Merge branch 'JuliaLinearAlgebra:master' into patch-2

mohamed82008 · web-flow · commit de99b367a2b7 · 2021-10-30T03:05:22.000+11:00
diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml
@@ -0,0 +1,19 @@
+name: CompatHelper
+
+on:
+  schedule:
+    - cron: '00 00 * * *'
+
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: julia -e 'using CompatHelper; CompatHelper.main()'
diff --git a/.github/workflows/Tagbot.yml b/.github/workflows/Tagbot.yml
@@ -0,0 +1,15 @@
+name: TagBot
+on:
+  issue_comment:
+    types:
+      - created
+  workflow_dispatch:
+jobs:
+  TagBot:
+    if: github.event_name == 'workflow_dispatch' || github.actor == 'JuliaTagBot'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: JuliaRegistries/TagBot@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+          ssh: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,49 @@
+name: CI
+env:
+  JULIA_NUM_THREADS: 2
+on:
+  pull_request:
+    branches:
+      - master
+  push:
+    branches:
+      - master
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1'
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - 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
+  
diff --git a/.travis.yml b/.travis.yml
@@ -1,37 +1,16 @@
-## Documentation: http://docs.travis-ci.com/user/languages/julia/
+# Documentation: http://docs.travis-ci.com/user/languages/julia/
 language: julia
+julia:
+  - 1.4
 os:
   - linux
-julia:
-  - 0.6
-  - 0.7
-  - 1.0
-  - 1.1
-  - nightly
+branches:
+  only:
+    - master
 notifications:
   email: false
-git:
-  depth: 99999999
-
-## uncomment the following lines to allow failures on nightly julia
-## (tests will run but not make your overall status red)
-matrix:
-  allow_failures:
-    - julia: nightly
-
-## uncomment and modify the following lines to manually install system packages
-addons:
-  apt: # apt-get for linux
-    packages:
-    - hdf5-tools
-#before_script: # homebrew for mac
-#  - if [ $TRAVIS_OS_NAME = osx ]; then brew install gcc; fi
-
-## uncomment the following lines to override the default test script
-script:
-  - julia -e 'VERSION >= v"0.7-" && using Pkg; Pkg.clone(pwd()); Pkg.build("AlgebraicMultigrid"); Pkg.test("AlgebraicMultigrid"; coverage=true)'
 after_success:
-  # push coverage results to Coveralls
-  - julia -e 'cd(Pkg.dir("AlgebraicMultigrid")); Pkg.add("Coverage"); using Coverage; Coveralls.submit(Coveralls.process_folder())'
-  # push coverage results to Codecov
-  - julia -e 'cd(Pkg.dir("AlgebraicMultigrid")); Pkg.add("Coverage"); using Coverage; Codecov.submit(Codecov.process_folder())'
+  - julia -e 'using Pkg;
+              Pkg.add("Coverage");
+              using Coverage;
+              Coveralls.submit(Coveralls.process_folder())'
diff --git a/LICENSE.md b/LICENSE.md
@@ -1,6 +1,6 @@
 The AMG.jl package is licensed under the MIT "Expat" License:
 
-> Copyright (c) 2017: ranjanan.
+> Copyright (c) 2017-20: ranjanan, Julia Computing.
 >
 > Permission is hereby granted, free of charge, to any person obtaining a copy
 > of this software and associated documentation files (the "Software"), to deal
diff --git a/Project.toml b/Project.toml
@@ -0,0 +1,26 @@
+name = "AlgebraicMultigrid"
+uuid = "2169fc97-5a83-5252-b627-83903c6c433c"
+version = "0.4.0"
+
+[deps]
+CompatHelper = "aa819f21-2bde-4658-8897-bab36330d9b7"
+DelimitedFiles = "8bb1440f-4735-579b-a4ab-409b98df4dab"
+IterativeSolvers = "42fd0dbc-a981-5370-80f2-aaf504508153"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
+[compat]
+CompatHelper = "1.3.0, 2.1, 3"
+IterativeSolvers = "0.9"
+julia = "1.4.0"
+
+[extras]
+FileIO = "5789e2e9-d7fb-5bc7-8068-2c6fae9b9549"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+
+[targets]
+test = ["FileIO", "JLD2", "Random"]
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 [![codecov.io](http://codecov.io/github/JuliaLinearAlgebra/AlgebraicMultigrid.jl/coverage.svg?branch=master)](http://codecov.io/github/JuliaLinearAlgebra/AlgebraicMultigrid.jl?branch=master)
 [![Build status](https://ci.appveyor.com/api/projects/status/0wnj4lhk1rvl5pjp?svg=true)](https://ci.appveyor.com/project/ranjanan/algebraicmultigrid-jl)
 
-This package lets you solve sparse linear systems using Algebraic Multigrid (AMG). This works especially well for symmetric positive definite matrices. 
+This package lets you solve sparse linear systems using Algebraic Multigrid (AMG). This works especially well for symmetric positive definite matrices.
 
 ## Usage
 
@@ -40,18 +40,18 @@ You can use AMG as a preconditioner for Krylov methods such as Conjugate Gradien
 ```julia
 import IterativeSolvers: cg
 p = aspreconditioner(ml)
-c = cg(A, A*ones(1000), Pl = p) 
+c = cg(A, A*ones(1000), Pl = p)
 ```
 
 ## Features and Roadmap
 
-This package currently supports: 
+This package currently supports:
 
 AMG Styles:
 * Ruge-Stuben Solver
 * Smoothed Aggregation (SA)
 
-Strength of Connection: 
+Strength of Connection:
 * Classical Strength of Connection
 * Symmetric Strength of Connection
 
@@ -60,12 +60,12 @@ Smoothers:
 * Damped Jacobi
 
 Cycling:
-* V cycle 
+* V, W and F cycles
 
 In the future, this package will support:
 1. Other splitting methods (like CLJP)
 2. SOR smoother
-3. W, F, AMLI cycles
+3. AMLI cycles
 
 #### Acknowledgements
-This package has been heavily inspired by the [`PyAMG`](http://github.com/pyamg/pyamg) project. 
+This package has been heavily inspired by the [`PyAMG`](http://github.com/pyamg/pyamg) project.
diff --git a/REQUIRE b/REQUIRE
diff --git a/appveyor.yml b/appveyor.yml
@@ -1,11 +1,8 @@
 environment:
   matrix:
-  - julia_version: 1.1
-  - julia_version: 1.0
-  - julia_version: 0.6
+  - julia_version: 1.4
 
 platform:
-  - x86 # 32-bit
   - x64 # 64-bit
 
 # # Uncomment the following lines to allow failures on nightly julia
diff --git a/src/AlgebraicMultigrid.jl b/src/AlgebraicMultigrid.jl
@@ -1,15 +1,13 @@
 module AlgebraicMultigrid
 
 import IterativeSolvers: gauss_seidel!
-using Compat, Compat.LinearAlgebra
-using Compat.SparseArrays, Compat.Printf
+using LinearAlgebra
+using SparseArrays, Printf
 using Base.Threads
 
-using Compat: rmul!
+using LinearAlgebra: rmul!
 
-if VERSION < v"0.7-"
-    const mul! = A_mul_B!
-end
+# const mul! = A_mul_B!
 
 const MT = false
 const AMG = AlgebraicMultigrid
diff --git a/src/aggregation.jl b/src/aggregation.jl
@@ -28,11 +28,7 @@ function smoothed_aggregation(A::TA,
     # agg = [aggregate for _ in 1:max_levels - 1]
     # sm = [smooth for _ in 1:max_levels]
 
-    @static if VERSION < v"0.7-"
-        levels = Vector{Level{TA, TA, TA}}()
-    else
-        levels = Vector{Level{TA, TA, Adjoint{T, TA}}}()
-    end
+    levels = Vector{Level{TA, TA, Adjoint{T, TA}}}()
     bsr_flag = false
     w = MultiLevelWorkspace(Val{bs}, eltype(A))
     residual!(w, size(A, 1))
diff --git a/src/classical.jl b/src/classical.jl
@@ -24,20 +24,12 @@ function ruge_stuben(_A::Union{TA, Symmetric{Ti, TA}, Hermitian{Ti, TA}},
         A = _A.data
         At = A
         symmetric = true
-        @static if VERSION < v"0.7-"
-            levels = Vector{Level{TA, TA}}()
-        else
-            levels = Vector{Level{TA, Adjoint{Ti, TA}, TA}}()
-        end
+        levels = Vector{Level{TA, Adjoint{Ti, TA}, TA}}()
     else
         symmetric = false
         A = _A
         At = adjoint(A)
-        @static if VERSION < v"0.7-"
-            levels = Vector{Level{TA, TA, TA}}()
-        else
-            levels = Vector{Level{TA, Adjoint{Ti, TA}, TA}}()
-        end
+        levels = Vector{Level{TA, Adjoint{Ti, TA}, TA}}()
     end
     w = MultiLevelWorkspace(Val{bs}, eltype(A))
     residual!(w, size(A, 1))
diff --git a/src/gallery.jl b/src/gallery.jl
@@ -1,3 +1,63 @@
-poisson(T, n) = sparse(Tridiagonal(fill(T(-1), n-1), 
+poisson(T, n) = sparse(Tridiagonal(fill(T(-1), n-1),
                         fill(T(2), n), fill(T(-1), n-1)))
 poisson(n) = poisson(Float64, n)
+
+function stencil_grid(T,stencil,sz)
+    # upper-bound for storage
+    n = prod(sz) * sum(.!iszero,stencil)
+
+    # indices and value of nonzero elements
+    Si = zeros(Int,n)
+    Sj = zeros(Int,n)
+    Ss = zeros(T,n)
+
+    linindices = LinearIndices(sz)
+    nnz = 0
+
+    stencil_sz = size(stencil)
+    offset = CartesianIndex((stencil_sz .+ 1) .÷ 2)
+
+    for i in CartesianIndices(sz)
+        for k in CartesianIndices(stencil_sz)
+            if stencil[k] != 0
+                j = i + k - offset
+                if checkbounds(Bool,linindices,j)
+                    nnz = nnz + 1
+                    Si[nnz] = linindices[i]
+                    Sj[nnz] = linindices[j]
+                    Ss[nnz] = stencil[k]
+                end
+            end
+        end
+    end
+
+    sparse((@view Si[1:nnz]),
+           (@view Sj[1:nnz]),
+           (@view Ss[1:nnz]),
+           prod(sz),prod(sz))
+end
+
+
+
+function poisson(T,sz::NTuple{N,Int}) where N
+    #=
+    In 2D stencil has the value:
+    stencil = [0  -1   0;
+               -1  4  -1;
+               0  -1   0]
+
+    =#
+    stencil = zeros(T,ntuple(i -> 3,Val(N)))
+    for i = 0:N-1
+        Ipre = CartesianIndex(ntuple(l -> 2,i))
+        Ipost = CartesianIndex(ntuple(l -> 2,N-i-1))
+        stencil[Ipre, 1, Ipost] = -1
+        stencil[Ipre, 3, Ipost] = -1
+    end
+    Icenter = CartesianIndex(ntuple(l -> 2,Val(N)))
+    stencil[Icenter] = 2*N
+
+    stencil_grid(T,stencil,sz)
+end
+
+poisson(sz::NTuple{N,Int}) where N = poisson(Float64,sz)
diff --git a/src/multilevel.jl b/src/multilevel.jl
diff --git a/src/preconditioner.jl b/src/preconditioner.jl
diff --git a/src/utils.jl b/src/utils.jl
diff --git a/test/cycle_tests.jl b/test/cycle_tests.jl
diff --git a/test/runtests.jl b/test/runtests.jl

Original file line number	Diff line number	Diff line change
`@@ -1,6 +1,6 @@`
`1`	`1`	`The AMG.jl package is licensed under the MIT "Expat" License:`
`2`	`2`
`3`		`-> Copyright (c) 2017: ranjanan.`
	`3`	`+> Copyright (c) 2017-20: ranjanan, Julia Computing.`
`4`	`4`	`>`
`5`	`5`	`> Permission is hereby granted, free of charge, to any person obtaining a copy`
`6`	`6`	`> of this software and associated documentation files (the "Software"), to deal`