using GLintptr = signed long int;
+ #endif

debian/patches/deb_run_tests

+--- a/run_tests
++++ b/run_tests
+@@ -10,8 +10,7 @@ cat > $LOGFILE <<EOD
+ 
+ EOD
+ 
+-echo -n "fetching test data... "
+-git submodule update --init >> $LOGFILE 2>&1
++echo -n "Debian build: Using available test data..." >> $LOGFILE
+ 
+ if [ $? != 0 ]; then
+   echo ERROR!

debian/patches/debian_build_cfg

+Description: Change buildsystem setup for Debian
+Forwarded: not-needed
+Author: Michael Hanke <michael.hanke@gmail.com>
+--- a/build
++++ b/build
+@@ -187,6 +187,15 @@ def pipe_errors_to_less_handler():
+     except:
+       raise
+ 
++# honor the environment
++try:
++  # the splitting is needed because the command is submitted as a list
++  # and we need individual options -- it may not be that simple though...
++  env_flags = os.environ['LDFLAGS'].split()
++  ld_flags.extend(env_flags)
++  ld_lib_flags.extend(env_flags)
++except:
++  pass
+ 
+ 
+ 

debian/patches/series

+up_blend_python
+changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff
+changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff
+deb_run_tests
+debian_build_cfg

debian/patches/up_blend_python

+--- a/bin/blend
++++ b/bin/blend
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2
++#!/usr/bin/env python
+ import os
+ import sys
+