Changes in version 0.99.0                        

Bug fixes

  - Corrected column name crack_coverage to crack_coverage_pct in
    vignette result subsets to match the actual output column from
    read_grayleafspot_results() (#1).
  - Added launch_grayleafspotr() to the pkgdown reference index to
    resolve a build error when exported topics were absent from
    _pkgdown.yml.

Initial release.

Analysis pipeline

  - SmallUNet segmentation pipeline
    (inst/python/pipeline/analysislocal.py) running inside rvenv_arm_311
    (ARM64 Python 3.11).
  - Sole model is models/best_area_w_0.7.pt; downloaded automatically
    from HuggingFace via grayleafspot_download_model() when not present
    locally.
  - Dish geometry calibrated from grayscale image edges using an
    assumed 90 mm petri dish diameter (configurable via
    plate_diameter_mm).
  - Classical crack detection on an internal-band mask; crack polylines
    drawn as yellow overlays on top of the red colony mask.
  - Colony expansion reported in mm and mm² from pixel-to-mm
    calibration.
  - Kinematics (radial velocity, area growth rate, relative growth rate)
    computed across the ordered time series.

R interface

  - grayleafspot_analyze() — run the pipeline on a folder of plate
    images.
  - grayleafspot_python_available() / grayleafspot_python_executable() —
    check and resolve the Python interpreter for rvenv_arm_311.
  - grayleafspot_download_model() — fetch best_area_w_0.7.pt from
    HuggingFace and cache to tools::R_user_dir("grayleafspotr",
    "cache").
  - read_grayleafspot_results() / write_grayleafspot_results() — load
    and save run directories (JSON + CSV + manifest).
  - as_grayleafspot_growth_data() — coerce a run to a tidy tibble.
  - example_grayleafspot_results() — load the built-in example run
    without running the pipeline.

Plotting

  - plot_colony_expansion() — equivalent radius over time.
  - plot_growth_roughness() — relative growth rate and edge roughness.
  - plot_stress_remodeling() — crack coverage and crack count.
  - plot_texture_organization() — Shannon entropy and center-to-edge
    delta.
  - plot_shape_vs_stress() — eccentricity vs crack coverage scatter.
  - plot_radial_growth_area() — colony area and radial growth by plate
    (faceted); connects points across time even when each plate appears
    only once.
  - plot_feature_heatmap() — Pearson correlation heatmap of numeric
    features.
  - plot_radial_profile() — radial intensity profile; auto-discovers the
    most recent analysis.json under outputs/ when given a plain data
    frame.

Package assets

  - Three bundled plate images in inst/extdata/testdata/06FEB/ for
    offline testing and vignette examples (original photographs, Apache
    License 2.0).
  - Example run in inst/extdata/example/ (JSON, CSV, manifest).
  - Full Roxygen2 documentation for all 17 exported functions (man/).
  - Integration tests in tests/testthat/test-pipeline.R; skip gracefully
    when Python or the model is not available.
  - inst/COPYRIGHTS enumerating copyright and license for every non-R
    asset.
  - NOTICE file in the package root (Apache 2.0 requirement).