scientificcomputing · finsberg · Jun 10, 2026
diff --git a/.github/workflows/create_legacy_checkpoint.yml b/.github/workflows/create_legacy_checkpoint.yml
@@ -15,7 +15,7 @@ jobs:
       adios4dolfinx_version: "0.7.1"
     runs-on: "ubuntu-latest"
     container: ghcr.io/fenics/dolfinx/dolfinx:v0.7.3
-  
+
     steps:
       - uses: actions/checkout@v6
 

diff --git a/.github/workflows/create_legacy_data.yml b/.github/workflows/create_legacy_data.yml
@@ -13,7 +13,7 @@ jobs:
   create-dolfin-data:
     env:
       data_dir: "legacy"
-  
+
     runs-on: "ubuntu-latest"
     container: ghcr.io/scientificcomputing/fenics:2024-02-19
     steps:

diff --git a/.github/workflows/test_dolfinx_versions.yml b/.github/workflows/test_dolfinx_versions.yml
@@ -27,8 +27,8 @@ jobs:
       fail-fast: false
       matrix:
         tag: ["nightly", "stable"]
-    
+
     # Call the reusable workflow
     uses: ./.github/workflows/test_workflow.yml
     with:
-      dolfinx_tag: ${{ matrix.tag }}
+      dolfinx_tag: ${{ matrix.tag }}
diff --git a/.github/workflows/test_workflow.yml b/.github/workflows/test_workflow.yml
@@ -67,4 +67,4 @@ jobs:
         with:
           name: code-coverage-report-${{ inputs.dolfinx_tag }}
           path: htmlcov
-          if-no-files-found: error
+          if-no-files-found: error
diff --git a/.gitignore b/.gitignore
@@ -139,4 +139,4 @@ output/
 *.xdmf
 *.bp/
 *.pvd
-*.vtu
+*.vtu
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -1,6 +1,17 @@
 # See https://pre-commit.com for more information
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+        args: ['--maxkb=3000']
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: check-toml
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: 'v0.15.16'

diff --git a/README.md b/README.md
@@ -66,7 +66,7 @@ For scalability, the code uses [MPI Neighbourhood collectives](https://www.mpi-f
 ### Mesh IO (Import/Export)
 Most meshing formats supports associating data with the nodes of the mesh (the mesh can be higher order) and the cells of the mesh. The node data can be read in as P-th order Lagrange functions (where P is the order of the grid), while the cell data can be read in as piecewise constant (DG-0) functions.
 
-- [VTKHDF](./docs/backends/vtkhdf.rst): The new scalable format from VTK, called [VTKHDF](https://docs.vtk.org/en/latest/vtk_file_formats/vtkhdf_file_format/index.html) is supported by the `vtkhdf` backend. 
+- [VTKHDF](./docs/backends/vtkhdf.rst): The new scalable format from VTK, called [VTKHDF](https://docs.vtk.org/en/latest/vtk_file_formats/vtkhdf_file_format/index.html) is supported by the `vtkhdf` backend.
 - [XDMF](./docs/backends/xdmf.rst) (eXtensible Model Data Format): `.xdmf`. The `xdmf` backend supports the `HDF5` encoding, to ensure performance in parallel.
 - [PyVista](./docs/backends/pyvista.rst) (IO backend is meshio): The [pyvista](https://pyvista.org/) backend uses {py:func}`pyvista.read` to read in meshes, point data and cell data. `pyvista` relies on [meshio](https://github.com/nschloe/meshio) for most reading operations (including the XDMF ascii format).
 
@@ -107,4 +107,4 @@ Please read [CONTRIBUTING.md](CONTRIBUTING.md) for details on our code of conduc
 
 
 ## LICENSE
-This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
+This project is licensed under the MIT License - see the [LICENSE](LICENSE) file for details.
diff --git a/_toc.yml b/_toc.yml
@@ -10,7 +10,7 @@ parts:
     - file: "docs/migration_guide"
     - file: "docs/testing.md"
     - file: "docs/reading_legacy_data"
-    
+
   - caption: Introduction to IPyParallel
     chapters:
     - file: "docs/ipyparallel_intro"
@@ -39,4 +39,4 @@ parts:
 
   - caption: Contributing
     chapters:
-    - file: "CONTRIBUTING"
+    - file: "CONTRIBUTING"
diff --git a/build-requirements.txt b/build-requirements.txt
@@ -2,4 +2,4 @@ scikit-build-core[pyproject]>=0.11.0
 nanobind>=1.3.2
 setuptools>=77.0.3
 packaging>=24.2
-pkgconfig
+pkgconfig
diff --git a/docs/adding_backend.md b/docs/adding_backend.md
@@ -98,4 +98,4 @@ def write_mesh(filename: Path | str, comm: MPI.Intracomm, mesh: MeshData,
     pass
 
 # ... Implement all other methods defined in IOBackend ...
-```
+```
diff --git a/docs/backends/adios2.rst b/docs/backends/adios2.rst
@@ -11,4 +11,4 @@ Therefore `ADIOS2` should not be install through PYPI/pip, but has to be install
 
 .. automodule:: io4dolfinx.backends.adios2.backend
     :members:
-    :exclude-members: read_point_data
+    :exclude-members: read_point_data
diff --git a/docs/backends/h5py.rst b/docs/backends/h5py.rst
@@ -34,4 +34,4 @@ Note that this code block does not install DOLFINx, it just illustrates how to g
 
 .. automodule:: io4dolfinx.backends.h5py.backend
     :members:
-    :exclude-members: read_point_data
+    :exclude-members: read_point_data
diff --git a/docs/backends/pyvista.rst b/docs/backends/pyvista.rst
@@ -5,4 +5,4 @@ PyVista-backend
 
 .. automodule:: io4dolfinx.backends.pyvista.backend
     :members:
-    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
+    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
diff --git a/docs/backends/vtkhdf.rst b/docs/backends/vtkhdf.rst
@@ -8,4 +8,4 @@ See that backend for detailed installation instructions.
 
 .. automodule:: io4dolfinx.backends.vtkhdf.backend
     :members:
-    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
+    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
diff --git a/docs/backends/xdmf.rst b/docs/backends/xdmf.rst
@@ -8,4 +8,4 @@ See that backend for detailed installation instructions.
 
 .. automodule:: io4dolfinx.backends.xdmf.backend
     :members:
-    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
+    :exclude-members: read_attributes, read_timestamps, write_attributes, write_mesh, write_meshtags, read_meshtags_data, read_dofmap, read_dofs, read_cell_perms, write_function, read_legacy_mesh, snapshot_checkpoint, read_hdf5_array
diff --git a/docs/migration_guide.md b/docs/migration_guide.md
@@ -80,5 +80,3 @@ io4dolfinx.write_function("solution.bp", u, time=0.0, backend="h5py")
 ```
 ````
 `````
-
-
diff --git a/docs/quickstart.md b/docs/quickstart.md
@@ -171,5 +171,3 @@ the `backend` argument to most functions.
 
 
 5.  **`xdmf`**: Basic support for reading XDMF data.
-
-
diff --git a/docs/reading_legacy_data.md b/docs/reading_legacy_data.md
@@ -66,7 +66,7 @@ filename = "legacy_data.h5"
 mesh = io4dolfinx.read_mesh_from_legacy_h5(filename, comm, group="/mesh")
 ```
 
-#### Create the appropriate FunctionSpace 
+#### Create the appropriate FunctionSpace
 You must know the element family and degree used in the legacy simulation
 ```python
 V = dolfinx.fem.functionspace(mesh, ("Lagrange", 1))

diff --git a/docs/testing.md b/docs/testing.md
@@ -110,4 +110,4 @@ To ensure broad support, specific workflows test against different configuration
 ### 3. Documentation (`build_docs.yml`)
 
 Ensures the documentation builds correctly with `jupyter-book` on every push and
-pull request, preventing documentation regressions.
+pull request, preventing documentation regressions.
diff --git a/pyproject.toml b/pyproject.toml
@@ -6,7 +6,7 @@ name = "io4dolfinx"
 version = "1.2.0"
 description = "Checkpointing functionality for DOLFINx meshes/functions with ADIOS2"
 authors = [
-    { name = "Jørgen S. Dokken", email = "dokken@simula.no" }, 
+    { name = "Jørgen S. Dokken", email = "dokken@simula.no" },
     { name = "Henrik N.T. Finsberg", email = "henriknf@simula.no" }
 ]
 license = { file = "LICENSE" }
@@ -15,11 +15,11 @@ dependencies = ["fenics-dolfinx>=0.10.0", "packaging"]
 
 [project.optional-dependencies]
 test = [
-    "pytest", 
-    "coverage", 
-    "ipyparallel", 
-    "io4dolfinx[h5py]", 
-    "io4dolfinx[pyvista]", 
+    "pytest",
+    "coverage",
+    "ipyparallel",
+    "io4dolfinx[h5py]",
+    "io4dolfinx[pyvista]",
     "io4dolfinx[xdmf]"
 ]
 dev = ["pdbpp", "ipython", "mypy", "ruff"]

diff --git a/src/io4dolfinx/comm_helpers.py b/src/io4dolfinx/comm_helpers.py
@@ -1,3 +1,7 @@
+"""
+Helpers for sending and receiving values for checkpointing
+"""
+
 from __future__ import annotations
 
 from mpi4py import MPI
@@ -13,9 +17,6 @@
     "send_dofs_and_recv_values",
     "numpy_to_mpi",
 ]
-"""
-Helpers for sending and receiving values for checkpointing
-"""
 
 numpy_to_mpi = {
     np.float64: MPI.DOUBLE,

diff --git a/src/io4dolfinx/structures.py b/src/io4dolfinx/structures.py
@@ -1,3 +1,4 @@
+"""Internal library classes for storing mesh and function data"""
 # Copyright (C) 2024 Jørgen Schartum Dokken
 #
 # This file is part of io4dolfinx
@@ -12,7 +13,6 @@
 import numpy.typing as npt
 from dolfinx.graph import AdjacencyList
 
-"""Internal library classes for storing mesh and function data"""
 __all__ = ["MeshData", "FunctionData", "ReadMeshData", "MeshTagsData"]
-Original file line number
+Diff line change
@@ Expand Up / @@ -139,4 +139,4 @@ output/ @@
     *.xdmf
     *.bp/
     *.pvd
-    *.vtu
+    *.vtu
Original file line number	Diff line number	Diff line change
Expand Up		@@ -80,5 +80,3 @@ io4dolfinx.write_function("solution.bp", u, time=0.0, backend="h5py")
		```
		````
		`````
Original file line number	Diff line number	Diff line change
Expand Up		@@ -171,5 +171,3 @@ the `backend` argument to most functions.


		5. `xdmf`: Basic support for reading XDMF data.