Updates for 1.0 (#24)

JuliaStats · Oct 6, 2018 · 63bafcf · 63bafcf
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commit 63bafcf
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Showing 16 changed files with 97 additions and 101 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -3,7 +3,8 @@ language: julia
 os:
   - linux
 julia:
-  - 0.6
+  - 0.7
+  - 1.0
   - nightly
 notifications:
   email: false
@@ -12,4 +13,4 @@ notifications:
 #  - if [[ -a .git/shallow ]]; then git fetch --unshallow; fi
 #  - julia -e 'Pkg.clone(pwd()); Pkg.build("NMF"); Pkg.test("NMF"; coverage=true)'
 after_success:
-  - julia -e 'cd(Pkg.dir("NMF")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())';
+  - julia -e 'using Pkg; Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())';
diff --git a/README.md b/README.md
@@ -4,7 +4,6 @@ A Julia package for non-negative matrix factorization (NMF).
 
 [![Build Status](https://travis-ci.org/JuliaStats/NMF.jl.svg?branch=master)](https://travis-ci.org/JuliaStats/NMF.jl)
 [![Coverage Status](https://coveralls.io/repos/github/JuliaStats/NMF.jl/badge.svg?branch=master)](https://coveralls.io/github/JuliaStats/NMF.jl?branch=master)
-[![NMF](http://pkg.julialang.org/badges/NMF_0.6.svg)](http://pkg.julialang.org/?pkg=NMF)
 
 ---------------------------
 

diff --git a/REQUIRE b/REQUIRE
@@ -1,3 +1,2 @@
-julia 0.6
-Compat 0.34.0
+julia 0.7
 StatsBase
diff --git a/examples/densenmf.jl b/examples/densenmf.jl
@@ -59,7 +59,7 @@ function main(args)
             run(a)
         end
     else
-        warn("Invalid command line arguments.")
+        @warn("Invalid command line arguments.")
         print_help()
     end
 end

diff --git a/src/NMF.jl b/src/NMF.jl
@@ -1,9 +1,8 @@
 module NMF
-    using Compat
     using StatsBase
-
-    import Compat: view
-    import Base: sum!
+    using Statistics
+    using Printf
+    using LinearAlgebra
 
     export nnmf
 

diff --git a/src/alspgrad.jl b/src/alspgrad.jl
@@ -49,20 +49,21 @@ struct ALSGradUpdH_State{T}
 
     function ALSGradUpdH_State{T}(X, W, H) where T
         k, n = size(H)
-        new{T}(Array{T,2}(k, n),
-               Array{T,2}(k, n),
-               Array{T,2}(k, n),
-               Array{T,2}(k, n),
-               Array{T,2}(k, k),
-               Array{T,2}(k, n),
-               Array{T,2}(k, n))
+        new{T}(Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, k),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, n))
     end
 end
 ALSGradUpdH_State(X, W::VecOrMat{T}, H::VecOrMat{T}) where {T} = ALSGradUpdH_State{T}(X, W, H)
 
 function set_w!(s::ALSGradUpdH_State, X, W)
-    At_mul_B!(s.WtW, W, W)
-    At_mul_B!(s.WtX, W, X)
+    Wt = transpose(W)
+    mul!(s.WtW, Wt, W)
+    mul!(s.WtX, Wt, X)
 end
 
 function alspgrad_updateh!(X,
@@ -120,7 +121,7 @@ function _alspgrad_updateh!(X,                      # size (p, n)
         t += 1
 
         # compute gradient
-        A_mul_B!(G, WtW, H)
+        mul!(G, WtW, H)
         for i = 1:length(G)
             G[i] -= WtX[i]
         end
@@ -150,7 +151,7 @@ function _alspgrad_updateh!(X,                      # size (p, n)
 
                 # compute criterion
                 dv1 = BLAS.dot(G, D)  # <G, D>
-                A_mul_B!(WtWD, WtW, D)
+                mul!(WtWD, WtW, D)
                 dv2 = BLAS.dot(WtWD, D)  # <D, WtW * D>
 
                 # back-track
@@ -164,20 +165,20 @@ function _alspgrad_updateh!(X,                      # size (p, n)
                     if !suff_decr
                         α *= β
                     else
-                        copy!(H, Hn)
+                        copyto!(H, Hn)
                         break
                     end
                 else
                     if suff_decr
                         if α/β < αmax
-                            copy!(Hp, Hn)
+                            copyto!(Hp, Hn)
                             α /= β
                         else
-                            copy!(H, Hn)
+                            copyto!(H, Hn)
                             break
                         end
                     else
-                        copy!(H, Hp)
+                        copyto!(H, Hp)
                         break
                     end
                 end
@@ -186,7 +187,7 @@ function _alspgrad_updateh!(X,                      # size (p, n)
 
         # print info
         if verbose
-            A_mul_B!(WH, W, H)
+            mul!(WH, W, H)
             preobjv = objv
             objv = sqL2dist(X, WH)
             @printf("%5d    %12.5e    %12.5e    %12.5e    %8.4f    %12d\n",
@@ -210,20 +211,21 @@ struct ALSGradUpdW_State{T}
 
     function ALSGradUpdW_State{T}(X, W, H) where T
         p, k = size(W)
-        new{T}(Array{T,2}(p, k),
-               Array{T,2}(p, k),
-               Array{T,2}(p, k),
-               Array{T,2}(p, k),
-               Array{T,2}(k, k),
-               Array{T,2}(p, k),
-               Array{T,2}(p, k))
+        new{T}(Matrix{T}(undef, p, k),
+               Matrix{T}(undef, p, k),
+               Matrix{T}(undef, p, k),
+               Matrix{T}(undef, p, k),
+               Matrix{T}(undef, k, k),
+               Matrix{T}(undef, p, k),
+               Matrix{T}(undef, p, k))
     end
 end
 ALSGradUpdW_State(X, W::VecOrMat{T}, H::VecOrMat{T}) where {T} = ALSGradUpdW_State{T}(X, W, H)
 
 function set_h!(s::ALSGradUpdW_State, X, H)
-    A_mul_Bt!(s.HHt, H, H)
-    A_mul_Bt!(s.XHt, X, H)
+    Ht = transpose(H)
+    mul!(s.HHt, H, Ht)
+    mul!(s.XHt, X, Ht)
 end
 
 
@@ -282,7 +284,7 @@ function _alspgrad_updatew!(X,                      # size (p, n)
         t += 1
 
         # compute gradient
-        A_mul_B!(G, W, HHt)
+        mul!(G, W, HHt)
         for i = 1:length(G)
             G[i] -= XHt[i]
         end
@@ -312,7 +314,7 @@ function _alspgrad_updatew!(X,                      # size (p, n)
 
                 # compute criterion
                 dv1 = BLAS.dot(G, D)  # <G, D>
-                A_mul_B!(DHHt, D, HHt)
+                mul!(DHHt, D, HHt)
                 dv2 = BLAS.dot(DHHt, D)  # <D * HHt, D>
 
                 # back-track
@@ -326,20 +328,20 @@ function _alspgrad_updatew!(X,                      # size (p, n)
                     if !suff_decr
                         α *= β
                     else
-                        copy!(W, Wn)
+                        copyto!(W, Wn)
                         break
                     end
                 else
                     if suff_decr
                         if α/β < αmax
-                            copy!(Wp, Wn)
+                            copyto!(Wp, Wn)
                             α /= β
                         else
-                            copy!(W, Wn)
+                            copyto!(W, Wn)
                             break
                         end
                     else
-                        copy!(W, Wp)
+                        copyto!(W, Wp)
                         break
                     end
                 end
@@ -348,7 +350,7 @@ function _alspgrad_updatew!(X,                      # size (p, n)
 
         # print info
         if verbose
-            A_mul_B!(WH, W, H)
+            mul!(WH, W, H)
             preobjv = objv
             objv = sqL2dist(X, WH)
             @printf("%5d    %12.5e    %12.5e    %12.5e    %8.4f    %12d\n",
@@ -419,6 +421,6 @@ function update_wh!(upd::ALSPGradUpd, s::ALSPGradUpd_State, X, W, H)
         upd.maxsubiter, 20, upd.tolg, convert(T, 0.2), convert(T, 0.01), false)
 
     # update WH
-    A_mul_B!(s.WH, W, H)
+    mul!(s.WH, W, H)
 end
 
diff --git a/src/common.jl b/src/common.jl
@@ -44,8 +44,8 @@ function nmf_skeleton!(updater::NMFUpdater{T},
 
     # init
     state = prepare_state(updater, X, W, H)
-    preW = Array{T,2}(size(W)...)
-    preH = Array{T,2}(size(H)...)
+    preW = Matrix{T}(undef, size(W))
+    preH = Matrix{T}(undef, size(H))
     if verbose
         objv = evaluate_objv(updater, state, X, W, H)
         @printf("%-5s     %-13s    %-13s    %-13s\n", "Iter", "objv", "objv.change", "(W & H).change")
@@ -57,8 +57,8 @@ function nmf_skeleton!(updater::NMFUpdater{T},
     t = 0
     while !converged && t < maxiter
         t += 1
-        copy!(preW, W)
-        copy!(preH, H)
+        copyto!(preW, W)
+        copyto!(preH, H)
 
         # update H
         update_wh!(updater, state, X, W, H)

diff --git a/src/initialization.jl b/src/initialization.jl
@@ -29,7 +29,7 @@ function _nndsvd!(X, W, Ht, inith::Bool, variant::Int)
     T = eltype(W)
 
     # compute SVD
-    (U, s, V) = svd(X, thin=true)
+    (U, s, V) = svd(X, full=false)
 
     # main loop
     v0 = variant == 0 ? zero(T) :
@@ -76,14 +76,14 @@ function nndsvd(X, k::Integer; zeroh::Bool=false, variant::Symbol=:std)
            variant == :ar  ? 2 :
            throw(ArgumentError("Invalid value for variant"))
 
-    W = Array{T,2}(p, k)
-    H = Array{T,2}(k, n)
+    W = Matrix{T}(undef, p, k)
+    H = Matrix{T}(undef, k, n)
     if zeroh
         Ht = reshape(view(H,:,:), (n, k))
         _nndsvd!(X, W, Ht, false, ivar)
         fill!(H, 0)
     else
-        Ht = Array{T,2}(n, k)
+        Ht = Matrix{T}(undef, n, k)
         _nndsvd!(X, W, Ht, true, ivar)
         for j = 1:k
             for i = 1:n

diff --git a/src/multupd.jl b/src/multupd.jl
@@ -53,10 +53,10 @@ struct MultUpdMSE_State{T}
     function MultUpdMSE_State{T}(X, W::Matrix{T}, H::Matrix{T}) where T
         p, n, k = nmf_checksize(X, W, H)
         new{T}(W * H,
-               Array{T,2}(k, n),
-               Array{T,2}(k, n),
-               Array{T,2}(p, k),
-               Array{T,2}(p, k))
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, p, k),
+               Matrix{T}(undef, p, k))
     end
 end
 
@@ -74,22 +74,24 @@ function update_wh!(upd::MultUpdMSE{T}, s::MultUpdMSE_State{T}, X, W::Matrix{T},
     WHHt = s.WHHt
 
     # update H
-    At_mul_B!(WtX, W, X)
-    At_mul_B!(WtWH, W, WH)
+    Wt = transpose(W)
+    mul!(WtX, Wt, X)
+    mul!(WtWH, Wt, WH)
 
     @inbounds for i = 1:length(H)
         H[i] *= (WtX[i] / (WtWH[i] + lambda))
     end
-    A_mul_B!(WH, W, H)
+    mul!(WH, W, H)
 
     # update W
-    A_mul_Bt!(XHt, X, H)
-    A_mul_Bt!(WHHt, WH, H)
+    Ht = transpose(H)
+    mul!(XHt, X, Ht)
+    mul!(WHHt, WH, Ht)
 
     @inbounds for i = 1:length(W)
         W[i] *= (XHt[i] / (WHHt[i] + lambda))
     end
-    A_mul_B!(WH, W, H)
+    mul!(WH, W, H)
 end
 
 
@@ -110,11 +112,11 @@ struct MultUpdDiv_State{T}
     function MultUpdDiv_State{T}(X, W::Matrix{T}, H::Matrix{T}) where T
         p, n, k = nmf_checksize(X, W, H)
         new{T}(W * H,
-               Array{T,2}(1, k),
-               Array{T,2}(k, 1),
-               Array{T,2}(p, n),
-               Array{T,2}(k, n),
-               Array{T,2}(p, k))
+               Matrix{T}(undef, 1, k),
+               Matrix{T}(undef, k, 1),
+               Matrix{T}(undef, p, n),
+               Matrix{T}(undef, k, n),
+               Matrix{T}(undef, p, k))
     end
 end
 
@@ -143,21 +145,21 @@ function update_wh!(upd::MultUpdDiv{T}, s::MultUpdDiv_State{T}, X, W::Matrix{T},
     @inbounds for i = 1:length(X)
         Q[i] = X[i] / (WH[i] + lambda)
     end
-    At_mul_B!(WtQ, W, Q)
+    mul!(WtQ, transpose(W), Q)
     sum!(fill!(sW, 0), W)
     @inbounds for j = 1:n, i = 1:k
         H[i,j] *= (WtQ[i,j] / sW[i])
     end
-    A_mul_B!(WH, W, H)
+    mul!(WH, W, H)
 
     # update W
     @inbounds for i = 1:length(X)
         Q[i] = X[i] / (WH[i] + lambda)
     end
-    A_mul_Bt!(QHt, Q, H)
+    mul!(QHt, Q, transpose(H))
     sum!(fill!(sH, 0), H)
     @inbounds for j = 1:k, i = 1:p
         W[i,j] *= (QHt[i,j] / sH[j])
     end
-    A_mul_B!(WH, W, H)
+    mul!(WH, W, H)
 end
-Original file line number
+Diff line change
@@ Expand Up / @@ -4,7 +4,6 @@ A Julia package for non-negative matrix factorization (NMF). @@
     [![Build Status](https://travis-ci.org/JuliaStats/NMF.jl.svg?branch=master)](https://travis-ci.org/JuliaStats/NMF.jl)
     [![Coverage Status](https://coveralls.io/repos/github/JuliaStats/NMF.jl/badge.svg?branch=master)](https://coveralls.io/github/JuliaStats/NMF.jl?branch=master)
-    [![NMF](http://pkg.julialang.org/badges/NMF_0.6.svg)](http://pkg.julialang.org/?pkg=NMF)
     ---------------------------
@@ Expand Down @@