refactor(python): harden support script parsing

[acgetchell]

• Require Python 3.13 for support-script tooling and align Ruff/Ty with that baseline.
• Replace mypy with strict Ty checking in the Python workflow.
• Parse TOML, JSON, argparse, and Semgrep inputs into typed boundary objects before downstream use.
• Reject malformed Criterion estimates, non-finite timings, invalid confidence intervals, and malformed Semgrep result shapes.

Closes #142

Summary by CodeRabbit

• Chores

  • Raised project Python requirement to 3.13 and updated tooling configs.
  • Switched type-checking to the new typechecker and tightened CI checks.
  • Converted key dataclasses to slot-based, improving runtime efficiency.

• New Features

  • Improved CLI and data-parsing validations with clearer error reporting.
  • Structured parsing for external tool results to reject malformed inputs.

• Tests

  • Added comprehensive tests covering parsing, validation, and error cases.

[coderabbitai]

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Reviewing files that changed from the base of the PR and between 87e1d00 and b9e0ba0.

📒 Files selected for processing (1)

• ty.toml

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📝 Walkthrough

Walkthrough

This PR upgrades the project to Python 3.13, migrates type checking from mypy to ty, and refactors development scripts to parse and validate external inputs (TOML, JSON, CLI args) at boundaries into typed, validated objects before computation.

Changes

Python 3.13 Upgrade and Parse-at-Boundaries Refactoring

Layer / File(s)	Summary
Python 3.13 & Type Checker Upgrade .python-version, pyproject.toml, justfile	Project requirement bumped to Python 3.13. Ruff target version updated to py313. Mypy configuration block and mypy dev dependency removed from pyproject.toml. Type checking recipe switched from mypy to ty over scripts/ with --error all.
check_docs_version_sync Type Safety scripts/check_docs_version_sync.py	Added ParsedObject alias and _is_parsed_object/_require_parsed_object TypeGuard helpers. PackageInfo and VersionMismatch dataclasses now include slots=True. _read_cargo_package_info refactored to use parsed-object validation.
check_semgrep_fixtures Structured Parsing scripts/check_semgrep_fixtures.py, scripts/tests/test_check_semgrep_fixtures.py	Introduced ParsedObject alias and SemgrepResults frozen dataclass. Rewrote _semgrep_results() to read SEMGREP_JSON, validate top-level shape and each results entry, and return SemgrepResults. Updated main() to consume structured output. Added tests for valid/malformed payloads and fixture integration.
criterion_dim_plot Data Types & Validation scripts/criterion_dim_plot.py	Added PlotCliArgs dataclass replacing argparse.Namespace. Row now implements __post_init__ validation enforcing dim>0, finite/non-negative timing values, and CI containment of point estimates. Added Protocols and ParsedObject alias for parsed content.
criterion_dim_plot Parsing & Function Signatures scripts/criterion_dim_plot.py, scripts/tests/test_criterion_dim_plot.py	Added _is_parsed_object/_require_parsed_object helpers. Rewrote _read_estimate to validate stat presence/type, parse numeric fields robustly, and enforce CI invariants. Cargo TOML parsing routed through validators. _parse_args now returns PlotCliArgs. _maybe_update_readme and _maybe_render_plot accept narrowed Protocol-typed args. Tests expanded with many _read_estimate error cases and Row validation tests; existing markdown-table tests updated with valid CI bounds.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Possibly related issues

• Update Python tooling to 3.13 and parse scripts at boundaries causal-triangulations#182: Implements the same Python 3.13 bump, migration to ty, and parse-at-boundaries refactors across scripts.
• Update Python tooling to 3.13 and parse scripts at boundaries markov-chain-monte-carlo#84: Mirrors the tooling bump and TypeGuard/dataclass boundary parsing approach used here.
• Update Python tooling to 3.13 and parse scripts at boundaries delaunay#429: Parallel changes for Python 3.13 and input validation refactors across repository scripts.

Possibly related PRs

• acgetchell/la-stack#19: Modifies scripts/criterion_dim_plot.py in the same area of Cargo/TOML extraction and test updates; code-level related.

"🐰 From mypy's gaze to ty's keen eye,
Three scripts now parse ere they apply,
With slots so slim and types so clear,
Boundary guards stand steadfast here.
Python three‑thirteen hops on stage — hooray!"

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 3.70% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title 'refactor(python): harden support script parsing' directly and concisely describes the main objective of the pull request - strengthening the type safety and validation in Python support scripts.
Linked Issues check	✅ Passed	The changes comprehensively address all coding requirements from issue #142: Python baseline upgraded to 3.13, mypy replaced with Ty, explicit boundary parsing implemented with typed dataclasses and TypeGuard validators, and validation tests added.
Out of Scope Changes check	✅ Passed	All changes are directly aligned with issue #142 objectives: version upgrades (Python, pyproject.toml, justfile, ty.toml), tooling replacement (mypy→Ty), and hardened parsing in all affected scripts.

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✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch refactor/142-python-boundary-parsing

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[codecov]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.61%. Comparing base (5bde071) to head (b9e0ba0).

Additional details and impacted files

@@           Coverage Diff           @@
##             main     #145   +/-   ##
=======================================
  Coverage   99.61%   99.61%           
=======================================
  Files           5        5           
  Lines        2846     2846           
=======================================
  Hits         2835     2835           
  Misses         11       11           

Flag	Coverage Δ
unittests	99.61% <ø> (ø)

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[coderabbitai]

Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@justfile`:
- Around line 495-496: Update ty.toml so ty type-checks against Python 3.13:
open ty.toml and change the python-version key from "3.12" to "3.13" to match
.python-version and pyproject.toml (this affects the python-typecheck target
invoked by the justfile); ensure there are no other references to 3.12 in
ty.toml that need updating so ty uses the correct stdlib/features for Python
3.13.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 06c993f2-92af-4139-ab4f-31bd3b67226a

📥 Commits

Reviewing files that changed from the base of the PR and between 5bde071 and 87e1d00.

⛔ Files ignored due to path filters (1)

• uv.lock is excluded by !**/*.lock

📒 Files selected for processing (8)

• .python-version
• justfile
• pyproject.toml
• scripts/check_docs_version_sync.py
• scripts/check_semgrep_fixtures.py
• scripts/criterion_dim_plot.py
• scripts/tests/test_check_semgrep_fixtures.py
• scripts/tests/test_criterion_dim_plot.py