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Initial commit for DiffDock-Web

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This is a thin wrapper, all the code is in the main DiffDock repository

Files changed (3) hide show
  1. .gitignore +162 -0
  2. Dockerfile +12 -0
  3. README.md +15 -1
.gitignore ADDED
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+ ### Python template
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+ # Byte-compiled / optimized / DLL files
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+ __pycache__/
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+ *.py[cod]
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+ *$py.class
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+
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+ # C extensions
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+ *.so
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+
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+ # Distribution / packaging
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+ .Python
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+ build/
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+ develop-eggs/
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+ dist/
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+ downloads/
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+ eggs/
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+ .eggs/
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+ lib/
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+ lib64/
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+ parts/
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+ sdist/
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+ var/
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+ wheels/
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+ share/python-wheels/
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+ *.egg-info/
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+ .installed.cfg
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+ *.egg
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+ MANIFEST
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+
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+ # PyInstaller
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+ # Usually these files are written by a python script from a template
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+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
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+ *.manifest
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+ *.spec
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+
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+ # Installer logs
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+ pip-log.txt
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+ pip-delete-this-directory.txt
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+
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+ # Unit test / coverage reports
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+ htmlcov/
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+ .tox/
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+ .nox/
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+ .coverage
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+ .coverage.*
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+ .cache
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+ nosetests.xml
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+ coverage.xml
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+ *.cover
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+ *.py,cover
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+ .hypothesis/
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+ .pytest_cache/
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+ cover/
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+
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+ # Translations
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+ *.mo
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+ *.pot
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+
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+ # Django stuff:
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+ *.log
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+ local_settings.py
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+ db.sqlite3
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+ db.sqlite3-journal
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+
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+ # Flask stuff:
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+ instance/
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+ .webassets-cache
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+
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+ # Scrapy stuff:
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+ .scrapy
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+
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+ # Sphinx documentation
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+ docs/_build/
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+
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+ # PyBuilder
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+ .pybuilder/
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+ target/
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+
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+ # Jupyter Notebook
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+ .ipynb_checkpoints
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+
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+ # IPython
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+ profile_default/
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+ ipython_config.py
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+
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+ # pyenv
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+ # For a library or package, you might want to ignore these files since the code is
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+ # intended to run in multiple environments; otherwise, check them in:
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+ # .python-version
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+
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+ # pipenv
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+ # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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+ # However, in case of collaboration, if having platform-specific dependencies or dependencies
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+ # having no cross-platform support, pipenv may install dependencies that don't work, or not
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+ # install all needed dependencies.
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+ #Pipfile.lock
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+
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+ # poetry
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+ # Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
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+ # This is especially recommended for binary packages to ensure reproducibility, and is more
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+ # commonly ignored for libraries.
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+ # https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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+ #poetry.lock
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+
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+ # pdm
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+ # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
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+ #pdm.lock
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+ # pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
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+ # in version control.
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+ # https://pdm.fming.dev/#use-with-ide
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+ .pdm.toml
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+
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+ # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
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+ __pypackages__/
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+
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+ # Celery stuff
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+ celerybeat-schedule
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+ celerybeat.pid
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+
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+ # SageMath parsed files
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+ *.sage.py
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+
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+ # Environments
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+ .env
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+ .venv
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+ env/
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+ venv/
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+ ENV/
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+ env.bak/
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+ venv.bak/
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+
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+ # Spyder project settings
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+ .spyderproject
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+ .spyproject
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+
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+ # Rope project settings
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+ .ropeproject
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+
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+ # mkdocs documentation
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+ /site
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+
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+ # mypy
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+ .mypy_cache/
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+ .dmypy.json
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+ dmypy.json
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+
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+ # Pyre type checker
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+ .pyre/
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+
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+ # pytype static type analyzer
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+ .pytype/
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+
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+ # Cython debug symbols
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+ cython_debug/
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+
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+ # PyCharm
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+ # JetBrains specific template is maintained in a separate JetBrains.gitignore that can
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+ # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
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+ # and can be added to the global gitignore or merged into this file. For a more nuclear
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+ # option (not recommended) you can uncomment the following to ignore the entire idea folder.
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+ #.idea/
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+
Dockerfile ADDED
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+ # This container is a basic web frontend, we do the heavy-lifting in the
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+ # main DiffDock image.
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+ FROM silterra/diffdock
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+
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+ USER $APPUSER
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+ WORKDIR $HOME/$DIR_NAME
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+
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+ # Expose port for web service
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+ EXPOSE 7860
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+
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+ # Run app under micromamba environment
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+ CMD ["sh", "-c", "micromamba run -n ${ENV_NAME} python3 app/main.py"]
README.md CHANGED
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  colorFrom: yellow
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  colorTo: indigo
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  sdk: docker
 
 
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  pinned: false
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- license: mit
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  ---
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  Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
 
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  colorFrom: yellow
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  colorTo: indigo
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  sdk: docker
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+ port: 7860
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+ app_file: main.py
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  pinned: false
 
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  ---
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+
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+ ## How to use this space
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+
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+ This is a simple app intended to showcase [DiffDock](https://github.com/gcorso/DiffDock).
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+ One can upload a protein and ligand, and calculate the predicted structure. The results are visualized in 3D and can be downloaded.
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+
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+ * This app is designed to take 1 protein (in PDB format) and 1 ligand (in SDF format) at a time. For bulk inference, use the [command line interface](https://github.com/gcorso/DiffDock).
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+
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+ * Our demonstration space uses a CPU, so it may take a few minutes to run. For faster results, use a GPU.
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+ One can duplicate this space (at their own expense) by selecting "â‹®" -> "Duplicate this space" in the top right corner, and then selecting a GPU in the "Settings" tab.
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+
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+ ----------
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+
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  Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference