Merge branch 'main' into wrapper_dev

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -0,0 +1,59 @@
+name: 🐞 Bug report
+description: Create a report to help us improve (use this to report bugs only).
+title: "[BUG] <title>"
+labels: [🐞 bug]
+body:
+  - type: checkboxes
+    attributes:
+      label: Is there an existing issue for this?
+      description: Please search to see if an issue already exists for the bug you encountered.
+      options:
+        - label: I have searched the existing issues
+          required: true
+  - type: textarea
+    attributes:
+      label: Describe the bug
+      description: A clear and concise description of what the bug is. Include images if relevant.
+      placeholder: A bug happened!
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Screenshots [optional]
+      description: |
+        Add screenshots to help explain your problem. You can also add a video here.
+
+        Tip: You can attach images or video files by clicking this area to highlight it and then dragging files in.
+    validations:
+      required: false
+  - type: textarea
+    attributes:
+      label: Steps To Reproduce
+      description: Steps to reproduce the bug.
+      placeholder: |
+        1. Visit '...'
+        2. Click on '...'
+        3. Scroll to '...'
+        4. See error
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Expected behavior
+      description: A clear and concise description of what you expected to happen
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: |
+        Links? References? Anything that will give us more context about the issue you are encountering!
+    validations:
+      required: false
+  - type: dropdown
+    id: assign
+    attributes:
+      label: Are you working on this?
+      options:
+        - "Yes"
+        - "No"

.github/ISSUE_TEMPLATE/feature_request.yml

@@ -0,0 +1,39 @@
+name: ✨ Idea [Feature request] 
+description: Tell us about the idea you have !
+title: "[Feature] <title>"
+labels: [idea]
+body:
+  - type: markdown
+    attributes:
+      value: |
+        Your suggestions are highly valuable.
+  - type: textarea
+    attributes:
+      label: Feature description
+      description: |
+        Is your feature request related to a problem? A clear and concise description of what the feature is.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe the solution
+      description: A clear and concise description of what you want to happen.
+    validations:
+      required: true
+  - type: textarea
+    attributes:
+      label: Describe alternatives
+      description: |
+        A clear and concise description of any alternative solutions or features you have considered.
+  - type: textarea
+    attributes:
+      label: Additional context
+      description: |
+        Add any other additional context or screenshots about the feature request here.
+  - type: dropdown
+    id: assign
+    attributes:
+      label: Are you working on this?
+      options:
+        - "Yes"
+        - "No"

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

@@ -0,0 +1,39 @@
+---
+name: Download Artifact
+description: Download artifact from the same or different workflow
+
+inputs:
+    name:
+        description: Artifact to be downloaded
+        required: true
+        type: string
+
+runs:
+    using: composite
+    steps:
+      - name: Download Artifact
+        uses: actions/github-script@v6
+        with:
+          script: |
+            var inputs = ${{ toJSON(inputs) }}
+            var artifactName = inputs['name']
+            let allArtifacts = await github.rest.actions.listWorkflowRunArtifacts({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               run_id: context.payload.workflow_run.id,
+            });
+            let matchArtifact = allArtifacts.data.artifacts.filter((artifact) => {
+              return artifact.name == artifactName
+            })[0];
+            let download = await github.rest.actions.downloadArtifact({
+               owner: context.repo.owner,
+               repo: context.repo.repo,
+               artifact_id: matchArtifact.id,
+               archive_format: 'zip',
+            });
+            let fs = require('fs');
+            fs.writeFileSync(`${process.env.GITHUB_WORKSPACE}/${artifactName}.zip`, Buffer.from(download.data));
+
+      - name: 'Unzip artifact'
+        run: unzip ${{ inputs.name }}.zip
+        shell: bash

.github/pull_request_template.md

@@ -0,0 +1,13 @@
+### Describe the changes you have made in this PR
+
+_A clear and concise description of what you want to happen_
+
+### Link this PR to an issue [optional]
+
+Fixes _#ISSUE-NUMBER_
+
+### Checklist
+
+- [ ] Self-review of changed code
+- [ ] Added automated tests where applicable
+- [ ] Update Docs & Guides

.github/workflows/analysis.yml

@@ -7,22 +7,106 @@ on:
       - 'analysis/**'
 
 jobs:
-  build:
+  algorithms:
+    runs-on: ubuntu-latest
+    outputs: # here we use the outputs from steps, and set outputs for the job `configure`
+      algorithms: ${{ steps.algorithms.outputs.algorithms }}
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        id: setup_python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
 
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Read algorithms
+        id: algorithms
+        run: |
+          echo 'algorithms<<EOF' >> $GITHUB_OUTPUT
+          cat ./tests/IVIMmodels/unit_tests/algorithms.json >> $GITHUB_OUTPUT
+          echo 'EOF' >> $GITHUB_OUTPUT
+      - name: Log algorithms
+        run: |
+          echo "${{fromJson(steps.algorithms.outputs.algorithms)}}"
+          echo "${{fromJson(steps.algorithms.outputs.algorithms).algorithms}}"
+      - name: Log algorithms file
+        run: cat ./tests/IVIMmodels/unit_tests/algorithms.json
+
+  build:
     runs-on: ubuntu-latest
+    needs: algorithms
     continue-on-error: false
     strategy:
       fail-fast: false
+      matrix:
+        algorithm: ${{fromJson(needs.algorithms.outputs.algorithms).algorithms}}
+        SNR: [10, 30, 50, 100, 200]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Set up Python
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: "3.11"
-      - name: Install dependencies
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+      - name: Restore cache
+        id: python-cache
+        uses: actions/cache@v3
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+
+      - name: Generate fitting data
         run: |
-          python -m pip install --upgrade pip
-          pip install -r requirements.txt
+          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 }}_${{ matrix.SNR }}.csv
+      - name: Upload raw data
+        uses: actions/upload-artifact@v3
+        with:
+            name: Working_Data
+            retention-days: 1
+            path: |
+              test_output_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
+              test_duration_${{ matrix.algorithm }}_${{ matrix.SNR }}.csv
+
+  merge:
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: artifacts
+      - name: Merge fitting results
+        run: |
+          head -n 1 $(ls artifacts/Working_Data/test_output_*.csv | head -n 1) > test_output.csv
+          tail -q -n +2 artifacts/Working_Data/test_output_*.csv >> test_output.csv
+      - name: Merge timing results
+        run: |
+          head -n 1 $(ls artifacts/Working_Data/test_duration_*.csv | head -n 1) > test_duration.csv
+          tail -q -n +2 artifacts/Working_Data/test_duration_*.csv >> test_duration.csv
+      - name: Upload merged artifacts
+        uses: actions/upload-artifact@v3
+        with:
+          name: Data
+          path: |
+            test_output.csv
+            test_duration.csv
+
+  analyze:
+    runs-on: ubuntu-latest
+    needs: merge
+    steps:
+      - uses: actions/checkout@v4
       - name: Set up R
         uses: r-lib/actions/setup-r@v2
         with: 
@@ -36,23 +120,17 @@ jobs:
             any::tidyverse
             any::data.table
             any::ggplot2
-      - name: Generate fitting data
-        run: |
-          pip install pytest
-          python -m pytest -m slow --saveFileName test_output.csv --SNR 10 30 50 100 200 --fitCount 300 --saveDurationFileName test_duration.csv
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: Data
       - name: Generate figures
         run: Rscript --vanilla tests/IVIMmodels/unit_tests/analyze.r test_output.csv test_duration.csv
-      - name: Upload raw data
-        uses: actions/upload-artifact@v3
-        with:
-            name: Raw data
-            path: |
-              test_output.csv
-              test_duration.csv
       - name: Upload figures
         uses: actions/upload-artifact@v3
+        if: always()
         with:
-            name: Fit figures
+            name: Figures
             path: |
               D.pdf
               f.pdf
@@ -63,3 +141,33 @@ jobs:
               durations.pdf
               curve_plot.pdf
               fitted_curves.pdf
+
+  compare:
+    runs-on: ubuntu-latest
+    needs: merge
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up R
+        uses: r-lib/actions/setup-r@v2
+        with: 
+          use-public-rspm: true
+      - name: Install R dependencies
+        uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          packages: |
+            any::tidyverse
+            any::assertr
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          name: Data
+      - name: Test against previous results
+        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
+      - name: Upload data
+        uses: actions/upload-artifact@v3
+        if: always()
+        with:
+            name: Comparison
+            path: |
+              test_reference.csv
+              test_results.csv

.github/workflows/documentation.yml

@@ -0,0 +1,66 @@
+name: Build & Deploy Documentation
+
+on:
+  workflow_run:
+    workflows: [Algorithm Analysis]
+    types:
+      - completed
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v4
+      - name: Set up Python
+        id: setup_python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+      - name: Cache pip
+        uses: actions/cache@v3
+        id: pip-cache
+        with:
+          key: ${{ runner.os }}-${{ env.pythonLocation }}-pip-${{ hashFiles('**/requirements.txt') }}
+          path: ${{ env.pythonLocation }}
+        if: steps.pip-cache.outputs.cache-hit != 'true'
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      # Action to download artifacts from a different workflow (analysis.yml)
+      - name: 'Download artifact'
+        if: ${{ github.event.workflow_run.conclusion == 'success' }}
+        uses: ./.github/actions/download-artifact
+        with:
+          name: 'Figures'
+
+      - name: Build html
+        run: |
+          mkdir docs/_static
+          mv *.pdf docs/_static/
+          sphinx-apidoc -o docs src
+          cd docs/
+          make html
+
+      - name: Upload docs artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: 'docs/_build/html'
+
+  deploy:
+    needs: build
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    runs-on: ubuntu-latest
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4