Fix GPU wheel versioning and polish JOSS paper for submission

.github/workflows/pypi-wheels-cpu.yml

@@ -18,6 +18,13 @@ jobs:
           submodules: recursive # Fetches Catch2, nlohmann/json, or pybind11 if needed
           fetch-depth: 0
 
+      - name: Extract version from tag
+        id: version
+        run: |
+          # Strip leading 'v' from tag (e.g. v4.0.2 -> 4.0.2)
+          VERSION="${GITHUB_REF_NAME#v}"
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -130,6 +137,7 @@ jobs:
             CMAKE_CXX_COMPILER="mpicxx"
             CMAKE_PREFIX_PATH="/usr/local"
             CMAKE_GENERATOR="Unix Makefiles"
+            SETUPTOOLS_SCM_PRETEND_VERSION="${{ steps.version.outputs.version }}"
 
           # Vendor libraries into the wheel, but exclude host-specific MPI and
           # runtime libraries that users must provide on their system.

.github/workflows/pypi-wheels-gpu.yml

@@ -18,6 +18,13 @@ jobs:
           submodules: recursive
           fetch-depth: 0
 
+      - name: Extract version from tag
+        id: version
+        run: |
+          # Strip leading 'v' from tag (e.g. v4.0.2 -> 4.0.2)
+          VERSION="${GITHUB_REF_NAME#v}"
+          echo "version=${VERSION}" >> "$GITHUB_OUTPUT"
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
@@ -143,6 +150,7 @@ jobs:
             CMAKE_PREFIX_PATH="/usr/local"
             CMAKE_GENERATOR="Unix Makefiles"
             CMAKE_ARGS="-DGPU_BACKEND=CUDA '-DCMAKE_CUDA_ARCHITECTURES=60;70;75;80;86;89;90' -DCMAKE_CUDA_HOST_COMPILER=/opt/rh/gcc-toolset-13/root/usr/bin/g++"
+            SETUPTOOLS_SCM_PRETEND_VERSION="${{ steps.version.outputs.version }}"
 
           # Vendor libraries but exclude host-specific MPI, OpenMP, Fortran runtime,
           # and CUDA runtime libraries (users must have CUDA toolkit installed).

figure.py

@@ -0,0 +1,112 @@
+"""Generate the architecture figure for the JOSS paper.
+
+Run: python figure.py
+Output: figure.png
+"""
+
+import matplotlib.pyplot as plt
+import matplotlib.patches as mpatches
+from matplotlib.patches import FancyBboxPatch, FancyArrowPatch
+
+fig, ax = plt.subplots(1, 1, figsize=(10, 6.5))
+ax.set_xlim(0, 10)
+ax.set_ylim(0, 7)
+ax.axis("off")
+
+# Colours
+c_io = "#3498db"
+c_solver = "#e74c3c"
+c_output = "#2ecc71"
+c_python = "#9b59b6"
+c_bg = "#ecf0f1"
+
+def box(x, y, w, h, text, color, fontsize=9, bold=False):
+    rect = FancyBboxPatch(
+        (x, y), w, h, boxstyle="round,pad=0.15",
+        facecolor=color, edgecolor="white", linewidth=2, alpha=0.9
+    )
+    ax.add_patch(rect)
+    weight = "bold" if bold else "normal"
+    ax.text(x + w / 2, y + h / 2, text, ha="center", va="center",
+            fontsize=fontsize, color="white", fontweight=weight,
+            linespacing=1.4)
+
+def arrow(x1, y1, x2, y2):
+    ax.annotate("", xy=(x2, y2), xytext=(x1, y1),
+                arrowprops=dict(arrowstyle="->,head_width=0.3,head_length=0.15",
+                                color="#7f8c8d", lw=2))
+
+# Title
+ax.text(5, 6.7, "OpenImpala Architecture", ha="center", va="center",
+        fontsize=14, fontweight="bold", color="#2c3e50")
+
+# ---- Python API layer (top) ----
+box(1.5, 5.8, 7, 0.7, "Python API:  import openimpala\n"
+    "Session  |  tortuosity()  |  volume_fraction()  |  percolation_check()",
+    c_python, fontsize=9, bold=True)
+
+# Arrow down
+arrow(5, 5.8, 5, 5.4)
+
+# ---- I/O Layer ----
+box(0.3, 4.2, 2.4, 1.1,
+    "I/O Layer\n\nTIFF | HDF5\nRAW | DAT",
+    c_io, fontsize=9, bold=False)
+
+# ---- Solver Layer ----
+box(3.1, 4.2, 3.8, 1.1,
+    "Physics Solvers\n\nHYPRE (Krylov + AMG)\nAMReX MLMG (matrix-free)",
+    c_solver, fontsize=9, bold=False)
+
+# ---- Output Layer ----
+box(7.3, 4.2, 2.4, 1.1,
+    "Output Layer\n\nJSON (BPX)\nCSV | Plotfiles",
+    c_output, fontsize=9, bold=False)
+
+# Arrows between layers
+arrow(2.7, 4.75, 3.1, 4.75)
+arrow(6.9, 4.75, 7.3, 4.75)
+
+# ---- Transport Properties (middle) ----
+box(0.3, 2.6, 4.3, 1.2,
+    "Transport Properties\n\n"
+    "Tortuosity factor  |  D_eff tensor\n"
+    "Multi-phase transport  |  Percolation",
+    "#e67e22", fontsize=9)
+
+box(5.0, 2.6, 4.7, 1.2,
+    "Microstructural Metrics\n\n"
+    "Volume fraction  |  SSA  |  PSD\n"
+    "Connected components  |  REV study",
+    "#e67e22", fontsize=9)
+
+# Arrows down from solvers
+arrow(3.5, 4.2, 2.5, 3.8)
+arrow(5.0, 4.2, 5.0, 3.8)
+arrow(6.5, 4.2, 7.3, 3.8)
+
+# ---- AMReX / HPC layer (bottom) ----
+box(0.3, 1.0, 9.4, 1.1,
+    "AMReX Infrastructure:   MPI + OpenMP + CUDA\n"
+    "iMultiFab (voxel data)  |  BoxArray (domain decomposition)  |  "
+    "Geometry  |  BL_PROFILE timers",
+    "#34495e", fontsize=9, bold=True)
+
+# Arrows down to AMReX
+arrow(2.5, 2.6, 2.5, 2.1)
+arrow(7.3, 2.6, 7.3, 2.1)
+
+# ---- External data (left of I/O) ----
+ax.text(0.15, 5.55, "3D voxel\nimages", ha="center", va="center",
+        fontsize=8, color="#7f8c8d", style="italic")
+arrow(0.15, 5.3, 0.8, 4.9)
+
+# ---- Downstream (right of output) ----
+ax.text(9.85, 5.55, "PyBaMM\nBPX", ha="center", va="center",
+        fontsize=8, color="#7f8c8d", style="italic")
+arrow(9.2, 4.9, 9.85, 5.3)
+
+plt.tight_layout()
+plt.savefig("figure.png", dpi=300, bbox_inches="tight", facecolor="white")
+plt.savefig("figure.pdf", bbox_inches="tight", facecolor="white")
+print("Saved figure.png and figure.pdf")

paper.bib

@@ -1,5 +1,5 @@
 @article{LeHoux2021OpenImpala,
-  title = {{{OpenImpala}}: {{OPEN}} source {{IMage}} based {{PArallisable}} {{Linear}} {{Algebra}} solver},
+  title = {{OpenImpala}: {OPEN} source {IMage} based {PArallisable} {Linear} {Algebra} solver},
   author = {Le Houx, James and Kramer, Denis},
   year = {2021},
   journal = {SoftwareX},
@@ -10,64 +10,132 @@ @article{LeHoux2021OpenImpala
 }
 
 @article{le2023statistical,
-  title={Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users},
-  author={Le Houx, James and Ruiz, Siul and McKay Fletcher, Daniel and Ahmed, Sharif and Roose, Tiina},
-  journal={Transport in Porous Media},
-  volume={150},
-  number={1},
-  pages={71--88},
-  year={2023},
-  publisher={Springer},
-  doi={10.1007/s11242-023-01993-7}
+  title = {Statistical Effective Diffusivity Estimation in Porous Media Using an Integrated On-site Imaging Workflow for Synchrotron Users},
+  author = {Le Houx, James and Ruiz, Siul and McKay Fletcher, Daniel and Ahmed, Sharif and Roose, Tiina},
+  journal = {Transport in Porous Media},
+  volume = {150},
+  number = {1},
+  pages = {71--88},
+  year = {2023},
+  publisher = {Springer},
+  doi = {10.1007/s11242-023-01993-7}
 }
 
 @article{amrex2019,
-  title={AMReX: a framework for block-structured adaptive mesh refinement},
-  author={Zhang, Weiqun and Almgren, Ann and Beckner, Vince and Bell, John and Blaschke, Johannes and Chan, Cy and Day, Marcus and Friesen, Brian and Gott, Kevin and Graves, Daniel and others},
-  journal={Journal of Open Source Software},
-  volume={4},
-  number={37},
-  pages={1370},
-  year={2019},
-  doi={10.21105/joss.01370}
-}
-
-@article{lu2025immersed,
-  title={An immersed interface Adaptive Mesh Refinement algorithm for Li-ion battery simulations. II. Multi-dimensional extension and separator modeling},
-  author={Lu, Jiawei and Nikiforakis, Nikolaos and Gokhale, Nandan},
-  journal={Journal of Applied Physics},
-  volume={138},
-  number={4},
-  pages={045002},
-  year={2025},
-  publisher={AIP Publishing},
-  doi={10.1063/5.0281626}
+  title = {{AMReX}: a framework for block-structured adaptive mesh refinement},
+  author = {Zhang, Weiqun and Almgren, Ann and Beckner, Vince and Bell, John and Blaschke, Johannes and Chan, Cy and Day, Marcus and Friesen, Brian and Gott, Kevin and Graves, Daniel and others},
+  journal = {Journal of Open Source Software},
+  volume = {4},
+  number = {37},
+  pages = {1370},
+  year = {2019},
+  doi = {10.21105/joss.01370}
 }
 
 @article{sulzer2021python,
-  title={{Python Battery Mathematical Modelling (PyBaMM)}},
-  author={Sulzer, Valentin and Marquis, Scott G and Timms, Robert and Robinson, Martin and Chapman, S Jon},
-  journal={Journal of Open Research Software},
-  volume={9},
-  number={1},
-  year={2021},
-  publisher={Ubiquity Press},
-  doi={10.5334/jors.309}
+  title = {{Python Battery Mathematical Modelling (PyBaMM)}},
+  author = {Sulzer, Valentin and Marquis, Scott G and Timms, Robert and Robinson, Martin and Chapman, S Jon},
+  journal = {Journal of Open Research Software},
+  volume = {9},
+  number = {1},
+  year = {2021},
+  publisher = {Ubiquity Press},
+  doi = {10.5334/jors.309}
 }
 
 @inproceedings{falgout2002hypre,
-  title={hypre: A library of high performance preconditioners},
-  author={Falgout, Robert D and Yang, Ulrike Meier},
-  booktitle={International Conference on Computational Science},
-  pages={632--641},
-  year={2002},
-  organization={Springer},
-  doi={10.1007/3-540-47789-6_66}
+  title = {hypre: A library of high performance preconditioners},
+  author = {Falgout, Robert D and Yang, Ulrike Meier},
+  booktitle = {International Conference on Computational Science},
+  pages = {632--641},
+  year = {2002},
+  organization = {Springer},
+  doi = {10.1007/3-540-47789-6_66}
 }
 
 @misc{jakob2017pybind11,
-   author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
-   year = {2017},
-   note = {https://github.com/pybind/pybind11},
-   title = {pybind11 -- Seamless operability between C++11 and Python}
+  author = {Wenzel Jakob and Jason Rhinelander and Dean Moldovan},
+  year = {2017},
+  title = {pybind11 -- Seamless operability between {C}++11 and {Python}},
+  url = {https://github.com/pybind/pybind11}
+}
+
+@article{cooper2016taufactor,
+  title = {{TauFactor}: An open-source application for calculating tortuosity factors from tomographic data},
+  author = {Cooper, Samuel J and Bertei, Antonio and Shearing, Paul R and Kilner, John A and Brandon, Nigel P},
+  journal = {SoftwareX},
+  volume = {5},
+  pages = {203--210},
+  year = {2016},
+  publisher = {Elsevier},
+  doi = {10.1016/j.softx.2016.09.002}
+}
+
+@article{gostick2019porespy,
+  title = {{PoreSpy}: A {Python} Toolkit for Quantitative Analysis of Porous Media Images},
+  author = {Gostick, Jeff T and Khan, Zohaib A and Tranter, Thomas G and Kok, Matthew D R and Agnaou, Mehrez and Sadeghi, Mohammadamin and Jervis, Rhodri},
+  journal = {Journal of Open Source Software},
+  volume = {4},
+  number = {37},
+  pages = {1296},
+  year = {2019},
+  doi = {10.21105/joss.01296}
+}
+
+@article{ferguson2018puma,
+  title = {{PuMA}: the Porous Microstructure Analysis software},
+  author = {Ferguson, Joseph C and Panerai, Francesco and Borner, Arnaud and Mansour, Nagi N},
+  journal = {SoftwareX},
+  volume = {7},
+  pages = {81--87},
+  year = {2018},
+  publisher = {Elsevier},
+  doi = {10.1016/j.softx.2018.03.001}
+}
+
+@article{lu2025immersed,
+  title = {An immersed interface Adaptive Mesh Refinement algorithm for {Li}-ion battery simulations. {II}. Multi-dimensional extension and separator modeling},
+  author = {Lu, Jiawei and Nikiforakis, Nikolaos and Gokhale, Nandan},
+  journal = {Journal of Applied Physics},
+  volume = {138},
+  number = {4},
+  pages = {045002},
+  year = {2025},
+  publisher = {AIP Publishing},
+  doi = {10.1063/5.0281626}
+}
+
+@article{tjaden2016origin,
+  title = {On the origin and application of the {Bruggeman} correlation for analysing transport phenomena in electrochemical systems},
+  author = {Tjaden, Bernhard and Cooper, Samuel J and Brett, Daniel JL and Kramer, Denis and Shearing, Paul R},
+  journal = {Current Opinion in Chemical Engineering},
+  volume = {12},
+  pages = {44--51},
+  year = {2016},
+  publisher = {Elsevier},
+  doi = {10.1016/j.coche.2016.02.006}
+}
+
+@article{epstein1989tortuosity,
+  title = {On tortuosity and the tortuosity factor in flow and diffusion through porous media},
+  author = {Epstein, Norman},
+  journal = {Chemical Engineering Science},
+  volume = {44},
+  number = {3},
+  pages = {777--779},
+  year = {1989},
+  publisher = {Elsevier},
+  doi = {10.1016/0009-2509(89)85053-5}
+}
+
+@article{withers2021xray,
+  title = {X-ray computed tomography},
+  author = {Withers, Philip J and Bouman, Charles and Carmignato, Simone and Cnudde, Veerle and Grimaldi, David and Hagen, Charlotte K and Maire, Eric and Manber, Mariam and Martini, Fabrizio and Stock, Stuart R},
+  journal = {Nature Reviews Methods Primers},
+  volume = {1},
+  number = {1},
+  pages = {18},
+  year = {2021},
+  publisher = {Nature Publishing Group},
+  doi = {10.1038/s43586-021-00015-4}
 }