.gitignore

# Ignore phyddle workspace dirs
workspace/*/simulate
workspace/*/format
workspace/*/train
workspace/*/estimate
workspace/*/plot
workspace/*/log
workspace/*/empirical

!tests/workspace/valid/simulate/
!tests/workspace/valid/format/
!tests/workspace/valid/estimate/
!tests/workspace/valid/train/
!tests/workspace/valid/plot/
!tests/workspace/valid/log/
!tests/workspace/valid/empirical/

tests/workspace/test/*
#simulate/
#tests/workspace/test/format/
#tests/workspace/test/estimate/
#tests/workspace/test/train/
#tests/workspace/test/plot/
#tests/workspace/test/log/
#tests/workspace/test/empirical/

# Ignore distribution files
dist/

# Ignore simulation tmp files
workspace/bisse_timehet_pj/bisse_timehet_*_parsed.pj

# Ignore extras in tests
#tests/workspace/*

# Ignore phyddle accessory dirs
sandbox/
paper/
code/
_old/
scripts/config

# Ignore phyddle accessory files
notes.txt
pkg_notes.txt

# Ignore everywhere
#.Rhistory
#.swp
#.vscode/
#.ipynb_checkpoints/
#__pycache__
#.DS_Store
#.DS_Store?
**/.Rhistory
**/*.swp
**/.vscode/
**/.ipynb_checkpoints/
**/__pycache__
**/.DS_Store
**/.DS_Store?

# Ignore JetBrains Rider project files
*.sln*
.idea/

# Ignore Sphinx extras
#docs/build/doctrees
#docs/build/doctrees/*
#docs/build/html
docs/build/*

# Ignore OS files

# Ignore programming files

# Ignore helper scripts
scripts/download_all.sh
scripts/download_plots.sh
build_all.sh

# Ignore notes
TODO.md

# Ignore random files
docs/source/tables/glossary_raw.csv
docs/source/tables/make_phyddle_settings_table.sh
workspace/levy_r/config_modeltest.py
workspace/levy_r/plot_tree.R