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Merge pull request #12 from apulverizer/develop
v 0.1.0
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‎.dockerignore

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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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*.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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.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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.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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# 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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# pyenv
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.python-version
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# celery beat schedule file
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celerybeat-schedule
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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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# lp
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.lp
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# Git
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.git

‎.github/workflows/build.yml

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name: Build
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on:
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pull_request:
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branches:
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- develop
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- master
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push:
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branches:
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- develop
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- master
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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@v1
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- name: Build docker image, build package, install package
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run: docker build . --file build.Dockerfile --tag apulverizer/allagash:build
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- name: Run tests
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run: docker run --user=allagash -v $PWD/tests:/home/allagash/tests -v $PWD/src-doc:/home/allagash/src-doc apulverizer/allagash:build /bin/bash -c "py.test --nbval"
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- name: Build documentation
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run: docker run --user=allagash -v $PWD/src-doc:/home/allagash/src-doc apulverizer/allagash:build /bin/bash -c "sphinx-build -b html ./src-doc ./doc -a"

‎.github/workflows/deploy.yml

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name: Deploy to PyPi and Docker Hub
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on:
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release:
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types: [published]
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jobs:
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deploy:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v1
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with:
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ref: master
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- name: Build docker image, build package, install package
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run: docker build . --file build.Dockerfile -t apulverizer/allagash:build
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- name: Test package
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run: docker run --user=allagash -v $PWD/tests:/home/allagash/tests -v $PWD/src-doc:/home/allagash/src-doc
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apulverizer/allagash:build /bin/bash -c "py.test --nbval"
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- name: Upload to PyPi
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env:
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PYPI_USERNAME: ${{ secrets.PYPI_USERNAME }}
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PYPI_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: docker run --user=allagash -w /home/allagash/src apulverizer/allagash:build
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/bin/bash -c "twine upload -u $PYPI_USERNAME -p $PYPI_PASSWORD dist/*"
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- name: Build public docker image
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run: VERSION=$(docker run --user=allagash apulverizer/allagash:build /bin/bash -c "python src/setup.py --version")
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&& docker build . -t apulverizer/allagash:latest -t apulverizer/allagash:$VERSION
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- name: Test docker image
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run: docker run --user=allagash apulverizer/allagash:latest /bin/bash -c "py.test --nbval"
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- name: Deploy to docker hub
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env:
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DOCKER_HUB_USERNAME: ${{ secrets.DOCKER_HUB_USERNAME }}
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DOCKER_HUB_PASSWORD: ${{ secrets.DOCKER_HUB_PASSWORD }}
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run: VERSION=$(docker run --user=allagash apulverizer/allagash:build /bin/bash -c "python src/setup.py --version")
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&& echo $DOCKER_HUB_PASSWORD | docker login -u $DOCKER_HUB_USERNAME --password-stdin
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&& docker push apulverizer/allagash:$VERSION
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&& docker push apulverizer/allagash:latest

‎.gitignore

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# Sphinx documentation
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docs/_build/
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docs/
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# PyBuilder
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target/

‎Dockerfile

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# Set the base image to Ubuntu
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FROM continuumio/miniconda3:4.7.10
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# File Author / Maintainer
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MAINTAINER Aaron Pulver <[email protected]>
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# Switch to root for install
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USER root
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ENV HOME /home/allagash
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# Install COINOR CBC and GLPK
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# Create the user
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RUN apt-get update -y && apt-get install -y \
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--no-install-recommends \
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coinor-cbc \
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glpk-utils \
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&& rm -rf /var/lib/apt/lists/* \
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&& useradd --create-home --home-dir $HOME allagash \
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&& chmod -R u+rwx $HOME \
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&& chown -R allagash:allagash $HOME \
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&& chown -R allagash:allagash /opt/conda
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# switch back to user
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USER allagash
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WORKDIR $HOME
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# Configure conda env
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RUN conda create -n allagash python=3.7 \
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&& conda install --name allagash -y geopandas=0.4.1 jupyter=1.0.0 matplotlib=3.1.1 pytest=5.0.1 \
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&& /opt/conda/envs/allagash/bin/pip install pulp==1.6.10 nbval==0.9.2 \
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&& /opt/conda/envs/allagash/bin/pip install allagash --no-deps \
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&& conda clean -a -f -y
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COPY --chown=allagash:allagash src-doc/examples examples
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ENV PATH /opt/conda/envs/allagash/bin:$PATH

‎README.md

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# allagash
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A spatial optmization library
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# Allagash [![build status](https://github.com/apulverizer/allagash/workflows/build/badge.svg)](https://github.com/apulverizer/allagash/actions)
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A spatial optimization library for covering problems
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### Running Locally
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1. Clone the repo `git clone [email protected]:apulverizer/allagash.git`
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2. Create the conda environment `conda env create --file environment.yml`
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3. Activate the new environment `conda activate allagash`
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4. Install allagash locally `pip install -e ./src --no-deps`
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5. Install a solver that is supported by [Pulp](https://github.com/coin-or/pulp)
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1. [GLPK](https://www.gnu.org/software/glpk/)
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2. [COIN-OR CBC](https://github.com/coin-or/Cbc)
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3. [CPLEX](https://www.ibm.com/analytics/cplex-optimizer)
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4. [Gurobi](https://www.gurobi.com/)
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6. Launch jupyter notebook `jupyter notebook`
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You should now be able to run the example notebooks.
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### Installing with pip
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You can install Allagash using `pip` but may need to manually configure certain dependencies if using Windows.
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1. Run `pip install allagash`
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### Running Tests Locally
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1. Run tests `pytest --nbval`
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### Building Documentation
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1. From the repo directory run `sphinx-build -b html ./src-doc ./docs -a`
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This will deploy html documentation to the docs folder.
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### Running with Docker
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You can build the local docker image that includes Allagash, Python, Jupyter, GLPK, and COIN-OR CBC.
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1. Builder the docker image `docker build . -t apulverizer/allagash:latest`
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2. Launch Jupyter notebook `docker run -i -t --user=allagash -p 8888:8888 apulverizer/allagash:latest /bin/bash -c "jupyter notebook --ip='*' --port=8888 --no-browser"`
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You should now be able to run the example notebooks.
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You can test the notebooks as well by running `docker run --user=allagash apulverizer/allagash:latest /bin/bash -c "py.test --nbval"`
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If you'd like to mount a directory of local data/files into the container, you can add `-v <your-local-dir>:/home/allagash/<dir-name>` when running `docker run`
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### Running Tests with Docker
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You can build a docker container that will run the tests (mounted into the container)
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1. `docker build . --file build.Dockerfile --tag apulverizer/allagash:build`
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2. `docker run --user=allagash -v $PWD/tests:/home/allagash/tests -v $PWD/src-doc:/home/allagash/src-doc apulverizer/allagash:build /bin/bash -c "py.test --nbval"`

‎build.Dockerfile

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# Set the base image to Ubuntu
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FROM continuumio/miniconda3:4.7.10
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# File Author / Maintainer
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MAINTAINER Aaron Pulver <[email protected]>
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# Switch to root for install
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USER root
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ENV HOME /home/allagash
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# Install COINOR CBC and GLPK
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# Create the user
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RUN apt-get update -y && apt-get install -y \
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--no-install-recommends \
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coinor-cbc \
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glpk-utils \
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&& rm -rf /var/lib/apt/lists/* \
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&& useradd --create-home --home-dir $HOME allagash \
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&& chmod -R u+rwx $HOME \
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&& chown -R allagash:allagash $HOME \
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&& chown -R allagash:allagash /opt/conda
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# switch back to user
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USER allagash
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WORKDIR $HOME
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COPY --chown=allagash:allagash environment.yml environment.yml
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COPY --chown=allagash:allagash src src
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# Configure conda env
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RUN conda env create -f environment.yml \
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&& cd src \
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&& /opt/conda/envs/allagash/bin/python setup.py sdist bdist_wheel \
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&& /opt/conda/envs/allagash/bin/pip install allagash --no-deps --find-links dist \
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&& conda clean -a -f -y
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ENV PATH /opt/conda/envs/allagash/bin:$PATH

‎environment.yml

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name: allagash
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channels:
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- defaults
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dependencies:
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- geopandas=0.4.1
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- jupyter=1.0.0
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- pip>=19.1.1
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- pytest>=5.0.1
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- python=3.7.4
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- sphinx>=2.1
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- conda-forge::nbsphinx>=0.4.2
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- twine>=1.13.0
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- conda-forge::setuptools>=41.2.0
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- pip:
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- pulp==1.6.10
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- sphinx-rtd-theme~=0.4.3
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- nbval~=0.9.2

‎src-doc/_static/overview_example.jpg

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‎src-doc/allagash.coverage.rst

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allagash.coverage module
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========================
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.. automodule:: allagash.coverage
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Coverage
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--------
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.. autoclass:: allagash.coverage.Coverage
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:members:
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:inherited-members:

‎src-doc/allagash.problem.rst

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allagash.problem module
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=======================
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.. automodule:: allagash.problem
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Problem
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-------
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.. autoclass:: allagash.problem.Problem
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:members:
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:inherited-members:
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InfeasibleException
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-------------------
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.. autoclass:: allagash.problem.NotSolvedException
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:members:
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:inherited-members:
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NotSolvedException
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------------------
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.. autoclass:: allagash.problem.InfeasibleException
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:members:
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:inherited-members:
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UnboundedException
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------------------
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.. autoclass:: allagash.problem.UnboundedException
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:members:
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:inherited-members:
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UndefinedException
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------------------
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.. autoclass:: allagash.problem.UndefinedException
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:members:
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:inherited-members:

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