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update workflow
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‎.github/workflows/style.yml‎

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name: Style
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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workflow_dispatch:
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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env:
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PYTHON_VERSION: "3.10"
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jobs:
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linter-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Set up Python ${{ env.PYTHON_VERSION }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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cache: pip
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- name: Install Python deps
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shell: bash
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run: |
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python -m pip install --upgrade pip
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python -m pip install black ruff
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python -m pip install -e .
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- name: Black Check
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shell: bash
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run: black . --diff --color --check
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# - name: ruff Check
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# shell: bash
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# run: ruff check src

‎.github/workflows/test-ci.yml‎

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name: CI
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name: CI-CD
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on:
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push:
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branches: [ "main" ]
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pull_request:
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branches: [ "main" ]
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workflow_dispatch:
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jobs:
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linter-check:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Set up Python "3.10"
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uses: actions/setup-python@v4
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with:
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python-version: "3.10"
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- name: Black setup
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shell: bash
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run: pip install black ruff mypy
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- name: Black Check
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shell: bash
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run: black . --diff --color --check
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test-cpu:
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test:
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runs-on: ubuntu-latest
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needs: linter-check
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strategy:
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fail-fast: true
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matrix:
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python-version: ["3.12", "3.10"]
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python-version: [3.11, 3.12] # Specify the desired Python versions
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steps:
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- uses: actions/checkout@v3
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v4
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install Dependencies
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shell: bash
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run: |
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python --version
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python -m pip install --upgrade pip
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python -m pip install .[test]
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- name: Run Tests
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shell: bash
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run: |
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export COVERAGE_FILE=coverage_${{ matrix.python-version }}
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pytest -n auto --cov --disable-pytest-warnings --cov-branch --cov-report=term
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- name: Upload coverage
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if: success()
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uses: actions/upload-artifact@v4
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with:
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name: coverage_${{ matrix.python-version }}
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path: coverage_${{ matrix.python-version }}
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get-commit-message:
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runs-on: ubuntu-latest
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outputs:
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message: ${{ steps.get_commit_message.outputs.message }}
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steps:
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- uses: actions/checkout@v3
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with:
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ref: ${{ github.event.pull_request.head.sha }}
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- name: Get commit message
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id: get_commit_message
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run: |
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COMMIT_MESSAGE=$(git log -1 --pretty=%B)
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echo "Commit message $COMMIT_MESSAGE"
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echo "::set-output name=message::$COMMIT_MESSAGE"
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coverage:
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runs-on: ubuntu-latest
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needs: [test-cpu, get-commit-message]
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if: ${{ always() }}
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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- name: Collect Coverages
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uses: actions/download-artifact@v4
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with:
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path: coverage_data
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pattern: coverage_*
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merge-multiple: true
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- name: Set up Python 3.10
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uses: actions/setup-python@v4
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with:
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python-version: ${{ env.PYTHON_VERSION }}
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- name: add the coverage tool
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shell: bash
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run: |
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python -m pip install --upgrade pip
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python -m pip install coverage[toml]
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python -m pip install -e .
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- name: Combine coverage
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run: |
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export COVERAGE_FILE=coverage_combined
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coverage combine -a coverage_data/*
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- name: Checkout code
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uses: actions/checkout@v4
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- name: Upload Combined coverage
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uses: actions/upload-artifact@v4
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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name: coverage_combined
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path: coverage_combined
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- name: Reports
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run: |
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export COVERAGE_FILE=coverage_combined
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coverage xml
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coverage report
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echo COVERAGE_PERC=$(coverage report | tail -n 1 | grep -oE [0-9\.]*?% | cut -d '%' -f1) >> $GITHUB_ENV
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python-version: ${{ matrix.python-version }}
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- name: Create a Coverage Badge
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if: ${{github.event_name == 'push'}}
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- name: Install dependencies
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run: |
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wget https://img.shields.io/badge/coverage-${{env.COVERAGE_PERC}}%25-green -O coverage_badge.svg
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pip install .[test]
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- name: Upload badge as artifact
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if: ${{github.event_name == 'push'}}
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uses: actions/upload-artifact@v4
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- name: Run tests
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run: pytest --cov --cov-report=xml tests
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- name: Upload coverage reports to Codecov
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uses: codecov/codecov-action@v4.0.1
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with:
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name: coverage_badge
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path: coverage_badge.svg
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token: ${{ secrets.CODECOV_TOKEN }}
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slug: INFN-MRI/torchsim
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BuildDocs:
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name: Build API Documentation
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runs-on: ubuntu-latest
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needs: get-commit-message
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if: ${{ contains(needs.get-commit-message.outputs.message, '!docs_build') || github.ref == 'refs/heads/main' }}
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docs:
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runs-on: ubuntu-20.04
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needs: test
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steps:
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- name: Checkout
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Get history and tags for SCM versioning to work
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run: |
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git fetch --prune --unshallow
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git fetch --depth=1 origin +refs/tags/*:refs/tags/*
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- name: Set up Python
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uses: actions/setup-python@v4
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uses: actions/setup-python@v5
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with:
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python-version: "3.10"
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- name: Restore cached ixi directory
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- name: Restore cached IXI directory
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uses: actions/cache/restore@v4
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id: cache-restore
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with:
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run: |
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python -m sphinx docs docs_build
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- name: Display data
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run: ls -R
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working-directory: docs_build/_static
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- name: Display structure of docs
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run: ls -R docs_build/
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- name: Cache ixi directory
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- name: Cache IXI directory
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uses: actions/cache/save@v4
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if: ${{ steps.cache-restore.outputs.cache-hit != 'true' }}
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with:
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path: ~/.ixi
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key: ${{ runner.os }}-ixi
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- name: Upload artifact
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id: artifact-upload-step
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uses: actions/upload-artifact@v4
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with:
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# Upload the docs
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name: docs
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path: 'docs_build'
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retention-days: 5
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CompileDocs:
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name: Compile the coverage badge in docs
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runs-on: ubuntu-latest
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if: ${{ github.ref == 'refs/heads/main' }}
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needs: [BuildDocs, coverage]
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steps:
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- name: Get the docs_build artifact
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uses: actions/download-artifact@v4
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with:
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name: docs
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path: docs_build
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overwrite: true
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- name: Get the badge from CI
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uses: actions/download-artifact@v4
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with:
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name: coverage_badge
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path: docs_build/_static
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github-token: ${{ secrets.GITHUB_TOKEN }}
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key: ${{ runner.os }}-ixi
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- name: ReUpload artifacts
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uses: actions/upload-artifact@v4
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- name: Deploy to GitHub Pages
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uses: peaceiris/actions-gh-pages@v4
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with:
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name: docs_final
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retention-days: 20
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path: docs_build
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github_token: ${{ secrets.GITHUB_TOKEN }}
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publish_dir: ./docs_build
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destination_dir: . # Ensure you deploy to the root of the gh-pages branch
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publish_branch: gh-pages
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keep_files: false
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‎README.rst‎

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|Coverage| |CI| |CD| |License| |Codefactor| |Sphinx| |PyPi| |Black| |PythonVersion|
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.. |Coverage| image:: https://infn-mri.github.io/torchsim/_static/coverage_badge.svg
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:target: https://infn-mri.github.io/torchsim
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.. |CI| image:: https://github.com/INFN-MRI/torchsim/workflows/CI/badge.svg
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:target: https://github.com/INFN-MRI/torchsim
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.. |Coverage| image:: https://codecov.io/gh/INFN-MRI/torchsim/graph/badge.svg?token=qtB53xANwI
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:target: https://codecov.io/gh/INFN-MRI/torchsim
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.. |CD| image:: https://github.com/INFN-MRI/torchsim/workflows/CD/badge.svg
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.. |CI/CD| image:: https://github.com/INFN-MRI/torchsim/workflows/CI-CD/badge.svg
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:target: https://github.com/INFN-MRI/torchsim
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.. |License| image:: https://img.shields.io/github/license/INFN-MRI/torchsim

‎docs/sg_execution_times.rst‎

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Computation times
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=================
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**01:31.589** total execution time for 4 files **from all galleries**:
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**01:07.135** total execution time for 4 files **from all galleries**:
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.. container::
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- Time
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- Mem (MB)
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* - :ref:`sphx_glr_generated_autoexamples_02-synth-data.py` (``../examples/02-synth-data.py``)
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- 00:41.073
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- 00:42.438
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* - :ref:`sphx_glr_generated_autoexamples_03-fitting.py` (``../examples/03-fitting.py``)
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- 00:24.580
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* - :ref:`sphx_glr_generated_autoexamples_04-derivatives.py` (``../examples/04-derivatives.py``)
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* - :ref:`sphx_glr_generated_autoexamples_01-simple-simulator.py` (``../examples/01-simple-simulator.py``)
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* - :ref:`sphx_glr_generated_autoexamples_04-derivatives.py` (``../examples/04-derivatives.py``)
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- 00:00.000
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- 0.0

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