InterSubMod/.gitignore at main · liaoyoyo/InterSubMod · GitHub

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###### Environment Variables ######
# Environment files (contain API keys and secrets)
.env
.env.local
.env.*.local
*.env

###### C++ General ######
# Prerequisites
*.d

# Compiled Object files
*.slo
*.lo
*.o
*.obj

# Precompiled Headers
*.gch
*.pch

# Linker files
*.ilk

# Debugger Files
*.pdb

# Compiled Dynamic libraries
*.so
*.dylib
*.dll

# Fortran module files
*.mod
*.smod

# Compiled Static libraries
*.lai
*.la
*.a
*.lib

# Executables
*.exe
*.out
*.app

# debug information files
*.dwo

###### VSCode settings ######
# VSCode settings
.vscode/

#CMake build artifacts
CMakeFiles/

# Output (Binary/Object/Library)
build*/
bin/

# Log files
*.log
logs/*

# Results and data (repo root only)
/results*/
/data/

# Output directory (repo root only)
/output/
/output

# Temporary and backup files
*~
*.swp
__pycache__/
*.cache

# Garbage files
*garbage*/

# Build artifacts
build*/
CMakeFiles/
CMakeCache.txt
Makefile
cmake_install.cmake

# Dependencies
_deps/

# Python virtual environment
.venv/

# Large data directories
data/

# Logs (specific)
heatmap_generation.log

# Large sequencing data files
*.bam
*.bai
*.vcf.gz
*.vcf.gz.tbi
*.tsv.gz
*.fastq
*.fastq.gz

# Python cache
*.pyc
*.pyo
.pytest_cache/

# Cycle result large files (keep summary only)
research/autoresearch/cycles/*/feature_obs.txt

# Build artifacts
# docs/*

# Analysis (repo root only)
/analysis/

# Other test files
# tests*/
# *test*/*.claude/skills/

# Slides
/slides/*