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Add OSBS tile mortality comparison workflow#178

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bw4sz wants to merge 1 commit into
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feat/osbs-mortality-clean
Open

Add OSBS tile mortality comparison workflow#178
bw4sz wants to merge 1 commit into
mainfrom
feat/osbs-mortality-clean

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@bw4sz bw4sz commented May 14, 2026

Summary

  • Adds an OSBS tile-scale mortality workflow that can download AOI-intersecting 2025 RGB tiles, run the existing detector plus Hugging Face alive/dead cropmodel, optionally run species inference, and aggregate alive/dead counts for 2017 vs 2025.
  • Writes per-year and change CSV/GPKG outputs plus GeoTIFF rasters for 2025 dead counts and 2017-to-2025 dead-count change.
  • Adds config, docs, a SLURM template, and focused tests for tile parsing, count aggregation, change flags, and raster output.

Test plan

  • uv run ruff check src/pipelines/osbs_mortality.py tests/test_osbs_mortality.py
  • uv run pytest tests/test_osbs_mortality.py tests/test_osbs_inference.py -q
  • uv run pytest -q currently fails on pre-existing absolute /blue/.../train_...csv paths in config-backed data/model tests.

Notes

  • This PR branch is a clean squashed snapshot from the local feature work because the local parent branch contains a tracked .env with a Comet key in its history. The pushed branch excludes .env and lightning_logs artifacts.

Made with Cursor

Squash the local feature branch into a clean PR branch without .env or lightning_logs artifacts.
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