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‎.github/workflows/ruff.yml‎

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name: Ruff
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on:
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workflow_dispatch:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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types: [opened, synchronize, reopened]
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# Cancel in-flight runs of the same PR/branch when a new commit is pushed.
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concurrency:
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group: ruff-${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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lint:
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name: ruff check
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runs-on: ubuntu-latest
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steps:
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- name: Checkout ARC
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uses: actions/checkout@v6
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- name: Set up Python
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uses: actions/setup-python@v6
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with:
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python-version: '3.12'
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cache: pip
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# Use the official astral-sh/ruff-action — it pins ruff and runs both
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# `ruff check` and `ruff format --check` against the configuration in
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# pyproject.toml. Pinning the action ref keeps the runner reproducible.
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#
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# NOTE on `continue-on-error: true`:
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# The ARC codebase predates ruff and currently has ~300 lint findings
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# against the configured rule set. We land ruff in non-blocking mode
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# first so the team can see the report on every PR without the gate
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# being red. To make ruff a hard gate (recommended once the residual
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# findings are cleaned up), remove `continue-on-error: true` from
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# both steps below.
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- name: Run ruff check
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uses: astral-sh/ruff-action@v3
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continue-on-error: true
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with:
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args: 'check arc/'
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- name: Run ruff format --check
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uses: astral-sh/ruff-action@v3
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continue-on-error: true
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with:
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args: 'format --check arc/'

‎README.md‎

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# Automated Rate Calculator | ARC
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![Build Status](https://github.com/ReactionMechanismGenerator/ARC/actions/workflows/cont_int.yml/badge.svg)
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[![Ruff](https://github.com/ReactionMechanismGenerator/ARC/actions/workflows/ruff.yml/badge.svg)](https://github.com/ReactionMechanismGenerator/ARC/actions/workflows/ruff.yml)
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[![codecov](https://codecov.io/gh/ReactionMechanismGenerator/ARC/branch/main/graph/badge.svg)](https://codecov.io/gh/ReactionMechanismGenerator/ARC)
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[![MIT license](http://img.shields.io/badge/license-MIT-brightgreen.svg)](http://opensource.org/licenses/MIT)
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![Release](https://img.shields.io/badge/version-1.1.0-blue.svg)

‎pyproject.toml‎

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"numpy",
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]
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build-backend = "setuptools.build_meta"
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# ---------------------------------------------------------------------------
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# Ruff configuration
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# ---------------------------------------------------------------------------
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# Ruff is the canonical linter for ARC. The selected rule set is intentionally
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# conservative for a working scientific codebase: bug-finding + import-sorting +
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# pyupgrade only. Stylistic rules (line length, naming, docstrings) are left
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# off until the team explicitly opts in. To run locally:
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#
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# ruff check arc/
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# ruff check --fix arc/ # auto-fix the safe ones
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# ruff format --check arc/ # check formatting only (does not modify)
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#
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# CI runs both `ruff check` and `ruff format --check` on every PR via
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# .github/workflows/ruff.yml. Both steps are currently non-blocking; see the
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# workflow file for the plan to make them gating.
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# ---------------------------------------------------------------------------
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[tool.ruff]
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# Match the Python pinned in environment.yml. Bumping this is the right
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# knob to enable newer pyupgrade rewrites once the conda env moves forward.
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target-version = "py312"
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line-length = 120
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extend-exclude = [
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"build",
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"dist",
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"*.egg-info",
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".eggs",
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"ipython", # notebook tutorials
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"arc/molecule", # Cython-compiled sources + tightly coupled modules
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]
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[tool.ruff.lint]
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# Rule families enabled (kept tight; can grow over time):
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# E pycodestyle errors (real syntactic / structural issues)
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# F pyflakes (unused imports, undefined names, …)
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# W pycodestyle warnings (trailing whitespace, blank-line issues)
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# I isort (import ordering — auto-fixable)
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# B flake8-bugbear (likely-bug patterns: mutable defaults, …)
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# UP pyupgrade (modernize old syntax for the target Python)
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# RUF ruff-specific (small high-signal correctness checks)
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# C4 flake8-comprehensions (clearer list/set/dict comprehensions)
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select = ["E", "F", "W", "I", "B", "UP", "RUF", "C4"]
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# Per-rule overrides — these are the rules that produce false positives on
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# scientific Python code more often than they catch real bugs, plus the
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# stylistic-modernization rules that would otherwise flood the inbox on a
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# mature codebase. Each ignore is justified inline so future maintainers can
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# see why it was added and revisit if the situation changes.
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ignore = [
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# --- whitespace / formatting (let `ruff format` handle these) ----------
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"E501", # line too long — allow long XYZ blocks, SMILES, docstrings
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"E731", # do not assign a lambda — common in numerical code
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"E741", # ambiguous variable name (l/I/O) — allowed for math/physics
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"W291", # trailing whitespace — formatter's job
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"W293", # blank-line whitespace — formatter's job
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# --- typing modernization (we keep the legacy form for now) -----------
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"UP006", # `list` instead of `List` — pre-PEP604 form is in heavy use
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"UP007", # `X | Y` instead of `Union[X, Y]` — same reason
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"UP035", # `typing.X` deprecated — same reason
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"UP045", # `X | None` instead of `Optional[X]` — same reason (1290+ hits)
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# --- pyupgrade modernizations that aren't worth a churn-PR ------------
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"UP009", # UTF-8 encoding declaration — harmless leftover
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"UP015", # redundant open mode `'r'` — harmless
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"UP025", # unicode kind prefix `u""` — harmless
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"UP030", # `format()` literal positional indexes — minor
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"UP032", # use f-string instead of `.format()` — minor
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# --- bugbear false positives on numerical code ------------------------
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"B007", # unused loop control variable — common with `for _, x in …`
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"B008", # function calls in arg defaults
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"B905", # zip() without strict — would require a churn PR
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# --- comprehension preferences (taste, not bugs) ----------------------
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"C408", # unnecessary `dict()` call
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"C416", # unnecessary comprehension
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"C419", # unnecessary comprehension in `any()`/`all()`/etc.
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# --- ruff-specific noise on chemistry text ----------------------------
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"RUF001", # ambiguous unicode in strings — Greek letters in chemistry text
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"RUF002", # ambiguous unicode in docstrings — same
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"RUF003", # ambiguous unicode in comments — same
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"RUF005", # collection literal concatenation — taste
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"RUF012", # mutable class attributes annotated with ClassVar — too noisy
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"RUF013", # implicit `Optional` — would need typing-wide cleanup
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"RUF059", # unused unpacked variable — taste
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]
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[tool.ruff.lint.per-file-ignores]
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# Tests routinely use long literal blocks (XYZ strings, expected dicts, …)
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# and `assert` patterns that some lint rules flag as "useless".
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"**/*test*.py" = ["E501", "F841", "B017", "RUF015"]
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"arc/testing/**" = ["E501", "F841"]
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# __init__.py files re-export symbols and need wildcard / unused-import patterns.
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"**/__init__.py" = ["F401", "F403"]
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# Standalone scripts run inside isolated envs and may import packages not
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# installed in the main env — don't flag those imports.
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"arc/job/adapters/scripts/*.py" = ["F401", "E402"]
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[tool.ruff.lint.isort]
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known-first-party = ["arc"]
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combine-as-imports = true
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force-sort-within-sections = false
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section-order = [
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"future",
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"standard-library",
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"third-party",
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"first-party",
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"local-folder",
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]
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[tool.ruff.format]
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# Format settings for `ruff format`. Not enforced by CI yet — the team can
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# opt in to a one-time mass reformat by running `ruff format arc/`.
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quote-style = "single"
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indent-style = "space"
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line-ending = "lf"
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docstring-code-format = false

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