phylocomr: Interface to 'Phylocom'

# context("phylomatic")
# test_that("phylomatic executable works", {
#   expect_output(phylomatic(), "Cam Webb")
#   expect_is(phylomatic(intern = TRUE), "character")
#   expect_match(phylomatic(intern = TRUE), "Cam Webb")
# })
#
#
# context("ph_phylomatic")
#
# taxa_file <- system.file("examples/taxa", package = "phylocomr")
# phylo_file <- system.file("examples/phylo", package = "phylocomr")
#
# taxa_str <- readLines(taxa_file)
# phylo_str <- readLines(phylo_file)
#
# test_that("ph_phylomatic works with chr string input", {
#   skip_on_appveyor()
#   skip_on_cran()
#
#   aa <- ph_phylomatic(taxa = taxa_str, phylo = phylo_str)
#
#   expect_is(aa, "character")
#   expect_is(attr(aa, "taxa_file"), "character")
#   expect_match(attr(aa, "taxa_file"), "taxa")
#   expect_is(attr(aa, "phylo_file"), "character")
#   expect_match(attr(aa, "phylo_file"), "phylo")
#
#   expect_match(aa, "lobelia_conferta")
#   expect_match(aa, "narcissus_cuatrecasasii")
#   expect_match(aa, "poales_to_asterales")
#
#   if (requireNamespace('ape')) {
#     library(ape)
#     tree <- read.tree(text = aa)
#     expect_is(tree, "phylo")
#   }
# })
#
# test_that("ph_phylomatic works with file input", {
#   skip_on_appveyor()
#   skip_on_cran()
#
#   taxa_file2 <- tempfile()
#   cat(taxa_str, file = taxa_file2, sep = '\n')
#   phylo_file2 <- tempfile()
#   cat(phylo_str, file = phylo_file2, sep = '\n')
#
#   aa <- ph_phylomatic(taxa = taxa_file2, phylo = phylo_file2)
#
#   expect_is(aa, "character")
#   expect_is(attr(aa, "taxa_file"), "character")
#   expect_is(attr(aa, "phylo_file"), "character")
#
#   expect_match(aa, "lobelia_conferta")
#   expect_match(aa, "narcissus_cuatrecasasii")
#   expect_match(aa, "poales_to_asterales")
#
#   if (requireNamespace('ape')) {
#     library(ape)
#     tree <- read.tree(text = aa)
#     expect_is(tree, "phylo")
#   }
# })
#
# test_that("ph_phylomatic fails well", {
#   # required inputs
#   expect_error(ph_phylomatic(),
#                "argument \"taxa\" is missing, with no default")
#   expect_error(ph_phylomatic("Adsf"),
#                "argument \"phylo\" is missing, with no default")
#
#   # types are correct
#   expect_error(ph_phylomatic(5, "asdfad"),
#                "taxa must be of class character")
#   expect_error(ph_phylomatic("adf", 5),
#                "phylo must be of class phylo, character")
#
#   expect_error(ph_phylomatic(taxa_str, phylo_str, tabular = 5),
#                "tabular must be of class logical")
#   expect_error(ph_phylomatic(taxa_str, phylo_str, lowercase = 5),
#                "lowercase must be of class logical")
#   expect_error(ph_phylomatic(taxa_str, phylo_str, nodes = 5),
#                "nodes must be of class logical")
# })