chore: Python 3.10+, remove legacy code, clean repo

[ericchansen]

Summary

Require Python 3.10+, remove all legacy/archived code, clean up .gitignore, and modernize the repo for a lean SDK.

Changes

Python 3.10+ minimum

• requires-python bumped from >=3.9 to >=3.10
• Ruff target-version updated to py310
• CI matrix drops Python 3.9
• Enable UP006/UP035 ruff rules -- auto-fix typing.List/Tuple to builtins in 7 files

Remove legacy code (-72K lines)

• Delete scripts/archived/ entirely (26 files -- Schrodinger-dependent tools)
• Delete psi4-output.dat and psi4-output-v2.dat (2.7 MB raw Psi4 logs; extracted .npy/.txt/.xyz data remains)
• Merge generate_qm_data_v2.py into generate_qm_data.py (remove v1)
• Rename test_new_pipeline.py to test_pipeline.py

Clean .gitignore (238 lines -> 55)

• Remove overly broad globs (*.fld, *.mol2, *.log, *.txt, *.fchk, *.mae, etc.) that were hiding legitimate example data
• Ethane example files (GS.fchk, GS.log, GS.mol2, TS.*) now properly tracked
• Test fixture optimization_golden.json now tracked

Update .vscode/launch.json

• Replace 7 legacy configs (referenced dead scripts like q2mm/loop.py, q2mm/seminario.py, q2mm/just_compare.py)
• Add 5 configs for current API: SN2 pipeline, test runner, current file tests, benchmarks, upstream validation

Testing

• ruff check . -- all checks passed
• ruff format --check -- 71 files already formatted
• pytest -q -- 153 passed, 8 skipped, 1 xfailed
• mkdocs build --strict -- clean build

[Copilot]

Pull request overview

This PR modernizes the repository into a leaner Python SDK by raising the minimum supported Python version to 3.10+, updating typing annotations to PEP 585 style, removing archived tooling/data, and tightening repo hygiene (CI, .gitignore, VS Code debug configs, fixtures/examples).

Changes:

• Require Python 3.10+ (packaging metadata, Ruff target version, CI matrix).
• Replace legacy typing.List/Tuple annotations with built-in generics (list[...], tuple[...]).
• Remove scripts/archived/ and consolidate SN2 QM data generation; add/track new fixtures and example data; simplify .gitignore and update .vscode/launch.json.

Reviewed changes

Copilot reviewed 43 out of 50 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
test/test_linear_algebra.py	Updates typing annotations to built-in generics.
test/fixtures/optimization_golden.json	Adds a pinned “golden” optimization fixture for regression testing.
scripts/validate_against_upstream.py	Modernizes typing import (Callable from collections.abc).
scripts/archived/tools/sumq.py	Removes archived script.
scripts/archived/tools/submit.py	Removes archived script.
scripts/archived/tools/setup_sh_from_com.py	Removes archived script.
scripts/archived/tools/setup_qm.py	Removes archived script.
scripts/archived/tools/many_sumq.py	Removes archived script.
scripts/archived/tools/invert-chirality.py	Removes archived script.
scripts/archived/tools/format-ff.py	Removes archived script.
scripts/archived/tools/file_converter.py	Removes archived script.
scripts/archived/tools/count_steps.py	Removes archived script.
scripts/archived/tools/clean_mae_same_update.py	Removes archived script.
scripts/archived/tools/clean_mae_same_restart.py	Removes archived script.
scripts/archived/tools/clean_mae_same.py	Removes archived script.
scripts/archived/tools/clean_mae.py	Removes archived script.
scripts/archived/tools/change_mae_atom_type.py	Removes archived script.
scripts/archived/smiles_to_catvs_example/template_diphos.mae	Removes archived example data.
scripts/archived/smiles_to_catvs_example/smi/strem_bisphosphines.smi	Removes archived example data.
scripts/archived/smiles_to_catvs_example/run	Removes archived example runner.
scripts/archived/smiles_to_catvs_example/atom.typ	Removes archived example data.
scripts/archived/smiles_to_catvs_example/allyl6.mae	Removes archived example data.
scripts/archived/smiles_to_catvs/scripts/search.py	Removes archived script.
scripts/archived/smiles_to_catvs/scripts/sdf_to_mae.py	Removes archived script.
scripts/archived/smiles_to_catvs/scripts/prepare.py	Removes archived script.
scripts/archived/smiles_to_catvs/scripts/finish.py	Removes archived script.
scripts/archived/README.md	Removes archived docs.
q2mm/parsers/mm3.py	Updates annotations to list[...] and adjusts internal typing.
q2mm/parsers/base.py	Updates annotations to list[...] in base parser APIs.
q2mm/parsers/amber_ff.py	Updates annotations to list[...] in Amber FF parser.
q2mm/models/hessian.py	Updates annotations (list[...], tuple[...]) in Hessian helpers.
q2mm/linear_algebra.py	Updates return type annotation to tuple[...].
pyproject.toml	Bumps requires-python to 3.10; Ruff target-version to py310; adjusts ignore list comments.
examples/sn2-test/test_pipeline.py	Adds a pipeline demo script using the “clean” model layer.
examples/sn2-test/generate_qm_data_v2.py	Removes v2 generator (merged into v1).
examples/sn2-test/generate_qm_data.py	Merges/improves QM data generation workflow (diffuse basis + complex).
examples/sn2-test/README.md	Updates docs to reflect renamed scripts and workflow.
examples/ethane/TS.mol2	Adds tracked TS mol2 example data.
examples/ethane/GS.mol2	Adds tracked GS mol2 example data.
.vscode/launch.json	Replaces legacy debug configs with configs targeting current scripts/tools.
.gitignore	Removes overly broad ignores; keeps only generated artifacts and standard tooling output.
.github/workflows/ci.yml	Drops Python 3.9 from the CI matrix.

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