Switch to `deepcell>12.0.7` requirement

[WeisLeDocto]

Starting from release 0.12.8, the deepcell library requires a token authentication for users to be able to download the weights of the AI models. Currently, we circumvent this limitation by enforcing the use of version 0.12.7, that allows to freely download the weights of the AI model.

On the long term, the possibility to provide a token and to install a newer version of DeepCell will however become necessary, as version 0.12.7 will age and eventually not be compatible with the evolution of Python. There are several requirements for integration in the basic interface of MyoFInDer:

• Upgrading from version 0.12.7 to a more recent one might entail re-installing a number of dependencies. We need to make sure that a token was given, and that it is valid, before triggering the upgrade.
• It would be convenient to ask the user for a token directly in the Windows installer, but there should always be an option for providing a token anytime in the interface of MyoFInDer.
• The solution for managing the token should also be compatible with use on Linux, macOS, and command-line use on Windows.

The default behavior should be to stick to version 0.12.7, maybe with regular messages advising users to request a token. For command-line users, it seems reasonable to request a manual update of DeepCell once they have provided their token. For regular Windows users, the bash script managing startup should be responsible for checking if a token was provided, and if it is valid. Once provided, the token could be stored in a __token__ file in the base folder of MyoFInDer.

The practical implementation of the token system is not straightforward to achieve in a clean way. Making use of the optional-dependencies of pyproject.toml could be an option, and work as follows:

• The default install doesn't specify a version for deepcell, and therefore installs the latest available
• MyoFInDer installs by default myofinder[no-token], that specifies deepcell==0.12.7 as a requirement
• If a valid token is provided, myofinder[token] is installed and specifies deepcell>0.12.7 as a requirement, thus installing the latest version

It should first be checked if it is allowed to have the same packages in the dependencies and optional-dependencies fields. Double-checking the validity of this system with a question on the Python Discourse would be safer. It would, at that point, also be good to check with the maintainers of DeepCell if they have any opinion on this solution.

[WeisLeDocto]

It should first be checked if it is allowed to have the same packages in the dependencies and optional-dependencies fields. Double-checking the validity of this system with a question on the Python Discourse would be safer. It would, at that point, also be good to check with the maintainers of DeepCell if they have any opinion on this solution.

In the light of this topic on the Python Discourse, it appears that having the version of DeepCell depend on an optional-dependencies would prove very hard, if not impossible. A more realistic approach will be to simply require users to provide a token when installing MyoFInDer, and raise an exception if no token is provided.

The new strategy is as follows:

• A new branch is created, that contains all the changes necessary for switching to a mandatory token policy
• This branch is not merged as long as the token-free version can still be reasonably used
• As soon as using a more recent version of DeepCell becomes mandatory (maximum supported Python version of DeepCell 12.0.7 becomes too old, critical performance improvement in newer version of DeepCell, end of support for the token-free DeepCell repository, etc.) the new branch is merged and using a DeepCell token becomes mandatory to use MyoFInDer
• Until then, any fixes or improvements are always merged into the token branch

The implementation would be the following:

• When starting MyoFInDer after a terminal installation, MyoFInDer checks if a text file containing a token is present in the application folder. If yes, it reads the token from this file and uses it. If not, a popup window appears in which the user can enter their token. If no token can be found, ~or if the provided one is not valid~, an error message is displayed in a popup window, and the user is invited to ~re~-enter a valid token. If the user exits, MyoFInDer stops. Otherwise, MyoFInDer continues as expected.
• When installing MyoFInDer with the Windows installer, the user is requested to enter a token before accepting the license agreement. If they don't, they cannot continue the installation. This token is written to a token file in the installation directory.

The changes in #44 now make it possible to request a token during installation with the Windows installer.

[WeisLeDocto]

if the provided one is not valid, an error message is displayed in a popup window, and the user is invited to re-enter a valid token

UPDATE: Won't be feasible as there is no way to preemptively check if a token is valid without actually downloading something. The error displayed in the terminal should be clear enough for users to know what's wrong, and should clearly provide the path to the file to modify.