[Debian-pan-maintainers] SOLEIL debian packaging status
Emmanuel FARHI
emmanuel.farhi at synchrotron-soleil.fr
Wed Aug 9 12:58:42 BST 2023
Hi Roland,
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.
There seem to be a similar error around QT5 on bookworm for packages
napari, quasar, refnx, xrt.
*nabu*: OK on bookworm
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 (https://tracker.debian.org/pkg/nabu
https://tracker.debian.org/pkg/tomoscan)
works as expected, it seems.
does not install on bullseye as the h5py version is too old (req.
h5py >=3)
*napari*: QT5 error on bookworm, pydantic error on bullseye, launcher
missing
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
/bookworm/: command 'napari' produces error:
$ napari
Traceback (most recent call last):
File "/usr/bin/napari", line 8, in <module>
sys.exit(main())
^^^^^^
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
556, in main
_maybe_rerun_with_macos_fixes()
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
442, in _maybe_rerun_with_macos_fixes
from napari._qt import API_NAME
File "/usr/lib/python3/dist-packages/napari/_qt/__init__.py",
line 64, in <module>
from napari._qt.qt_event_loop import get_app, gui_qt, quit_app, run
File
"/usr/lib/python3/dist-packages/napari/_qt/qt_event_loop.py", line
11, in <module>
from qtpy.QtGui import QIcon
File "/usr/lib/python3/dist-packages/qtpy/QtGui.py", line 14, in
<module>
from PyQt5.QtGui import *
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE, version Qt_5
bullseye: command 'napari' produces error:
$ napari
Traceback (most recent call last):
File "/usr/bin/napari", line 5, in <module>
from napari.__main__ import main
File "/usr/lib/python3/dist-packages/napari/__main__.py", line
17, in <module>
from napari.utils.translations import trans
File "/usr/lib/python3/dist-packages/napari/utils/__init__.py",
line 2, in <module>
from napari.utils.colormaps import Colormap
File
"/usr/lib/python3/dist-packages/napari/utils/colormaps/__init__.py",
line 2, in <module>
from napari.utils.colormaps.colormap import Colormap
File
"/usr/lib/python3/dist-packages/napari/utils/colormaps/colormap.py",
line 9, in <module>
from napari.utils.events import EventedModel
File
"/usr/lib/python3/dist-packages/napari/utils/events/__init__.py",
line 17, in <module>
from napari.utils.events.evented_model import EventedModel
File
"/usr/lib/python3/dist-packages/napari/utils/events/evented_model.py",
line 8, in <module>
from app_model.types import KeyBinding
File "/usr/lib/python3/dist-packages/app_model/__init__.py", line
10, in <module>
from ._app import Application
File "/usr/lib/python3/dist-packages/app_model/_app.py", line 9,
in <module>
from .registries import (
File
"/usr/lib/python3/dist-packages/app_model/registries/__init__.py",
line 3, in <module>
from ._keybindings_reg import KeyBindingsRegistry
File
"/usr/lib/python3/dist-packages/app_model/registries/_keybindings_reg.py",
line 7, in <module>
from app_model.types._keys import KeyBinding
File
"/usr/lib/python3/dist-packages/app_model/types/__init__.py", line
2, in <module>
from ._action import Action
File "/usr/lib/python3/dist-packages/app_model/types/_action.py",
line 7, in <module>
from app_model._pydantic_compat import validator
File
"/usr/lib/python3/dist-packages/app_model/_pydantic_compat.py", line
5, in <module>
from pydantic import BaseModel, __version__
ImportError: cannot import name '__version__' from 'pydantic'
(/usr/lib/python3/dist-packages/pydantic/__init__.py)
*orange-quasar*: QT5 error on bookworm, quasar not installed as a
module, nor launcher.
installs correctly on bookworm, not on bullseye (req py >= 3.11)
bookworm: the command 'orange-canvas' produces error
$ orange-canvas
Traceback (most recent call last):
File "/usr/bin/orange-canvas", line 5, in <module>
from Orange.canvas.__main__ import main
File "/usr/lib/python3/dist-packages/Orange/__init__.py", line
33, in <module>
import pyqtgraph # import pyqtgraph first so that it can
detect Qt5
^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pyqtgraph/__init__.py", line
18, in <module>
from .colors import palette
File
"/usr/lib/python3/dist-packages/pyqtgraph/colors/palette.py", line
1, in <module>
from ..Qt import QtGui
File "/usr/lib/python3/dist-packages/pyqtgraph/Qt/__init__.py",
line 156, in <module>
import PyQt5.QtGui
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE, version Qt_5
I can not find a way to launch quasar itself (there should be a
launcher)
farhie at grades-vm:~/persistent_area/debs$ python3 -m quasar
/usr/bin/python3: No module named quasar
*pyimagetool*: data files not writable (!!)
installs OK on bookworm and bullseye
(https://tracker.debian.org/pkg/pyimagetool)
but does not launch with 'python3 -m pyimagetool' (there should be a
launcher)
python3 -m pyimagetool
Traceback (most recent call last):
File "<frozen runpy>", line 189, in _run_module_as_main
File "<frozen runpy>", line 148, in _get_module_details
File "<frozen runpy>", line 112, in _get_module_details
File "/usr/lib/python3/dist-packages/pyimagetool/__init__.py",
line 2, in <module>
from .ImageTool import ImageTool
File "/usr/lib/python3/dist-packages/pyimagetool/ImageTool.py",
line 8, in <module>
from .widgets import InfoBar
File "/usr/lib/python3/dist-packages/pyimagetool/widgets.py",
line 6, in <module>
from .cmaps import CMap
File
"/usr/lib/python3/dist-packages/pyimagetool/cmaps/__init__.py", line
1, in <module>
from .CMap import CMap
File "/usr/lib/python3/dist-packages/pyimagetool/cmaps/CMap.py",
line 66, in <module>
raise OSError(
OSError: Packaged data files are not writeable, use a helper
script.See /usr/share/pyimagetool/debian_pyimagetool.py
*refnx*: QT5 error on bookworm, invalid C extensions and missing
numpy.typing on bullseye
installs OK on both bookworm and bullseye.
but there is an error launching command 'refnx'
bookworm error:
$ refnx
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:200:
UserWarning: Can't use the C abeles backend
warnings.warn("Can't use the C abeles backend")
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:233:
UserWarning: Using the SLOW reflectivity calculation.
warnings.warn("Using the SLOW reflectivity calculation.")
Traceback (most recent call last):
File "/usr/bin/refnx", line 33, in <module>
sys.exit(load_entry_point('refnx==0.1.33', 'gui_scripts',
'refnx')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/usr/lib/python3/dist-packages/refnx/reflect/_app/__init__.py",
line 54, in main
sys.exit(gui(expt_file=expt_file))
^^^^^^^^^^^^^^^^^^^^^^^^
File
"/usr/lib/python3/dist-packages/refnx/reflect/_app/__init__.py",
line 5, in gui
from qtpy import QtGui, QtWidgets, QtCore
File "/usr/lib/python3/dist-packages/qtpy/QtGui.py", line 14, in
<module>
from PyQt5.QtGui import *
ImportError: /usr/lib/python3/dist-packages/PyQt5/QtGui.abi3.so:
undefined symbol: _ZN15QSessionManager16staticMetaObjectE, version Qt_5
bullseye error:
$ refnx
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:200:
UserWarning: Can't use the C abeles backend
warnings.warn("Can't use the C abeles backend")
/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py:233:
UserWarning: Using the SLOW reflectivity calculation.
warnings.warn("Using the SLOW reflectivity calculation.")
Traceback (most recent call last):
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 196, in get_reflect_backend
from refnx.reflect import _creflect as _c
ImportError: cannot import name '_creflect' from partially
initialized module 'refnx.reflect' (most likely due to a circular
import) (/usr/lib/py
thon3/dist-packages/refnx/reflect/__init__.py)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/bin/refnx", line 33, in <module>
sys.exit(load_entry_point('refnx==0.1.33', 'gui_scripts',
'refnx')())
File "/usr/bin/refnx", line 25, in importlib_load_entry_point
return next(matches).load()
File "/usr/lib/python3.9/importlib/metadata.py", line 77, in load
module = import_module(match.group('module'))
File "/usr/lib/python3.9/importlib/__init__.py", line 127, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "<frozen importlib._bootstrap>", line 1030, in _gcd_import
File "<frozen importlib._bootstrap>", line 1007, in _find_and_load
File "<frozen importlib._bootstrap>", line 986, in
_find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 680, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 790, in
exec_module
File "<frozen importlib._bootstrap>", line 228, in
_call_with_frames_removed
File "/usr/lib/python3/dist-packages/refnx/reflect/__init__.py",
line 3, in <module>
from refnx.reflect.reflect_model import (
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 242, in <module>
kernel = get_reflect_backend("c")
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 201, in get_reflect_backend
return get_reflect_backend("python")
File
"/usr/lib/python3/dist-packages/refnx/reflect/reflect_model.py",
line 236, in get_reflect_backend
from refnx.reflect import _reflect as _py
File "/usr/lib/python3/dist-packages/refnx/reflect/_reflect.py",
line 28, in <module>
import numpy.typing as npt
ModuleNotFoundError: No module named 'numpy.typing'
*ufo-tofu*: opencl error
installs OK on bookworm and bullseye.
'tofu flow' command brings an error related to OpenCL. Hard to
debug. 'tofu ez' works.
*bioxtas-raw*: error with colorcet version
installs ok on bookworm, not on bullseye (req py >= 3.11)
error when launching command bioxtas_raw and launcher
$ more bioxtas-raw-README.txt
$ bioxtas_raw
Traceback (most recent call last):
File "/usr/bin/bioxtas_raw", line 33, in <module>
sys.exit(load_entry_point('bioxtasraw==2.1.1', 'gui_scripts',
'bioxtas_raw')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/bin/bioxtas_raw", line 25, in importlib_load_entry_point
return next(matches).load()
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/importlib/metadata/__init__.py", line
202, in load
module = import_module(match.group('module'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/importlib/__init__.py", line 126, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
File "<frozen importlib._bootstrap>", line 1149, in
_find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in
exec_module
File "<frozen importlib._bootstrap>", line 241, in
_call_with_frames_removed
File "/usr/lib/python3/dist-packages/bioxtasraw/RAW.py", line 61,
in <module>
import pyFAI, pyFAI.calibrant, pyFAI.control_points
File "/usr/lib/python3/dist-packages/pyFAI/__init__.py", line 54,
in <module>
from .utils import decorators
File "/usr/lib/python3/dist-packages/pyFAI/utils/__init__.py",
line 55, in <module>
from .. import resources
File
"/usr/lib/python3/dist-packages/pyFAI/resources/__init__.py", line
72, in <module>
import pkg_resources
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3248, in <module>
@_call_aside
^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3223, in _call_aside
f(*args, **kwargs)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 3261, in _initialize_master_working_set
working_set = WorkingSet._build_master()
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 617, in _build_master
ws.require(__requires__)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 956, in require
needed = self.resolve(parse_requirements(requirements))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 815, in resolve
dist = self._resolve_dist(
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 844, in _resolve_dist
env = Environment(self.entries)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1044, in __init__
self.scan(search_path)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1077, in scan
self.add(dist)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 1096, in add
dists.sort(key=operator.attrgetter('hashcmp'), reverse=True)
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 2631, in hashcmp
self.parsed_version,
^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py",
line 2679, in parsed_version
self._parsed_version = parse_version(self.version)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/usr/lib/python3/dist-packages/pkg_resources/_vendor/packaging/version.py",
line 266, in __init__
raise InvalidVersion(f"Invalid version: '{version}'")
pkg_resources.extern.packaging.version.InvalidVersion: Invalid
version: 'None'
(package: colorcet)
*xrt*: QT5 error on bookworm (as above)
installs OK on both bookworm and bullseye
error when starting on bookworm
*tomopy*: wrong naming of lib.so files on bookworm
import tomopy brings
ModuleNotFoundError: The following shared library is missing:
/usr/lib/python3/dist-packages/tomopy/util/extern/libtomopy-recon.so
$ ls /usr/lib/python3/dist-packages/tomopy/util/extern/
__init__.py libtomopy-accel.cpython-311-x86_64-linux-gnu.so misc.py
__pycache__ libtomopy-misc.cpython-311-x86_64-linux-gnu.so prep.py
accel.py libtomopy-prep.cpython-311-x86_64-linux-gnu.so recon.py
gridrec.py libtomopy-recon.cpython-311-x86_64-linux-gnu.so
so the debian library naming scheme is not compatible with what
tomopy expects
*tomogui/freeart and xrstools*: not installable (SID)
seems to be uninstalable on both bookworm (req py < 3.11) and
bullseye (req py > 3.10)
even if not maintained anymore, could we build/push a version that
works on bookworm ?
*navarp*:
install OK on both bookworm and bullseye
works OK on bullseye, error on bookworm with command 'navarp'
$ navarp
Traceback (most recent call last):
File "/usr/bin/navarp", line 33, in <module>
sys.exit(load_entry_point('navarp==1.3.0', 'console_scripts',
'navarp')())
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/bin/navarp", line 25, in importlib_load_entry_point
return next(matches).load()
^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/importlib/metadata/__init__.py", line
202, in load
module = import_module(match.group('module'))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/usr/lib/python3.11/importlib/__init__.py", line 126, in
import_module
return _bootstrap._gcd_import(name[level:], package, level)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "<frozen importlib._bootstrap>", line 1206, in _gcd_import
File "<frozen importlib._bootstrap>", line 1178, in _find_and_load
File "<frozen importlib._bootstrap>", line 1149, in
_find_and_load_unlocked
File "<frozen importlib._bootstrap>", line 690, in _load_unlocked
File "<frozen importlib._bootstrap_external>", line 940, in
exec_module
File "<frozen importlib._bootstrap>", line 241, in
_call_with_frames_removed
File "/usr/lib/python3/dist-packages/navarp/navarp_gui.py", line
38, in <module>
from matplotlib.backends.backend_qt5agg import (
File
"/usr/lib/python3/dist-packages/matplotlib/backends/backend_qt5agg.py",
line 7, in <module>
from .backend_qtagg import ( # noqa: F401, E402 # pylint:
disable=W0611
File
"/usr/lib/python3/dist-packages/matplotlib/backends/backend_qtagg.py",
line 9, in <module>
from .qt_compat import QT_API, _enum, _setDevicePixelRatio
File
"/usr/lib/python3/dist-packages/matplotlib/backends/qt_compat.py",
line 137, in <module>
raise ImportError(
ImportError: Failed to import any of the following Qt binding
modules: PyQt6, PySide6, PyQt5, PySide2
the error persists even after installing python3-pyside2.*
python3-pyqt5.* python3-pyqt6.*
*genx*: install and works OK (3.6) on both bookworm and bullseye
Cheers, Emmanuel.
--
signature
/ ___|__/\_| | | ____|_ _| | FARHI Emmanuel
\___ \\ | | | _| | || | Div Exp/Data Reduction and Analysis Team
___) /_ _| |___| |___ | || |___ Tel : +33 (1) 69 35 96 04
<callto:+33%20%281%29%2069%2035%2096%2004>
|____/ \/ |_____|_____|___|_____| Saint-Aubin BP 48 - 91192 GIF/YVETTE
CEDEX
SYNCHROTRON http://www.synchrotron-soleil.fr
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://alioth-lists.debian.net/pipermail/debian-pan-maintainers/attachments/20230809/d9f4cf79/attachment-0001.htm>
More information about the Debian-pan-maintainers
mailing list