Fix codecov CI and update template

[grst]

This PR fixes some problems with the CI setup of the scverse-cookiecutter template repo. Last night, the codecov package was pulled from PyPI. This can easily be replaced, however we've realized our automatic template sync system does not allow us to modify github actions (a security precaution from github), so we need to roll out this update manually.

We're also taking this opportunity to make several other intended changes for to the CI workflow.

We're still looking into how we can avoid this in the future, which will likely require us changing how our template sync system works. This is being tracked in the scverse/cookiecutter-scverse#138.

Changes

These changes constitute the 0.2.1 release of the template and make the following changes:

• Remove codecov as a dependency since it's been pulled from pypi (scverse/cookiecutter-scverse#161)
• Remove usage of deprecated GitHub actions environment variables (these will be removed in a month) (scverse/cookiecutter-scverse#161)
• Fix some spurious ruff errors (scverse/cookiecutter-scverse#156, scverse/cookiecutter-scverse#159)
• Replace the example citation with the scverse manuscript (scverse/cookiecutter-scverse#160)
• automatically cancel running CI jobs on new commit ( scverse/cookiecutter-scverse#158)

Additional remarks

• If there are merge conflicts, they either show up inline (>>>>>>>) or a .rej file will have been created for the respective files. You need to address these conflicts manually. Make sure to enable pre-commit.ci (see below) to detect such files.
• The scverse template works best when the pre-commit.ci, readthedocs and codecov services are enabled. Make sure to activate those apps if you haven't already.

[codecov]

Codecov Report

Patch and project coverage have no change.

Comparison is base (0259448) 52.58% compared to head (8ed8d19) 52.58%.

Additional details and impacted files

@@           Coverage Diff           @@
##             main       #6   +/-   ##
=======================================
  Coverage   52.58%   52.58%           
=======================================
  Files           6        6           
  Lines         831      831           
=======================================
  Hits          437      437           
  Misses        394      394           

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