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ChangeLog
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version: 3.9.2
date: 2020-10-15
author: Melanie Loth <mloth1@jhmi.edu>
- Updated license to BSD 3
- Added Melanie (self) as maintainer
version: 3.5.13
date: 2019-9-9
author: Tom Sherman <tomsherman159@gmail.com>
- fixed patternMarkers function, allow axis to be specified
- added snapshots functionality
version: 3.5.12
date: 2019-8-30
author: Tom Sherman <tomsherman159@gmail.com>
- fixed failing error with calcZ
version: 3.5.11
date: 2019-8-30
author: Tom Sherman <tomsherman159@gmail.com>
- Change zereos in standard deviation matrix to a warning when calculating Z-Scores, in this case 1e-6 will be used instead
- set the minimum p-value to 1/numPerm in calcCoGAPSStat
version: 3.5.10
date: 2019-8-30
author: Tom Sherman <tomsherman159@gmail.com>
- Fix bogus error check in calcCoGAPSStat
version: 3.5.9
date: 2019-8-29
author: Tom Sherman <tomsherman159@gmail.com>
- added option to use P matrix for calcCoGAPSStat
version: 3.5.8
date: 2019-7-22
author: Tom Sherman <tomsherman159@gmail.com>
- scientific notation allowed in input files
version: 3.5.7
date: 2019-7-22
author: Tom Sherman <tomsherman159@gmail.com>
- fixed error in mtx parsing
version: 3.5.6
date: 2019-7-2
author: Tom Sherman <tomsherman159@gmail.com>
- disable checkpoint system until repairs are made for the new version
version: 3.5.5
date: 2019-7-2
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bug that caused installation on windows to fail
version: 3.5.4
date: 2019-6-28
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bug where workers wouldn't print status during distributed runs
version: 3.5.3
date: 2019-6-26
author: Tom Sherman <tomsherman159@gmail.com>
- refactored several portions of the backend
- added an option for running a sequential gibbs sampler so the overhead of
multi-threading is not paid unless requested, this mode is enabled when running
distributed cogaps since it can't be run on more than one thread anyways
- fixed the atomic domain bottleneck when reaching millions of atoms
- add warning if multiple threads requested and OpenMP was not supported by compiler
- fixed issues with reading csv/tsv/gct files
- added amplitude markers function
- log transformed sample GIST data
- track number of updates and total running time
- added more robust assert statements for debugging
- added debugRuns script for an extra step of testing
version: 3.5.2
date: 2019-6-26
author: Tom Sherman <tomsherman159@gmail.com>
- fixed name of Equilibration phase
version: 3.5.1
date: 2019-6-4
author: Tom Sherman <tomsherman159@gmail.com>
- bumped version for new bioc release
version: 3.3.45
date: 2019-6-4
author: Tom Sherman <tomsherman159@gmail.com>
- added a clearer display message in for the number of atoms in each domain
- added a warning message when using scCoGAPS or GWCoGAPS instead of the main
function CoGAPS with the distributed argument
version: 3.3.44
date: 2019-5-1
author: Tom Sherman <tomsherman159@gmail.com>
- fixed internal issues that would result in parameters being misread
on some systems
version: 3.3.43
date: 2019-4-3
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bug where feature/sample names would get re-ordered in distributed runs
- add warning when data is sparse, but sparseOptimization is not enabled
- display feature/sample name information in parameters object
- remove debug pring statement when pattern matching results in NA's
version: 3.3.42
date: 2019-3-7
author: Tom Sherman <tomsherman159@gmail.com>
- add warning when not using a file as input for distributed cogaps
version: 3.3.41
date: 2019-3-5
author: Tom Sherman <tomsherman159@gmail.com>
- fix bug where not all workers would start
- no longer ignore custom value for BPPARAM
version: 3.3.40
date: 2019-2-22
author: Tom Sherman <tomsherman159@gmail.com>
- more sensible default parameters
- fixed critical bug introduced in 3.3.37 where fixedPatterns was
ignored in the second phase of distributed runs
version: 3.3.39
date: 2019-2-20
author: Tom Sherman <tomsherman159@gmail.com>
- fix bug when reading mtx and not ignoring comments
- allow setDistributedParams to be called to reset params
version: 3.3.38
date: 2019-2-18
author: Tom Sherman <tomsherman159@gmail.com>
- print message when each worker starts
version: 3.3.37
date: 2019-2-18
author: Tom Sherman <tomsherman159@gmail.com>
- move all critical parameters to CogapsParams class
- allow RDS files to be passed for parameters
- runs should be reproducible now with the data file and the parameters file
version: 3.3.36
date: 2019-2-13
author: Tom Sherman <tomsherman159@gmail.com>
- fix bug when recording initial phase of distributed cogaps
version: 3.3.35
date: 2019-2-12
author: Tom Sherman <tomsherman159@gmail.com>
- correctly subset gene/sample names
version: 3.3.34
date: 2019-2-8
author: Tom Sherman <tomsherman159@gmail.com>
- optionally disable checkpoints, disable on windows by default
version: 3.3.33
date: 2019-2-7
author: Tom Sherman <tomsherman159@gmail.com>
- internal design changes, should have no visible effect
version: 3.3.32
date: 2019-2-4
author: Tom Sherman <tomsherman159@gmail.com>
- allow "none" to be the argument type for distributed parameter
version: 3.3.31
date: 2019-1-31
author: Tom Sherman <tomsherman159@gmail.com>
- allow rds files to be passed
version: 3.3.30
date: 2019-1-29
author: Tom Sherman <tomsherman159@gmail.com>
- added check for value of params@distributed
version: 3.3.29
date: 2019-1-22
author: Tom Sherman <tomsherman159@gmail.com>
- check for user interrupt more often when reading data
version: 3.3.28
date: 2019-1-15
author: Tom Sherman <tomsherman159@gmail.com>
- return average asynchronous queue length in metadata
version: 3.3.27
date: 2019-1-9
author: Tom Sherman <tomsherman159@gmail.com>
- stop running examples for scCoGAPS/GWCoGAPS to reduce R CMD check time
version: 3.3.26
date: 2019-1-8
author: Tom Sherman <tomsherman159@gmail.com>
- allow for selectively disabling AVX instructions
version: 3.3.25
date: 2019-1-7
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bugs with new build configuration
version: 3.3.24
date: 2019-1-4
author: Tom Sherman <tomsherman159@gmail.com>
- dont compile C++ unit tests by default
version: 3.3.23
date: 2019-1-4
author: Tom Sherman <tomsherman159@gmail.com>
- better handle setting nPatterns after cut
version: 3.3.22
date: 2019-1-3
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bug when reading csv/tsv files and using sparseOptimization
version: 3.3.21
date: 12-20-19
author: Tom Sherman <tomsherman159@gmail.com>
- added PUMP back to CoGAPS
version: 3.3.20 (jumped from 3.3.16)
date: 2018-12-19
author: Tom Sherman <tomsherman159@gmail.com>
- allow for fixed matrix in standard CoGAPS
version: 3.3.16
date: 2018-11-22
author: Tom Sherman <tomsherman159@gmail.com>
- flush output when printing time
version: 3.3.15
date: 2018-11-22
author: Tom Sherman <tomsherman159@gmail.com>
- clarify internal parameters
version: 3.3.14
date: 2018-11-16
author: Tom Sherman <tomsherman159@gmail.com>
- added how much time the run took in the worker output message
version: 3.3.13
date: 2018-11-16
author: Tom Sherman <tomsherman159@gmail.com>
- added a print message when a worker has finished during distributed CoGAPS
version: 3.3.12
date: 2018-11-16
author: Tom Sherman <tomsherman159@gmail.com>
- fixed bug where rows/cols would get re-ordered in GWCoGAPS/scCoGAPS
version: 3.3.11
date: 2018-11-15
author: Tom Sherman <tomsherman159@gmail.com>
- store chisq and atom count history in result object
version: 3.3.10
date: 2018-11-15
author: Tom Sherman <tomsherman159@gmail.com>
- display size of subsets created by GWCoGAPS/scCoGAPS