v2.1.1 — Docs overhaul, multispectral + predict/outputs upgrades, CI refresh

Compare: v2.0.1...v2.1.1 Stats: 53 commits · 40 files · +2,918 / −2,126 LOC

Highlights

• Multispectral support in prediction/training: predict.py now reads .tif stacks via rasterio and handles H×W×C ordering; training docs cover MS workflows.
• Smarter crown de-overlap (clean_crowns): rewritten around spatial join + union-find clustering; more robust, faster on big scenes.
• Docs: major restructure: new tutorial series, API reference, and an HPC/cluster guide; docs build is more reliable via mocked heavy deps.
• CI refresh: runners moved to Ubuntu 22.04, pin/upgrade key pieces (GDAL in CI, NumPy bound for tests), and a cleaner Sphinx workflow with gh-pages deploy.
• Dependency modernisation: shapely ≥2, geopandas/rasterio/fiona ranges updated; stale geospatial deps removed.

New / Improved

Models & pipeline

• predict.py

  • Accepts .png (RGB via OpenCV) and .tif (multispectral via rasterio).
  • Safer filename handling and JSON output naming.
  • Clearer logging and mode detection via get_filenames(...).

• outputs.py

  • New clean_crowns algorithm:

    • bbox-based spatial join to find candidates;
    • union-find to cluster overlaps by IoU;
    • keep best per cluster by field (default Confidence_score);
    • filters invalid/empty geometry; configurable area_threshold (now default 2 m²).

• evaluation.py

  • More robust geometry ops:

    • handles GEOSException, uses make_valid fallback;
    • consistent union_area/IoU computation;
    • safer handling of test/pred file naming.

• train.py

  • Large update (see docs): clarified config path, support surfaced for MS training, early-stopping usage, and advanced options captured in docs.

Documentation

• Restructure

  • New docs/source/tutorials/ series:

    • 01_getting_started, 02_data_preparation, 03_training_and_evaluation,
    • 04_prediction, 05_advanced_topics.

  • API reference via sphinx-apidoc (docs/source/api.rst).

  • Cluster/HPC guide with CSD3 examples and GPU setup (cluster.rst).

• Build reliability

  • conf.py: add repo root to sys.path; mock heavy deps (torch, detectron2, rasterio, geopandas, shapely, etc.) so docs build without native libs.
  • release string set to 2.1.1.
  • docs/requirements.txt added.

• Model garden

  • Updated Zenodo links; added notes for 230717_base, 230729_05dates, and 250312_flexi; example wget commands updated.

Continuous Integration

• python-ci.yml

  • Runner: ubuntu-22.04.
  • GDAL in CI from 3.6.4; explicit numpy>=1.20,<2.0 for tests; add pytest-order.
  • Keep flake8 erroring on syntax/undefined names; soften general run with --exit-zero for metrics only.

• sphinx-ci.yml

  • Renamed to "Sphinx Documentation"; runner ubuntu-22.04.
  • Streamlined: setup-python@v4, build, upload artifact (v4), and deploy to GitHub Pages on master.

Repo/Meta

• .gitattributes: make *.py detectable, ignore notebooks for linguist.
• New dark/light logos updated.
• README: contributors updated (incl. Christopher Kotthoff).

Removals / Potentially Breaking

• Removed data loaders:

  • detectree2/data_loading/gdrive.py
  • gdrivePull.sh
  • gee_download.py
  • quickstart.py

  If you relied on these, migrate to your own fetch scripts or keep them pinned at ≤ v2.0.1.

• Docs cleanup: legacy tutorial.rst and tutorial_multi.rst removed (replaced by new tutorial set).

Dependency changes (setup.py)

• Now requires

  • shapely>=2.0, geopandas>=0.13,
  • rasterio>=1.2,<1.4, fiona>=1.8,<1.10,
  • numpy>=1.20, pandas>=1.3, opencv-python>=4.5, tqdm>=4.60, pycocotools>=2.0.4,
  • detectron2 from GitHub.

• Removed: proj, geos, pygeos, pypng, pycrs, descartes, hard-pinned prerelease rasterio, etc.

Tests

• tests/test_preprocessing.py: updated expected ybox_coords (reflects tiling math tweak).

Upgrade notes

• If your environment is older (e.g., shapely <2), create a fresh venv and reinstall.
• For MS .tif predictions, ensure rasterio can open your imagery and that channel order matches expectations.
• The new clean_crowns defaults are stricter (area_threshold=2). If you need tiny crowns, lower that or post-filter by Confidence_score.

Contributors

Thanks to everyone who pushed on CI, docs, MS support, and the crown cleaning logic. Also updated contributor credits in README.

What's Changed

• Added Compute Cluster Guide by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/154
• fixed the random rotation augmentation inconsistency by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/155
• Fixed Layout for the Cluster Guide by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/156
• Jb/dec24 by @PatBall1 in https://github.com/PatBall1/detectree2/pull/158
• Github Workflow Fix (python-ci.yml) by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/172
• [Re-Opened] Added Adaptive Tiling by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/173
• Masks and Other Features for Tiling by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/165
• Random Tiles Subset Generation by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/166
• Additional Custom nodata-Values by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/167
• Conversion of all Multispectral Tiles to the Range 0-255 by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/168
• Overlapping Tiles - More Training Data by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/169
• Fix typo in tutorial by @CiSong10 in https://github.com/PatBall1/detectree2/pull/175
• visualization feature with clean_crowns bugfix by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/179
• Weight Initialization for MS by repeating RGB Channel Weights in the First Layer by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/170
• Create an RGB clone of a MS Tiles Folder by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/180
• Ignoring certain Bands during the Tiling Process by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/181
• Remove non-annotated image data from training-tiles by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/182
• Fixing sphinx-ci Workflow + Optimization by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/185
• Fixed failing Pytest by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/186
• Fix FileNotFoundError and shapely.errors.GEOSException for models/evaluation.py by @CiSong10 in https://github.com/PatBall1/detectree2/pull/187
• Jb/sept25 by @PatBall1 in https://github.com/PatBall1/detectree2/pull/203
• Enhancing RGB Tile Contrast by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/202
• Tutorial Modifications and Extension by @ChristopherKotthoff in https://github.com/PatBall1/detectree2/pull/204

New Contributors

• @CiSong10 made their first contribution in https://github.com/PatBall1/detectree2/pull/175

Full Changelog: https://github.com/PatBall1/detectree2/compare/v2.0.1...v2.1.1