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‎.github/ISSUE_TEMPLATE/feature-request.yml

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name: Feature request
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description: Request a new feature
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labels: "enhancement"
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body:
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- type: markdown
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attributes:
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value: |
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Thank you for taking the time to let us know what gget is missing!
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- type: dropdown
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id: request-type
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attributes:
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label: Request type
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description: Are you requesting the extension of an existing module or a new module?
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options:
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- Extension of existing module
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- New module
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validations:
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required: true
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- type: textarea
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id: description
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attributes:
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label: Request description
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description: Please describe your request.
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placeholder: Include links to references/databases if applicable.
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validations:
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required: true
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- type: textarea
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id: command
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attributes:
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label: Example command
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description: Please provide an example command as you envision it.
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render: shell
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- type: textarea
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id: command-output
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attributes:
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label: Example return value
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description: Please describe what the above-mentioned command should return.
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placeholder: What is the most important information? Which format would be most useful?

‎.github/ISSUE_TEMPLATE/issue_report.yml

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name: Issue / Bug Report
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description: Create a report to help us improve
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body:
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- type: markdown
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attributes:
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value: |
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Thank you for taking the time to fill out this report and help us improve! :)
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- type: textarea
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id: what-happened
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attributes:
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label: What happened?
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description: Please provide a clear and concise description of what the issue is.
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validations:
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required: true
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- type: textarea
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id: version
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attributes:
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label: gget version
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description: Which version of gget are you using?
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placeholder: 0.27.2
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validations:
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required: true
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- type: dropdown
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id: os
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attributes:
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label: Operating System (OS)
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description: Which Operating System (OS) did you use?
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multiple: true
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options:
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- Linux
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- macOS
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- Windows
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- Other (please specify above)
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- Not applicable
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validations:
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required: true
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- type: dropdown
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id: interface
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attributes:
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label: User interface
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description: Did the problem occur when calling gget from the command-line or Python? (Select all that apply.)
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multiple: true
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options:
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- Command-line
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- Python
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- Google Colab (please include a shareable link above)
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- R (please specify Python wrapper above)
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- Not applicable
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validations:
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required: true
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- type: dropdown
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id: m1
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attributes:
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label: Are you using a computer with an Apple M1 chip?
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description: We are asking this because the M1 chip has been causing [problems](https://github.com/pachterlab/gget/issues/30) for some `gget alphafold` dependencies.
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options:
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- Not M1
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- M1
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- Not applicable
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validations:
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required: true
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- type: textarea
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id: command
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attributes:
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label: What is the exact command that was run?
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description: Please copy-paste the gget command that caused the problem.
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render: shell
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- type: textarea
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id: command-output
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attributes:
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label: Which output/error did you get?
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description: Please copy-paste the complete output/error returned by the command entered above.
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render: shell

‎.github/workflows/ci.yml

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name: CI
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on:
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schedule:
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- cron: "0 16 * * 1,4"
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push:
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paths:
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- 'gget/**'
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- 'tests/**'
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jobs:
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build:
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runs-on: ubuntu-22.04
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strategy:
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fail-fast: false
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matrix:
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python: ['3.8', '3.9', '3.10', '3.11', '3.12']
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os: ['ubuntu-22.04']
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name: Test on Python ${{ matrix.python }}
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steps:
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- name: Checkout branch
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uses: actions/checkout@main
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- name: Setup python
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uses: actions/setup-python@v1
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with:
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python-version: ${{ matrix.python }}
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architecture: x64
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- name: Install dependencies
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run: pip install -r requirements.txt && pip install -r dev-requirements.txt
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- name: Run tests
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run: coverage run -m pytest -ra -v tests && coverage report --omit=main.py,tests*

‎.github/workflows/deploy.yml

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name: Deploy
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on:
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push:
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branches:
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- main
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paths:
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- 'docs/**'
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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@v2
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with:
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fetch-depth: 0
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- name: Install mdbook
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run: |
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mkdir mdbook
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curl -sSL https://github.com/rust-lang/mdBook/releases/download/v0.4.34/mdbook-v0.4.34-x86_64-unknown-linux-gnu.tar.gz | tar -xz --directory=./mdbook
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echo `pwd`/mdbook >> $GITHUB_PATH
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- name: Deploy GitHub Pages
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run: |
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cd docs/
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mdbook build
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git worktree add gh-pages
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git config user.name "Deploy from CI"
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git config user.email ""
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cd gh-pages
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# Delete the ref to avoid keeping history.
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git update-ref -d refs/heads/gh-pages
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rm -rf *
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mv ../book/* .
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git add .
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git commit -m "Deploy $GITHUB_SHA to gh-pages"
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git push --force --set-upstream origin gh-pages

‎.github/workflows/traffic.yml

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name: Traffic
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on:
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schedule:
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# Runs every week
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- cron: "0 0 */7 * *"
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jobs:
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# This workflow stores repository traffic and clones past the default 2 week period
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traffic:
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# The type of runner that the job will run on
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runs-on: ubuntu-latest
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steps:
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# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
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- uses: actions/checkout@v2
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with:
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ref: "traffic"
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# Calculates traffic and clones and stores them in a CSV file
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# This workflow is based on https://github.com/marketplace/actions/repository-traffic
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- name: GitHub traffic
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uses: sangonzal/[email protected]
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env:
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TRAFFIC_ACTION_TOKEN: ${{ secrets.TRAFFIC_ACTION_TOKEN }}
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# Commits files to traffic branch
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- name: Commit changes
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uses: EndBug/add-and-commit@v4
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with:
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author_name: Laura Luebbert
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message: "GitHub traffic"
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add: "./traffic/*"
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ref: "traffic"

‎.gitignore

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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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# Mac OS file that stores custom attributes of its containing folder
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.DS_Store
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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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pip-wheel-metadata/
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share/python-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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/gget/elm_files/
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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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.nox/
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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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*.py,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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db.sqlite3-journal
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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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# IPython
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profile_default/
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ipython_config.py
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# pyenv
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.python-version
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# pipenv
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# According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
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# However, in case of collaboration, if having platform-specific dependencies or dependencies
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# having no cross-platform support, pipenv may install dependencies that don't work, or not
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# install all needed dependencies.
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#Pipfile.lock
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# PEP 582; used by e.g. github.com/David-OConnor/pyflow
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__pypackages__/
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# Celery stuff
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celerybeat-schedule
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celerybeat.pid
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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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.dmypy.json
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dmypy.json
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# Pyre type checker
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.pyre/
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# PyCharm
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/.idea/
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# mdbook documentation
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/docs/book/
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# Scratch directory
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/scratch/

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