jupytext --to notebook call from a paired script fails with InconsistentPath

[MPKonst]

First of all, thank you for creating and maintaining jupytext! I have been using it for quite some time and it has been incredibly useful. However, it seems like the changes introduced in 1.11.2 in response to #765 have broken some of my automated jupytexting scripts. The minimal setup to reproduce the problem seems to be the following:

1. With a directory structure

nb
├── scripts
└── test.ipynb

where scripts is a subdirectory and test.ipynb is some notebook
2. Run jupytext --set-formats "ipynb,scripts//py:percent" test.ipynb to create a paired script test.py in the scripts subdirectory.
3. Delete the notebook test.ipynb to simulate just having pulled test.py.
4. Try to recreate the notebook from the script: jupytext --to notebook --output test.ipynb ./scripts/test.py
Result: the notebook is correctly created but the call still fails with:

[jupytext] Reading ./scripts/test.py in format py
[jupytext] Writing test.ipynb
Traceback (most recent call last):
  File "/usr/local/bin/jupytext", line 8, in <module>
    sys.exit(jupytext())
  File "/usr/local/lib/python3.7/site-packages/jupytext/cli.py", line 427, in jupytext
    exit_code += jupytext_single_file(nb_file, args, log)
  File "/usr/local/lib/python3.7/site-packages/jupytext/cli.py", line 826, in jupytext_single_file
    for alt_path, _ in paired_paths(nb_file, fmt, formats)
  File "/usr/local/lib/python3.7/site-packages/jupytext/paired_paths.py", line 248, in paired_paths
    short_form_multiple_formats(formats),
jupytext.paired_paths.InconsistentPath: Paired paths './scripts/test.ipynb','./scripts/scripts/test.py' do not include the current notebook path './scripts/test.py'. Current format is 'py:percent', and paired formats are 'ipynb,scripts//py:percent'.

[mwouts]

Thank you @MPKonst for reporting this!
Sorry for the regression - I'll size the opportunity to add one more test and make sure we get our use case covered.

[DancingQuanta]

I have the same issue. I have started using 1.11.3 from 1.9.1 when I wanted to use --use-source-timestamp in my project.
I tried this following command with --output and this still fails.

jupytext --output notebooks/02-00-probe-temperature.ipynb markdown/02-00-probe-temperature.md
[jupytext] Reading markdown/02-00-probe-temperature.md in format md
[jupytext] Writing notebooks/02-00-probe-temperature.ipynb (destination file replaced [use --update to preserve cell outputs and ids])
Traceback (most recent call last):
  File "C:\tools\Anaconda3\envs\sthm\Scripts\jupytext-script.py", line 9, in <module>
    sys.exit(jupytext())
  File "C:\tools\Anaconda3\envs\sthm\lib\site-packages\jupytext\cli.py", line 434, in jupytext
    exit_code += jupytext_single_file(nb_file, args, log)
  File "C:\tools\Anaconda3\envs\sthm\lib\site-packages\jupytext\cli.py", line 846, in jupytext_single_file
    for alt_path, _ in paired_paths(nb_file, fmt, formats)
  File "C:\tools\Anaconda3\envs\sthm\lib\site-packages\jupytext\paired_paths.py", line 248, in paired_paths
    short_form_multiple_formats(formats),
jupytext.paired_paths.InconsistentPath: Paired paths 'markdown/markdown/02-00-probe-temperature.md','markdown/notebooks/02-00-probe-temperature.ipynb','markdown/scripts/02-00-probe-temperature.py' do not include the current notebook path 'markdown/02-00-probe-temperature.md'. Current format is 'md', and paired formats are 'markdown//md,notebooks//ipynb,scripts//py:percent'.