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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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- '!tests/pytest_results_py*.txt'
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workflow_dispatch:
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permissions:
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contents: write
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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: ['3.11', '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@v4
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with:
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fetch-depth: 0
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- name: Setup python
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python }}
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- name: Install dependencies
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run: pip install -r requirements.txt && pip install -r dev-requirements.txt
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# Always run tests on push
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- name: Run tests
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if: github.event_name == 'push'
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run: pytest -ra -v --tb=long --maxfail=5 --durations=10 --cov=gget --cov-report=term-missing tests
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# On schedule/manual, run tests AND save output (and capture real pytest exit code)
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- name: Run tests (save output to file)
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id: pytest_saved
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if: github.event_name == 'schedule' || github.event_name == 'workflow_dispatch'
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continue-on-error: true
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shell: bash
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run: |
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set -o pipefail
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OUT="tests/pytest_results_py${{ matrix.python }}.txt"
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echo "Pytest results (Python ${{ matrix.python }}) - $(date -u +"%Y-%m-%dT%H:%M:%SZ")" > "$OUT"
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echo "" >> "$OUT"
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pytest -ra -v --tb=long --maxfail=5 --durations=10 \
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--cov=gget --cov-report=term-missing tests 2>&1 | tee -a "$OUT"
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code=${PIPESTATUS[0]}
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echo "exit_code=$code" >> "$GITHUB_OUTPUT"
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echo "pytest exit code: $code"
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- name: Upload pytest results artifact
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# create and commit results only for one python version to avoid matrix push races
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if: always() && matrix.python == '3.12' && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch')
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uses: actions/upload-artifact@v4
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with:
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name: pytest-results-py${{ matrix.python }}
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path: tests/pytest_results_py${{ matrix.python }}.txt
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- name: Commit and push pytest results
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# create and commit results only for one python version to avoid matrix push races
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if: always() && matrix.python == '3.12' && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch')
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shell: bash
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run: |
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set -euo pipefail
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git config user.name "github-actions[bot]"
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git config user.email "github-actions[bot]@users.noreply.github.com"
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git add -A tests/pytest_results_py*.txt
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if git diff --cached --quiet; then
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echo "No changes to commit."
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exit 0
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fi
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git commit -m "CI: update pytest results"
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# Keep branch up-to-date (handles concurrent updates) + retry push
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for attempt in 1 2 3 4 5; do
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echo "Push attempt $attempt..."
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# autostash prevents "cannot rebase: You have unstaged changes" if anything is modified locally
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git pull --rebase --autostash origin main || true
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if git push origin main; then
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exit 0
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fi
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sleep $((attempt * 5))
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done
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echo "Push failed after retries."
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exit 1
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# Make schedule/manual runs still fail if pytest failed
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- name: Fail job if pytest failed
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if: always() && (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch')
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shell: bash
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run: |
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code="${{ steps.pytest_saved.outputs.exit_code }}"
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if [ -n "$code" ] && [ "$code" != "0" ]; then
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exit "$code"
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fi

‎.github/workflows/deploy.yml‎

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name: Deploy Website
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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/gdrive_backup.yml‎

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name: Backup gget Repo on Google Drive
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on:
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schedule:
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- cron: "0 0 1 * *" # Runs at midnight on the 1st of every month
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workflow_dispatch:
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jobs:
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backup:
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runs-on: ubuntu-latest
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steps:
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- name: Set backup filename
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run: echo "BACKUP_FILE=$(echo \"${{ github.repository }}-backup-$(date +%F).tar.gz\" | sed 's/\//-/g')" >> $GITHUB_ENV
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- name: Clone the repository (mirror all branches and history)
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run: |
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git clone --mirror https://github.com/${{ github.repository }}.git repo-mirror
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- name: Create backup archive
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run: |
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tar -czvf "$BACKUP_FILE" repo-mirror
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- name: Check if backup archive exists
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run: |
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if [ -f "$BACKUP_FILE" ]; then
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echo "Backup file found: $BACKUP_FILE"
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ls -lh "$BACKUP_FILE"
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else
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echo "Backup file not found!"
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exit 1
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fi
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- name: Create credentials.json
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id: create-json
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uses: jsdaniell/create-json@v1.2.3
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with:
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name: "credentials.json"
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json: ${{ secrets.GDRIVE_BACKUP_CREDENTIALS }}
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- name: Install rclone
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run: |
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curl https://rclone.org/install.sh | sudo bash
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- name: Configure rclone
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run: |
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mkdir -p ~/.config/rclone/
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rclone config create gdrive drive \
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--config ~/.config/rclone/rclone.conf \
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service_account_file credentials.json || exit 1
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- name: Upload archive to Google Drive
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run: |
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rclone copy "$BACKUP_FILE" gdrive:/GitHub_backups --drive-shared-with-me --verbose || exit 1
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- name: Clean up
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run: |
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rm -rf repo-mirror
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rm -f "$BACKUP_FILE"
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rm -f credentials.json

‎.github/workflows/plot_traffic.yml‎

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name: Plot Repo Traffic
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on:
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# Trigger on pushes to traffic branch
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push:
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branches:
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- traffic
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# Allow manual trigger
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workflow_dispatch:
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# Trigger when Traffic workflow finishes
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workflow_run:
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workflows: ["Traffic"]
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types:
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- completed
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- name: Check out traffic branch
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uses: actions/checkout@v4
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with:
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ref: traffic
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- name: Setup Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.8'
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- name: Configure pip caching
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uses: actions/cache@v4
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with:
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path: ~/.cache/pip
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key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
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restore-keys: |
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${{ runner.os }}-pip-
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- name: Install Python dependencies
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run: |
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python -m pip install -r requirements.txt
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- name: Execute Jupyter notebook
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run: jupyter nbconvert --to 'html' --execute gget_traffic.ipynb
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- name: Commit and push new data to traffic branch
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run: |
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git config user.name "Automated"
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git config user.email "actions@users.noreply.github.com"
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git add plots/*
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if ! git diff --cached --quiet; then
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timestamp=$(date -u)
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git commit -m "Latest data: ${timestamp}"
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git push origin traffic
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else
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echo "No changes to commit"
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fi
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- name: Clean up
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run: rm gget_traffic.html

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