RcppML/.gitignore at main · zdebruine/RcppML · GitHub

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# R project files
.Rproj.user
.Rhistory
.RData
.Ruserdata

# IDE
.vscode/

# Manuscript (not part of the R package)
GuidedNMFManuscript/

# Superseded plans (now archived to docs/dev/)
/HARDENING_PLAN.md
/WORKSTREAMS.md

# Compiled files
src/*.o
src/*.so
src/*.dll
inst/lib/*.so
tests/cpp/*.o

# pkgdown site (auto-generated)
docs/site/
inst/doc

# GPU profiling
dcgm-gpu-stats-*.out
*.nsys-rep
*.ncu-rep

# SLURM output
*.err
*.out
*.log

# Background processes
nohup.out

# Binary dataset snapshots
benchmarks/**/*.bin

# R CMD check output
RcppML.Rcheck/
*.tar.gz

# Test artifacts
test_output.txt
tests/testthat/_problems/

# Python virtual environment
.venv/
__pycache__/
*.pyc

# LaTeX artifacts
manuscript/**/*.aux
manuscript/**/*.log
manuscript/**/*.bbl
manuscript/**/*.blg
manuscript/**/*.out

# Benchmark data (large, regenerable)
benchmarks/**/*.rds
benchmarks/**/*.csv
benchmarks/**/*.spz
benchmarks/**/cellcensus_*_binary/
benchmarks/results/overfitting_log.txt

# Development artifacts (not part of package distribution)
logs/
rendered_vignettes/
sandbox/
NEWS.md.bak
inst/lib/.nfs*

# tools/ generated outputs (keep scripts, ignore results)
tools/*.log
tools/*.rds
tools/*.png
tools/*.html
tools/*_progress.txt
tools/*_log.txt

# GuidedNMFManuscript generated outputs (keep scripts & reports)
GuidedNMFManuscript/**/*.log
GuidedNMFManuscript/**/*.rds
GuidedNMFManuscript/**/*.csv
GuidedNMFManuscript/**/results/
GuidedNMFManuscript/**/plots/
GuidedNMFManuscript/**/logs/
GuidedNMFManuscript/**/combined/
GuidedNMFManuscript/**/tsv2_*/
GuidedNMFManuscript/dead_code/
GuidedNMFManuscript/sandbox/