Bump dependency version in Dockerfiles (#3394)

* Version bumps in Dockerfile

* Fix cython install

* Revert HDF5 version bump

* Format fixes

* HDF5 filename updates

* Fix HDF5 tarball names

* More HDF5 updates

.github/workflows/pyvista.yml

@@ -20,8 +20,8 @@ jobs:
       # For pyvista/pyvistaqt
       DISPLAY: ":99.0"
       PYVISTA_OFF_SCREEN: true
-      PYVISTA_QT_VERSION: 0.11.0
-      PYVISTA_VERSION: 0.43.10
+      PYVISTA_QT_VERSION: 0.11.1
+      PYVISTA_VERSION: 0.44.1
       QT_DEBUG_PLUGINS: 1
 
       PETSC_ARCH: ${{ matrix.petsc_arch }}

docker/Dockerfile.end-user

@@ -34,7 +34,7 @@
 #    echo "FROM dolfinx/dolfinx-onbuild:nightly" | docker build -f- .
 #
 
-ARG PYVISTA_VERSION=0.43.8
+ARG PYVISTA_VERSION=0.44.1
 
 # Used to set the correct PYTHONPATH for the real and complex install of
 # DOLFINx
@@ -170,7 +170,7 @@ RUN dpkgArch="$(dpkg --print-architecture)"; \
       pip install --no-cache-dir pyvista[trame]==${PYVISTA_VERSION} ;; \
     esac; \
     case "$dpkgArch" in arm64) \
-      pip install --no-cache-dir https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.3.0-cp312/vtk-9.3.0.dev0-cp312-cp312-linux_aarch64.whl && \ 
+      pip install --no-cache-dir https://github.com/finsberg/vtk-aarch64/releases/download/vtk-9.3.0-cp312/vtk-9.3.0.dev0-cp312-cp312-linux_aarch64.whl && \
       pip install --no-cache-dir pyvista[trame]==${PYVISTA_VERSION} ;; \
     esac; \
     pip cache purge

docker/Dockerfile.redhat

@@ -7,10 +7,8 @@ FROM rockylinux/rockylinux:9
 
 ARG BUILD_NP=4
 
-ARG HDF5_SERIES=1.14
-ARG HDF5_PATCH=3
-ARG HDF5_FIX=
-ARG PETSC_VERSION=3.21.3
+ARG HDF5_VERSION=1.14.4.3
+ARG PETSC_VERSION=3.21.5
 ARG MPICH_VERSION=4.2.2
 
 WORKDIR /tmp
@@ -54,9 +52,9 @@ RUN curl -L -O https://www.mpich.org/static/downloads/${MPICH_VERSION}/mpich-${M
     rm -rf /tmp/*
 
 # Build HDF5
-RUN curl -L -O https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    tar -xf hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    cd hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX} && \
+RUN curl -L -O https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${HDF5_VERSION}.tar.gz && \
+    tar -xf hdf5_${HDF5_VERSION}.tar.gz && \
+    cd hdf5-hdf5_${HDF5_VERSION} && \
     ./configure --prefix=/usr/local --enable-parallel --enable-shared --enable-static=no && \
     make -j${BUILD_NP} install && \
     rm -rf /tmp/*

docker/Dockerfile.test-env

@@ -13,14 +13,12 @@
 #
 
 ARG ADIOS2_VERSION=2.10.1
-ARG DOXYGEN_VERSION=1_11_0
+ARG DOXYGEN_VERSION=1_12_0
 ARG GMSH_VERSION=4_13_1
-ARG HDF5_SERIES=1.14
-ARG HDF5_PATCH=3
-ARG HDF5_FIX=
+ARG HDF5_VERSION=1.14.4.3
 ARG KAHIP_VERSION=3.16
-ARG NUMPY_VERSION=1.26.4
-ARG PETSC_VERSION=3.21.3
+ARG NUMPY_VERSION=2.1.1
+ARG PETSC_VERSION=3.21.5
 ARG SLEPC_VERSION=3.21.1
 
 ARG MPICH_VERSION=4.2.2
@@ -35,9 +33,7 @@ LABEL description="FEniCS testing and development environment with PETSc real, c
 
 ARG DOXYGEN_VERSION
 ARG GMSH_VERSION
-ARG HDF5_SERIES
-ARG HDF5_PATCH
-ARG HDF5_FIX
+ARG HDF5_VERSION
 ARG PETSC_VERSION
 ARG SLEPC_VERSION
 ARG ADIOS2_VERSION
@@ -149,7 +145,7 @@ RUN python3 -m venv ${VIRTUAL_ENV}
 
 # Install Python packages (via pip)
 RUN pip install --no-cache-dir --upgrade pip setuptools wheel && \
-    pip install --no-cache-dir numpy==${NUMPY_VERSION} && \
+    pip install --no-cache-dir cython numpy==${NUMPY_VERSION} && \
     pip install --no-cache-dir --no-build-isolation mpi4py
 
 # Install KaHIP
@@ -165,9 +161,9 @@ RUN wget -nc --quiet https://github.com/kahip/kahip/archive/v${KAHIP_VERSION}.ta
 # HDF5 overrides CMAKE_INSTALL_PREFIX by default, hence it is set
 # below to ensure that HDF5 is installed into a path where it can be
 # found.
-RUN wget -nc --quiet https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${HDF5_SERIES}/hdf5-${HDF5_SERIES}.${HDF5_PATCH}/src/hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    tar xfz hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX}.tar.gz && \
-    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-${HDF5_SERIES}.${HDF5_PATCH}${HDF5_FIX} && \
+RUN wget -nc --quiet https://github.com/HDFGroup/hdf5/archive/refs/tags/hdf5_${HDF5_VERSION}.tar.gz && \
+    tar xfz hdf5_${HDF5_VERSION}.tar.gz && \
+    cmake -G Ninja -DCMAKE_INSTALL_PREFIX=/usr/local -DCMAKE_BUILD_TYPE=Release -DHDF5_ENABLE_PARALLEL=on -DHDF5_ENABLE_Z_LIB_SUPPORT=on -B build-dir -S hdf5-hdf5_${HDF5_VERSION} && \
     cmake --build build-dir && \
     cmake --install build-dir && \
     rm -rf /tmp/*
@@ -316,9 +312,7 @@ RUN apt-get -qq update && \
     make PETSC_ARCH=linux-gnu-complex128-64 ${MAKEFLAGS} all && \
     # Install petsc4py
     cd src/binding/petsc4py && \
-    pip install --no-cache-dir cython && \
     PETSC_ARCH=linux-gnu-real32-32:linux-gnu-complex64-32:linux-gnu-real64-32:linux-gnu-complex128-32:linux-gnu-real64-64:linux-gnu-complex128-64 pip -v install --no-cache-dir --no-build-isolation . && \
-    pip3 uninstall --yes cython && \
     # Cleanup
     apt-get -y purge bison flex && \
     apt-get -y autoremove && \
@@ -359,9 +353,7 @@ RUN git clone --depth=1 -b v${SLEPC_VERSION} https://gitlab.com/slepc/slepc.git
     make && \
     # Install slepc4py
     cd src/binding/slepc4py && \
-    pip3 install --no-cache-dir cython && \
     PETSC_ARCH=linux-gnu-real32-32:linux-gnu-complex64-32:linux-gnu-real64-32:linux-gnu-complex128-32:linux-gnu-real64-64:linux-gnu-complex128-64 pip -v install --no-cache-dir --no-build-isolation . && \
-    pip3 uninstall --yes cython && \
     rm -rf ${SLEPC_DIR}/CTAGS ${SLEPC_DIR}/TAGS ${SLEPC_DIR}/docs ${SLEPC_DIR}/src/ ${SLEPC_DIR}/**/obj/ ${SLEPC_DIR}/**/test/ && \
     rm -rf /tmp/*
 

python/dolfinx/wrappers/la.cpp

@@ -138,7 +138,7 @@ void declare_objects(nb::module_& m, const std::string& type)
              std::size_t nrows = self.num_all_rows() * bs[0];
              std::size_t ncols = self.index_map(1)->size_global() * bs[1];
              auto dense = self.to_dense();
-             assert(nrows*ncols == dense.size());
+             assert(nrows * ncols == dense.size());
              return dolfinx_wrappers::as_nbarray(std::move(self.to_dense()),
                                                  {nrows, ncols});
            })

python/dolfinx/wrappers/refinement.cpp

@@ -47,8 +47,9 @@ void export_refinement_with_variable_mesh_type(nb::module_& m)
       [](const dolfinx::mesh::Mesh<T>& mesh, bool redistribute,
          dolfinx::mesh::GhostMode ghost_mode)
       {
-        auto [mesh_refined, parent_cells] = dolfinx::refinement::refine_interval(
-            mesh, std::nullopt, redistribute, ghost_mode);
+        auto [mesh_refined, parent_cells]
+            = dolfinx::refinement::refine_interval(mesh, std::nullopt,
+                                                   redistribute, ghost_mode);
         return std::tuple(std::move(mesh_refined),
                           as_nbarray(std::move(parent_cells)));
       },