Add Google Earth Engine accessor for satellite imagery (#53) - #76
Add Google Earth Engine accessor for satellite imagery (#53)#76KarnakOza wants to merge 3 commits into
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- Implement GoogleEarthEngineAccessor with NDVI, NDWI, NDBI, and NDBI-change methods covering the use cases in fccoelho#53 (vegetation coverage/breeding sites, urban density, informal settlement growth) - Register earthengine-api as an optional extra and add entry point so the accessor is discoverable via the standard source registry - Add tests covering initialization, list_countries, and indicator sign/range sanity checks against real-world reference points - Raise a clear ValueError when no cloud-free Landsat imagery is available for a given area/date range, instead of a cryptic band-not-found error Closes fccoelho#53
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👋 PR Review Reminder This pull request has been open for over a week without review. Maintainers will review soon! If you need immediate feedback, feel free to tag us. Thanks for your contribution! 🙏 |
fccoelho
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Thanks for this contribution @KarnakOza — the accessor is well-structured and closely follows the conventions of copernicus_cds.py (optional-import guard, ClassVar metadata, clear ImportError/RuntimeError messages). The index math and the no-imagery ValueError are good. However, there are two blocking issues that contradict the PR's own description, plus some correctness and test-hygiene concerns.
Blocking
1. Entry point was never registered — The PR description promises "add the entry point so the accessor is discoverable via the standard source registry", but pyproject.toml only adds the optional extra. There is no line under [project.entry-points."epidatasets.sources"] (pyproject.toml:136). Without it:
epidatasets.get_source("google_earth_engine")raisesKeyError,- the source won't appear in
list_sources(), _registry.py:24(_load_entry_points) won't find it.
The README still says "33 registered (via plugin registry)" — and after this PR that number is still correct, which is exactly the symptom of the missing registration.
➕ Please add, e.g.:
google_earth_engine = "epidatasets.sources.google_earth_engine:GoogleEarthEngineAccessor"2. Not added to sources/__init__.py — Every other accessor is listed in src/epidatasets/sources/__init__.py:14-47 (under TYPE_CHECKING) and in __all__. GEE is missing from both, breaking the convention every other source follows. Please add it to both sections.
Correctness
3. Landsat C2 L2 surface-reflectance scaling is not applied (google_earth_engine.py:181). SR_B4/5/6 are raw DNs; reflectance = DN * 0.0000275 − 0.2. For normalized-difference ratios the multiplicative factor cancels, but the additive offset (−0.2) does not, biasing every index. Please either apply image.multiply(0.0000275).add(-0.2) or document explicitly why the offset is ignored.
4. Sentinel-2 / MODIS are advertised but unused — COLLECTIONS declares sentinel2_sr and modis_vi, the docstring lists them, but every method hardcodes Landsat 8. In tropical epidemiology (the stated use case), Landsat's 16-day revisit + the 20% cloud filter means the ValueError in _landsat_composite will fire frequently. Consider a sensor="landsat8"|"sentinel2" parameter, or at least drop the unused entries to avoid false advertising.
Test hygiene
5. TestGoogleEarthEngine.test_initialization will ERROR (not skip) on any machine without EE auth (test_accessors.py:893). The accessor fixture instantiates the class, which calls ee.Initialize() in __init__. Since test_initialization lacks @requires_external_api, CI without earthengine-api installed/authenticated will report an error during setup rather than a skip. Options:
- mark
test_initializationwith@requires_external_apitoo, or - add
pytest.importorskip("ee")in the fixture, or - split into a mocked unit test + a live external test (best — matches the
responses-based pattern used byTestDiseaseSh).
6. test_no_imagery_raises_clear_error is flaky (test_accessors.py:937) — it assumes a 1-day Amazon window has zero <20%-cloud Landsat scenes. A single cloud-free acquisition on 2021-03-01 would flip this. Better to monkeypatch the collection size.
Minor / nits
- 7.
logging.basicConfig(level=logging.INFO)at module import (google_earth_engine.py:43) reconfigures the root logger on every import. (Same anti-pattern exists incopernicus_cds.py:52, so it's consistent — but worth fixing repo-wide eventually.) - 8.
_reduce_meansilently returnsNoneon a bad band name rather than raising (google_earth_engine.py:188). - 9.
earthengineis intentionally excluded from theallextra (pyproject.toml:105) — reasonable given interactive auth, just confirming it's deliberate. - 10. Modern
str | Nonehints here vs.Optional[str]incopernicus_cds.py— minor style drift; the new style is preferable. - 11. README's "Optional extras: 11" update is correct, but the "Data sources: 33 registered" line was not touched (already stale — the entry-point list has 34 — but this PR doesn't fix it).
Suggested changes before merge
- Add entry point to
pyproject.toml(item 1) - Register in
sources/__init__.py(item 2) - Fix
test_initializationso it skips cleanly without EE (item 5) - Apply Landsat SR scaling or document the omission (item 3)
The accessor code itself is solid; once these are addressed the PR will deliver what its description claims and keep CI green on machines without GEE credentials.
📋 Description
Adds a Google Earth Engine (GEE) accessor providing satellite-imagery-derived
indicators for epidemiological modeling, as requested in #53.
GoogleEarthEngineAccessorwithget_ndvi,get_ndwi,get_built_up_index, andget_built_up_changemethods, covering theuse cases in 🛰️ Add Google Earth Engine accessor (Satellite imagery) #53 (vegetation coverage/breeding sites, urban density,
informal settlement growth)
earthengine-apias an optional extra and add the entry pointso the accessor is discoverable via the standard source registry
list_countries, and indicatorsign/range sanity checks against real-world reference points
ValueErrorwhen no cloud-free Landsat imagery isavailable for a given area/date range, instead of a cryptic
band-not-found error
🎯 Type of Change
🔗 Related Issues
Closes #53
🧪 Testing
pytest)Test commands:
📊 Data Source Details
registration at https://signup.earthengine.google.com/, plus a linked
GEE Cloud Project (set via
EE_PROJECTenv var orproject=argument)Example usage:
📚 Documentation
✅ Checklist
Code Quality
Functionality
🌍 Impact Assessment
Who will benefit:
urban-density proxies
without a separate GEE integration
Breaking changes:
🔄 Testing Evidence
Validated NDBI sign convention against known land cover: positive for
dense urban core (São Paulo), negative for Amazon rainforest — confirming
the built-up index behaves correctly across contrasting terrain.