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VirtualPhotonics / VTS

Virtual Tissue Simulator
https://virtualphotonics.org
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Feature/sonar cloud cleanup #63

Closed lmalenfant closed 1 year ago

lmalenfant commented 1 year ago

Hi Carole,

Our code smells are down to 397: https://sonarcloud.io/summary/overall?id=VirtualPhotonics_VTS

Hopefully I didn't break anything :)

hayakawa16 commented 1 year ago

Hi Lisa,

I will review code changes, then run branch code on linux before I accept.

Carole

On 2023-04-13 15:26, Lisa Malenfant wrote:

Hi Carole,

Our code smells are down to 397: https://sonarcloud.io/summary/overall?id=VirtualPhotonics_VTS [1]

Hopefully I didn't break anything :)

YOU CAN VIEW, COMMENT ON, OR MERGE THIS PULL REQUEST ONLINE AT:

https://github.com/VirtualPhotonics/VTS/pull/63 [2]

COMMIT SUMMARY

  • 6f9baff [3] Spectral converter cleanup
  • 1ae032b [4] Fixed some of the blocker and critical code smells
  • 62b0b89 [5] Code cleanup and renaming a misspelled property
  • c2c0d44 [6] Fixed the introduced bug and code smells
  • 372930c [7] Fix for code smell: Refactor 'Regions' into a method, properties should not copy collections.
  • c38fabc [8] Fixed the remailing code smells for Refactor 'Regions' into a method, properties should not copy collections.

FILE CHANGES

(54 files [9])

  • M src/Vts.Test/MonteCarlo/Sources/PointAndLineSources/LineSources/CustomLineSourceTests.cs [10] (2)
  • M src/Vts.Test/MonteCarlo/Sources/PointAndLineSources/LineSources/DirectionalLineSourceTests.cs [11] (2)
  • M src/Vts.Test/MonteCarlo/Sources/PointAndLineSources/LineSources/IsotropicLineSourcesTests.cs [12] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/CustomCircularSourceTests.cs [13] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/DirectionalCircularSourceTests.cs [14] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Elliptical/CustomEllipticalSourceTests.cs [15] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Elliptical/DirectionalEllipticalSourceTests.cs [16] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/CustomRectangularSourceTests.cs [17] (2)
  • M src/Vts.Test/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/DirectionalRectangularSourceTests.cs [18] (2)
  • M src/Vts/Modeling/ForwardSolvers/TwoLayerSDAForwardSolver.cs [19] (24)
  • M src/Vts/Modeling/Spectroscopy/SpectralConverter.cs [20] (165)
  • M src/Vts/MonteCarlo/Controllers/HistoryDetectorController.cs [21] (13)
  • M src/Vts/MonteCarlo/Controllers/pMCDatabaseWriterController.cs [22] (20)
  • M src/Vts/MonteCarlo/Detectors/AOfXAndYAndZDetector.cs [23] (3)
  • M src/Vts/MonteCarlo/Detectors/ATotalBoundingVolumeDetector.cs [24] (8)
  • M src/Vts/MonteCarlo/Detectors/ATotalDetector.cs [25] (3)
  • M src/Vts/MonteCarlo/Detectors/ReflectedMTOfRhoAndSubRegionHistDetector.cs [26] (5)
  • M src/Vts/MonteCarlo/Detectors/ReflectedMTOfXAndYAndSubregionHistDetector.cs [27] (3)
  • M src/Vts/MonteCarlo/Detectors/SurfaceFiberDetector.cs [28] (3)
  • M src/Vts/MonteCarlo/Detectors/TransmittedMTOfRhoAndSubregionHistDetector.cs [29] (3)
  • M src/Vts/MonteCarlo/Detectors/TransmittedMTOfXAndYAndSubregionHistDetector.cs [30] (3)
  • M src/Vts/MonteCarlo/Detectors/pMCATotalDetector.cs [31] (2)
  • M src/Vts/MonteCarlo/Helpers/CylinderTissueRegionToolbox.cs [32] (31)
  • M src/Vts/MonteCarlo/Helpers/SourceDefaults.cs [33] (7)
  • M src/Vts/MonteCarlo/Interfaces/IDetector.cs [34] (2)
  • M src/Vts/MonteCarlo/Interfaces/IDetectorController.cs [35] (4)
  • M src/Vts/MonteCarlo/Sources/PointAndLineSources/LineSources/CustomLineSource.cs [36] (4)
  • M src/Vts/MonteCarlo/Sources/PointAndLineSources/LineSources/DirectionalLineSource.cs [37] (4)
  • M src/Vts/MonteCarlo/Sources/PointAndLineSources/LineSources/IsotropicLineSource.cs [38] (4)
  • M src/Vts/MonteCarlo/Sources/PointAndLineSources/LineSources/LineAngledFromLine.cs [39] (4)
  • M src/Vts/MonteCarlo/Sources/PointAndLineSources/LineSources/LineSourceBase.cs [40] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/CircularAngledFromCircleSource.cs [41] (2)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/CircularAngledFromPointSource.cs [42] (2)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/CircularSourceBase.cs [43] (2)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/CustomCircularSource.cs [44] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Circular/DirectionalCircularSource.cs [45] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Elliptical/CustomEllipticalSource.cs [46] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Elliptical/DirectionalEllipticalSource.cs [47] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Elliptical/EllipticalSourceBase.cs [48] (2)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/CustomRectangularSource.cs [49] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/DirectionalRectangularSource.cs [50] (4)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/RectangularAngledFromCircleSource.cs [51] (2)
  • M src/Vts/MonteCarlo/Sources/SurfaceEmittingFlatSources/Rectangular/RectangularSourceBase.cs [52] (2)
  • M src/Vts/MonteCarlo/Sources/VolumetricSources/FluorescenceEmission/FluorescenceEmissionAOfRhoAndZSource.cs [53] (2)
  • M src/Vts/MonteCarlo/Sources/VolumetricSources/FluorescenceEmission/FluorescenceEmissionAOfXAndYAndZSource.cs [54] (2)
  • M src/Vts/MonteCarlo/Tissues/BoundingCylinderTissue.cs [55] (31)
  • M src/Vts/MonteCarlo/Tissues/MultiConcentricInfiniteCylinderTissue.cs [56] (52)
  • M src/Vts/MonteCarlo/Tissues/MultiEllipsoidTissue.cs [57] (43)
  • M src/Vts/MonteCarlo/Tissues/MultiLayerWithSurfaceFiberTissue.cs [58] (43)
  • M src/Vts/MonteCarlo/Tissues/SingleCylinderTissue.cs [59] (31)
  • M src/Vts/MonteCarlo/Tissues/SingleEllipsoidTissue.cs [60] (31)
  • M src/Vts/MonteCarlo/Tissues/SingleInfiniteCylinderTissue.cs [61] (31)
  • M src/Vts/MonteCarlo/Tissues/SingleVoxelTissue.cs [62] (27)
  • M src/Vts/MonteCarlo/Types/PhotonStateType.cs [63] (8)

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lmalenfant commented 1 year ago

Hi Carole (@hayakawa16),

I just realized that I sent you the link to the Sonar Cloud analysis but since I added it to the repo, you can now see the analysis directly in this PR. It is in the "Checks" tab at the top. We still have quite a lot of duplications so I had to increase the percentage to 20% to pass the quality gate until we can address it.

hayakawa16 commented 1 year ago

Hi Lisa,

I just viewed it. Is that a new capability to GitHub? Or is it just because you added it to the repo. That is nice! I do still like the screen capture I've been keeping because will this tab and information go away when this PR is closed?

Carole

On 2023-04-13 15:55, Lisa Malenfant wrote:

Hi Carole,

I just realized that I sent you the link to the Sonar Cloud analysis but since I added it to the repo, you can now see the analysis directly in this PR. It is in the "Checks" tab at the top. We still have quite a lot of duplications so I had to increase the percentage to 20% to pass the quality gate until we can address it.

-- Reply to this email directly, view it on GitHub [1], or unsubscribe [2]. You are receiving this because your review was requested.Message ID: @.***>

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lmalenfant commented 1 year ago

The Sonar Cloud scanning has been a part of GitHub for a while, it has always been connected but I have to run the analysis separately. Eventually, I hope to have it working with a pipeline but I have to automate the code coverage results first (I'm almost there). You're right, this will go away when we merge the PR and the history is available but we don't view it the same way on Sonar Cloud so keeping a screenshot of the progress is still good.

I'll fix that one name and then merge, yes, let's merge master into the branches together.

lmalenfant commented 1 year ago

Hi Carole (@hayakawa16),

I made the name change, could you verify that it looks right? I believe it should be fFtTimeSequence.

hayakawa16 commented 1 year ago

Hi Lisa,

I think that is correct, however when I wrote it out it seemed funny to me and so I looked in the code for other acronyms and what we did. That is when I found pMc for pMC. I deferred to you because you know more about the right thing to do here.

Carole

On 2023-04-13 17:02, Lisa Malenfant wrote:

Hi Carole @.*** [1]),

I made the name change, could you verify that it looks right? I believe it should be fFtTimeSequence.

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