Pre commit test

[pavelvazquez]

Tested the pre-commit requirement for developers but seems to be very slow

[sveinugu]

Sorry for the very late review. Have had to prioritise stuff related to biohackathon/conferences.

As I understand it, you have tried to make poetry work well with pre-commit and your solution works, but I found that it was not recommended by the developer of pre-commit (https://stackoverflow.com/a/72888197). Due to the complexity of this, I went ahead and reconfigured pre-commit to handle the dependencies for formatting and linting alone (removing these dependencies from poetry). PyCharm File Watch config needs to be changed accordingly (info in CONTRIBUTING.md). Documentation on installation, use, and development setup has been added.

However, I discovered that the Flake8 config has been incorrect for a long time, perhaps always, which have caused most errors to be ignored. I started fixing some of the errors that now appeared, but then understood that fixing the rest is good training for you. So fix the rest of the flake8 errors before I will merge the PR.

GitHub Actions workflows have been updated.