Tests functions

• all in runtests.jl, which calls other test files
• to see deprecation warnings when running things locally, start julia with

  julia --depwarn=yes

  and possibly other options (like --project).
• generally, code in file src/x.jl is tested by test/test_x.jl, but see below for what older test files do (related to SNaQ).
  checkout PhyloNetworks v0.9.1 or older to see those older files.

add hybridization

test_add2hyb.jl add a first hybrid, then a second hybrid that makes a bad triangle, and the functions should identify it

delete hybridization

test_deleteHybridizationUpdate.jl checks that all attributes are correctly updated after deleting a hybridization (1 and 2 hybrids)

read topology

test_5taxon_readTopology.jl runs all the tests for the eight 5taxon networks by reading from parenthetical format and then updating

aux functions: test_functions_5taxon_read.jl

calculate exp CF

test_calculateExpCF.jl runs all the tests for Case G, bad diamond and bad triangle for calculation of expCF

test_calculateExpCF2.jl computes the expCF for the n6 network

has Edge

test_hasEdge.jl tests if the attribute qnet.hasEdge is correctly updated after extracting quartets for case G. It also checks if net.ht, net.numht, qnet.indexht are correctly set for Case G.

parts of optBL

test_optBLparts.jl tests the parts of optBL separately to see if they work.

parameters

test_parameters.jl get net.ht and net.numht for all the 5 taxon networks

Likelihood

test_correctLik.jl computes the pseudolik for a tree and a network with 1 hybrid and checks that it is correctly computed

partition

test_partition.jl (1 hybrid) and test_partition2.jl (2 hybrids) check if the attribute of partition is correctly set