Cleanup: remove duplicate and unused #include statements by mirams · Pull Request #516 · Chaste/Chaste

mirams · 2026-04-30T16:17:41Z

Removes 99 include lines across 48 files:

30 exact-duplicate includes (same header in same file twice)
69 unused class headers where the included type is never referenced in that translation unit (verified: class name absent from all code outside the include line, or already pulled in transitively by another included header)

Removes 67 net include lines across 48 files: - 30 duplicate includes (second occurrence of same header in same file) - 41 unused class headers where the included type is never referenced in that translation unit Two corrections applied after build verification: - SlidingBoundaryCondition.cpp: replaced implicit AbstractOffLatticeCellPopulation (was pulled in transitively) with a direct include of its own header - LinearSpringWithVariableSpringConstantsForce.cpp: replaced implicit AbstractVanLeeuwen2009WntSwatCellCycleModel with a direct include Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

mirams · 2026-04-30T17:38:40Z

@copilot, implement the two changes in my comments above

- Restore #include "CellBasedEventHandler.hpp" in TestCryptSimulation2dNightly.hpp (line 440, inside a comment) - Restore #include "CheckpointArchiveTypes.hpp" in SerializationExportWrapper.hpp (needed to prevent test failures) Agent-Logs-Url: https://github.com/Chaste/Chaste/sessions/700e2e49-eb95-4d02-99b8-16207f5546c0 Co-authored-by: mirams <858776+mirams@users.noreply.github.com>

Copilot

Pull request overview

This PR cleans up C++ #include lists across the codebase by removing duplicate includes and trimming headers that are no longer directly needed, reducing compile-time overhead and improving translation-unit hygiene.

Changes:

Remove exact-duplicate #include lines within the same file.
Remove headers for types not referenced in the translation unit (or already included elsewhere).
In a few places, replace overly-specific headers with a more appropriate/common header.

Reviewed changes

Copilot reviewed 46 out of 46 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
pde/test/TestSolveLaplacianWithQuadratics.hpp	Removes an unnecessary include from the test TU.
ode/src/solver/BackwardEulerIvpOdeSolver.hpp	Removes a redundant include from the solver header.
mesh/src/vertex/VertexMeshWriter.cpp	Drops unused mesh-type includes from the writer TU.
lung/test/ventilation/TestDynamicVentilation.hpp	Removes an unnecessary include from the test TU.
lung/src/airway_generation/AirwayGenerator.cpp	Removes an unused VTK include from the TU.
heart/test/tutorials/TestCardiacElectroMechanicsTutorial.hpp	Removes a duplicate include.
heart/test/tutorials/TestAnotherCardiacElectroMechanicsTutorial.hpp	Removes a duplicate include.
heart/test/postprocessing/TestPseudoEcgCalculator.hpp	Removes duplicate/unused includes from the test TU.
heart/test/monodomain/TestMonodomainPurkinjeProblemLong.hpp	Removes an unnecessary mesh include.
heart/test/monodomain/TestMonodomainPurkinjeAssemblersAndSolver.hpp	Removes an unnecessary mesh include.
heart/test/ionicmodels/TestCvodeCells.hpp	Removes an unused include from the test TU.
heart/test/extended_bidomain/TestStimulusFactory.hpp	Removes an unused stimulus-factory include.
heart/test/bidomain/TestBidomainTissue.hpp	Removes an unnecessary include from the test TU.
heart/src/postprocessing/PostProcessingWriter.cpp	Removes unused converter includes from the TU.
global/src/Exception.cpp	Removes a duplicate/unused include from the TU.
crypt/src/simulation/CryptSimulation2d.cpp	Removes unused concrete-model includes from the TU.
crypt/src/forces/LinearSpringWithVariableSpringConstantsForce.cpp	Replaces concrete-model includes with the abstract base model include.
continuum_mechanics/test/TestCompressibleNonlinearElasticitySolver.hpp	Removes a duplicate include.
cell_based/test/tutorial/TestCreatingAndUsingANewSrnModelTutorial.hpp	Removes an include and keeps export macro usage in the tutorial TU.
cell_based/test/simulation/TestOnLatticeSimulationWithPdes.hpp	Removes an unused simulation include.
cell_based/test/simulation/TestOffLatticeSimulationWithPdes.hpp	Removes an unnecessary PETSc setup include.
cell_based/test/population/TestMeshBasedCellPopulationWithGhostNodes.hpp	Removes unused writer includes.
cell_based/test/population/TestCellWriters.hpp	Removes a duplicate include.
cell_based/test/cell/TestCellSrn.hpp	Removes an unused include.
cell_based/test/cell/TestCell.hpp	Removes unused proliferative-type includes.
cell_based/test/cell_based_pde/TestSimulationsWithEllipticGrowingDomainPdeModifier.hpp	Removes an unused include.
cell_based/src/writers/population_writers/VoronoiDataWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/VertexT3SwapLocationsWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/VertexT2SwapLocationsWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/VertexT1SwapLocationsWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/VertexIntersectionSwapLocationsWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/NodeVelocityWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/CellPopulationAreaWriter.cpp	Removes an unused base population include.
cell_based/src/writers/population_writers/AbstractCellPopulationWriter.cpp	Removes unused concrete-population includes.
cell_based/src/writers/population_count_writers/AbstractCellPopulationCountWriter.cpp	Removes unused concrete-population includes.
cell_based/src/writers/cell_writers/ImmersedBoundaryNeighbourNumberWriter.cpp	Removes an unused immersed-boundary include.
cell_based/src/writers/cell_writers/CellProliferativeTypesWriter.cpp	Removes unused property/mutation includes.
cell_based/src/simulation/numerical_methods/AbstractNumericalMethod.cpp	Removes an unused population include.
cell_based/src/simulation/modifiers/DeltaNotchEdgeTrackingModifier.cpp	Removes an unused SRN-model include.
cell_based/src/population/VertexBasedCellPopulation.cpp	Removes an unused SRN-model include.
cell_based/src/population/NodeBasedCellPopulationWithParticles.cpp	Removes unused writer includes.
cell_based/src/population/MeshBasedCellPopulation.cpp	Removes an unused mesh include.
cell_based/src/population/forces/DiffusionForce.cpp	Removes an unused population include.
cell_based/src/population/boundary_conditions/SlidingBoundaryCondition.cpp	Replaces overly-specific population includes with the off-lattice base include.
cell_based/src/population/AbstractCellPopulation.cpp	Removes unused count-writer includes.
cell_based/src/cell/Cell.cpp	Removes an unused property include.

💡 Add Copilot custom instructions for smarter, more guided reviews. Learn how to get started.

fcooper8472

Other than those two copilot suggestions, this looks good to me!

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Copilot · 2026-06-03T15:49:23Z

@copilot, implement the two changes in my comments above

Implemented in 533bd70 and a8b5fb0.

…into modernize/include-cleanup

mirams force-pushed the modernize/include-cleanup branch from eb5bb0a to fde6e88 Compare April 30, 2026 16:51

mirams commented Apr 30, 2026

View reviewed changes

Comment thread crypt/test/simulation/TestCryptSimulation2dNightly.hpp

mirams commented Apr 30, 2026

View reviewed changes

Comment thread global/src/checkpointing/SerializationExportWrapper.hpp

Copilot started work on behalf of mirams April 30, 2026 17:38 View session

Copilot finished work on behalf of mirams April 30, 2026 17:41

mirams marked this pull request as ready for review May 19, 2026 12:33

mirams requested review from Copilot, fcooper8472 and jmpf May 19, 2026 12:33

Copilot started reviewing on behalf of mirams May 19, 2026 12:33 View session

Copilot AI reviewed May 19, 2026

View reviewed changes

Comment thread crypt/src/simulation/CryptSimulation2d.cpp

Comment thread cell_based/test/tutorial/TestCreatingAndUsingANewSrnModelTutorial.hpp Outdated

fcooper8472 reviewed May 19, 2026

View reviewed changes

Comment thread cell_based/test/tutorial/TestCreatingAndUsingANewSrnModelTutorial.hpp Outdated

Comment thread crypt/src/simulation/CryptSimulation2d.cpp

Copilot started work on behalf of mirams June 2, 2026 08:56 View session

mirams and others added 2 commits June 2, 2026 09:57

Potential fix for pull request finding

533bd70

Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>

Fix explicit Wnt cell cycle include

a8b5fb0

Copilot finished work on behalf of mirams June 2, 2026 09:01

Copilot started work on behalf of mirams June 3, 2026 15:46 View session

Move PDE modifier include to end

b1e7053

mirams added 2 commits June 3, 2026 16:49

Make sure petsc setup and finalise is where it should be

be8f09d

Merge branch 'modernize/include-cleanup' of github.com:Chaste/Chaste …

32eda0c

…into modernize/include-cleanup

Copilot finished work on behalf of mirams June 3, 2026 15:49

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Cleanup: remove duplicate and unused #include statements#516

Cleanup: remove duplicate and unused #include statements#516
mirams wants to merge 7 commits into
developfrom
modernize/include-cleanup

mirams commented Apr 30, 2026

Uh oh!

Uh oh!

Uh oh!

mirams commented Apr 30, 2026

Uh oh!

Copilot AI left a comment

Uh oh!

Uh oh!

Uh oh!

fcooper8472 left a comment

Uh oh!

Uh oh!

Uh oh!

Copilot AI commented Jun 3, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants

Conversation

mirams commented Apr 30, 2026

Uh oh!

Uh oh!

Uh oh!

mirams commented Apr 30, 2026

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Pull request overview

Reviewed changes

Uh oh!

Uh oh!

Uh oh!

fcooper8472 left a comment

Choose a reason for hiding this comment

Uh oh!

Uh oh!

Uh oh!

Copilot AI commented Jun 3, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

4 participants