feat: GeoZarr minispec validator, compliant converter output, and doc fixes - #7 by d-v-b · Pull Request #237 · EOPF-Explorer/data-model

d-v-b · 2026-08-10T12:37:38Z

This PR fixes a variety of issues related to stale content in the minispec, as well as deviations from the spec in our geozarr output. Closes #233. See the full ai-generated PR summary below:

🤖 AI text below 🤖

Responds to #233: the documented conversion sample produced output matching neither the published GeoZarr conventions nor the repo's own minispec, and eopf-geozarr validate could not detect any of it (#88).

What this does

1. A real minispec validator (eopf-geozarr validate, backed by data_api/geozarr/validation.py)

Replaces the legacy per-variable CF checks with a declarative validator built on the pydantic-zarr store models. It snapshots the hierarchy with GroupSpec.from_zarr (metadata-only, no chunk reads) and checks:

store root: zarr_conventions declaration, spatial:bbox, at least one proj:* CRS key
multiscale datasets: all three conventions declared; spatial:bbox/spatial:dimensions/CRS present; every layout entry carries spatial:shape + spatial:transform (and transform when derived_from is set); layout assets resolve to members; every level qualifies as a GeoZarr dataset
datasets: used proj:/spatial: conventions validate and are declared (group declarations inherited by direct child arrays only, per the spec)
structural rules: no scalar arrays (0-D CF grid-mapping containers tolerated), unique string dimension_names, and a matching 1-D coordinate array for every data-variable dimension
Zarr V3 only; malformed metadata (e.g. a non-array zarr_conventions) is diagnosed with its node path instead of crashing

Each violation is reported with its Zarr node path; the CLI exits non-zero on a non-compliant store. Note: stores converted with releases <= 0.10.x predate the store-root requirements and will report as non-compliant until reconverted (migration note included in the docs).

2. Converter fixes so both paths produce validator-clean output

create_geozarr_dataset writes the store-root footprint (zarr_conventions + spatial:bbox + proj:code), shared with convert_s2_optimized (which previously wrote the bbox but not the declaration)
root bbox reprojection uses transform_bounds (edge densification) instead of two corner points — the corner-only math understated a UTM tile's footprint by ~4 km at the N/S edges and inverted across the antimeridian; CRS is resolved from proj:code/proj:wkt2/proj:projjson, unresolvable groups are skipped with a warning, and antimeridian-crossing footprints fall back to the full longitude range
calculate_overview_levels always emits level 0, so groups smaller than min_dimension no longer silently lose all their geo metadata
overview level groups carry their own spatial:/proj: conventions and keep 1-D non-spatial coordinates (e.g. time)
sanitize_array_attrs strips geo-proj convention keys that source products carry on arrays without the required declaration; the variable's CRS is captured before sanitizing so proj:code-only sources keep their CRS
the optimized path drops scalar (0-D) source coordinates (e.g. band labels) from dataset groups

3. Docs

every sample now uses the real /measurements/reflectance/r10m paths — the /measurements/r10m paths in the previous samples were silently skipped, which reproduces the empty output described in Mismatch between code sample output // GeoZarr MiniSpec // GeoZarr conventions #233
remaining GeoZarr-0.4-era requirement lists replaced with the conventions the converter actually writes; S2 auto-routing and the validator documented

Testing

23 validator unit tests (one compliant-store case, one per error case)
integration tests assert both converter paths produce validator-clean stores; the level-0 fix is pinned directly (it was previously mutation-survivable); the CLI's non-compliant exit path is covered
recorded example structures regenerated through the tests' own regeneration hooks
full suite green; pyright and ruff clean apart from one pre-existing finding in s2_resampling.py

The last commit addresses findings from a multi-agent adversarial review (five reviewers with distinct lenses; every fixed finding was reproduced before fixing).

Known loose end: the minispec's Members section says all resolution levels must have "the exact same set of variable names", which contradicts the spec's own Sentinel-2 example and the shipped layout — deliberately not enforced; needs a spec-text fix in a follow-up.

🤖 Generated with Claude Code

Replace the legacy per-variable CF attribute checks in `eopf-geozarr validate` with a declarative validator built on the pydantic-zarr store models. The validator snapshots the hierarchy with GroupSpec.from_zarr and checks every normative minispec requirement: - store root: zarr_conventions declaration, spatial:bbox, exactly one CRS key - multiscale datasets: all three conventions declared, spatial:bbox / spatial:dimensions / CRS present, layout entries carry spatial:shape and spatial:transform (and transform when derived_from is set), layout assets resolve to members, and every level qualifies as a GeoZarr dataset - any node using proj:/spatial: convention keys: keys validate and the convention is declared (group declarations are inherited by direct child arrays) - Zarr V3 only; stores with no convention-bearing nodes are reported The store models in data_api/geozarr/store.py are tightened to carry these requirements (root zarr_conventions, multiscale group conventions/CRS/ dimensions, transform-with-derived_from). The CLI exits non-zero on a non-compliant store and reports each violation with its node path. Refs EOPF-Explorer#233, EOPF-Explorer#163, EOPF-Explorer#88 Assisted-by: ClaudeCode:claude-fable-5

Fixes surfaced by the new minispec validator, reproducing issue EOPF-Explorer#233: - create_geozarr_dataset now writes the store-root spatial footprint (zarr_conventions + spatial:bbox + proj:code in EPSG:4326); the root writer moved to conversion.utils and is shared with convert_s2_optimized, which previously wrote the bbox but not the conventions declaration - calculate_overview_levels always emits level 0, so groups smaller than min_dimension no longer lose their multiscales/proj/spatial metadata to a swallowed empty-layout validation error - overview level groups (r2, r4, ...) now carry their own spatial + proj convention attributes, as the minispec requires of every layout member - multiscales layout entries always carry spatial:transform (previously skipped when the transform was degenerate) - sanitize_array_attrs strips geo-proj convention keys (proj:code, proj:wkt2, proj:projjson) that source products carry on arrays without the required declaration; legacy external keys like proj:epsg are kept Integration tests assert both converter paths produce validator-clean stores; the recorded example structures are regenerated accordingly. Fixes EOPF-Explorer#233 Assisted-by: ClaudeCode:claude-fable-5

The Python API samples pointed at /measurements/r10m, but Sentinel-2 products nest reflectance under /measurements/reflectance/r10m; following the samples verbatim silently skipped every group and produced a store with no GeoZarr metadata at all (issue EOPF-Explorer#233). All samples now use the real paths. Also replaces the remaining GeoZarr-0.4-era requirement lists (_ARRAY_DIMENSIONS, mandatory CF names) with the conventions the converter actually writes, documents the S2 auto-routing to the optimized layout, and describes the new minispec validator. Refs EOPF-Explorer#233 Assisted-by: ClaudeCode:claude-fable-5

Findings from a multi-agent adversarial review of the minispec branch, each independently reproduced before fixing: Validator (data_api/geozarr): - malformed zarr_conventions values (wrong type, non-mapping entries) are now diagnosed as validation issues instead of raising TypeError - convention declarations are inherited by direct child arrays only; child groups no longer inherit them (matches the minispec inheritance rule) - empty multiscales.layout is rejected (spec: layout must not be empty) - the store root accepts redundant CRS encodings; the invented at-most-one rule (inherited from the pre-existing model) is relaxed to the spec's at-least-one - new structural Members/DataArray checks: no scalar arrays (0-D CF grid-mapping containers tolerated), unique string dimension_names, and a matching 1-D coordinate array for every data-variable dimension Converters: - write_store_root_geo_metadata reprojects with transform_bounds (edge densification) instead of two corner points, resolves the CRS from proj:code/proj:wkt2/proj:projjson instead of assuming degrees when the code is absent, skips-with-warning groups whose CRS cannot be resolved, falls back to the full longitude range for antimeridian-crossing footprints, and derives S3 storage options from the output path; the create_geozarr_dataset call site is guarded so a late failure cannot abort a finished conversion - the CRS of a source variable is captured (proj:epsg, then proj:code/wkt2) before sanitize_array_attrs strips the convention keys - overview datasets carry over 1-D non-spatial coordinates (e.g. time) so every data-variable dimension keeps its coordinate array - the optimized path drops scalar (0-D) coordinates such as source band labels when writing dataset groups Tests: error cases for each fix, the level-0 overview fix is pinned directly (mutation-detected), the CLI validate non-compliant exit path is covered, and the recorded example structures are regenerated. Assisted-by: ClaudeCode:claude-fable-5

+
+    for name, arr in data_arrays.items():
+        dims = arr.dimension_names
+        assert dims is not None  # narrowed above


codecov-commenter · 2026-08-10T12:45:11Z

⚠️ Please install the to ensure uploads and comments are reliably processed by Codecov.

Codecov Report

❌ Patch coverage is 84.86486% with 56 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
src/eopf_geozarr/data_api/geozarr/validation.py	89.23%	21 Missing ⚠️
src/eopf_geozarr/cli.py	5.26%	18 Missing ⚠️
src/eopf_geozarr/conversion/utils.py	85.33%	11 Missing ⚠️
src/eopf_geozarr/conversion/geozarr.py	85.18%	4 Missing ⚠️
src/eopf_geozarr/data_api/geozarr/store.py	95.55%	2 Missing ⚠️

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pip-audit blocks CI on aiohttp 3.14.1 (PYSEC-2026-3545, PYSEC-2026-3546, PYSEC-2026-3547, all fixed by 3.14.3). Raise the floor and update the lock; the lock also picks up the 0.10.2 package version from the release commit, which had not been re-locked. Assisted-by: ClaudeCode:claude-fable-5

+
+    for name, arr in data_arrays.items():
+        dims = arr.dimension_names
+        assert dims is not None  # narrowed above


emmanuelmathot

LGTM but I would wait an E2E test in the data pipele by @lhoupert before putting in production.

emmanuelmathot · 2026-08-11T11:03:38Z

Merging it for now to have the docs updated and published but we will wait next release to go in prod

…uilders (#216) * feat: Phase 0 — S1 GRD RTC design, S1Tiling integration, and real-data GeoTIFF→GeoZarr V3 prototype - Implementation plan with Zarr V3 store structure, conventions, and phased roadmap - S1Tiling Docker instructions with EODAG 4.0.0 patch (5 breaking changes fixed) - GeoTIFF inspector script for S1Tiling output validation - Synthetic prototype validating sharding, resize/append, overview generation - Real-data conversion: 3 acquisitions (31TCH) → 1.8 GB Zarr store with 6 overview levels - Key findings: chunk divisibility constraint, datetime format, coverage variability * phase 0: integrate all lessons learned into plan and docs - Update §2 array metadata example to actual zarr-python 3.1.1 on-disk format (sharding codec in codecs array, chunk_grid holds shard shape, inner chunks 366) - Update conditions group: per-orbit naming (gamma_area_{orbit}), mark LIA and incidence_angle as aspirational (not confirmed as S1Tiling outputs) - Add Operational Findings subsection: EODAG 4.0.0 patch, DEM tile extent, GAMMA_AREA filename format - Fix docker instructions: CALIBRATION tag is GammaNaughtRTC (not gamma_naught_rtc) - Mark Phase 0 checklist fully complete - Update §9 API corrections to reflect plan is now corrected * phase 1: S1 RTC Pydantic models aligned with S2 pattern - Add src/eopf_geozarr/data_api/s1_rtc.py — Zarr V3 Pydantic models for S1 GRD γ0T RTC GeoZarr stores, using pyz.v3 GroupSpec/ArraySpec with TypedDict members (same pattern as s2.py uses pyz.v2) - Models: S1RtcRoot, S1RtcOrbitGroup, S1RtcNativeResolutionDataset, S1RtcOverviewResolutionDataset, S1RtcConditionsGroup - Validation: convention UUIDs, spatial:dimensions, multiscales layout, required data arrays (vv/vh/border_mask), gamma_area presence - Add tests/_test_data/s1_rtc_examples/s1-grd-rtc-31TCH.json — realistic fixture with 3 timesteps, 6 overview levels, 3 gamma_area conditions - Add tests/test_data_api/test_s1_rtc.py — 11 tests: round-trip, structure validation, negative cases (missing orbit, r10m, UUIDs, etc.) - Add conftest fixture s1_rtc_json_example parametrized over all fixtures * refactor: improve Pydantic model definitions and streamline imports in S1 RTC module * docs: update Phase 1 checklist, add Phase 1 findings, link tracking issue #139 * fix: standardize spatial dimensions to lowercase in S1 RTC models and test cases * fix: add 1D spatial coordinate arrays and use lowercase dimension names in S1 GRD RTC prototype * feat: add detailed implementation plan for Phase 2 GeoTIFF ingestion pipeline * fix: update Phase 2 GeoTIFF ingestion plan to include 1D spatial coordinate arrays and enforce lowercase dimension names * feat: Phase 2 — S1 GRD RTC GeoTIFF ingestion pipeline Productionise the GeoTIFF → Zarr V3 ingestion pipeline for S1Tiling gamma-naught RTC outputs. New module: src/eopf_geozarr/conversion/s1_ingest.py (~500 lines) - extract_geotiff_metadata(): rasterio-based metadata extraction with tag validation and S1Tiling datetime normalisation - create_s1_store(): Zarr V3 store creation with full GeoZarr conventions (multiscales, proj:, spatial:), sharded arrays, 1D spatial coordinate arrays at every resolution level - ingest_s1tiling_acquisition(): main API — create-or-open store, read GeoTIFFs, generate overviews (average/nearest), write all levels, append coordinate variables. CRS/shape consistency validation on append. - consolidate_s1_store(): post-batch metadata consolidation - discover_s1tiling_acquisitions(): file discovery with grouping Tests: tests/test_s1_rtc_ingest.py (27 tests) - Metadata extraction, store creation, ingestion (create + append), data integrity, xarray roundtrip, CRS/shape mismatch rejection, consolidation, file discovery Uses zarr_cm CMO dicts for convention metadata (not hardcoded UUIDs). Reuses calculate_aligned_chunk_size() from utils.py. Exports wired in conversion/__init__.py. Refs: #139 * refactor: use zcm.Multiscales typed model per reviewer feedback - Replace dict[str, Any] multiscales field with zcm.Multiscales import - Remove inline MultiscalesTransform/ScaleLevel/Multiscales classes - Update spatial:dimensions validator to lowercase ['y', 'x'] (Python 3.12) - Remove typing_extensions import (native in Python 3.12) - Update test assertions for Pydantic model attribute access - Auto-format fixes from ruff (imports, fixture parens, line length) * fix: configure ruff TC001 for Pydantic runtime-evaluated base classes - Add [tool.ruff.lint.flake8-type-checking] runtime-evaluated-base-classes for pydantic.BaseModel so Pydantic field type imports aren't flagged - Remove 4 stale noqa comments auto-fixed by ruff * feat: implement S1Tiling conditions ingestion and discovery commands in CLI * feat(stac): add build_s1_rtc_stac_item and generate-stac-s1 CLI (#173) * feat(stac): add build_s1_rtc_stac_item and generate-stac-s1 CLI command Adds eopf_geozarr.stac.s1_rtc.build_s1_rtc_stac_item, which reads a consolidated S1 GRD RTC Zarr V3 store and returns a pystac.Item with SAR/SAT/projection extensions, WGS84 bbox derived via pyproj, and vv/vh asset sub-paths. Ascending orbit is preferred when both are present. Also adds the generate-stac-s1 CLI subcommand that prints the item as JSON. 8 unit tests cover all acceptance criteria from the plan. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix: support s3:// URIs in S1Tiling discovery and ingest (#175) Four functions in s1_ingest.py silently failed for s3:// paths: - discover_s1tiling_acquisitions / discover_s1tiling_conditions used pathlib.Path.glob(), which normalises s3:// to s3:/ and returns 0 matches - ingest_s1tiling_acquisition / ingest_s1tiling_conditions coerced paths via Path(), corrupting s3:// URIs, and called .exists() which always returns False for S3 (existence checks now use path_exists() from fs_utils) Adds three private helpers: - _list_tifs(): uses s3fs.S3FileSystem.glob for s3:// prefixes - _coerce_input_path(): preserves str for s3://, returns Path otherwise - _rasterio_env(): rasterio.Env(AWSSession) context for s3:// paths; strips https:// from AWS_ENDPOINT_URL since GDAL expects hostname only Tested: rasterio.open("s3://...") confirmed working on OVH S3 with AWS_S3_ENDPOINT or AWS_ENDPOINT_URL set; hostname-only required by GDAL. Refs #139 Co-authored-by: Claude Sonnet 4.6 <[email protected]> * fix(stac): point vv/vh asset hrefs to orbit group root; add tile_matrix_set Per Emmanuel's review on #173: - vv/vh asset hrefs now point to {store}/{orbit} (the zarr group that carries multiscales), matching how S2 reflectance assets point to measurements/reflectance. TiTiler reads tile_matrix_set from that group's multiscales attributes. - create_s1_store now writes tile_matrix_set into the orbit group's multiscales so TiTiler can discover the tiling scheme without error. - Updated test_asset_hrefs to assert the new orbit-group href. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix(ingest): add proj:code to resolution group attrs for TiTiler compatibility TiTiler's _validate_zarr checks ds.rio.crs on the native resolution group (r10m). Without proj:code in the resolution group's attrs, rioxarray returns None and the group is excluded → groups=[] → bounds unpack error. S2 zarr already has proj:code at the resolution group level; mirror that for S1. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix(s1): write CF grid_mapping, drop tile_matrix_set from RTC store (#176) The deployed titiler-eopf reader resolves a group's CRS via rioxarray, which reads a CF spatial_ref/crs_wkt coordinate -- not the GeoZarr proj:code attr. S1 GRD RTC stores carried only proj:code, so rio.crs was None and every multiscale group was rejected (HTTP 500 on render/info). The S2 converter already writes a spatial_ref grid-mapping; this brings S1 in line. Also stop writing tile_matrix_set into the orbit-group multiscales: the data-model owner confirmed it is not part of the S1 GRD RTC data model, and the data_api reader already treats it as optional (MISSING default). - add _add_grid_mapping() using pyproj CRS.to_cf() (the same source rioxarray uses, so no hard-coded projection) and call it for every resolution level (both store-creation paths) and the conditions group - remove _create_tile_matrix_set() and its multiscales entry - tests: assert no tile_matrix_set, spatial_ref present + rio.crs resolves to the native EPSG, conditions group carries grid_mapping This fixes at the source what data-pipeline currently works around in ingest_v1_s1_rtc.py (_patch_cf_grid_mapping / _patch_tile_matrix_limits). Co-authored-by: Claude Opus 4.8 <[email protected]> * Merge #172 (deprecate v0, fix fill values, sanitize attrs) into s1-rtc (#178) * chore: release 0.9.0 * feat: implement scale-offset and data type casting via codecs * fix: fix dependency declaration * chore: use latest version of cast value * chore: make cast-value a project dependency * test: expand test coverage * fix: upgrade pytest to 9.0.3 (CVE-2025-71176) Fixes insecure /tmp directory handling on UNIX systems. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * - Use zarr-python's presumptive implementation of scale-offset - use scalar map for handling NaN - ensure that downsampled arrays use scalar map + cast value - improve tests across parametrization of relelvant functions * feat: add store-root spatial:bbox and tighten minispec requirements (#164) * feat: add store-root spatial:bbox and tighten minispec requirements Introduces a GeoZarr "Store Root" layer in the minispec so clients can read a summary footprint without walking into child groups, and tightens the multiscale profile so `spatial:bbox` at the root and `spatial:transform` + `spatial:shape` on every layout entry are mandatory. Adds a new `geozarr.store` pydantic module (`GeoZarrStoreAttrs`, `GeoZarrMultiscaleGroupAttrs`, `GeoZarr`) enforcing the tightened profile, and updates the S2 converter to union child-group bboxes into an EPSG:4326 footprint written at the store root. Closes #156. Addresses the clear parts of #163; the array-level and non-multiscale-group parts of that issue need further clarification. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]> * feat: update GeoZarr store model and optimize S2 converter for improved bbox handling * Addresses review feedback on #164: - Adds a "GeoZarr Hierarchy & Identification" subsection to the Store Root section of the minispec, codifying d-v-b's proposed rules: single root, root prefix ends with `.zarr`, suffix occurs at most once in the hierarchy, and explicit terminal-path conditions. - Promotes the store-root CRS to mandatory: at least one of `proj:code`, `proj:wkt2`, `proj:projjson` MUST be set; there is no implicit EPSG:4326 default. Per @vincentsarago's review. - Promotes `zarr_conventions` declaration at the store root from RECOMMENDED to required. - Converter now writes `proj:code: "EPSG:4326"` at the root alongside `spatial:bbox`. - Pydantic `GeoZarrStoreAttrs` enforces the new CRS-required rule. Cross-links the new hierarchy + spatial:extent follow-ups upstream: zarr-developers/geozarr-spec#132 (hierarchy & root identification, also addresses #124 URL parsing) and #133 (STAC-style spatial:extent). --------- Co-authored-by: Claude Opus 4.7 (1M context) <[email protected]> * chore: uv.lock * refactor: use zarr-python 3.2.0 * chore: lockfile * fix: pin fill value based on data type instead of relying on xarray * test: update tests to consistently use nan fill value for floats * chore: bump urllib3 to 2.7.0 * chore: skip quicklook groups (#165) * chore: group dependabot updates for actions and pip (#160) * chore: group dependabot updates for actions and pip - Group all GitHub Actions bumps (minor, patch, major) into one PR - Group minor and patch pip bumps into one PR; major bumps remain ungrouped for individual review Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * chore: change dependabot schedule day to wednesday * ci: add comment_on option to security auditing action * ci: switch dependabot Python ecosystem from pip to uv uv ecosystem reads uv.lock directly, enabling Dependabot to raise PRs for lockfile-pinned versions including security patches. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> --------- Co-authored-by: Claude Sonnet 4.6 <[email protected]> * fix: derive coarse spatial transforms from coordinates (#168) * fix: derive coarse spatial transforms from coordinates * refactor: improve function definitions for clarity and consistency * chore: release 0.10.0 (#162) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * 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: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Davis Vann Bennett <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Emmanuel Mathot <[email protected]> --------- Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Davis Vann Bennett <[email protected]> Co-authored-by: Emmanuel Mathot <[email protected]> * Revert "feat(stac): add build_s1_rtc_stac_item and generate-stac-s1 CLI (#173)" (#179) This reverts commit f749368ac3870790a69b250926f0af1aa6b58d0e. * fix(s1-ingest): discover multi-frame acquisitions with a masked timestamp (#183) (#184) discover_s1tiling_acquisitions returned 0 acquisitions for multi-frame S1Tiling products: their GeoTIFF filenames mask the acquisition time as '…txxxxxx', which the filename regex (\d{8}t\d{6}) rejected, so parse_s1tiling_filename returned None and every file was skipped — silently, with no error. - Relax the acq_stamp pattern to accept a masked time (\d{6}|x{6}), so masked files are no longer dropped. - In discover, when the stamp is masked, resolve the real YYYYMMDDtHHMMSS stamp from the GeoTIFF ACQUISITION_DATETIME tag (via extract_geotiff_metadata) and use it for grouping + downstream STAC datetime. This is the durable upstream fix for the data-pipeline #237 workaround (which renamed masked products before discovery); that workaround can now be retired. Closes #183. Co-authored-by: Claude Opus 4.8 <[email protected]> * chore: merge main into s1-tiling (#190) * chore: release 0.9.0 * feat: implement scale-offset and data type casting via codecs * fix: fix dependency declaration * chore: use latest version of cast value * chore: make cast-value a project dependency * test: expand test coverage * fix: upgrade pytest to 9.0.3 (CVE-2025-71176) Fixes insecure /tmp directory handling on UNIX systems. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * - Use zarr-python's presumptive implementation of scale-offset - use scalar map for handling NaN - ensure that downsampled arrays use scalar map + cast value - improve tests across parametrization of relelvant functions * feat: add store-root spatial:bbox and tighten minispec requirements (#164) * feat: add store-root spatial:bbox and tighten minispec requirements Introduces a GeoZarr "Store Root" layer in the minispec so clients can read a summary footprint without walking into child groups, and tightens the multiscale profile so `spatial:bbox` at the root and `spatial:transform` + `spatial:shape` on every layout entry are mandatory. Adds a new `geozarr.store` pydantic module (`GeoZarrStoreAttrs`, `GeoZarrMultiscaleGroupAttrs`, `GeoZarr`) enforcing the tightened profile, and updates the S2 converter to union child-group bboxes into an EPSG:4326 footprint written at the store root. Closes #156. Addresses the clear parts of #163; the array-level and non-multiscale-group parts of that issue need further clarification. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]> * feat: update GeoZarr store model and optimize S2 converter for improved bbox handling * Addresses review feedback on #164: - Adds a "GeoZarr Hierarchy & Identification" subsection to the Store Root section of the minispec, codifying d-v-b's proposed rules: single root, root prefix ends with `.zarr`, suffix occurs at most once in the hierarchy, and explicit terminal-path conditions. - Promotes the store-root CRS to mandatory: at least one of `proj:code`, `proj:wkt2`, `proj:projjson` MUST be set; there is no implicit EPSG:4326 default. Per @vincentsarago's review. - Promotes `zarr_conventions` declaration at the store root from RECOMMENDED to required. - Converter now writes `proj:code: "EPSG:4326"` at the root alongside `spatial:bbox`. - Pydantic `GeoZarrStoreAttrs` enforces the new CRS-required rule. Cross-links the new hierarchy + spatial:extent follow-ups upstream: zarr-developers/geozarr-spec#132 (hierarchy & root identification, also addresses #124 URL parsing) and #133 (STAC-style spatial:extent). --------- Co-authored-by: Claude Opus 4.7 (1M context) <[email protected]> * chore: uv.lock * refactor: use zarr-python 3.2.0 * chore: lockfile * fix: pin fill value based on data type instead of relying on xarray * test: update tests to consistently use nan fill value for floats * chore: bump urllib3 to 2.7.0 * chore: skip quicklook groups (#165) * chore: group dependabot updates for actions and pip (#160) * chore: group dependabot updates for actions and pip - Group all GitHub Actions bumps (minor, patch, major) into one PR - Group minor and patch pip bumps into one PR; major bumps remain ungrouped for individual review Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * chore: change dependabot schedule day to wednesday * ci: add comment_on option to security auditing action * ci: switch dependabot Python ecosystem from pip to uv uv ecosystem reads uv.lock directly, enabling Dependabot to raise PRs for lockfile-pinned versions including security patches. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> --------- Co-authored-by: Claude Sonnet 4.6 <[email protected]> * fix: derive coarse spatial transforms from coordinates (#168) * fix: derive coarse spatial transforms from coordinates * refactor: improve function definitions for clarity and consistency * chore: release 0.10.0 (#162) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * enh: deprecate v0, fix fill values and sanitize attributes (#172) * 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]> * ci(deps): bump the actions group across 1 directory with 8 updates (#167) 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](https://github.com/actions/checkout/compare/93cb6efe18208431cddfb8368fd83d5badbf9bfd...de0fac2e4500dabe0009e67214ff5f5447ce83dd) Updates `astral-sh/setup-uv` from 7.6.0 to 8.1.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/37802adc94f370d6bfd71619e3f0bf239e1f3b78...08807647e7069bb48b6ef5acd8ec9567f424441b) 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](https://github.com/actions/cache/compare/668228422ae6a00e4ad889ee87cd7109ec5666a7...27d5ce7f107fe9357f9df03efb73ab90386fccae) 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](https://github.com/codecov/codecov-action/compare/1af58845a975a7985b0beb0cbe6fbbb71a41dbad...57e3a136b779b570ffcdbf80b3bdc90e7fab3de2) 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](https://github.com/googleapis/release-please-action/compare/16a9c90856f42705d54a6fda1823352bdc62cf38...45996ed1f6d02564a971a2fa1b5860e934307cf7) Updates `actions/upload-artifact` from 6.0.0 to 7.0.1 - [Release notes](https://github.com/actions/upload-artifact/releases) - [Commits](https://github.com/actions/upload-artifact/compare/b7c566a772e6b6bfb58ed0dc250532a479d7789f...043fb46d1a93c77aae656e7c1c64a875d1fc6a0a) Updates `actions/download-artifact` from 7.0.0 to 8.0.1 - [Release notes](https://github.com/actions/download-artifact/releases) - [Commits](https://github.com/actions/download-artifact/compare/37930b1c2abaa49bbe596cd826c3c89aef350131...3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c) 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](https://github.com/pypa/gh-action-pypi-publish/compare/ed0c53931b1dc9bd32cbe73a98c7f6766f8a527e...cef221092ed1bacb1cc03d23a2d87d1d172e277b) --- 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> * deps(deps-dev): bump mypy from 1.20.2 to 2.1.0 (#170) 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](https://github.com/python/mypy/compare/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> * deps(deps): bump the uv-minor-patch group across 1 directory with 4 updates (#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](https://github.com/pydantic/pydantic/compare/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](https://github.com/numpy/numpy/compare/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](https://github.com/xarray-contrib/cf-xarray/compare/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](https://github.com/facelessuser/pymdown-extensions/compare/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> * fix(deps): bump aiohttp to >=3.14.0 to resolve CVE-2026-34993 and CVE-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]> * chore: release 0.10.1 (#181) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * ci(deps): bump the actions group with 3 updates (#185) Bumps the actions group with 3 updates: [actions/checkout](https://github.com/actions/checkout), [astral-sh/setup-uv](https://github.com/astral-sh/setup-uv) and [codecov/codecov-action](https://github.com/codecov/codecov-action). Updates `actions/checkout` from 6.0.2 to 6.0.3 - [Release notes](https://github.com/actions/checkout/releases) - [Changelog](https://github.com/actions/checkout/blob/main/CHANGELOG.md) - [Commits](https://github.com/actions/checkout/compare/de0fac2e4500dabe0009e67214ff5f5447ce83dd...df4cb1c069e1874edd31b4311f1884172cec0e10) Updates `astral-sh/setup-uv` from 8.1.0 to 8.2.0 - [Release notes](https://github.com/astral-sh/setup-uv/releases) - [Commits](https://github.com/astral-sh/setup-uv/compare/08807647e7069bb48b6ef5acd8ec9567f424441b...fac544c07dec837d0ccb6301d7b5580bf5edae39) Updates `codecov/codecov-action` from 6.0.0 to 6.0.1 - [Release notes](https://github.com/codecov/codecov-action/releases) - [Changelog](https://github.com/codecov/codecov-action/blob/main/CHANGELOG.md) - [Commits](https://github.com/codecov/codecov-action/compare/57e3a136b779b570ffcdbf80b3bdc90e7fab3de2...e79a6962e0d4c0c17b229090214935d2e33f8354) --- updated-dependencies: - dependency-name: actions/checkout dependency-version: 6.0.3 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions - dependency-name: astral-sh/setup-uv dependency-version: 8.2.0 dependency-type: direct:production update-type: version-update:semver-minor dependency-group: actions - dependency-name: codecov/codecov-action dependency-version: 6.0.1 dependency-type: direct:production update-type: version-update:semver-patch dependency-group: actions ... Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Davis Vann Bennett <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Emmanuel Mathot <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * feat(s1-rtc): STAC item builders + ingest fixes for TiTiler rendering (#180) * feat(stac): add build_s1_rtc_stac_item and generate-stac-s1 CLI command Adds eopf_geozarr.stac.s1_rtc.build_s1_rtc_stac_item, which reads a consolidated S1 GRD RTC Zarr V3 store and returns a pystac.Item with SAR/SAT/projection extensions, WGS84 bbox derived via pyproj, and vv/vh asset sub-paths. Ascending orbit is preferred when both are present. Also adds the generate-stac-s1 CLI subcommand that prints the item as JSON. 8 unit tests cover all acceptance criteria from the plan. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix: support s3:// URIs in S1Tiling discovery and ingest (#175) Four functions in s1_ingest.py silently failed for s3:// paths: - discover_s1tiling_acquisitions / discover_s1tiling_conditions used pathlib.Path.glob(), which normalises s3:// to s3:/ and returns 0 matches - ingest_s1tiling_acquisition / ingest_s1tiling_conditions coerced paths via Path(), corrupting s3:// URIs, and called .exists() which always returns False for S3 (existence checks now use path_exists() from fs_utils) Adds three private helpers: - _list_tifs(): uses s3fs.S3FileSystem.glob for s3:// prefixes - _coerce_input_path(): preserves str for s3://, returns Path otherwise - _rasterio_env(): rasterio.Env(AWSSession) context for s3:// paths; strips https:// from AWS_ENDPOINT_URL since GDAL expects hostname only Tested: rasterio.open("s3://...") confirmed working on OVH S3 with AWS_S3_ENDPOINT or AWS_ENDPOINT_URL set; hostname-only required by GDAL. Refs #139 Co-authored-by: Claude Sonnet 4.6 <[email protected]> * fix(stac): point vv/vh asset hrefs to orbit group root; add tile_matrix_set Per Emmanuel's review on #173: - vv/vh asset hrefs now point to {store}/{orbit} (the zarr group that carries multiscales), matching how S2 reflectance assets point to measurements/reflectance. TiTiler reads tile_matrix_set from that group's multiscales attributes. - create_s1_store now writes tile_matrix_set into the orbit group's multiscales so TiTiler can discover the tiling scheme without error. - Updated test_asset_hrefs to assert the new orbit-group href. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix(ingest): add proj:code to resolution group attrs for TiTiler compatibility TiTiler's _validate_zarr checks ds.rio.crs on the native resolution group (r10m). Without proj:code in the resolution group's attrs, rioxarray returns None and the group is excluded → groups=[] → bounds unpack error. S2 zarr already has proj:code at the resolution group level; mirror that for S1. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * fix(s1): write CF grid_mapping, drop tile_matrix_set from RTC store (#176) The deployed titiler-eopf reader resolves a group's CRS via rioxarray, which reads a CF spatial_ref/crs_wkt coordinate -- not the GeoZarr proj:code attr. S1 GRD RTC stores carried only proj:code, so rio.crs was None and every multiscale group was rejected (HTTP 500 on render/info). The S2 converter already writes a spatial_ref grid-mapping; this brings S1 in line. Also stop writing tile_matrix_set into the orbit-group multiscales: the data-model owner confirmed it is not part of the S1 GRD RTC data model, and the data_api reader already treats it as optional (MISSING default). - add _add_grid_mapping() using pyproj CRS.to_cf() (the same source rioxarray uses, so no hard-coded projection) and call it for every resolution level (both store-creation paths) and the conditions group - remove _create_tile_matrix_set() and its multiscales entry - tests: assert no tile_matrix_set, spatial_ref present + rio.crs resolves to the native EPSG, conditions group carries grid_mapping This fixes at the source what data-pipeline currently works around in ingest_v1_s1_rtc.py (_patch_cf_grid_mapping / _patch_tile_matrix_limits). Co-authored-by: Claude Opus 4.8 <[email protected]> * Merge #172 (deprecate v0, fix fill values, sanitize attrs) into s1-rtc (#178) * chore: release 0.9.0 * feat: implement scale-offset and data type casting via codecs * fix: fix dependency declaration * chore: use latest version of cast value * chore: make cast-value a project dependency * test: expand test coverage * fix: upgrade pytest to 9.0.3 (CVE-2025-71176) Fixes insecure /tmp directory handling on UNIX systems. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * - Use zarr-python's presumptive implementation of scale-offset - use scalar map for handling NaN - ensure that downsampled arrays use scalar map + cast value - improve tests across parametrization of relelvant functions * feat: add store-root spatial:bbox and tighten minispec requirements (#164) * feat: add store-root spatial:bbox and tighten minispec requirements Introduces a GeoZarr "Store Root" layer in the minispec so clients can read a summary footprint without walking into child groups, and tightens the multiscale profile so `spatial:bbox` at the root and `spatial:transform` + `spatial:shape` on every layout entry are mandatory. Adds a new `geozarr.store` pydantic module (`GeoZarrStoreAttrs`, `GeoZarrMultiscaleGroupAttrs`, `GeoZarr`) enforcing the tightened profile, and updates the S2 converter to union child-group bboxes into an EPSG:4326 footprint written at the store root. Closes #156. Addresses the clear parts of #163; the array-level and non-multiscale-group parts of that issue need further clarification. Co-Authored-By: Claude Opus 4.7 (1M context) <[email protected]> * feat: update GeoZarr store model and optimize S2 converter for improved bbox handling * Addresses review feedback on #164: - Adds a "GeoZarr Hierarchy & Identification" subsection to the Store Root section of the minispec, codifying d-v-b's proposed rules: single root, root prefix ends with `.zarr`, suffix occurs at most once in the hierarchy, and explicit terminal-path conditions. - Promotes the store-root CRS to mandatory: at least one of `proj:code`, `proj:wkt2`, `proj:projjson` MUST be set; there is no implicit EPSG:4326 default. Per @vincentsarago's review. - Promotes `zarr_conventions` declaration at the store root from RECOMMENDED to required. - Converter now writes `proj:code: "EPSG:4326"` at the root alongside `spatial:bbox`. - Pydantic `GeoZarrStoreAttrs` enforces the new CRS-required rule. Cross-links the new hierarchy + spatial:extent follow-ups upstream: zarr-developers/geozarr-spec#132 (hierarchy & root identification, also addresses #124 URL parsing) and #133 (STAC-style spatial:extent). --------- Co-authored-by: Claude Opus 4.7 (1M context) <[email protected]> * chore: uv.lock * refactor: use zarr-python 3.2.0 * chore: lockfile * fix: pin fill value based on data type instead of relying on xarray * test: update tests to consistently use nan fill value for floats * chore: bump urllib3 to 2.7.0 * chore: skip quicklook groups (#165) * chore: group dependabot updates for actions and pip (#160) * chore: group dependabot updates for actions and pip - Group all GitHub Actions bumps (minor, patch, major) into one PR - Group minor and patch pip bumps into one PR; major bumps remain ungrouped for individual review Co-Authored-By: Claude Sonnet 4.6 <[email protected]> * chore: change dependabot schedule day to wednesday * ci: add comment_on option to security auditing action * ci: switch dependabot Python ecosystem from pip to uv uv ecosystem reads uv.lock directly, enabling Dependabot to raise PRs for lockfile-pinned versions including security patches. Co-Authored-By: Claude Sonnet 4.6 <[email protected]> --------- Co-authored-by: Claude Sonnet 4.6 <[email protected]> * fix: derive coarse spatial transforms from coordinates (#168) * fix: derive coarse spatial transforms from coordinates * refactor: improve function definitions for clarity and consistency * chore: release 0.10.0 (#162) Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * 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: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Davis Vann Bennett <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Emmanuel Mathot <[email protected]> * feat(s1-stac): add render extension with dual-pol RGB composite preview The previous S1 RTC preview rendered a single VH band as grayscale with an incorrect rescale (0,219), unsuitable for linear gamma0 RTC values. Declare a render-extension `renders.rgb` config producing the standard dual-pol false- colour composite (R=VV, G=VH, B=VV/VH ratio) with rescale 0–0.1 and tilesize 256, referencing the preferred orbit group. Downstream titiler-based services consume this to generate previews/tiles/tilejson. Co-Authored-By: Claude Opus 4.8 <[email protected]> * refactor(s1-stac): emit a single rescale pair in the RGB render A single [min, max] pair applies to all bands in titiler, so emitting three identical pairs was redundant (and forced collapse logic in the consumer). Same rendered output. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): TEMPORARY name store as s1-rtc-{tile} to match titiler render path (#246) titiler-eopf reconstructs the store path as s3://{bucket}/tests-output/{collection}/{item_id}.zarr and ignores the STAC asset href, so the GeoZarr cube must be named after the item id (s1-rtc-{tile}) for new tiles to preview. Parse the tile from the s1-rtc- prefix (was s1-grd-rtc-); the item id (s1-rtc-{tile}) is unchanged, so filename == item id by construction. Pairs with the data-pipeline direct-write change (store written at the tests-output path) which replaces the #250 auto-copy. Dev-phase, no consumers — disposable test data. Revert to s1-grd-rtc- when titiler-eopf#108 (resolve store from href) lands. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): build STAC item from a non-consolidated cube store build_s1_rtc_stac_item opened the cube with zarr.open_consolidated, which raises `ValueError: Consolidated metadata ... not found` when the store lacks root consolidated metadata. A per-tile cube grown by appending a time-slice to an existing same-orbit group ends up in exactly that state — re-consolidating an append on the S3 store is unreliable — so live STAC registration failed on the 2nd+ same-orbit acquisition for a tile (it broke the Pyrenees S1 RTC soak). The builder must not require consolidated metadata: titiler reads these stores fine without it. Fall back to a direct zarr.open_group(mode="r") read when the consolidated metadata is absent; re-raise any other ValueError. Adds a regression test: build from a 2-slice same-orbit store created with consolidate=False (fails before the fix in open_consolidated, passes after). Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): CF-encode `time` at every level for datetime-based rendering (#192) (#193) Per-acquisition previews render via titiler `sel=time={INTEGER index}` — a positional index that breaks once a cube's time axis goes non-monotonic (a cross-run append of an earlier-dated scene; proved on 31TEH: `[06-08, 06-07]` → the 06-07 item has no preview). Keeping positional indices correct would need cube reorder + full re-registration on every append (not scalable). The deployed titiler (v0.5.0) already does label-based `da.sel(..., method=...)` via `open_datatree(decode_times=True)`; the only gap is the cube's `time` array, which is a bare int64 with no CF datetime metadata, so it can't be a datetime index. Encoding it lets previews select by exact datetime, which works even on a non-monotonic axis — no reorder, register only the new item. titiler picks a multiscale level by zoom (previews use a coarse level), so `time` must resolve there. Putting it only at the orbit-group level and inheriting fails to open while r10m stays bare int64 (AlignmentError: int64 vs datetime64 on the shared dim). So encode `time` consistently at EVERY level: - new `_create_time_coordinate_array` + `TIME_CF_ATTRS` (units/calendar/ standard_name); created at every level in create + append-group paths. - the append write resizes/writes `time` at every level (was r10m only). - absolute_orbit/relative_orbit/platform stay at r10m (not selected on). - stored dtype stays int64 ns, so register_per_acquisition's raw read is unaffected. Adds TestTimeCFDatetime incl. exact datetime `.sel` on a non-monotonic axis at the native and a coarse level. 55 passed. Refs EOPF-Explorer/data-model#192 Co-authored-by: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): enrich STAC items & consolidate construction into the library (#195) (#196) * fix(s1-rtc): enrich cube STAC item + fix vv/vh asset model (#195) The S1 RTC cube STAC item carried duplicate vv/vh assets with byte-identical hrefs (bug #1), exposed no asset for the descending orbit group of a dual-orbit cube (bug #2), and was missing most of the metadata the S2 L2A reference carries. Rework `build_s1_rtc_stac_item`: - Asset model: replace the two indistinguishable vv/vh assets with one `gamma0-rtc-backscatter-{asc,desc}` asset per present orbit group, exposing VV/VH as named STAC 1.1 `bands` (no more duplicate hrefs), plus a `border-mask-{orbit}` asset for the valid-data mask. Each γ⁰ asset carries data_type/nodata/unit/gsd. - Identity: add `constellation`, `instruments: [c-sar]`, `gsd` (platform stays per-acquisition — a cube can mix S1A/S1C). - Projection: add proj:bbox, and proj:shape/proj:transform (best-effort from the r10m group attrs). - Datacube extension: cube:dimensions (time as a bounded extent — not a values list, the cube grows by appending — plus x/y) + cube:variables. - Descriptive: title/description; created (earliest acquisition, stable across rebuilds) / updated (build time) via the timestamps extension. - Fold the corrected render rescale (0.0,0.2) into `_rgb_render`. Out of scope (tracked follow-ups): statistics (#157), processing:software / DEM lineage, and per-product CDSE fields are not in the store; per-acquisition item construction is moved in a follow-up commit. Co-Authored-By: Claude Opus 4.8 <[email protected]> * feat(s1-rtc): move per-acquisition + coverage STAC construction into the library Consolidate the *pure* S1 RTC STAC construction in eopf_geozarr.stac.s1_rtc so item shape has a single owner (the library); registration (STAC-API upsert, S3 alternates, gateway rewrite, TiTiler links, CDSE discovery) stays in data-pipeline. Adds, ported from the data-pipeline scripts (deployment URLs stripped): - acquisition_id(tile_id, when) - build_s1_rtc_per_acquisition_items(store, *, orbit, collection_id) -> list[pystac.Item]: one single-datetime item per cube time slice of an orbit, reoriented to that orbit (sat:orbit_state + render expression + only that orbit's γ⁰/mask assets), per-slice platform, datacube structure dropped (a single acquisition is not a cube). Deployment-agnostic: carries the render config + datetime; the registration layer derives the cube-endpoint TiTiler links (sel=time={datetime}) from it. - Slice / pick_slice / slice_coverages: coverage-based preview-slice selection (reads border_mask at r720m). Ported the construction unit tests (pick_slice, slice_coverages, and the per-acquisition construction subset); the link/thumbnail/alternate-asset and rescale-override tests stay in data-pipeline as registration concerns. Follow-up (separate data-pipeline PR): bump the data-model pin, delete the moved functions from register_per_acquisition.py / register_v1_s1_rtc.py, and rewire them to consume this library output. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): per-acquisition items carry their own orbit footprint Review follow-up. A per-acquisition item cloned the cube base, so on a dual-orbit cube every item inherited the WGS84 union bbox/geometry of both orbits and the preferred (ascending) orbit's proj:bbox — advertising a footprint wider than, and a data bbox from the wrong orbit relative to, the acquisition's own orbit. Recompute bbox/geometry/proj:bbox from the run orbit's spatial:bbox (factored the bbox->polygon construction into `_bbox_to_geometry`, shared with the cube builder), and give per-acquisition items a single-acquisition description rather than the cube's "datacube" wording. Tests: per-acq footprint = run orbit (not the union); `created` = earliest acquisition (idempotent across rebuilds); ValueError on an invalid or absent orbit. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): omit orbit_state on dual-orbit cubes; expose datacube dimension sizes Two review observations from inspecting the live items: - sat:orbit_state is single-valued, so on a dual-orbit cube (both ascending and descending groups present) a single value mislabels half the slices. Set it (and declare the SAT extension) only for a single-orbit cube; per-acquisition items, which are single-orbit, still carry the real per-orbit value. Ensure per-acq items declare the SAT extension even when cloned from a dual-orbit base that omitted it. - cube:dimensions previously carried only `extent`, so the number of elements per dimension wasn't visible. The time axis is irregularly sampled, so list its discrete `values` (count = number of acquisitions); the regular x/y axes get a `step` (size derivable from extent; exact pixel count is also in proj:shape). Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): datacube time axis carries extent only (drop values enumeration) Enumerating every acquisition as cube:dimensions.time.values does not scale as the cube is appended over the mission. No STAC extension provides a scalable temporal element-count field (datacube temporal_dimension offers only values/step/extent, and step is null for S1's irregular sampling; projection proj:shape is spatial-only; raster has no dimension shape). So the time axis carries a bounded `extent` only. x/y element counts remain available via proj:shape (exact) and the datacube x/y extent+step. The number of acquisitions is obtained from the per-acquisition collection (STAC search count), which stays correct as the cube grows. Co-Authored-By: Claude Opus 4.8 <[email protected]> * fix(s1-rtc): correct datacube variable_type, platform value, created, time values Review of the live items surfaced several metadata issues: - cube:variables used `type` (a non-standard, silently-ignored key) instead of the datacube extension's `variable_type`; border_mask is now `auxiliary`, vv/vh `data`. - per-acquisition `platform` carried the store's short code (e.g. `s1a`); normalize to the STAC convention `sentinel-1a` (mirrors the Sentinel-2 reference). - `created` (timestamps ext) was set to an acquisition time, which misuses the field (it means the item's creation instant); omit it and keep `updated` = build time. - the cube's irregular time axis now lists its discrete `values` (the acquisition instants) so the number of time steps is visible; the regular x/y axes stay extent + step (their pixel count is in proj:shape). Co-Authored-By: Claude Opus 4.8 <[email protected]> * refactor(s1-rtc): robust EPSG parse for datacube reference_system + clarify per-acq proj inheritance Review follow-ups (no behaviour change for the EPSG:NNNN stores in use): - derive the datacube reference_system via pyproj.CRS(...).to_epsg() instead of splitting the proj:code string, so non-"EPSG:NNNN" CRS forms don't break it. - comment why per-acquisition items recompute proj:bbox from their orbit but inherit proj:code/shape/transform (the MGRS grid is shared across orbits). Co-Authored-By: Claude Opus 4.8 <[email protected]> * docs(s1-rtc): note the dual-orbit time axis spans both orbits in the datacube A dual-orbit cube merges two per-orbit sub-cubes (disjoint time axes) onto a shared grid. Modelling orbit as a dimension would imply a sparse, mostly-empty orbit×time grid; instead orbit stays an attribute of each acquisition, conveyed via the per-orbit assets. Add a `description` on the time dimension so the merged axis isn't misread. Single-orbit cubes …

d-v-b added 4 commits August 10, 2026 10:36

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Comment thread src/eopf_geozarr/data_api/geozarr/validation.py

for name, arr in data_arrays.items():

dims = arr.dimension_names

assert dims is not None # narrowed above

emmanuelmathot self-requested a review August 10, 2026 13:14

d-v-b marked this pull request as ready for review August 10, 2026 13:36

github-advanced-security Bot found potential problems Aug 10, 2026

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Comment thread src/eopf_geozarr/data_api/geozarr/validation.py

for name, arr in data_arrays.items():

dims = arr.dimension_names

assert dims is not None # narrowed above

emmanuelmathot approved these changes Aug 11, 2026

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emmanuelmathot requested a review from lhoupert August 11, 2026 07:23

emmanuelmathot merged commit da604dd into EOPF-Explorer:main Aug 11, 2026
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github-actions Bot mentioned this pull request Aug 11, 2026

chore: release 0.11.0 #235

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emmanuelmathot mentioned this pull request Sep 2, 2026

eopf-geozarr validate returns 0 compliant and 0 non compliant variables #88

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lhoupert mentioned this pull request Jun 9, 2026

S1 RTC: discover_s1tiling_acquisitions returns 0 for multi-frame products (masked acq timestamp) #183

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emmanuelmathot mentioned this pull request Sep 24, 2026

feat!: reintegrate cpm-geozarr into main #277

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feat: GeoZarr minispec validator, compliant converter output, and doc fixes - #7 - #237

feat: GeoZarr minispec validator, compliant converter output, and doc fixes - #7#237
emmanuelmathot merged 5 commits into
EOPF-Explorer:mainfrom
d-v-b:claude/spec-compliance-validation-464b38

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