Update JOSS paper branch with first set of reviewers' comments (#149)

Co-authored-by: menon-karthik <[email protected]>

Author: menon-karthik

.github/workflows/codechecks.yml

@@ -8,10 +8,11 @@ jobs:
       - uses: actions/checkout@v3
       - name: Install dependencies
         run: |
-          sudo apt install clang-format
+          wget -O - https://apt.llvm.org/llvm-snapshot.gpg.key | sudo apt-key add -
+          sudo apt-get install clang-format-19
       - name: Run clang-format
         run: |
           mkdir Release
           cd Release
           cmake ..
-          make codecheck
+          make codecheck

.github/workflows/documentation.yml

@@ -18,7 +18,7 @@ jobs:
           doxyfile-path: 'docs/Doxyfile'
           enable-latex: true
       - name: Save documentation
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: documentation
           path: ./docs/build/html

.github/workflows/draft-pdf.yml

@@ -23,7 +23,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/test.yml

@@ -8,7 +8,10 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-22.04, ubuntu-latest, macos-13, macos-latest]
+        version: [13] # GCC version
       fail-fast: false
+    env:
+      GCC_V: ${{ matrix.version }}
     steps:
       - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v3
@@ -17,12 +20,21 @@ jobs:
       - name: Install ubuntu dependencies
         if: startsWith(matrix.os, 'ubuntu')
         run: sudo apt update && sudo apt install build-essential cmake lcov
-      - name: Install svZeroDSolver
+      - name: Create conda environment
         run: |
           #export PATH="/usr/share/miniconda/bin:$PATH"
           #alias conda="$CONDA/bin/conda"
           conda create -n zerod python=3.11.4
-          conda run -n zerod pip install -e ".[dev]"
+      - name: Install dependencies to get correct version numbers (Ubuntu)
+        if: startsWith(matrix.os, 'ubuntu')
+        run: conda install -n zerod -c conda-forge libstdcxx-ng=${GCC_V} gcc=${GCC_V}
+      - name: Install dependencies to get correct version numbers (MacOS)
+        if: startsWith(matrix.os, 'macos')
+        run: |
+          brew install gcc@${GCC_V}
+          ln -s /usr/local/bin/gcc-${GCC_V} /usr/local/bin/gcc
+      - name: Install svZeroDSolver
+        run: conda run -n zerod pip install -e ".[dev]"
       - name: Install Networkx
         run: |
             conda run -n zerod pip install networkx
@@ -59,7 +71,7 @@ jobs:
           make coverage
       - name: Save coverage report
         if: startsWith(matrix.os, 'ubuntu-22.04')
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: coverage_report
           path: Release/coverage
@@ -74,7 +86,7 @@ jobs:
           cpack
           cp distribution/svZeroDSolver_* ..
       - name: Upload installer
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: ${{ matrix.os }} installer
           path: svZeroDSolver_*

LICENSE.txt

@@ -8,4 +8,6 @@ Permission is hereby granted, free of charge, to any person obtaining a copy of
 
 The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+License type: MIT License

paper/paper.bib

@@ -79,7 +79,8 @@ @article{pfaller2019importance
   volume={18},
   pages={503--529},
   year={2019},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s10237-018-1098-4}
 }
 
 @article{menon2023predictors,
@@ -99,7 +100,8 @@ @article{sankaran2012patient
   volume={40},
   pages={2228--2242},
   year={2012},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s10439-012-0579-3}
 }
 
 @article{kerckhoffs2007coupling,
@@ -109,7 +111,8 @@ @article{kerckhoffs2007coupling
   volume={35},
   pages={1--18},
   year={2007},
-  publisher={Springer}
+  publisher={Springer},
+  doi={10.1007/s10439-006-9212-7}
 }
 
 @article{menon2024cardiovascular, 
@@ -178,7 +181,7 @@ @article{TAYLOR2023
 year = {2023},
 note = {A Special Issue in Honor of the Lifetime Achievements of T. J. R. Hughes},
 issn = {0045-7825},
-doi = {https://doi.org/10.1016/j.cma.2023.116414},
+doi = {10.1016/j.cma.2023.116414},
 url = {https://www.sciencedirect.com/science/article/pii/S0045782523005388},
 author = {Charles A. Taylor and Kersten Petersen and Nan Xiao and Matthew Sinclair and Ying Bai and Sabrina R. Lynch and Adam UpdePac and Michiel Schaap},
 keywords = {Patient-specific modeling, Blood flow, Deep learning, Coronary artery},
@@ -200,7 +203,7 @@ @article{Updegrove2017
 
 @article{Lee2024,
 author = {Lee, John D and Richter, Jakob and Pfaller, Martin R and Szafron, Jason M and Menon, Karthik and Zanoni, Andrea and Ma, Michael R and Feinstein, Jeffrey A and Kreutzer, Jacqueline and Marsden, Alison L and Schiavazzi, Daniele E},
-doi = {https://doi.org/10.1002/cnm.3820},
+doi = {10.1002/cnm.3820},
 journal = {International Journal for Numerical Methods in Biomedical Engineering},
 keywords = { neural network emulator, parameterization of complex interventional repairs,digital twin for interventional planning},
 number = {5},
@@ -213,7 +216,7 @@ @article{Lee2024
 
 @article{zanoni2024,
 author = {Zanoni, Andrea and Geraci, Gianluca and Salvador, Matteo and Menon, Karthik and Marsden, Alison L and Schiavazzi, Daniele E},
-doi = {https://doi.org/10.1016/j.cma.2024.117119},
+doi = {10.1016/j.cma.2024.117119},
 issn = {0045-7825},
 journal = {Computer Methods in Applied Mechanics and Engineering},
 keywords = { Active subspaces, Autoencoders, Monte Carlo estimators, Normalizing flows, Uncertainty quantification,Multifidelity},
@@ -245,18 +248,21 @@ @incollection{PFALLER2024449
 year = {2024},
 series = {Biomechanics of Living Organs},
 isbn = {978-0-323-95484-6},
-doi = {https://doi.org/10.1016/B978-0-323-95484-6.00016-6},
+doi = {10.1016/B978-0-323-95484-6.00016-6},
 url = {https://www.sciencedirect.com/science/article/pii/B9780323954846000166},
-author = {Martin R. Pfaller and Luca Pegolotti and Jonathan Pham and Natalia L. Rubio and Alison L. Marsden},
+author = {Martin R. Pfaller and Luca Pegolotti and Jonathan Pham and Natalia L. Rubio and Alison L. Marsden}
 }
 
 @article{rubio2024,
-title={Hybrid Physics-Based and Data-Driven Modeling of Vascular Bifurcation Pressure Differences},
-author={Natalia L. Rubio and Luca Pegolotti and Martin R. Pfaller and Eric F. Darve and Alison L. Marsden},
-year={2024},
-volume={2402.15651},
-journal={arXiv},
-url={https://arxiv.org/abs/2402.15651},
+title = {Hybrid physics-based and data-driven modeling of vascular bifurcation pressure differences},
+journal = {Computers in Biology and Medicine},
+volume = {184},
+pages = {109420},
+year = {2025},
+issn = {0010-4825},
+doi = {10.1016/j.compbiomed.2024.109420},
+url = {https://www.sciencedirect.com/science/article/pii/S0010482524015051},
+author = {Natalia L. Rubio and Luca Pegolotti and Martin R. Pfaller and Eric F. Darve and Alison L. Marsden}
 }
 
 @article{Vignon-Clementel2006,
@@ -293,3 +299,33 @@ @article{menon2024personalizeduncertainty
       journal={arXiv},
       url={https://arxiv.org/abs/2409.02247},
 }
+
+@article{AFRICA2024109039,
+title = {lifex-cfd: An open-source computational fluid dynamics solver for cardiovascular applications},
+journal = {Computer Physics Communications},
+volume = {296},
+pages = {109039},
+year = {2024},
+issn = {0010-4655},
+doi = {10.1016/j.cpc.2023.109039},
+url = {https://www.sciencedirect.com/science/article/pii/S0010465523003843},
+author = {Pasquale Claudio Africa and Ivan Fumagalli and Michele Bucelli and Alberto Zingaro and Marco Fedele and Luca Dede' and Alfio Quarteroni},
+}
+
+@article{crimson2021,
+    doi = {10.1371/journal.pcbi.1008881},
+    author = {Arthurs, Christopher J. AND Khlebnikov, Rostislav AND Melville, Alex AND Marčan, Marija AND Gomez, Alberto AND Dillon-Murphy, Desmond AND Cuomo, Federica AND Silva Vieira, Miguel AND Schollenberger, Jonas AND Lynch, Sabrina R. AND Tossas-Betancourt, Christopher AND Iyer, Kritika AND Hopper, Sara AND Livingston, Elizabeth AND Youssefi, Pouya AND Noorani, Alia AND Ben Ahmed, Sabrina AND Nauta, Foeke J. H. AND van Bakel, Theodorus M. J. AND Ahmed, Yunus AND van Bakel, Petrus A. J. AND Mynard, Jonathan AND Di Achille, Paolo AND Gharahi, Hamid AND Lau, Kevin D. AND Filonova, Vasilina AND Aguirre, Miquel AND Nama, Nitesh AND Xiao, Nan AND Baek, Seungik AND Garikipati, Krishna AND Sahni, Onkar AND Nordsletten, David AND Figueroa, C. Alberto},
+    journal = {PLOS Computational Biology},
+    publisher = {Public Library of Science},
+    title = {CRIMSON: An open-source software framework for cardiovascular integrated modelling and simulation},
+    year = {2021},
+    month = {05},
+    volume = {17},
+    url = {https://doi.org/10.1371/journal.pcbi.1008881},
+    pages = {1-21},
+    number = {5},
+}
+
+@article{Hirschvogel2024, doi = {10.21105/joss.05744}, url = {https://doi.org/10.21105/joss.05744}, year = {2024}, publisher = {The Open Journal}, volume = {9}, number = {93}, pages = {5744}, author = {Marc Hirschvogel}, title = {Ambit – A FEniCS-based cardiovascular multi-physics solver}, journal = {Journal of Open Source Software} }
+
+@article{Agdestein2018, doi = {10.21105/joss.01107}, url = {https://doi.org/10.21105/joss.01107}, year = {2018}, publisher = {The Open Journal}, volume = {3}, number = {32}, pages = {1107}, author = {Syver D. Agdestein and Kristian Valen-Sendstad and Alexandra K. Diem}, title = {Artery.FE: An implementation of the 1D blood flow equations in FEniCS}, journal = {Journal of Open Source Software} }