package PhylogeneticTrees.m2

[kroner]

Beginning at the MRC on algebraic statistics this past summer in Snowbird, our team wrote a package to compute the invariants of phylogenetic tree models with several different algorithms. We're planning to submit the package to JSAG shortly.

The team consists of Hector Banos, Nathaniel Bushek, Ruth Davidson, Elizabeth Gross, Pamela Harris, Robert Krone, Colby Long, AJ Stewart, Robert Walker.

[DanGrayson]

This package doesn't load:

Macaulay2, version 1.9.2
with packages: ConwayPolynomials, Elimination, IntegralClosure, LLLBases,
               PrimaryDecomposition, ReesAlgebra, TangentCone

i1 : installPackage "PhylogeneticTrees"
--loading configuration for package "Graphs" from file /Users/dan/Library/Application Support/Macaulay2/init-Graphs.m2
--loading configuration for package "FourTiTwo" from file /Users/dan/Library/Application Support/Macaulay2/init-FourTiTwo.m2
--loading configuration for package "Posets" from file /Users/dan/Library/Application Support/Macaulay2/init-Posets.m2
Macaulay2/packages/PhylogeneticTrees.m2:2251:6:(0):[10]: error: EOF in string /// ... /// beginning here
stdio:1:1:(3): --backtrace: parse error--

[kroner]

Sorry, somehow an extra "/" got added to a "///" that broke things. It should load now.

[DanGrayson]

I get two errors when installing the package. One of them is this one:

-- -*- M2-comint -*- {* hash: 1324183505 *}

i1 : T = leafTree(4,{{0,1}})

o1 = {{0, 1, 2, 3}, {set {0, 1}, set {0}, set {1}, set {2}, set {3}}}

o1 : LeafTree

i2 : P = edgeCut(T, set {0,1});
stdio:2:5:(3): error: no method found for applying edgeCut to:
     argument 1 :  {{0, 1, 2, 3}, {set {0, 1}, set {0}, se. (of class LeafTree)
     argument 2 :  set {0, 1} (of class Set)

The package name should be added to the list in =distributed-packages.

One of the tests fails with this output:

-- -*- M2-comint -*- {* hash: 434041771 *}

i1 : --/home2/dan/src/M2/M2/Macaulay2/packages/PhylogeneticTrees.m2:1803: location of test code
     
     assert( (2+2) === 5 )
stdio:3:1:(3): error: assertion failed

How could it ever work?

[DanGrayson]

@kroner or @antonleykin ?

[DanGrayson]

PS: What about also adding the name of this package to the list of packages? (... in addition to making it work.)

[antonleykin]

I was not a part of this one...

[DanGrayson]

@kroner Any comments on repairing this pull request?

[kroner]

@DanGrayson Sorry it took me some time to address this. Those bugs should be fixed and the examples and tests run now for me. I also added it to =distributed-packages.

I was neglecting to uninstallPackage before installing or run the check function, but now hopefully I'm actually testing everything.

[DanGrayson]

Thanks!