Add source code from caponetto/bhc repository.

.coveragerc

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

.gitattributes

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+bhc/_version.py export-subst

.github/ISSUE_TEMPLATE/bug_report.md

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

.github/ISSUE_TEMPLATE/feature_request.md

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

.github/ISSUE_TEMPLATE/question.md

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+---
+name: Question
+about: Ask a question
+title: ''
+labels: question
+assignees: ''
+
+---
+
+

.github/workflows/ci.yml

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

.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+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
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+coverage_report
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# 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/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# 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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.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/
+
+# vscode
+.vscode/

MANIFEST.in

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

bhc/__init__.py

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