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Merge pull request #154 from boutproject/packaging-update
Packaging update, auto-publish to PyPi
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‎.git_archival.txt‎

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ref-names: $Format:%D$

‎.gitattributes‎

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.git_archival.txt export-subst

‎.github/workflows/master.yml‎

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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
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# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
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#
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# This workflow should be an exact duplicate of 'Python package' in
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# pythonpackage.yml, except that it only runs on pushes to master. This is done
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# so that we can refer to this workflow specifically in the status badge in
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# README.md
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name: master
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on:
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push:
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branches:
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- master
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jobs:
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pytest:
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runs-on: ubuntu-latest
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if: always()
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strategy:
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matrix:
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python-version: [3.6, 3.7, 3.8]
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pip-packages:
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- "setuptools pip pytest pytest-cov coverage codecov boutdata xarray!=0.14.0 numpy>=1.16.0"
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- "setuptools pip pytest pytest-cov coverage codecov boutdata xarray==0.16.0 dask==2.10.0 numpy==1.16.0 natsort==5.5.0 matplotlib==3.1.1 animatplot==0.4.1 netcdf4==1.4.2 Pillow==6.1.0 fsspec" # test with oldest supported version of packages. Note, using numpy==1.16.0 as a workaround for some weird fails on Travis, in principle we should work with numpy>=1.13.3. We should not need to install fsspec explicitly, but at the moment are getting import errors in the tests due to fsspec not being present - should remove in future, probably when dask version is increased.
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fail-fast: false
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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sudo apt-get install libhdf5-dev libnetcdf-dev
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python -m pip install --upgrade pip
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pip install --upgrade ${{ matrix.pip-packages }}
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pip install -e .
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- name: Test with pytest
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run: |
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pip install pytest
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pytest -v --long --cov
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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fail_ci_if_error: true
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# Need to tidy up the things that flake8 finds before we activate this
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#flake8:
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# runs-on: ubuntu-latest
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# if: always()
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# steps:
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# - uses: actions/checkout@v2
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# - name: Set up Python
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# uses: actions/setup-python@v1
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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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# - name: Lint with flake8
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# run: |
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# pip install flake8
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# flake8
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black:
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runs-on: ubuntu-latest
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if: always()
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v1
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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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- name: Check formatting with black
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run: |
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pip install black
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black --check .

‎.github/workflows/pythonpackage.yml‎

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name: Python package
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on:
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[push, pull_request]
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push:
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branches-ignore:
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- master
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pull_request:
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jobs:
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pytest:
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sudo apt-get install libhdf5-dev libnetcdf-dev
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python -m pip install --upgrade pip
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pip install --upgrade ${{ matrix.pip-packages }}
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pip install -r requirements.txt
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pip install -e .
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- name: Test with pytest
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run: |
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pip install pytest
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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 -r requirements.txt
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# - name: Lint with flake8
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# run: |
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# pip install flake8

‎.github/workflows/pythonpublish.yml‎

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# This workflows will upload a Python Package using Twine when a release is created
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# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
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name: Upload Python Package
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on:
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release:
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types: [created]
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jobs:
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pytest:
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runs-on: ubuntu-latest
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if: always()
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strategy:
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matrix:
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python-version: [3.6, 3.7, 3.8]
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pip-packages:
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- "setuptools pip pytest pytest-cov coverage codecov boutdata xarray!=0.14.0 numpy>=1.16.0"
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- "setuptools pip pytest pytest-cov coverage codecov boutdata xarray==0.16.0 dask==2.10.0 numpy==1.16.0 natsort==5.5.0 matplotlib==3.1.1 animatplot==0.4.1 netcdf4==1.4.2 Pillow==6.1.0 fsspec" # test with oldest supported version of packages. Note, using numpy==1.16.0 as a workaround for some weird fails on Travis, in principle we should work with numpy>=1.13.3. We should not need to install fsspec explicitly, but at the moment are getting import errors in the tests due to fsspec not being present - should remove in future, probably when dask version is increased.
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fail-fast: true
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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sudo apt-get install libhdf5-dev libnetcdf-dev
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python -m pip install --upgrade pip
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pip install --upgrade ${{ matrix.pip-packages }}
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pip install -e .
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- name: Test with pytest
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run: |
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pip install pytest
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pytest -v --long --cov
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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fail_ci_if_error: true
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# Need to tidy up the things that flake8 finds before we activate this
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#flake8:
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# runs-on: ubuntu-latest
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# if: always()
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# steps:
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# - uses: actions/checkout@v2
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# - name: Set up Python
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# uses: actions/setup-python@v1
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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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# - name: Lint with flake8
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# run: |
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# pip install flake8
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# flake8
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black:
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runs-on: ubuntu-latest
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if: always()
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v1
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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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- name: Check formatting with black
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run: |
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pip install black
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black --check .
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deploy:
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runs-on: ubuntu-latest
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needs: [pytest, black]
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steps:
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- uses: actions/checkout@v2
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- name: Set up Python
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uses: actions/setup-python@v1
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with:
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python-version: '3.x'
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- name: Install dependencies
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run: |
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sudo apt-get install libhdf5-dev libnetcdf-dev
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python -m pip install --upgrade pip
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pip install --upgrade setuptools wheel twine
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pip install -e .
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- name: Build and publish
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env:
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TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
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TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
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run: |
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git fetch --tags --unshallow
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python setup.py sdist bdist_wheel
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twine upload dist/*

‎LICENSE‎

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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright [yyyy] [name of copyright owner]
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Copyright 2020 The contributors to the xBOUT project.
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xBOUT provides an interface for collecting the output data from a BOUT++
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simulation into an xarray dataset in an efficient and scalable way, as well
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as accessor methods for common BOUT++ analysis and plotting tasks.
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.

‎README.md‎

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# xBOUT
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[![Build Status](https://travis-ci.org/boutproject/xBOUT.svg?branch=master)](https://travis-ci.org/boutproject/xBOUT.svg?branch=master)
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[![Build Status](https://github.com/boutproject/xBOUT/workflows/master/badge.svg)](https://github.com/boutproject/xBOUT/actions)
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[![codecov](https://codecov.io/gh/boutproject/xBOUT/branch/master/graph/badge.svg)](https://codecov.io/gh/boutproject/xBOUT)
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Documentation: https://xbout.readthedocs.io
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### Installation
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xBOUT is not currently on pip or conda. Therefore to install xBOUT on
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your system you must first clone the repository using:
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```bash
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git clone [email protected]:boutproject/xBOUT.git
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```
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or
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With pip:
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```bash
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git clone https://github.com/boutproject/xBOUT.git
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pip install --user xbout
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```
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Once cloned navigate to the `xBOUT` directory and run the following command:
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With conda:
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```bash
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pip3 install --user ./
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```
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or
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```bash
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python3 setup.py install
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conda install xbout
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```
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You can run the tests by navigating to the `/xBOUT/` directory and
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entering `pytest`. You can also test your installation of `xBOUT` by
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running `pytest --pyargs xbout`.
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You can test your installation of `xBOUT` by running `pytest --pyargs xbout`.
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xBOUT requires other python packages, which will be installed when you
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this repository too.
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### Developers
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Clone the repository with:
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```bash
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git clone [email protected]:boutproject/xBOUT.git
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```
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The recommended way to work with `xBOUT` from the git repo is to do an editable
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install with pip. Run this command from the `xBOUT/` directory:
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```bash
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pip install --user -e .
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```
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which will also install all the required dependencies. Dependencies can also be
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installed using pip
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```bash
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pip install --user -r requirements.txt
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```
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or conda
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```
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conda install --file requirements.txt
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```
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It is possible to use `xBOUT` by adding the `xBOUT/` directory to your
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`$PYTHONPATH`.
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Test by running `pytest` in the `xBOUT/` directory.
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### Development plan
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Things which definitely need to be included (see the 1.0 milestone):

‎pyproject.toml‎

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[build-system]
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requires = ["setuptools >= 42", "wheel", "setuptools_scm[toml]>=3.4", "setuptools_scm_git_archive"]
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build-backend = "setuptools.build_meta"
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[tool.setuptools_scm]
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write_to = "xbout/_version.py"

‎requirements.txt‎

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xarray >= 0.16.0
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dask[array] >= 2.10.0
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natsort >= 5.5.0
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matplotlib >= 3.1.1
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animatplot >= 0.4.1
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netcdf4 >= 1.4.0
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Pillow >= 6.1.0
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xarray>=0.16.0
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boutdata>=0.1.2
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dask[array]>=2.10.0
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natsort>=5.5.0
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matplotlib>=3.1.1
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animatplot>=0.4.1
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netcdf4>=1.4.0
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Pillow>=6.1.0
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# Not required for Python>=3.8, but included because conda does not support
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# conditional expressions in --file arguments.
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# This file should only be used by developers, so the odd extra package is not
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# a big issue. If it is not wanted, you can install these dependencies by hand.
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importlib-metadata
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# for version number in non-installed package:
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setuptools>=42
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setuptools_scm[toml]>=3.4
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# for tests
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pytest>=3.3.0

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