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spyder-ide / spyder

Official repository for Spyder - The Scientific Python Development Environment
https://www.spyder-ide.org
MIT License
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Spyder fails to start in Wayland only desktop environment #20206

Open pemd-sys opened 1 year ago

pemd-sys commented 1 year ago

Issue Report Checklist

Problem Description

Spyder install fails after following the installation steps for pip according to the installation guide https://docs.spyder-ide.org/current/installation.html

What steps reproduce the problem?

  1. python3 -m venv spyder-env
  2. source spyder-env/bin/activate
  3. pip install spyder

What is the expected output? What do you see instead?

Check initial Pip packages 

matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ pip3 list

Package                Version
---------------------- ---------------
apturl                 0.5.2
blinker                1.4
Brlapi                 0.8.3
certifi                2020.6.20
chardet                4.0.0
click                  8.0.3
colorama               0.4.4
command-not-found      0.3
cryptography           3.4.8
cupshelpers            1.0
dbus-python            1.2.18
defer                  1.0.6
distlib                0.3.6
distro                 1.7.0
distro-info            1.1build1
filelock               3.8.2
httplib2               0.20.2
idna                   3.3
importlib-metadata     4.6.4
jeepney                0.7.1
keyring                23.5.0
language-selector      0.1
launchpadlib           1.10.16
lazr.restfulclient     0.14.4
lazr.uri               1.0.6
louis                  3.20.0
macaroonbakery         1.3.1
more-itertools         8.10.0
netifaces              0.11.0
oauthlib               3.2.0
olefile                0.46
pexpect                4.8.0
Pillow                 9.0.1
pip                    22.0.2
platformdirs           2.6.0
protobuf               3.12.4
ptyprocess             0.7.0
pycairo                1.20.1
pycups                 2.0.1
PyGObject              3.42.1
PyJWT                  2.4.0
pymacaroons            0.13.0
PyNaCl                 1.5.0
pyparsing              2.4.7
pyRFC3339              1.1
python-apt             2.3.0+ubuntu2.1
python-dateutil        2.8.1
python-debian          0.1.43ubuntu1
pytz                   2022.1
pyxdg                  0.27
PyYAML                 5.4.1
reportlab              3.6.8
requests               2.25.1
SecretStorage          3.3.1
setuptools             59.6.0
six                    1.16.0
systemd-python         234
ubuntu-advantage-tools 27.9
ubuntu-drivers-common  0.0.0
ufw                    0.36.1
unattended-upgrades    0.1
urllib3                1.26.5
virtualenv             20.17.1
wadllib                1.3.6
wheel                  0.37.1
xdg                    5
xkit                   0.0.0
zipp                   1.0.0

Install Virtual Environment package

matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ sudo apt-get install python3-venv
[sudo] password for matrix: 
Reading package lists... Done
Building dependency tree... Done
Reading state information... Done
The following package was automatically installed and is no longer required:
  systemd-hwe-hwdb
Use 'sudo apt autoremove' to remove it.
The following additional packages will be installed:
  python3-pip-whl python3-setuptools-whl python3.10-venv
The following NEW packages will be installed
  python3-pip-whl python3-setuptools-whl python3-venv python3.10-venv
0 to upgrade, 4 to newly install, 0 to remove and 183 not to upgrade.
Need to get 2,474 kB of archives.
After this operation, 2,888 kB of additional disk space will be used.
Do you want to continue? [Y/n] Y
Get:1 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64 python3-pip-whl all 22.0.2+dfsg-1 [1,679 kB]
Get:2 http://gb.archive.ubuntu.com/ubuntu jammy/universe amd64 python3-setuptools-whl all 59.6.0-1.2 [788 kB]
Get:3 http://gb.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3.10-venv amd64 3.10.6-1~22.04.2 [5,722 B]
Get:4 http://gb.archive.ubuntu.com/ubuntu jammy-updates/universe amd64 python3-venv amd64 3.10.6-1~22.04 [1,038 B]
Fetched 2,474 kB in 2s (1,000 kB/s)
Selecting previously unselected package python3-pip-whl.
(Reading database ... 180980 files and directories currently installed.)
Preparing to unpack .../python3-pip-whl_22.0.2+dfsg-1_all.deb ...
Unpacking python3-pip-whl (22.0.2+dfsg-1) ...
Selecting previously unselected package python3-setuptools-whl.
Preparing to unpack .../python3-setuptools-whl_59.6.0-1.2_all.deb ...
Unpacking python3-setuptools-whl (59.6.0-1.2) ...
Selecting previously unselected package python3.10-venv.
Preparing to unpack .../python3.10-venv_3.10.6-1~22.04.2_amd64.deb ...
Unpacking python3.10-venv (3.10.6-1~22.04.2) ...
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Unpacking python3-venv (3.10.6-1~22.04) ...
Setting up python3-setuptools-whl (59.6.0-1.2) ...
Setting up python3-pip-whl (22.0.2+dfsg-1) ...
Setting up python3.10-venv (3.10.6-1~22.04.2) ...
Setting up python3-venv (3.10.6-1~22.04) ...

Activate virtual Environment and install spyder

matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ python3 -m venv spyder-env

matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ source spyder-env/bin/activate

(spyder-env) matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ pip install spyder
Collecting spyder
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Requirement already satisfied: setuptools>=49.6.0 in ./spyder-env/lib/python3.10/site-packages (from spyder) (59.6.0)
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  Using cached pytoolconfig-1.2.4-py3-none-any.whl (16 kB)
Collecting cryptography>=2.0
  Using cached cryptography-38.0.4-cp36-abi3-manylinux_2_28_x86_64.whl (4.2 MB)
Collecting webencodings>=0.4
  Using cached webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
Collecting soupsieve>1.2
  Using cached soupsieve-2.3.2.post1-py3-none-any.whl (37 kB)
Collecting six>=1.9.0
  Using cached six-1.16.0-py2.py3-none-any.whl (11 kB)
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Collecting cffi>=1.12
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Collecting pycparser
  Using cached pycparser-2.21-py2.py3-none-any.whl (118 kB)
Using legacy 'setup.py install' for atomicwrites, since package 'wheel' is not installed.
Using legacy 'setup.py install' for intervaltree, since package 'wheel' is not installed.
Using legacy 'setup.py install' for jellyfish, since package 'wheel' is not installed.
Building wheels for collected packages: lazy-object-proxy
  Building wheel for lazy-object-proxy (pyproject.toml) ... done
  Created wheel for lazy-object-proxy: filename=lazy_object_proxy-1.8.0-cp310-cp310-linux_x86_64.whl size=58666 sha256=fc1a340d8352fa034fef62a82f62378a488bda7900b0d11c403b75b59be90d7b
  Stored in directory: /home/matrix/.cache/pip/wheels/14/14/c4/2ae0f79a7e70a883c6f54368f6ec4b847018dbcf555546dded
Successfully built lazy-object-proxy
Installing collected packages: yapf, webencodings, wcwidth, text-unidecode, sortedcontainers, snowballstemmer, pyxdg, pytz, PyQtWebEngine-Qt5, PyQt5-Qt5, ptyprocess, pickleshare, mypy-extensions, mistune, ipython-genutils, fastjsonschema, backcall, alabaster, zipp, wurlitzer, wrapt, whatthepatch, watchdog, urllib3, ujson, traitlets, tornado, tomlkit, tomli, toml, tinycss2, textdistance, sphinxcontrib-serializinghtml, sphinxcontrib-qthelp, sphinxcontrib-jsmath, sphinxcontrib-htmlhelp, sphinxcontrib-devhelp, sphinxcontrib-applehelp, soupsieve, six, rtree, pyzmq, pyyaml, python-slugify, pyrsistent, PyQt5-sip, pylint-venv, pygments, pyflakes, pydocstyle, pycparser, pycodestyle, psutil, prompt-toolkit, pluggy, platformdirs, pexpect, pathspec, parso, pandocfilters, packaging, nest-asyncio, more-itertools, mccabe, markupsafe, lazy-object-proxy, jupyterlab-pygments, jellyfish, jeepney, isort, intervaltree, inflection, imagesize, idna, entrypoints, docutils, docstring-to-markdown, dill, diff-match-patch, defusedxml, decorator, debugpy, cloudpickle, click, charset-normalizer, chardet, certifi, babel, attrs, atomicwrites, three-merge, requests, qtpy, qstylizer, pytoolconfig, python-lsp-jsonrpc, python-dateutil, pyqt5, matplotlib-inline, jupyter-core, jsonschema, Jinja2, jedi, jaraco.classes, importlib-metadata, flake8, comm, cffi, bleach, black, binaryornot, beautifulsoup4, autopep8, astroid, sphinx, qtawesome, qdarkstyle, python-lsp-server, pyqtwebengine, pylint, nbformat, jupyter-client, ipython, cryptography, arrow, SecretStorage, rope, python-lsp-black, pyls-spyder, numpydoc, nbclient, jinja2-time, ipykernel, spyder-kernels, qtconsole, nbconvert, keyring, cookiecutter, spyder
  Running setup.py install for jellyfish ... done
  Running setup.py install for intervaltree ... done
  Running setup.py install for atomicwrites ... done
Successfully installed Jinja2-3.1.2 PyQt5-Qt5-5.15.2 PyQt5-sip-12.11.0 PyQtWebEngine-Qt5-5.15.2 SecretStorage-3.3.3 alabaster-0.7.12 arrow-1.2.3 astroid-2.12.13 atomicwrites-1.4.1 attrs-22.1.0 autopep8-1.6.0 babel-2.11.0 backcall-0.2.0 beautifulsoup4-4.11.1 binaryornot-0.4.4 black-22.12.0 bleach-5.0.1 certifi-2022.12.7 cffi-1.15.1 chardet-5.1.0 charset-normalizer-2.1.1 click-8.1.3 cloudpickle-2.2.0 comm-0.1.2 cookiecutter-2.1.1 cryptography-38.0.4 debugpy-1.6.4 decorator-5.1.1 defusedxml-0.7.1 diff-match-patch-20200713 dill-0.3.6 docstring-to-markdown-0.11 docutils-0.19 entrypoints-0.4 fastjsonschema-2.16.2 flake8-5.0.4 idna-3.4 imagesize-1.4.1 importlib-metadata-5.1.0 inflection-0.5.1 intervaltree-3.1.0 ipykernel-6.19.2 ipython-7.34.0 ipython-genutils-0.2.0 isort-5.11.2 jaraco.classes-3.2.3 jedi-0.18.2 jeepney-0.8.0 jellyfish-0.9.0 jinja2-time-0.2.0 jsonschema-4.17.3 jupyter-client-7.4.8 jupyter-core-5.1.0 jupyterlab-pygments-0.2.2 keyring-23.11.0 lazy-object-proxy-1.8.0 markupsafe-2.1.1 matplotlib-inline-0.1.6 mccabe-0.7.0 mistune-2.0.4 more-itertools-9.0.0 mypy-extensions-0.4.3 nbclient-0.7.2 nbconvert-7.2.6 nbformat-5.7.0 nest-asyncio-1.5.6 numpydoc-1.5.0 packaging-22.0 pandocfilters-1.5.0 parso-0.8.3 pathspec-0.10.3 pexpect-4.8.0 pickleshare-0.7.5 platformdirs-2.6.0 pluggy-1.0.0 prompt-toolkit-3.0.36 psutil-5.9.4 ptyprocess-0.7.0 pycodestyle-2.9.1 pycparser-2.21 pydocstyle-6.1.1 pyflakes-2.5.0 pygments-2.13.0 pylint-2.15.8 pylint-venv-2.3.0 pyls-spyder-0.4.0 pyqt5-5.15.7 pyqtwebengine-5.15.6 pyrsistent-0.19.2 python-dateutil-2.8.2 python-lsp-black-1.2.1 python-lsp-jsonrpc-1.0.0 python-lsp-server-1.6.0 python-slugify-7.0.0 pytoolconfig-1.2.4 pytz-2022.6 pyxdg-0.28 pyyaml-6.0 pyzmq-24.0.1 qdarkstyle-3.0.3 qstylizer-0.2.2 qtawesome-1.2.1 qtconsole-5.4.0 qtpy-2.3.0 requests-2.28.1 rope-1.6.0 rtree-1.0.1 six-1.16.0 snowballstemmer-2.2.0 sortedcontainers-2.4.0 soupsieve-2.3.2.post1 sphinx-5.3.0 sphinxcontrib-applehelp-1.0.2 sphinxcontrib-devhelp-1.0.2 sphinxcontrib-htmlhelp-2.0.0 sphinxcontrib-jsmath-1.0.1 sphinxcontrib-qthelp-1.0.3 sphinxcontrib-serializinghtml-1.1.5 spyder-5.4.0 spyder-kernels-2.4.0 text-unidecode-1.3 textdistance-4.5.0 three-merge-0.1.1 tinycss2-1.2.1 toml-0.10.2 tomli-2.0.1 tomlkit-0.11.6 tornado-6.2 traitlets-5.7.1 ujson-5.6.0 urllib3-1.26.13 watchdog-2.2.0 wcwidth-0.2.5 webencodings-0.5.1 whatthepatch-1.0.3 wrapt-1.14.1 wurlitzer-3.0.3 yapf-0.32.0 zipp-3.11.0

Launch Spyder

(spyder-env) matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ spyder
Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
Could not load the Qt platform plugin "xcb" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: eglfs, linuxfb, minimal, minimalegl, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, webgl, xcb.

Aborted (core dumped)
(spyder-env) matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$

Paste Traceback/Error Below (if applicable)


PASTE TRACEBACK HERE

Versions

Dependencies

PASTE DEPENDENCIES HERE
ccordoba12 commented 1 year ago

Hey @pemd-sys, thanks for reporting. I think this happens because you're running a Wayland session and not an Xorg one, which can be inferred from the first line of the messages shows when Spyder is launched:

Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.

The message also seems to give the solution to your problem, i.e. that you need to start Spyder like this:

QT_QPA_PLATFORM=wayland spyder

Please try that and let us know if it works for you.

pemd-sys commented 1 year ago

Thank you @ccordoba12. Spyder Works ! I got a few messages in the terminal (see below) when i run with the suggested command, but otherwise it loads just fine. On another note is there a install guide for using it inside a docker. I got a scientific package which runs inside docker container and i was wondering if there is already documented guide to doing this properly.

(spyder-env) matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ QT_QPA_PLATFORM=wayland spyder &
[1] 2414
(spyder-env) matrix@matrix-Standard-PC-i440FX-PIIX-1996:~$ Warning: Ignoring XDG_SESSION_TYPE=wayland on Gnome. Use QT_QPA_PLATFORM=wayland to run on Wayland anyway.
QSocketNotifier: Can only be used with threads started with QThread
fromIccProfile: failed minimal tag size sanity
Wayland does not support QWindow::requestActivate()
ccordoba12 commented 1 year ago

Thank you @ccordoba12. Spyder Works !

Great! I'm glad it works for you now.

On another note is there a install guide for using it inside a docker

No, there isn't. But in that case I wouldn't recommend you to install Spyder inside your docker instance. Instead, you should install Spyder-kernels and then connect to it using our instructions here.

berniyh commented 1 year ago

Hm, for me it doesn't work even when specifying the Qt platform plugin:

(base) berniyh@orionis:~ [i] $ QT_QPA_PLATFORM=wayland spyder              

Could not load the Qt platform plugin "wayland" in "" even though it was found.
This application failed to start because no Qt platform plugin could be initialized. Reinstalling the application may fix this problem.

Available platform plugins are: minimal, offscreen, vnc, wayland-egl, wayland, wayland-xcomposite-egl, wayland-xcomposite-glx, xcb, eglfs, minimalegl, webgl.

zsh: IOT instruction (core dumped)  QT_QPA_PLATFORM=wayland spyder

Just did a fresh anaconda installation + conda update. Out of the given options, only eglfs starts up, but it's fullscreen and not really usable. Also, I removed ~/.config/spyder-py3, just to be sure it's not some config problem, but that didn't help either.

berniyh commented 1 year ago

Here is what I get with coredumpctl: https://gist.github.com/berniyh/f9f2e0e0a47ea185a3ea710b33bebd66

berniyh commented 1 year ago

Ok, I got it working. The problem, which I already suspected, but wasn't sure about, was that it tried to use the system Qt instead of the one by anaconda. Doing unset QT_PLUGIN_PATH in the anaconda environment did the trick and spyder came up fine.

ccordoba12 commented 1 year ago

Great! I'm glad you figured it out how to solve that problem.

thinktankmohan commented 7 months ago

QT_QPA_PLATFORM=wayland spyder

Based on yours recommendation. It works! Thanks a Lot