Include all the possible workflows

.github/workflows/profile_orig_cbds_bfgs_big.yml

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+name: Profile original cbds and bfgs using optiprofiler, big
+
+on:
+  # Trigger the workflow on # push or pull request
+  push:
+  # Trigger the workflow manually
+  schedule:
+  - cron: '0 0 */2 * *'
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Profile original CBDS and bfgs, big
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        matlab: [latest]
+        dim: [big]
+        with_optim_toolbox: [yes]
+        solver: [cbds-orig]
+        competitor: [fminunc]
+        run_plain: [false]
+        summarize_log_ratio_profiles: [false]
+        feature: [plain, perturbed_x0_0.001, perturbed_x0_1, perturbed_x0_10, perturbed_x0_100, noisy_1e-1, noisy_1e-2, noisy_1e-3, noisy_1e-4, truncated_1, truncated_2, truncated_3, truncated_4, permuted, linearly_transformed, random_nan_5, random_nan_10, random_nan_20, quantized_1, quantized_2, quantized_3, quantized_4, rotation_noisy_1e-1, rotation_noisy_1e-2, rotation_noisy_1e-3, rotation_noisy_1e-4]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Checkout OptiProfiler
+        uses: actions/checkout@v4
+        with:
+          repository: optiprofiler/optiprofiler
+          ref: matlab
+          path: optiprofiler
+
+      - name: Install Texlive
+        run: sudo apt-get update && sudo apt-get install texlive
+
+      - name: Check whether LaTeX is installed
+        run: pdflatex --version
+
+      - name: Cache MATLAB
+        id: cache-matlab
+        uses: actions/cache@v4.0.1
+        with:
+          path: ${{ runner.tool_cache }}/MATLAB
+          key: ${{ matrix.os }}-${{ matrix.matlab }}-${{ matrix.with_optim_toolbox }}
+
+      - name: Set up MATLAB with optimization toolbox
+        if: ${{ matrix.with_optim_toolbox == 'yes' }}
+        uses: matlab-actions/setup-matlab@v2.1.2
+        with:
+          release: ${{ matrix.matlab }}
+          products: Optimization_Toolbox
+
+      - name: Run test
+        uses: matlab-actions/run-command@v2.1.1
+        with:
+            command: |
+              root_dir = pwd()
+              ls
+  
+              % Setup optiprofiler
+              cd(fullfile(root_dir, 'optiprofiler'));
+              setup
+              cd(root_dir);
+
+              % Setup bds
+              setup
+              cd(fullfile(root_dir, 'tests', 'competitors'));
+              addpath(pwd);
+
+              % profile
+              cd(fullfile(root_dir, 'tests'));
+              options = struct();
+              options.feature_name = '${{ matrix.feature }}';
+              options.solver_names = {'${{ matrix.solver }}', '${{ matrix.competitor }}'};
+              options.dim = '${{ matrix.dim }}';
+              options.run_plain = ${{ matrix.run_plain }};
+              options.summarize_log_ratio_profiles = ${{ matrix.summarize_log_ratio_profiles }};
+              profile_optiprofiler(options);
+              cd(root_dir);
+              cd(fullfile(root_dir, 'tests', 'out'));
+              ls -R
+              cd(root_dir);
+
+      - name: Change the summary file name
+        run: |
+          cd ./tests/out
+          ls -R
+          find . -type f -name 'summary.pdf' | while read -r file; do
+            # Obtain the parent directory and name
+            parent_dir=$(dirname "$file")
+            parent_name=$(basename "$parent_dir")
+
+            # Obtain the new name(Why the fifth underline? Because the last five parts are the time stamp)
+            new_name=$(echo "$parent_name" | awk -F'_' '{if(NF>=5) {for(i=1;i<=NF-5;i++) printf "%s%s", $i, (i<NF-5?"_":"")} else print $0}')
+
+            # Print the new name
+            echo "New name: $new_name"
+
+            # Obtain the directory name
+            dir_name=$(dirname "$file")
+            
+            # Establish the new file name
+            new_file="$dir_name/summary_$new_name.pdf"
+            
+            # Check if the source and destination are the same
+            if [ "$file" != "$new_file" ]; then
+              mv "$file" "$new_file"
+              echo "Renamed $file to $new_file"
+            else
+              echo "Source and destination are the same, skipping: $file"
+            fi
+          done
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3.1.2
+        with:
+          name: profile_optiprofiler_${{ matrix.solver }}_${{ matrix.competitor }}_${{ matrix.dim }}_${{ matrix.feature }}_${{ matrix.run_plain }}
+          path: ./tests/out/**
+
+  merge_artifacts:
+    name: Merge Artifacts
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      actions: read
+      contents: read
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Install PDF tools
+        run: sudo apt-get update && sudo apt-get install -y poppler-utils
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: tests/testdata/downloaded_artifacts
+
+      - name: List all files
+        run: |
+          cd tests/testdata/downloaded_artifacts
+          ls -R
+
+      - name: Merge PDF files
+        run: |
+          cp tests/tools/merge_pdf.sh tests/testdata/downloaded_artifacts
+          cd tests/testdata/downloaded_artifacts/
+
+          ARTIFACT_NAME=$(ls | grep "profile_optiprofiler" | head -n 1)
+          BASE_INFO=$(echo $ARTIFACT_NAME | sed -n 's/.*optiprofiler_\([^_]*_[^_]*_\(small\|big\)\).*/\1/p')
+          echo "Base info extracted: ${BASE_INFO}"
+          echo "BASE_INFO=${BASE_INFO}" >> $GITHUB_ENV
+
+          # Merge PDF files
+          mkdir summary
+          for f in $(find . -maxdepth 3 -type f -name 'summary*.pdf'); do
+              if [ ! -f "summary/$(basename $f)" ]; then
+                  cp "$f" summary/
+              fi
+          done
+          cd summary
+          ls
+          bash ../merge_pdf.sh
+          mv merged.pdf "summary_${BASE_INFO}.pdf"
+          cd ..
+          if [ -d "summary" ]; then
+            mv summary "summary_${BASE_INFO}"
+          fi
+
+      - name: Upload merged artifact
+        uses: actions/upload-artifact@v3
+        env:
+          BASE_INFO: ${{ env.BASE_INFO }}
+        with:
+          name: merged_profiles_${{ env.BASE_INFO }}
+          path: tests/testdata/downloaded_artifacts/**
+
+      - name: Upload summary files
+        uses: actions/upload-artifact@v3
+        env:
+          BASE_INFO: ${{ env.BASE_INFO }}
+        with:
+          name: summary_files_${{ env.BASE_INFO }}
+          path: tests/testdata/downloaded_artifacts/summary_${{ env.BASE_INFO }}/**

.github/workflows/profile_orig_cbds_bfgs_small.yml

@@ -0,0 +1,195 @@
+name: Profile original cbds and bfgs using optiprofiler, small
+
+on:
+  # Trigger the workflow on # push or pull request
+  push:
+  # Trigger the workflow manually
+  schedule:
+  - cron: '0 6 */2 * *'
+  workflow_dispatch:
+
+jobs:
+  test:
+    name: Profile original CBDS and bfgs, small
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest]
+        matlab: [latest]
+        dim: [small]
+        with_optim_toolbox: [yes]
+        solver: [cbds-orig]
+        competitor: [fminunc]
+        run_plain: [false]
+        summarize_log_ratio_profiles: [false]
+        feature: [plain, perturbed_x0_0.001, perturbed_x0_1, perturbed_x0_10, perturbed_x0_100, noisy_1e-1, noisy_1e-2, noisy_1e-3, noisy_1e-4, truncated_1, truncated_2, truncated_3, truncated_4, permuted, linearly_transformed, random_nan_5, random_nan_10, random_nan_20, quantized_1, quantized_2, quantized_3, quantized_4, rotation_noisy_1e-1, rotation_noisy_1e-2, rotation_noisy_1e-3, rotation_noisy_1e-4]
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Checkout OptiProfiler
+        uses: actions/checkout@v4
+        with:
+          repository: optiprofiler/optiprofiler
+          ref: matlab
+          path: optiprofiler
+
+      - name: Install Texlive
+        run: sudo apt-get update && sudo apt-get install texlive
+
+      - name: Check whether LaTeX is installed
+        run: pdflatex --version
+
+      - name: Cache MATLAB
+        id: cache-matlab
+        uses: actions/cache@v4.0.1
+        with:
+          path: ${{ runner.tool_cache }}/MATLAB
+          key: ${{ matrix.os }}-${{ matrix.matlab }}-${{ matrix.with_optim_toolbox }}
+
+      - name: Set up MATLAB with optimization toolbox
+        if: ${{ matrix.with_optim_toolbox == 'yes' }}
+        uses: matlab-actions/setup-matlab@v2.1.2
+        with:
+          release: ${{ matrix.matlab }}
+          products: Optimization_Toolbox
+
+      - name: Run test
+        uses: matlab-actions/run-command@v2.1.1
+        with:
+            command: |
+              root_dir = pwd()
+              ls
+  
+              % Setup optiprofiler
+              cd(fullfile(root_dir, 'optiprofiler'));
+              setup
+              cd(root_dir);
+
+              % Setup bds
+              setup
+              cd(fullfile(root_dir, 'tests', 'competitors'));
+              addpath(pwd);
+
+              % profile
+              cd(fullfile(root_dir, 'tests'));
+              options = struct();
+              options.feature_name = '${{ matrix.feature }}';
+              options.solver_names = {'${{ matrix.solver }}', '${{ matrix.competitor }}'};
+              options.dim = '${{ matrix.dim }}';
+              options.run_plain = ${{ matrix.run_plain }};
+              options.summarize_log_ratio_profiles = ${{ matrix.summarize_log_ratio_profiles }};
+              profile_optiprofiler(options);
+              cd(root_dir);
+              cd(fullfile(root_dir, 'tests', 'out'));
+              ls -R
+              cd(root_dir);
+
+      - name: Change the summary file name
+        run: |
+          cd ./tests/out
+          ls -R
+          find . -type f -name 'summary.pdf' | while read -r file; do
+            # Obtain the parent directory and name
+            parent_dir=$(dirname "$file")
+            parent_name=$(basename "$parent_dir")
+
+            # Obtain the new name(Why the fifth underline? Because the last five parts are the time stamp)
+            new_name=$(echo "$parent_name" | awk -F'_' '{if(NF>=5) {for(i=1;i<=NF-5;i++) printf "%s%s", $i, (i<NF-5?"_":"")} else print $0}')
+
+            # Print the new name
+            echo "New name: $new_name"
+
+            # Obtain the directory name
+            dir_name=$(dirname "$file")
+            
+            # Establish the new file name
+            new_file="$dir_name/summary_$new_name.pdf"
+            
+            # Check if the source and destination are the same
+            if [ "$file" != "$new_file" ]; then
+              mv "$file" "$new_file"
+              echo "Renamed $file to $new_file"
+            else
+              echo "Source and destination are the same, skipping: $file"
+            fi
+          done
+
+      - name: Upload artifact
+        uses: actions/upload-artifact@v3.1.2
+        with:
+          name: profile_optiprofiler_${{ matrix.solver }}_${{ matrix.competitor }}_${{ matrix.dim }}_${{ matrix.feature }}_${{ matrix.run_plain }}
+          path: ./tests/out/**
+
+  merge_artifacts:
+    name: Merge Artifacts
+    runs-on: ubuntu-latest
+    needs: test
+    permissions:
+      actions: read
+      contents: read
+
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Install PDF tools
+        run: sudo apt-get update && sudo apt-get install -y poppler-utils
+
+      - name: Download artifacts
+        uses: actions/download-artifact@v3
+        with:
+          path: tests/testdata/downloaded_artifacts
+
+      - name: List all files
+        run: |
+          cd tests/testdata/downloaded_artifacts
+          ls -R
+
+      - name: Merge PDF files
+        run: |
+          cp tests/tools/merge_pdf.sh tests/testdata/downloaded_artifacts
+          cd tests/testdata/downloaded_artifacts/
+
+          ARTIFACT_NAME=$(ls | grep "profile_optiprofiler" | head -n 1)
+          BASE_INFO=$(echo $ARTIFACT_NAME | sed -n 's/.*optiprofiler_\([^_]*_[^_]*_\(small\|big\)\).*/\1/p')
+          echo "Base info extracted: ${BASE_INFO}"
+          echo "BASE_INFO=${BASE_INFO}" >> $GITHUB_ENV
+
+          # Merge PDF files
+          mkdir summary
+          for f in $(find . -maxdepth 3 -type f -name 'summary*.pdf'); do
+              if [ ! -f "summary/$(basename $f)" ]; then
+                  cp "$f" summary/
+              fi
+          done
+          cd summary
+          ls
+          bash ../merge_pdf.sh
+          mv merged.pdf "summary_${BASE_INFO}.pdf"
+          cd ..
+          if [ -d "summary" ]; then
+            mv summary "summary_${BASE_INFO}"
+          fi
+
+      - name: Upload merged artifact
+        uses: actions/upload-artifact@v3
+        env:
+          BASE_INFO: ${{ env.BASE_INFO }}
+        with:
+          name: merged_profiles_${{ env.BASE_INFO }}
+          path: tests/testdata/downloaded_artifacts/**
+
+      - name: Upload summary files
+        uses: actions/upload-artifact@v3
+        env:
+          BASE_INFO: ${{ env.BASE_INFO }}
+        with:
+          name: summary_files_${{ env.BASE_INFO }}
+          path: tests/testdata/downloaded_artifacts/summary_${{ env.BASE_INFO }}/**