Update lock files plus test fixes - #7270
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #7270 +/- ##
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- Coverage 90.42% 90.35% -0.07%
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Files 93 93
Lines 25816 25816
Branches 4796 4796
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- Hits 23344 23327 -17
- Misses 1693 1709 +16
- Partials 779 780 +1 ☔ View full report in Codecov by Harness. 🚀 New features to boost your workflow:
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Closes #7243 |
trexfeathers
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Thanks @trexfeathers, all looks good!
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⏱️ Performance Benchmark Report: 31016d7Performance shiftsFull benchmark resultsGenerated by GHA run |
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The branch was cut from main at c508ac8; greenfield carries SciTools#7270 on top of that, which re-solved all three lock files. The lock additions here are re-derived against those fresh locks, and remain minimal - the myst-parser dependency closure and the input_hash, nothing else. The cube.py line references the spec cites are unaffected: SciTools#7270's changes are confined to rolling_window, some 4500 lines below the merge and concatenate methods. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com>
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… and configurable (#7274) * Add design spec for merge/concatenate improvement programme Specifies a twelve-PR programme to make cube merge and concatenate more robust, efficient, configurable, extensible, lazy and lenient, without a rewrite. Each PR is either a behaviour-preserving refactor or a standalone user-visible improvement; together they grow a shared substrate beneath both engines. Includes a confirmed diagnosis and fix for the separability bug open since 2017 (#2761), verified end-to-end against the reporter's case. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * Record design-spec location in AGENTS.md Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * docs: publish design specs as MyST Markdown Adopt the spec/plan convention used in bjlittle/tephpy. Agreed design specs now live in `docs/src/developers_guide/specs/` and are published as part of the documentation. They are written in MyST Markdown, are living documents revised as a design evolves, and each declares a citation prefix so its sections can be cited from issues and pull requests. Implementation plans live in the sibling `docs/src/developers_guide/plans/`. A plan is point-in-time and frozen once its pull request merges, so plans are tracked in the repository but excluded from the Sphinx build. This requires `myst-parser`, added to `requirements/py*.yml` and inserted into the three lock files following the precedent of #7095 and #7100. Markdown is used only for specs; all other documentation remains reStructuredText. The merge/concatenate design spec moves here from `docs/superpowers/specs/` and is reworked to the new conventions. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * docs: add a plan roadmap and decision register to the merge spec The spec described a twelve-PR programme but had nowhere to record how far it had got, which assumptions it rested on, or what it had left open. Restructure §6 from a static table of work into the programme's live progress record: dependencies as a partial order rather than a chain, a status vocabulary, an "Outside the roadmap" list, and a numbered register of assumptions and open decisions - each item owned by the pull request that must resolve it. Add §10 for the questions the programme raises but does not answer, renumbering References to §11. Also exclude "_build" and "_static" from the Sphinx build. myst-parser makes ".md" a source suffix, so the README of each was being read as a document. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * docs: record how agentic contributions are pushed and labelled This work is long-running partly because it is also an exercise in earning core-developer buy-in for agentic contributions, so the mechanics of how it reaches them are worth writing down rather than re-deciding each session. Add a "Contribution Workflow" section to AGENTS.md carrying the general rule: branches to the fork, pull requests to a feature branch rather than main, honest "Agentic" labelling, clear attribution, and ask before doing anything outward-facing when unsure. Drop the "Getting Help" link list to stay inside the file's 200-line budget - the links it held are all reachable from CONTRIBUTING.md. The programme-specific parts - base branch "greenfield" and the "Feature: Merge/Concatenate" label - go in the spec's cross-cutting rules instead, where a reviewer can see why these pull requests do not target main. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * docs: add changelog fragments for the design spec Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * docs: rebase the spec baseline onto greenfield The branch was cut from main at c508ac8; greenfield carries #7270 on top of that, which re-solved all three lock files. The lock additions here are re-derived against those fresh locks, and remain minimal - the myst-parser dependency closure and the input_hash, nothing else. The cube.py line references the spec cites are unaffected: #7270's changes are confined to rolling_window, some 4500 lines below the merge and concatenate methods. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> * Spell out spec section citation runs Give every cited section its own section sign, and separate a run of them with a comma or a solidus rather than a dash. A dashed range such as "5.6-5.7" reads as a single citation carrying a stray suffix, so only its first section is unambiguously identified -- by a reader now, and by any cross-reference tooling later. Records the rule on the Design Specs index page, next to the citation prefix table it belongs with, and applies it to the one occurrence in the merge/concatenate spec. Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5 <noreply@anthropic.com>
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* undo the whatsnew changes * fix for doctest warnings * Add unit tests for Cube.coord_dims (#7198) * Add unit tests for Cube.coord_dims * Add What's New changelog fragment for #4552 * Refactor Test_coord_dims._setup for readability Address review feedback from @ESadek-MO: - Move hybrid-height set-up into the single test that uses it - Group _setup into clear blocks: cube → DimCoords → AuxCoords → assigns * Move hybrid-height set-up into a dedicated fixture Address review feedback from @ESadek-MO on #7198: move the hybrid-height construction (delta/sigma/orography, HybridHeightFactory, add_aux_factory) out of the test body and into its own pytest fixture, so that set-up failures can be isolated by PyTest. --------- Co-authored-by: 01luyicheng <01luyicheng@users.noreply.github.com> * Bump the gha group across 1 directory with 9 updates (#7215) Bumps the gha group with 9 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `7.0.0` | `7.0.1` | | [actions/setup-python](https://github.com/actions/setup-python) | `6.3.0` | `7.0.0` | | [lycheeverse/lychee-action](https://github.com/lycheeverse/lychee-action) | `2.8.0` | `2.9.0` | | [scitools/workflows/.github/workflows/ci-manifest.yml](https://github.com/scitools/workflows) | `2026.06.0` | `2026.07.1` | | [scitools/workflows/.github/workflows/ci-template-check.yml](https://github.com/scitools/workflows) | `2026.06.0` | `2026.07.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.14.0` | `1.14.2` | | [actions/labeler](https://github.com/actions/labeler) | `6.1.0` | `7.0.0` | | [scitools/workflows/.github/workflows/refresh-lockfiles.yml](https://github.com/scitools/workflows) | `2026.06.0` | `2026.07.1` | | [actions/stale](https://github.com/actions/stale) | `10.3.0` | `11.0.0` | Updates `actions/checkout` from 7.0.0 to 7.0.1 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@9c091bb...3d3c42e) Updates `actions/setup-python` from 6.3.0 to 7.0.0 - [Release notes](https://github.com/actions/setup-python/releases) - [Commits](actions/setup-python@ece7cb0...5fda3b9) Updates `lycheeverse/lychee-action` from 2.8.0 to 2.9.0 - [Release notes](https://github.com/lycheeverse/lychee-action/releases) - [Commits](lycheeverse/lychee-action@8646ba3...e747777) Updates `scitools/workflows/.github/workflows/ci-manifest.yml` from 2026.06.0 to 2026.07.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@1f21414...7c41342) Updates `scitools/workflows/.github/workflows/ci-template-check.yml` from 2026.06.0 to 2026.07.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@1f21414...7c41342) Updates `pypa/gh-action-pypi-publish` from 1.14.0 to 1.14.2 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@cef2210...dc37677) Updates `actions/labeler` from 6.1.0 to 7.0.0 - [Release notes](https://github.com/actions/labeler/releases) - [Commits](actions/labeler@f27b608...bf12e9b) Updates `scitools/workflows/.github/workflows/refresh-lockfiles.yml` from 2026.06.0 to 2026.07.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@1f21414...7c41342) Updates `actions/stale` from 10.3.0 to 11.0.0 - [Release notes](https://github.com/actions/stale/releases) - [Changelog](https://github.com/actions/stale/blob/main/CHANGELOG.md) - [Commits](actions/stale@eb5cf3a...4391f3d) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: gha - dependency-name: actions/labeler dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: gha - dependency-name: actions/setup-python dependency-version: 7.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: gha - dependency-name: actions/stale dependency-version: 10.4.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: gha - dependency-name: lycheeverse/lychee-action dependency-version: 2.9.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: gha - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: gha - dependency-name: scitools/workflows/.github/workflows/ci-manifest.yml dependency-version: 2026.07.1 dependency-type: direct:production dependency-group: gha - dependency-name: scitools/workflows/.github/workflows/ci-template-check.yml dependency-version: 2026.07.1 dependency-type: direct:production dependency-group: gha - dependency-name: scitools/workflows/.github/workflows/refresh-lockfiles.yml dependency-version: 2026.07.1 dependency-type: direct:production dependency-group: gha ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Bump the gha group across 1 directory with 3 updates (#7256) Bumps the gha group with 3 updates in the / directory: [scitools/workflows/.github/workflows/ci-manifest.yml](https://github.com/scitools/workflows), [scitools/workflows/.github/workflows/ci-template-check.yml](https://github.com/scitools/workflows) and [scitools/workflows/.github/workflows/refresh-lockfiles.yml](https://github.com/scitools/workflows). Updates `scitools/workflows/.github/workflows/ci-manifest.yml` from 2026.07.1 to 2026.08.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@7c41342...28aea7a) Updates `scitools/workflows/.github/workflows/ci-template-check.yml` from 2026.07.1 to 2026.08.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@7c41342...28aea7a) Updates `scitools/workflows/.github/workflows/refresh-lockfiles.yml` from 2026.07.1 to 2026.08.1 - [Release notes](https://github.com/scitools/workflows/releases) - [Commits](SciTools/workflows@7c41342...28aea7a) --- updated-dependencies: - dependency-name: scitools/workflows/.github/workflows/ci-manifest.yml dependency-version: 2026.08.1 dependency-type: direct:production dependency-group: gha - dependency-name: scitools/workflows/.github/workflows/ci-template-check.yml dependency-version: 2026.08.1 dependency-type: direct:production dependency-group: gha - dependency-name: scitools/workflows/.github/workflows/refresh-lockfiles.yml dependency-version: 2026.08.1 dependency-type: direct:production dependency-group: gha ... Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * Fix TEST_DATA_DIR default behaviour (#7257) * fix TEST_DATA_DIR default behaviour * add whatsnew * Add option for steps in Cube rolling windows (#7236) * Add option for steps in Cube rolling windows * Add changelog entry * Fix bug with mesh indexing for start_index=1 (#7253) * fix bug with mesh indexing for start_index=1 * add test * add whatsnew * add unit tests * CI compatibility with PROJ 9.8 (#7254) * CI compatibility with PROJ 9.8. * review comments (#97) --------- Co-authored-by: Elias <110238618+ESadek-MO@users.noreply.github.com> * Update lock files plus test fixes (#7270) * Updated environment lockfiles * Temporary gallery test fix. * Revert "Temporary gallery test fix." This reverts commit 6403701. * Skip Proj 9.8 incompatible gallery tests. Proven by 6403701. * Modernise graphics tests. * What's New entry. --------- Co-authored-by: Lockfile bot <noreply@github.com> Co-authored-by: Elias <110238618+ESadek-MO@users.noreply.github.com> * DOC BLD: get scipy objects inventory from their static site (#7269) * Move developers' conda yml to environment.yml (#7267) * Move developers' conda yml to environment.yml * Fix readthedocs.yml * Add environment.yml to manifest * Add code trial for encode/decode of lazy data. * Some extra debug. * Apply encode/decode to load/save shortcutting, and support lazy data. * Small changes to support scalar character variables. * Replace complex VariableEncoder constructor with a .from_var classmethod. * Apply scalar adjustment whether lazy or real. * Remove debug print. * Extend get_cf_var to test dataset-shortcutting of strings and real/lazy data. * Fix typo in tests. * Remove temporary tests. * With CoPilot: tests for handling of ncdata-style direct data transfers in '_lazy_stream_data'. * Added changelog fragment. * Review changes. --------- Signed-off-by: dependabot[bot] <support@github.com> Co-authored-by: Henry Wright <henrywright@sky.com> Co-authored-by: Martin Yeo <40734014+trexfeathers@users.noreply.github.com> Co-authored-by: 陆奕丞 <01luyicheng@gmail.com> Co-authored-by: 01luyicheng <01luyicheng@users.noreply.github.com> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: stephenworsley <49274989+stephenworsley@users.noreply.github.com> Co-authored-by: Andrew Creswick <89418171+mo-AndrewCreswick@users.noreply.github.com> Co-authored-by: Elias <110238618+ESadek-MO@users.noreply.github.com> Co-authored-by: Lockfile bot <noreply@github.com> Co-authored-by: Ruth Comer <10599679+rcomer@users.noreply.github.com>
pp-mo
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* Updated environment lockfiles * Temporary gallery test fix. * Revert "Temporary gallery test fix." This reverts commit 6403701. * Skip Proj 9.8 incompatible gallery tests. Proven by SciTools/iris@6403701. * Modernise graphics tests. * What's New entry. --------- Co-authored-by: Lockfile bot <noreply@github.com> Co-authored-by: Elias <110238618+ESadek-MO@users.noreply.github.com>
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Description
Closes #7243
Have tested and proven that the remaining failures result from the incompatible combination of PROJ>=9.8 and Cartopy <0.26. Have therefore skipped the relevant tests.
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