refactor: pyproject.toml migration + ruff lint clean-up - #13

Node.js 20 is deprecated. The following actions target Node.js 20 but are being forced to run on Node.js 24: actions/checkout@v4, conda-incubator/setup-miniconda@v3. For more information see: https://github.blog/changelog/2025-09-19-deprecation-of-node-20-on-github-actions-runners/

`auto-activate-base` is deprecated. Please use `auto-activate`. If your installer does not use the `base` environment as the default environment, also add `activate-environment: base`.

warning libmamba You are using 'pip' as an additional package manager. Be aware that packages installed with 'pip' are managed independently from 'conda-forge' channel.

'nodefaults' channel detected: will remove 'defaults' if added implicitly. In the future, 'nodefaults' to remove 'defaults' won't be supported. Please set 'conda-remove-defaults' = 'true' in setup-miniconda to remove this warning.