Dev

[Arvindiyer]

Summary

Reorganize non-standard files, rewrite INSTALLATION.md, and clean up compiled binaries from git tracking.

Changes

• Move CONTRIBUTING.md, CODE_OF_CONDUCT.md → .github/ (GitHub still surfaces them)
• Move environment.yml, cran-comments.md → dev/
• Rewrite INSTALLATION.md: prerequisites, 3 install options (pak, micromamba, pinned env), verification, troubleshooting
• Switch install examples from deprecated devtools::install_github() to pak::pak(); update README accordingly
• Add *.tar.gz, src/*.so, src/*.o to .gitignore; untrack compiled SelectSim.so
• Trim .Rbuildignore to remove entries now covered by .github/ and dev/ rules

Test plan

• devtools::document() run to regenerate NAMESPACE / man pages
• devtools::check() passes with 0 errors, 0 warnings, 0 notes
• New or changed behaviour covered by tests in tests/testthat/
• Documentation updated (roxygen tags, vignette, README) if applicable

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 8d346f69-34cb-4aa1-af20-d3b98d67dcab

📥 Commits

Reviewing files that changed from the base of the PR and between a4128fe and b7d93aa.

⛔ Files ignored due to path filters (1)

• src/SelectSim.so is excluded by !**/*.so

📒 Files selected for processing (52)

• .Rbuildignore
• .github/CODE_OF_CONDUCT.md
• .github/CONTRIBUTING.md
• .gitignore
• INSTALLATION.md
• README.Rmd
• README.md
• dev/cran-comments.md
• dev/environment.yml
• man/GENIE_maf_schema.Rd
• man/TCGA_maf_schema.Rd
• man/add.Rd
• man/al.pairwise.alteration.stats.Rd
• man/al.stats.Rd
• man/am.pairwise.alteration.coverage.Rd
• man/am.pairwise.alteration.overlap.Rd
• man/am.stats.Rd
• man/am.weight.pairwise.alteration.overlap.Rd
• man/binary.yule.Rd
• man/effectSize.Rd
• man/estimateFDR2.Rd
• man/estimate_p_val.Rd
• man/estimate_pairwise_p.Rd
• man/filter_maf_column.Rd
• man/filter_maf_complex.Rd
• man/filter_maf_gene.name.Rd
• man/filter_maf_ignore.Rd
• man/filter_maf_missense.Rd
• man/filter_maf_mutation.type.Rd
• man/filter_maf_mutations.Rd
• man/filter_maf_sample.Rd
• man/filter_maf_schema.Rd
• man/filter_maf_truncating.Rd
• man/generateS.Rd
• man/generateW_block.Rd
• man/generateW_mean_tmb.Rd
• man/get.blocks.Rd
• man/interaction.table.Rd
• man/maf2gam.Rd
• man/mutation_type.Rd
• man/new.AL.general.Rd
• man/new.ALS.Rd
• man/new.AMS.Rd
• man/null_model_parallel.Rd
• man/r.am.pairwise.alteration.overlap.Rd
• man/r.effectSize.Rd
• man/retrieveOutliers.Rd
• man/stat_maf_column.Rd
• man/stat_maf_gene.Rd
• man/stat_maf_sample.Rd
• man/template.obj.gen.Rd
• man/w.r.am.pairwise.alteration.overlap.Rd

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch dev

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