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Merge branch 'dev' into ndefries/flusurv-new-columns
2 parents b18c898 + 2487f8b commit b8897d7

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‎.dockerignore‎

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‎.editorconfig‎

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[*]
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# Change these settings to your own preference
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indent_style = space
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indent_size = 4
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[*.md]
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trim_trailing_whitespace = false
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[*.yml]
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indent_size = 2

‎.git-blame-ignore-revs‎

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# Run repo through formatter
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c7831fc0fa1367d8517831996539ce0c6c48aa58
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# Run repo through formatter
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57908fc0099685a6cad6bfe6996182e6295411df

‎.github/workflows/ci.yaml‎

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‎.github/workflows/ci.yml‎

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name: ci
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on: push
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jobs:
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build:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.8]
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steps:
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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cache: "pip"
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- name: Install Dependencies
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run: |
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make install
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- name: Check Formatting
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run: |
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make lint_ruff
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- name: Check Linting
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run: |
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make lint_pylint
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- name: Check Types
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run: |
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make lint_mypy
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- name: Test
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run: |
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make test

‎.github/workflows/create_release.yml‎

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description: "Semantic Version Number (i.e., 5.5.0 or patch, minor, major, prepatch, preminor, premajor, prerelease)"
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required: true
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default: patch
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jobs:
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create_release:
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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ref: main
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ssh-key: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_SSH }}
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git fetch origin dev:dev
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git reset --hard dev
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
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- name: Change version number
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id: version
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# See this issue for explanation and testing:
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# https://github.com/cmu-delphi/delphi-epidata/pull/1473
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run: |
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python -m pip install bump2version
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echo -n "::set-output name=next_tag::"
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bump2version --list ${{ github.event.inputs.versionName }} | grep new_version | sed -r s,"^.*=",,
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if [[ ${{ github.event.inputs.versionName }} =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
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# use given version number
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NEXT_TAG="${{ github.event.inputs.versionName }}"
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elif [[ ${{ github.event.inputs.versionName }} =~ ^(major|minor|patch)$ ]]; then
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# calculate new version number based on given tag
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NEXT_TAG=$(bump2version --dry-run --list ${{ github.event.inputs.versionName }} | grep ^new_version | sed -r s,"^.*=",,)
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else
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echo "\nInvalid version name: ${{ github.event.inputs.versionName }}"
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exit 1
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fi
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# apply given or calculated version number
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bump2version --new-version $NEXT_TAG _ignored_arg_
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# save version number for later
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echo "next_tag=$NEXT_TAG" >> $GITHUB_OUTPUT
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- name: Create pull request into main
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uses: peter-evans/create-pull-request@v3
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uses: peter-evans/create-pull-request@v6
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with:
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branch: release/${{ steps.version.outputs.next_tag }}
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commit-message: "chore: release ${{ steps.version.outputs.next_tag }}"
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base: main
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title: Release ${{ steps.version.outputs.next_tag }}
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labels: chore
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# reviewers:
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assignees: melange396
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assignees: dshemetov
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body: |
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Releasing ${{ steps.version.outputs.next_tag }}.

‎.github/workflows/documentation.yml‎

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name: documentation
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on:
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push:
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branches:
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- main
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permissions:
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contents: write
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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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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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DELPHI_EPIDATA_KEY: ${{ secrets.DELPHI_GITHUB_ACTIONS_EPIDATA_API_KEY }}
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steps:
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- uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- uses: actions/setup-python@v5
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- name: Install dependencies
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run: |
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python3.8 -m venv .venv
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.venv/bin/python -m pip install --upgrade pip
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.venv/bin/pip install -e ".[dev]"
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- uses: siacodelabs/setup-pandoc@v1
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- name: Sphinx build
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run: |
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.venv/bin/sphinx-build -b html docs docs/_build
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v3
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with:
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publish_branch: gh-pages
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: docs/_build/
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force_orphan: true

‎.github/workflows/release_helper.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
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- name: Extract version
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id: extract_version
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run: |
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python -m pip install bump2version
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echo -n "::set-output name=version::"
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bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,
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NEXT_TAG=$(bump2version --dry-run --list patch | grep ^current_version | sed -r s,"^.*=",,)
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echo "version=$NEXT_TAG" >> $GITHUB_OUTPUT
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- name: Create Release
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id: create_release
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uses: release-drafter/release-drafter@v5
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uses: release-drafter/release-drafter@v6
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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with:
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upload_url: ${{ steps.create_release.outputs.upload_url }}
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tag_name: ${{ steps.create_release.outputs.tag_name }}
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release_package:
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needs: create_release
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lint:
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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- name: Set up Python 3.8
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uses: actions/setup-python@v2
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
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- name: Install build dependencies
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run: |
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python -m pip install --upgrade pip
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pip install --use-feature=2020-resolver -r requirements.txt -r requirements-dev.txt
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make install
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- name: Linting
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run: |
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. venv/bin/activate
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inv lint
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make lint
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- name: Testing
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run: |
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. venv/bin/activate
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inv test
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- name: Create release
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make test
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build:
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needs: [create_release, lint]
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v4
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- name: Set up Python 3.8
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uses: actions/setup-python@v5
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with:
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python-version: 3.8
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- name: Install build dependencies
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run: |
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make install
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- name: Build
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run: |
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inv dist
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- uses: actions/upload-artifact@v2
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make dist
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release_package:
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needs: [create_release, lint]
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runs-on: ubuntu-latest
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# TODO: Make sure this works, copied from best practices here
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# https://github.com/pypa/gh-action-pypi-publish/tree/release/v1/?tab=readme-ov-file#trusted-publishing
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environment:
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name: pypi
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url: https://pypi.org/p/epidatpy
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permissions:
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id-token: write
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steps:
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- uses: actions/upload-artifact@v4
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with:
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name: epidatpy
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path: dist/*.tar.gz
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- name: Upload Release Asset
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uses: AButler/upload-release-assets@v2.0
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uses: AButler/upload-release-assets@v3.0
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with:
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files: "dist/*.tar.gz"
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repo-token: ${{ secrets.GITHUB_TOKEN }}
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release-tag: ${{ needs.create_release.outputs.tag_name }}
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- name: Publish a Python distribution to PyPI
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.DELPHI_PYPI_PROD_TOKEN }}
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skip_existing: true
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skip-existing: true
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# repository_url: https://test.pypi.org/legacy/
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sync_dev:
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needs: correct_repository
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runs-on: ubuntu-latest
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steps:
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- name: Check out code
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uses: actions/checkout@v2
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uses: actions/checkout@v4
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with:
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ref: dev
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ssh-key: ${{ secrets.CMU_DELPHI_DEPLOY_MACHINE_SSH }}
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git fetch origin main:main
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git reset --hard main
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- name: Create pull request into dev
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uses: peter-evans/create-pull-request@v3
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uses: peter-evans/create-pull-request@v6
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with:
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branch: bot/sync-main-dev
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commit-message: "chore: sync main-dev"
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base: dev
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title: "chore: sync main->dev"
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labels: chore
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# reviewers:
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assignees: melange396
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# reviewers:
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assignees: dshemetov
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body: |
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Syncing Main->Dev.

‎.gitignore‎

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.mypy_cache
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*.pyc
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__pycache__
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/venv
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/docs/_build
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.coverage
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.pytest_cache
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.DS_Store
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*.egg-info
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/dist
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.DS_Store
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dist/
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build/
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docs/_build
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.venv/

‎.pylintrc‎

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