[med-svn] [Git][med-team/mrtrix3][master] 35 commits: packaging from mrtrix project
Andreas Tille
gitlab at salsa.debian.org
Tue Jan 21 08:53:01 GMT 2020
Andreas Tille pushed to branch master at Debian Med / mrtrix3
Commits:
b0b5f88a by Yaroslav Halchenko at 2018-08-28T22:53:51-04:00
packaging from mrtrix project
- - - - -
0688f717 by Yaroslav Halchenko at 2018-08-28T23:01:23-04:00
initial tune ups for mrtrix3 package
- - - - -
263976d1 by Yaroslav Halchenko at 2018-08-29T09:49:34-04:00
tune rules to config,build,clean
- - - - -
966f350a by Yaroslav Halchenko at 2018-08-30T10:06:36-04:00
Initial set of updates to build as mrtrix3 pkg
- - - - -
319f37e4 by Yaroslav Halchenko at 2018-08-30T10:36:45-04:00
libeigen3 and opengl into b-depends, recommend numpy
- - - - -
7872caad by Yaroslav Halchenko at 2018-08-30T16:01:57-04:00
No extra priority
- - - - -
b67e8110 by Yaroslav Halchenko at 2018-08-30T22:07:43-04:00
a note
- - - - -
195e47d8 by Yaroslav Halchenko at 2018-09-04T13:08:43-04:00
Symlink only mrview for now
- - - - -
5f261636 by Yaroslav Halchenko at 2018-09-04T13:10:13-04:00
Python into dependencies
- - - - -
51906a09 by Yaroslav Halchenko at 2018-09-04T13:11:36-04:00
And python2 explicitely since some scripts need python2
- - - - -
31204e8f by Yaroslav Halchenko at 2018-09-04T19:39:09-04:00
Various tune ups and placing under Debian Med umbrella
- - - - -
1ef673a1 by Yaroslav Halchenko at 2018-09-04T19:39:52-04:00
hardening
- - - - -
022a0bf7 by Yaroslav Halchenko at 2018-09-04T19:41:17-04:00
debian/watch based on the one from mrtrix, thanks Andreas T
- - - - -
0666e46f by Yaroslav Halchenko at 2018-09-04T20:02:08-04:00
try enabling build time testing
- - - - -
1efc3191 by Yaroslav Halchenko at 2018-09-04T20:04:08-04:00
assure no online interactions
- - - - -
e8952c54 by Yaroslav Halchenko at 2018-09-04T22:26:55-04:00
Do not use git to get test data, dump testing log if fail, need bc for tests
- - - - -
b4fb914a by Yaroslav Halchenko at 2018-09-05T09:19:35-04:00
Try to provide CFLAGS for consistent operation across x86 platforms
- - - - -
9a3aaec1 by Yaroslav Halchenko at 2018-09-05T09:57:17-04:00
BF: project is under MPL-2.0 now
- - - - -
a89cbaf0 by Yaroslav Halchenko at 2018-09-05T10:07:25-04:00
Lets upload to Debian proper
- - - - -
9d491a2d by Yaroslav Halchenko at 2018-09-05T11:58:13-04:00
removed too old .dsc patches -- we do not build there any longer anyways
- - - - -
16e96112 by Yaroslav Halchenko at 2018-09-07T16:25:23-04:00
README.source to clarify source package generation
- - - - -
ddf257bb by Yaroslav Halchenko at 2018-11-21T23:08:20-05:00
Need to disable PIE on older systems
- - - - -
1c6f44b5 by Yaroslav Halchenko at 2018-12-13T12:55:33-05:00
debian/gbp.conf - adjusted to relfect used branches layout, where debian branch is based on (original) upstream's master branch.
- - - - -
610d7131 by Yaroslav Halchenko at 2018-12-13T17:34:00-05:00
Merge commit '3.0_RC3-135-g2b8e7d0c2' into debian
* commit '3.0_RC3-135-g2b8e7d0c2': (23 commits)
only include xmmintrin.h header if actually used
TravisCI: try using git repo to fetch Eigen
dwipreproc: Search PATH for 'eddy_cpu'
Streamline::calc_length(): Make no assumptions
dwipreproc: Compatibility with FSL6.0.0
_5ttgen/gif.py: Remove extraneous pylint directive
5ttgen GIF algorithm: fix for pylint errors
run_pylint: fix to report correct version information
run_pylint: log version information for potential debugging
MRView: fix translation in camera coordinates in screen capture tool
DICOM: be more lenient with slice timing vector is Siemens mosaics
mrtrix3.image.statistic(): Fix parameter naming
dwiextract: Fix extraction based on TRT
further updated test data for mrpad
merge updated test data for mrpad
mrpad: fix header translation of y and z axes
DICOM: increase resilience to errors and empty fields
mrview: fix -norealign option
dcminfo: fix -tags output
Fix bug json.load() -> json.loads()
...
- - - - -
55474e9d by Yaroslav Halchenko at 2018-12-13T17:34:18-05:00
Adjusted changelog entry for new snapshot
- - - - -
825d3939 by Yaroslav Halchenko at 2019-01-07T11:38:23-05:00
added patch changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff to "cherry-pick" 7fb509cf35d5862f073faaa7e136e987486960d9 (gl_core_3_3.h: simplify and fix typedefs)
- - - - -
0f9168a2 by Yaroslav Halchenko at 2019-01-07T11:38:32-05:00
added patch changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff to "cherry-pick" 1c1d3304791bd029bca744ff6634bfa4824f6938 (gl_core_3_3.h: fix missing semicolon)
- - - - -
d66ef424 by Yaroslav Halchenko at 2019-01-07T11:42:44-05:00
changelog entry
- - - - -
61f0c969 by Yaroslav Halchenko at 2019-01-07T11:44:36-05:00
Fix symlinks for the manpages to point to mrtrix3.1.gz not the absent mrtrix.1.gz (Closes: #916775)
- - - - -
556ad2a7 by Yaroslav Halchenko at 2019-01-21T23:38:00-05:00
Ship Python mrtrix3 module for internal use:
* Ship Python mrtrix3 module for internal use:
- Many tools rely on Python (2) support module, which was omitted
- - - - -
667393d7 by Yaroslav Halchenko at 2019-01-22T16:28:57-05:00
Clean up *.py? files upon install
- - - - -
45965c4f by Yaroslav Halchenko at 2019-01-22T16:29:06-05:00
debian/control, debian/patches/up_blend_python - just ask/use default Python (currently python2)
- - - - -
45f43ce3 by Yaroslav Halchenko at 2019-01-22T18:57:54-05:00
Override dh_install instead of dh_auto_install for pruning .pyc files
- - - - -
b3a5d28e by Andreas Tille at 2020-01-20T21:41:57+01:00
Update upstream source from tag '3.0_rc3+git135-g2b8e7d0c2'
Update to upstream version '3.0~rc3+git135-g2b8e7d0c2'
with Debian dir e87262d348856b5bc9024c486bf3277ed938270f
- - - - -
974ad5c3 by Andreas Tille at 2020-01-20T22:07:07+01:00
Get the build at least starting
- - - - -
23 changed files:
- + debian/README.Debian
- + debian/README.source
- + debian/changelog
- + debian/compat
- + debian/control
- + debian/copyright
- + debian/gbp.conf
- + debian/mrtrix3-doc.install
- + debian/mrtrix3.1
- + debian/mrtrix3.desktop
- + debian/mrtrix3.install
- + debian/mrtrix3.links
- + debian/mrtrix3.links.in
- + debian/mrtrix3.manpages
- + debian/patches/changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff
- + debian/patches/changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff
- + debian/patches/deb_run_tests
- + debian/patches/debian_build_cfg
- + debian/patches/series
- + debian/patches/up_blend_python
- + debian/rules
- + debian/source/format
- + debian/watch
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,24 @@
+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 at onerussian.com>, Thu, 30 Aug 2018 09:32:03 -0400
=====================================
debian/README.source
=====================================
@@ -0,0 +1,14 @@
+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 at onerussian.com>, Fri, 7 Sep 2018 16:25:08 -0400
=====================================
debian/changelog
=====================================
@@ -0,0 +1,51 @@
+mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-4) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * s/libqt4-opengl-dev/libqt5opengl5-dev/
+
+ -- Andreas Tille <tille at 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 at 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 at 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 at 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 at 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 at onerussian.com> Wed, 05 Sep 2018 10:07:15 -0400
=====================================
debian/compat
=====================================
@@ -0,0 +1 @@
+9
=====================================
debian/control
=====================================
@@ -0,0 +1,55 @@
+Source: mrtrix3
+Maintainer: Debian Med Packaging Team <debian-med-packaging at alioth-lists.debian.net>
+Uploaders: Michael Hanke <mih at debian.org>,
+ Yaroslav Halchenko <debian at 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
=====================================
@@ -0,0 +1,40 @@
+Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: MRtrix3
+Upstream-Contact: Donald Tournier <jdtournier at 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 at gmail.com>
+ 2018, Yaroslav Halchenko <debian at 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
=====================================
@@ -0,0 +1,9 @@
+[DEFAULT]
+submodules = True
+debian-tag = debian/%(version)s
+upstream-tag = %(version)s
+upstream-branch = master
+debian-branch = debian
+
+
+
=====================================
debian/mrtrix3-doc.install
=====================================
@@ -0,0 +1 @@
+src/doc/* usr/share/doc/mrtrix3-doc/html
=====================================
debian/mrtrix3.1
=====================================
@@ -0,0 +1,23 @@
+.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 at brain.org.au)
+.PP
+This manual page was written by Michael Hanke <michael.hanke at 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
=====================================
@@ -0,0 +1,10 @@
+[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
=====================================
@@ -0,0 +1,7 @@
+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
=====================================
@@ -0,0 +1,48 @@
+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.links.in
=====================================
=====================================
debian/mrtrix3.manpages
=====================================
@@ -0,0 +1 @@
+debian/mrtrix3.1
=====================================
debian/patches/changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff
=====================================
@@ -0,0 +1,14 @@
+From: J-Donald Tournier <jdtournier at 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/changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff
=====================================
The diff for this file was not included because it is too large.
=====================================
debian/patches/deb_run_tests
=====================================
@@ -0,0 +1,12 @@
+--- 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 [ $? != 0 ]; then
+ echo ERROR!
=====================================
debian/patches/debian_build_cfg
=====================================
@@ -0,0 +1,21 @@
+Description: Change buildsystem setup for Debian
+Forwarded: not-needed
+Author: Michael Hanke <michael.hanke at gmail.com>
+--- a/build
++++ b/build
+@@ -187,6 +187,15 @@ def pipe_errors_to_less_handler():
+ except:
+ raise
+
++# honor the environment
++try:
++ # the splitting is needed because the command is submitted as a list
++ # and we need individual options -- it may not be that simple though...
++ env_flags = os.environ['LDFLAGS'].split()
++ ld_flags.extend(env_flags)
++ ld_lib_flags.extend(env_flags)
++except:
++ pass
+
+
+
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,5 @@
+up_blend_python
+changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff
+changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff
+deb_run_tests
+debian_build_cfg
=====================================
debian/patches/up_blend_python
=====================================
@@ -0,0 +1,8 @@
+--- a/bin/blend
++++ b/bin/blend
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python2
++#!/usr/bin/env python
+ import os
+ import sys
+
=====================================
debian/rules
=====================================
@@ -0,0 +1,73 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# get octave paths (have to build-depend on octave-headers)
+include /usr/share/octave/debian/defs.make
+# same for Matlab
+include /usr/share/matlab/debian/defs.make
+
+# on older systems such as 16.04 PIE is not enabled by default and
+# configure them fails # to link
+DISABLE_HARDENING_OPTS=$(shell g++ -v 2>&1 | grep -q -e --enable-default-pie || echo ",-pie")
+export DEB_BUILD_MAINT_OPTIONS=hardening=+all$(DISABLE_HARDENING_OPTS)
+
+# To avoid --match=native since wouldn't be supported on some platforms
+export CPP_MARCH=
+
+DEB_HOST_ARCH=$(shell dpkg-architecture -qDEB_HOST_ARCH)
+# guarantee the same precision on x86 platforms for tests
+ifneq (,$(findstring z$(DEB_HOST_ARCH)z,zamd64z zi386z))
+ CFLAGS+=-mmmx -msse -msse2 -mfpmath=sse
+endif
+
+# To prevent any online interactions
+export http_proxy=http://127.0.0.1:9/
+export https_proxy=http://127.0.0.1:9/
+
+export QT_SELECT=qt5
+
+%:
+ dh $@
+
+override_dh_auto_configure:
+ ./configure -openmp # -debug
+
+override_dh_auto_build:
+ ./build -verbose
+
+override_dh_install:
+ dh_install
+ # .pyc files get generated, so we remove all the .pyc/.pyo etc
+ -find debian -iname *.py? -delete
+
+override_dh_auto_test:
+ ./run_tests || { cat testing.log; exit 1; }
+
+override_dh_link:
+ cp debian/mrtrix3.links.in debian/mrtrix3.links
+ : # Generate symlinks for all the mr* commands
+ for f in debian/mrtrix3/usr/lib/mrtrix3/bin/mrview; do \
+ bn=$$(basename $$f); \
+ echo "usr/lib/mrtrix3/bin/$$bn usr/bin/$$bn" >> debian/mrtrix3.links; \
+ echo "/usr/share/man/man1/mrtrix.1.gz /usr/share/man/man1/$$bn.1.gz" >> debian/mrtrix3.links; \
+ done
+ echo "/usr/share/mrtrix3/matlab $(MATLAB_MDIR)/mrtrix" >> debian/mrtrix3.links
+ echo "/usr/share/mrtrix3/matlab $(MDIR)/mrtrix" >> debian/mrtrix3.links
+ dh_link
+
+# we want immediately useable docs and example data, they are in a dedicated
+# package already
+override_dh_compress:
+ dh_compress -X.html
+
+override_dh_clean:
+ ./build clean
+ find . -name '*.pyc' -delete
+ -rm clean \
+ config configure.log build.log \
+ core/version.cpp lib/mrtrix3/_version.py src/exec_version.cpp
+ dh_clean
+ @rm -f debian/mrtrix.links
+
+override_dh_shlibdeps:
+ dh_shlibdeps -l $(CURDIR)/lib
=====================================
debian/source/format
=====================================
@@ -0,0 +1 @@
+3.0 (quilt)
=====================================
debian/watch
=====================================
@@ -0,0 +1,4 @@
+version=4
+
+http://github.com/MRtrix3/mrtrix3/releases .*/archive/@ANY_VERSION@@ARCHIVE_EXT@
+
View it on GitLab: https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008
--
View it on GitLab: https://salsa.debian.org/med-team/mrtrix3/compare/e5f6ed5b1a5306e354f31af9ad93b7b3caacbc6c...974ad5c338b7e0c65bd46c12aa83509ef5e8c008
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