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Merge pull request #70 from OSIPI/main
abdominal phantom up to date
2 parents 11445d7 + b099579 commit 77fe390

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‎.github/ISSUE_TEMPLATE/bug_report.yml‎

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name: 🐞 Bug report
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description: Create a report to help us improve (use this to report bugs only).
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title: "[BUG] <title>"
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labels: [🐞 bug]
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body:
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- type: checkboxes
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attributes:
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label: Is there an existing issue for this?
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description: Please search to see if an issue already exists for the bug you encountered.
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options:
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- label: I have searched the existing issues
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required: true
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- type: textarea
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attributes:
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label: Describe the bug
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description: A clear and concise description of what the bug is. Include images if relevant.
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placeholder: A bug happened!
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validations:
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required: true
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- type: textarea
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attributes:
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label: Screenshots [optional]
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description: |
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Add screenshots to help explain your problem. You can also add a video here.
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Tip: You can attach images or video files by clicking this area to highlight it and then dragging files in.
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validations:
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required: false
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- type: textarea
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attributes:
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label: Steps To Reproduce
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description: Steps to reproduce the bug.
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placeholder: |
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1. Visit '...'
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2. Click on '...'
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3. Scroll to '...'
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4. See error
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validations:
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required: true
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- type: textarea
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attributes:
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label: Expected behavior
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description: A clear and concise description of what you expected to happen
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validations:
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required: true
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- type: textarea
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attributes:
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label: Additional context
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description: |
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Links? References? Anything that will give us more context about the issue you are encountering!
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validations:
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required: false
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- type: dropdown
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id: assign
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attributes:
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label: Are you working on this?
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options:
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- "Yes"
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- "No"

‎.github/ISSUE_TEMPLATE/feature_request.yml‎

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name: ✨ Idea [Feature request]
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description: Tell us about the idea you have !
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title: "[Feature] <title>"
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labels: [idea]
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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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Your suggestions are highly valuable.
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- type: textarea
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attributes:
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label: Feature description
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description: |
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Is your feature request related to a problem? A clear and concise description of what the feature is.
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validations:
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required: true
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- type: textarea
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attributes:
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label: Describe the solution
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description: A clear and concise description of what you want to happen.
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validations:
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required: true
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- type: textarea
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attributes:
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label: Describe alternatives
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description: |
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A clear and concise description of any alternative solutions or features you have considered.
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- type: textarea
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attributes:
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label: Additional context
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description: |
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Add any other additional context or screenshots about the feature request here.
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- type: dropdown
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id: assign
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attributes:
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label: Are you working on this?
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options:
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- "Yes"
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- "No"

‎.github/actions/download-artifact/action.yml‎

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---
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name: Download Artifact
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description: Download artifact from the same or different workflow
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inputs:
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name:
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description: Artifact to be downloaded
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required: true
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type: string
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runs:
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using: composite
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steps:
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- name: Download Artifact
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uses: actions/github-script@v6
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with:
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script: |
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var inputs = ${{ toJSON(inputs) }}
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var artifactName = inputs['name']
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let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
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owner: context.repo.owner,
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repo: context.repo.repo,
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run_id: context.payload.workflow_run.id,
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});
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let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
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return artifact.name == artifactName
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})[0];
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let download = await github.rest.actions.downloadArtifact({
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owner: context.repo.owner,
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repo: context.repo.repo,
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artifact_id: matchArtifact.id,
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archive_format: 'zip',
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});
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let fs = require('fs');
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fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/${artifactName}.zip`, Buffer.from(download.data));
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- name: 'Unzip artifact'
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run: unzip ${{ inputs.name }}.zip
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shell: bash

‎.github/pull_request_template.md‎

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### Describe the changes you have made in this PR
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_A clear and concise description of what you want to happen_
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### Link this PR to an issue [optional]
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Fixes _#ISSUE-NUMBER_
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### Checklist
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- [ ] Self-review of changed code
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- [ ] Added automated tests where applicable
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- [ ] Update Docs & Guides

‎.github/workflows/analysis.yml‎

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name: Algorithm Analysis
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on:
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push:
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branches:
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- 'main'
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- 'analysis/**'
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jobs:
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algorithms:
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runs-on: ubuntu-latest
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outputs: # here we use the outputs from steps, and set outputs for the job `configure`
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algorithms: ${{ steps.algorithms.outputs.algorithms }}
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steps:
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- uses: actions/checkout@v4
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- name: Set up Python
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id: setup_python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Cache pip
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uses: actions/cache@v3
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id: pip-cache
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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- name: Read algorithms
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id: algorithms
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run: |
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echo 'algorithms<<EOF' >> $GITHUB_OUTPUT
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cat ./tests/IVIMmodels/unit_tests/algorithms.json >> $GITHUB_OUTPUT
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echo 'EOF' >> $GITHUB_OUTPUT
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- name: Log algorithms
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run: |
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echo "${{fromJson(steps.algorithms.outputs.algorithms)}}"
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echo "${{fromJson(steps.algorithms.outputs.algorithms).algorithms}}"
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- name: Log algorithms file
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run: cat ./tests/IVIMmodels/unit_tests/algorithms.json
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build:
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runs-on: ubuntu-latest
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needs: algorithms
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continue-on-error: false
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strategy:
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fail-fast: false
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matrix:
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algorithm: ${{fromJson(needs.algorithms.outputs.algorithms).algorithms}}
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SNR: [10, 30, 50, 100, 200]
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steps:
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- uses: actions/checkout@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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python-version: "3.11"
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Restore cache
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id: python-cache
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uses: actions/cache@v3
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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- name: Generate fitting data
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run: |
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python -m pytest -m slow --selectAlgorithm ${{ matrix.algorithm }} --saveFileName test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv --SNR ${{ matrix.SNR }} --fitCount 300 --saveDurationFileName test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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- name: Upload raw data
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uses: actions/upload-artifact@v3
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with:
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name: Working_Data
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retention-days: 1
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path: |
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test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
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merge:
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runs-on: ubuntu-latest
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needs: build
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steps:
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- name: Download artifacts
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uses: actions/download-artifact@v3
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with:
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path: artifacts
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- name: Merge fitting results
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run: |
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head -n 1 $(ls artifacts/Working_Data/test_output_*.csv | head -n 1) > test_output.csv
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tail -q -n +2 artifacts/Working_Data/test_output_*.csv >> test_output.csv
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- name: Merge timing results
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run: |
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head -n 1 $(ls artifacts/Working_Data/test_duration_*.csv | head -n 1) > test_duration.csv
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tail -q -n +2 artifacts/Working_Data/test_duration_*.csv >> test_duration.csv
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- name: Upload merged artifacts
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uses: actions/upload-artifact@v3
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with:
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name: Data
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path: |
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test_output.csv
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test_duration.csv
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analyze:
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runs-on: ubuntu-latest
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needs: merge
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steps:
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- uses: actions/checkout@v4
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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packages: |
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any::plyr
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any::dplyr
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any::tidyverse
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any::data.table
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any::ggplot2
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- name: Download artifacts
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uses: actions/download-artifact@v3
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with:
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name: Data
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- name: Generate figures
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run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv
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- name: Upload figures
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uses: actions/upload-artifact@v3
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if: always()
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with:
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name: Figures
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path: |
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D.pdf
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f.pdf
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Dp.pdf
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D_limited.pdf
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f_limited.pdf
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Dp_limited.pdf
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durations.pdf
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curve_plot.pdf
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fitted_curves.pdf
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compare:
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runs-on: ubuntu-latest
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needs: merge
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steps:
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- uses: actions/checkout@v4
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- name: Set up R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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packages: |
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any::tidyverse
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any::assertr
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- name: Download artifacts
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uses: actions/download-artifact@v3
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with:
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name: Data
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- name: Test against previous results
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run: Rscript --vanilla tests/IVIMmodels/unit_tests/compare.r test_output.csv test_reference.csv tests/IVIMmodels/unit_tests/reference_output.csv test_results.csv
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- name: Upload data
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uses: actions/upload-artifact@v3
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if: always()
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with:
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name: Comparison
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path: |
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test_reference.csv
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test_results.csv

‎.github/workflows/documentation.yml‎

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name: Build & Deploy Documentation
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on:
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workflow_run:
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workflows: [Algorithm Analysis]
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types:
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- completed
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permissions:
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contents: read
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pages: write
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id-token: write
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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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- uses: actions/checkout@v4
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- name: Setup Pages
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uses: actions/configure-pages@v4
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- name: Set up Python
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id: setup_python
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uses: actions/setup-python@v5
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with:
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python-version: "3.11"
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- name: Cache pip
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uses: actions/cache@v3
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id: pip-cache
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with:
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key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
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path: ${{ env.pythonLocation }}
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if: steps.pip-cache.outputs.cache-hit != 'true'
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- name: Install dependencies
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run: |
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pip install -r requirements.txt
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# Action to download artifacts from a different workflow (analysis.yml)
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- name: 'Download artifact'
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if: ${{ github.event.workflow_run.conclusion == 'success' }}
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uses: ./.github/actions/download-artifact
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with:
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name: 'Figures'
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- name: Build html
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run: |
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mkdir docs/_static
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mv *.pdf docs/_static/
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sphinx-apidoc -o docs src
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cd docs/
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make html
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- name: Upload docs artifact
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uses: actions/upload-pages-artifact@v3
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with:
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path: 'docs/_build/html'
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deploy:
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needs: build
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environment:
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name: github-pages
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url: ${{ steps.deployment.outputs.page_url }}
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runs-on: ubuntu-latest
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steps:
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- name: Deploy to GitHub Pages
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id: deployment
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uses: actions/deploy-pages@v4

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