Add treescanr R package MVP, devcontainer, and CI - #1
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- New R package `treescanr` at the repo root with a pipeable core pipeline: ts_visits()/ts_visits_nssp() -> ts_counts() -> ts_run() -> ts_results(), plus ts_prm_*() helpers for TreeScan parameter files and ts_binary(). - ts_counts() is a port of treescan_project/code/3_create_count_file.R; an integration test checks it reproduces the legacy output exactly. - Toy data (subset of the 2026/2027 trees + synthetic visits) in inst/extdata, generated by data-raw/toy_data.R. - tinytest integration tests, quarto README and vignette, NEWS.md. - Private devcontainer image (ghcr.io/epiforesite/treescanr-dev) bundling TreeScan 2.4.1, and a GitHub Action running R CMD check inside it. - Legacy scripts kept in treescan_project/ (README moved there). Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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Summary
treescanrR package at the repo root. The core pipeline ists_visits()→ts_counts()→ts_run()→ts_results()(native|>, onlydata.tableandutilsas dependencies).ts_counts()portstreescan_project/code/3_create_count_file.R. A tinytest integration test checks that it reproduces the legacy count file exactly on the toy data.ghcr.io/epiforesite/treescanr-dev, which bundles TreeScan 2.4.1 (.devcontainer/), and anR-CMD-checkworkflow that runs inside it. This means the tests that call the real TreeScan binary also run in CI.treescan_project/.Notes
R CMD checkpassed locally with Status OK and all 17 tests passing, including a real TreeScan run that detects the injected A08.4 cluster.GITHUB_TOKENandpackages: read. This repo needs read access to the package ("Manage Actions access"). PRs from forks cannot pull the image.🤖 Generated with Claude Code