Comparing changes

@vincentsarago

* fix(converter): align convert layout to S2, strip _eopf_attrs, fix _FillValue (#171) - Remove TMS layout and /0 /1 /2 numeric overview groups from the general 'convert' CLI; produce S2-style sibling r{2**level} overviews instead. 'convert-s2-optimized' continues to emit the same layout. - Drop the '--tile-width' CLI option. - Sanitize array attrs in all converters: strip stale '_eopf_attrs' and source-only '_FillValue' / 'dtype' / 'valid_min' / 'valid_max' on decoded floats; rewrite 'units: digital_counts' -> 'units: 1'. The sanitizer now returns a new dict and callers reassign 'attrs', so stale keys are actually removed (a previous '.update()' pattern left them in place). - Sanitize coord attrs too (datetime coords in /conditions/meteorology were leaking '_eopf_decode_datetime64' via '_eopf_attrs'). - Set '_FillValue' properly for float measurements so xarray's CF encoder produces the base64-NaN representation needed for 'use_zarr_fill_value_as_mask=True' round-trip (xarray#11345). Fixes #171. - Remove dead 'utils.encode_cf_fill_value' (no callers). - Tests: open each r{N} multiscale level separately; migrate 'test_multiscales_round_trip' from deprecated tms.Multiscales to zcm.Multiscales (with tuplify_json to handle extra='allow' fields). - Regenerate snapshot fixtures; verified 0 '_eopf_attrs', 'tile_matrix*', or 'digital_counts' markers across S2A/S2B/S2C. * test: add guardrails for converter output attrs (#171) Walks the snapshotted GroupSpec JSON fixtures and asserts: - no '_eopf_attrs' anywhere; - no 'tile_matrix*' markers (TMS removal); - no 'units: digital_counts' on float arrays (decoded scale/offset); - every float array under '/measurements/' has '_FillValue' set (required for CF NaN-mask round-trip, xarray#11345). * docs: deprecate v0 references, document r{N} overview layout (#171) - Drop 'tile_width' parameter from API examples (option removed from CLI/API). - Replace '/measurements/r10m/{0,1,2}' nested-pyramid examples with the current flat 'r{2**level}' sibling-group layout. - Remove the V0 vs V1 split in converter.md / examples.md / quickstart.md; the general 'convert' command now produces the same flat layout as 'convert-s2-optimized'. The S2-optimized section is reframed as a feature description rather than a 'V1 vs V0' comparison. - Update architecture.md multiscales snippet to the new model ('layout' / 'asset' / 'derived_from' / 'transform'). - Update faq.md inspection snippet to walk the new layout. * refactor: clean up code formatting and enhance attribute handling in geozarr conversion * fix(cli-e2e): drop deprecated --tile-width flag from tests and example * refactor: remove deprecated v0 layout, sanitize attributes, and fix _FillValue handling * test: add _FillValue masking roundtrip test (#172) Addresses @vincentsarago's PR review: assert float arrays written with the converter's _FillValue convention round-trip through xarray's use_zarr_fill_value_as_mask=True so NaN cells come back masked. * test: drive _FillValue masking test through create_geozarr_dataset (#172) Replace the standalone xarray write with a real converter run: build a small float DataTree, invoke create_geozarr_dataset, then reopen the output with use_zarr_fill_value_as_mask=True and assert masking on the nodata patch. Exercises the converter's _FillValue + encoding path end-to-end, per @vincentsarago's review. * fix: green CI for #172 — S2 convert flat layout + idna CVE (#177) * fix(security): bump idna 3.13 -> 3.17 to clear CVE-2026-45409 pip-audit in the Security Audit workflow blocks on idna 3.13 (CVE-2026-45409, incomplete fix of CVE-2024-3651; fixed in 3.15). Bump the transitive pin via uv lock. pip-audit now reports no known vulnerabilities. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(cli): route Sentinel-2 convert through the optimized flat layout Generic `convert` emitted GeoZarr-0.4 multiscales with native data at the group root and overviews as nested r{2**N} sub-groups. That tree cannot be opened by xr.open_datatree (an overview child's x/y conflict with the parent's inherited x/y), so the `info` and `validate` CLI commands crashed on the converter's own Sentinel-2 output. Detect Sentinel-2 inputs and delegate to the existing, tested convert_s2_optimized path, which emits flat sibling r{N}m levels (the layout PR #172 documents). Non-S2 inputs keep the generic create_geozarr_dataset path. Detection is best-effort and never aborts conversion. Regenerate the geozarr_examples structure snapshots to the flat layout. Co-Authored-By: Claude Opus 4.8 <[email protected]> * test: make CLI e2e assertions debuggable and fix multiscale round-trip - The CLI logs errors to stdout via structlog; assert on stdout+stderr in test_cli_e2e so a non-zero exit shows the actual error instead of an empty stderr. - test_multiscale_attrs_round_trip tuplified only one side of its equality, so flat-layout level groups carrying list-valued attrs (e.g. spatial:bbox) broke a check that is only about JSON list/tuple normalisation. Tuplify both sides; the model still round-trips losslessly. Co-Authored-By: Claude Opus 4.8 <[email protected]> --------- Co-authored-by: Claude Opus 4.8 <[email protected]> --------- Co-authored-by: Loïc Houpert <[email protected]> Co-authored-by: Claude Opus 4.8 <[email protected]>

) Bumps the actions group with 8 updates in the / directory: | Package | From | To | | --- | --- | --- | | [actions/checkout](https://github.com/actions/checkout) | `5.0.1` | `6.0.2` | | [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) | `7.6.0` | `8.1.0` | | [actions/cache](https://github.com/actions/cache) | `5.0.4` | `5.0.5` | | [codecov/codecov-action](https://github.com/codecov/codecov-action) | `5.5.3` | `6.0.0` | | [googleapis/release-please-action](https://github.com/googleapis/release-please-action) | `4.4.0` | `5.0.0` | | [actions/upload-artifact](https://github.com/actions/upload-artifact) | `6.0.0` | `7.0.1` | | [actions/download-artifact](https://github.com/actions/download-artifact) | `7.0.0` | `8.0.1` | | [pypa/gh-action-pypi-publish](https://github.com/pypa/gh-action-pypi-publish) | `1.13.0` | `1.14.0` | Updates `actions/checkout` from 5.0.1 to 6.0.2 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](actions/checkout@93cb6ef...de0fac2) Updates `astral-sh/setup-uv` from 7.6.0 to 8.1.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](astral-sh/setup-uv@37802ad...0880764) Updates `actions/cache` from 5.0.4 to 5.0.5 - [Release notes](https://github.com/actions/cache/releases) - [Changelog](https://github.com/actions/cache/blob/main/RELEASES.md) - [Commits](actions/cache@6682284...27d5ce7) Updates `codecov/codecov-action` from 5.5.3 to 6.0.0 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](codecov/codecov-action@1af5884...57e3a13) Updates `googleapis/release-please-action` from 4.4.0 to 5.0.0 - [Release notes](https://github.com/googleapis/release-please-action/releases) - [Changelog](https://github.com/googleapis/release-please-action/blob/main/CHANGELOG.md) - [Commits](googleapis/release-please-action@16a9c90...45996ed) Updates `actions/upload-artifact` from 6.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](actions/upload-artifact@b7c566a...043fb46) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](actions/download-artifact@37930b1...3e5f45b) Updates `pypa/gh-action-pypi-publish` from 1.13.0 to 1.14.0 - [Release notes](https://github.com/pypa/gh-action-pypi-publish/releases) - [Commits](pypa/gh-action-pypi-publish@ed0c539...cef2210) --- updated-dependencies: - dependency-name: actions/cache dependency-version: 5.0.5 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: actions/checkout dependency-version: 6.0.2 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/download-artifact dependency-version: 8.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: actions/upload-artifact dependency-version: 7.0.1 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 8.1.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: googleapis/release-please-action dependency-version: 5.0.0 dependency-type: direct:production update-type: version-update:semver-major dependency-group: actions - dependency-name: pypa/gh-action-pypi-publish dependency-version: 1.14.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

Bumps [mypy](https://github.com/python/mypy) from 1.20.2 to 2.1.0. - [Changelog](https://github.com/python/mypy/blob/master/CHANGELOG.md) - [Commits](python/mypy@v1.20.2...v2.1.0) --- updated-dependencies: - dependency-name: mypy dependency-version: 2.1.0 dependency-type: direct:development update-type: version-update:semver-major ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…pdates (#174) Bumps the uv-minor-patch group with 4 updates in the / directory: [pydantic](https://github.com/pydantic/pydantic), [numpy](https://github.com/numpy/numpy), [cf-xarray](https://github.com/xarray-contrib/cf-xarray) and [pymdown-extensions](https://github.com/facelessuser/pymdown-extensions). Updates `pydantic` from 2.13.3 to 2.13.4 - [Release notes](https://github.com/pydantic/pydantic/releases) - [Changelog](https://github.com/pydantic/pydantic/blob/main/HISTORY.md) - [Commits](pydantic/pydantic@v2.13.3...v2.13.4) Updates `numpy` from 2.4.4 to 2.4.6 - [Release notes](https://github.com/numpy/numpy/releases) - [Changelog](https://github.com/numpy/numpy/blob/main/doc/RELEASE_WALKTHROUGH.rst) - [Commits](numpy/numpy@v2.4.4...v2.4.6) Updates `cf-xarray` from 0.11.0 to 0.11.1 - [Release notes](https://github.com/xarray-contrib/cf-xarray/releases) - [Commits](xarray-contrib/cf-xarray@v0.11.0...v0.11.1) Updates `pymdown-extensions` from 10.21.2 to 10.21.3 - [Release notes](https://github.com/facelessuser/pymdown-extensions/releases) - [Commits](facelessuser/pymdown-extensions@10.21.2...10.21.3) --- updated-dependencies: - dependency-name: pydantic dependency-version: 2.13.4 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: uv-minor-patch - dependency-name: numpy dependency-version: 2.4.6 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: uv-minor-patch - dependency-name: cf-xarray dependency-version: 0.11.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: uv-minor-patch - dependency-name: pymdown-extensions dependency-version: 10.21.3 dependency-type: direct:development update-type: version-update:semver-patch dependency-group: uv-minor-patch ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

…-2026-47265 (#182) The Security Audit job's pip-audit step flagged aiohttp 3.13.5 for CVE-2026-34993 and CVE-2026-47265 (both fixed in 3.14.0). Raise the floor and refresh the lock to 3.14.1. Co-authored-by: Claude Opus 4.8 <[email protected]>

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>

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