Update force class names following Chaste force restructure by Copilot · Pull Request #3 · Chaste/CellBasedComparison2017

Copilot · 2026-05-03T09:26:53Z

Following the Chaste force restructure (#513), several force classes were renamed. This PR updates all four test files to use the correct replacement classes.

Changes

TestCylindricalCryptLiteratePaper.hpp — adds LinearSpringForce.hpp and PathmanathanInteractionForce.hpp; removes unused RepulsionForce.hpp
TestDeltaNotchLiteratePaper.hpp — replaces GeneralisedLinearSpringForce.hpp with LinearSpringForce.hpp and PathmanathanInteractionForce.hpp; removes unused RepulsionForce.hpp
TestMorphogenMonolayerLiteratePaper.hpp — same include swaps as above
TestCellSortingLiteratePaper.hpp — replaces DifferentialAdhesionGeneralisedLinearSpringForce.hpp with DifferentialAdhesionPathmanathanInteractionForce.hpp (node-based) and DifferentialAdhesionLinearSpringForce.hpp (mesh-based)

In each file, MAKE_PTR usages are updated accordingly:

// NodeBasedCellPopulation — was GeneralisedLinearSpringForce
MAKE_PTR(PathmanathanInteractionForce<2>, p_linear_force);

// MeshBasedCellPopulation — was GeneralisedLinearSpringForce
MAKE_PTR(LinearSpringForce<2>, p_linear_force);

// Node-based cell sorting — was DifferentialAdhesionGeneralisedLinearSpringForce
MAKE_PTR(DifferentialAdhesionPathmanathanInteractionForce<2>, p_differential_adhesion_force);

// Mesh-based cell sorting — was DifferentialAdhesionGeneralisedLinearSpringForce
MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force);

Copilot

Copilot wasn't able to review any files in this pull request.

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

…hanInteractionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/900d25b2-02ee-49b4-a57c-9484fa59c3e8 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com>

jmosborne · 2026-05-03T09:32:32Z

@copilot Also replace DifferentialAdhesionGeneralisedLinearSpringForce and RepulsionForce as per the instructions in Chaste/Chaste#513

…ulsionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/5b619335-e853-4cb5-b76a-ee1e7e6c54a5 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com>

Copilot · 2026-05-03T09:34:47Z

@copilot Also replace DifferentialAdhesionGeneralisedLinearSpringForce and RepulsionForce as per the instructions in Chaste/Chaste#513

Done in commit 87c1aeb:

DifferentialAdhesionGeneralisedLinearSpringForce → DifferentialAdhesionLinearSpringForce (include + 2× MAKE_PTR in TestCellSortingLiteratePaper.hpp)
RepulsionForce → LogarithmicRepulsionForce (include rename in TestCylindricalCryptLiteratePaper.hpp, TestDeltaNotchLiteratePaper.hpp, and TestMorphogenMonolayerLiteratePaper.hpp)

jmosborne

@copilot make these changes

jmosborne · 2026-05-03T09:39:50Z


        // Create a force law and pass it to the simulation
-        MAKE_PTR(DifferentialAdhesionGeneralisedLinearSpringForce<2>, p_differential_adhesion_force);
+        MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force);


Suggested change

MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force);

MAKE_PTR(DifferentialAdhesionPathmanathanInteractionForce<2>, p_differential_adhesion_force);

Updated in commit 45fb0ec — node-based test now uses DifferentialAdhesionPathmanathanInteractionForce<2>, mesh-based test keeps DifferentialAdhesionLinearSpringForce<2>.

jmosborne · 2026-05-03T09:40:33Z


 #include "NagaiHondaForce.hpp"
-#include "RepulsionForce.hpp"
+#include "LogarithmicRepulsionForce.hpp"


Suggested change

#include "LogarithmicRepulsionForce.hpp"

Removed in commit 45fb0ec.

jmosborne · 2026-05-03T09:41:13Z

 #include "DiffusionForce.hpp"
-#include "RepulsionForce.hpp"
-#include "GeneralisedLinearSpringForce.hpp"
+#include "LogarithmicRepulsionForce.hpp"


Suggested change

#include "LogarithmicRepulsionForce.hpp"

Removed in commit 45fb0ec.

jmosborne · 2026-05-03T09:41:32Z


 #include "NodeBasedCellPopulation.hpp"
-#include "RepulsionForce.hpp"
+#include "LogarithmicRepulsionForce.hpp"


Suggested change

#include "LogarithmicRepulsionForce.hpp"

Removed in commit 45fb0ec.

…Force for node-based, remove LogarithmicRepulsionForce includes Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/e5f2f4ab-5362-4bf4-b7fe-7e898948ccde Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com>

Copilot · 2026-05-03T09:44:18Z

@copilot make these changes

Done in commit 45fb0ec.

Co-authored-by: Copilot <copilot@github.com>

jmosborne

All Pass on my local machine with the correct branch

Initial plan

fed549e

Copilot AI assigned Copilot and jmosborne May 3, 2026

Copilot started work on behalf of jmosborne May 3, 2026 09:26 View session

Copilot AI linked an issue May 3, 2026 that may be closed by this pull request

Update User Project following Force restructure in https://github.com/Chaste/Chaste/issues/417 #2

Open

jmosborne marked this pull request as ready for review May 3, 2026 09:28

Copilot AI review requested due to automatic review settings May 3, 2026 09:28

Copilot AI reviewed May 3, 2026

View reviewed changes

Replace GeneralisedLinearSpringForce with LinearSpringForce/Pathmanat…

cec147a

…hanInteractionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/900d25b2-02ee-49b4-a57c-9484fa59c3e8 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com>

jmosborne marked this pull request as draft May 3, 2026 09:29

Copilot AI changed the title ~~[WIP] Update user project forces following restructure~~ Replace GeneralisedLinearSpringForce with LinearSpringForce/PathmanathanInteractionForce May 3, 2026

Copilot finished work on behalf of jmosborne May 3, 2026 09:30

Copilot AI requested a review from jmosborne May 3, 2026 09:30

Copilot started work on behalf of jmosborne May 3, 2026 09:32 View session

Also replace DifferentialAdhesionGeneralisedLinearSpringForce and Rep…

87c1aeb

…ulsionForce Agent-Logs-Url: https://github.com/Chaste/CellBasedComparison2017/sessions/5b619335-e853-4cb5-b76a-ee1e7e6c54a5 Co-authored-by: jmosborne <2212095+jmosborne@users.noreply.github.com>

Copilot AI changed the title ~~Replace GeneralisedLinearSpringForce with LinearSpringForce/PathmanathanInteractionForce~~ Update force class names following Chaste force restructure May 3, 2026

Copilot finished work on behalf of jmosborne May 3, 2026 09:35

jmosborne reviewed May 3, 2026

View reviewed changes

Copilot started work on behalf of jmosborne May 3, 2026 09:42 View session

Copilot finished work on behalf of jmosborne May 3, 2026 09:44

Copilot AI requested a review from jmosborne May 3, 2026 09:44

Updating User Project to Latest Force Hierachy

c9aaded

Co-authored-by: Copilot <copilot@github.com>

jmosborne approved these changes May 3, 2026

View reviewed changes

jmosborne marked this pull request as ready for review May 3, 2026 11:52

	MAKE_PTR(DifferentialAdhesionLinearSpringForce<2>, p_differential_adhesion_force);
	MAKE_PTR(DifferentialAdhesionPathmanathanInteractionForce<2>, p_differential_adhesion_force);

Conversation

Copilot AI commented May 3, 2026 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Changes

Uh oh!

Copilot AI left a comment

Choose a reason for hiding this comment

Uh oh!

jmosborne commented May 3, 2026

Uh oh!

Copilot AI commented May 3, 2026

Uh oh!

jmosborne left a comment

Choose a reason for hiding this comment

Uh oh!

jmosborne May 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI May 3, 2026

Choose a reason for hiding this comment

Uh oh!

jmosborne May 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI May 3, 2026

Choose a reason for hiding this comment

Uh oh!

jmosborne May 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI May 3, 2026

Choose a reason for hiding this comment

Uh oh!

jmosborne May 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI May 3, 2026

Choose a reason for hiding this comment

Uh oh!

Copilot AI commented May 3, 2026

Uh oh!

jmosborne left a comment

Choose a reason for hiding this comment

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Copilot AI commented May 3, 2026 •

edited

Loading