.gitignore

*~
# KDE directory preferences
 .directory
# # Linux trash folder which might appear on any partition or disk
 .Trash-*


#VIM backup and swap
[a-w][a-z]
[._]s[a-w][a-z]
*.un~
Session.vim
.netrwhist
*~
.ropeproject/

#python compiled files
# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
# C extensions
*.so
# Distribution / packaging
.Python
env/
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
*.egg-info/
.installed.cfg
*.egg
# 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
# Translations
*.mo
*.pot
# Django stuff:
*.log
# Sphinx documentation
docs/_build/
# PyBuilder
target/

#file for sublime text
*.tmlanguage.cache
*.tmPreferences.cache
*.stTheme.cache
# workspace files are user-specific
*.sublime-workspace
# project files should be checked into the repository, unless a significant
# proportion of contributors will probably not be using SublimeText
*.sublime-project
# sftp configuration file
sftp-config.json

#data files other resources
*.svg

!data/

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

__pycache__

#folders
compare_lineages/output_files/

#figures with dates
figures/overall_trends-2020*
figures/S222_S477_compare-2020*
figures/logistic_fits-2020*
figures/pie_tree-2020*
figures/United Kingdom-newcases-seqs-2020*
figures/uk_pie_tree-2020*
figures/EUClusters_compare-2020*
figures/compare_lineages_Switzerland-2020*

# Some of emma's rough scripts
clusterDynamics_weekFreq.py
clusterManuDraft.docx
figures/uk_pie_tree.png
networkTrial2.py
old_swiss_tree/
figures/pie_tree-EBH.png
tree_pie_plot_EBH.py

#back up file
manu_backup-2020-10-10.txt
Swiss_intro_notes_old.md