jupytext: Wrong paired paths when syncing with the --pre-commit flag

I have the following directory structure, where the nb/test.ipynb is paired with the py/test.py.

├── nb
│   └── test.ipynb
└── py
    └── test.py

The notebook and Python file are paired with "jupytext": {"formats": "py//py,nb//ipynb"}. (using jupytext --set-formats py//py,nb//ipynb nb/test.ipynb) This works fine when syncing with jupytext --sync nb/test.ipynb, but when syncing with jupytext --sync --pre-commit I get the following exception:

[jupytext] Notebooks in git index are:
py/test.py
[jupytext] Reading py/test.py
Traceback (most recent call last):
  File "PATH/jupytext", line 8, in <module>
    sys.exit(jupytext())
  File "PATH/jupytext/cli.py", line 292, in jupytext
    exit_code += jupytext_single_file(nb_file, args, log)
  File "PATH/jupytext/cli.py", line 389, in jupytext_single_file
    notebook, inputs_nb_file, outputs_nb_file = load_paired_notebook(notebook, fmt, nb_file, log)
  File "PATH/jupytext/cli.py", line 596, in load_paired_notebook
    for alt_path, alt_fmt in paired_paths(nb_file, fmt, formats):
  File "PATH/jupytext/paired_paths.py", line 128, in paired_paths
    raise InconsistentPath(u"Paired paths '{}' do not include the current notebook path '{}'. "
jupytext.paired_paths.InconsistentPath: Paired paths 'py/py/test.py','py/nb/test.ipynb' do not include the current notebook path 'py/test.py'. Current format is 'py:light', and paired formats are 'py//py,nb//ipynb'.

I have tried all sorts of pairings (taken from/inspired by the comments in #180), among them:

• ..//py,ipynb (and ipynb,…//py`)
• nb//ipynb,..//py
• nb//ipynb,py//py but they all throw a similar exception (and work fine with a regular sync).

Addition As a current workaround I’m using jupytext --sync nb/*.ipynb in my pre-commit hook, which seems to work fine.