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Integrate Segway Toolkit into Segway#181

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isaiahah wants to merge 95 commits intohoffmangroup:develophoffmangroup/segway:developfrom isaiahah:gmtk-apiisaiahah/segway:gmtk-apiCopy head branch name to clipboard

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Commits

Commits on Jul 25, 2023

• Change output to proper BED

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  05936cb

• Last file of BED format change

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  ef92989

• Fix simpleseg test

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  c6c873c

• Bugfix color assignment and posterior

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  4356d20

• Fix data test

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  a4edc87

• Fix multipledatasets test

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  29cc1b8

• Fix runroundinstance test

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  e6eafb1

• Fix simpleconcat test

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  eb5525e

Commits on Jul 26, 2023

• Fix simpleidentifysteps test

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  5db5629

• Fixed simplerecover test

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  7a60723

• Fixed simpleresolution test

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  7b389b1

• Fixed simplesemisupervised test

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  178ac84

• Attempt to fix simplesubseg test

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  eeffe89

• Fixed simpletrainsteps test

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  431a578

• Fixed simplevirtualevidence test

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  775301e

• Fix Pyflakes warnings

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  75b1b2c

• Change to coloring by superlabel

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  e0878b9

• Bugfix extract_superlabel return type

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  028f261

• Bugfix color assignment to superlabel

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  82914c7

Commits on Jul 27, 2023

• Begin addressing Eric's comments

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  70854a5

• Remove unneeded import

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  852886f

Commits on Jul 28, 2023

• Begin responding to Eric's comments

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  77fdf95

• Complete posterior track output

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  0cecaec

• Fix data test

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  committed
  1cc687f

• Fix runroundinstance test

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  committed
  478e321

• Attempt to fix simplesubseg test

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  committed
  a6707ee

• Bugfix multi-item context manager for py<3.9

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  bb3e7e1

• Cleanup comments and documentation

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  87cc8c4

Commits on Jul 31, 2023

• Address Eric's comments

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  035040e

Commits on Sep 1, 2023

• In progress GMTK API integration

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  d488be3

Commits on Oct 6, 2023

• Rename API files

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  4138d48

• Merge Segway main into GMTK API

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  72b11f6

• flake8 fixes

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  354240a

• Merge branch 'master' of https://github.com/hoffmangroup/segway into gmtk-api

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  6b892aa

• flake8 fixes

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  8c9afde

Commits on Oct 7, 2023

• Convert Virtual Evidence to hard coded string

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  0aff1e1

• Remove extra test files

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  0077e3b

Commits on May 22, 2024

• Draft GMTK API integration

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  8908295

• Bugfix DenseCPT DirichletTable implementation

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  c7eea28

• Place format strings on one line

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  63615eb

• Reorder sections to match template

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  eff60d6

Commits on May 23, 2024

• Add conditional statement on INPUT_PARAMS_FILENAME

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  ebe17ea

• Add clause to print condition on INPUT_PARAMS_FILENAME

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  7947649

• Use Segway toolkit as official input.master

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  f3d9819

• Fix segCountDown_seg_segTransition prob shape

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  c7e3ab1

• Print from-template input.master for testing

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  39a8f20

• Bugfix filename suffix

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  6e61b11

• Bugfix template input.master suffix

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  39c3d58

• Undo previous bugfix

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  f91348c

• Attempt to debug segCountDown_seg_segTransition dimension

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  dd7b63c

Commits on May 24, 2024

• Remove support for Segway toolkit gamma distribution

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  edb2074

• Bugfix removing Gamma distribution

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  ec4ba8d

Commits on May 27, 2024

• Add preprocessor condition on VIRTUAL_EVIDENCE

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  5035df7

• Add keep_shape for Dirichlet Table

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  0ebf3a1

• Fix get_header_info for Dirichlet Tables

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  904cb42

• Remove calls to InputMasterSaver class

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  3d47d64

• Attempt to fix filename creation

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  cfb36e0

• Hardcode input.master.tmpl resource name

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  e5f5564

• Bugfix new file creation

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  2520f26

• Bugfix filename assignment

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  ae9d1ee

• Add header and footers to sections for preprocessor conditions

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  853531f

• Bugfix line_before

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  44d2255

• Add VirtualEvidence class

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  00a419a

• Fix type of VirtualEvidence section

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  380ed43

• Cleanup VirtualEvidence string

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  ff66b3e

Commits on May 29, 2024

• Minor code cleanup

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  f57ff1f

Commits on May 30, 2024

• Move testing to generate input.master into save_input_master

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  9b376e8

• Re-add INPUT_MASTER_FILENAME

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  5889962

• Fix exported filename

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  committed
  b02316b

• Bugfix code change

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  d096ea2

• Attempt to bugfix input_master_filename

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  a038925

• Undo attempted changes from today

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  97d75cf

• Merge branch 'gmtk-api' of https://github.com/isaiahah/segway into gmtk-api

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  f7f8e7b

• Revert changes from today

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  9c26a70

Commits on Jun 6, 2024

• Remove old template system for input.master

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  f15876a

• Cleanup code checking if input.master exists

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  f9a5f31

Commits on Jun 11, 2024

• Continue cleanup

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  f1a873e

Commits on Jun 12, 2024

• Additional code cleanup and flake8 fixes

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  622f892

• input.master cleanup

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  f3a1e52

Commits on Jun 13, 2024

• Rename segway_input_master

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  6c4245d

• Implement DirichletConst line in DPMF header

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  3e960f4

• Remove input.master.tmpl

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  e397c7f

• flake8 fixes

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  f4e28dc

• Add default preamble to support CNVway backward compatability

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  c3ed1ec

Commits on Jun 14, 2024

• Load decision trees from data files

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  20378f2

• Bugfix for Python3.9 (cannot check instance with generic)

  isaiahah

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  679fe0a

Commits on Jun 24, 2024

• Address Eric's comments

  isaiahah

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  a087573

Commits on Jul 2, 2024

• Remove RealMat class

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  8c9703b

Commits on Jul 5, 2024

• Address Eric's comments

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  df8c2db

Commits on Jul 8, 2024

• Update OBJ_KIND for Generic String

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  62917f9

Commits on Jul 10, 2024

• Remove references to ArbitraryString

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  72a38f8

• flake8 fixes

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  committed
  6a6e60b

Commits on Jul 12, 2024

• Rename toolkit file to params.py

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  b1bef31

Commits on Aug 30, 2024

• Address Michael's comments

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  74ebfe1

• Call make_cardinality_line more

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  072d3e8