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Porting projects to Qt5 and Python3

We have chosen to go for a compatible sources set, which can work with Qt4 or Qt5, Python2 or Python3. Porting to Qt5 and to Python3 are two independent tasks.

Projects list

  • baby
  • Brainrat
  • casa-distro
  • CatiDB
  • Constellation
  • cortical_surface (must be tested)
  • data_storage_client
  • DISCO
  • freesurfer (must be tested)
  • longitudinal
  • Neuroimaging toolbox (nit)
  • QualiCATI
  • Sacha
  • Snapbase (must be tested)
  • SPM
  • Whasa

How to setup a build workflow using Qt5 and/or python3

Building

  • Your system must have Qt5 / python3 + all modules installed. In casa-distro, Ubuntu-16.04 and ubuntu-18.04 develpment images are already ready for that.

  • Edit the bv_maker.cfg file, and change in the [ build ] section:

      cmake_options = -DDESIRED_QT_VERSION=5 -DPYTHON_EXECUTABLE=/usr/bin/python3

  • then run bv_maker to configure and build (either in casa-distro or directly depending on your config/setup)

Running

To run programs using python3, either run explicitely python3:

python3 <build_workflow>/bin/morphologist

But this is not very convenient, and many python scripts start with the standard shebang:

#!/usr/bin/env python

which would normally call python2 because python2 is what is called via the python command on many systems up to now. A simple fix for that is to make a symlink from python3 to python in the bin directory of the build workflow:

ln -s /usr/bin/python3 <builmd_workflow>/bin/python

Then once the build-workflow is setup (bv_env.sh has been sourced from this build workflow) and it is in the paths, the python command will switch to python3, and all python scripts will do the same.

Qt4 / Qt5

imports:

Don't import directly PyQt5 or PyQt4. We have a compatibility module: soma.qt_gui.qt_backend which replaces the explicit imports:

    from soma.qt_gui.qt_backend import Qt
    widget = Qt.QWidget()
    # etc.

The qt_backend module supports PyQt4, PyQt5 and PySide transparently, and offers a few functions to help links with matplotlib (see init_matplotlib_backend) or for the few functions which do not have the same API in the different implementations (like QFileDialog.getOpenFileName). If you need to explicitly initialize the backend to a specific Qt implementation, do it only in main scripts directly called from the user, not in modules/libraries which may be imported.

    from soma.qt_gui import qt_backend
    qt_backend.set_qt_backend('PyQt5')
    from soma.qt_gui.qt_backend import Qt
    widget = Qt.QWidget()
    # etc.

But the best way is not to force this, and rely on the QT_API environment variable that any user can set:

    export QT_API=pyqt5
    soma_workflow_gui # will use PyQt5.

The QT_API variable is already set by the bv_env program according to the settings of the build workflow, so you even don't have to care about it in bv_makerand casa-distro.

major changes:

  • No very deep changes in the API, most code written for Qt4 will work with Qt5.
  • One of the most important points however is in Pyqt4/PyQt5 handling of slots: in a slot function, when an exception is raised, in PyQt4 the slot would end silently and the program would go on its normal life, but in PyQt5, an exception would cause the whole program to end with an error. So check / catch exceptions in callbacks
  • The QtWebKit module has been deprecated, and removed in Ubuntu 18/Qt4. This needs to explicitely switch between QtWebKit (Qt4) and QtWebEngine (Qt5) instead (with a if in codes).
  • A layout problem seems to exist in QGLWidget with Qt5, which causes sometimes GL widgets to appear outside of their parent widget (in a non-reproducible way). We're working on replacing it with QOpenGLWidget in Qt5 in Anatomist.

Python2 / python3

official porting doc

Things to check:

  • use from __future__ import print_function at the beginning of source files

  • print "babar" -> print("babar")

  • print >> file, "babar" -> print("babar", file=file)

  • print "babar", -> print("babar", end='')

  • use six

  • dict.iteritems() -> six.iteritems(dict)

  • dict.iterkeys() -> six.iterkeys(dict)

  • dict.itervalues() -> six.itervalues(dict)

  • check what is made from results of dict.keys(), dict.values(), dict.items(): they were lists in pyton2, they are generators (iterators) in python3. Sometimes needs to wrap them into real lists: list(dict.values()) is a list (but there is a double list, copied in python2, hence an overhead).

  • imports are absolute: relative imports should be prefixed with .:

          import .submodule
      from .submodule import babar

    also possible to use (for python2):

          from __future__ import absolute_import

  • unicode does not exist, str is actually unicode. Sometimes just defining if sys.version_info[0] >= 3: unicode=str is enough, sometimes not...

  • metaclasses are different: use six.with_metaclass()

  • apply(func, list) -> func(*list)

  • some modules have changed name/position in python3. six.moves may help:

  • import cPickle -> from six.moves import cPickle (or use the regular import pickle)

  • import StringIO -> from six.moves import StringIO

  • types.StringTypes -> six.string_types

  • urllib2.urlopen() -> six.moves.urllib.request.urlopen()

  • execfile() -> with open(file[, encoding='utf-8']) as f: six.exec_(f.read()[, ...]), or use soma.importer.execfile()

  • raise (exc_type, exc_instance, exc_traceback) -> six.reraise(exc_type, exc_instance, exc_traceback)

  • try: .. ; except Exception, e: -> try: ...; except Exception as e:

  • iterators: iterator.next() -> next(iterator)

  • to get the 1st item of a generator: next(iter(generator))

  • comparison / sorting operators: redefine something.__hash__() when needed,

  • __cmp__ is deprecated and not called anymore, sometimes needs to redefine __lt__, __gt__, __eq__ etc.

  • map(func, list) -> [func(x) for x in list], or (func(x) for x in list) if a generator is OK

  • reduce(func, list) -> six.moves.reduce(func, list)

  • filter(func, list) -> [x for x in list if func(x)], or (x for x in list if func(x)) if a generator is OK

  • 0777 -> 0o777: 0777 is a syntax error in python3

  • dict ordering / iteration order is different and non-reproducible in python 3.0-3.6

  • The real nightmare is strings: str, unicode, bytes, and encoding...

  • Encoding also causes problems to open text files.

  • Some functions used to return str and now return bytes, for instance file.read() when no encoding is used, sqlite3 requests results...

  • sharing pickled objects between python 2 and 3 is almost impossible, mainly because of these str/unicode/bytes/encoding problems

  • int divisions: in python2:

              >>> 3 / 2
          1

    in python3:

              >>> 3 / 2
          1.5

    thus, use 3 // 2 when possible.

  • in python2, there are two types int and long: 2L. In python3, all ints are longs, and long does not exist any longer. 2L is a syntax error.