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spyder-ide / spyder

Official repository for Spyder - The Scientific Python Development Environment
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Update mechanism not working for Spyder 6.0 installed from Fedora distro package #22407

Closed dvlierop closed 4 weeks ago

dvlierop commented 2 months ago

Description

What steps will reproduce the problem?

I closed a tab in the IPython Console view, and then it crashed

Versions

Dependencies

# Mandatory:
atomicwrites >=1.2.0              :  1.4.1 (OK)
chardet >=2.0.0                   :  5.2.0 (OK)
cloudpickle >=0.5.0               :  3.0.0 (OK)
cookiecutter >=1.6.0              :  2.6.0 (OK)
diff_match_patch >=20181111       :  20230430 (OK)
intervaltree >=3.0.2              :  3.1.0 (OK)
IPython >=8.13.0,<9.0.0,!=8.17.1  :  8.23.0 (OK)
jedi >=0.17.2,<0.20.0             :  0.19.1 (OK)
jellyfish >=0.7                   :  0.9.0 (OK)
jsonschema >=3.2.0                :  4.19.1 (OK)
keyring >=17.0.0                  :  24.3.1 (OK)
nbconvert >=4.0                   :  7.16.0 (OK)
numpydoc >=0.6.0                  :  1.6.0 (OK)
parso >=0.7.0,<0.9.0              :  0.8.3 (OK)
pexpect >=4.4.0                   :  4.9.0 (OK)
pickleshare >=0.4                 :  0.7.5 (OK)
psutil >=5.3                      :  5.9.8 (OK)
pygments >=2.0                    :  2.17.2 (OK)
pylint >=3.1                      :  3.2.5 (OK)
pylint_venv >=3.0.2               :  3.0.2 (OK)
pyls_spyder >=0.4.0               :  0.4.0 (OK)
pylsp >=1.11.0,<1.12.0            :  1.11.0 (OK)
pylsp_black >=2.0.0,<3.0.0        :  2.0.0 (OK)
pyuca >=1.2                       :  1.2 (OK)
qdarkstyle >=3.2.0,<3.3.0         :  3.2.3 (OK)
qstylizer >=0.2.2                 :  0.2.2 (OK)
qtawesome >=1.3.1,<1.4.0          :  1.3.1 (OK)
qtconsole >=5.5.1,<5.6.0          :  5.5.1 (OK)
qtpy >=2.4.0                      :  2.4.1 (OK)
rtree >=0.9.7                     :  1.3.0 (OK)
setuptools >=49.6.0               :  69.0.3 (OK)
sphinx >=0.6.6                    :  7.2.6 (OK)
spyder_kernels >=3.0.0b5,<3.0.0b6 :  3.0.0b5 (OK)
superqt >=0.6.1,<1.0.0            :  0.6.7 (OK)
textdistance >=4.2.0              :  4.6.2 (OK)
three_merge >=0.1.1               :  0.1.1 (OK)
watchdog >=0.10.3                 :  3.0.0 (OK)
xdg >=0.26                        :  0.27 (OK)
zmq >=24.0.0                      :  25.1.1 (OK)

# Optional:
cython >=0.21                     :  None (NOK)
matplotlib >=3.0.0                :  3.8.4 (OK)
numpy >=1.7                       :  1.26.4 (OK)
pandas >=1.1.1                    :  2.2.1 (OK)
scipy >=0.17.0                    :  1.11.3 (OK)
sympy >=0.7.3                     :  None (NOK)

Environment

Environment ``` Package Version ----------------------------- ------------------- aiodns 3.0.0 aiohttp 3.9.5 aiosignal 1.3.1 alabaster 0.7.16 appdirs 1.4.4 argcomplete 3.3.0 arrow 1.2.3 astroid 3.2.3 asttokens 2.4.1 atomicwrites 1.4.1 attrs 23.2.0 autopep8 2.0.4 babel 2.16.0 Beaker 1.12.1 beautifulsoup4 4.12.3 binaryornot 0.4.4 black 24.4.2 bleach 6.1.0 blivet 3.10.0 blivet-gui 2.5.0 blosc2 2.5.1 boto3 1.34.162 botocore 1.34.162 Bottleneck 1.3.7 Brlapi 0.8.5 Brotli 1.1.0 cachetools 5.3.2 cffi 1.16.0 chardet 5.2.0 charset-normalizer 3.3.2 click 8.1.7 cloudpickle 3.0.0 comm 0.2.1 contourpy 1.2.0 cookiecutter 2.6.0 cryptography 41.0.7 cssselect 1.1.0 cupshelpers 1.0 cycler 0.11.0 dasbus 1.7 dbus-python 1.3.2 decorator 5.1.1 defusedxml 0.7.1 diff-match-patch 20230430 dill 0.3.8 distro 1.9.0 dnf 4.21.1 docstring-to-markdown 0.15 docutils 0.20.1 entrypoints 0.4 et-xmlfile 1.1.0 executing 2.0.1 fastjsonschema 2.18.0 fedora-third-party 0.10 file-magic 0.4.0 flake8 6.0.0 fonttools 4.50.0 fros 1.1 frozenlist 1.4.1 fs 2.4.16 fsspec 2024.6.1 gcsfs 2023.6.0+1.g7cc53d9 google-api-core 2.11.1 google-auth 2.34.0 google-auth-oauthlib 0.8.0 google-cloud-core 2.3.3 google-cloud-storage 2.14.0 google-crc32c 1.5.0 google-resumable-media 2.7.2 googleapis-common-protos 1.63.0 greenlet 3.0.3 grpcio 1.48.4 grpcio-status 1.48.4 helpdev 0.7.1 html5lib 1.1 humanize 3.13.1 idna 3.7 imagesize 1.4.1 importlib-metadata 6.9.0 inflection 0.5.1 inkex 1.3.1 intervaltree 3.1.0 ipykernel 6.29.3 ipython 8.23.0 iso639 0.1.4 isort 5.13.2 jaraco.classes 3.3.0 jdcal 1.4.1 jedi 0.19.1 jeepney 0.8.0 jellyfish 0.9.0 Jinja2 3.1.4 jinja2-time 0.2.0 jmespath 1.0.1 jsonschema 4.19.1 jsonschema-specifications 2023.11.2 jupyter_client 7.4.9 jupyter_core 5.1.0 jupyterlab_pygments 0.3.0 keyring 24.3.1 kiwisolver 1.4.5 langtable 0.0.68 libcomps 0.1.20 libdnf 0.73.3 libsass 0.23.0 louis 3.28.0 lxml 5.1.0 Mako 1.2.3 markdown-it-py 3.0.0 MarkupSafe 2.1.3 matplotlib 3.8.4 matplotlib-inline 0.1.6 mccabe 0.7.0 mdurl 0.1.2 mistune 2.0.4 more-itertools 10.1.0 msgpack 1.0.6 multidict 6.0.5 mypy-extensions 1.0.0 nbclient 0.9.0 nbconvert 7.16.0 nbformat 5.9.2 ndindex 1.7 nest-asyncio 1.6.0 netifaces 0.11.0 nftables 0.1 numexpr 2.8.5 numpy 1.26.4 numpydoc 1.6.0 oauthlib 3.2.2 odfpy 1.4.1 olefile 0.47 openpyxl 3.1.2 packaging 23.2 pandas 2.2.1 pandocfilters 1.5.1 parso 0.8.3 Paste 3.7.1 pathspec 0.12.1 pexpect 4.9.0 pickleshare 0.7.5 pid 2.2.3 pillow 10.3.0 pip 23.3.2 platformdirs 3.11.0 pluggy 1.3.0 ply 3.11 pooch 1.8.2 productmd 1.38 prompt-toolkit 3.0.41 protobuf 3.19.6 psutil 5.9.8 psycopg2 2.9.9 ptyprocess 0.7.0 pure-eval 0.2.2 pwquality 1.4.5 py-cpuinfo 9.0.0 pyarrow 15.0.2 pyasn1 0.5.1 pyasn1-modules 0.3.0 pycairo 1.25.1 pycares 4.3.0 pycodestyle 2.10.0 pycparser 2.20 pycrypto 2.6.1 pycups 2.0.4 pydocstyle 6.3.0 pyenchant 3.2.2 pyflakes 3.0.1 Pygments 2.17.2 PyGObject 3.48.2 pykickstart 3.52 pylint 3.2.5 pylint-venv 3.0.2 pyls-spyder 0.4.0 PyMySQL 1.1.1 pyOpenSSL 23.2.0 pyparsing 3.1.2 pyparted 3.13.0 PyQt5 5.15.10 PyQt5-sip 12.13.0 PyQtWebEngine 5.15.6 pyserial 3.5 PySocks 1.7.1 python-augeas 1.1.0 python-dateutil 2.8.2 python-gettext 4.0 python-lsp-black 2.0.0 python-lsp-jsonrpc 1.1.2 python-lsp-server 1.11.0 python-manatools 0.0.4 python-meh 0.51 python-pam 2.0.2 python-slugify 6.1.2 pytoolconfig 1.3.1 pytz 2024.1 pyuca 1.2 pyudev 0.24.1 pyxdg 0.27 PyYAML 6.0.1 pyzmq 25.1.1 QDarkStyle 3.2.3 qstylizer 0.2.2 QtAwesome 1.3.1 qtconsole 5.5.1 QtPy 2.4.1 qtsass 0.4.0 referencing 0.31.1 regex 2024.4.16 requests 2.31.0 requests-file 2.0.0 requests-ftp 0.3.1 requests-oauthlib 1.3.1 rich 13.7.0 rope 1.13.0 rpds-py 0.18.1 rpm 4.19.1.1 rsa 4.9 Rtree 1.3.0 s3transfer 0.10.2 SciPy 1.11.3 scour 0.38.2 SecretStorage 3.3.3 selinux 3.6 sepolicy 3.6 setools 4.5.1 setuptools 69.0.3 shtab 1.6.1 simpleaudio 1.0.4 simpleline 1.9.0 six 1.16.0 snowballstemmer 2.2.0 sortedcontainers 2.4.0 sos 4.7.2 soupsieve 2.5 Sphinx 7.2.6 sphinxcontrib-devhelp 1.0.5 sphinxcontrib-htmlhelp 2.0.4 sphinxcontrib-qthelp 1.0.6 sphinxcontrib-serializinghtml 1.1.9 spyder 6.0.0a5 spyder-kernels 3.0.0b5 SQLAlchemy 2.0.32 stack-data 0.6.3 superqt 0.6.7 systemd-python 235 tables 3.9.2 tabulate 0.9.0 Tempita 0.5.2 text-unidecode 1.3 textdistance 4.6.3 three-merge 0.1.1 tinycss2 1.2.1 tomli 2.0.1 tomlkit 0.12.3 tornado 6.3.3 traitlets 5.14.1 typing_extensions 4.12.2 ujson 5.9.0 urllib3 1.26.19 watchdog 3.0.0 wcwidth 0.2.13 webencodings 0.5.1 whatthepatch 1.0.2 wurlitzer 3.1.1 wxPython 4.2.1 xarray 2023.8.0 xkbregistry 0.3 xlrd 2.0.1 XlsxWriter 3.1.9 yapf 0.40.2 yarl 1.9.4 zipp 3.17.0 zstandard 0.22.0 ```
dvlierop commented 2 months ago

Fedora 40, Wayland, should that be of interest. This happens to any empty console, without any history of code being ran, even immediately after startup, on a system that was freshly installed only a few days ago.

When started from a terminal, I see this output, printed at startup, so WAY BEFORE the crash: `` QSocketNotifier: Can only be used with threads started with QThread

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: GFileInfo created without standard::icon

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: GFileInfo created without standard::icon

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: GFileInfo created without standard::icon

(python3:34009): GLib-GIO-CRITICAL **: 14:42:50.656: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached Wayland does not support QWindow::requestActivate() /usr/lib/python3.12/site-packages/jupyter_client/threaded.py:73: RuntimeWarning: ZMQStream only supports the base zmq.Socket class.

            Use zmq.Socket(shadow=other_socket)
            or `ctx.socket(zmq.DEALER, socket_class=zmq.Socket)`
            to create a base zmq.Socket object,
            no matter what other kind of socket your Context creates.

self.stream = zmqstream.ZMQStream(self.socket, self.ioloop) /usr/lib/python3.12/site-packages/jupyter_client/threaded.py:73: RuntimeWarning: ZMQStream only supports the base zmq.Socket class.

            Use zmq.Socket(shadow=other_socket)
            or `ctx.socket(zmq.SUB, socket_class=zmq.Socket)`
            to create a base zmq.Socket object,
            no matter what other kind of socket your Context creates.

self.stream = zmqstream.ZMQStream(self.socket, self.ioloop)

dalthviz commented 1 month ago

Hi @dvlierop thank you for the report and sorry for the late response! Could it be possible for you to check if this keeps happening with the latest release (Spyder 6.0.1)? Let us know!

dvlierop commented 1 month ago

Hi @dalthviz, thanks a lot! No need to be sorry, your reply is appreciated!

I took the lazy route and upgraded to Fedora 41; This installed 6.0.0-1.fc41 from the updates-testing repository. The frequent crashes have disappeared, so I'm happy.

Next, I tried installing 6.0.1 through the integrated automatic updater, which indeed downloaded the new version. The installation process itself however doesn't appear to get started. If you want to, then I can file a separate report for this issue, but personally I don't care as much. I'm happy to wait for updates through the Fedora channels.

I still see some warnings on the command line (although less than before), but I'm not noticing any related issues.


QSocketNotifier: Can only be used with threads started with QThread

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: GFileInfo created without standard::icon

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: GFileInfo created without standard::icon

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: GFileInfo created without standard::icon

(python3:6913): GLib-GIO-CRITICAL **: 22:33:46.534: file ../gio/gfileinfo.c: line 1765 (g_file_info_get_icon): should not be reached
Wayland does not support QWindow::requestActivate()
``
dalthviz commented 1 month ago

I took the lazy route and upgraded to Fedora 41; This installed 6.0.0-1.fc41 from the updates-testing repository. The frequent crashes have disappeared, so I'm happy.

Oh I see, so you are using the Fedora package for Spyder, we don't directly maintain that (or any of the available distro packages) but glad to hear that the latest version available works for you!

Next, I tried installing 6.0.1 through the integrated automatic updater, which indeed downloaded the new version. The installation process itself however doesn't appear to get started. If you want to, then I can file a separate report for this issue, but personally I don't care as much. I'm happy to wait for updates through the Fedora channels.

Yes please! If you think something is off with that update mechanism I think it could be worthy to give that a check :+1: In fact, do we have any logic over the update manager to detect a Spyder installation that comes from a distro package @ccordoba12 @mrclary ? As the current logic is, probably Spyder shows the same information/update message as if Spyder has been installed via pip? 🤔

I still see some warnings on the command line (although less than before), but I'm not noticing any related issues.

Maybe those are related with the Fedora's Qt/PyQt package but no idea to be honest 😅

mrclary commented 1 month ago

do we have any logic over the update manager to detect a Spyder installation that comes from a distro package @ccordoba12 @mrclary ? As the current logic is, probably Spyder shows the same information/update message as if Spyder has been installed via pip? 🤔

I still see some warnings on the command line (although less than before), but I'm not noticing any related issues.

Maybe those are related with the Fedora's Qt/PyQt package but no idea to be honest 😅

No, we don't have logic to detect distro installations; however, I think it should show up as pip, as you suspect. I don't have access to Fedora to check, though.

Next, I tried installing 6.0.1 through the integrated automatic updater, which indeed downloaded the new version. The installation process itself however doesn't appear to get started.

Yes, please open a new issue for that. If the update downloaded, but the update did not start, it may be a bash script issue on Fedora.

ccordoba12 commented 1 month ago

@mrclary, an easy fix could be to disable the auto-update mechanism if we detect we're on Linux and sys.executable in ["/usr/bin/python3", "/usr/bin/python", "/usr/local/bin/python3", "/usr/local/bin/python"]

That's where the Python executable is usually placed on Linux (the last two entries are necessary to cover custom global installations).