Add AGENTS.md

AGENTS.md

@@ -0,0 +1,221 @@
+# AGENTS.md
+
+Agent instructions for the [Iris](https://scitools-iris.readthedocs.io/) repository.
+Iris is a Python package for analysing and visualising Earth science data, built around
+CF-compliant multi-dimensional arrays ("Cubes").
+
+Subdirectory AGENTS.md files take precedence for their subtrees:
+- [`docs/AGENTS.md`](docs/AGENTS.md) — documentation-specific rules
+- [`lib/iris/tests/AGENTS.md`](lib/iris/tests/AGENTS.md) — test-specific rules
+
+
+## Project Overview
+
+| | |
+|---|---|
+| **Language** | Python 3.12 / 3.13 / 3.14 |
+| **Licence** | BSD-3-Clause |
+| **Distribution** | conda-forge (`iris`), PyPI (`scitools-iris`) |
+| **Key dependencies** | NumPy, Dask, SciPy, Cartopy, CF-Python, NetCDF4 |
+| **Linter / formatter** | Ruff (88-char line length) |
+| **Test runner** | pytest + pytest-xdist (`-n auto`) |
+| **Env management** | nox + conda |
+
+### Main source layout
+
+```
+lib/iris/
+    cube.py            # Core Cube / CubeList data structures
+    coords.py          # DimCoord, AuxCoord, CellMeasure, AncillaryVariable
+    loading.py         # File-loading entry points
+    analysis/          # Collapse, regrid, statistics, calculus
+    fileformats/       # NetCDF, PP, GRIB, NIMROD format handlers
+    io/                # I/O registry and URI handling
+    common/            # Shared metadata, mixins, resolvers
+    mesh/              # Unstructured grid (UGRID) support
+    experimental/      # Unstable / in-progress features
+    tests/             # All tests (unit/, integration/, graphics/)
+docs/src/              # Sphinx documentation source
+benchmarks/            # ASV performance benchmarks
+requirements/          # Conda environment specs and lock files
+```
+
+
+## Setup
+
+### Conda environment (recommended)
+
+Always use a conda environment, reuse the iris-dev conda environment if it
+already exists but confirm with the user before installing or removing packages.
+
+If a package cannot be installed via conda then you can use pip that is in the conda
+environment.
+
+```bash
+# Create and activate a development environment
+conda env create -f requirements/py312.yml
+conda activate iris-dev
+pip install --no-build-isolation -e .
+```
+
+Alternatively, use lock files for exact reproducibility:
+
+```bash
+conda create -n iris-dev --file requirements/locks/py312-linux-64.lock
+conda activate iris-dev
+pip install --no-build-isolation -e .
+```
+
+### Environment variables
+
+```bash
+# Disable CPU features that can cause SIGILL in some CI environments
+export NPY_DISABLE_CPU_FEATURES="AVX512F,AVX512CD,AVX512_SKX"
+
+# Point to iris-test-data for tests that need external data files
+export OVERRIDE_TEST_DATA_REPOSITORY=/path/to/iris-test-data/test_data
+
+# Override Cartopy cache directory if needed
+export CARTOPY_CACHE_DIR=~/.local/share/cartopy
+```
+
+
+
+## Testing
+
+- [`lib/iris/tests/AGENTS.md`](lib/iris/tests/AGENTS.md) — test-specific 
+
+
+
+## Code Style
+
+```bash
+# Lint
+ruff check lib/iris
+
+# Auto-fix safe lint issues
+ruff check --fix lib/iris
+
+# Format
+ruff format lib/iris
+
+# Check formatting without writing
+ruff format --check lib/iris
+```
+
+- **Line length**: 88 characters (Ruff default).
+- **Docstrings**: NumPy style; strictly validated.
+- **Copyright header**: Every new Python file must start with:
+
+  ```python
+  # Copyright Iris contributors
+  #
+  # This file is part of Iris and is released under the BSD license.
+  # See LICENSE in the root of the repository for full licensing details.
+  ```
+
+- **Imports**: Ruff-managed ordering. No direct `import netCDF4` — always use
+  `iris.fileformats.netcdf._thread_safe_nc` for thread safety.
+
+
+
+## Development Conventions
+
+### Core data model
+
+- `iris.cube.Cube` — multi-dimensional array with CF-compliant metadata.
+- Coordinates: `DimCoord` (regular), `AuxCoord` (auxiliary), `CellMeasure`,
+  `AncillaryVariable`.
+- Data may be **lazy** (Dask array). Always preserve laziness; never call `.data`
+  unnecessarily inside library code.
+- Operations return **new** Cubes (functional style); do not mutate in place.
+- All metadata must be **CF-convention** compliant.
+
+### Deprecation
+
+- Use `iris._deprecation.warn_deprecated()` or issue a custom warning class.
+- Warning classes live in `iris.warnings` (e.g., `IrisUserWarning`, `IrisCfWarning`).
+- Follow the NEP29 deprecation schedule (same as NumPy).
+- All `UserWarning` subclasses must ultimately inherit from `IrisUserWarning`.
+
+### Exception hierarchy
+
+Base class: `iris.exceptions.IrisError`. Common subclasses:
+`CoordinateNotFoundError`, `CoordinateCollapseError`, `IgnoreCubeException`.
+
+### Versioning
+
+Version is derived from git tags via `setuptools_scm`. Do not hard-code version
+strings.
+
+
+## Documentation
+
+Documentation lives under `docs/` and is built with Sphinx. See
+[`docs/AGENTS.md`](docs/AGENTS.md) for full rules.
+
+
+
+## Lock-file Maintenance
+
+```bash
+# Regenerate lock files for all supported Python versions
+python tools/update_lockfiles.py -o requirements/locks requirements/py*.yml
+# Shortcut via Makefile
+make lockfiles
+```
+
+
+
+## Pull Request Guidelines
+
+- **Title format**: `[component] Brief description` (e.g., `[netcdf] Fix chunking for large files`).
+- Run before opening a PR:
+  ```bash
+  ruff check lib/iris
+  ruff format --check lib/iris
+  pytest -n auto lib/iris/tests
+  ```
+- Keep changes focused; avoid unrelated refactors in the same PR.
+- Add or update tests for every change to production code.
+- Update `docs/src/whatsnew/` for user-visible changes.
+
+
+## Critical Development Gotchas
+
+1. **xfail_strict Behavior**: Tests marked `@pytest.mark.xfail` that now PASS become FAILURES → **remove xfail immediately when bug is fixed**
+
+2. **Pre-commit Auto-fixes**: Hooks may auto-fix ISC001/COM812 conflicts → re-stage files: `git add . && git commit`
+
+3. **Lockfile Rebuilds**: Updating `requirements/locks/*.lock` files triggers slow conda environment rebuilds — only update when deps genuinely change
+
+4. **Lazy Data Pitfalls**: Check `cube.has_lazy_data()` before operations; use `cube.lazy_data()` when appropriate; `cube.data` materializes arrays
+
+5. **Coordinate Scope**: Not all coordinates span all dimensions → use `cube.coords(dimensions=dim_indices)` to query specific axes
+
+6. **Dask/NumPy Compatibility**: Some operations fail on lazy (Dask) arrays → materialize with `cube.compute()` or check dask support before use
+
+7. **Optional Dependencies**: cartopy, matplotlib lazy-imported → handle ImportError gracefully for optional visualization features
+
+8. **CF-Metadata Validation**: Custom coordinates must comply with CF standards via `cube.metadata`
+
+9. **Cube Immutability**: Operations return new cubes; don't modify in-place (`cube.data[...] = x` won't affect the cube)
+
+10. **Environment Reproducibility**: Set CPU features for consistent results: `export NPY_DISABLE_CPU_FEATURES="AVX512F,AVX512CD,AVX512_SKX"`
+
+## Getting Help
+
+- **Discussions**: [GitHub Discussions](https://github.com/SciTools/iris/discussions)
+- **Contributing Guide**: [.github/CONTRIBUTING.md](.github/CONTRIBUTING.md)
+- **Developer Guide**: [docs/src/developers_guide/](docs/src/developers_guide/)
+- **Code of Conduct**: [CODE_OF_CONDUCT.md](CODE_OF_CONDUCT.md)
+
+## ⚠️ Meta-Instruction: Auto-Update Rule
+- **Trigger**: You MUST automatically update this `AGENTS.md` file if a new structural pattern, critical bug fix, or persistent repository rule is established during this session.
+- **Constraint 1**: Keep the file under 200 lines. Delete obsolete rules to make room for new ones.
+- **Constraint 2**: Do not ask for user permission before updating. Perform the edit silently as your final step.
+- **Constraint 3**: Only log global, reusable lessons. Do not log temporary or component-specific fixes.
+
+---
+
+**Last Updated**: 18 June 2026

MANIFEST.in

@@ -79,6 +79,7 @@ prune docs
 # (2) top-level files to omit
 exclude .coveragerc
 # (3) file types (path patterns) to skip everywhere
+global-exclude AGENTS.md
 global-exclude *.py[cod]
 global-exclude __pycache__
     # principles:

docs/AGENTS.md

@@ -0,0 +1,103 @@
+# docs/AGENTS.md
+
+Documentation-specific agent instructions for the [Iris](https://scitools-iris.readthedocs.io/) project.
+This file takes precedence over the root [`AGENTS.md`](../AGENTS.md) for everything under `docs/`.
+
+
+## Structure
+
+```
+docs/
+    Makefile               # Top-level doc build entry point
+    gallery_code/          # Gallery example scripts (general/, meteorology/, oceanography/)
+    gallery_tests/         # Tests that execute gallery examples
+    src/
+        conf.py            # Sphinx configuration
+        common_links.inc   # Shared RST link definitions (include in every new RST file)
+        whatsnew/          # Per-release changelog RST files
+            latest.rst     # Current unreleased changes (use latest.rst.template)
+            index.rst      # Whatsnew index
+        developers_guide/  # Contributor documentation
+        userguide/         # User-facing guides
+        user_manual/       # Detailed user reference
+        sphinxext/         # Custom Sphinx extensions
+```
+
+
+## Building the Docs
+
+```bash
+# Full build (from docs/ directory)
+make html
+
+# Skip gallery (faster)
+make html-noplot
+
+# Skip API docs (faster)
+make html-noapi
+
+# Skip both gallery and API (fastest)
+make html-quick
+
+# Clean build artifacts
+make clean
+
+# Live rebuild on file changes (requires sphinx-autobuild)
+cd docs/src && make livehtml
+```
+
+Build output goes to `docs/src/_build/html/`.
+
+
+## Whatsnew Entries
+
+- Every **user-visible change** must have an entry in `docs/src/whatsnew/latest.rst`.
+- Use the `latest.rst.template` as the template when starting a new release file.
+- Sections: *New Features*, *Deprecations*, *Bugs Fixed*, *Internal*, *Dependencies*.
+- Reference issues/PRs with ``:issue:`123` `` and `` :pull:`123` `` roles.
+- Keep entries concise — one or two sentences with a code example if helpful.
+
+
+## RST / Sphinx Conventions
+
+- All new RST files must include `.. include:: ../common_links.inc` (adjust relative path as needed) to access shared link definitions.
+- Use NumPy-style docstrings for all Python API pages; Sphinx autodoc pulls these automatically.
+- Warnings are treated as errors in the standard build (`-W --keep-going`). Fix all Sphinx warnings before merging.
+- Do **not** commit build artifacts (`docs/src/_build/`).
+- Cross-reference Iris symbols with ``:class:`iris.cube.Cube` ``, ``:func:`iris.load` ``, etc.
+- Gallery scripts live under `docs/gallery_code/` and must be valid standalone Python files executable by `matplotlib` / `sphinx-gallery`.
+
+
+## Gallery Examples
+
+- Each gallery script must have a module-level docstring that becomes its title and description.
+- Scripts are grouped by subdirectory: `general/`, `meteorology/`, `oceanography/`.
+- Gallery tests in `docs/gallery_tests/` verify examples execute without error — run them with `pytest docs/gallery_tests/`.
+- Keep examples self-contained; prefer `iris.sample_data_path()` for data files rather than absolute paths.
+
+
+## Doctest / Inline Code Examples
+
+- Doctests in RST files are run via `make doctest` (from `docs/src/`).
+- Use `# doctest: +SKIP` sparingly and only when execution is genuinely impossible (e.g., requires a display).
+- Ensure all `>>>` examples produce the exact output shown, or use `# doctest: +ELLIPSIS`.
+
+
+## Critical Gotchas
+
+1. **Sphinx warnings = errors**: The standard `make html` build uses `-W`. Any new warning breaks CI.
+2. **`common_links.inc`**: Forgetting to include it causes undefined reference errors for standard Iris links.
+3. **`latest.rst` conflicts**: Multiple contributors adding entries may cause merge conflicts — add entries under the correct section heading and keep them alphabetically ordered by PR number.
+4. **Gallery data files**: Use `iris.sample_data_path()` — hard-coded paths will break in CI.
+5. **API doc changes**: Moving or renaming public symbols requires updating any manual cross-references in the RST files.
+
+
+## ⚠️ Meta-Instruction: Auto-Update Rule
+- **Trigger**: You MUST automatically update this `AGENTS.md` file if a new structural pattern, critical bug fix, or persistent repository rule is established during this session.
+- **Constraint 1**: Keep the file under 200 lines. Delete obsolete rules to make room for new ones.
+- **Constraint 2**: Do not ask for user permission before updating. Perform the edit silently as your final step.
+- **Constraint 3**: Only log global, reusable lessons. Do not log temporary or component-specific fixes.
+
+---
+
+**Last Updated**: 16 June 2026  

docs/src/whatsnew/latest.rst

@@ -172,11 +172,16 @@ This document explains the changes made to Iris for this release
 #. `@trexfeathers` set the link checking workflow to accept redirect HTTP codes, as
    the reports were getting too noisy. (:pull:`7148`)
 
-#. `@HGWright`_ changed the default of the private switch :obj:`~iris.loading._LAZY_DERIVED_LOADING` (formerly `.CONCRETE_DERIVED_LOADING`)
-   for controlling laziness of coordinates from pp loading, now the switch must be set to True for lazy loading to be enabled.
-   Note: this object is temporary and is likely to be replaced by a permanent solution or else be renamed.
+#. `@HGWright`_ changed the default of the private switch
+   :obj:`~iris.loading._LAZY_DERIVED_LOADING` (formerly `.CONCRETE_DERIVED_LOADING`)
+   for controlling laziness of coordinates from pp loading, now the switch must be set
+   to True for lazy loading to be enabled.  Note: this object is temporary and is
+   likely to be replaced by a permanent solution or else be renamed.
    (:issue:`7094`, :pull:`7134`)
 
+#. :user:`tkknight` Added ``AGENTS.md`` for AI-assisted development guidelines across
+   the project root, ``docs/`` and ``tests/`` directories. (:pull:`7160`)
+
 #. `@rcomer`_ fixed the capitalisation of a pytest marker. (:pull:`7163`)
 
 .. comment