# For docs / outputs from example notebooks;
examples/*.cif

# User-defined custom metrics
configs/metrics/custom_metrics/
src/rfproteina/metrics/custom_metrics/

# User-defined custom sampling transforms
src/rfproteina/transforms/sampling/

# Checkpoints
**.ckpt
**.pt

# Base .gitignore from https://github.com/github/gitignore/blob/main/Python.gitignore
*.lock
**.nfs**
**.dat

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

# C extensions
*.so

# Distribution / packaging
.Python
build/
develop-eggs/
dist/
downloads/
eggs/
.eggs/
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

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

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

# 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/
docs/auto_examples/
docs/sg_execution_times.rst

# PyBuilder
.pybuilder/
target/

# Jupyter Notebooks (unless explicitly not ignored)
.ipynb_checkpoints
**/.ipynb

# IPython
profile_default/
ipython_config.py

# 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
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

# 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__/

# Celery stuff
celerybeat-schedule
celerybeat.pid

# SageMath parsed files
*.sage.py

# Environments
.env
/.env.*
!/.env.local.example
# Private user-created runtime profile
.ipd/.env.local
.venv
env/
venv/
ENV/
env.bak/
venv.bak/

# 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
#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
#  and can be added to the global gitignore or merged into this file.  For a more nuclear
#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
#.idea/

# VS Code
.vscode
.cursor
.history/

# Ruff
ruff.toml
.ruff_cache

# Development
dev.py

# Pytest
*.benchmarks/

# Images
*.png
*.pdf
*.svg
*.jpg
*.jpeg
*.gif
*.bmp
*.tiff
# The docs ship their own images, and the blanket ignore above drops them silently: the build
# still succeeds locally off the working tree, so the loss only shows up as broken images on the
# published site. Keep the whole static dir exempt rather than naming files one at a time.
!docs/_static/*.png
!docs/_static/*.svg
!assets/readme/*.png
!assets/readme/*.gif

# Versioning
**/version.py

# W&B
wandb/

# Hydra
.hydra/

# Logs
logs/

# Other
*.sif
*.out

# Misc
model_weights/
**/notebooks/
**/scratch/
**/tmp/
**/tmp_ae/
scripts/slurm/
tests/data/pdb/*

# Run outputs (default to ./runs/<run_name>/; override with out_dir for external storage)
**/runs/
**/store/
**/inference/
**/inference_samples/
**/inference_metrics/
**/evaluation_results*/
**/slurm_run_outputs/
**/slurm_logs/
**/lightning_logs/
**/outputs/

# Model weights and checkpoints (covered by **.ckpt above)

# Benchmarks (except rfproteina benchmarks which are source-controlled)
**/benchmarks/
!website/benchmarks/
!website/benchmarks/**
!website/assets/**
!data/benchmarks
!data/benchmarks/**
# Downloaded by scripts/download_assets.sh from Hugging Face (nvidia/RFD4-Proteina, benchmarks/); not stored in git.
data/benchmarks/ae_pdb_temporal_holdout_2026_10_04/
data/benchmarks/nanobody/
src/rfproteina/metrics/cdr_torsion_data/
!.ipd/benchmarks
!.ipd/benchmarks/**

# Distillation artifacts
**/distillation/

# AI
**/.claude/*
!**/.claude/commands/
!**/.claude/skills
claude_experiments/**

# User info files contain secrets; private templates live under .ipd.
**/scripts/.user_info*

# Exceptions
!.ipd/apptainer/latent-dev.sif
# CCD benchmark files (extracted from ccd.tar.gz)
data/benchmarks/structure_prediction/ccd/*.cif

#backup
.merge_backup_*

# --- generated at runtime by the entrypoints / test suite ---
hydra_outputs/
inference/
# Committed regression baselines live inside an otherwise-ignored inference/ dir
!/tests/e2e/baselines/inference/
outputs/
store/
runs/
.benchmarks/

# Local DATA_PATH created by the setup docs (checkpoints, test dataset)
data_path/
