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docs: add AGENTS.md for the repository, monai/transforms and tests - #9200
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Introduce the AGENTS.md convention described in Project-MONAI#9199: a root file that routes to the package files, plus leaf files for monai/transforms and tests, and a pointer from CONTRIBUTING.md. Every fact in the files was checked against the code, and the files link to CONTRIBUTING.md instead of duplicating it. Assisted-by: OpenCode <noreply@opencode.ai> Signed-off-by: Ayan Zahid <220202667+AyanZahid-Code@users.noreply.github.com>
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📝 Walkthrough
Merge Risk: ⚪ Minimal · up to
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| Check name | Status | Explanation |
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| Title check |  |
The title clearly identifies the main change: adding AGENTS.md guidance for the repository, transforms, and tests. It is concise and specific. |
| Description check | |
The description clearly explains the scope, file contents, validation process, authorship, and issue addressed. It does not reproduce the template headings or checklist, but it provides the required i… |
| 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… |
| Linked Issues check | |
Check skipped because no linked issues were found for this pull request. |
| 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 clearly explains the scope, file contents, validation process, authorship, and issue addressed. It does not reproduce the template headings or checklist, but it provides the required information and is mostly complete.
Full details: Docstring Coverage
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Explanation
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. (2 skipped: 2 unsupported.)
✨ Finishing Touches
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Actionable comments posted: 2
- 🪄 Fix comments: Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at @AGENTS.md:
- Line 38: Update the docs entry in the repository map to describe all Sphinx
sources under docs/source/, including Markdown files, rather than limiting the
scope to *.rst files.
Review comments at @tests/AGENTS.md:
- Line 25: Update the inline comment for the ./runtests.sh command to describe
it as recommended before opening a pull request, rather than claiming it is the
exact CI command.
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📒 Files selected for processing: 4
AGENTS.mdCONTRIBUTING.mdmonai/transforms/AGENTS.mdtests/AGENTS.md
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CodeRabbit's review of the AGENTS.md pull request pointed out that the repository map described only the reStructuredText sources under docs/source, while Sphinx also includes the Markdown ones, and that the full test command is the one CONTRIBUTING.md recommends before a pull request rather than the one CI runs. Assisted-by: OpenCode <noreply@opencode.ai> Signed-off-by: Ayan Zahid <220202667+AyanZahid-Code@users.noreply.github.com>
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I checked the claims against the code: the tests.test_utils helpers, the min_tests unused/duplicate assertion, the functional.py/batch.py layout, the extra_info collate restriction, the DCO commit-msg hook and every CONTRIBUTING anchor all hold. One security suggestion: AGENTS.md files are loaded as instructions by contributors' coding assistants, so changes to them deserve the same review gate as code. The leaf files are covered by CODEOWNERS through /monai/ and /tests/, but /AGENTS.md and /CONTRIBUTING.md are not; adding /AGENTS.md (or **/AGENTS.md) to .github/CODEOWNERS would close that. Note #9212 overlaps with this PR.
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| ```bash | ||
| ./runtests.sh --setup # install the pre-commit hooks (black, isort, ruff, DCO sign-off) | ||
| ./runtests.sh --autofix # format the working tree (isort + black) |
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--autofix also runs ruff check --fix --unsafe-fixes and the copyright-header fixer, not only isort and black. Worth saying, since an assistant will run it across the whole tree and should expect those edits.
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This is steps 1 and 2 of #9199: the root file plus the two highest-traffic leaf files.
What is in the pull request
AGENTS.md(root): project overview, a repository map of every top-level folder, a routing table, the setup and command list, the repo-wide conventions, a link to the tool-assisted contribution policy, and a short "do not" list.monai/transforms/AGENTS.md: thearray.py/dictionary.py/functional.py/batch.pylayout of each family, and the traps specific to the package —MetaTensormetadata must survive the call, randomness goes throughself.R, thepush_transform/pop_transformcontract ofInvertibleTransform, and the deferred resampling ofLazyTransform.tests/AGENTS.md: the file naming rules, how to run one module, and the traps — optional dependencies are handled with theSkipIfNoModuledecorators orexclude_casesintests/min_tests.py, test data is downloaded rather than committed, and the shared helpers are imported fromtests.test_utils.CONTRIBUTING.md: a pointer toAGENTS.mdand the expectation to keep it current.How the facts were checked
Every statement was verified against the code in this branch, not from memory:
optional_importlives inmonai/utils/module.py, and the deprecation helpers inmonai/utils/deprecate_utils.py.tests.test_utils(thetests.utilspackage holds the tests ofmonai.utilsitself).QUICKTEST=true python -m tests.min_tests, as documented intests/min_tests.py.ResampleModeandtrace_back_transformdo not exist in this tree, so neither file mentions them; the lazy machinery is described throughLazyTrait,LazyTransformandApplyPending.monai.module.exportdecorator thatCONTRIBUTING.mdstill mentions is not in the code any more, so the files point at the package__init__.pyre-exports instead.The commands listed in the root file are the ones
./runtests.sh -hprints;./runtests.sh -hand the help output were run for this pull request, while the test commands need the full development environment (pip install -e .[testing]).Note on authorship
This documentation was drafted with an AI assistant, under the tool-assisted contribution policy in
CONTRIBUTING.md. The commit carries anAssisted-by:trailer and a DCO sign-off, and the content was reviewed against the code before submitting.Addresses step 1 and step 2 of #9199.