Add dependencies for Ubuntu 25.10

Dockerfile.custom

@@ -107,8 +107,9 @@ RUN source /etc/profile.d/modules.sh && \
     rm -rf ${MODULES_DIR}/src/* && \
     rm -rf /tmp/*
 
-# TODO: This RUN section is a temporary workaround for backwards compatibility.
-# Remove once the combined PETSc/HDF5 module is no longer needed.
+# TODO: This RUN section adds an additional petsc_hdf5 environment module which 
+# is a temporary workaround for backwards compatibility.
+# It can be removed once a combined PETSc/HDF5 module is no longer needed.
 # See https://github.com/Chaste/dependency-modules/issues/84
 RUN source /etc/profile.d/modules.sh && \
     module use ${MODULES_DIR}/modulefiles && \

scripts/system/install_modulefiles.sh

@@ -127,8 +127,9 @@ module-whatis "This adds the environment variables for petsc ${petsc_version} wi
 conflict petsc
 EOF
 
-# TODO: This adds PETSc/HDF5 modulefile stub as a temporary workaround for backwards compatibility.
-# Remove once the combined PETSc/HDF5 module is no longer needed.
+# TODO: This next sections adds a combined petsc_hdf5 modulefile stub as a temporary
+# workaround for backwards compatibility.
+# It can be removed once a combined PETSc/HDF5 module is no longer needed.
 # See https://github.com/Chaste/dependency-modules/issues/84
 
 mkdir -p ${base_dir}/modulefiles/petsc_hdf5/${petsc_version}_${hdf5_version}

scripts/system/setup_system.sh

@@ -36,7 +36,27 @@ apt-get install -y --no-install-recommends \
 codename="$(. /etc/os-release && echo ${VERSION_CODENAME} | sed 's/\.//')"
 
 if [ "${codename}" = 'plucky' ]; then
-  # Install manually: Ubuntu Plucky repository not yet available
+  # Install manually: Ubuntu 25.04 Plucky Puffin repository not yet available
+  apt-get install -y --no-install-recommends \
+    hdf5-tools \
+    libboost-serialization-dev \
+    libboost-filesystem-dev \
+    libboost-program-options-dev \
+    libhdf5-openmpi-dev \
+    libmetis-dev \
+    libopenmpi-dev \
+    libpetsc-real3.22 \
+    libpetsc-real3.22-dbg \
+    libpetsc-real3.22-dev \
+    libscotchparmetis-dev \
+    libsundials-dev \
+    libvtk9.3 \
+    libvtk9-dev \
+    libxerces-c-dev \
+    petsc-dev \
+    xsdcxx
+elif [ "${codename}" = 'questing' ]; then
+  # Install manually: Ubuntu 25.10 Questing Quokka repository not yet available
   apt-get install -y --no-install-recommends \
     hdf5-tools \
     libboost-serialization-dev \