WIP: Update for paper

.github/workflows/4-1-partitioned-oscillator.yml

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+name: Section 4.1 partitioned oscillator
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+  pull_request:
+
+jobs:
+  section_4_1:
+    name: Perform experiments from Section 4.1
+    strategy:
+      matrix:
+        experiment:
+        - name: Figure 10 constant
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/fig10_dts.csv -tss runge_kutta_4 generalized_alpha -wd 0 -o results/Fig10/data/constant.csv'
+        - name: Figure 10 linear
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/fig10_dts.csv -tss runge_kutta_4 generalized_alpha -wd 1 -o results/Fig10/data/linear.csv'
+        - name: Figure 10 piecewise linear
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/fig10_dts.csv -tss runge_kutta_4 generalized_alpha -wd 1 --exchange-substeps -o results/Fig10/data/piecewise_linear.csv'
+        - name: Figure 10 third-order B-spline
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/fig10_dts.csv -tss runge_kutta_4 generalized_alpha -wd 3 --exchange-substeps -o results/Fig10/data/third_degree_b-spline.csv'
+        - name: Figure 11
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/fig11_dts.csv -tss runge_kutta_4 generalized_alpha -wd 3 --exchange-substeps -o results/Fig11/data/contour_data.csv'
+        - name: Table 1 fixed-point (shown)
+          args: 'precice-config-FP.xml.jinja2 --silent --executor Github --config configs/tab1_dts.csv -tss runge_kutta_4 generalized_alpha -wd 3 --exchange-substeps -o results/Tab1/data/FP.csv'
+        - name: Table 1 reduced quasi-Newton (not shown)
+          args: 'precice-config-rQN.xml.jinja2 --silent --executor Github --config configs/tab1_dts.csv -tss runge_kutta_4 generalized_alpha -wd 3 --exchange-substeps -o results/Tab1/data/rQN.csv'
+        - name: Table 1 full quasi-Newton (not shown)
+          args: 'precice-config-fQN.xml.jinja2 --silent --executor Github --config configs/tab1_dts.csv -tss runge_kutta_4 generalized_alpha -wd 3 --exchange-substeps -o results/Tab1/data/fQN.csv'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: experiments/oscillator-overlap
+    container: precice/precice:3.2.0
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Install Dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install software-properties-common python3-dev python3-pip python3.12-venv git apt-utils pkg-config
+          rm -rf /var/lib/apt/lists/*
+      - name: Create venv
+        run: |
+          ./make-venv.sh
+      - name: Activate venv
+        # see https://stackoverflow.com/a/74669486
+        run: |
+          . .venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
+      - name: Run tutorial
+        run: |
+          python3 doConvergenceStudy.py ${{matrix.experiment.args}}
+      - name: Store results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: oscillator-overlap ${{ matrix.experiment.name }}
+          path: |
+            # working directory is ignored by actions/upload-artifact
+            experiments/oscillator-overlap/results
+
+  visualize:
+    name: Create plots and tables to visualize experiments from Section 4.1
+    needs: section_4_1
+    runs-on: ubuntu-latest
+    container: 
+      image: benjaminrodenberg/latex:wi-paper
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Download results from stage "experiment"
+        uses: actions/download-artifact@v5
+        with:
+          pattern: oscillator-overlap*
+          merge-multiple: true
+          path: artifacts
+      - name: Show structure for debugging
+        run: |
+          ls -R artifacts
+      - name: Replace pre-computed results with newly computed ones
+        run: |
+          rm -r plotting/oscillator-overlap/Fig10/data
+          mv artifacts/Fig10/data plotting/oscillator-overlap/Fig10/data
+          rm -r plotting/oscillator-overlap/Fig11/data
+          mv artifacts/Fig11/data plotting/oscillator-overlap/Fig11/data
+          rm -r plotting/oscillator-overlap/Tab1/data
+          mv artifacts/Tab1/data plotting/oscillator-overlap/Tab1/data
+      - name: Install Python dependencies
+        working-directory: plotting
+        run: pip install --break-system-packages -r requirements.txt
+      - name: Create visualizations
+        working-directory: plotting/oscillator-overlap
+        run: make
+      - name: Store results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: visualizations
+          path: |
+            plotting/oscillator-overlap/Fig10/main.pdf
+            plotting/oscillator-overlap/Fig11/main.pdf
+            plotting/oscillator-overlap/Tab1/FP.pdf
+            plotting/oscillator-overlap/Tab1/fQN.pdf
+            plotting/oscillator-overlap/Tab1/rQN.pdf
+
+  merge:
+    name: Merge output artifacts
+    runs-on: ubuntu-latest
+    needs: section_4_1
+    steps:
+      - name: Merge results
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: results
+
+  publish-pages:
+    permissions:
+      contents: write
+    needs: 
+      - merge
+      - visualize
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download merge output
+        uses: actions/download-artifact@v4
+        with:
+          name: results
+          path: pages/oscillator-overlap/results
+
+      - name: Download visualizations
+        uses: actions/download-artifact@v4
+        with:
+          name: visualizations
+          path: pages/oscillator-overlap/visualizations
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: pages

.github/workflows/4-2-partitioned-heat-conduction.yml

@@ -0,0 +1,192 @@
+name: Section 4.2 partitioned heat conduction
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+  pull_request:
+
+jobs:
+  section_4_2_partitioned:
+    name: Perform experiments from Section 4.2 (partitioned)
+    strategy:
+      matrix:
+        experiment:
+        - name: Figure 13 IE, p=3
+          args: '--experiment sincos -w 6 -s 1 -wd 3 -sb 5 5 -dt 1 -tss BackwardEuler BackwardEuler --exchange-substeps -o results/Fig13/data/IE_3.csv'
+        - name: Figure 13 GL(2), p=2
+          args: '--experiment sincos -w 6 -s 1 -wd 2 -sb 5 5 -dt 1 -tss GaussLegendre2 GaussLegendre2 --exchange-substeps -o results/Fig13/data/GL2_2.csv'
+        - name: Figure 13 GL(2), p=3
+          args: '--experiment sincos -w 6 -s 1 -wd 3 -sb 5 5 -dt 1 -tss GaussLegendre2 GaussLegendre2 --exchange-substeps -o results/Fig13/data/GL2_3.csv'
+        - name: Figure 13 GL(2), p=5
+          args: '--experiment sincos -w 6 -s 1 -wd 5 -sb 5 5 -dt 1 -tss GaussLegendre2 GaussLegendre2 --exchange-substeps -o results/Fig13/data/GL2_5.csv'
+        - name: Figure 13 GL(3), p=3
+          args: '--experiment sincos -w 6 -s 1 -wd 3 -sb 5 5 -dt 1 -tss GaussLegendre3 GaussLegendre3 --exchange-substeps -o results/Fig13/data/GL3_3.csv'
+        - name: Figure 13 GL(3), p=5
+          args: '--experiment sincos -w 6 -s 1 -wd 5 -sb 5 5 -dt 1 -tss GaussLegendre3 GaussLegendre3 --exchange-substeps -o results/Fig13/data/GL3_5.csv'
+        - name: Figure 13 LIIIC(3), p=2
+          args: '--experiment sincos -w 6 -s 1 -wd 2 -sb 5 5 -dt 1 -tss LobattoIIIC3 LobattoIIIC3 --exchange-substeps -o results/Fig13extra/data/LIIIC3_2.csv'
+        - name: Figure 13 LIIIC(3), p=3
+          args: '--experiment sincos -w 6 -s 1 -wd 3 -sb 5 5 -dt 1 -tss LobattoIIIC3 LobattoIIIC3 --exchange-substeps -o results/Fig13extra/data/LIIIC3_3.csv'
+        - name: Figure 13 LIIIC(3), p=5
+          args: '--experiment sincos -w 6 -s 1 -wd 5 -sb 5 5 -dt 1 -tss LobattoIIIC3 LobattoIIIC3 --exchange-substeps -o results/Fig13extra/data/LIIIC3_5.csv'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: experiments/partitioned-heat-conduction
+    container: precice/precice:3.2.0
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Install Dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install software-properties-common python3-dev python3-pip python3.12-venv git apt-utils pkg-config
+          add-apt-repository -y ppa:fenics-packages/fenics
+          apt-get -qq install --no-install-recommends fenics
+          rm -rf /var/lib/apt/lists/*
+      - name: Create venv
+        run: |
+          ./make-venv.sh
+      - name: Activate venv
+        # see https://stackoverflow.com/a/74669486
+        run: |
+          . .venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
+      - name: Run tutorial
+        run: |
+          python3 doConvergenceStudy.py precice-config.xml.jinja2 --silent --executor Github ${{matrix.experiment.args}}
+      - name: Store results
+        uses: actions/upload-artifact@v4
+        with:
+          name: partitioned-heat-conduction-convergence ${{ matrix.experiment.name }}
+          path: |
+            # working directory is ignored by actions/upload-artifact
+            experiments/partitioned-heat-conduction/results
+
+  section_4_2_monolithic:
+    name: Perform experiments from Section 4.2 (monolithic)
+    strategy:
+      matrix:
+        experiment:
+        - name: Figure 13 IE, mono
+          args: '--experiment sincos -s 6 -dt 0.2 -tss BackwardEuler -o results/Fig13/data/IE_mono.csv'
+        - name: Figure 13 GL(2), mono
+          args: '--experiment sincos -s 6 -dt 0.2 -tss GaussLegendre2 -o results/Fig13/data/GL2_mono.csv'
+        - name: Figure 13 GL(3), mono
+          args: '--experiment sincos -s 6 -dt 0.2 -tss GaussLegendre3 -o results/Fig13/data/GL3_mono.csv'
+        - name: Figure 13 LIIIC(3), mono
+          args: '--experiment sincos -s 6 -dt 0.2 -tss LobattoIIIC3 -o results/Fig13extra/data/LIIIC3_mono.csv'
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: experiments/partitioned-heat-conduction
+    container: precice/precice:3.2.0
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Install Dependencies
+        run: |
+          apt-get -qq update
+          apt-get -qq install software-properties-common python3-dev python3-pip python3.12-venv git apt-utils pkg-config
+          add-apt-repository -y ppa:fenics-packages/fenics
+          apt-get -qq install --no-install-recommends fenics
+          rm -rf /var/lib/apt/lists/*
+      - name: Create venv
+        run: |
+          ./make-venv.sh
+      - name: Activate venv
+        # see https://stackoverflow.com/a/74669486
+        run: |
+          . .venv/bin/activate
+          echo PATH=$PATH >> $GITHUB_ENV
+      - name: Run tutorial
+        run: |
+          python3 doConvergenceStudyMonolithic.py --silent --executor Github ${{matrix.experiment.args}}
+      - name: Store results
+        uses: actions/upload-artifact@v4
+        with:
+          name: partitioned-heat-conduction ${{ matrix.experiment.name }}
+          path: |
+            # working directory is ignored by actions/upload-artifact
+            experiments/partitioned-heat-conduction/results
+
+  visualize:
+    name: Create plots to visualize experiments from Section 4.2
+    needs: 
+      - section_4_2_partitioned
+      - section_4_2_monolithic
+    runs-on: ubuntu-latest
+    container: 
+      image: benjaminrodenberg/latex:wi-paper
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v4
+      - name: Download results from stage "experiment"
+        uses: actions/download-artifact@v5
+        with:
+          pattern: partitioned-heat-conduction*
+          merge-multiple: true
+          path: artifacts
+      - name: Show structure for debugging
+        run: |
+          ls -R artifacts
+      - name: Replace pre-computed results with newly computed ones
+        run: |
+          rm -r plotting/partitioned-heat-conduction/Fig13/data
+          mv artifacts/Fig13/data plotting/partitioned-heat-conduction/Fig13/data
+          rm -r plotting/partitioned-heat-conduction/Fig13extra/data
+          mv artifacts/Fig13extra/data plotting/partitioned-heat-conduction/Fig13extra/data
+      - name: Install Python dependencies
+        working-directory: plotting
+        run: pip install --break-system-packages -r requirements.txt
+      - name: Create visualizations
+        working-directory: plotting/partitioned-heat-conduction
+        run: make
+      - name: Store results
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: visualizations
+          path: |
+            plotting/partitioned-heat-conduction/Fig13/main.pdf
+            plotting/partitioned-heat-conduction/Fig13extra/main.pdf
+
+  merge:
+    name: Merge output artifacts
+    runs-on: ubuntu-latest
+    needs: 
+      - section_4_2_partitioned
+      - section_4_2_monolithic
+    steps:
+      - name: Merge results
+        uses: actions/upload-artifact/merge@v4
+        with:
+          name: results
+
+  publish-pages:
+    permissions:
+      contents: write
+    needs: 
+      - merge
+      - visualize
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Download merge output
+        uses: actions/download-artifact@v4
+        with:
+          name: results
+          path: pages/partitioned-heat-conduction/results
+
+      - name: Download visualizations
+        uses: actions/download-artifact@v4
+        with:
+          name: visualizations
+          path: pages/partitioned-heat-conduction/visualizations
+
+      - name: Deploy to GitHub Pages
+        uses: peaceiris/actions-gh-pages@v4
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: pages