NEWS

grayleafspotr 0.99.2

Replaced \donttest{} wrappers with plain runnable code in four man pages (launch_grayleafspotr, write_grayleafspot_results, grayleafspot_python_available, grayleafspot_python_executable) so that BiocCheck counts them toward the required 80% runnable-examples threshold. launch_grayleafspotr uses an if (interactive()) guard; grayleafspot_python_executable uses tryCatch() to handle environments where Python is absent without aborting the check.

Added runnable @examples to all 18 exported man pages to satisfy the Bioconductor BiocCheck requirement (>= 80% of pages must have examples). Functions requiring Python or a network connection use \donttest{}; pure-R functions use the bundled example_grayleafspot_results() data.
Changed \dontrun{} to \donttest{} in launch_grayleafspotr() man page (BiocCheck does not count \dontrun{} as a runnable example).

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.

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.

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.

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.

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).