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<p>Hi Roland,</p>
<p>I took time during this very steady August to test a few recent
packages that have been pushed to debian thanks to you. Here are
my toughts and conclusions. If you ever find some time, please
have a look.</p>
<p>There seem to be a similar error around QT5 on bookworm for
packages napari, quasar, refnx, xrt.<br>
</p>
<p><b>nabu</b>: OK on bookworm<br>
</p>
<blockquote>
<p>installs correctly on bookworm with the
'python3-nabu_2023.1.1-2_all.deb
python3-tomoscan_1.2.2-2_all.deb' packages from SID
(<a class="moz-txt-link-freetext" href="https://tracker.debian.org/pkg/nabu">https://tracker.debian.org/pkg/nabu</a>
<a class="moz-txt-link-freetext" href="https://tracker.debian.org/pkg/tomoscan">https://tracker.debian.org/pkg/tomoscan</a>)<br>
</p>
<p>works as expected, it seems.</p>
<p>does not install on bullseye as the h5py version is too old
(req. h5py >=3)</p>
</blockquote>
<p><b>napari</b>: QT5 error on bookworm, pydantic error on bullseye,
launcher missing<br>
</p>
<blockquote>
<p>installs correctly on bookworm and bullseye with the packages
python3-app-model_0.2.0-1_all.deb
python3-in-n-out_0.1.8-1_all.deb
python3-napari-plugin-engine_0.2.0-1_all.deb
python3-cachey_0.2.1-1_all.deb
python3-magicgui_0.7.2-1_all.deb python3-npe2_0.7.2-1_all.deb
python3-docstring-parser_0.15-1_all.deb
python3-napari_0.5.0~a1-1_all.deb
python3-psygnal_0.9.1-1_all.deb <br>
</p>
<p><i>bookworm</i>: command 'napari' produces error: <br>
</p>
<p>$ napari<br>
Traceback (most recent call last):<br>
File "/usr/bin/napari", line 8, in <module><br>
sys.exit(main())<br>
^^^^^^<br>
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
556, in main<br>
_maybe_rerun_with_macos_fixes()<br>
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
442, in _maybe_rerun_with_macos_fixes<br>
from napari._qt import API_NAME<br>
File "/usr/lib/python3/dist-packages/napari/_qt/__init__.py",
line 64, in <module><br>
from napari._qt.qt_event_loop import get_app, gui_qt,
quit_app, run<br>
File
"/usr/lib/python3/dist-packages/napari/_qt/qt_event_loop.py",
line 11, in <module><br>
from qtpy.QtGui import QIcon<br>
File "/usr/lib/python3/dist-packages/qtpy/QtGui.py", line 14,
in <module><br>
from PyQt5.QtGui import *<br>
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE,
version Qt_5</p>
<p>bullseye: command 'napari' produces error: <br>
</p>
<p>$ napari<br>
Traceback (most recent call last):<br>
File "/usr/bin/napari", line 5, in <module><br>
from napari.__main__ import main<br>
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
17, in <module><br>
from napari.utils.translations import trans<br>
File
"/usr/lib/python3/dist-packages/napari/utils/__init__.py", line
2, in <module><br>
from napari.utils.colormaps import Colormap<br>
File
"/usr/lib/python3/dist-packages/napari/utils/colormaps/__init__.py",
line 2, in <module><br>
from napari.utils.colormaps.colormap import Colormap<br>
File
"/usr/lib/python3/dist-packages/napari/utils/colormaps/colormap.py",
line 9, in <module><br>
from napari.utils.events import EventedModel<br>
File
"/usr/lib/python3/dist-packages/napari/utils/events/__init__.py",
line 17, in <module><br>
from napari.utils.events.evented_model import EventedModel<br>
File
"/usr/lib/python3/dist-packages/napari/utils/events/evented_model.py",
line 8, in <module><br>
from app_model.types import KeyBinding<br>
File "/usr/lib/python3/dist-packages/app_model/__init__.py",
line 10, in <module><br>
from ._app import Application<br>
File "/usr/lib/python3/dist-packages/app_model/_app.py", line
9, in <module><br>
from .registries import (<br>
File
"/usr/lib/python3/dist-packages/app_model/registries/__init__.py",
line 3, in <module><br>
from ._keybindings_reg import KeyBindingsRegistry<br>
File
"/usr/lib/python3/dist-packages/app_model/registries/_keybindings_reg.py",
line 7, in <module><br>
from app_model.types._keys import KeyBinding<br>
File
"/usr/lib/python3/dist-packages/app_model/types/__init__.py",
line 2, in <module><br>
from ._action import Action<br>
File
"/usr/lib/python3/dist-packages/app_model/types/_action.py",
line 7, in <module><br>
from app_model._pydantic_compat import validator<br>
File
"/usr/lib/python3/dist-packages/app_model/_pydantic_compat.py",
line 5, in <module><br>
from pydantic import BaseModel, __version__<br>
ImportError: cannot import name '__version__' from 'pydantic'
(/usr/lib/python3/dist-packages/pydantic/__init__.py)<br>
</p>
</blockquote>
<p><b>orange-quasar</b>: QT5 error on bookworm, quasar not installed
as a module, nor launcher.<br>
</p>
<blockquote>
<p>installs correctly on bookworm, not on bullseye (req py >=
3.11)</p>
<p>bookworm: the command 'orange-canvas' produces error</p>
<p>$ orange-canvas <br>
Traceback (most recent call last):<br>
File "/usr/bin/orange-canvas", line 5, in <module><br>
from Orange.canvas.__main__ import main<br>
File "/usr/lib/python3/dist-packages/Orange/__init__.py", line
33, in <module><br>
import pyqtgraph # import pyqtgraph first so that it can
detect Qt5<br>
^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pyqtgraph/__init__.py",
line 18, in <module><br>
from .colors import palette<br>
File
"/usr/lib/python3/dist-packages/pyqtgraph/colors/palette.py",
line 1, in <module><br>
from ..Qt import QtGui<br>
File
"/usr/lib/python3/dist-packages/pyqtgraph/Qt/__init__.py", line
156, in <module><br>
import PyQt5.QtGui<br>
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE,
version Qt_5</p>
<p>I can not find a way to launch quasar itself (there should be a
launcher)<br>
</p>
<p>farhie@grades-vm:~/persistent_area/debs$ python3 -m quasar<br>
/usr/bin/python3: No module named quasar<br>
</p>
</blockquote>
<p><b>pyimagetool</b>: data files not writable (!!)<br>
</p>
<blockquote>
<p>installs OK on bookworm and bullseye
(<a class="moz-txt-link-freetext" href="https://tracker.debian.org/pkg/pyimagetool">https://tracker.debian.org/pkg/pyimagetool</a>)</p>
<p>but does not launch with 'python3 -m pyimagetool' (there should
be a launcher)</p>
<p>python3 -m pyimagetool<br>
Traceback (most recent call last):<br>
File "<frozen runpy>", line 189, in _run_module_as_main<br>
File "<frozen runpy>", line 148, in _get_module_details<br>
File "<frozen runpy>", line 112, in _get_module_details<br>
File "/usr/lib/python3/dist-packages/pyimagetool/__init__.py",
line 2, in <module><br>
from .ImageTool import ImageTool<br>
File
"/usr/lib/python3/dist-packages/pyimagetool/ImageTool.py", line
8, in <module><br>
from .widgets import InfoBar<br>
File "/usr/lib/python3/dist-packages/pyimagetool/widgets.py",
line 6, in <module><br>
from .cmaps import CMap<br>
File
"/usr/lib/python3/dist-packages/pyimagetool/cmaps/__init__.py",
line 1, in <module><br>
from .CMap import CMap<br>
File
"/usr/lib/python3/dist-packages/pyimagetool/cmaps/CMap.py", line
66, in <module><br>
raise OSError(<br>
OSError: Packaged data files are not writeable, use a helper
script.See /usr/share/pyimagetool/debian_pyimagetool.py<br>
<br>
</p>
</blockquote>
<p><b>refnx</b>: QT5 error on bookworm, invalid C extensions and
missing numpy.typing on bullseye<br>
</p>
<blockquote>
<p>installs OK on both bookworm and bullseye.</p>
<p>but there is an error launching command 'refnx'</p>
<p>bookworm error:</p>
<p>$ refnx<br>
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:200:
UserWarning: Can't use the C abeles backend<br>
warnings.warn("Can't use the C abeles backend")<br>
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:233:
UserWarning: Using the SLOW reflectivity calculation.<br>
warnings.warn("Using the SLOW reflectivity calculation.")<br>
Traceback (most recent call last):<br>
File "/usr/bin/refnx", line 33, in <module><br>
sys.exit(load_entry_point('refnx==0.1.33', 'gui_scripts',
'refnx')())<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/_app/__init__.py",
line 54, in main<br>
sys.exit(gui(expt_file=expt_file))<br>
^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/_app/__init__.py",
line 5, in gui<br>
from qtpy import QtGui, QtWidgets, QtCore<br>
File "/usr/lib/python3/dist-packages/qtpy/QtGui.py", line 14,
in <module><br>
from PyQt5.QtGui import *<br>
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE,
version Qt_5<br>
</p>
<p>bullseye error:</p>
<p>$ refnx<br>
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:200:
UserWarning: Can't use the C abeles backend<br>
warnings.warn("Can't use the C abeles backend")<br>
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:233:
UserWarning: Using the SLOW reflectivity calculation.<br>
warnings.warn("Using the SLOW reflectivity calculation.")<br>
Traceback (most recent call last):<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 196, in get_reflect_backend<br>
from refnx.reflect import _creflect as _c<br>
ImportError: cannot import name '_creflect' from partially
initialized module 'refnx.reflect' (most likely due to a
circular import) (/usr/lib/py<br>
thon3/dist-packages/refnx/reflect/__init__.py)<br>
<br>
During handling of the above exception, another exception
occurred:<br>
<br>
Traceback (most recent call last):<br>
File "/usr/bin/refnx", line 33, in <module><br>
sys.exit(load_entry_point('refnx==0.1.33', 'gui_scripts',
'refnx')())<br>
File "/usr/bin/refnx", line 25, in importlib_load_entry_point<br>
return next(matches).load()<br>
File "/usr/lib/python3.9/importlib/metadata.py", line 77, in
load<br>
module = import_module(match.group('module'))<br>
File "/usr/lib/python3.9/importlib/__init__.py", line 127, in
import_module<br>
return _bootstrap._gcd_import(name[level:], package, level)<br>
File "<frozen importlib._bootstrap>", line 1030, in
_gcd_import<br>
File "<frozen importlib._bootstrap>", line 1007, in
_find_and_load<br>
File "<frozen importlib._bootstrap>", line 986, in
_find_and_load_unlocked<br>
File "<frozen importlib._bootstrap>", line 680, in
_load_unlocked<br>
File "<frozen importlib._bootstrap_external>", line 790,
in exec_module<br>
File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/__init__.py", line
3, in <module><br>
from refnx.reflect.reflect_model import (<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 242, in <module><br>
kernel = get_reflect_backend("c")<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 201, in get_reflect_backend<br>
return get_reflect_backend("python")<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 236, in get_reflect_backend<br>
from refnx.reflect import _reflect as _py<br>
File
"/usr/lib/python3/dist-packages/refnx/reflect/_reflect.py", line
28, in <module><br>
import numpy.typing as npt<br>
ModuleNotFoundError: No module named 'numpy.typing'<br>
</p>
</blockquote>
<p><b>ufo-tofu</b>: opencl error<br>
</p>
<blockquote>
<p>installs OK on bookworm and bullseye.</p>
<p>'tofu flow' command brings an error related to OpenCL. Hard to
debug. 'tofu ez' works.<br>
</p>
</blockquote>
<p><b>bioxtas-raw</b>: error with colorcet version<br>
</p>
<blockquote>
<p>installs ok on bookworm, not on bullseye (req py >= 3.11)</p>
<p>error when launching command bioxtas_raw and launcher</p>
$ more bioxtas-raw-README.txt <br>
$ bioxtas_raw <br>
Traceback (most recent call last):<br>
File "/usr/bin/bioxtas_raw", line 33, in <module><br>
sys.exit(load_entry_point('bioxtasraw==2.1.1', 'gui_scripts',
'bioxtas_raw')())<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/bin/bioxtas_raw", line 25, in
importlib_load_entry_point<br>
return next(matches).load()<br>
^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3.11/importlib/metadata/__init__.py", line
202, in load<br>
module = import_module(match.group('module'))<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3.11/importlib/__init__.py", line 126, in
import_module<br>
return _bootstrap._gcd_import(name[level:], package, level)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "<frozen importlib._bootstrap>", line 1206, in
_gcd_import<br>
File "<frozen importlib._bootstrap>", line 1178, in
_find_and_load<br>
File "<frozen importlib._bootstrap>", line 1149, in
_find_and_load_unlocked<br>
File "<frozen importlib._bootstrap>", line 690, in
_load_unlocked<br>
File "<frozen importlib._bootstrap_external>", line 940,
in exec_module<br>
File "<frozen importlib._bootstrap>", line 241, in
_call_with_frames_removed<br>
File "/usr/lib/python3/dist-packages/bioxtasraw/RAW.py", line
61, in <module><br>
import pyFAI, pyFAI.calibrant, pyFAI.control_points<br>
File "/usr/lib/python3/dist-packages/pyFAI/__init__.py", line
54, in <module><br>
from .utils import decorators<br>
File "/usr/lib/python3/dist-packages/pyFAI/utils/__init__.py",
line 55, in <module><br>
from .. import resources<br>
File
"/usr/lib/python3/dist-packages/pyFAI/resources/__init__.py", line
72, in <module><br>
import pkg_resources<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3248, in <module><br>
@_call_aside<br>
^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3223, in _call_aside<br>
f(*args, **kwargs)<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3261, in _initialize_master_working_set<br>
working_set = WorkingSet._build_master()<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 617, in _build_master<br>
ws.require(__requires__)<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 956, in require<br>
needed = self.resolve(parse_requirements(requirements))<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 815, in resolve<br>
dist = self._resolve_dist(<br>
^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 844, in _resolve_dist<br>
env = Environment(self.entries)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1044, in __init__<br>
self.scan(search_path)<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1077, in scan<br>
self.add(dist)<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1096, in add<br>
dists.sort(key=operator.attrgetter('hashcmp'), reverse=True)<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 2631, in hashcmp<br>
self.parsed_version,<br>
^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 2679, in parsed_version<br>
self._parsed_version = parse_version(self.version)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File
"/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/version.py",
line 266, in __init__<br>
raise InvalidVersion(f"Invalid version: '{version}'")<br>
pkg_resources.extern.packaging.version.InvalidVersion: Invalid
version: 'None'<br>
(package: colorcet)<br>
</blockquote>
<p><b>xrt</b>: QT5 error on bookworm (as above)</p>
<blockquote>
<p>installs OK on both bookworm and bullseye</p>
<p>error when starting on bookworm<br>
</p>
</blockquote>
<p><b>tomopy</b>: wrong naming of lib.so files on bookworm<br>
</p>
<blockquote>
<p>import tomopy brings</p>
<p>ModuleNotFoundError: The following shared library is missing:<br>
/usr/lib/python3/dist-packages/tomopy/util/extern/libtomopy-recon.so<br>
<br>
$ ls /usr/lib/python3/dist-packages/tomopy/util/extern/<br>
__init__.py libtomopy-accel.cpython-311-x86_64-linux-gnu.so
misc.py<br>
__pycache__ libtomopy-misc.cpython-311-x86_64-linux-gnu.so
prep.py<br>
accel.py libtomopy-prep.cpython-311-x86_64-linux-gnu.so
recon.py<br>
gridrec.py libtomopy-recon.cpython-311-x86_64-linux-gnu.so<br>
so the debian library naming scheme is not compatible with what
tomopy expects<br>
</p>
</blockquote>
<p><b>tomogui/freeart and xrstools</b>: not installable (SID)<br>
</p>
<blockquote>
<p>seems to be uninstalable on both bookworm (req py < 3.11)
and bullseye (req py > 3.10)</p>
<p>even if not maintained anymore, could we build/push a version
that works on bookworm ?</p>
</blockquote>
<p><b>navarp</b>:</p>
<blockquote>
<p>install OK on both bookworm and bullseye</p>
<p>works OK on bullseye, error on bookworm with command 'navarp'</p>
<p>$ navarp <br>
Traceback (most recent call last):<br>
File "/usr/bin/navarp", line 33, in <module><br>
sys.exit(load_entry_point('navarp==1.3.0',
'console_scripts', 'navarp')())<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/bin/navarp", line 25, in importlib_load_entry_point<br>
return next(matches).load()<br>
^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3.11/importlib/metadata/__init__.py",
line 202, in load<br>
module = import_module(match.group('module'))<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "/usr/lib/python3.11/importlib/__init__.py", line 126, in
import_module<br>
return _bootstrap._gcd_import(name[level:], package, level)<br>
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^<br>
File "<frozen importlib._bootstrap>", line 1206, in
_gcd_import<br>
File "<frozen importlib._bootstrap>", line 1178, in
_find_and_load<br>
File "<frozen importlib._bootstrap>", line 1149, in
_find_and_load_unlocked<br>
File "<frozen importlib._bootstrap>", line 690, in
_load_unlocked<br>
File "<frozen importlib._bootstrap_external>", line 940,
in exec_module<br>
File "<frozen importlib._bootstrap>", line 241, in
_call_with_frames_removed<br>
File "/usr/lib/python3/dist-packages/navarp/navarp_gui.py",
line 38, in <module><br>
from matplotlib.backends.backend_qt5agg import (<br>
File
"/usr/lib/python3/dist-packages/matplotlib/backends/backend_qt5agg.py",
line 7, in <module><br>
from .backend_qtagg import ( # noqa: F401, E402 # pylint:
disable=W0611<br>
File
"/usr/lib/python3/dist-packages/matplotlib/backends/backend_qtagg.py",
line 9, in <module><br>
from .qt_compat import QT_API, _enum, _setDevicePixelRatio<br>
File
"/usr/lib/python3/dist-packages/matplotlib/backends/qt_compat.py",
line 137, in <module><br>
raise ImportError(<br>
ImportError: Failed to import any of the following Qt binding
modules: PyQt6, PySide6, PyQt5, PySide2<br>
</p>
</blockquote>
<blockquote>
<p>the error persists even after installing python3-pyside2.*
python3-pyqt5.* python3-pyqt6.* <br>
</p>
</blockquote>
<p><b>genx</b>: install and works OK (3.6) on both bookworm and
bullseye</p>
<p><br>
</p>
<p>Cheers, Emmanuel.<br>
</p>
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