test_nb = read_nb('../../tests/image.ipynb')
assert test_nb.cells[0].outputs[0].data['image/png'][-1] == "\n" # Make sure it was not converted by acccident
clean_nb(test_nb)
assert test_nb.cells[0].outputs[0].data['image/png'][-1] != "\n"clean
Strip superfluous metadata from notebooks
To avoid pointless conflicts while working with jupyter notebooks (with different execution counts or cell metadata), it is recommended to clean the notebooks before committing anything (done automatically if you install the git hooks with nbdev_install_hooks). The following functions are used to do that.
Trust
nbdev_trust
nbdev_trust (fname:str=None, force_all:bool=False)
Trust notebooks matching fname
| Type | Default | Details | |
|---|---|---|---|
| fname | str | None | A notebook name or glob to trust |
| force_all | bool | False | Also trust notebooks that haven’t changed |
Clean
clean_nb
clean_nb (nb, clear_all=False, allowed_metadata_keys:list=None, allowed_cell_metadata_keys:list=None, clean_ids=True)
Clean nb from superfluous metadata
| Type | Default | Details | |
|---|---|---|---|
| nb | The notebook to clean | ||
| clear_all | bool | False | Remove all cell metadata and cell outputs? |
| allowed_metadata_keys | list | None | Preserve the list of keys in the main notebook metadata |
| allowed_cell_metadata_keys | list | None | Preserve the list of keys in cell level metadata |
| clean_ids | bool | True | Remove ids from plaintext reprs? |
Jupyter adds a trailing to images in cell outputs. Vscode-jupyter does not.
Notebooks should be brought to a common style to avoid unnecessary diffs:
The test notebook has metadata in both the main metadata section and contains cell level metadata in the second cell:
test_nb = read_nb('../../tests/metadata.ipynb')
assert {'meta', 'jekyll', 'my_extra_key', 'my_removed_key'} <= test_nb.metadata.keys()
assert {'meta', 'hide_input', 'my_extra_cell_key', 'my_removed_cell_key'} == test_nb.cells[1].metadata.keys()After cleaning the notebook, all extra metadata is removed, only some keys are allowed by default:
clean_nb(test_nb)
assert {'jekyll', 'kernelspec'} == test_nb.metadata.keys()
assert {'hide_input'} == test_nb.cells[1].metadata.keys()We can preserve some additional keys at the notebook or cell levels:
test_nb = read_nb('../../tests/metadata.ipynb')
clean_nb(test_nb, allowed_metadata_keys={'my_extra_key'}, allowed_cell_metadata_keys={'my_extra_cell_key'})
assert {'jekyll', 'kernelspec', 'my_extra_key'} == test_nb.metadata.keys()
assert {'hide_input', 'my_extra_cell_key'} == test_nb.cells[1].metadata.keys()Passing clear_all=True removes everything from the cell metadata:
test_nb = read_nb('../../tests/metadata.ipynb')
clean_nb(test_nb, clear_all=True)
assert {'jekyll', 'kernelspec'} == test_nb.metadata.keys()
test_eq(test_nb.cells[1].metadata, {})Passing clean_ids=True removes ids from plaintext repr outputs, to avoid notebooks whose contents change on each run since they often lead to git merge conflicts. For example:
<PIL.PngImagePlugin.PngImageFile image mode=L size=28x28 at 0x7FB4F8979690>becomes:
<PIL.PngImagePlugin.PngImageFile image mode=L size=28x28>process_write
process_write (warn_msg, proc_nb, f_in, f_out=None, disp=False)
nbdev_clean
nbdev_clean (fname:str=None, clear_all:bool=False, disp:bool=False, stdin:bool=False)
Clean all notebooks in fname to avoid merge conflicts
| Type | Default | Details | |
|---|---|---|---|
| fname | str | None | A notebook name or glob to clean |
| clear_all | bool | False | Remove all cell metadata and cell outputs? |
| disp | bool | False | Print the cleaned outputs |
| stdin | bool | False | Read notebook from input stream |
By default (fname left to None), all the notebooks in config.nbs_path are cleaned. You can opt in to fully clean the notebook by removing every bit of metadata and the cell outputs by passing clear_all=True.
If you want to keep some keys in the main notebook metadata you can set allowed_metadata_keys in settings.ini. Similarly for cell level metadata use: allowed_cell_metadata_keys. For example, to preserve both k1 and k2 at both the notebook and cell level adding the following in settings.ini:
...
allowed_metadata_keys = k1 k2
allowed_cell_metadata_keys = k1 k2
...clean_jupyter
clean_jupyter (path, model, **kwargs)
Clean Jupyter model pre save to path
This cleans notebooks on-save to avoid unnecessary merge conflicts. The easiest way to install it for both Jupyter Notebook and Lab is by running nbdev_install_hooks. It works by implementing a pre_save_hook from Jupyter’s file save hook API.
Hooks
nbdev_install_hooks
nbdev_install_hooks ()
Install Jupyter and git hooks to automatically clean, trust, and fix merge conflicts in notebooks
See clean_jupyter and nbdev_merge for more about how each hook works.