\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.@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.\dontrun{} to \donttest{} in launch_grayleafspotr() man page
(BiocCheck does not count \dontrun{} as a runnable example).crack_coverage to crack_coverage_pct in vignette
result subsets to match the actual output column from read_grayleafspot_results()
(#1).launch_grayleafspotr() to the pkgdown reference index to resolve a
build error when exported topics were absent from _pkgdown.yml.Initial release.
inst/python/pipeline/analysislocal.py)
running inside rvenv_arm_311 (ARM64 Python 3.11).models/best_area_w_0.7.pt; downloaded automatically from
HuggingFace via grayleafspot_download_model() when not present locally.plate_diameter_mm).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.inst/extdata/testdata/06FEB/ for offline
testing and vignette examples (original photographs, Apache License 2.0).inst/extdata/example/ (JSON, CSV, manifest).man/).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).