#############################################################################
# COMPREHENSIVE .GITIGNORE FILE
#############################################################################

#############################################################################
# 1. OPERATING SYSTEM SPECIFIC FILES
#############################################################################

# macOS
# -----
# General
.DS_Store
.AppleDouble
.LSOverride

# Thumbnails
._*

# Files that might appear in the root of a volume
.DocumentRevisions-V100
.fseventsd
.Spotlight-V100
.TemporaryItems
.Trashes
.VolumeIcon.icns
.com.apple.timemachine.donotpresent

# Directories potentially created on remote AFP share
.AppleDB
.AppleDesktop
Network Trash Folder
Temporary Items
.apdisk

# Windows
# -------
# Windows thumbnail cache files
Thumbs.db
Thumbs.db:encryptable
ehthumbs.db
ehthumbs_vista.db

# Dump file
*.stackdump

# Folder config file
[Dd]esktop.ini

# Recycle Bin used on file shares
$RECYCLE.BIN/

# Windows Installer files
*.cab
*.msi
*.msix
*.msm
*.msp

# Windows shortcuts
*.lnk

# Linux
# -----
# temporary files which can be created if a process still has a handle open of a deleted file
.fuse_hidden*

# KDE directory preferences
.directory

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

# .nfs files are created when an open file is removed but is still being accessed
.nfs*

#############################################################################
# 2. PYTHON RELATED FILES
#############################################################################

# 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/
share/python-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/
.nox/
.coverage
.coverage.*
.cache
nosetests.xml
coverage.xml
*.cover
*.py,cover
.hypothesis/
.pytest_cache/
cover/
coverage-report/

# Translations
*.mo
*.pot

# Django stuff:
*.log
local_settings.py
db.sqlite3
db.sqlite3-journal

# Flask stuff:
instance/
.webassets-cache

# Scrapy stuff:
.scrapy

# Sphinx documentation
docs/_build/

# 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/

# Python type checking
.mypy_cache/
.dmypy.json
dmypy.json
.pyre/
.pytype/

# Cython debug symbols
cython_debug/

# Pixi package manager
.pixi

#############################################################################
# 3. R RELATED FILES
#############################################################################

# History files
.Rhistory
.Rapp.history

# Session Data files
.RData
.RDataTmp

# User-specific files
.Ruserdata

# Example code in package build process
*-Ex.R

# Output files from R CMD build
/*.tar.gz

# Output files from R CMD check
/*.Rcheck/

# RStudio files
.Rproj.user/

# produced vignettes
vignettes/*.html
vignettes/*.pdf

# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
.httr-oauth

# knitr and R markdown default cache directories
*_cache/
/cache/

# Temporary files created by R markdown
*.utf8.md
*.knit.md

# R Environment Variables
.Renviron

# RStudio Connect folder
rsconnect/

#############################################################################
# 4. IDE/EDITOR SPECIFIC FILES
#############################################################################

# PyCharm
.idea/
*.iml
*.iws
*.ipr
*.iws
*.idea/
out/
.idea_modules/

# Visual Studio Code
.vscode/*
!.vscode/settings.json
!.vscode/tasks.json
!.vscode/launch.json
!.vscode/extensions.json
*.code-workspace
.history/
.ionide/

# Sublime Text
*.sublime-project
*.sublime-workspace

# VIM
[._]*.s[a-v][a-z]
[._]*.sw[a-p]
[._]s[a-rt-v][a-z]
[._]ss[a-gi-z]
[._]sw[a-p]
*~
Session.vim
Sessionx.vim
.netrwhist

# Emacs
*~
\#*\#
/.emacs.desktop
/.emacs.desktop.lock
*.elc
auto-save-list
tramp
.\#*

# Cursor
.cursorignore
.cursorindexingignore

#############################################################################
# 5. DEPENDENCY MANAGEMENT
#############################################################################

# Despite the standard using pixi, I'm sure people will use other dependency management tools.
# so this is just to protect against the common ones lol.

# pyenv
#   For a library or package, you might want to ignore these files since the code is
#   intended to run in multiple environments; otherwise, check them in:
# .python-version

# pipenv
#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
#   However, in case of collaboration, if having platform-specific dependencies or dependencies
#   having no cross-platform support, pipenv may install dependencies that don't work, or not
#   install all needed dependencies.
#Pipfile.lock

# UV
#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#uv.lock

# poetry
#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
#   This is especially recommended for binary packages to ensure reproducibility, and is more
#   commonly ignored for libraries.
#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
#poetry.lock
#poetry.toml

# pdm
#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
#pdm.lock
#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
#   in version control.
#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
.pdm.toml
.pdm-python
.pdm-build/

# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
__pypackages__/

# Abstra
# Abstra is an AI-powered process automation framework.
# Ignore directories containing user credentials, local state, and settings.
# Learn more at https://abstra.io/docs
.abstra/

#############################################################################
# 6. BUILD/TEST ARTIFACTS
#############################################################################

# Ruff cache
.ruff_cache/

# PyPI configuration file
.pypirc

# Recipe files
recipe.yaml

# Cache directories for various tools
**/__pycache__/*
*./**/.pyc
**.pyc

# Log files
logs/

#############################################################################
# 7. DOCUMENTATION BUILDS
#############################################################################

# mkdocs documentation
/site
site/

#############################################################################
# 8. PROJECT-SPECIFIC ENTRIES
#############################################################################

# Add your project-specific entries here
# For example:
# models/
# sandbox/
# etc.


data/
docs/data_sources.md
docs/usage.md
docs/devnotes.md

workflow/scripts/example_script_1.py
workflow/scripts/example_script_2.py
workflow/scripts/ICB_Inspect.py

workflow/notebooks/preproccesing_kidney_ureteral.ipynb
workflow/notebooks/preproccesing_melanoma.ipynb
workflow/notebooks/preproccesing_pancancer.ipynb
workflow/notebooks/results_analysis.ipynb

workflow/notebooks/preproccesing.ipynb
workflow/notebooks/README.md
workflow/notebooks/example_notebook.ipynb

__pycache__/
dist/
build/
*.egg-info/

src/__pycache__

dist/
src/*.egg-info

pixi.lock 

prueba.py
.pixi/