Forthcoming fixes - cmu-phil/tetrad GitHub Wiki

Updates since 7.6.3

  1. Added elapsed wall time of algorithm run to the Stats List editor if a GeneralAlgorithmRunner is a parent of it.
  2. Updated the manual so that all algorithms, tests, and scores have documentation in the Search box in the interface.
  3. Added a method to MarkovCheck to print out a Markov check result as a string for use in Causal Command.
  4. Resolved all JavaDoc warnings.
  5. Made the handling of threads more uniform, using a ForkJoinPool for everything. A new ForkJoinPool is created for each algorithm's run, allowing all threads for that pool to be stopped by calling shutdownNow() on the pool when the current thread is interrupted.
  6. For parallelized algorithms, add (where not already available) a parameter to specify the number of threads to use.
  7. For bootstrapping, also added a parameter for the number of threads to use (for the bootstrapping itself).
  8. This fixes a long-standing bug in the interface where clicking the stop button would not stop all threads associated with a multi-threaded algorithm.
  9. Added a parameter for the number of threads to BFCI and GFCI since BOSS and FGES have this parameter.
  10. Fixed the stop button in the interface so that partial work is not returned if an algorithm is stopped.
  11. Added a method to test whether a given graph is a legal CPDAG.
  12. Set as default for bootstrapping not to include the original dataset as an extra sample.
  13. Cleaned up the TetradLogger class to use immediate logging throughout the code.
  14. Cleaned up logging for PC and FCI and several other algorithms.
  15. Moved the session package from the lib package to the GUI package.
  16. Corrected null and alternative hypotheses for Bayes Estimator.
  17. Increased the factor for off-peak randomizations for rows in CPTs for BayesIM randomization.
  18. Improved deserialization procedure for LoadSessionAction.
  19. Reduced the size of the initial application windows.
  20. Fixed the stop button in the interface so that partial work is not returned if an algorithm is stopped.
  21. Made a correction to the whitening step of FastICA, affecting ICA LiNGAM and ICA LiNG-D.
  22. Did another cleanup/documentation update pass through the search package, using IntelliJ's AI Assistant.
  23. Did another cleanup/documentation update pass through the test package, using IntelliJ's AI Assistant.
  24. Fixed bug in SemSimulation where when different graphs were specified, data would not be simulated using the novel graphs.
  25. Refactored the generalized SEM editors.
  26. In the generalized SEM IM, for simulation, switched to a recursive method for acyclic models; the Fisher method is only used for cyclic models.
  27. Fixed bug in generalized sem PM where edits to formulas would eventually cause Tetrad to hang.
  28. Refactored GeneralizedSemSimulation and SemSimulation.
  29. Added IDA minimum beta values to the MarkovCheck and MarkovCheckEditor classes.