Merge pull request dillondaudert#18 from dillondaudert/nnd_0.3

Update compat: Julia >=1.3, NNDescent.jl 0.3

.appveyor.yml

@@ -1,6 +1,6 @@
 environment:
   matrix:
-  - julia_version: 1
+  - julia_version: 1.3
   - julia_version: nightly
 
 platform:

.travis.yml

@@ -4,12 +4,14 @@ os:
   - osx
 
 julia:
-  - 1.0
-  - 1.2
+  - 1.3
   - nightly
 
-script:
-  - julia -e 'import Pkg; Pkg.build(); Pkg.test(; coverage=true)'
+script: travis_wait julia --project -e 'using Pkg; Pkg.test(; coverage=true)'
+matrix:
+  - fast_finish: true
+  - allow_failures:
+    - julia: nightly
 
 codecov: true
 coveralls: true

Project.toml

@@ -12,11 +12,11 @@ NearestNeighborDescent = "dd2c4c9e-a32f-5b2f-b342-08c2f244fce8"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [compat]
-Arpack = "0.3, 0.4"
+Arpack = "0.4"
 Distances = "0.8"
-LsqFit = "0.6, 0.8"
-NearestNeighborDescent = "0.2"
-julia = "1.0"
+LsqFit = "0.6, 0.7, 0.8"
+NearestNeighborDescent = "0.3"
+julia = "1.3"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

src/UMAP.jl

@@ -1,11 +1,11 @@
 module UMAP
 
-using Distances: evaluate, pairwise!, Euclidean, SqEuclidean, SemiMetric
-using NearestNeighborDescent: DescentGraph
+using Arpack
+using Distances
+using LinearAlgebra
 using LsqFit: curve_fit
-using SparseArrays: SparseMatrixCSC, sparse, dropzeros, nzrange, rowvals, nonzeros
-using LinearAlgebra: Symmetric, Diagonal, issymmetric, I
-using Arpack: eigs, ARPACKException
+using NearestNeighborDescent
+using SparseArrays
 
 include("utils.jl")
 include("umap_.jl")

src/utils.jl

@@ -65,8 +65,8 @@ function knn_search(X::AbstractMatrix{S},
                     k,
                     metric,
                     ::Val{:approximate}) where {S <: Real}
-    knngraph = DescentGraph(X, k, metric)
-    return knngraph.indices, knngraph.distances
+    knngraph = nndescent(X, k, metric)
+    return knn_matrices(knngraph)
 end
 
 function _knn_from_dists(dist_mat::AbstractMatrix{S}, k) where {S <: Real}