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Merge pull request #45 from softwareunderground/t21-main
Part I of the T21 hackathon - versioning and autodeploy to PyPI/conda-forge
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‎.github/workflows/docs.yml‎

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name: docs
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the master branch
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push:
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branches:
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- main
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release:
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types:
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- published
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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docs:
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runs-on: ubuntu-latest
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env:
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DISPLAY: ':99.0'
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PYVISTA_OFF_SCREEN: 'True'
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ALLOW_PLOTTING: true
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SHELLOPTS: 'errexit:pipefail'
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steps:
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- uses: actions/checkout@v2
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- name: Setup Headless Display
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run: |
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sudo apt-get install libgl1-mesa-glx
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sudo apt-get install -y xvfb
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Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
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sleep 3
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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'
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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_dev.txt
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pip install -e .
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- name: Generate Sphinx Docs
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working-directory: docs/
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run: make html
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- name: Publish generated content to GitHub Pages
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uses: tsunematsu21/[email protected]
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with:
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dir: docs/build/html
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branch: gh-pages
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token: ${{ secrets.ACCESS_TOKEN }}

‎.github/workflows/main.yml‎

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# This is a basic workflow to help you get started with Actions
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name: linux
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name: subsurface CI
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# Controls when the action will run.
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# Controls when the action will run.
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on:
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# Triggers the workflow on push or pull request events but only for the master branch
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push:
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branches: [ main, mig_dev, main_candidate, t21-main ]
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pull_request:
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branches: [ main, t21-main ]
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release:
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types:
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- published
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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# A workflow run is made up of one or more jobs that can run sequentially or in parallel
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jobs:
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# This workflow contains a single job called "build"
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pytest:
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runs-on: ubuntu-latest
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env:
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DISPLAY: ':99.0'
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PYVISTA_OFF_SCREEN: 'True'
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ALLOW_PLOTTING: true
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SHELLOPTS: 'errexit:pipefail'
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# The type of runner that the job will run on
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steps:
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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'
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- uses: actions/checkout@v2
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- name: Setup Headless Display
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run: |
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sudo apt-get install libgl1-mesa-glx
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sudo apt-get install -y xvfb
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Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
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sleep 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 -r requirements.txt
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pip install -r optional_requirements.txt
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- name: Test with pytest
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run: |
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pip install pytest
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pip install pytest-cov
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pytest
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docs:
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runs-on: ubuntu-latest
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name: ${{ matrix.case.os }} py${{ matrix.case.python-version }} ${{ matrix.case.name }}
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runs-on: ${{ matrix.case.os }}-latest
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu, ] # macos, windows] # Only Linux currently.
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case:
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- python-version: 3.8
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name: basic
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os: ubuntu
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# - python-version: 3.9
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# name: basic
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# os: ubuntu
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env:
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DISPLAY: ':99.0'
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PYVISTA_OFF_SCREEN: 'True'
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ALLOW_PLOTTING: true
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SHELLOPTS: 'errexit:pipefail'
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OS: ${{ matrix.case.os }}
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PYTHON: ${{ matrix.case.python-version }}
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steps:
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# Cancel any previous run of the test job; [pin v0.8.0 (2021-02-13)]
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- name: Cancel Previous Runs
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uses: styfle/cancel-workflow-action@3d86a7cc43670094ac248017207be0295edbc31d
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with:
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access_token: ${{ github.token }}
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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: ${{ matrix.case.python-version }}
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- uses: actions/checkout@v2
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- name: Setup Headless Display
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run: |
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Xvfb :99 -screen 0 1024x768x24 > /dev/null 2>&1 &
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sleep 3
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- name: Set up Python
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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_dev.txt
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- name: Test with pytest
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run: pytest --cov=subsurface
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# # # # DEPLOY # # #
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deploy:
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needs: pytest
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name: Deploy to PyPI
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runs-on: ubuntu-latest
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# Only from the origin repository, not forks; only main and tags.
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if: github.repository_owner == 'softwareunderground' && (github.ref == 'refs/heads/main' || startsWith(github.ref, 'refs/tags/'))
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE
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- name: Checkout
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uses: actions/checkout@v2
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with:
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# Need to fetch more than the last commit so that setuptools_scm can
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# create the correct version string. If the number of commits since
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# the last release is greater than this, the version will still be
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# wrong. Increase if necessary.
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fetch-depth: 100
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# The GitHub token is preserved by default but this job doesn't need
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# to be able to push to GitHub.
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persist-credentials: false
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# Need the tags so that setuptools_scm can form a valid version number
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- name: Fetch git tags
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run: git fetch origin 'refs/tags/*:refs/tags/*'
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- name: Setup Python
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uses: actions/setup-python@v2
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with:
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python-version: '3.8'
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python-version: "3.8"
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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 wheel setuptools_scm
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pip install -r requirements.txt
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pip install -r optional_requirements.txt
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pip install -r dev_requirements.txt
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pip install -e .
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- name: Generate Sphinx Docs
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working-directory: docs/
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run: make html
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- name: Publish generated content to GitHub Pages
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uses: tsunematsu21/[email protected]
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- name: Build source and wheel distributions
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if: github.ref == 'refs/heads/main'
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run: |
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# Change setuptools-scm local_scheme to "no-local-version" so the
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# local part of the version isn't included, making the version string
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# compatible with Test PyPI.
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sed --in-place "s/'root'/'local_scheme':'no-local-version','root'/g" setup.py
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- name: Build source and wheel distributions
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run: |
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# Build source and wheel packages
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python setup.py sdist
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python setup.py bdist_wheel
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echo ""
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echo "Generated files:"
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ls -lh dist/
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- name: Publish to Test PyPI
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if: success()
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# Hash corresponds to v1.4.1
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uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
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with:
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dir: docs/build/html
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branch: gh-pages
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token: ${{ secrets.ACCESS_TOKEN }}
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user: __token__
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password: ${{ secrets.TEST_PYPI_PASSWORD }}
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repository_url: https://test.pypi.org/legacy/
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# Allow existing releases on test PyPI without errors.
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# NOT TO BE USED in PyPI!
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skip_existing: true
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- name: Publish to PyPI
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# Only for releases
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if: success() && github.event_name == 'release'
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# Hash corresponds to v1.4.1
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uses: pypa/gh-action-pypi-publish@54b39fb9371c0b3a6f9f14bb8a67394defc7a806
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with:
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user: __token__
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password: ${{ secrets.PYPI_PASSWORD }}

‎.gitignore‎

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subsurface/_version.py
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# vscode
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.vscode/*
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!/docs/source/_templates/
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/data/
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.idea
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.idea

‎DevelopersGuide.md‎

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Before a release.
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NOTES
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-----
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TODO: Re-work and automate this. Steps that should be necessary:
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**Important.** Due to the use of ``setuptools_scm``, everything is by default
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added to the wheel on PyPI. Documents that should not be in a release have to
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be excluded by adding it to the ``MANIFEST.in``.
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Making a release
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----------------
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# set version number in setup.py, also in the config file of the documentation and init of the package
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- [ ] setup.py
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- [ ] subsurface._version
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> Note: in the config for sphinx~ this is taken from subsurface._version
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Github release
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--------------
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# add new tag
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$ git tag X.X -m "Add X.X tag for PyPI"
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# push git tag
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$ git push --tags origin master
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PyPi release
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------------
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# First create the dist
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python3 setup.py sdist bdist_wheel
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# Second upload the distributions
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twine upload dist/*
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Create a release on GitHub. This will run the tests, and then automatically
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deploy it to PyPI, from where conda-forge will pick it up as well.
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If everything works fine it should be available from PyPI within minutes after
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the tests passed, and within an hour or two from conda-forge.
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### Type of commits:

‎MANIFEST.in‎

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prune docs
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prune examples
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prune tests
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prune .github
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exclude CONTRIBUTING.md
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exclude DevelopersGuide.md
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exclude MANIFEST.in
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exclude requirements.txt
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exclude requirements_dev.txt
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exclude requirements_opt.txt
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exclude .gitignore

‎README.md‎

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**Human**
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\=================================/'
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\===============================/ ' \
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\==========geo_format=========/ ' \ -> Additional context/meta information about the data
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\===========================/' ' \
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\=======geo_object========/ ' ' \ -> Elements that represent some
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\=======================/ ' ' / geological concept. E.g: faults, seismic
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\=====================/' ' ' ' /
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\======element======/' ' ' ' / -> type of geometric object: PointSet,
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\=================/' ' ' ' / TriSurf, LineSet, Tetramesh
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\=primary_struct/ '' / - > Set of arrays that define a geometric object:
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\=============/ ' ' / e.g. *StructuredData* **UnstructuredData**
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\============/'' /
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\DF/Xarray/ ' '/ -> Label numpy.arrays
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\=======/'' /
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\array/' / -> Memory allocation
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\===/ /
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\=//
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'
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\‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾‾/\
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\= = = = = = = = = = = = = = /. \ -> Additional context/meta information about the data
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\= = = = geo_format= = = = /. . \
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\= = = = = = = = = = = = /. . . \ -> Elements that represent some
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\= = = geo_object= = = /. . . . \ geological concept. E.g: faults, seismic
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\= = = = = = = = = = /. . . . ./
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\= = element = = = /. . . . / -> type of geometric object: PointSet,
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\= = = = = = = = /. . . ./ TriSurf, LineSet, Tetramesh
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\primary_struct/. . . / -> Set of arrays that define a geometric object:
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\= = = = = = /. . ./ e.g. *StructuredData* **UnstructuredData**
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\DF/Xarray /. . / -> Label numpy.arrays
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\= = = = /. ./
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\array /. / -> Memory allocation
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\= = /./
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\= //
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\/
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**Computer**
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## Documentation (WIP)
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An early version of the documentation can be found here:
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https://softwareunderground.github.io/subsurface/
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## Installation
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`pip install subsurface`
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#### Original statement
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The goal of this project is to support other subsurface geoscience and
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engineering projects with a set of classes for common subsurface data entities,
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such as seismic and GPR datasets, log curves, and so on. The current plan is to
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The goal of this project is to support other subsurface geoscience and
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engineering projects with a set of classes for common subsurface data entities,
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such as seismic and GPR datasets, log curves, and so on. The current plan is to
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use `xarray` under the hood, with `pint` for units support and `cartopy` for CRS and map support.
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It's early days, everything might change. Help us figure it out!

‎dev_requirements.txt‎

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‎docs/logos/subsurface_place_holder.png‎

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