Adopt ruff as the central tool for linting and formatting

[tomvothecoder]

Description

• Closes [DevOps]: Adopt ruff as the central tool for linting, formatting, and import sorting #918
• Closes [Doc]: Update Anaconda badge link to the conda-forge page #809
• Closes Remove deprecated setup.py (reintroduced due to rebase on main) #922

Summary of Changes

• Replace black, isort, flake8, and flake8-isortwithruff
  • Affected files: .pre-commit-config.yaml, e3sm_diags.code-workspace, Makefile, dev.yml, ci.yml, pyproject.toml, project-standards.rst
  • Delete setup.cfg
• Address ruff issues
  • raise-without-from-inside-except (B904) Within an except clause, raise exceptions with raise ... from err or raise ... from None to distinguish them from errors in exception handling
  • unused-loop-control-variable (B007) Loop control variable variable not used within loop body

Future ruff issues to address (ignored)

• zip-without-explicit-strict (B905) zip() without an explicit strict= parameter
• function-call-in-default-argument (B008) Do not perform function call CoreParser in argument defaults; instead, perform the call within the function, or read the default from a module-level singleton variable
  • e3sm_diags_driver.py,
• mutable-argument-default (B006) Do not use mutable data structures for argument defaults
  • e3sm_diags_driver.py, `core_parser.py
• star-arg-unpacking-after-keyword-arg (B026) Star-arg unpacking after a keyword argument is strongly discouraged
  • Most/all *_parser.py files, core_parser.py

Checklist

• My code follows the style guidelines of this project
• I have performed a self-review of my own code
• My changes generate no new warnings
• Any dependent changes have been merged and published in downstream modules

If applicable:

• New and existing unit tests pass with my changes (locally and CI/CD build)
• I have added tests that prove my fix is effective or that my feature works
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• I have noted that this is a breaking change for a major release (fix or feature that would cause existing functionality to not work as expected)

[tomvothecoder]

FYI @chengzhuzhang and @forsyth2 this PR consolidates the DevOps tooling to just ruff. You just need to rebuild the e3sm_diags dev env to use it

conda env create -f conda/dev.yml
conda activate e3sm_diags_dev
pre-commit install
pre-commit run --all-files