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‎.gitignore‎

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dist/*
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*egg*/*
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*stop*
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files.txt
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files.txt
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# Created by https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks
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# Edit at https://www.toptal.com/developers/gitignore?templates=python,jupyternotebooks
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### JupyterNotebooks ###
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# gitignore template for Jupyter Notebooks
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# website: http://jupyter.org/
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.ipynb_checkpoints
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*/.ipynb_checkpoints/*
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# IPython
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profile_default/
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ipython_config.py
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# Remove previous ipynb_checkpoints
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# git rm -r .ipynb_checkpoints/
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### Python ###
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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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# C extensions
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*.so
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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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# 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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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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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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# Translations
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*.mo
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*.pot
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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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# Flask stuff:
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instance/
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.webassets-cache
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# Scrapy stuff:
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.scrapy
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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.pybuilder/
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target/
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# Jupyter Notebook
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# IPython
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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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# 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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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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# SageMath parsed files
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*.sage.py
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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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# Spyder project settings
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.spyderproject
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.spyproject
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# Rope project settings
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.ropeproject
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# mkdocs documentation
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/site
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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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# Pyre type checker
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.pyre/
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# pytype static type analyzer
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.pytype/
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# Cython debug symbols
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cython_debug/
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# End of https://www.toptal.com/developers/gitignore/api/python,jupyternotebooks

‎docs/API/index.html‎

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This file was deleted.

‎docs/Makefile‎

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = source
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BUILDDIR = build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

‎docs/make.bat‎

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@ECHO OFF
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pushd %~dp0
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REM Command file for Sphinx documentation
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if "%SPHINXBUILD%" == "" (
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set SPHINXBUILD=sphinx-build
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)
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set SOURCEDIR=source
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set BUILDDIR=build
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if "%1" == "" goto help
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%SPHINXBUILD% >NUL 2>NUL
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if errorlevel 9009 (
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echo.
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echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
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echo.installed, then set the SPHINXBUILD environment variable to point
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echo.to the full path of the 'sphinx-build' executable. Alternatively you
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echo.may add the Sphinx directory to PATH.
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echo.
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echo.If you don't have Sphinx installed, grab it from
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echo.http://sphinx-doc.org/
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exit /b 1
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)
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%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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goto end
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:help
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%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
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:end
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popd

‎docs/source/api.rst‎

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API
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===
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.. autosummary::
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:toctree: generated
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lumache

‎docs/source/conf.py‎

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# Configuration file for the Sphinx documentation builder.
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# -- Project information
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project = 'PyMIC'
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copyright = '2021, HiLab'
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author = 'HiLab'
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release = '0.1'
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version = '0.1.0'
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# -- General configuration
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extensions = [
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'sphinx.ext.duration',
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'sphinx.ext.doctest',
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'sphinx.ext.autodoc',
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'sphinx.ext.autosummary',
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'sphinx.ext.intersphinx',
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]
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intersphinx_mapping = {
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'python': ('https://docs.python.org/3/', None),
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'sphinx': ('https://www.sphinx-doc.org/en/master/', None),
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}
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intersphinx_disabled_domains = ['std']
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templates_path = ['_templates']
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# -- Options for HTML output
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html_theme = 'sphinx_rtd_theme'
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# -- Options for EPUB output
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epub_show_urls = 'footnote'

‎docs/source/index.rst‎

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Welcome to PyMIC's documentation!
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===================================
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PyMIC is a pytorch-based toolkit for medical image computing with annotation-efficient deep learning.
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PyMIC is developed to support learning with imperfect labels, including semi-supervised and weakly supervised learning, and learning with noisy annotations.
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Check out the :doc:`usage` section for further information, including
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how to :ref:`installation` the project.
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.. note::
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This project is under active development.
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Contents
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--------
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.. toctree::
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usage
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api

‎docs/source/usage.rst‎

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Usage
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=====
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.. _installation:
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Installation
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------------
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To use Lumache, first install it using pip:
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.. code-block:: console
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(.venv) $ pip install lumache
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Creating recipes
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----------------
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To retrieve a list of random ingredients,
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you can use the ``lumache.get_random_ingredients()`` function:
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.. autofunction:: lumache.get_random_ingredients
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The ``kind`` parameter should be either ``"meat"``, ``"fish"``,
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or ``"veggies"``. Otherwise, :py:func:`lumache.get_random_ingredients`
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will raise an exception.
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.. autoexception:: lumache.InvalidKindError
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For example:
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>>> import lumache
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>>> lumache.get_random_ingredients()
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['shells', 'gorgonzola', 'parsley']
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‎pyproject.toml‎

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[build-system]
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requires = ["flit_core >=3.2,<4"]
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build-backend = "flit_core.buildapi"
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[project]
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name = "PyMIC"
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authors = [{name = "Graziella", email = "graziella@lumache"}]
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dynamic = ["version", "description"]

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