Regression in 1.3.1 due to #407 when scripts and notebooks are in a separate folder.

The directory structure looks like this:

├── ./notebooks
│   ├── ./notebooks/01_tabular_data_exploration.ipynb
├── ./python_scripts
│   ├── ./python_scripts/01_tabular_data_exploration.py

I am running jupytext like this:

jupytext --set-formats python_scripts//py:percent,notebooks//ipynb python_scripts/01_tabular_data_exploration.py

Output:

[jupytext] Reading python_scripts/01_tabular_data_exploration.py
[jupytext] Updating notebook metadata with '{"jupytext": {"formats": "python_scripts//py:percent,notebooks//ipynb"}}'
Traceback (most recent call last):
  File "/home/lesteve/miniconda3/envs/scikit-learn-tutorial/bin/jupytext", line 10, in <module>
    sys.exit(jupytext())
  File "/home/lesteve/miniconda3/envs/scikit-learn-tutorial/lib/python3.7/site-packages/jupytext/cli.py", line 271, in jupytext
    exit_code += jupytext_single_file(nb_file, args, log)
  File "/home/lesteve/miniconda3/envs/scikit-learn-tutorial/lib/python3.7/site-packages/jupytext/cli.py", line 464, in jupytext_single_file
    for alt_path, alt_fmt in paired_paths(nb_file, fmt, formats)[::-1]:
  File "/home/lesteve/miniconda3/envs/scikit-learn-tutorial/lib/python3.7/site-packages/jupytext/paired_paths.py", line 126, in paired_paths
    short_form_multiple_formats(formats)))
jupytext.paired_paths.InconsistentPath: Paired paths 'python_scripts/python_scripts/01_tabular_data_exploration.py','python_scripts/notebooks/01_tabular_data_exploration.ipynb' do not include the current notebook path 'python_scripts/01_tabular_data_exploration.py'. Current format is 'py:percent', and paired formats are 'python_scripts//py:percent,notebooks//ipynb'.

If I try to change the format to avoid the error then jupytext --sync does not seem to create the notebook in the right place. Maybe I was doing something fishy all along in which case I would appreciate advice how to use jupytext better …

Here is a way to reproduce:

pip install jupytext==1.3.1
cd /tmp && git clone https://github.com/lesteve/scikit-learn-tutorial && cd scikit-learn-tutorial
jupytext --set-formats python_scripts//py:percent,notebooks//ipynb python_scripts/01_tabular_data_exploration.py

Same thing works fine with jupytext 1.3:

pip install jupytext==1.3
cd /tmp && git clone https://github.com/lesteve/scikit-learn-tutorial && cd scikit-learn-tutorial
jupytext --set-formats python_scripts//py:percent,notebooks//ipynb python_scripts/01_tabular_data_exploration.py

git bisecting points to #407.

[lesteve]

Great thanks a lot for this! I just tested with 1.3.5 and it does fix the issue.

[lesteve]

I don’t know much about Makefile unfortunately, but yours look nice!

I don’t know much either about Makefiles and just to be explicit, nobody should use my Makefile because it is horrible and it does not really work!

OK if I end up doing something not too hacky, I will let you know. My feeling is that it will be very hacky though, at least the first iteration.