BioJulia / Bio.jl / 1495
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Jobs 2
Files 66
Run time 9min
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Ben J. Ward 
Squashed Previous Phylo rework commits (#157)

edited Phylo, phylogeny, runtests.

Added a few more methods for new phylogenies.

Added some tests for phylogenies

Edited Bio.jl file

Started incorporating the SingleIndex datastructure I initially designed for genotype count arrays.

Added using Bio.Util.Indexing to Phylo module

Changed constructor of phylogeny.

Added tokenizer to utils, edited Phylo.jl and tokenizer.jl

Added tokenizer to utils, edited Phylo.jl and tokenizer.jl

Rearranged includes

Rearranged includes

changed tokenizer module to tokenize module

Commented out PhyNode function

Corrected type parameter in graft function

Changes to phylogeny.jl

Edited phylogeny type

Added more methods to phylogeny.jl

Rearranged a few tests

Edited basic constructor

Added two functions for calculating the number of possible trees for n taxa.

max_vertices function added, Phylogeny construction edited.

Added convinience constructor.

Added more phylogeny methods

Some new methods, re-org of code, and added module exports.

Renamed some methods and added internal structural function

added more internal methods for structural manipulation

More structural methods for phylogenies

Added base copy method for phylogenies

Edited phylogeny.jl header file

Added is_redundant method

Added header to PHylo.jl

Rearranged methods into new files

Edited branch_basics.jl and manipulation.jl

Deleted dangling clades function as there should never be the occasion where they exist

added methods to get parent and child branches, as well as a delete method for deleting nodes from a phylogeny.

Working on test suite

Added comments clarifying internal structure of phylogenies.

Implemented review suggestions

Added tests for hasparent, noparent, nchildren, haschildren, and nochildren

Corrected Phylo.jl file

Implemented more review suggestions.

Removed depreceated syntax in tests

Addressed more review comments

Addressed more review comments including changes to hasparent and noparent

Made ASCIIString String in Tokenizer types/methods

Made string Compat.String

Conflict resolution in src/util/windows.jl

Added using Compat to tokenize.jl

Changed name of Indexing module to Indexers

Remove noparent and nochildren methods

Fixed manipulation methods due to removal of hnoparent and nochildren

Fixed module exports

3600 of 4491 relevant lines covered (80.16%)

1856545.72 hits per line

Jobs
ID Job ID Ran Files Coverage
1 1495.1 0
80.16
 Travis Job 1495.1
3 1495.3 0
80.14
 Travis Job 1495.3
Source Files on build 1495
Detailed source file information is not available for this build.