Make code flake8, mypy, black and isort compliant 🥸

[laulopezreal]

pre-commit is a useful tool for managing linters and checking your code for simple errors before comitting. Some advantages are:

Users don't need to install linting tools (other than pre-commit), and tool versions are shared across users / workflows.
pre-commit can be installed locally to prevent committing unless the checks have passed, enforcing a high code quality
Some of the useful built-in hooks are: trim whitespacemypy, pyroma, check-manifest)

[slobentanzer]

very cool @laulopezreal, many thanks!

we don't have pre-commit in the adapters/pipelines so far, so this is a very welcome addition. will review as soon as possible. :)

[kpto]

@laulopezreal Thanks for your contribution! There are a few issues needed to be sorted.

1. I think you modified the pyproject.toml directly, this makes the lock file unsync one will not be able to run poetry install. You should run poetry update {package_name} to update a package instead.
2. The data folder should be omitted by the formatter/linter as they are resources, not code.
3. The add of file import.report seems to be a mistake to me? I think that should be ignored by Git?

These are my initial comments, I will have a more thorough review later.

[slobentanzer]

Hi @kpto,
modifying the pyproject.toml directly is definitely possible, I don't think that is the reason for the failure. You can usually just run poetry lock to update.

[slobentanzer]

The dependency issue I get is that the packages we install from our other git repositories still depend on a previous biocypher version (they are defined as dmb and bccb for the DepMap and CROssBAR repositories). I used these as imports for (originally) demonstrating the workflow of importing adapters from other places on GitHub.

I would suggest to deactivate these imports in the pyproject.toml. I have added these changes to the other PR (the first one, #11).