Fix bug with mesh indexing for start_index=1 - #7253
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trexfeathers merged 5 commits intoAug 20, 2026
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Codecov Report✅ All modified and coverable lines are covered by tests. Additional details and impacted files@@ Coverage Diff @@
## main #7253 +/- ##
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stephenworsley
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August 20, 2026 12:38
trexfeathers
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Thanks @stephenworsley. I have confirmed that this fixes the problems reported in #7246 (and without it I can replicate those problems).
Couple of comments on the tests for you
trexfeathers
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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>
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Closes #7246.
This ought to fix the problems with face_node_connectivities in #7246, but won't yet address the other connectivities (it might be worth just throwing away these connectivities from the returned MeshIndexSet for the time being). This PR seems to work with the file in #7246 when I experimented with it locally, but this PR will want a bit more testing to ensure coverage for these cases.