debian/changelog

 mrtrix3 (3.0~rc3+git135-g2b8e7d0c2-4) UNRELEASED; urgency=medium
 
   * Team upload.
-  * s/libqt4-opengl-dev/libqt5opengl5-dev/
+  * QT4 -> Qt5
+     - s/libqt4-opengl-dev/libqt5opengl5-dev/
+     - Add some missing Build-Depends
+     - d/rules: export QT_SELECT=qt5
+    Closes: #939627
+  * Standards-Version: 4.4.1
+  * Build using python3 instead of python2
+    Closes: #937091
+  * Use /usr/share/dpkg/architecture.mk to obtain architecture
+  * Trim trailing whitespace.
+  * Bump debhelper from old 9 to 10.
+  * Remove deprecated Encoding key from desktop file
+    debian/mrtrix3.desktop.
+  * Use secure URI in Homepage field.
+  * Set upstream metadata fields: Bug-Database, Bug-Submit.
 
  -- Andreas Tille <tille@debian.org>  Mon, 20 Jan 2020 21:42:52 +0100
 

debian/compat

-9
+10

debian/control

@@ -4,14 +4,15 @@ Uploaders: Michael Hanke <mih@debian.org>,
            Yaroslav Halchenko <debian@onerussian.com>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 9~),
+Build-Depends: debhelper (>= 10~),
+               dh-python,
                liboctave-dev,
                libgsl-dev | libgsl0-dev,
                libeigen3-dev,
                libqt5opengl5-dev,
                qtbase5-dev-tools,
                libqt5svg5-dev,
-               python,
+               python3,
                pkg-config,
                libgtkmm-2.4-dev,
                libgtkglext1-dev,
@@ -19,18 +20,18 @@ Build-Depends: debhelper (>= 9~),
                libtiff-dev,
                matlab-support-dev,
                bc,
-Standards-Version: 4.2.1
+Standards-Version: 4.4.1
 Vcs-Browser: https://salsa.debian.org/med-team/mrtrix3
 Vcs-Git: https://salsa.debian.org/med-team/mrtrix3.git
-Homepage: http://www.mrtrix.org
+Homepage: https://www.mrtrix.org
 
 Package: mrtrix3
 Architecture: any
 Section: science
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         python,
-Recommends: python-numpy
+         python3,
+Recommends: python3-numpy
 Conflicts: mrtrix
 Suggests: mrtrix3-doc,
           octave,

debian/mrtrix3.desktop

 [Desktop Entry]
-Encoding=UTF-8
 GenericName=MRI Tractography View
 Name=MRview
 Exec=mrview %F

debian/patches/python3.patch

+Description: Build using python3 instead of python2
+Bug-Debian: https://bugs.debian.org/937091
+Author: Andreas Tille <tille@debian.org>
+Last-Update: Mon, 20 Jan 2020 21:42:52 +0100
+
+--- a/build
++++ b/build
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ usage_string = '''
+ USAGE
+--- a/configure
++++ b/configure
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ usage_string = '''
+ USAGE
+@@ -150,7 +150,7 @@ system = platform.system().lower()
+ 
+ # on Windows, need to use MSYS2 version of python - not MinGW version:
+ if sys.executable[0].isalpha() and sys.executable[1] == ':':
+-  python_cmd = subprocess.check_output ([ 'cygpath.exe', '-w', '/usr/bin/python' ]).splitlines()[0].strip()
++  python_cmd = subprocess.check_output ([ 'cygpath.exe', '-w', '/usr/bin/python3' ]).splitlines()[0].strip()
+   sys.exit (subprocess.call ([ python_cmd ] + sys.argv))
+ 
+ 
+@@ -1301,7 +1301,7 @@ sys.stdout.write ('\nwriting configurati
+ 
+ cache = open (cache_filename, 'w')
+ 
+-cache.write ("""#!/usr/bin/python
++cache.write ("""#!/usr/bin/python3
+ #
+ # autogenerated by MRtrix configure script
+ #
+--- a/bin/population_template
++++ b/bin/population_template
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Generates an unbiased group-average template via image registration of images to a midway space.
+ 
+--- a/bin/5ttgen
++++ b/bin/5ttgen
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script that generates a five-tissue-type (5TT) segmented image: the format appropriate for ACT
+ #
+--- a/bin/average_response
++++ b/bin/average_response
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import sys
+ 
+ def errorMessage(msg):
+--- a/bin/blend
++++ b/bin/blend
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ import os
+ import sys
+ 
+--- a/bin/convert_bruker
++++ b/bin/convert_bruker
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import sys, os.path
+ 
+--- a/bin/dwi2response
++++ b/bin/dwi2response
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script for estimating response functions for spherical deconvolution
+ # A number of different approaches are available within this script for performing response function estimation.
+--- a/bin/dwibiascorrect
++++ b/bin/dwibiascorrect
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script that performs B1 field inhomogeneity correction for a DWI volume series
+ # Bias field is estimated using the mean b=0 image, and subsequently used to correct all volumes
+--- a/bin/dwigradcheck
++++ b/bin/dwigradcheck
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script for checking the orientation of the diffusion gradient table
+ 
+--- a/bin/dwiintensitynorm
++++ b/bin/dwiintensitynorm
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ 
+ # Make the corresponding MRtrix3 Python libraries available
+--- a/bin/dwipreproc
++++ b/bin/dwipreproc
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script for performing DWI pre-processing using FSL 5.0 tools eddy / topup / applytopup
+ 
+--- a/bin/labelsgmfix
++++ b/bin/labelsgmfix
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # Script for 'repairing' a FreeSurfer parcellation image
+ # FreeSurfer's sub-cortical structure segmentation has been observed to be highly variable
+--- a/docs/format_config_options
++++ b/docs/format_config_options
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ import sys
+ 
+--- a/generate_bash_completion.py
++++ b/generate_bash_completion.py
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ #
+ # Generates bash completion file for MRtrix commands
+ # MRtrix needs to be built prior to running this
+--- a/run_pylint
++++ b/run_pylint
+@@ -15,7 +15,7 @@ if [ $# == 0 ]; then
+     fi
+   done
+   for bin_path in bin/*; do
+-    if head ${bin_path} -n1 | grep -q "#!/usr/bin/env python"; then
++    if head ${bin_path} -n1 | grep -q "#!/usr/bin/python3"; then
+       tests="$tests $bin_path"
+     fi
+   done
+--- a/set_path
++++ b/set_path
+@@ -1,4 +1,4 @@
+-#!/usr/bin/env python
++#!/usr/bin/python3
+ 
+ # automatically set the PATH environment variable to include the MRtrix3
+ # executables and scripts. This script must be run after a successful build,

debian/patches/series

@@ -3,3 +3,4 @@ changeset_7fb509cf35d5862f073faaa7e136e987486960d9.diff
 changeset_1c1d3304791bd029bca744ff6634bfa4824f6938.diff
 deb_run_tests
 debian_build_cfg
+python3.patch

debian/rules

@@ -14,7 +14,7 @@ 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=$(shell dpkg-architecture -qDEB_HOST_ARCH)
+include /usr/share/dpkg/architecture.mk
 # guarantee the same precision on x86 platforms for tests
 ifneq (,$(findstring z$(DEB_HOST_ARCH)z,zamd64z zi386z))
     CFLAGS+=-mmmx -msse -msse2 -mfpmath=sse
@@ -37,8 +37,8 @@ override_dh_auto_build:
 
 override_dh_install:
 	dh_install
-	# .pyc files get generated, so we remove all the .pyc/.pyo etc
-	-find debian -iname *.py? -delete
+	# Remove __pycache__ dirs that were created in build time tests
+	find debian -name __pycache__ -type d | xargs rm -rf
 
 override_dh_auto_test:
 	./run_tests || { cat testing.log; exit 1; }
@@ -71,3 +71,6 @@ override_dh_clean:
 
 override_dh_shlibdeps:
 	dh_shlibdeps -l $(CURDIR)/lib
+
+override_dh_python3:
+	dh_python3 --shebang=/usr/bin/python3

debian/upstream/metadata

+Bug-Database: https://github.com/MRtrix3/mrtrix3/issues
+Bug-Submit: https://github.com/MRtrix3/mrtrix3/issues/new