Allow ruff to discover all files, instead of hardcoding every path which
can be error prone, e.g. including "tests/" in the list meant that
nested Python files were not being linted, while other paths were stale.
There is no need for this list since we truly want to lint all Python
files, which ruff does by default.

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Drop the explicit ruff.format configuration from the pyproject.toml file
since it corresponds to ruff's default values, making it harder for
someone familiar with the tool to tell deviations from the default
behaviour. Given that ruff strives to maintain compatibility with black,
these defaults are unlikely to change.

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Drop configuration settings that match ruff's default values (also see
previous commit for the changes in ruff.format).

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Drop E501 and E226 from ruff.lint's ignore list:
* E226 does not appear in the codebase therefore there's no reason to
  include it there
* Given that our line-length limit is already high, we shouldn't ignore
  E501

Ignoring C901 is not a good idea; the only reason I'm leaving it in is
because it would require a lot of refactoring to fix it. We should
address this in the future.

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Imports are highly inconsistent throughout the project, using a mix of
absolute as well as explicit and implicit relative imports. For this
reason, we have to explicitly specify the known first-party and local
folders for isort to work correctly.

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

I strongly believe that the limit should be reduced, but feel free to
drop this commit if you disagree.

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>

Run 'ruff check --fix' followed by 'ruff format' and resolve remaining
errors manually. For the most part, the manual changes involved one of
the 3 following actions:
* Split long strings into multiple lines wrapped with parentheses
* Refactor code, e.g. retrieve dict values and evaluate conditionals
  before using the results in f-strings
* Move long strings to files (this can be done in many more places
  around the codebase)

Signed-off-by: Phoevos Kalemkeris <phoevos.kalemkeris@ucl.ac.uk>