File permissions in WSL2 are not preserved when saving with a Windows installation of Spyder

[jtziebarth]

Issue Report Checklist

• [x] Searched the issues page for similar reports
• [x] Read the relevant sections of the Spyder Troubleshooting Guide and followed its advice
• [x] Reproduced the issue after updating with conda update spyder (or pip, if not using Anaconda)
• [x] Could not reproduce inside jupyter qtconsole (if console-related)
• [x] Tried basic troubleshooting (if a bug/error)
  • [x] Restarted Spyder
  • [x] Reset preferences with spyder --reset
  • [x] Reinstalled the latest version of Anaconda
  • [x] Tried the other applicable steps from the Troubleshooting Guide
• [x] Completed the Problem Description, Steps to Reproduce and Version sections below

Problem Description

Permissions of a file in WSL2 are not preserved when editing and saving the file using a Windows installation of Spyder.

This problem seems to have appeared before, but I'm encountering it under different circumstances.

What steps reproduce the problem?

1. Create a new file "test.py" in Windows installation of Spyder and save it to a location under the WSL2 filesystem
2. In WSL2, run stat -c '%a' test.py
3. In WSL2, run chmod +x test.py
4. In WSL2, run stat -c '%a' test.py
5. Edit the test.py in the Windows installation of Spyder and save your changes.
6. In WSL2, run stat -c '%a' test.py

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

Expected Output: 644 755 755

Actual Output: 644 755 644

Versions

• Spyder version: 5.4.2 (conda)
• Python version: 3.10.10 64-bit
• Qt version: 5.15.2
• PyQt5 version: 5.15.9
• Operating System: Windows 10

Dependencies

# Mandatory:
atomicwrites >=1.2.0          :  1.4.1 (OK)
chardet >=2.0.0               :  5.1.0 (OK)
cloudpickle >=0.5.0           :  2.2.1 (OK)
cookiecutter >=1.6.0          :  2.1.1 (OK)
diff_match_patch >=20181111   :  20200713 (OK)
intervaltree >=3.0.2          :  3.1.0 (OK)
IPython >=7.31.1;<9.0.0       :  8.11.0 (OK)
jedi >=0.17.2;<0.19.0         :  0.18.2 (OK)
jellyfish >=0.7               :  0.11.0 (OK)
jsonschema >=3.2.0            :  4.17.3 (OK)
keyring >=17.0.0              :  23.13.1 (OK)
nbconvert >=4.0               :  7.2.10 (OK)
numpydoc >=0.6.0              :  1.5.0 (OK)
paramiko >=2.4.0              :  3.1.0 (OK)
parso >=0.7.0;<0.9.0          :  0.8.3 (OK)
pexpect >=4.4.0               :  4.8.0 (OK)
pickleshare >=0.4             :  0.7.5 (OK)
psutil >=5.3                  :  5.9.4 (OK)
pygments >=2.0                :  2.14.0 (OK)
pylint >=2.5.0;<3.0           :  2.17.1 (OK)
pylint_venv >=2.1.1           :  3.0.1 (OK)
pyls_spyder >=0.4.0           :  0.4.0 (OK)
pylsp >=1.7.1;<1.8.0          :  1.7.1 (OK)
pylsp_black >=1.2.0           :  1.2.1 (OK)
qdarkstyle >=3.0.2;<3.1.0     :  3.0.3 (OK)
qstylizer >=0.2.2             :  0.2.2 (OK)
qtawesome >=1.2.1             :  1.2.3 (OK)
qtconsole >=5.4.0;<5.5.0      :  5.4.1 (OK)
qtpy >=2.1.0                  :  2.3.0 (OK)
rtree >=0.9.7                 :  1.0.1 (OK)
setuptools >=49.6.0           :  65.6.3 (OK)
sphinx >=0.6.6                :  6.1.3 (OK)
spyder_kernels >=2.4.2;<2.5.0 :  2.4.2 (OK)
textdistance >=4.2.0          :  4.5.0 (OK)
three_merge >=0.1.1           :  0.1.1 (OK)
watchdog >=0.10.3             :  3.0.0 (OK)
zmq >=22.1.0                  :  25.0.2 (OK)

# Optional:
cython >=0.21                 :  None (NOK)
matplotlib >=3.0.0            :  3.7.1 (OK)
numpy >=1.7                   :  1.24.2 (OK)
pandas >=1.1.1                :  1.5.3 (OK)
scipy >=0.17.0                :  1.10.1 (OK)
sympy >=0.7.3                 :  1.11.1 (OK)

[ccordoba12]

Hey @jtziebarth, thanks for reporting. We'll see what we can do about this.

@dalthviz, are you able to reproduce this problem on your side?

[ccordoba12]

Pinging again @dalthviz about this one (it seems he forgot it).

[dalthviz]

Checked with Spyder 5.4.3 from the standalone installer on Windows and I was able to reproduce this :+1:

[ccordoba12]

Ok, and how easy do you think it is to solve? I'm asking that to know if we should try to address it in 5.4.4 or leave it for Spyder 6.

[dalthviz]

No idea what could be happening here so probably something to check for Spyder 6?