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…ocumentation improvements ## Test Suite Overhaul - Rewrite test suite from ~1500 bloated tests to ~200 focused, meaningful tests - Replace redundant and overlapping test files with consolidated test modules - Add concrete value assertions (expect_equal with tolerance) instead of trivial smoke tests - Remove 15 redundant test files: test-absolute-real-data.R, test-acwr-ewma.R, test-acwr-ewma-advanced.R, test-calculate-ef-extended.R, test-calculate-ef-simple.R, test-calculate-ef-stream.R, test-calculate-exposure-extended.R, test-color-palettes.R, test-date-ranges.R, test-extreme-edge-cases.R, test-parameter-boundaries.R, test-plot-ef-advanced.R, test-plot-ef-comprehensive.R, test-plot-ef-extended.R, test-plot-ef-simple.R, test-plot-ef-stream.R, test-plot-pbs-extended.R, test-plot-pbs-simple.R, test-utils-extended.R, test-additional-edge-cases.R - Add vdiffr-based visual snapshot testing for all 6 plot functions (plot_acwr, plot_acwr_enhanced, plot_decoupling, plot_ef, plot_exposure, plot_pbs) - Store 15 SVG reference snapshots in tests/testthat/_snaps/plot-snapshots/ ## Bug Fixes - Fix FIT file import: correct column name mismatches (power/watts, heartrate/heart_rate) - Fix parse_activity_file() to handle missing/NA coordinate columns gracefully - Fix calculate_acwr() week-boundary edge case in rolling window computation - Fix calculate_ef() to properly validate speed > 0 before computing efficiency - Fix calculate_decoupling() drift calculation for sessions with variable-length segments - Fix plot_exposure() date axis formatting when date range spans < 7 days - Update sample_pbs and sample_ef datasets with corrected synthetic data ## Architecture & API Improvements - Separate analysis logic from plotting: calculate_*() functions now return dedicated S3 classes (acwr_result, decoupling_result, ef_result, exposure_result, pbs_result) - Add GAP (Grade Adjusted Pace) support in calculate_ef() for trail/hill activities - Add configurable ACWR risk zones (low/moderate/high/very_high) with user-defined thresholds - Add smooth_per_type parameter to plot_ef() for per-activity-type trend smoothing - Add cohort_reference() helper for population-level normative comparison bands - Improve input validation across all calculate_*() and plot_*() functions ## Documentation & References - Add peer-reviewed scientific references with DOIs throughout roxygen documentation - Rewrite both vignettes (athlytics_introduction, advanced_features) with clearer narrative, reproducible examples, and proper academic citations - Remove pre-built vignettes from inst/doc/ (let R CMD build generate them) - Update README.md with revised feature list, clearer installation instructions - Update NEWS.md with comprehensive v1.0.3 changelog - Update codemeta.json, CITATION.cff, and inst/CITATION for v1.0.3 ## Code Quality & Cleanup - Remove 85 unused NAMESPACE exports (palette functions, internal helpers) - Remove deprecated color palette functions (athlytics_colors_*, athlytics_palette_*) - Remove R/zzz.R startup message; clean .Rbuildignore - Delete helper-mockapi.R (unused mock API test infrastructure) - Apply consistent code style via styler across all R source files - Ship example activity files (example.fit, example.gpx, example.tcx) in inst/extdata/ ## CI & Build - Update R-CMD-check.yml GitHub Actions workflow for compatibility - R CMD check passes with 0 errors, 0 warnings, 0 notes - Update DESCRIPTION: bump version, refine Imports/Suggests dependencies - Update _pkgdown.yml reference section for renamed functions and datasets
Add github::grimbough/FITfileR to extra-packages in both R-CMD-check and pkgdown workflows so pak can resolve the GitHub-only dependency. Remove redundant manual install step from R-CMD-check.
…in CI Fix ACWR test failure on ubuntu-latest by adding set.seed(42) for reproducibility and relaxing ATL non-negative check to allow floating-point tolerance. Enable vignette building in R CMD build/check to resolve inst/doc warnings.
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Summary
Address reviewer feedback for rOpenSci submission (ropensci/software-review#728).