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/")