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Migration

Almost all versions of coppafisher will automatically warn you about any incompatibilities when the pipeline is run on a new version. Below contains specific migration guides for special cases.

Coppafisher \(\leq\) 1.5 Migration

The extraction directory (labelled tile_dir under the config) is deprecated. Update the directory by

from coppafisher.extract import update_tile_dir

update_tile_dir("/path/to/config.ini")

The notebook from versions <= 1.5.0 will open as normal. The data can be zipped at any time to be the same as versions > 1.5.0 by

from coppafisher import Notebook

nb = Notebook("/path/to/notebook")
nb.zip()

You may be prompted to install the 7-zip CLI if it is not found.

Specify drive to zip from

By default, the default drive is used for zipping notebook variables (i.e. within /tmp/... on Linux). If you do not have sufficient disk space on this drive and wish to use a different location, specify your own existing temporary directory by doing

from coppafisher import Notebook

nb = Notebook("/path/to/notebook")
nb.zip("/path/to/temporary/directory/")