Add pre-commit, mypy, and related dependencies to copilot-setup-steps.yml

[Copilot]

Summary

This PR adds the necessary dependencies for pre-commit and mypy to the .github/workflows/copilot-setup-steps.yml workflow, enabling the Copilot agent to properly work with code quality and type checking tools in the repository.

Changes

Added a single line to install the following packages via micromamba:

• pre-commit - For running pre-commit hooks and code quality checks
• mypy - For static type checking
• types-setuptools - Type stubs for setuptools
• scipy-stubs - Type stubs for scipy
• pandas - Required to run the mypy script (scripts/run_mypy.py)

These packages are sourced from the environment.yml file and match the development environment setup used in other workflows (e.g., mypy.yml).

Note on mypy-extensions

The mypy-extensions package mentioned in the issue is automatically installed as a dependency of mypy (mypy requires mypy_extensions>=1.0.0), so it does not need to be explicitly listed. This is consistent with the approach used in environment.yml.

Testing

• Verified YAML syntax is valid
• Confirmed minimal changes (1 line added)
• Package list matches what's in environment.yml for the development environment

Original prompt

The steps in .github/workflows/copilot-setup-steps.yml don't install pre-commit, or mypy and mypy-extensions. These are also needed by the agent to work correctly with the repo. Can you add them? Try to reuse the settings from the relevant workflows that install pre-commit and mypy

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💡 You can make Copilot smarter by setting up custom instructions, customizing its development environment and configuring Model Context Protocol (MCP) servers. Learn more Copilot coding agent tips in the docs.

[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 81.65%. Comparing base (2fdd67a) to head (20d142d).
⚠️ Report is 1 commits behind head on main.

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #1644   +/-   ##
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  Coverage   81.65%   81.65%           
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  Files         232      232           
  Lines       53087    53087           
  Branches     9403     9403           
=======================================
  Hits        43348    43348           
  Misses       7286     7286           
  Partials     2453     2453           

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