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.gitignore
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.DS_Store
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class
# C extensions
*.so
# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST
# PyInstaller
# Usually these files are written by a python script from a template
# before PyInstaller builds the exe, so as to inject date/other infos into it.
*.manifest
*.spec
# Installer logs
pip-log.txt
pip-delete-this-directory.txt
# Unit test / coverage reports
htmlcov/
.tox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
.hypothesis/
.pytest_cache/
# Translations
*.mo
*.pot
# Django stuff:
*.log
local_settings.py
db.sqlite3
# Flask stuff:
instance/
.webassets-cache
# Scrapy stuff:
.scrapy
# PyBuilder
target/
# Jupyter Notebook
.ipynb_checkpoints
.~*.ipynb
# pyenv
.python-version
# celery beat schedule file
celerybeat-schedule
# SageMath parsed files
*.sage.py
# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
# Spyder project settings
.spyderproject
.spyproject
# Rope project settings
.ropeproject
# mkdocs documentation
/site
# mypy
.mypy_cache/
#files I don't want tracked
*.snakemake*
seasonal-flu
seasonal-flu-nextstrain/mafft_7.467-1_amd64.deb
chromedriver.exe
tex2pdf.21972/
fauna/
zika-nextstrain/.snakemake
zika-nextstrain/.snakemake/metadata/
seasonal-flu-nextstrain/.snakemake/
seasonal-flu-nextstrain/results-outlier/
seasonal-flu-nextstrain/auspice-outlier/
seasonal-flu-nextstrain/results-20182020/
seasonal-flu-nextstrain/logs/
seasonal-flu-nextstrain/auspice-20182020/
seasonal-flu-nextstrain-2018-2020/results
zika-nextstrain/results-20182020/
zika-nextstrain/auspice/
zika-nextstrain/logs/
mers-nextstrain/logs/
sars-cov-2-nextstrain/logs/
notebooks/2019-07-18-view-auspice-tree-json-with-altair.ipynb
notebooks/2019-08-01DistanceMatrixCode.ipynb
notebooks/PairwiseVsEuclidean.ipynb
notebooks/zika_tree.json
source/docs/_build
.vscode/
manuscript/cartography.aux
manuscript/cartography.bbl
manuscript/cartography.blg
manuscript/cartography.suppinfo
# Adding gridsearch but not results
**/seasonal-flu-nextstrain/results/*
**/seasonal-flu-nextstrain-2018-2020/results/*
**/ha-na-nextstrain/results/*
**/sars-cov-2-nextstrain/results/*
**/sars-cov-2-nextstrain-2022-2023/results/*
**/sars-cov-2-nextstrain/data/*
**/sars-cov-2-nextstrain-2022-2023/data/*
!**/sars-cov-2-nextstrain/results/gridsearch/gridsearch.tsv
!**/zika-nextstrain/results/gridsearch/gridsearch.tsv
!**/mers-nextstrain/results/gridsearch/gridsearch.tsv
!**/seasonal-flu-nextstrain/results/gridsearch/gridsearch.tsv
!**/ha-na-nextstrain/results/gridsearch/gridsearch.tsv
!**/outlier_analysis/results/gridsearch/gridsearch.tsv
!**/ha-na-ma-nextstrain/results/gridsearch/gridsearch.tsv
!**/sars-cov-2-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/zika-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/mers-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/seasonal-flu-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/ha-na-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/outlier_analysis/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/ha-na-ma-nextstrain/results/gridsearch/mcc_by_method_and_distance_threshold.pdf
!**/sars-cov-2-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/zika-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/mers-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/seasonal-flu-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/ha-na-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/outlier_analysis/results/gridsearch/mcc_by_mds_parameters.pdf
!**/ha-na-ma-nextstrain/results/gridsearch/mcc_by_mds_parameters.pdf
!**/sars-cov-2-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/zika-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/mers-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/seasonal-flu-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/ha-na-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/outlier_analysis/results/gridsearch/mcc_by_umap_parameters.pdf
!**/ha-na-ma-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/sars-cov-2-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/zika-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/mers-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/seasonal-flu-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/ha-na-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/outlier_analysis/results/gridsearch/mcc_by_umap_parameters.pdf
!**/ha-na-ma-nextstrain/results/gridsearch/mcc_by_umap_parameters.pdf
!**/sars-cov-2-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/zika-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/mers-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/seasonal-flu-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/ha-na-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/outlier_analysis/results/gridsearch/mcc_by_t-sne_parameters.pdf
!**/ha-na-ma-nextstrain/results/gridsearch/mcc_by_t-sne_parameters.pdf
# Ignore log files.
logs/
slurm_logs/
*.out
replicate-*/
benchmarks/
.auctex-auto
auspice