docs: updated publications and fixed broken links with button-ref

src/coreComponents/fileIO/doc/InputXMLFiles.rst

@@ -266,7 +266,7 @@ Advanced XML Features
 =================================
 
 The `geosx_xml_tools` python package adds a set of advanced features to the GEOS xml format: units, parameters, and symbolic expressions.
-See`Python Tools Setup <https://geosx-geosx.readthedocs-hosted.com/projects/geosx-geospythonpackages/en/latest/>`_ for details on setup instructions, and `XML Parser Documentation <https://geosx-geosx.readthedocs-hosted.com/projects/geosx-geospythonpackages/en/latest/geosx_xml_tools.html>`_ for package API details.
+See `Python Tools Setup <https://geosx-geosx.readthedocs-hosted.com/projects/geosx-geospythonpackages/en/latest>`_ for details on setup instructions, and `XML Parser Documentation <https://geosx-geosx.readthedocs-hosted.com/projects/geosx-geospythonpackages/en/latest/geos-xml-tools.html>`_ for package API details.
 
 
 Usage

src/coreComponents/fileIO/doc/OutputTasks.rst

@@ -195,7 +195,7 @@ time history datat.
 
 .. _SILO: https://wci.llnl.gov/simulation/computer-codes/silo
 .. _VTK: https://vtk.org/wp-content/uploads/2015/04/file-formats.pdf
-.. _HDF5: https://portal.hdfgroup.org/display/HDF5/HDF5
+.. _HDF5: https://www.hdfgroup.org/solutions/hdf5
 .. _VisIT: https://wci.llnl.gov/simulation/computer-codes/visit/downloads
 .. _Paraview: https://www.paraview.org/
 .. _MatPlotLib: https://matplotlib.org/

src/coreComponents/linearAlgebra/docs/LinearSolvers.rst

@@ -305,14 +305,14 @@ This section provides a brief description of the available preconditioners.
 * **ILUK**: incomplete LU factorization with fill level k of the original matrix: :math:`\mathsf{M}^{-1} = \mathsf{U}^{-1} \mathsf{L}^{-1}`.
   Further details can be found in:
 
-  - `HYPRE documentation <https://hypre.readthedocs.io/en/latest/solvers-hypre-ilu.html>`__,
+  - `HYPRE documentation <https://hypre.readthedocs.io/en/latest/solvers-ilu.html>`__,
   - `PETSc documentation <https://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/PC/PCILU.html>`__,
   - `Trilinos documentation <https://docs.trilinos.org/dev/packages/ifpack/doc/html/classIfpack__ILU.html>`__.
 
 * **ILUT**: a dual threshold incomplete LU factorization: :math:`\mathsf{M}^{-1} = \mathsf{U}^{-1} \mathsf{L}^{-1}`.
   Further details can be found in:
 
-  - `HYPRE documentation <https://hypre.readthedocs.io/en/latest/solvers-hypre-ilu.html>`__,
+  - `HYPRE documentation <https://hypre.readthedocs.io/en/latest/solvers-ilu.html>`__,
   - not yet available through PETSc interface,
   - `Trilinos documentation <https://docs.trilinos.org/dev/packages/ifpack/doc/html/classIfpack__ILUT.html>`__.
 

src/coreComponents/mesh/mpiCommunications/docs/SpatialPartition.rst

@@ -81,6 +81,6 @@ Therefore, it is a good practice or habit to hide ghost objects using ghostRank
 If the visualization method involves interpolation, such as interpolating a zonal field into a nodal field or generating contours, 
 the interpretation near partition boundaries is not accurate.
 
-.. _METIS: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview
-.. _PARMETIS: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
+.. _METIS: https://github.com/KarypisLab/METIS
+.. _PARMETIS: https://github.com/KarypisLab/ParMETIS
 .. _PTSCOTCH: https://www.labri.fr/perso/pelegrin/scotch/

src/coreComponents/physicsSolvers/solidMechanics/contact/docs/SolidMechanicsEmbeddedFractures.rst

@@ -43,9 +43,9 @@ The following data are allocated and used by the solver:
 References
 ==========
 
-1. Simo JC, Rifai MS. A class of mixed assumed strain methods and the method of incompatible modes. *Int J Numer Methods Eng.* 1990;29(8):1595-1638. Available at: http://arxiv.org/abs/https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.1620290802.
+1. Simo JC, Rifai MS. A class of mixed assumed strain methods and the method of incompatible modes. *Int J Numer Methods Eng.* 1990;29(8):1595-1638. Available at: https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.1620290802.
 
-2. Foster CD, Borja RI, Regueiro RA. Embedded strong discontinuity finite elements for fractured geomaterials with variable friction. *Int J Numer Methods Eng.* 2007;72(5):549-581. Available at: http://arxiv.org/abs/https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.2020.
+2. Foster CD, Borja RI, Regueiro RA. Embedded strong discontinuity finite elements for fractured geomaterials with variable friction. *Int J Numer Methods Eng.* 2007;72(5):549-581. Available at: https://onlinelibrary.wiley.com/doi/pdf/10.1002/nme.2020.
 
 3. Wells G, Sluys L. Three-dimensional embedded discontinuity model for brittle fracture. *Int J Solids Struct.* 2001;38(5):897-913. Available at: https://doi.org/10.1016/S0020-7683(00)00029-9.
 

src/docs/sphinx/Publications.rst

@@ -2,7 +2,7 @@
 Publications
 ###############################################################################
 
-Last updated 10-October-2025
+Last updated 07-July-2026
 
 Referencing GEOS  
 =========================
@@ -20,25 +20,6 @@ Referencing GEOS
 Preprints and Early-Views
 =========================
 
-.. list-table::
-   :widths: 100
-   :header-rows: 0
-
-   * - | **A robust framework for frictional fault contact in geological formations using a stabilized augmented Lagrangian approach**
-       | M Frigo, N Castelletto, M Cusini, RR Settgast, HA Tchelepi
-       | arXiv preprint
-       | `arXiv:2509.20528 <https://doi.org/10.48550/arXiv.2509.20528>`_
-
-   * - | **Recurrent Transformer U-Net surrogate for flow modeling and data assimilation in subsurface formations with faults**
-       | Y Han, LJ Durlofsky
-       | arXiv preprint
-       | `arXiv:2508.16631 <https://doi.org/10.48550/arXiv.2508.16631>`_
-
-   * - | **Semi-Analytical Approaches for Addressing Thermal Debonding Issues in Cased Wellbores**
-       | T Nguyen-Sy, J Huang, H Gross, FP Hamon
-       | SSRN preprint
-       | `doi:10.2139/ssrn.5208966 <https://doi.org/10.2139/ssrn.5208966>`_
-
 
 2026
 ====
@@ -52,6 +33,31 @@ Preprints and Early-Views
        | Computer Methods in Applied Mechanics and Engineering
        | `doi:10.1016/j.cma.2025.118399 <https://doi.org/10.1016/j.cma.2025.118399>`_
 
+   * - | **A robust framework for frictional fault contact in geological formations using a stabilized augmented Lagrangian approach**
+       | M Frigo, N Castelletto, M Cusini, RR Settgast, HA Tchelepi
+       | Journal of Computational Physics
+       | `doi:10.1016/j.jcp.2026.114988 <https://doi.org/10.1016/j.jcp.2026.114988>`_
+
+   * - | **Recurrent Transformer U-Net surrogate for flow modeling and data assimilation in subsurface formations with faults**
+       | Y Han, LJ Durlofsky
+       | Journal of Computational Physics
+       | `doi:10.1016/j.jcp.2026.114801 <https://doi.org/10.1016/j.jcp.2026.114801>`_
+
+   * - | **Simulation of Multiphase Flow and Poromechanical Effects Around Injection Wells in CO2 Storage Sites**
+       | J Huang, F Hamon, M Cusini, T Gazzola, RR Settgast, JA White, H Gross
+       | Rock Mechanics and Rock Engineering
+       | `doi:10.1007/s00603-024-04051-w <https://doi.org/10.1007/s00603-024-04051-w>`_ 
+
+   * - | **High-Resolution Simulations of Geological CO2 Injection: Application to the SPE11 Benchmark**
+       | D Kachuma, R Hasanzade, P Tomin, ME Thomadakis, J Franc, VAP Magri, TJ Byer, M Cusini, RR Settgast, H Gross, N Castelletto
+       | SPE Journal
+       | `doi:10.2118/231182-PA <https://doi.org/10.2118/231182-PA>`_ 
+
+   * - | **Basin-scale analysis of Mokelumne River Formation for multi-well CO2 injection**
+       | A  Zibitsker, B Schmidt, T Byer, N Castelletto, J Iyer
+       | International Journal of Greenhouse Gas Control
+       | `doi:10.1016/j.ijggc.2026.104703 <https://doi.org/10.1016/j.ijggc.2026.104703>`_ 
+
 
 2025
 ====
@@ -113,11 +119,6 @@ Preprints and Early-Views
        | Advances in Water Resources
        | `doi:10.1016/j.advwatres.2024.104678 <https://doi.org/10.1016/j.advwatres.2024.104678>`_
 
-   * - | **Simulation of Multiphase Flow and Poromechanical Effects Around Injection Wells in CO2 Storage Sites**
-       | J Huang, F Hamon, M Cusini, T Gazzola, RR Settgast, JA White, H Gross
-       | Rock Mechanics and Rock Engineering
-       | `doi:10.1007/s00603-024-04051-w <https://doi.org/10.1007/s00603-024-04051-w>`_ 
-
    * - | **Learning CO2 plume migration in faulted reservoirs with Graph Neural Networks**
        | X Ju, FP Hamon, G Wen, R Kanfar, M Araya-Polo, HA Tchelepi
        | Computers & Geosciences

src/docs/sphinx/advancedExamples/validationStudies/carbonStorage/buckleyLeverett/Example.rst

@@ -9,7 +9,7 @@
 **Context**
 
 In this example, we simulate a CO2 core flood experiment representing immiscible transport of two-phase
-flow (CO2 and water) through porous media `(Ekechukwu et al., 2022) <https://arxiv.org/pdf/2203.05021.pdf>`__. This problem is solved using the multiphase flow solver in GEOS to obtain the temporal evolution of saturation along the flow direction, and verified against the Buckley-Leverett analytical solutions `(Buckley and Leverett, 1942;  <https://onepetro.org/TRANS/article/146/01/107/161720/Mechanism-of-Fluid-Displacement-in-Sands>`__ `Arabzai and Honma, 2013)  <http://bulletin.soe.u-tokai.ac.jp/english_vol38/20_25.pdf>`__.
+flow (CO2 and water) through porous media `(Ekechukwu et al., 2022) <https://arxiv.org/pdf/2203.05021.pdf>`__. This problem is solved using the multiphase flow solver in GEOS to obtain the temporal evolution of saturation along the flow direction, and verified against the Buckley-Leverett analytical solutions `(Buckley and Leverett, 1942;  <https://onepetro.org/TRANS/article/146/01/107/161720/Mechanism-of-Fluid-Displacement-in-Sands>`__ `Arabzai and Honma, 2013)  <https://www.researchgate.net/profile/Abidullah-Arabzai-2/publication/385085530_Numerical_Simulation_of_the_Buckley-Leverett_Problem/links/6714f783d796f96b8ec38491/Numerical-Simulation-of-the-Buckley-Leverett-Problem.pdf>`__.
 
 
 **Input file**

src/docs/sphinx/advancedExamples/validationStudies/hydraulicFracture/kgdValidation/Example.rst

@@ -8,7 +8,7 @@ Validating KGD Hydraulic Fracture with Experiment
 
 **Context**
 
-In this example, we use GEOS to model a planar hydraulic fracture propagating in a finite domain subject to traction-free external boundaries. Contrary to the classic KGD problems, we do not assume an infinite rock domain. Existing analytical solutions cannot model fracture behavior in this scenario, so this problem is solved using the hydrofracture solver in GEOS. We validate the simulation results against a benchmark experiment `(Rubin, 1983)  <http://citeseerx.ist.psu.edu/viewdoc/download;jsessionid=BBFD63D08B444221B5546F7AAC3FC159?doi=10.1.1.1052.2551&rep=rep1&type=pdf>`__. 
+In this example, we use GEOS to model a planar hydraulic fracture propagating in a finite domain subject to traction-free external boundaries. Contrary to the classic KGD problems, we do not assume an infinite rock domain. Existing analytical solutions cannot model fracture behavior in this scenario, so this problem is solved using the hydrofracture solver in GEOS. We validate the simulation results against a benchmark experiment `(Rubin, 1983)  <https://asmedigitalcollection.asme.org/energyresources/article-abstract/105/2/116/405848/Experimental-Study-of-Hydraulic-Fracturing-in-an?redirectedFrom=fulltext>`__. 
 
 
 **Input file**

src/docs/sphinx/advancedExamples/validationStudies/thermoPoromechanics/thermalConsolidation/Example.rst

@@ -8,7 +8,7 @@ Thermoporoelastic Consolidation
 **Context**
 
 Thermoporoelastic consolidation is a typical fully coupled problem which involves solid deformation, fluid flow and heat transfer in saturated porous media.
-In this example, we use the GEOS coupled solvers to solve a one-dimensional thermoporoelastic consolidation problem with a non-isothermal boundary condition, and we verify the accuracy of the results using the analytical solution provided in `(Bai, 2005) <http://gclx.xml-journal.net/en/article/id/3369>`__ 
+In this example, we use the GEOS coupled solvers to solve a one-dimensional thermoporoelastic consolidation problem with a non-isothermal boundary condition, and we verify the accuracy of the results using the analytical solution provided in `(Bai, 2005) <https://engineeringmechanics.cn/article/id/3369>`__ 
 
 **InputFile**
 

src/docs/sphinx/buildGuide/ContinuousIntegration.rst

@@ -6,9 +6,7 @@ Continuous Integration process
 To save building time, the third party libraries (that do not change so often) and GEOS are build separately.
 
 Everytime a pull is requested in the TPL repository, docker images are generated and deployed on `dockerhub <https://hub.docker.com/r/geosx>`_.
-The repository names (`ubuntu18.04-gcc8 <https://hub.docker.com/r/geosx/ubuntu18.04-gcc8>`_,
-`centos7.7.1908-clang9.0.0 <https://hub.docker.com/r/geosx/centos7.5.1804-clang6.0.1>`_, `centos7.6.1810-gcc8.3.1-cuda10.1.243 <https://hub.docker.com/r/geosx/centos7.6.1810-gcc8.3.1-cuda10.1.243>`_ etc.)
-obviously reflect the OS and the compiler flavour used.
+The repository names (e.g. `ubuntu24.04-gcc13-cuda12.9.1 <https://hub.docker.com/r/geosx/ubuntu24.04-gcc13-cuda12.9.1>`_) obviously reflect the OS and the compiler flavour used.
 For each image, the unique tag ``${PULL_REQUEST_NUMBER}-${BUILD_NUMBER}`` (defined as ``${{ github.event.number }}-${{ github.run_number }}`` in github actions) is used so we can connect the related code source in a rather convenient way.
 Each docker contains the ``org.opencontainers.image.created`` and ``org.opencontainers.image.revision`` labels to provide additional information.
 

src/docs/sphinx/buildGuide/Dependencies.rst

@@ -57,10 +57,10 @@ uncrustify_   401a409    :code:`ENABLE_UNCRUSTIFY`   :code:`UNCRUSTIFY_EXECUTABL
 .. _conduit: https://github.com/LLNL/conduit
 .. _CHAI : https://github.com/LLNL/CHAI
 .. _RAJA : https://github.com/LLNL/RAJA
-.. _hdf5 : https://portal.hdfgroup.org/display/HDF5/HDF5
+.. _hdf5 : https://www.hdfgroup.org/solutions/hdf5
 .. _mathpresso : https://github.com/kobalicek/mathpresso
 .. _pugixml : https://pugixml.org
-.. _parmetis : http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview
+.. _parmetis : https://github.com/KarypisLab/ParMETIS
 .. _silo : https://wci.llnl.gov/simulation/computer-codes/silo
 .. _VTK : https://vtk.org/
 .. _suitesparse : https://people.engr.tamu.edu/davis/suitesparse.html

src/docs/sphinx/tutorials/step01/Tutorial.rst

@@ -137,7 +137,7 @@ In production runs, you may want to suppress most console output.
 
 For solvers of the ``SinglePhaseFVM`` family, one required attribute is a discretization scheme.
 Here, we use a Two-Point Flux Approximation (TPFA) finite volume discretization scheme called ``singlePhaseTPFA``.
-To know the list of admissible values of an attribute, please see `GEOS's XML schema <https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/CompleteXMLSchema.html#>`_.
+To know the list of admissible values of an attribute, please see `GEOS's XML schema <https://geosx-geosx.readthedocs-hosted.com/en/latest/docs/sphinx/datastructure/CompleteXMLSchema.html#>`_.
 This discretization type must know how to find permeability values that it uses internally to compute transmissibilities.
 The ``permeabilityNames`` attribute tells the solver the user-defined name (the *handle*)
 of the permeability values that will be defined elsewhere in the input file.

src/index.rst

@@ -39,7 +39,7 @@ you have suggestions for improving the guides below, please post an issue on our
 
         +++
 
-        .. button-ref:: QuickStart
+        .. button-link:: docs/sphinx/QuickStart.html
             :expand:
             :color: info
             :click-parent:
@@ -55,7 +55,7 @@ you have suggestions for improving the guides below, please post an issue on our
 
         +++
 
-        .. button-ref:: Tutorials
+        .. button-link:: docs/sphinx/tutorials/Index.html
             :expand:
             :color: info
             :click-parent:
@@ -71,7 +71,7 @@ you have suggestions for improving the guides below, please post an issue on our
 
         +++
 
-        .. button-ref:: BasicExamples
+        .. button-link:: docs/sphinx/basicExamples/Index.html
             :expand:
             :color: info
             :click-parent:
@@ -87,7 +87,7 @@ you have suggestions for improving the guides below, please post an issue on our
 
         +++
 
-        .. button-ref:: AdvancedExamples
+        .. button-link:: docs/sphinx/advancedExamples/Index.html
             :expand:
             :color: info
             :click-parent:
@@ -103,7 +103,7 @@ you have suggestions for improving the guides below, please post an issue on our
 
         +++
 
-        .. button-ref:: UserGuide
+        .. button-link:: docs/sphinx/userGuide/Index.html
             :expand:
             :color: info
             :click-parent: