.gitignore

s3cache
*~
*.py[cod]

# C extensions
*.so

# Packages
*.egg
*.egg-info
build
eggs
parts
bin
var
sdist
develop-eggs
.installed.cfg
lib
lib64

# Installer logs
pip-log.txt

# Unit test / coverage reports
.coverage
.tox
.pytest_cache
.cache
.mypy_cache
nosetests.xml
inputs.rds
outputs.rds

# Translations
*.mo

# Mr Developer
.mr.developer.cfg
.project
.pydevproject

# Complexity
output/*.html
output/*/index.html

# Sphinx
docs/_build

.webassets-cache
dist

# Virtualenvs
env/
.idea/
Procfile
__pycache__/

# Assets
portal-backend/depmap/static/libs/
portal-backend/depmap/static/css/*.css
portal-backend/depmap/static/js/common.js
portal-backend/depmap/static/js/pre_common.js

# Webpack
portal-backend/depmap/static/webpack
npm-debug.log

# Database
dev.db

# Mac filesystem
.DS_Store

# Screening quality
portal-backend/sample_data/cell_line/avana-essential-genes.csv
portal-backend/sample_data/cell_line/avana-nonessential-genes.csv
portal-backend/sample_data/cell_line/avana-guide-qced-reduced.csv
portal-backend/sample_data/cell_line/avana-guide-qced.csv
portal-backend/sample_data/cell_line/avana-replicate-map.csv
portal-backend/sample_data/cell_line/negative_avana-guide-qced.csv
portal-backend/sample_data/cell_line/positive_avana-guide-qced.csv

s3cache
webapp_data*
methylation.sqlite3

# Pipeline
pipeline/state
pipeline/state-external
pipeline/conseq-debug.log
nonquarterly-pipeline/state

webapp_data_prod_copy
.ipynb_checkpoints
scratch
profiling
pipeline/.gcloud
build-db/.kubeque-cached-file-hashes

travis/depmap-deploy-svc-acct.json
sparkles/.kubeque-cached-file-hashes
pipeline/conseq-debug.log

# these change depending on when we run build-depmap-base, changes are just noise
depmap-base/prod_copy.txt
depmap-base/dev_copy.txt

results
depmap-base/requirements

.RData
.Rhistory
yarn-error.log
storybook-static
node_modules
documentation/cell_lines.png
documentation/*.png
*.orig
pipeline/pipeline-run-docker/minicdsr.tar.gz
pipeline/pipeline-run-docker/conseq-*.zip
pipeline/tda-docker/conseq-*.zip
pipeline/.sparkles-cache
pipeline/DEADJOE
pipeline/state

# celery/redis
dump.rdb

# ignore files downloaded in release-scripts
release-scripts/**/*.csv
release-scripts/**/*.md
release-scripts/**/depmap-gumbo-pull-sa.json
# used for generating download entries
metadata.csv
pipeline/xrefs-internal-DO-NOT-EDIT-ME
pipeline/xrefs-external-DO-NOT-EDIT-ME
pipeline/xrefs-dmc-DO-NOT-EDIT-ME
Untitled*.ipynb
pipeline/test/state
pipeline/ensemble_564f3670e5

release-scripts/release-diff.cache.db
.*
!.importlinter
backup

!.github/
hack-docker
preprocess-logs
pipeline/state-1
pipeline/state-2
pipeline/state-*
hack-docker
preprocess-logs
sparkles.log
release_schema.json
release_schema.txt
public-20q4.md
pipeline/html
nonquarterly-pipeline/html
.env

.vscode
.*_cache

# local breadbox db and dataset storage directory
sql_app.db
app_datasets/
*.db-shm 
*.db-wal

# breadbox
breadbox/install
breadbox/breadbox/static
breadbox/breadbox/result
# generated file
portal-backend/depmap/utilities/color_palette.py
breadbox/app_datasets
secrets

# data access logs
portal-backend/access.log

# predictability output_data from local run
output_data/