Ci and lint update 20260227

[AmandaBirmingham]

No description provided.

[Copilot]

Pull request overview

Updates the project’s CI and linting setup by removing legacy flake8/pep8 dependencies/config and introducing ruff, along with some formatting-only reflows to satisfy stricter lint rules.

Changes:

• Switch CI linting from flake8 to ruff and add ruff configuration in pyproject.toml.
• Remove flake8/pep8 from packaging and conda environment dependencies.
• Reformat a number of source/test lines (line wrapping) and add .DS_Store to .gitignore.

Reviewed changes

Copilot reviewed 11 out of 12 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
setup.py	Drops flake8/pep8 from install_requires (but still includes nose).
setup.cfg	Removes the old [flake8] configuration block.
pyproject.toml	Adds initial ruff lint rule selection.
environment.yml	Replaces flake8/pep8 with ruff in the conda environment.
.github/workflows/main.yaml	Updates CI python matrix and switches lint step to ruff check.
.gitignore	Ignores macOS .DS_Store.
pysyndna/src/quant_orfs.py	Formatting-only line wrap.
pysyndna/src/calc_cell_counts.py	Formatting-only line wraps.
pysyndna/tests/test_util.py	Formatting-only line wrap.
pysyndna/tests/test_quant_orfs.py	Formatting-only line wraps (comprehensions/DF construction).
pysyndna/tests/test_fit_syndna_models.py	Formatting-only line wraps; introduces a couple readability issues in comments/continuations.
pysyndna/tests/test_calc_cell_counts.py	Formatting-only line wraps; adds # noqa: E501 for long test names.

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