Nothing
# Tests buildHnsw().
# library(BiocNeighbors); library(testthat); source("test-build-hnsw.R")
set.seed(250000)
test_that("buildHnsw() works as expected", {
tmp.dir <- dirname(file.path(tempdir(), ".")) # convert Windows back slash to forward slash.
for (ndim in c(1, 5, 10)) {
for (nobs in c(500, 1000, 2000)) {
X <- matrix(runif(nobs * ndim), nrow=nobs)
out <- buildHnsw(X)
expect_identical(dirname(HnswIndex_path(out)), tmp.dir)
expect_identical(dim(out), dim(X))
expect_identical(bndistance(out), "Euclidean")
}
}
})
set.seed(2500001)
test_that("buildHnsw() respects path changes", {
nobs <- 500
ndim <- 5
X <- matrix(runif(nobs * ndim), nrow=nobs)
out <- buildHnsw(X, fname="whee.idx")
expect_identical(HnswIndex_path(out), "whee.idx")
out <- buildHnsw(X, directory=".")
expect_identical(dirname(HnswIndex_path(out)), ".")
unlink(list.files(pattern="\\.idx$"))
})
set.seed(250001)
test_that("buildHnsw() preserves dimension names", {
nobs <- 1011
ndim <- 23
X <- matrix(runif(nobs * ndim), nrow=nobs)
rownames(X) <- paste0("POINT", seq_len(nobs))
colnames(X) <- paste0("DIM", seq_len(ndim))
out <- buildHnsw(X)
expect_identical(rownames(out), rownames(X))
# Still true if there are no cells.
out <- buildHnsw(X[0,,drop=FALSE])
expect_identical(rownames(out), NULL)
})
set.seed(2500011)
test_that("buildHnsw() responds to transposition", {
nobs <- 1011
ndim <- 10
X <- matrix(runif(nobs * ndim), nrow=nobs)
rownames(X) <- paste0("POINT", seq_len(nobs))
colnames(X) <- paste0("DIM", seq_len(ndim))
set.seed(101)
ref <- buildHnsw(X)
set.seed(101)
out <- buildHnsw(t(X), transposed=TRUE)
expect_identical(bndata(ref), bndata(out))
expect_identical(rownames(ref), rownames(out))
expect_identical(bnorder(ref), bnorder(out))
# Check it works in a function.
ref <- findHnsw(X, k=5)
out <- findHnsw(t(X), k=5, transposed=TRUE)
expect_identical(out, ref)
})
set.seed(250002)
test_that("choice of parameters in buildHnsw() has an effect", {
nobs <- 2101
ndim <- 23
X <- matrix(runif(nobs * ndim), nrow=nobs)
idx1 <- buildHnsw(X, nlinks=10)
out1 <- findHnsw(precomputed=idx1, k=20)
idx2 <- buildHnsw(X, nlinks=50)
out2 <- findHnsw(precomputed=idx2, k=20)
expect_false(identical(out1$index, out2$index))
# As a control for randomness:
idx3 <- buildHnsw(X, nlinks=10)
out3 <- findHnsw(precomputed=idx3, k=20)
expect_true(identical(out1$index, out3$index))
})
set.seed(250003)
test_that("choice of 'ef.search' in buildHnsw() has an effect", {
nobs <- 2101
ndim <- 23
X <- matrix(runif(nobs * ndim), nrow=nobs)
idx <- buildHnsw(X)
expect_identical(HnswIndex_ef_search(idx), 10L)
idx <- buildHnsw(X, ef.search=100)
expect_identical(HnswIndex_ef_search(idx), 100L)
})
set.seed(2500021)
test_that("buildHnsw() works with the Manhattan distance", {
nobs <- 1011
ndim <- 10
X <- matrix(runif(nobs * ndim), nrow=nobs)
set.seed(102)
ref <- buildHnsw(X, distance="Manhattan")
expect_identical(bndistance(ref), "Manhattan")
res <- findHnsw(precomputed=ref, k=5)
val <- findHnsw(X, k=5, distance="Manhattan")
expect_identical(res, val)
})
set.seed(250003)
test_that("buildHnsw() behaves sensibly with silly inputs", {
nobs <- 100L
ndim <- 10L
X <- matrix(runif(nobs * ndim), nrow=nobs)
# What happens when there are no cells.
out <- buildHnsw(X[0,,drop=FALSE])
expect_identical(dim(out), c(0L, ndim))
# What happens when there are no dimensions.
out <- buildHnsw(X[,0,drop=FALSE])
expect_identical(dim(out), c(nobs, 0L))
# Checking that it behaves without distinct data points.
expect_error(prec <- buildHnsw(matrix(0, 10,10)), NA)
# We get a sane result when 'X' is not, strictly, a matrix.
Y <- data.frame(X, check.names=FALSE, fix.empty.names=FALSE)
colnames(Y) <- NULL
expect_error(out <- buildHnsw(Y), NA)
})
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