add CI and docs deployment (#1)

KristofferC · ViralBShah · web-flow · commit 3df2e8d3ce1c · 2021-11-07T17:31:03.000-05:00
* add CI and docs deployment * All the linalg tests are moved to SuiteSparse.jl JuliaSparse/SuiteSparse.jl#53 * Disable the ambiguity tests for the moment. Co-authored-by: Viral B. Shah <viral@mayin.org>
diff --git a/.ci/test_and_change_uuid.jl b/.ci/test_and_change_uuid.jl
@@ -0,0 +1,28 @@
+@static if Base.VERSION >= v"1.6"
+    using TOML
+    using Test
+else
+    using Pkg: TOML
+    using Test
+end
+
+# To generate the new UUID, we simply modify the first character of the original UUID
+const original_uuid = "3f01184e-e22b-5df5-ae63-d93ebab69eaf"
+const new_uuid      = "4f01184e-e22b-5df5-ae63-d93ebab69eaf"
+
+# `@__DIR__` is the `.ci/` folder.
+# Therefore, `dirname(@__DIR__)` is the repository root.
+const project_filename = joinpath(dirname(@__DIR__), "Project.toml")
+
+@testset "Test that the UUID is unchanged" begin
+    project_dict = TOML.parsefile(project_filename)
+    @test project_dict["uuid"] == original_uuid
+end
+
+write(
+    project_filename,
+    replace(
+        read(project_filename, String),
+        r"uuid = .*?\n" => "uuid = \"$(new_uuid)\"\n",
+    ),
+)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -0,0 +1,69 @@
+name: CI
+on:
+  pull_request:
+    branches:
+      - 'main'
+      - 'release-*'
+  push:
+    branches:
+      - 'main'
+      - 'release-*'
+    tags: '*'
+jobs:
+  test:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          # - '1.6'
+          - 'nightly'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+          - x86
+        exclude:
+          - os: macOS-latest
+            arch: x86
+    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 }}-
+            ${{ runner.os }}-test-${{ matrix.os }}
+            ${{ runner.os }}-
+      - run: julia --color=yes .ci/test_and_change_uuid.jl
+      - 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
+  docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v1.0.0
+      - uses: julia-actions/setup-julia@latest
+        with:
+          # version: '1.6'
+          version: 'nightly'
+      - name: Generate docs
+        run: |
+          julia --color=yes -e 'write("Project.toml", replace(read("Project.toml", String), r"uuid = .*?\n" =>"uuid = \"3f01184e-e22b-5df5-ae63-d93ebab69eaf\"\n"));'
+          julia --project --color=yes -e 'using Pkg; Pkg.activate("docs"); Pkg.instantiate(); Pkg.develop(PackageSpec(path = pwd()))'
+          julia --project=docs --color=yes docs/make.jl pdf
+        env:
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }}
diff --git a/Project.toml b/Project.toml
@@ -1,5 +1,5 @@
 name = "SparseArrays"
-uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+uuid = "3f01184e-e22b-5df5-ae63-d93ebab69eaf"
 
 [deps]
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
diff --git a/README.md b/README.md
@@ -0,0 +1,22 @@
+# SparseArrays
+
+| **Documentation**                                                 | **Build Status**                                                                                |
+|:-----------------------------------------------------------------:|:-----------------------------------------------------------------------------------------------:|
+|  [![][docs-img]][docs-url] | [![][ci-img]][ci-url] [![][codecov-img]][codecov-url] |
+
+[docs-img]: https://img.shields.io/badge/docs-blue.svg
+[docs-url]: https://sparsearrays.juliasparse.org/dev/
+
+[docs-v1-img]: https://img.shields.io/badge/docs-v1-blue.svg
+[docs-v1-url]: https://sparsearrays.juliasparse.org/v1/
+
+[ci-img]: https://github.com/JuliaLang/sparsearrays.jl/workflows/Run%20tests/badge.svg?branch=master
+[ci-url]: https://github.com/JuliaLang/sparsearrays.jl/actions?query=workflow%3A%22Run+tests%22
+
+[codecov-img]: https://codecov.io/gh/JuliaLang/sparsearrays.jl/branch/master/graph/badge.svg
+[codecov-url]: https://codecov.io/gh/JuliaLang/sparsearrays.jl
+
+This package ships as part of the Julia stdlib.
+
+SparseArrays.jl provides functionality for working with sparse arrays in Julia.
+
diff --git a/docs/Project.toml b/docs/Project.toml
@@ -0,0 +1,2 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
diff --git a/docs/make.jl b/docs/make.jl
@@ -0,0 +1,11 @@
+using Documenter, SparseArrays
+
+makedocs(
+    modules = [SparseArrays],
+    sitename = "SparseArrays",
+    pages = Any[
+        "SparseArrays" => "index.md"
+        ]
+    )
+
+deploydocs(repo = "github.com/JuliaLang/SparseArrays.jl.git")
diff --git a/test/ambiguous_exec.jl.disable b/test/ambiguous_exec.jl.disable
diff --git a/test/sparse.jl b/test/sparse.jl
@@ -273,119 +273,6 @@ end
     @test B*A ≈ B*Array(A)
 end
 
-@testset "complex matrix-vector multiplication and left-division" begin
-    if Base.USE_GPL_LIBS
-    for i = 1:5
-        a = I + 0.1*sprandn(5, 5, 0.2)
-        b = randn(5,3) + im*randn(5,3)
-        c = randn(5) + im*randn(5)
-        d = randn(5) + im*randn(5)
-        α = rand(ComplexF64)
-        β = rand(ComplexF64)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(mul!(similar(b), a, b) - Array(a)*b)) < 100*eps()) # for compatibility with present matmul API. Should go away eventually.
-        @test (maximum(abs.(mul!(similar(c), a, c) - Array(a)*c)) < 100*eps()) # for compatibility with present matmul API. Should go away eventually.
-        @test (maximum(abs.(mul!(similar(b), transpose(a), b) - transpose(Array(a))*b)) < 100*eps()) # for compatibility with present matmul API. Should go away eventually.
-        @test (maximum(abs.(mul!(similar(c), transpose(a), c) - transpose(Array(a))*c)) < 100*eps()) # for compatibility with present matmul API. Should go away eventually.
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-        @test (maximum(abs.((a'*c + d) - (Array(a)'*c + d))) < 1000*eps())
-        @test (maximum(abs.((α*transpose(a)*c + β*d) - (α*transpose(Array(a))*c + β*d))) < 1000*eps())
-        @test (maximum(abs.((transpose(a)*c + d) - (transpose(Array(a))*c + d))) < 1000*eps())
-        c = randn(6) + im*randn(6)
-        @test_throws DimensionMismatch α*transpose(a)*c + β*c
-        @test_throws DimensionMismatch α*transpose(a)*fill(1.,5) + β*c
-
-        a = I + 0.1*sprandn(5, 5, 0.2) + 0.1*im*sprandn(5, 5, 0.2)
-        b = randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        a = I + tril(0.1*sprandn(5, 5, 0.2))
-        b = randn(5,3) + im*randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        a = I + tril(0.1*sprandn(5, 5, 0.2) + 0.1*im*sprandn(5, 5, 0.2))
-        b = randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        a = I + triu(0.1*sprandn(5, 5, 0.2))
-        b = randn(5,3) + im*randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        a = I + triu(0.1*sprandn(5, 5, 0.2) + 0.1*im*sprandn(5, 5, 0.2))
-        b = randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        a = I + triu(0.1*sprandn(5, 5, 0.2))
-        b = randn(5,3) + im*randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        # UpperTriangular/LowerTriangular solve
-        a = UpperTriangular(I + triu(0.1*sprandn(5, 5, 0.2)))
-        b = sprandn(5, 5, 0.2)
-        @test (maximum(abs.(a\b - Array(a)\Array(b))) < 1000*eps())
-        # test error throwing for bwdTrisolve
-        @test_throws DimensionMismatch a\Matrix{Float64}(I, 6, 6)
-        a = LowerTriangular(I + tril(0.1*sprandn(5, 5, 0.2)))
-        b = sprandn(5, 5, 0.2)
-        @test (maximum(abs.(a\b - Array(a)\Array(b))) < 1000*eps())
-        # test error throwing for fwdTrisolve
-        @test_throws DimensionMismatch a\Matrix{Float64}(I, 6, 6)
-
-
-
-        a = sparse(Diagonal(randn(5) + im*randn(5)))
-        b = randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-
-        b = randn(5,3) + im*randn(5,3)
-        @test (maximum(abs.(a*b - Array(a)*b)) < 100*eps())
-        @test (maximum(abs.(a'b - Array(a)'b)) < 100*eps())
-        @test (maximum(abs.(transpose(a)*b - transpose(Array(a))*b)) < 100*eps())
-        @test (maximum(abs.(a\b - Array(a)\b)) < 1000*eps())
-        @test (maximum(abs.(a'\b - Array(a')\b)) < 1000*eps())
-        @test (maximum(abs.(transpose(a)\b - Array(transpose(a))\b)) < 1000*eps())
-    end
-    end
-end
 
 @testset "matrix multiplication" begin
     for (m, p, n, q, k) in (
@@ -1641,14 +1528,6 @@ end
     @test count(!iszero, sparsevec(Diagonal(Int[]))) == 0
 end
 
-@testset "explicit zeros" begin
-    if Base.USE_GPL_LIBS
-        a = SparseMatrixCSC(2, 2, [1, 3, 5], [1, 2, 1, 2], [1.0, 0.0, 0.0, 1.0])
-        @test lu(a)\[2.0, 3.0] ≈ [2.0, 3.0]
-        @test cholesky(a)\[2.0, 3.0] ≈ [2.0, 3.0]
-    end
-end
-
 @testset "issue #9917" begin
     @test sparse([]') == reshape(sparse([]), 1, 0)
     @test Array(sparse([])) == zeros(0)
@@ -2088,43 +1967,6 @@ end
     @test_throws ArgumentError opnorm(rowM, 3)
 end
 
-@testset "sparse matrix cond" begin
-    local A = sparse(reshape([1.0], 1, 1))
-    Ac = sprandn(20, 20,.5) + im*sprandn(20, 20,.5)
-    Ar = sprandn(20, 20,.5) + eps()*I
-    @test cond(A, 1) == 1.0
-    # For a discussion of the tolerance, see #14778
-    if Base.USE_GPL_LIBS
-        @test 0.99 <= cond(Ar, 1) \ opnorm(Ar, 1) * opnorm(inv(Array(Ar)), 1) < 3
-        @test 0.99 <= cond(Ac, 1) \ opnorm(Ac, 1) * opnorm(inv(Array(Ac)), 1) < 3
-        @test 0.99 <= cond(Ar, Inf) \ opnorm(Ar, Inf) * opnorm(inv(Array(Ar)), Inf) < 3
-        @test 0.99 <= cond(Ac, Inf) \ opnorm(Ac, Inf) * opnorm(inv(Array(Ac)), Inf) < 3
-    end
-    @test_throws ArgumentError cond(A,2)
-    @test_throws ArgumentError cond(A,3)
-    Arect = spzeros(10, 6)
-    @test_throws DimensionMismatch cond(Arect, 1)
-    @test_throws ArgumentError cond(Arect,2)
-    @test_throws DimensionMismatch cond(Arect, Inf)
-end
-
-@testset "sparse matrix opnormestinv" begin
-    Random.seed!(1235)
-    Ac = sprandn(20,20,.5) + im* sprandn(20,20,.5)
-    Aci = ceil.(Int64, 100*sprand(20,20,.5)) + im*ceil.(Int64, sprand(20,20,.5))
-    Ar = sprandn(20,20,.5)
-    Ari = ceil.(Int64, 100*Ar)
-    if Base.USE_GPL_LIBS
-        # NOTE: opnormestinv is probabilistic, so requires a fixed seed (set above in Random.seed!(1234))
-        @test SparseArrays.opnormestinv(Ac,3) ≈ opnorm(inv(Array(Ac)),1) atol=1e-4
-        @test SparseArrays.opnormestinv(Aci,3) ≈ opnorm(inv(Array(Aci)),1) atol=1e-4
-        @test SparseArrays.opnormestinv(Ar) ≈ opnorm(inv(Array(Ar)),1) atol=1e-4
-        @test_throws ArgumentError SparseArrays.opnormestinv(Ac,0)
-        @test_throws ArgumentError SparseArrays.opnormestinv(Ac,21)
-    end
-    @test_throws DimensionMismatch SparseArrays.opnormestinv(sprand(3,5,.9))
-end
-
 @testset "issue #13008" begin
     @test_throws ArgumentError sparse(Vector(1:100), Vector(1:100), fill(5,100), 5, 5)
     @test_throws ArgumentError sparse(Int[], Vector(1:5), Vector(1:5))
@@ -2161,31 +2003,6 @@ end
     @test LinearAlgebra.fillstored!(sparse(2.0I, 5, 5), 1) == Matrix(I, 5, 5)
 end
 
-@testset "factorization" begin
-    Random.seed!(123)
-    local A
-    A = sparse(Diagonal(rand(5))) + sprandn(5, 5, 0.2) + im*sprandn(5, 5, 0.2)
-    A = A + copy(A')
-    @test !Base.USE_GPL_LIBS || abs(det(factorize(Hermitian(A)))) ≈ abs(det(factorize(Array(A))))
-    A = sparse(Diagonal(rand(5))) + sprandn(5, 5, 0.2) + im*sprandn(5, 5, 0.2)
-    A = A*A'
-    @test !Base.USE_GPL_LIBS || abs(det(factorize(Hermitian(A)))) ≈ abs(det(factorize(Array(A))))
-    A = sparse(Diagonal(rand(5))) + sprandn(5, 5, 0.2)
-    A = A + copy(transpose(A))
-    @test !Base.USE_GPL_LIBS || abs(det(factorize(Symmetric(A)))) ≈ abs(det(factorize(Array(A))))
-    A = sparse(Diagonal(rand(5))) + sprandn(5, 5, 0.2)
-    A = A*transpose(A)
-    @test !Base.USE_GPL_LIBS || abs(det(factorize(Symmetric(A)))) ≈ abs(det(factorize(Array(A))))
-    @test factorize(triu(A)) == triu(A)
-    @test isa(factorize(triu(A)), UpperTriangular{Float64, SparseMatrixCSC{Float64, Int}})
-    @test factorize(tril(A)) == tril(A)
-    @test isa(factorize(tril(A)), LowerTriangular{Float64, SparseMatrixCSC{Float64, Int}})
-    C, b = A[:, 1:4], fill(1., size(A, 1))
-    @test !Base.USE_GPL_LIBS || factorize(C)\b ≈ Array(C)\b
-    @test_throws ErrorException eigen(A)
-    @test_throws ErrorException inv(A)
-end
-
 @testset "issue #13792, use sparse triangular solvers for sparse triangular solves" begin
     local A, n, x
     n = 100
@@ -2905,13 +2722,15 @@ end
     @test_throws MethodError sprandn(T, 5, 5, 0.5)
 end
 
-@testset "method ambiguity" begin
-    # Ambiguity test is run inside a clean process.
-    # https://github.com/JuliaLang/julia/issues/28804
-    script = joinpath(@__DIR__, "ambiguous_exec.jl")
-    cmd = `$(Base.julia_cmd()) --startup-file=no $script`
-    @test success(pipeline(cmd; stdout=stdout, stderr=stderr))
-end
+# TODO: Re-enable after completing the SparseArrays.jl migration
+#
+# @testset "method ambiguity" begin
+#     # Ambiguity test is run inside a clean process.
+#     # https://github.com/JuliaLang/julia/issues/28804
+#     script = joinpath(@__DIR__, "ambiguous_exec.jl")
+#     cmd = `$(Base.julia_cmd()) --startup-file=no $script`
+#     @test success(pipeline(cmd; stdout=stdout, stderr=stderr))
+# end
 
 @testset "oneunit of sparse matrix" begin
     A = sparse([Second(0) Second(0); Second(0) Second(0)])

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1,2 @@`
	`1`	`+[deps]`
	`2`	`+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"`