PhyloNetworks v0.16 to v1 refactoring: re-naming guide

This document lists the main changes to names in PhyloNetworks when the package was refactored, in Nov. 2024. It is intended to help users update scripts developed under PhyloNetworks v0.16 or older, to work with v1 and later.

While PhyloNetwork’s documentation should be help: each package version has its own documentation. We can switch between documentations by clicking on the desired package version in the “version” menu on the lower left corner. This documentation should help to update code that uses exported functions, especially using the search box (near the top left corner) when we don’t know the exact function name. But changes in internal field names, in particular, are not typically documented, so here they are.

types and functions moved away

Many functions were moved to SNaQ.jl. Obviously, snaq! is one of them.

Internal utilities specific to quartets were moved also, including types DataCF and Quartet, and methods that used these objects, possibly renamed. Here is a non-exhaustive list.

old name	new name
`readTopologyLevel1`	`readnewicklevel1`
`readMultiTopologyLevel1`	`readmultinewicklevel1`
`unionTaxa`	`tiplabels`
`unionTaxaTree`	`tiplabelsTree`
`readTrees2CF`	`readtrees2CF`

and these internals, not renamed:

readInputData, allQuartets, randQuartets, readListQuartets, taxadiff, sameTaxa, calculateObsCFAll!, calculateObsCFAll_noDataCF!, taxaTreesQuartets, taxonTrees, taxonQuartets, descData, summarizeDataCF updateBL!, edgesParts, getDescendants!, makeTable, and more.

renamed functions: CamelCase to lowercase

To follow julia conventions, most exported methods and many internal methods had their names changed to be “lowercase” if they were not already.

exported functions

An old name (typically “CamelCase”) was deprecated in v0.1 if it was exported in v0.16, to make it usable without breaking old code. In many cases, the function name was also changed to be more descriptive.

Most notably:

old name	new name
`tipLabels`	`tiplabels`
`readTopology`	`readnewick`
`writeTopology`	`writenewick`
`writeMultiTopology`	`writemultinewick`
`readMultiTopology`	`readmultinewick`

For the full list, see v1.0.0 deprecated.jl. Note that using a deprecated name does not trigger a deprecation message by default, so users may not know that their scripts should be updated. To see deprecation warnings, start julia with option depwarn=yes like this:

julia --depwarn=yes

internal functions

Some methods that were internal in v0.16 were renamed to be “lowercase”, but not deprecated in v1 (because not exported, and not expected to be used in scripts). Some are now exported in v1.

blobInfo, displayedNetworks!,
resetEdgeNumbers!, resetNodeNumbers!,
sampleBootstrapTrees → samplebootstrap_multiloci,
inheritanceWeight, pairwiseTaxonDistanceMatrix!,
pairwiseTaxonDistanceGrad → pairwisetaxondistance_gradient
readFastaToArray (exported in v1), readCSVtoArray
writeTableCF (internal in v0.16) → tablequartetCF (exported in v1)
writeSubTree! (exported, but should not: so not deprecated),
readSubtree! → readnewick_subtree!,
parseRemainingSubtree! → parsenewick_remainingsubtree!,
readFloat → readnewick_float,
getDataValue! → parsenewick_getfloat!,
parseEdgeData! → parsenewick_edgedata!,
parseHybridNode! → parsenewick_hybridnode!,
readnodename → readnewick_nodename,
parseTreeNode! → parsenewick_treenode!, synchronizePartnersData!, updatePostOrder! → postorder_nodeupdate!,
updatePreOrder! → preorder_nodeupdate!,
remove_edgeLengthsGammas!,
solvePolytomyRecursive! and solvePolytomy! → re-written and replaced by resolvetreepolytomy!

also many others in parsimony.jl.

Some keyword arguments were renamed to be lowercase also. Notably: checkPreorder → checkpreorder or simply preorder.

renamed internal fields

These field names are very internal! They should not be used. If they are, document which package version is used to make the code reproducible, and expect un-documented changes. Use exported methods instead, such as getroot etc.

Edge’s:

old field name	new field name
`isChild1`	`ischild1`
`isMajor`	`ismajor`
`containRoot`	`containroot`
`inCycle`	`inte1`
`istIdentifiable`	`boole1`
`fromBadDiamondI`	`boole2`

Node’s:

old field name	new field name
`gammaz`	`fvalue`
`hasHybEdge`	`booln1`
`isBadDiamondI`	`booln2`
`isBadDiamondII`	`booln3`
`isExtBadTriangle`	`booln4`
`isVeryBadTriangle`	`booln5`
`isBadTriangle`	`booln6`
`inCycle`	`intn1`
`k`	`intn2`
`typeHyb`	`int8n3`

HybridNetwork’s:

old field name	new field name
`numTaxa`	`numtaxa`
`numNodes`	`numnodes`
`numEdges`	`numedges`
`root`	`rooti`
`numHybrids`	`numhybrids`
`cladewiseorder_nodeIndex`	`vec_int1`
`visited`	`vec_bool`
`edges_changed`	`vec_edge`
`nodes_changed`	`vec_node`
`ht`	`vec_float`
`numht`	`vec_int2`
`numBad`	`intg1`
`hasVeryBadTriangle`	`boolg1`
`index`	`vec_int3`
`loglik`	`fscore`
`blacklist`	`vec_int4`
`cleaned`	`boolg2`
`isRooted`	`isrooted` (don’t trust it!)