Code

Merging 7.6.0 to master#1704

Code

Merged

jdramsey merged 141 commits intomastercmu-phil/tetrad:masterfrom developmentcmu-phil/tetrad:developmentCopy head branch name to clipboardOct 31, 2023

+6,705-3,975

Commits

Commits on Aug 3, 2023

• Update README.md

  jdramsey

  authored
  151dbff

Commits on Aug 4, 2023

• Update README.md

  jdramsey

  authored
  640c62c

Commits on Aug 6, 2023

• Updated to 7.5.0.

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  f0961ee

Commits on Aug 7, 2023

• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

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• Pushing FX examples to my brnach.

  jdramsey

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• Pushing FX examples to my brnach.

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  1fdd595

• Pushing FX examples to my brnach.

  jdramsey

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  098967d

• Pushing FX examples to my brnach.

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  aa31354

Commits on Aug 8, 2023

• Adjusted circle layout so that it automatically adjusts the size of the circle so you can see all of the nodes.

  jdramsey

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  8f80c9b

• Adjusted circle layout so that it automatically adjusts the size of the circle so you can see all of the nodes.

  jdramsey

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  4f07b41

Commits on Aug 9, 2023

• Added threshold option to bootstrapping.

  jdramsey

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  48c8a26

• Merge remote-tracking branch 'origin/joe-work-2023-8-4' into joe-work-2023-8-4

  jdramsey

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  d819ff3

• Adjusted circle layout so that it automatically adjusts the size of the circle so you can see all of the nodes.

  jdramsey

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  28383cf

Commits on Aug 11, 2023

• Fixed usedataorder for BOSS.

  jdramsey

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  6f923a7

• Merge remote-tracking branch 'origin/joe-work-2023-8-4' into joe-work-2023-8-4

  jdramsey

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  5bf37c0

• Fixed usedataorder for BOSS.

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  5b6226d

Commits on Aug 12, 2023

• Reverting Matrix.

  jdramsey

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  b361e70

Commits on Aug 15, 2023

• added gst synchronization

  bja43

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  b261a7d

• switched to atomic booleans and got rid of the allow randomness within parameter since it breaks num starts

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  456a419

Commits on Aug 16, 2023

• doesnt work, dont know why

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  b81f344

• switched to fjp and now it works!

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  c9fcc77

Commits on Aug 17, 2023

• Joe's adjustments.

  jdramsey

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  79ccd91

• Joe's adjustments.

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  146e0ef

• made the pool a class variable

  bja43

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  72da77a

• Joe's adjustments.

  jdramsey

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  5b398b1

• Merge remote-tracking branch 'origin/boss_parallel' into boss_parallel

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  df2162a

• Joe's adjustments.

  jdramsey

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  934d0e7

• Reverted to working version, put pool back to class level.

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  3bd81ab

Commits on Aug 18, 2023

• Working version that doesn't scale to 2000:10:1000 pd 8.

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  8f4e6d2

• Working version that doesn't scale to 2000:10:1000 pd 8.

  jdramsey

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  89528d8

Commits on Aug 22, 2023

• Streamlined graph display in the interface.

  jdramsey

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  76aafa3

Commits on Aug 23, 2023

• fixed make valid knowledge order

  bja43

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  c959210

• Merge pull request #1679 from cmu-phil/required_knowledge_fix

  Show description for 5d17003
  jdramsey

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  5d17003

• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe-work-2023-8-4

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  f9aa227

Commits on Aug 24, 2023

• modified boss parallel and fixed required edge code

  bja43

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  a7254cc

• Added NUM_THREADS parameter for BOSS and tested required knowledge for BOSS and GRaSP.

  jdramsey

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  f1d2f9d

• Changed name of GRASP_USE_DATA_ORDER to USE_DATA_ORDER throughout and added this parameter to BOSS.

  jdramsey

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  20423b7

• Merge pull request #1682 from cmu-phil/boss_parallel

  Show description for e029775
  bja43

  authored
  e029775

• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe-work-2023-8-4

  Show description for 6f8a007
  jdramsey

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  6f8a007

• Changed name of GRASP_USE_DATA_ORDER to USE_DATA_ORDER throughout and added this parameter to BOSS.

  jdramsey

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  755fba3

• Updating some versions of plugins in the poms, responding to warnings.

  jdramsey

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  385ac36

• Merge pull request #1680 from cmu-phil/joe-work-2023-8-4

  Show description for 6023db4
  bja43

  authored
  6023db4

Commits on Aug 26, 2023

• Update README.md

  jdramsey

  authored
  4d8be74

• Merge pull request #1684 from cmu-phil/jdramsey-patch-2

  Show description for c9ac3d8
  jdramsey

  authored
  c9ac3d8

• Update README.md

  jdramsey

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  7c54842

Commits on Aug 27, 2023

• Update README.md

  jdramsey

  authored
  d559669

• Update README.md

  jdramsey

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  4cadfc6

• Update README.md

  jdramsey

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  5ca1ebe

• Update README.md

  jdramsey

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  a8e9047

• Merge pull request #1685 from cmu-phil/jdramsey-patch-3

  Show description for fd59303
  jdramsey

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  fd59303

• Update README.md

  jdramsey

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  9021c49

• Update README.md

  jdramsey

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  e10d9fc

• Update README.md

  jdramsey

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  5c0f5a4

• Update README.md

  jdramsey

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  e176c42

• Update README.md

  jdramsey

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  4f5eff6

• Update README.md

  jdramsey

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  e6dc7dd

Commits on Aug 30, 2023

• Update README.md

  jdramsey

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  043c65b

• Update README.md

  jdramsey

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  8eee94e

Commits on Sep 9, 2023

• parallel boss + polish

  bja43

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  680f5e7

Commits on Sep 11, 2023

• parallel boss + polish

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  e39f98e

Commits on Sep 18, 2023

• fixed a few knowledge bugs for boss and grasp

  bja43

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  433872f

Commits on Sep 19, 2023

• Merge pull request #1691 from cmu-phil/boss-updates

  Show description for 1b696a2
  jdramsey

  authored
  1b696a2

Commits on Sep 29, 2023

• Fixed kurtosis centering.

  jdramsey

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  84f117b

• Fixed an issue Clark found where if you draw a graph in the Graph Editor and change the name of a variable, the edges incident to that variable disappered. This is fixed, but oddly a GFCI unit test…

  Show description for 78ca6f5
  jdramsey

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  78ca6f5

• Fixed the GFCI test issue by copying code over from BFCI into GFCI.

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  2288016

Commits on Oct 1, 2023

• Fixed the GFCI test issue by copying code over from BFCI into GFCI.

  jdramsey

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  b7c5e3d

• 1. Fixed the self-inflicted bug of layout requiring acyclic graphs.

  Show description for cbca548
  jdramsey

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  cbca548

• Added a note to the bootstrapping section of the manual, in response to a request from Frederick.

  jdramsey

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Commits on Oct 2, 2023

• Formatted the manual.

  jdramsey

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  18468a3

• Formatted the manual.

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  0ccc7f1

Commits on Oct 3, 2023

• New branch to reconcile other branches.

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  2956a57

• New branch to reconcile other branches.

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  7fc4fc1

• New branch to reconcile other branches.

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  f386d2f

• Fixed variable orderign 1.2.3... for knowledge required/forbidden edge editor.

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  ad0f298

• Fixed variable orderign 1.2.3... for knowledge required/forbidden edge editor.

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  a99fcb9

Commits on Oct 5, 2023

• Collapsed existsSemiDirectedPaths() methods in Paths.

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  cb04147

• Collapsed existsSemiDirectedPaths() methods in Paths.

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  078b0d7

• Fixed private static long serialVerUids

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  2b3dbff

• Fixed private static long serialVerUids

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  a1af3de

• Working on the determnistic SEM IM issue.

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  351a959

• Working on the determnistic SEM IM issue.

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  229c5ba

• Working on the determnistic SEM IM issue.

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  d63102c

• Copyed some layouts from Tetrad-FX.

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  4095f43

• Substituted continuous and discrete data loader methods from Tetrad-FX in SimpleDataLoader.

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  13b08b2

• Same for mixed data loader.

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  d78c058

• Copied over the mixed loader and also methods to save and load JSON files.

  jdramsey

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  7329ec6

• Copied data transforms and graph transforms over from tetrad-fx; need to inline the uses of these methods at some point. Some stuff from the Changed class I put in the Utils in Tetrad-FX instead.

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  95f6a2a

Commits on Oct 6, 2023

• Added a menu item to the PlotMatrix to remove the minimum points per plot. This does not work for regressions though.

  jdramsey

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  528aa27

• Switched that manu item to remove zeros from the data instead of minima.

  jdramsey

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  b6cb41f

Commits on Oct 7, 2023

• Switched that manu item to remove zeros from the data instead of minima.

  jdramsey

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  6096c6a

Commits on Oct 12, 2023

• Changed the default layout for graphs to circle if # nodes <= 20 and square otherwise.

  jdramsey

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  1def095

• Added remove zero points per plot feature for Histogram.

  Show description for 0598206
  jdramsey

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  0598206

• Inlined DataTransforms methods in DataUtils.

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  65105c8

• For all tests, throwing an exception if singularities, undefined p-values, or undefined score bumps are encountered. These should be handled by the calling algorithm.

  jdramsey

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  78a3dc6

• Fixed this issues:

  Show description for 640cd00
  jdramsey

  committed
  640cd00

Commits on Oct 13, 2023

• Fixed PC-LiNGAM and added it back into the interface.

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  79cbf87

• Factored out the method in Markov Check that generates all of the independence facts to check for the all-subsets case.

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  d74d125

• Factored out the method in Markov Check that generates all of the independence facts to check for the all-subsets case.

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  6e22d4b

• Fixed tests.

  jdramsey

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  9e886e7

• Fixing some javadoc errors insisted on by the new Javadoc builder.

  jdramsey

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  6a199a6

• Fixing some javadoc errors insisted on by the new Javadoc builder.

  jdramsey

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  e77e8f6

• Fixing some javadoc errors insisted on by the new Javadoc builder.

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  a2729a5

Commits on Oct 15, 2023

• Trying to fix a persistent bug in knowledge where when you delete required edges in the interface, and toggle show explicitly required only, the edges reappear.

  jdramsey

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  1f3d6ba

Commits on Oct 19, 2023

• Trying to fix a persistent bug in knowledge where when you delete required edges in the interface, and toggle show explicitly required only, the edges reappear.

  jdramsey

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  90a0272

Commits on Oct 20, 2023

• Trying to fix a bug in FCI-like algorithms where with R1 or R9 directed edges could be oriented against knowledge. Also, putting CFCI back in the interface.

  jdramsey

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  3bd738e

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  8e6b52a

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  559f803

Commits on Oct 21, 2023

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

  committed
  e0c1cec

• Actually fixed the FCI knowledge but this time. The issue was that the forbidden edges iterator was wrong.

  jdramsey

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  91e62f6

• Fixed some unit tests.

  jdramsey

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  3e00658

Commits on Oct 23, 2023

• Update README.md

  jdramsey

  authored
  ba2531d

• Create InstallApplication.md

  Show description for 9234705
  jdramsey

  authored
  9234705

• Rename InstallApplication.md to INSTALL_APPLICATION.md

  jdramsey

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  8003854

• Update README.md

  jdramsey

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  2e91c11

• Update README.md

  jdramsey

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  483cdbb

• Fixed a typing error in README.md

  daulatojha17

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  1a2ef42

• Update INSTALL_APPLICATION.md

  jdramsey

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  987815a

• Update INSTALL_APPLICATION.md

  jdramsey

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  4c14763

• Update README.md

  jdramsey

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  f0ff6d1

• Merge pull request #1700 from daulatojha17/development

  Show description for 09df9bd
  jdramsey

  authored
  09df9bd

• Update README.md

  Show description for 321df68
  jdramsey

  authored
  321df68

• Merge pull request #1702 from cmu-phil/jdramsey-patch-8

  Show description for af4e626
  jdramsey

  authored
  af4e626

• Update README.md

  jdramsey

  authored
  b107e6c

• Update README.md

  jdramsey

  authored
  547f04a

• Update README.md

  jdramsey

  authored
  d81dd7d

Commits on Oct 24, 2023

• Fixed some unit tests.

  jdramsey

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  18fa2ab

Commits on Oct 27, 2023

• Fixed some knowledge issues.

  jdramsey

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  8dc9855

• Fixed some knowledge issues.

  jdramsey

  committed
  3aecff1

• Fixed some knowledge issues.

  jdramsey

  committed
  6aaca9c

Commits on Oct 30, 2023

• Fixed some knowledge issues.

  jdramsey

  committed
  66b920b

Commits on Oct 31, 2023

• Fixed a problem with Fisher Z with testwise deletion.

  jdramsey

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  43c260d

• Merge pull request #1699 from cmu-phil/joe-work-2023-10-2

  Show description for dccf96d
  jdramsey

  authored
  dccf96d

• Changing version to 7.6.0-SNAPSHOT

  jdramsey

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  7161428

• Merge remote-tracking branch 'origin/development' into development

  Show description for 9ff1c39
  jdramsey

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  9ff1c39