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Releases: bredelings/BAli-Phy

Release 4.0-beta5

27 Jun 23:04
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A lot of small things.

  • New Singularity executable to run on clusters with old software.
  • Fix problem with Covarion models (affected RNA-editting model).
  • Temporarily remove pre-burnin.
  • If --tree is specified then scales default to a constant 1.0 so that the likelihood tests work
  • Remove eigen sources from git, automatically download if not installed.
  • Allow printing trees and alignments efficiently from Haskell.
  • Implement Haskell File IO.
  • Move loggers for almost everything from C++ into Haskell.
  • Compute parsimony score in Haskell.
  • Move slice-sampling and MH moves from C++ into Haskell.
  • Don't treat JSON integers as if they were floating point.
  • Make it a lot easier to define new IO operations.
  • Stop running C++ MCMC moves -- just run Haskell moves.
  • Stop exporting the scale from Haskell to C++.
  • Add Data.IORef for mutable values.
  • Add Data.Unique and Data.Unique.Id.

Release 4.0-beta4

12 May 07:04
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Fixes:

  • update R script
  • fix bug where exponential / gamma variables weren't sampled.

Features:

  • alignment-consensus implements strict consensus with --cutoff=1 or --strict=1
  • give better errors with overlapping instances in Haskell.

Release 4.0-beta3

22 Apr 04:16
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This release starts changing the command-line model language:

  • You can now use +, -, *, and / for numeric operations.
  • Models are now stacked with +> instead of +
  • Functions are now called with parenthesis (e.g. f(x) instead of f[x])
  • List and tuples can be specified like [x,y] and (x,y)` respectively.
  • Dictionaries can be specified like {"A":x,"B",y}.

Additionally,

  • Improve MCMC mixing when extending/shrinking I.I.D. lists.
  • Add new numeric type Prob that handles numbers very close to 1 without having (1-p) = 0.
  • Make Geometric, Bernoulli, Binomial, etc. use the new Prob type.

Release 4.0-beta2

22 Mar 02:42
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This release updates the command-line model syntax to look like f(x) instead of f[x]. Other changes include:

  • Allow sequences names to contain Newick special characters, but give a warning.
  • Optimization: eliminate unused error paths.
  • Decrease memory usage from compilation.

Release 4.0-beta1

09 Mar 20:02
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Fixes:

  • Fix bug with fixed alignments that was introduced in 4.0alpha-10.
  • Check likelihoods for fixed alignments as well as variable alignments in CI.
  • Fix sample_ancestral_sequences

Other changes

  • Allow compiling with gcc-13
  • Better error messages in case type variable escapes its scope.

Release 4.0-alpha10

22 Feb 04:44
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This release decreases memory usage for large trees. This fixes a problem that goes back to the version 3 series.

It also

  • refactors the Tree data structure
  • simplifies the dependency graph
  • adds the unbounded type Integer, in addition to the bound type Int.
  • allows importing and exporting types
  • further improves error messages

Release 4.0-alpha9

10 Jan 15:25
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This release mostly improves the model language by adding (i) associated types, (ii) readable error messages, and (iii) the unbounded Integer type.

It also contains a few new models and fixes.

  • Models
    • Add Covarion.gtr to allow more flexible rates between classes.
    • Add the (iid_on objects sub_distribution) distribution.
  • Fixes
    • Fix tree MDS plots

Release 4.0-alpha8

15 Nov 18:40
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Release 4.0-alpha8 Pre-release
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This release mostly improves the typechecking code by

  • adding support for GADTs and equality constraints like (a ~ [b]).
  • making the Random monad into a GADT.

This is mostly invisible to users, unless you are using the probabilistic programming stuff.

It also

  • fixes some Inf/NaN output in trees-bootstrap
  • accepts '?' again as maybe-an-N-maybe-a-gap.

Release 4.0-alpha7

19 Aug 01:50
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Release 4.0-alpha7 Pre-release
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A few changes:

  • make BES work with typechecking
  • make read_phase_file and read_phase2_file into IO actions for BES.
  • allow specifying model arguments as just -m Model arg1 arg2 instead of -m Model.hs ... --- arg1 arg2.
  • use std::filesystem for file operations.
  • target OS X 10.15
  • alignment-consensus and alignment-gild can take a list of alignment files

Release 4.0-alpha6

17 Jul 01:30
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Release 4.0-alpha6 Pre-release
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The main new feature of 4.0-alpha6 is Haskell model code is type-checked.