.gitignore

# ============================================================================
# Generalized Notation Notation (GNN) - Git Ignore Configuration
# ============================================================================
# This file contains comprehensive ignore patterns for the GNN project
# including Python, scientific computing, and pipeline-specific artifacts
# ============================================================================

# ============================================================================
# PYTHON VIRTUAL ENVIRONMENTS
# ============================================================================
/src/.venv
.venv/
venv/
env/
ENV/
.pytest_cache/
src/.pytest_cache/
*/.pytest_cache/
*.pytest_cache/

# ============================================================================
# ENVIRONMENT AND CONFIGURATION FILES
# ============================================================================
# Environment variables (NEVER commit these!)
.env
.env*
*.env
.env.local
.env.production
.env.development

# Configuration files with secrets
config.local.json
config.local.yaml
secrets.json
secrets.yaml
credentials.json

# ============================================================================
# PYTHON ARTIFACTS
# ============================================================================
# Python bytecode and cache (never `git add` these; if tracked historically, `git rm -r --cached **/__pycache__`)
__pycache__/
*.py[cod]
*$py.class
*.pyo
*.pyd
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg

# Specific module cache directories
/src/export/__pycache__/
/src/setup/__pycache__/
/src/utils/__pycache__/
/src/*/activeinference_jl/.julia
/src/execute/activeinference_jl/.julia

# ============================================================================
# GENERATED TREES INSIDE src/ (NOT SOURCE)
# ============================================================================
# Root `output/` is tracked in git (selective ignores below for temp/audio/cache).
# Optional fixture copies under `src/output/` may be tracked when committed.
src/tests/output/

# ============================================================================
# TESTING AND COVERAGE
# ============================================================================
# Coverage reports (allow output/coverage.json)
htmlcov/
.coverage
coverage.xml
*.cover
*.log
nosetests.xml
coverage.json
src/tests/htmlcov/
*/htmlcov/

# Testing artifacts
.pytest_cache/
.tox/
.coverage.*
.cache
.pytest_cache/
pytest.ini.local
# Local Bandit JSON from CI-parity runs (see .github/workflows/ci.yml artifact name)
bandit-results.json

# ============================================================================
# DOCUMENTATION BUILD ARTIFACTS
# ============================================================================
docs/_build/
docs/build/
target/
site/
_build/
build/

# Sphinx documentation
docs/_build/
*.doctrees

# Jekyll
_site/
.jekyll-cache/

# ============================================================================
# IDE AND EDITOR FILES
# ============================================================================
# VSCode
.vscode/
*.code-workspace

# PyCharm / IntelliJ
.idea/
*.iml
*.ipr
*.iws

# Sublime Text
*.tmlanguage.cache
*.tmPreferences.cache
*.stTheme.cache

# Vim
[._]*.s[a-v][a-z]
[._]*.sw[a-p]
[._]s[a-rt-v][a-z]
[._]ss[a-gi-z]
[._]sw[a-p]

# Emacs
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*

# Atom
.atom/

# ============================================================================
# OPERATING SYSTEM FILES
# ============================================================================
# macOS
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
ehthumbs.db
Thumbs.db
*~

# Windows
Thumbs.db
ehthumbs.db
Desktop.ini
$RECYCLE.BIN/
*.cab
*.msi
*.msix
*.msm
*.msp
*.lnk

# Linux
*~
.fuse_hidden*
.directory
.Trash-*

# ============================================================================
# SCIENTIFIC COMPUTING FRAMEWORKS
# ============================================================================
# Julia
*.jl.cov
*.jl.mem
.julia/
.jl/

# JAX / TensorFlow
*.pb
*.pbtxt
*.ckpt
*.index
*.data-*
*.meta

# Julia package manager
/Manifest.toml
/LocalPreferences.toml

# ============================================================================
# AUDIO AND MEDIA FILES
# ============================================================================
# Audio processing artifacts
*.wav
*.mp3
*.flac
*.ogg
*.m4a
*.wma
*.aac

# Generated audio from pipeline
output/*/audio/
cache/audio/
temp_audio_*


# ============================================================================
# PIPELINE OUTPUTS (Selective - root output/ is tracked)
# ============================================================================
# Commit substantive pipeline artifacts under output/. Patterns below drop volatile
# subtrees only (temp, debug, large generated audio), not the whole tree.

# Ignore temporary and intermediate files
output/*/temp/
output/*/tmp/
output/*/cache/
output/*/*_temp_*
output/*/*_tmp_*

# Debug and development outputs
output/*/debug/
output/*/dev/

# ============================================================================
# LOGS AND DEBUGGING
# ============================================================================
# Log files
*.log
logs/
log/
*.log.*

# Debug files
debug/
debug_*
*_debug.*

# Profiling outputs
*.prof
*.pstat
profiling/

# ============================================================================
# TEMPORARY AND CACHE FILES
# ============================================================================
# Temporary files
*.tmp
*.temp
tmp/
temp/
.tmp/
.temp/

# Cache directories
.cache/
*/cache/
cache/
*.cache
*.cache.*

# Backup files
*.bak
*.backup
*~

# ============================================================================
# LARGE DATA FILES (Optional - uncomment if needed)
# ============================================================================
# Uncomment these if you want to ignore large data files
# *.csv
# *.jsonl
# *.parquet
# *.hdf5
# *.h5
# *.nc
# data/
# datasets/

# ============================================================================
# DEVELOPMENT AND DEPLOYMENT
# ============================================================================
# Docker
.docker/
docker-compose.override.yml

# Deployment artifacts
deploy/
deployment/
!doc/deployment/
dist/
build/

# Package build artifacts
*.whl
*.tar.gz
*.zip

# ============================================================================
# MISCELLANEOUS
# ============================================================================
# Lock files (keep uv.lock, ignore others)
poetry.lock
Pipfile.lock
requirements.txt.lock
constraints.txt.lock

# Node.js (if used for documentation)
node_modules/
npm-debug.log*
yarn-debug.log*
yarn-error.log*

# R (if used for statistics)
*.RData
*.rda
*.rds
.Rhistory
.Rproj.user/

*.timelock.*
*.jl.mem

# ============================================================================
# GITKEEP FILES (Always keep these)
# ============================================================================
# Important directories that should be tracked but may be empty
!output/.gitkeep
!cache/.gitkeep
!logs/.gitkeep

# ============================================================================
# CUSTOM PATTERNS
# ============================================================================
# Add any project-specific patterns below this line

# ============================================================================
# SETUP AND MAINTENANCE NOTES
# ============================================================================
#
# To clean ignored files: git clean -fdx
# To see what would be cleaned: git clean -fdxn
# To update this file: Review and test patterns before committing
#
# Last updated: March 23, 2026
# ============================================================================
/.desloppify
/.claude
/.desloppify
/src/.desloppify