Skip to content

Latest commit

 

History

History
148 lines (90 loc) · 3.83 KB

ChangeLog.md

File metadata and controls

148 lines (90 loc) · 3.83 KB
Raw

Revision history for ELynx

Unreleased changes

Version 0.8.0.0

  • Adapt to breaking changes in upstream libraries (data-default).

Version 0.7.2.0

  • slynx: Allow global normalization of mixture models.

Version 0.7.1.0

  • Be less strict with quoted identifiers/names in phylogenetic trees.
  • Be less strict with FASTA identifiers.
  • Update tooling (GHC 9.2.4).

Version 0.7.0.1

  • Random 1.2: Parallel functions now require an `IOGenM` random number generator.
  • Fix splitting of the random number generator.

Version 0.6.1.1

  • Remove plotting functionality (gnuplot incompatible with ghc922).
  • Read files strictly.
  • Refactor; flatten model hierarchy.

Version 0.6.1.0

  • Split ELynx.Tools into separate modules because the package will be reduced.
  • Remove the following modules from ELynx.Tools: Concurrent, LinearAlgebra, List, Misc, and Numeric.

Version 0.6.0.0

  • elynx-tree: remove parallel folds with layers (parBranchFoldMapWithLayer too special and slow).
  • elynx-tree: fix various tree instances; add zip trees with appropriate instances.
  • Remove monad-logger dependency and implement lighter alternative.
  • Significant changes to the tool chain.

Version 0.5.1.0

  • elynx-tree: new functions isValidPath, isLeaf, depth; add conversion topology -> tree; various internal algorithmic improvements; improved error messages; simplified interface to Newick parsers; parallel fold map; Nix flake.
  • Remove unneeded dependencies.

Version 0.5.0.2

  • Speed up mixture model simulation.
  • Improve rooting functions.
  • Improve Topology data type (but still a lot to do).
  • Various additions to the documentation.
  • Rename Measurable to HasLength, Supported to HasSupport, and Named to HasLength.
  • Cabal and stack file changes.

Version 0.5.0.1

  • modLen, modSup.
  • Newtype wrappers for branch length, branch support, and node name. Those data types and some functions were also renamed.
  • Add Path, and getSubTreeUnsafe to tree zipper.
  • Rename unsafe functions so that unsafe is at the end.
  • Many small changes.

Version 0.4.1

  • Improve TimeSpec (Point process).
  • Parallel evaluation strategies.
  • Change names of some functions involving partitions. For example, mp was renamed to pt.
  • Improve documentation for (bi)partitions.
  • Bugfix tlynx compare; do not throw error when branch support values are not set.
  • Add no-elynx-file option.
  • Also parse Nexus files with tlynx commands.
  • Bugfix subSample; the sub sample was reversed.

Version 0.4.0

  • Major refactor of elynx-tree. All required function can now conveniently reexported by ELynx.Tree.

Version 0.3.4

  • Improve slynx examine; show hamming distance; show constant sites.
  • PhyloStrict -> PhyloExplicit; and some conversion functions were changed.
  • tlynx coalesce was merged into tlynx simulate, the syntax has changed; see tlynx simulate --help.

Version 0.3.3

  • Fix test suites.

Version 0.3.2

  • Remove llvm dependency.
  • Move away from hpack.

Version 0.3.1

  • Use Attoparsec.
  • Use ByteString consistently.
  • Remove elynx-tools dependency from libaries.

Version 0.3.0

  • elynx-nexus: library to import and export Nexus files.
  • elynx-tree: major refactor and big cleanup; use rose trees with branch labels.
  • elynx-tree: provide zippers.

Version 0.2.2

  • Validation and repetition of previous analyses is finally possible with the new elynx binary.
  • A library elynx-markov for running Markov processes along phylogenetic trees has been split off elynx-seq. This library performs the computations when executing slynx simulate ....
  • Many other small improvements.