.gitignore

# =============================================================================
# PROJECT-SPECIFIC IGNORES
# =============================================================================

# Project keys and sensitive data
anonymization_key.pkl
credentials.py

# Project directories and outputs
output_directory/
output_directory/*
notebooks/output_directory/
notebooks/output_directory
backups/
logs/
notebooks/test_project/
notebooks/example_searches_test/*
# Development and testing
dev_test/
test_dev.ipynb
live_test.ipynb
paths.py
temp_annot_file.csv
notebooks/temp_annot_file.csv

# Project-specific notebooks and files
t1.ipynb
example_usage_DEV.ipynb
notebooks/treatment_doc_extract/
treatment_doc_extract/
notebooks/treatment_docs.csv

# Pat2vec specific
notebooks/pat2vec_projects/
notebooks/pat2vec_projects/notebooks/example_usage_dev.ipynb
notebooks/pat2vec_projects/new_project/
notebooks/pat2vec_projects/new_project/*
notebooks/pat2vec_projects/new_project_ipw/
notebooks/pat2vec_projects/new_project_ipw/*
pat2vec/notebooks/
pat2vec/notebooks/*

# Project directories
new_project/
new_project_ipw/
notebooks/new_project/
notebooks/new_project/*
notebooks/new_project_ipw/
notebooks/new_project_ipw/*

# Utility and cohort files
util/cohort_searcher_dummy.ipynb
util/medcat_models/
util/medcat_models/*

# Project-specific data files
notebooks/anonymization_log.json
notebooks/my_project_outputfile_name_missing_dict.pickle
notebooks/ipw_dataframe.csv

# =============================================================================
# PYTHON STANDARD IGNORES
# =============================================================================

# Byte-compiled / optimized / DLL files
__pycache__/
*.py[cod]
*$py.class

# C extensions
*.so

# Compiled files
*.o
*.out

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
lib/
lib64/
parts/
sdist/
var/
wheels/
share/python-wheels/
*.egg-info/
.installed.cfg
*.egg
MANIFEST

# PyInstaller
*.manifest
*.spec

# Installer logs
pip-log.txt
pip-delete-this-directory.txt

# Unit test / coverage reports
htmlcov/
.tox/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/

# Translations
*.mo
*.pot

# Django stuff
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff
instance/
.webassets-cache

# Scrapy stuff
.scrapy

# Sphinx documentation
docs/_build/
docs/source/generated/

# PyBuilder
.pybuilder/
target/

# Jupyter Notebook
.ipynb_checkpoints

# IPython
profile_default/
ipython_config.py

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
.venv
env/
venv/
ENV/
env.bak/
venv.bak/
myenv/
myenv
pat2vec_env

# Spyder project settings
.spyderproject
.spyproject

# Rope project settings
.ropeproject

# mkdocs documentation
/site

# mypy
.mypy_cache/
.dmypy.json
dmypy.json

# Pyre type checker
.pyre/

# pytype static type analyzer
.pytype/

# Cython debug symbols
cython_debug/

# PyCharm
#.idea/

# PEP 582
__pypackages__/

# pdm
.pdm.toml

.env
# =============================================================================
# DEVELOPMENT TOOLS AND EDITORS
# =============================================================================

# IDE and editor files
.idea/
.vscode/

# =============================================================================
# SYSTEM AND TEMPORARY FILES
# =============================================================================

# Log files
*.log

# Temporary files
*.tmp

# macOS system files
.DS_Store

# Backup files
*~

# Node.js
node_modules/

# =============================================================================
# REQUIREMENTS AND DEPENDENCIES
# =============================================================================

requirements.in
notebooks/requirements.in
notebooks/treatment_docs_dummy.csv