error 128: clean filter 'filter_name' failed

[Paulo Macedo]

In order to use git with my Jupyter notebooks, I used jq (https://stedolan.github.io/jq/download/) to create a filter, call it 'clean_ipynb', following the instructions on http://timstaley.co.uk/posts/making-git-and-jupyter-notebooks-play-nice/. While this does make Git and Jupyter notebooks work fine together, I've been having many issues with Sourcetree. In particular, every time I open a repo containing a Jupyter notebook I get an error: 

'git status' failed with code 128:'jq --indent 1         '(.cells[] | select(has("outputs")) | .outputs) = []          | (.cells[] | select(has("execution_count")) | .execution_count) = null          | .metadata = {"language_info": {"name": "python", "pygments_lexer": "ipython2"}}         | .cells[].metadata = {}         ': jq: command not found

error: external filter jq --indent 1         '(.cells[] | select(has("outputs")) | .outputs) = []          | (.cells[] | select(has("execution_count")) | .execution_count) = null          | .metadata = {"language_info": {"name": "python", "pygments_lexer": "ipython2"}}         | .cells[].metadata = {}         ' failed -1

error: external filter jq --indent 1         '(.cells[] | select(has("outputs")) | .outputs) = []          | (.cells[] | select(has("execution_count")) | .execution_count) = null          | .metadata = {"language_info": {"name": "python", "pygments_lexer": "ipython2"}}         | .cells[].metadata = {}         ' failed

fatal: src/file.ipynb: clean filter 'clean_ipynb' failed

Can you please help me fix this? All git commands are working fine, and I'm using System Git with Sourcetree, so I'm not sure where this could be coming from. Thanks!

[Paulo Macedo]

I fixed the issue by fixing the permission settings with jq. It wasn't a Sourcetree error! Thanks.

[Axel Perschmann]

What exactly did you do to fix the permission settings with jq? I'm facing the exact same problem with Sourcetree right now.

[Kim Scott]

For anyone else in the same boat: It seems Sourcetree doesn't use the same PATH as the regular shell. (Similar to the issue w/ using jq in launchd described here: https://stackoverflow.com/questions/23598328/using-jq-to-parse-json-in-launchd)

I fixed the same issue just by providing the full path to jq in the .gitconfig file defining the clean filter (i.e., using /usr/local/bin/jq instead of just jq).