add rawupdateindex! and dropzeros! methods

Author: j-fu

.github/workflows/ci.yml

@@ -43,9 +43,9 @@ jobs:
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
       - uses: julia-actions/julia-processcoverage@v1
-      # - uses: codecov/codecov-action@v1
-      #   with:
-      #     file: lcov.info
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info
   docs:
     name: Documentation
     runs-on: ubuntu-latest

Project.toml

@@ -1,7 +1,7 @@
 name = "ExtendableSparse"
 uuid = "95c220a8-a1cf-11e9-0c77-dbfce5f500b3"
 authors = ["Juergen Fuhrmann <juergen.fuhrmann@wias-berlin.de>"]
-version = "0.4.1"
+version = "0.4.2"
 
 [deps]
 DocStringExtensions = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"

src/ExtendableSparse.jl

@@ -6,7 +6,7 @@ using LinearAlgebra
 include("sparsematrixcsc.jl")
 include("sparsematrixlnk.jl")
 include("extendable.jl")
-export SparseMatrixLNK,ExtendableSparseMatrix,flush!,nnz, updateindex!, colptrs
+export SparseMatrixLNK,ExtendableSparseMatrix,flush!,nnz, updateindex!, rawupdateindex!, colptrs
 
 include("preconditioners.jl")
 export JacobiPreconditioner, ILU0Preconditioner, ParallelJacobiPreconditioner

src/extendable.jl

@@ -80,7 +80,7 @@ Base.similar(m::ExtendableSparseMatrix{Tv,Ti}) where {Tv,Ti}=ExtendableSparseMat
 """
 $(SIGNATURES)
 
-Update element of the matrix  with operation `op`. 
+Update element of the matrix  with operation `op`.
 This can replace the following code and save one index
 search during acces:
 
@@ -98,6 +98,8 @@ A=ExtendableSparseMatrix(3,3)
 updateindex!(A,+,0.1,1,2)
 A
 ```
+
+If `v` is zero, no new entry is created.
 """
 function updateindex!(ext::ExtendableSparseMatrix{Tv,Ti}, op,v, i,j) where {Tv,Ti<:Integer}
     k=findindex(ext.cscmatrix,i,j)
@@ -113,11 +115,31 @@ function updateindex!(ext::ExtendableSparseMatrix{Tv,Ti}, op,v, i,j) where {Tv,T
 end
 
 
+"""
+$(SIGNATURES)
+Like [`updateindex!`](@ref) but without 
+checking if v is zero.
+
+"""
+function rawupdateindex!(ext::ExtendableSparseMatrix{Tv,Ti}, op,v, i,j) where {Tv,Ti<:Integer}
+    k=findindex(ext.cscmatrix,i,j)
+    if k>0
+        ext.cscmatrix.nzval[k]=op(ext.cscmatrix.nzval[k],v)
+    else
+        if ext.lnkmatrix==nothing
+            ext.lnkmatrix=SparseMatrixLNK{Tv, Ti}(ext.cscmatrix.m, ext.cscmatrix.n)
+        end
+        rawupdateindex!(ext.lnkmatrix,op,v,i,j)
+    end
+    ext
+end
+
+
 """
 $(SIGNATURES)
 
 Find index in CSC matrix and set value if it exists. Otherwise,
-set index in extension.
+set index in extension if `v` is nonzero.
 """
 
 function Base.setindex!(ext::ExtendableSparseMatrix{Tv,Ti}, v, i,j) where {Tv,Ti}
@@ -189,7 +211,7 @@ function flush!(ext::ExtendableSparseMatrix)
     if ext.lnkmatrix!=nothing && nnz(ext.lnkmatrix)>0
         ext.cscmatrix=ext.lnkmatrix+ext.cscmatrix
         ext.lnkmatrix=nothing
-        ext.pattern_timestamp
+        ext.pattern_timestamp=time()
     end
     return ext
 end
@@ -380,3 +402,12 @@ function Base.:-(csc::SparseMatrixCSC,ext::ExtendableSparseMatrix)
     @inbounds flush!(ext)
     return csc - ext.cscmatrix
 end
+
+
+"""
+$(SIGNATURES)
+"""
+function SparseArrays.dropzeros!(ext::ExtendableSparseMatrix)
+    @inbounds flush!(ext)
+    dropzeros!(ext.cscmatrix)
+end

src/sparsematrixcsc.jl

@@ -23,7 +23,9 @@ end
 """
 $(SIGNATURES)
 
-Update element of the matrix  with operation `op`. 
+Update element of the matrix  with operation `op` whithout
+introducing new nonzero elements.
+
 This can replace the following code and save one index
 search during acces:
 
@@ -42,17 +44,19 @@ A=spzeros(3,3)
 updateindex!(A,+,0.1,1,2)
 A
 ```
+
 """
 function updateindex!(csc::SparseMatrixCSC{Tv,Ti}, op, v,i, j) where{Tv,Ti<:Integer}
     k=findindex(csc,i,j)
     if k>0 # update existing value
         csc.nzval[k]=op(csc.nzval[k],v)
     else # insert new value
-        csc[i,j]= op(zero(Tv),v)
+        csc[i,j]=op(zero(Tv),v)
     end
     csc
 end
 
+
 """
 $(SIGNATURES)
 

src/sparsematrixlnk.jl

@@ -211,7 +211,8 @@ end
 $(SIGNATURES)
 
 Update element of the matrix  with operation `op`. 
-It assumes that `op(0,0)==0` 
+It assumes that `op(0,0)==0`. If `v` is zero, no new 
+entry is created.
 """
 function updateindex!(lnk::SparseMatrixLNK{Tv,Ti},op, v, i,j) where {Tv,Ti}
     # Set the first  column entry if it was not yet set.
@@ -233,6 +234,31 @@ function updateindex!(lnk::SparseMatrixLNK{Tv,Ti},op, v, i,j) where {Tv,Ti}
     lnk
 end
 
+"""
+$(SIGNATURES)
+
+Update element of the matrix  with operation `op`. 
+It assumes that `op(0,0)==0`. If `v` is zero a new entry
+is created nevertheless.
+"""
+function rawupdateindex!(lnk::SparseMatrixLNK{Tv,Ti},op, v, i,j) where {Tv,Ti}
+    # Set the first  column entry if it was not yet set.
+    if lnk.rowval[j]==0
+        lnk.rowval[j]=i       
+        lnk.nzval[j]=op(lnk.nzval[j],v)
+        lnk.nnz+=1
+        return lnk
+    end
+    k,k0=findindex(lnk,i,j)
+    if k>0
+        lnk.nzval[k]=op(lnk.nzval[k],v)
+    else
+        k=addentry!(lnk,i,j,k,k0)
+        lnk.nzval[k]=op(zero(Tv),v)
+    end
+    lnk
+end
+
 
 """
 $(SIGNATURES)

test/runtests.jl

@@ -21,6 +21,24 @@ using BenchmarkTools
     @test test_constructors()
 end
 
+#################################################################
+
+@testset "Updates" begin
+    A=ExtendableSparseMatrix(10,10)
+    @test nnz(A)==0
+    A[1,3]=5
+    updateindex!(A,+,6.0,4,5)
+    updateindex!(A,+,0.0,2,3)
+    @test nnz(A)==2
+    rawupdateindex!(A,+,0.0,2,3)
+    @test nnz(A)==3
+    dropzeros!(A)
+    @test nnz(A)==2
+    rawupdateindex!(A,+,0.1,2,3)
+    @test nnz(A)==3
+    dropzeros!(A)
+    @test nnz(A)==3
+end
 #################################################################
 function test_timing(k,l,m)
     t1=@belapsed fdrand($k,$l,$m,matrixtype=$SparseMatrixCSC) seconds=1
@@ -171,6 +189,26 @@ end
   @test  test_fdrand_coo(10,10,10)
 end
 
+
+
+##############################################
+function test_fdrand_update(k,l,m)
+    A1=fdrand(k,l,m,rand=()->1,matrixtype=ExtendableSparseMatrix,update = (A,v,i,j)-> A[i,j]+=v)
+    A2=fdrand(k,l,m,rand=()->1,matrixtype=ExtendableSparseMatrix,update = (A,v,i,j)-> rawupdateindex!(A,+,v,i,j))
+    A3=fdrand(k,l,m,rand=()->1,matrixtype=ExtendableSparseMatrix,update = (A,v,i,j)-> updateindex!(A,+,v,i,j))
+
+    A1≈A2 && A1 ≈ A3
+end
+
+@testset "fdrand_update" begin
+  @test  test_fdrand_update(1000,1,1)
+  @test  test_fdrand_update(20,20,1)
+  @test  test_fdrand_update(10,10,10)
+end
+
+
+
+
 ##############################################
 
 function test_precon(Precon,k,l,m;maxiter=10000)
@@ -236,3 +274,6 @@ end
     @test test_hermitian(300,:U)
     @test test_hermitian(300,:L)
 end
+
+
+