.gitignore

# For augur repo #
environment*
temp*
results*
dengue/utils/
prepared/
processed/
auspice/
test_input/
test_output/
scratch/
s3/
build/
dist/
*stderr
/docs/_build/

# Output files from running tests
tests/functional/tree/data/full_aligned-delim.fasta.contree
tests/functional/tree/data/full_aligned-delim.fasta.splits.nex
tests/functional/tree/data/full_aligned-delim.fasta.ufboot
tests/functional/tree/data/masked_aligned-delim.iqtree.log.xz
tests/functional/tree/data/masked_aligned.fasta.xz

# Transient error outputs from tests
/tests/**/*.t.err

# For Python #
##############
*.pyc
__pycache__/
.cache/
.coverage
htmlcov/
augur.egg-info/
.mypy_cache/
nextstrain_augur.egg-info/
env/
.pytest_cache

# Compiled source #
###################
*.com
*.class
*.dll
*.exe
*.o
*.so

# OS generated files #
######################
.DS_Store
.DS_Store?
._*
.Spotlight-V100
.Trashes
Icon?
ehthumbs.db
Thumbs.db

# autosave #
############
*~

# IDE #
#######
*sublime*
.vscode

# Recursively ignore log files
**/*.log