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Add source code from caponetto/bhc repository.
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‎.coveragerc‎

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[run]
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omit =
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bhc/tests/*
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bhc/_*
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*/.local/*

‎.gitattributes‎

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bhc/_version.py export-subst

‎.github/ISSUE_TEMPLATE/bug_report.md‎

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---
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name: Bug report
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about: Create a report to help us improve
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title: ''
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labels: ''
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assignees: ''
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---
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**Describe the bug**
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A clear and concise description of what the bug is.
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**To Reproduce**
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Steps to reproduce the behavior:
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1. Go to '...'
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2. Click on '....'
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3. Scroll down to '....'
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4. See error
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**Expected behavior**
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A clear and concise description of what you expected to happen.
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**Screenshots**
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If applicable, add screenshots to help explain your problem.
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**Desktop (please complete the following information):**
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- OS: [e.g. Ubuntu]
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- Version [e.g. 20.04 LTS]
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**Additional context**
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Add any other context about the problem here.

‎.github/ISSUE_TEMPLATE/feature_request.md‎

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---
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name: Feature request
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about: Suggest an idea for this project
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title: ''
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labels: ''
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assignees: ''
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---
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**Is your feature request related to a problem? Please describe.**
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A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
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**Describe the solution you'd like**
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A clear and concise description of what you want to happen.
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**Describe alternatives you've considered**
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A clear and concise description of any alternative solutions or features you've considered.
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**Additional context**
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Add any other context or screenshots about the feature request here.

‎.github/ISSUE_TEMPLATE/question.md‎

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---
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name: Question
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about: Ask a question
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title: ''
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labels: question
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assignees: ''
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---
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‎.github/workflows/ci.yml‎

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name: Python application
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on:
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push:
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branches: [main]
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pull_request:
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branches: [main]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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with:
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fetch-depth: 0
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- name: Set up Python
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uses: actions/setup-python@v2
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with:
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python-version: 3.8.3
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- name: Install dependencies
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run: |
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python -m pip install --upgrade pip
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pip install pytest coverage wheel flake8-black
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pip install -r requirements.txt
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- name: Lint with flake8
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run: |
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flake8 . --count --show-source --statistics
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flake8 . --count --exit-zero --statistics
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- name: Test and coverage
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run: |
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coverage run -m pytest
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coverage html -d coverage_report
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- name: Build package
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run: |
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python setup.py sdist bdist_wheel
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- name: Upload artifacts
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uses: actions/upload-artifact@v2
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with:
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name: bhc
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path: dist/
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- name: Upload coverage report
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uses: actions/upload-artifact@v2
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with:
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name: coverage
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path: coverage_report/

‎.gitignore‎

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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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pip-wheel-metadata/
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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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coverage_report
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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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# 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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target/
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# Jupyter Notebook
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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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# 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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# vscode
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.vscode/

‎MANIFEST.in‎

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include LICENSE
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include versioneer.py
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include bhc/_version.py
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exclude README.md
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recursive-exclude * __pycache__
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recursive-exclude * *.pyc
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recursive-exclude * *.pyo
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recursive-exclude * *.orig

‎README.md‎

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![Python application](https://github.com/caponetto/bhc/workflows/Python%20application/badge.svg) [![License: GPL v3](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
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# Bayesian Hierarchical Clustering in python
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This is a python implementation of the Bayesian Hierarchical Clustering algorithm proposed by Heller & Ghahramani (2005).
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> HELLER, Katherine A.; GHAHRAMANI, Zoubin. Bayesian hierarchical clustering. In: **Proceedings of the 22nd international conference on Machine learning**. 2005. p. 297-304.
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It also includes the Bayesian Rose Trees extension proposed by Blundell et al (2012).
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> BLUNDELL, Charles; TEH, Yee Whye; HELLER, Katherine A. Bayesian rose trees. arXiv preprint arXiv:1203.3468, 2012.
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## How to build from source
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1. Create an anaconda environment using the [environment.yml](environment.yml) file.
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`$ conda env create -f environment.yml`
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2. Activate the environment after the installation is completed.
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`$ conda activate bayesian-hierarchical-clustering`
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3. Install the following libraries: `pytest`, `coverage` and `flake8`.
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`$ conda install pytest coverage flake8`
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4. Run the `build_dev.sh` script.
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`$ ./build_dev.sh`
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The files will be available in the `dist` folder.
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## Contribute
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All contributions are welcome, so don't hesitate to submit a pull request. ;-)
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## License
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This code is released under GPL 3.0 License.
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Check [LICENSE](LICENSE) file for more information.

‎bhc/__init__.py‎

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# -*- coding: utf-8 -*-
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# License: GPL 3.0
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from bhc.core.bhc import BayesianHierarchicalClustering
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from bhc.core.brt import BayesianRoseTrees
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from bhc.core.prior import NormalInverseWishart
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from ._version import get_versions
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__version__ = get_versions()['version']
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del get_versions

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