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Scoped to Project-MONAI#9199's root file: PRs target dev, DCO sign-off required, ./runtests.sh --autofix is the formatter, optional deps go through monai.utils.optional_import, new public API needs a docs/source/*.rst entry, slow tests go in tests/min_tests.py. Cross-references the AI/tool-assisted contribution policy from Project-MONAI#9106 rather than duplicating it. Nested, package-level AGENTS.md files are left for a follow-up PR per the discussion on the issue. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Signed-off-by: arxh80 <archie.mullins1807@gmail.com>
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| Check name | Status | Explanation |
|---|---|---|
| Title check |  |
The title clearly and concisely identifies the main change: adding a root-level AGENTS.md file for AI coding assistants. |
| Description check | |
The description explains the change, scope, related issue, deferred work, and change type. It omits the template's explicit issue-reference line and leaves the documentation checkbox unchecked despite… |
| Docstring Coverage | |
No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0… |
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| Out of Scope Changes check | |
Check skipped because no linked issues were found for this pull request. |
Full details: Description check
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Explanation
The description explains the change, scope, related issue, deferred work, and change type. It omits the template's explicit issue-reference line and leaves the documentation checkbox unchecked despite adding repository documentation, but it is otherwise complete.
Full details: Docstring Coverage
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No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 0 files. (1 skipped: 1 unsupported.)
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garciadias
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Thanks for picking this up. Two points beyond the inline ones. First, #9200 covers the same root file plus the transforms and tests leaf files and was opened earlier, so maintainers will need to choose one or combine them; it may be worth coordinating with that author. Second, on security: AGENTS.md is read as instructions by every contributor's coding assistant, so an edit to it is effectively a change to tooling behaviour and a prompt-injection surface. The root path is not covered by .github/CODEOWNERS today (only /monai/, /docs/, /tests/ and /.github/ are), so I'd suggest adding /AGENTS.md there whichever PR lands.
| `import`, so the package stays usable without every extra installed. | ||
| - A new public API needs a corresponding entry in `docs/source/*.rst` (or the matching `.md` file for guides), | ||
| not just a docstring. | ||
| - A slow test belongs in `tests/min_tests.py`'s exclusion list, not in the default fast suite. |
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This line sends slow tests to the wrong place. exclude_cases in tests/min_tests.py is for modules that need external/optional dependencies (see the comment on that list), not for slow tests. Slow tests are marked with skip_if_quick from tests/test_utils.py, which --quick honours. An assistant reading this will remove slow tests from the minimal run instead of decorating them. (The same wording in #9199 is my mistake; I'll correct the issue.) Suggested: "A slow test is decorated with skip_if_quick (tests/test_utils.py); a test module that needs an optional dependency is added to exclude_cases in tests/min_tests.py."
| ## Project overview | ||
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| MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging. See | ||
| [setup.cfg](setup.cfg) / [pyproject.toml](pyproject.toml) for the supported Python and PyTorch versions. |
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setup.cfg does not exist on dev, so this link is broken. The versions are declared in pyproject.toml and setup.py.
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| Guidance for AI coding assistants (Claude Code, Codex, Copilot agent mode, Cursor, Gemini CLI, Jules, Aider, ...) | ||
| working in this repository. See [CONTRIBUTING.md](CONTRIBUTING.md) for the full human contributor guide and | ||
| [the AI/tool-assisted contribution policy](CONTRIBUTING.md) for what is and isn't acceptable when using these |
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Both links point to the top of CONTRIBUTING.md; the policy one can target CONTRIBUTING.md#tool-assisted-contribution-policy.
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Thanks for the review. Pushed fixes for all three inline points:
Re: #9200 — thanks for flagging it, hadn't seen it. It's broader (adds Left the CODEOWNERS addition for |
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Small note: the fix commit had reached my fork yesterday, but this PR never picked it up and kept showing only the first commit. I've re-pushed it (same content, now |
- Fix broken CONTRIBUTING.md link/anchor for the tool-assisted contribution policy. - setup.cfg doesn't exist on dev; point to pyproject.toml and setup.py instead. - Correct the slow-test guidance: skip_if_quick marks a slow test, exclude_cases in tests/min_tests.py is for optional-dependency modules, not slow tests. Per review from garciadias on Project-MONAI#9212. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01STJRQtEaEPSLfiWGMn8Syr Signed-off-by: arxh80 <archie.mullins1807@gmail.com>
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Actionable comments posted: 1
- 🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @AGENTS.md:
- Around line 28-29: Update the AGENTS.md guidance for ./runtests.sh --autofix
to describe it as formatting only, not linting, and direct contributors to run
./runtests.sh --ruff or the full style check for linting; keep the existing
pre-commit hook guidance accurate.
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AGENTS.md
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--autofix sets doRuffFix and doRuffFormat as well as the isort and black fixes, so it runs `ruff check --fix --unsafe-fixes` too (runtests.sh lines 291-297 and 626). The parenthetical only named isort and black. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01STJRQtEaEPSLfiWGMn8Syr Signed-off-by: arxh80 <archie.mullins8@gmail.com>
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Description
Adds a root-level
AGENTS.md, as requested in #9199, scoped to just the repo-wide rules an AI codingassistant needs on every session: PRs target
dev, every commit needs DCO sign-off,./runtests.sh --autofixis the formatter, optional dependencies go through
monai.utils.optional_import, a new public API needs adocs/source/*.rstentry, and a slow test goes intests/min_tests.py.It cross-references the AI/tool-assisted contribution policy merged in #9106 rather than duplicating it —
this file is about how the codebase works, not whether AI assistance is allowed.
Per the discussion on #9199, nested package-level
AGENTS.mdfiles (formonai/transforms,monai/networks,etc.) are left for a follow-up PR rather than bundled into this one.
Types of changes
(Docs-only change — no code paths touched, so the usual test/docs checkboxes above don't apply.)
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