v1.0.0

PhyloNetworks v1.0.0

Diff since v0.17.0

PhyloNetworks v1.0.0 is a major change from version v0.16.4, to serve as a "core" for the manipulation of phylogenies, used by other packages with more specialized functionalities.

• many functionalities were moved to other packages (e.g. SNaQ.jl and PhyloTraits.jl)
• new core functionalities are available.

Merged pull requests:

• tagbot fix; new: getlevel, istreechild, isgalled (#219) (@cecileane)
• v1.0.0 (#221) (@cecileane)

v0.17.0

PhyloNetworks v0.17.0

major changes to lighten PhyloNetworks to make it a better "core".
new features include: traversal routines, getting node heights, check for time-consistency

breaking changes include:

• snaq! moved to new package SNaQ.jl
• phylolm moved to new package PhyloTraits.jl
• many function names and internal field names were modified -- older exported names are deprecated
• function to search for most parsimony network left in (not exported), but not working (was limited to level-1 networks)
• phylinc moved to new package: PhyLiNC.jl

v0.16.4

PhyloNetworks v0.16.4

Diff since v0.16.3

• breaking change to internal function: addleaf! returns new leaf, not net
• modified RNG within snaq!: will generate different network proposals, compared to same seed but v0.16.3

Merged pull requests:

• fix bug: when deleting a hybrid edge leads to simplification of parallel edges at hybrid with 2 children (#207) (@cecileane)
• Fix for the slow but constant increase in memory usage (#209) (@NathanKolbow)
• fix 2-cycle (parallel edges) bug in snaq (#211) (@cecileane)
• documentation: workflow, badges, workshop link, ftest warnings (#212) (@cecileane)

Closed issues:

• MrBayer error (#208)
• 2-cycle (parallel edges) proposed in SNaQ (#210)

v0.16.3

PhyloNetworks v0.16.3

Diff since v0.16.2

Merged pull requests:

• CompatHelper: bump compat for NLopt to 1, (keep existing compat) (#202) (@github-actions[bot])
• fix #201 and #205 (#206) (@cecileane)

Closed issues:

• infinite loop in readTopologyLevel1 (#201)
• Feedback on Detected EXCEPTION-HANDLING (#203)
• The confusion of starting topology (#204)
• fitdiscrete error with new String7 from CSV (#205)

v0.16.2

PhyloNetworks v0.16.2

Diff since v0.16.1

Closed issues:

• Get rid of TableRegressionModel (#185)
• Support extended Newick? (#193)
• Inheritance Probability Confidence Interval? (#198)

Merged pull requests:

• CompatHelper: bump compat for StatsBase to 0.34, (keep existing compat) (#199) (@github-actions[bot])
• for v0.16.2 (#200) (@cecileane)

v0.16.1

PhyloNetworks v0.16.1

• better method to read a 'trees' block from a nexus-formatted file
• writeTableCF more generally applicable to convert a vector of QuartetTs to a data frame

Diff since v0.16.0

Merged pull requests:

• read nexus tree blocks: with translate tables and networks (#197) (@cecileane)

v0.16.0

PhyloNetworks v0.16.0

Diff since v0.15.3

breaking changes:

• Getter names (getchild, getparent etc.) were changed with standardized names, and are now exported.
  Old getter names are deprecated, so users should run julia with deprecation warnings (julia --depwarn=yes) to get info on new names to update their code.
• PhyloNetworkLinearModel's are no longer wrapped in a TableRegressionModel
• Evolutionary model of TraitSimulation and PhyloNetworkLinearModel objects: now in field 'evomodel'

new:

• more accessors, e.g. getroot, isleaf, isexternal, isrootof, isparentof, ischildof

bug fixes:

• in get and setGammas: fixed to work with non-tree-child networks
• in addAlternativeHybridizations!

Closed issues:

• performance suggestion make trees more type stable (#155)
• Ghost introgression (#192)

Merged pull requests:

• CompatHelper: bump compat for Functors to 0.4, (keep existing compat) (#189) (@github-actions[bot])
• standardize and export getter names (#190) (@cecileane)
• Get rid of Tableregressionmodel (#194) (@pbastide)
• CompatHelper: bump compat for StatsModels to 0.7, (keep existing compat) (#195) (@github-actions[bot])
• near v0.16.0 (#196) (@cecileane)

v0.15.3

PhyloNetworks v0.15.3

Diff since v0.15.2

Edge type: parametrized by its Node type to use a vector of concrete type
Improved manual & tests about multiple alleles

bug fixes:

removal of degree-2 nodes, used in deleteleaf!
removal of hybrid edges with low inheritance
read table of qCFs: bug due to compatibility; now requires DataFrames v1.3

Closed issues:

• multiple alleles: bug in mapAllelesCFtable? (#143)

Merged pull requests:

• better handling of 2-cycle at the root (#186) (@cecileane)
• parametric EdgeT with vector of concrete node type (#187) (@cecileane)
• bug fix to read table of qCFs (#188) (@cecileane)

v0.15.2

PhyloNetworks v0.15.2

Diff since v0.15.1

new features:

• shrinkedge! e.g. to create a polytomy
• least stable ancestor: find it, delete what's above

bug fixes in:

• rootatnode!: redirect edges before error, if re-rooting failed (and better error message, keyword argument 'verbose' removed)
• biconnectedComponents, when there were parallel edges

Merged pull requests:

• bug fix for biconnected components (#182) (@cecileane)
• CompatHelper: bump compat for FASTX to 2, (keep existing compat) (#183) (@github-actions[bot])
• v0.15.2: redirect edges if re-rooting failed. new: shrinkedge! (#184) (@cecileane)

v0.15.1

PhyloNetworks v0.15.1

Diff since v0.15.0

Merged pull requests:

• CompatHelper: bump compat for Functors to 0.3, (keep existing compat) (#178) (@github-actions[bot])
• Error when the network has negative or missing branches for phylolm (#180) (@pbastide)
• removedegree2nodes! : option to keep the root (#181) (@cecileane)