Add ElasticSource class for the elastic solver by qiUip · Pull Request #129 · ucl-bug/k-wave-ii

qiUip · 2024-06-17T15:28:04Z

See issues #120 for the solver requirements and progress, and #126 for this PR.

Straight forward class adding only the initial pressure. It will be expanded to include more source terms in the future.

github-actions · 2024-06-17T15:31:30Z

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 · 2024-06-17T15:31:59Z

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 99.22%. Comparing base (c36c5a3) to head (d71980a).
⚠️ Report is 1 commits behind head on develop.

Additional details and impacted files

@@           Coverage Diff            @@
##           develop     #129   +/-   ##
========================================
  Coverage    99.22%   99.22%           
========================================
  Files           47       47           
  Lines         1027     1027           
========================================
  Hits          1019     1019           
  Misses           8        8

Flag	Coverage Δ
unit	`99.22% <0.00%> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

🚀 New features to boost your workflow:

❄️ Test Analytics: Detect flaky tests, report on failures, and find test suite problems.

* #49: Work in progress to save .m files to .md * #49: Removes folder helpfilesweb from tracking * #49: Clean-up function mToMarkdown * #49: Change mToMarkdown input from namespace name to filename with full file path * First attempt at mkdocs. Requires the literate-nav plugin. * Generate md the same way as html. mToMarkdown is not used anymore. * Fix bug if duplicated unit test docs files. Some refactoring. * Fix documentation files titles. * Generate sections for markdown toc by creating subfolders and SUMMARY.md files. * Evaluate and show the code when converting to md as well (same as html). * Move static documentation out of .m files and into md * Clean up tutorials * #147: Fix all broken links and matlab markup syntax errors in all .m docs. * Apply suggestions from code review Co-authored-by: Devaraj Gopinathan <36169767+Devaraj-G@users.noreply.github.com> * #147: Address code review comments: Rename generateHTML function, since now it does more than generating html. Move link fixing to its own function, to de-clutter generateDocFiles function a bit. * Add the Template Class documentation to the html toc. * #156: remove helpfiles subdir - to be re-generated on the fly, not commited to the repo. * #156: add some static md files in docs, and clean up the folder. * #156: add placeholder for helpfilesweb folder and softlink for README * #156: Update instructions on generating documentation. * #156: Fix LaTeX rendering * #156: Tidy up folders for generated documentation. * #156: Move instructions for building the docs into the developer docs only. * #156: Try to make the GA runner pick up the latest release of matlab... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 2... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 3... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 4... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 5... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 6... * #156: Try to make the GA runner pick up the latest release of matlab - attempt 7... * #156: Save docs files as artifacts in runner * #156: Save docs files as artifacts in runner - attempt 2 * #156: Save docs files as artifacts in runner - attempt 3 * #156: Save docs files as artifacts in runner - attempt 4 * #156: Save docs files as artifacts in runner - attempt 5 * #156: Save docs files as artifacts in runner - attempt 6 * #156: Save docs files as artifacts in runner - attempt 7 * #156: Save docs files as artifacts in runner - attempt 8 * #156: Save docs files as artifacts in runner - attempt 9 * #156: Save docs files as artifacts in runner - attempt 10 * #156: Save docs files as artifacts in runner - attempt 11 * #156: put all python package requirements into requirements.txt * #156: write test to count docs files and run in GA * #156: try number of doc files test with powershell * #156: retry number of doc files test with python * #156: remove number of doc files test with python from workflow, but have script ready for future use. * #156: Address review comments and re-attempt python test. - Fix security warning in js package - Get order of folders in mkdocs the same as in generated matlab help page - Fix broken licence link - Re-attempt soft link to README.md file from index.md, instead of the other way round. * #156: retry python test - attempt 2. * #156: retry python test - attempt 3. * #156: use bash test instead. * #156: Re-shuffle utilities folder, separate docs of interest to the user and the developer. * #156: correct script location in GA. * #164: Separate user from contributor docs, in files and mkdocs side bar. * #164: update workflow in contributor docs, add maintainer docs placeholder. * #164: add maintainer docs. * #164: Clarify some bits in the docs after discussions. * #13: add help files for helptoc section headings. * #13: fix links in the section headings. * #13: update documentation about link fixing. * Apply suggestions from code review Co-authored-by: Ben Cox <b.cox@ucl.ac.uk> * #164: Address more review comments. * #172 Removed EM medium and source from develop branch * #132 Acoustic sensor class and tests added from MKingEndBranch * #132 Updated t02_AcousticSolverExamples.m * #132 Updated TestAcousticSensor.m * #132 Many small changes found while improving code check coverage * #132 Tidied up header text in sensor and related classes and tidied up simple tutorials * #132 Bug fix to pass tests * Stop CI from running on draft PRs (#186) * Do not run CI workflows for draft pull requests * run code_quality workflow on draft PRs * Update workflow triggers to exclude draft PRs * Also run on push (to main) * gate non-draft PR trigger through workflow_call * Revert "gate non-draft PR trigger through workflow_call" This reverts commit a313e3c. * Clarify that jobs are skipped on draft PRs * Add vscode settings folder to gitignore (#185) ignore VSCode settings * add pre-commit hooks * Add codespell, remove markdownlint-fix and forbid-tabs * Add environment setup and pre-commit instructions * Add pre-commit workflow configuration * Use ubuntu-latest in pre-commit workflow * 179: update docs that we use squash commits. (#187) * Create top level docs table of contents (#189) #37: Create top level docs toc. * Fix spelling mistakes (#194) * fix spelling mistakes * Apply suggestions from code review Some symbols are rendering strange, fix them. --------- Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * add ilekra's suggestion https://github.com/ucl-bug/k-wave-ii/pull/195/changes#r2840666954 * add pre-commit to requirments.txt https://github.com/ucl-bug/k-wave-ii/pull/195/changes#r2840644366 * Add ilektra's suggestion https://github.com/ucl-bug/k-wave-ii/pull/195/changes#r2840634706 * exclude markdown from trailing whitespace checks #195 (comment) * Sp/release (#207) * Add issue templates copied from k-wave-i * fix folder hiearchy for PR template * Test old PR template hierarchy * Add pull request template for better contributions Added a pull request template to guide contributors in providing necessary information. * Delete .github/PULL_REQUEST_TEMPLATE directory * Update to v4 and add deploy to gh pages * test gh pages deployment Replace GitHub Actions deployment step with mkdocs command. * test deploy gh pages Updated deployment steps for GitHub Pages in workflow. * Update deployment steps for GitHub Pages * test deploy docs Updated the GitHub Actions workflow for documentation generation and deployment. Added permissions, changed the runner to 'windows-latest', and modified steps for building and deploying MkDocs site. * Update branch reference from main to develop in workflow configuration * test workfow trigger * use orginal docs workflow * trigger on push to develop * Update workflow to build and deploy to gh pages * use ubuntu runner * use mathworks actions * Add semantic release configuration and workflow * Update release workflow to include npm caching and consistent versioning * Add node modules to gitignore * add package(-lock) jsons * Revert "Sp/release (#207)" This reverts commit f64df90. * Deploy the documentation to GitHub Pages (#202) * Update to v4 and add deploy to gh pages * Add GitHub Pages ("site") directory to .gitignore * Deploy when push to sp/49-deploy_gh_pages branch * add build mkdocs step to docs workflow Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * add python setup (comment out build docs to speed up testing) Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * change to windows-latest Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * upload to site instead of docs Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Added venv to gitignore Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Trying to deploy Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Write permissions given? Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Upload to github pages Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Naming error Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Damn you windows! Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Added Matlab helpfile documentation Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Testing Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Order! Order! Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Connect the two jobs Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Version upgrade due to deprecation Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Trying Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Trying 2 Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Trying 3 Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Done! Removing unnecessary if statements Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * More descriptive runner name Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Workflow to run only when of develop branch Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Deployment skipped on PR's Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> --------- Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> Co-authored-by: Arindam Saha <arindamsaha1507@gmail.com> Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> * Added guidelines on use of AI Policy (#203) * Add issue templates and fix PR template hierarchy (#192) * Add issue templates copied from k-wave-i * fix folder hiearchy for PR template * Update .github/ISSUE_TEMPLATE/bug-form.yml Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * remove custom issues and enable blank issues * Add ilektra's suggestion for PR checklist (to better match contribution guidelines) --------- Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * Add contributor agreement (#201) * Fixes issue 178 also added the link in the PR template, did not change anything else there since it is an issue assigned to Stella * Moved legal to the end after merge removed it * #178: fix merge conflict mess * #178: remove superfluous PR template file --------- Co-authored-by: blaze <blaze@ITX.broadband> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * Added a code of conduct (#198) * Added basic code of conduct * Added the page to nav bar * Better list rendering due to correct tabbing * Made it concise * Add contact information in codeOfConduct.md --------- Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * remove space to fix broken badge link Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * test branch protection (remove redundent blank line from README) Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * test branch protection (remove redundent blank line from README) Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * test branch protection (#213) test branch protection (remove redundent blank line from README) Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * add contributors workflow (#210) * add contributors workflow Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Add Ben as project owder Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * Add badge and lis tags to README Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * remove bots and add co authors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * remove contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * remove readme tags Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * fix indentation Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * use scan Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * change back to working workflow Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * Add contributors section header Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * exclude bots as contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * set custom type fields to null (instead of empty string) Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * adjust custom type * docs: update contributors * remove contributorsfooter * docs: update contributors * set link to usage to false and add footer Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * add reference to all contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * include co authors as contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * include co authors as contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * exclude bots as contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * remove bot Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * properly install all-contributors and add contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * replace old tags in readme * docs: update contributors * add contributors Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * fix all contributors src file Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * docs: update contributors * clarify where the all contributors information is sourced from (GDPR) * docs: update contributors * change wording slightly * add forum contact details in case people want to request to be removed * docs: update contributors * skip commit and push if no changes in .all-contributorsrc detected * remove redundent blank lines in readme (and test whether bot commits) * add Ben's email as contact point instead of forum. * add workflow for protecting npm package jsons Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * change workflow triggers for protecting npm package jsons Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * break package-lock.json Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * fix package-lock.json using `npm install --package-lock-only` sugestion Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * try to break package.json Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * add _comment to package json file Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * change version of all contributors cli in package json Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * pick better descriptive workflow name and revert previous commit Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Added proper link Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> --------- Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Arindam Saha <arindamsaha1507@gmail.com> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * Remove `package.json` and `package-lock.json` files and workflow (#215) * take into account non-PR triggers * remove lockflow workflow * remove `package.json` and `package-lock.json` Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * remove npm installation from contributors workflow Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * add npm dependency (but not using npm ci) * remove Arindam from .all-contributorssrc file * update contributors --------- Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> * add ilektra's suggestion about running pre-commit on all files * add contributors (#218) * docs: update README.md * docs: update .all-contributorsrc * change code to custom for jarosjir * try to add Eleanor * add ellymartin and ellwise as contributors --------- Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: Stella <30465823+stellaprins@users.noreply.github.com> * Move README.md to docs folder (#226) * Move README.md to docs folder * Refer to docs/README.md in .all-contributorsrc and contributors workflow * Add "development lead" section to README (#222) * Update README.md to include development lead group (BUG) * Add Ben's suggested changes Co-authored-by: Ben Cox <b.cox@ucl.ac.uk> --------- Co-authored-by: Ben Cox <b.cox@ucl.ac.uk> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * Improve contributors grid (#228) * adjust .all-contributorsrc - change order profiles (Bradley first) - slightly smaller thumbnails (100->80 pixels) - 6 instead of 7 profiles per row * update contributors * change order grid * fix: correct JSON syntax in .all-contributorsrc * update contributors * add back Devaraj (accidentily deleted him!) --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> * Add contributor counter badge (#221) * Update README.md to include new contributors badge * Remove the badge that is not working * Replace deprecated `<tt>` tags (#234) * replace tt tages by code tags in published html files Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Replace deprecated <tt> tags with <code> tags in generated HTML files --------- Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Add `CITATION.cff` (#232) * add cff file * remove hyphens from keyword labels (and use spaces instead) Treeby, B. E., Jaros, J., Rendell, A. P., & Cox, B. T. (2012). Modeling nonlinear ultrasound propagation in heterogeneous media with power law absorption using a k-space pseudospectral method. The Journal of the Acoustical Society of America, 131(6), 4324–4336. https://doi.org/10.1121/1.4712021 * #188 Fixed how tutorial docs display (#204) * #188 Fixed how tutorial docs display * #188: fix t01_AcousticSolverExamples1D to display correctly. * #188 Updated two tutorial files so they format correctly when converted to html. * #188: Fix some aesthetic things and add documentation about markup peculiarities. --------- Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> * #142 medium class updates (#205) * #142 New Materials class for materials to be passed to the Medium class * #142 Updated Materials class definition and added unit tests * #142 Rewritten Medium class to work with Materials class object. Also Medium class unit test. * #142 Tutorial example and various debugged files that it flagged up. Deleted unused files. * #142 Bug fixes to ensure unit tests all pass * #142 Rewrote TestMedium and TestMaterials to improve unit test coverage. * #142 updated header to Materials.m so docs compile * #142 updated header to Materials.m again so docs compile * #142 Minor updates to improve test coverage of Medium and Materials classes. * #142 Updated Materials and TestMaterials to improve unit test coverage, and tighten class definition * #142 Updated Medium and TestMedium to improve coverage. Small changes to tutorial example. * #142 updates following comments, and some other largely cosmetic tidying up of the code. * fix docs error (#233) * remove (potentially) problematic | markers and replace with backticks * use disp(table) so it displays properly in the documentation * update tutorial documentation Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com> Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> * Explain where to run the GenerateDocumentation script from. (#240) 193: Explain where to run the GenerateDocumentation script from. * added script and linter option for checking/adding license block (#212) * added script and linter option for checking/adding license block * #14: Move yaml configuration to workflow folder, to run as GA. Fix bug in script. * #14: Fixed some comments * #14: adjust triggers to run new action. Fix trigger for tests action. * style: automatically apply LGPL license headers to .m files * Revert "style: automatically apply LGPL license headers to .m files" This reverts commit b9398ba. * 14: Remove legacy files from copyright check. Debugging stuff still in the script. * 14: Fix search for existing wrong Copyright header. Add some verbose print statements * style: automatically apply LGPL license headers to .m files * style: automatically apply LGPL license headers to .m files * 14: Remove files brought back with the merge by mistake. --------- Co-authored-by: blaze <blaze@ITX.broadband> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> Co-authored-by: ilectra <22891967+ilectra@users.noreply.github.com> Co-authored-by: Stella Prins <30465823+stellaprins@users.noreply.github.com> * Update pre-commit configuration to exclude legacy files * exclude site directory and don't use prettier on docs or markdown files * add pre-commit changes to all files (lots of white space trimmings!) * style: automatically apply LGPL license headers to .m files * update contributors --------- Co-authored-by: Bradley Treeby <b.treeby@ucl.ac.uk> Co-authored-by: Devaraj Gopinathan <d.gopinathan@ucl.ac.uk> Co-authored-by: Ilektra Christidi <ilektra.christidi@ucl.ac.uk> Co-authored-by: Devaraj Gopinathan <36169767+Devaraj-G@users.noreply.github.com> Co-authored-by: Ben Cox <b.cox@ucl.ac.uk> Co-authored-by: MatthewJohnKing <137497118+MatthewJohnKing@users.noreply.github.com> Co-authored-by: Arindam Saha <arindamsaha1507@users.noreply.github.com> Co-authored-by: Arindam Saha <arindamsaha1507@gmail.com> Co-authored-by: Stella Prins <stellaprins@users.noreply.github.com> Co-authored-by: nicolin <n.govender@ucl.ac.uk> Co-authored-by: blaze <blaze@ITX.broadband> Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: allcontributors[bot] <46447321+allcontributors[bot]@users.noreply.github.com> Co-authored-by: ilectra <22891967+ilectra@users.noreply.github.com>

bencox · 2026-06-02T10:01:02Z

I have closed this PR. The branch will remain, and should perhaps be first pulled into an 'elastic model' feature branch.As it's not a complete feature yet I won't move it into develop yet.

#126: Added ElasticSource class and a unit test for it

19f6ca9

bencox self-requested a review November 12, 2024 14:13

bencox self-assigned this Nov 12, 2024

bencox and others added 3 commits July 16, 2025 09:56

Merge branch 'main' into 126-ElasticSource

86d87f9

Merge branch 'develop' into 126-ElasticSource

d71980a

bencox closed this Jun 2, 2026

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Uh oh!

Add ElasticSource class for the elastic solver - #129

Add ElasticSource class for the elastic solver#129
qiUip wants to merge 4 commits into
developfrom
126-ElasticSource

qiUip commented Jun 17, 2024

Uh oh!

github-actions Bot commented Jun 17, 2024 •

edited

Loading

Uh oh!

codecov Bot commented Jun 17, 2024 •

edited

Loading

Uh oh!

bencox commented Jun 2, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

Uh oh!

Conversation

qiUip commented Jun 17, 2024

Uh oh!

github-actions Bot commented Jun 17, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Cyclomatic Complexity Check

Uh oh!

codecov Bot commented Jun 17, 2024 • edited Loading Uh oh! There was an error while loading. Please reload this page.

Uh oh!

Codecov Report

Uh oh!

bencox commented Jun 2, 2026

Uh oh!

Reviewers

Assignees

Labels

Projects

Milestone

Development

Uh oh!

3 participants

github-actions Bot commented Jun 17, 2024 •

edited

Loading

codecov Bot commented Jun 17, 2024 •

edited

Loading