Update README.md by bencox · Pull Request #245 · ucl-bug/k-wave-ii

bencox · 2026-05-28T15:53:45Z

Summary

Updated README.md, contributor guidelines, etc

I've changed this quite a bit to lower both the apparent and actual barriers to getting users started on contributing. I've slightly relaxed the requirements for very small contributions, while maintaining them for significant contributions.

minor URL update

Tiny change to a title

Added instructions on how to install matlab and create the documentation.

Minor re-wording and rearrangements.

Link update.

Minor typo

typo

Few minor changes.

Small changes, as we will allow PRs into develop for minor fixes. Not everything tiny change must rigidly go through a feature branch.

github-actions · 2026-05-28T21:31:29Z

Cyclomatic Complexity Check

L 97 (C 22-41): The McCabe cyclomatic complexity of 'initialiseSensorData' is 19.
L 153 (C 24-39): The McCabe cyclomatic complexity of 'recordSensorData' is 6.
L 159 (C 24-37): The McCabe cyclomatic complexity of 'AcousticSolver' is 5.
L 189 (C 29-40): The McCabe cyclomatic complexity of 'get.pressure' is 1.
L 192 (C 33-48): The McCabe cyclomatic complexity of 'get.densitySplit' is 1.
L 195 (C 29-40): The McCabe cyclomatic complexity of 'get.velocity' is 1.
L 38 (C 21-39): The McCabe cyclomatic complexity of 'autoComputeTimeStep' is 3.
L 35 (C 10-24): The McCabe cyclomatic complexity of 'executeTimeStep' is 25.
L 61 (C 7): The McCabe cyclomatic complexity of the anonymous function on line 61 is 1.
L 62 (C 9): The McCabe cyclomatic complexity of the anonymous function on line 62 is 1.
L 63 (C 12): The McCabe cyclomatic complexity of the anonymous function on line 63 is 1.
L 64 (C 14): The McCabe cyclomatic complexity of the anonymous function on line 64 is 1.
L 68 (C 54-77): The McCabe cyclomatic complexity of 'buildAbsorptionOperators' is 2.
L 49 (C 23-42): The McCabe cyclomatic complexity of 'kappaSplitCorrection' is 2.
L 47 (C 10-34): The McCabe cyclomatic complexity of 'setAbsorptionCoefficients' is 5.
L 38 (C 10-29): The McCabe cyclomatic complexity of 'setInitialConditions' is 2.
L 36 (C 10-28): The McCabe cyclomatic complexity of 'setkSpaceCorrection' is 2.

L 67 (C 41-64): The McCabe cyclomatic complexity of 'get.sourceFieldMagnitude' is 1.
L 72 (C 37-56): The McCabe cyclomatic complexity of 'get.sourceFieldPhase' is 1.

L 170 (C 24-41): The McCabe cyclomatic complexity of 'FourierCollocation' is 1.
L 207 (C 18-26): The McCabe cyclomatic complexity of 'set.kappa' is 2.
L 60 (C 14-17): The McCabe cyclomatic complexity of 'curl' is 2.
L 65 (C 14-23): The McCabe cyclomatic complexity of 'divergence' is 1.
L 67 (C 14-28): The McCabe cyclomatic complexity of 'divergenceSplit' is 16.
L 59 (C 16-28): The McCabe cyclomatic complexity of 'fracLaplacian' is 4.
L 65 (C 15-22): The McCabe cyclomatic complexity of 'gradient' is 15.
L 38 (C 10-18): The McCabe cyclomatic complexity of 'plotField' is 4.
L 37 (C 14-17): The McCabe cyclomatic complexity of 'sinc' is 1.
L 61 (C 17-23): The McCabe cyclomatic complexity of 'stagger' is 17.
L 193 (C 24-27): The McCabe cyclomatic complexity of 'Grid' is 6.
L 220 (C 23-28): The McCabe cyclomatic complexity of 'get.Nx' is 1.
L 224 (C 23-28): The McCabe cyclomatic complexity of 'get.Ny' is 1.
L 228 (C 23-28): The McCabe cyclomatic complexity of 'get.Nz' is 1.
L 232 (C 23-28): The McCabe cyclomatic complexity of 'get.dx' is 1.
L 236 (C 23-28): The McCabe cyclomatic complexity of 'get.dy' is 1.
L 240 (C 23-28): The McCabe cyclomatic complexity of 'get.dz' is 1.
L 245 (C 25-32): The McCabe cyclomatic complexity of 'get.xVec' is 1.
L 249 (C 25-32): The McCabe cyclomatic complexity of 'get.yVec' is 1.
L 253 (C 25-32): The McCabe cyclomatic complexity of 'get.zVec' is 1.
L 259 (C 22-26): The McCabe cyclomatic complexity of 'get.x' is 4.
L 270 (C 22-26): The McCabe cyclomatic complexity of 'get.y' is 4.
L 281 (C 22-26): The McCabe cyclomatic complexity of 'get.z' is 4.
L 293 (C 26-34): The McCabe cyclomatic complexity of 'get.xSize' is 1.
L 297 (C 26-34): The McCabe cyclomatic complexity of 'get.ySize' is 1.
L 301 (C 26-34): The McCabe cyclomatic complexity of 'get.zSize' is 1.
L 306 (C 22-40): The McCabe cyclomatic complexity of 'get.totalGridPoints' is 1.
L 311 (C 26-34): The McCabe cyclomatic complexity of 'get.kxVec' is 1.
L 315 (C 26-34): The McCabe cyclomatic complexity of 'get.kyVec' is 1.
L 319 (C 26-34): The McCabe cyclomatic complexity of 'get.kzVec' is 1.
L 324 (C 22-26): The McCabe cyclomatic complexity of 'get.k' is 4.
L 344 (C 23-28): The McCabe cyclomatic complexity of 'get.kx' is 4.
L 355 (C 23-28): The McCabe cyclomatic complexity of 'get.ky' is 4.
L 366 (C 23-28): The McCabe cyclomatic complexity of 'get.kz' is 4.
L 378 (C 26-34): The McCabe cyclomatic complexity of 'get.kxMax' is 1.
L 382 (C 26-34): The McCabe cyclomatic complexity of 'get.kyMax' is 1.
L 386 (C 26-34): The McCabe cyclomatic complexity of 'get.kzMax' is 1.
L 390 (C 25-32): The McCabe cyclomatic complexity of 'get.kMax' is 1.
L 43 (C 25-45): The McCabe cyclomatic complexity of 'assignWithGridPadding' is 4.
L 30 (C 10-24): The McCabe cyclomatic complexity of 'displayGridSize' is 2.
L 39 (C 10-22): The McCabe cyclomatic complexity of 'printGridSize' is 4.
L 40 (C 17-30): The McCabe cyclomatic complexity of 'getWavenumbers' is 3.
L 41 (C 22-40): The McCabe cyclomatic complexity of 'highestPrimeFactors' is 1.
L 39 (C 19-42): The McCabe cyclomatic complexity of 'returnWithoutGridPadding' is 4.
L 68 (C 10-21): The McCabe cyclomatic complexity of 'validateSize' is 7.
L 69 (C 24-32): The McCabe cyclomatic complexity of 'GridField' is 1.
L 44 (C 22-40): The McCabe cyclomatic complexity of 'createGridFieldsMap' is 2.

L 158 (C 24-32): The McCabe cyclomatic complexity of 'GridInput' is 2.
L 182 (C 29-38): The McCabe cyclomatic complexity of 'properties' is 1.
L 195 (C 23-34): The McCabe cyclomatic complexity of 'get.gridSize' is 1.
L 40 (C 10-32): The McCabe cyclomatic complexity of 'checkRequiredProperties' is 3.
L 48 (C 20-36): The McCabe cyclomatic complexity of 'getPropertyGroups' is 2.
L 52 (C 16-23): The McCabe cyclomatic complexity of 'subsasgn' is 4.
L 47 (C 22-28): The McCabe cyclomatic complexity of 'subsref' is 4.

L 119 (C 24-29): The McCabe cyclomatic complexity of 'Logger' is 1.
L 126 (C 18-27): The McCabe cyclomatic complexity of 'logMessage' is 4.
L 151 (C 35-45): The McCabe cyclomatic complexity of 'getInstance' is 3.
L 165 (C 18-20): The McCabe cyclomatic complexity of 'log' is 1.
L 175 (C 18-22): The McCabe cyclomatic complexity of 'reset' is 1.
L 180 (C 18-28): The McCabe cyclomatic complexity of 'setLogLevel' is 1.
L 186 (C 18-29): The McCabe cyclomatic complexity of 'setLogToFile' is 1.
L 192 (C 18-36): The McCabe cyclomatic complexity of 'setLogToCommandLine' is 1.
L 198 (C 18-30): The McCabe cyclomatic complexity of 'showTimeStamp' is 1.
L 204 (C 18-22): The McCabe cyclomatic complexity of 'debug' is 1.
L 209 (C 18-21): The McCabe cyclomatic complexity of 'info' is 1.
L 214 (C 18-24): The McCabe cyclomatic complexity of 'warning' is 1.
L 220 (C 18-22): The McCabe cyclomatic complexity of 'error' is 1.
L 84 (C 24-43): The McCabe cyclomatic complexity of 'validateNonNegScalar' is 2.
L 100 (C 24-41): The McCabe cyclomatic complexity of 'validateIndexField' is 6.
L 115 (C 24-32): The McCabe cyclomatic complexity of 'Materials' is 1.
L 140 (C 32-42): The McCabe cyclomatic complexity of 'addMaterial' is 20.
L 238 (C 22-34): The McCabe cyclomatic complexity of 'listMaterials' is 4.
L 270 (C 22-40): The McCabe cyclomatic complexity of 'listMaterialIndices' is 1.
L 279 (C 26-41): The McCabe cyclomatic complexity of 'getMaterialNames' is 1.
L 286 (C 45-76): The McCabe cyclomatic complexity of 'getMaterialNamesAndIndicesSorted' is 2.
L 144 (C 24-29): The McCabe cyclomatic complexity of 'Medium' is 1.
L 157 (C 24-31): The McCabe cyclomatic complexity of 'subsasgn' is 5.
L 187 (C 24-30): The McCabe cyclomatic complexity of 'refresh' is 1.
L 195 (C 18-40): The McCabe cyclomatic complexity of 'set.soundSpeedReference' is 2.
L 201 (C 18-39): The McCabe cyclomatic complexity of 'set.diffusionReference' is 2.
L 212 (C 24-46): The McCabe cyclomatic complexity of 'updateDerivedPaddedMaps' is 10.
L 262 (C 25-35): The McCabe cyclomatic complexity of 'mapProperty' is 6.
L 300 (C 22-40): The McCabe cyclomatic complexity of 'get.absorptionPower' is 4.
L 57 (C 36-56): The McCabe cyclomatic complexity of 'get.totalSensorPoints' is 1.
L 67 (C 33-49): The McCabe cyclomatic complexity of 'ProcessSensorData' is 4.

L 87 (C 24-29): The McCabe cyclomatic complexity of 'Solver' is 5.
L 104 (C 24-36): The McCabe cyclomatic complexity of 'SplitFieldPML' is 1.
L 126 (C 18-25): The McCabe cyclomatic complexity of 'set.pmlX' is 1.
L 131 (C 18-34): The McCabe cyclomatic complexity of 'set.pmlXStaggered' is 1.
L 136 (C 18-25): The McCabe cyclomatic complexity of 'set.pmlY' is 1.
L 141 (C 18-34): The McCabe cyclomatic complexity of 'set.pmlYStaggered' is 1.
L 146 (C 18-25): The McCabe cyclomatic complexity of 'set.pmlZ' is 1.
L 151 (C 18-34): The McCabe cyclomatic complexity of 'set.pmlZStaggered' is 1.
L 156 (C 24-31): The McCabe cyclomatic complexity of 'get.pmlX' is 1.
L 160 (C 24-31): The McCabe cyclomatic complexity of 'get.pmlY' is 1.
L 164 (C 24-31): The McCabe cyclomatic complexity of 'get.pmlZ' is 1.
L 168 (C 24-40): The McCabe cyclomatic complexity of 'get.pmlXStaggered' is 1.
L 172 (C 24-40): The McCabe cyclomatic complexity of 'get.pmlYStaggered' is 1.
L 176 (C 24-40): The McCabe cyclomatic complexity of 'get.pmlZStaggered' is 1.
L 49 (C 14-21): The McCabe cyclomatic complexity of 'applyPML' is 10.
L 62 (C 20-39): The McCabe cyclomatic complexity of 'getQuarticPMLProfile' is 5.
L 40 (C 10-24): The McCabe cyclomatic complexity of 'setupQuarticPML' is 3.

L 119 (C 24-36): The McCabe cyclomatic complexity of 'ThermalSolver' is 3.
L 142 (C 32-46): The McCabe cyclomatic complexity of 'get.temperature' is 1.
L 38 (C 21-39): The McCabe cyclomatic complexity of 'autoComputeTimeStep' is 3.
L 35 (C 10-24): The McCabe cyclomatic complexity of 'executeTimeStep' is 7.
L 32 (C 10-29): The McCabe cyclomatic complexity of 'setInitialConditions' is 3.

L 82 (C 24-39): The McCabe cyclomatic complexity of 'TimeDomainSolver' is 1.
L 111 (C 18-37): The McCabe cyclomatic complexity of 'setInitialConditions' is 1.
L 58 (C 10-12): The McCabe cyclomatic complexity of 'run' is 5.
L 1 (C 1): The McCabe cyclomatic complexity is 0.
L 76 (C 27-38): The McCabe cyclomatic complexity of 'expandMatrix' is 17.

codecov · 2026-05-28T21:45:13Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.22%. Comparing base (c12cb8e) to head (26a30ec).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #245   +/-   ##
========================================
  Coverage    99.22%   99.22%           
========================================
  Files           47       47           
  Lines         1027     1027           
========================================
  Hits          1019     1019           
  Misses           8        8

Flag	Coverage Δ
unit	`99.22% <ø> (ø)`

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Updated minimum requirements date

stellaprins

I like your changes they make the text more clear and concise in places (always a good thing!)

A few small comments and make sure to run pre-commit on all files to address the CI failure.

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Minor changes following Stella's comments.

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Added a bit more description on conda.

minor changes

Small changes to pre-commit description.

* Remove no-commit-to-branch hook from pre-commit config * Remove push trigger from pre-commit workflow Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

stellaprins

Looks good, just add the line of instructions to install pre-commit, see earlier comment
.

… moment.

…r beginners

bencox added 11 commits May 28, 2026 16:52

Update README.md

5187094

Update CONTRIBUTING.md

0f3caa8

I've changed this quite a bit to lower both the apparent and actual barriers to getting users started on contributing. I've slightly relaxed the requirements for very small contributions, while maintaining them for significant contributions.

Update README.md

afb8cf6

minor URL update

Update CONTRIBUTING.md

97a801a

Tiny change to a title

Update README.md

a715961

Added instructions on how to install matlab and create the documentation.

Update README.md

e601ac1

Minor re-wording and rearrangements.

Update CONTRIBUTING.md

99dba51

Link update.

Update codingStandard.md

17ef1b4

Minor typo

Update CONTRIBUTING.md

bc5a2a2

typo

Update developerIntroduction.md

40a2c77

Few minor changes.

Update maintainerDocs.md

5d449cf

Small changes, as we will allow PRs into develop for minor fixes. Not everything tiny change must rigidly go through a feature branch.

bencox marked this pull request as ready for review May 28, 2026 21:21

bencox requested a review from stellaprins May 28, 2026 21:21

Update README.md

e382597

Updated minimum requirements date

stellaprins reviewed May 29, 2026

View reviewed changes

bencox and others added 10 commits June 2, 2026 09:21

Update docs/CONTRIBUTING.md

ba9b6b0

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Update docs/README.md

9ac3eee

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Update CONTRIBUTING.md

aec33c9

Minor changes following Stella's comments.

Update docs/developerIntroduction.md

48d6ce9

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

Merge branch 'develop' into updated_README

4167868

Update CONTRIBUTING.md

4d99289

Added a bit more description on conda.

Update CONTRIBUTING.md

be44d33

minor changes

Update CONTRIBUTING.md

d0e0f1d

Small changes to pre-commit description.

pre-commit changes

7617363

Remove no-commit-to-branch hook from pre-commit config (#249) (#251)

6c63ade

* Remove no-commit-to-branch hook from pre-commit config * Remove push trigger from pre-commit workflow Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

stellaprins self-requested a review June 3, 2026 10:03

stellaprins reviewed Jun 3, 2026

View reviewed changes

Comment thread docs/CONTRIBUTING.md Outdated

stellaprins self-requested a review June 3, 2026 11:10

Update docs/CONTRIBUTING.md

27be9af

Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com>

stellaprins approved these changes Jun 3, 2026

View reviewed changes

bencox added 8 commits June 3, 2026 12:20

Merge branch 'develop' into updated_README

63cf361

Updated README.md again, minor tweaks.

5c18723

changed BUG website address to github as UCL website is broken at the…

351241e

… moment.

Small updates to CONTRIBUTING.md

4362c97

small update to CONTRIBUTING.md

58563f9

pre-commit whitespace changes

655e33d

Quite significant re-ordering of CONTRIBUTING.md to make it easier fo…

53f6b8c

…r beginners

pre-commit whitespace changes

26a30ec

bencox merged commit b7a2d76 into develop Jun 5, 2026
6 checks passed

bencox deleted the updated_README branch June 5, 2026 15:33

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Update README.md - #245

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Cyclomatic Complexity Check

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bencox commented May 28, 2026 •

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