# ======================================================================
# Docker Ignore File for Rxiv-Maker Base Image
# ======================================================================
# This file ensures that NO rxiv-maker code or user data is included
# in the Docker base image. The image should only contain system
# dependencies and tools.
# ======================================================================

# Ignore ALL files by default (base image should be minimal)
*

# But allow specific files needed for Docker build
!Dockerfile
!.dockerignore
!build.sh
!README.md

# ======================================================================
# Explicitly ignore rxiv-maker code and data
# ======================================================================

# Python source code
src/py/
*.py
*.pyc
__pycache__/
*.pyo
*.pyd
.Python
env/
venv/
.venv/
pip-log.txt
pip-delete-this-directory.txt
.tox/
.coverage
.pytest_cache/
htmlcov/
.cache/
nosetests.xml
coverage.xml
*.cover
.hypothesis/

# LaTeX and manuscript files
*.tex
*.pdf
*.aux
*.bbl
*.blg
*.log
*.out
*.toc
*.fdb_latexmk
*.fls
*.synctex.gz
*.nav
*.snm
*.vrb
*.bib
*.md
*.yml
*.yaml

# Output and build directories
output/
build/
dist/
*.egg-info/

# Configuration files
.env
.env.local
.env.*.local
config.json
settings.json

# Manuscript and example directories
MANUSCRIPT/
EXAMPLE_MANUSCRIPT/
manuscripts/
examples/
docs/

# Figure directories and files
FIGURES/
figures/
*.png
*.jpg
*.jpeg
*.gif
*.svg
*.pdf
*.eps
*.mmd

# Data files
*.csv
*.json
*.xlsx
*.xls
*.parquet
*.hdf5
*.h5
*.pkl
*.pickle

# Temporary files
*.tmp
*.temp
*.swp
*.swo
*~
.DS_Store
Thumbs.db

# Version control
.git/
.gitignore
.gitattributes
.gitmodules

# IDE and editor files
.vscode/
.idea/
*.sublime-project
*.sublime-workspace
.atom/
.brackets.json

# OS generated files
.DS_Store?
ehthumbs.db
Icon?
Thumbs.db

# Archives
*.tar
*.zip
*.gz
*.bz2
*.xz
*.7z

# Logs
*.log
logs/

# Node.js (if any local node_modules exist)
node_modules/
npm-debug.log*
yarn-debug.log*
yarn-error.log*

# Python package files
*.whl
*.tar.gz

# R files
*.RData
*.Rhistory
.Rproj.user/

# Test files
tests/
test_*

# Documentation
docs/
documentation/

# GitHub Actions
.github/

# Makefile (not needed in Docker image)
Makefile

# CI/CD files
.travis.yml
.circleci/
.gitlab-ci.yml
azure-pipelines.yml

# Package managers
requirements.txt
pyproject.toml
setup.py
setup.cfg
poetry.lock
Pipfile
Pipfile.lock

# Any other project-specific files
README.md
LICENSE
CHANGELOG.md
CONTRIBUTING.md
AUTHORS
MANIFEST.in
tox.ini
noxfile.py
.pre-commit-config.yaml
.bandit
.mypy.ini
.ruff.toml
