Code

joe_work_2024_6-13#1800

Code

Merged

jdramsey merged 162 commits intodevelopmentcmu-phil/tetrad:developmentfrom joe_work_2024_6-13cmu-phil/tetrad:joe_work_2024_6-13Copy head branch name to clipboardAug 11, 2024

+12,065-5,355

Commits

Commits on Jun 14, 2024

• Add new statistic calculation classes and update depth control in search algorithms

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Commits on Jun 16, 2024

• Add graph viewing functionality to GridSearch GUI

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• Add depth setting methods and refactor statistics calculation

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• Update Maven plugin versions and add documentation comments

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Commits on Jun 17, 2024

• Make GUI components transient and refactor button creation

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• Redirect verbose output to System.out and ensure parameter serialization

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Commits on Jun 18, 2024

• Remove unused MagSemBicScore and add new Scoring Implementations

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Commits on Jun 20, 2024

• Refactor likelihood tests and update data handling in multiple files

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• Reduce histogram bins and optimize variable removal in Markov check

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• Remove unused MyWatchedProcess call

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• Implement prevention of graph cycles in Meek rules

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Commits on Jun 21, 2024

• Added meekPreventCycles flag with default setting

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• Refactor MeekRules class with better documentation

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• Refactor logging and collider checks in MeekRules and PcCommon

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• Move directed edge addition in MeekRules

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• Add ability to prevent cycles in Meek orientation

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• Replace "meekPreventCycles" with "guaranteeCpdag" across multiple files

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• Refactor markov check logic and add new statistic classes

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• Enable cycle prevention in MeekRules and improve documentation

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• Add additional argument in compareFromSimulations method

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Commits on Jun 22, 2024

• Add MagDgBicScore class and update depth in GraspFci

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Commits on Jun 23, 2024

• Improve comments and refactor method parameters in tetrad-gui

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• Refactor graph comparison methods and adjust collider orientation

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• Rename orientCollidersAndRemoveEdges to orientAndRemove

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• Update LvLite algorithm mechanics

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• Rename "equalityThreshold" to "bayesFactorThreshold"

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• Update description in LV-Lite procedure documentation

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Commits on Jun 25, 2024

• Update LvLite classes and methods to use allowableThreshold

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• Update rules and methods to repair faulty PAGs in various graph-related classes

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Commits on Jun 26, 2024

• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe_work_2024_6-13

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• Refactor code and fix orientation issue

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• Update repairFaultyPag method and enhance logging in GraphUtils

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• Refactor LvLite and LvLiteDsepFriendly classes

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Commits on Jun 28, 2024

• Update calculation methods in GraphUtils and optimize various search methods

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• Refactor LvLite.java for parallel execution

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Commits on Jun 29, 2024

• Update Grasp and TeyssierScorer constructor arguments

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• Update exception message in LvLite.java

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• Update attribute names and improve parallel computations

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• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe_work_2024_6-13

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• Refactor edge removal methods in LvLite

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Commits on Jun 30, 2024

• Refactor LvLite.java and SessionEditorNode.java for better performance

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• Update parameters and add documentation to existing methods

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Commits on Jul 2, 2024

• Refactor LvLite and related classes for clarity and performance; ensured edge specialization in the interface is done only for directed edges.

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• Refactor LvLite class and update edge type documentation

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• Add 'knowledge' parameter to graph processing methods

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• Add option to remove extraneous variables in MarkovCheckEditor

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• Update parameter descriptions and add new option in conditioning set type

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• Remove LvLiteDsepFriendly class from the project

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Commits on Jul 5, 2024

• Update LvLite and related classes

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Commits on Jul 6, 2024

• Update graph algorithm and remove unnecessary debug log

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• Refactor LvLite algorithm and update GraphUtils

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• Add statistics for adjacencies in PAG graphs

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• Refactor collider addition logic in LvLite.java

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Commits on Jul 7, 2024

• Refactor LvLite search, improve path handling, and enhance PAG adjustments

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• Refactor LvLite.java and add maxBlockingPathLength field

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• Refactor LvLite and FciOrient classes for enhanced code optimization

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• Rename LV_LITE_MAX_PATH_LENGTH to MAX_BLOCKING_PATH_LENGTH

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• Update LvLite algorithm and related files

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• Rename and modify NumInducedAdjacenciesInPag to NumEdgeInEstInTrue

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• Refactor comparison process to use WatchedProcess

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• Update StatsListEditor class documentation

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Commits on Jul 8, 2024

• Refactor LvLite and BFci classes for clarity and performance

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• Refactor LvLite and update search methods

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• Refine wording and adjust parameters in LvLite class

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• Refine LvLite algorithm and documentation

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Commits on Jul 10, 2024

• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe_work_2024_6-13

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• Refactor LvLite and update FciOrient; add tucking and testing flags

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• Refactor code for better handling of directed acyclic graphs.

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Commits on Jul 13, 2024

• Refined LvLite algorithm and updated graph statistics

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• Remove unused checkTucked2 method and comments

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• Refactor FciOrient for better path tracking mechanism

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• Refactor FciOrient configuration and adjust usages

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Commits on Jul 14, 2024

• Refactor FciOrient method and update classes

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Commits on Jul 15, 2024

• Add getSepset2 method in LvLite class and fix typo in TestLvFromOracle class

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• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe_work_2024_6-13

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• Update search parameters in TestFci.java

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• Change methods to return Set instead of List

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Commits on Jul 16, 2024

• Change methods to return Set instead of List

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• This version of LV-Lite is regularly passing a Markov check.

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• Refactor code across multiple files and methods

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• Refactor graph manipulation in search algorithms

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Commits on Jul 18, 2024

• Add option to skip final orientation step in algorithms

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• Remove redundant 'repairFaultyPag' method

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• Add new SepsetFinder class and refactor related classes

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• Refactor Sepset classes for efficiency

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Commits on Jul 19, 2024

• Refactor SepsetsGreedy to improve performance

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• Add selection of sepset finder method in SpFci and BFci

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• Update sepset finding methods in docs

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• Update sepset finding methods in docs

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Commits on Jul 21, 2024

• Add depth parameter to sepset finding functions

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• Refactor sepset path blocking method in SepsetFinder

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• Refactor SepsetFinder and related methods

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Commits on Jul 22, 2024

• Refactor LvLite and SepsetFinder and enhance code consistency

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• Refactor sepset finder and remove unnecessary code

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• Refactor SepsetFinder and TestSepsetMethods

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• Update method name in output message

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• Update test parameters in SepsetMethods test cases

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• Merge branch 'development' of https://github.com/cmu-phil/tetrad into joe_work_2024_6-13

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• Refactor SepsetFinder methods and update tests

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Commits on Jul 24, 2024

• Add new functions for graph conversion and update existing ones

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• Update search methods and remove tucking steps

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• Refactor separation set logic and improve sepset handling

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Commits on Jul 25, 2024

• Remove discriminating path rules from DAG to PAG conversions

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• Enhance D-SEP computation for MAGs and IPGs

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• Add FCI orientation rules with data examination strategies

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• Refactor and streamline LvLite and related classes

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Commits on Jul 26, 2024

• Refactor AlmostCycleRemover for clarity and flexibility

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• Refactor LvLite orientation methods and improve cycle removal

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• Refactor cycle-removal logic and cleanup LvLite class

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Commits on Jul 27, 2024

• Refactor handling of almost cycles and sepsets

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• Disable cycle removal and add allPathsOutOf3 method

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• Refactor sepset path blocking logic and update tests.

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• Merge remote-tracking branch 'origin/joe_work_2024_6-13' into joe_work_2024_6-13

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Commits on Jul 28, 2024

• Update path blocking methods and clean up comments

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Commits on Jul 29, 2024

• Refactor LvLite to use 'dag' instead of 'cpdag'

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• Update FciOrient initialization in LvLite class

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• Remove debug println statements for cleaner code

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• Remove debug println statements for cleaner code

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Commits on Jul 30, 2024

• Refactor edge removal method and improve exception clarity

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• Refactor: Add blank line for code readability

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• Remove redundant blank line in LvLite.java

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• Add extra edge removal strategy to LvLite

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• Update various classes with JavaDoc comments and final modifiers

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• space

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Commits on Jul 31, 2024

• Update LV-Lite parallel execution and add timeout handling

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• Refactor doDiscriminatingPathOrientation method signature

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• Refactor SepsetFinder and update discriminatingPathOrient

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• Introduce timeout for extra edge removals and FciOrient steps

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• Refactor timeout handling and synchronize methods

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Commits on Aug 1, 2024

• Implement Pair return type for path orientation methods

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Commits on Aug 2, 2024

• Implement support for allowed colliders in FCI algorithms

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• Refactor FciOrient and LvLite for consistency

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Commits on Aug 3, 2024

• Refactor logging for better readability and context

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• Add detailed logging to LvLite.java

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Commits on Aug 5, 2024

• Add detailed logging to LvLite.java

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• Remove redundant methods and cleanup SepsetFinder.

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• Refactor graph pathfinding to use Dijkstra's algorithm

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Commits on Aug 6, 2024

• Add "Make All Edges Nondirected" functionality

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• Add "Make All Edges Nondirected" functionality

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• Improve Dijkstra implementations for FciOrient and Graph handling

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• Rename Dijkstra utility to FciOrientDijkstra for specialization

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• Rename Dijkstra utility to FciOrientDijkstra for specialization

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• Rename Dijkstra utility to FciOrientDijkstra for specialization

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• Remove FciOrientDijkstra and Rename FciOrient Strategies

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• Rename R4Strategy to R0R4Strategy and update related references.

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• Remove extraneous newline in FciOrient.java

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• Add handling for partially oriented edges and refactor rules

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• Refactor GraphUtils handling and adjust FciOrient signature

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Commits on Aug 7, 2024

• Refactor discriminating path methods

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• Refactor: Move R5R9Dijkstra to search.utils package

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• Simplify discriminating path orientation methods

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• Merge remote-tracking branch 'origin/joe_work_2024_6-13' into joe_work_2024_6-13

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• Remove unused import in FciOrient.java

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• Remove SvarFciOrient.java

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• Rename isValidForGraph to existsInGraph in DiscriminatingPath

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Commits on Aug 8, 2024

• Refactor DiscriminatingPath and related classes/methods.

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• Refine edge orientation rules and simplify documentation

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• Make fciOrientbk method public

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• Refactor visibility check logic in Paths.java

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• Conditionally log messages based on verbosity

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Commits on Aug 9, 2024

• Fix newline formatting in FciOrient.java

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• Add Javadoc to various classes and methods

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