Merge pull request #8 from SciML/ap/fix-copy

Fix copy

Author: avik-pal

.JuliaFormatter.toml

@@ -1,2 +1,3 @@
 style = "sciml"
 annotate_untyped_fields_with_any = false
+join_lines_based_on_source = false

.github/workflows/CI.yml

@@ -13,18 +13,22 @@ concurrency:
   cancel-in-progress: ${{ startsWith(github.ref, 'refs/pull/') }}
 jobs:
   test:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         version:
           - "1"
+        os:
+          - ubuntu-latest
+          - macos-latest
+          - windows-latest
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
-      - uses: actions/cache@v3
+      - uses: actions/cache@v4
         env:
           cache-name: cache-artifacts
         with:
@@ -36,7 +40,16 @@ jobs:
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@v1
       - uses: julia-actions/julia-runtest@v1
+        env:
+          JULIA_NUM_THREADS: 11
+          RETESTITEMS_NWORKERS: 4
+          RETESTITEMS_NWORKER_THREADS: 2
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
         with:
-          files: lcov.info
+          directories: src
+      - uses: codecov/codecov-action@v4
+        with:
+          file: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          verbose: true
+          fail_ci_if_error: true

.github/workflows/Downstream.yml

@@ -54,6 +54,8 @@ jobs:
             exit(0)  # Exit immediately, as a success
           end
       - uses: julia-actions/julia-processcoverage@v1
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           files: lcov.info
+          token: ${{ secrets.CODECOV_TOKEN }}
+          fail_ci_if_error: true

.github/workflows/FormatPR.yml

@@ -15,7 +15,7 @@ jobs:
       # https://github.com/peter-evans/create-pull-request#reference-example
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@v5
+        uses: peter-evans/create-pull-request@v6
         with:
           token: ${{ secrets.GITHUB_TOKEN }}
           commit-message: Format .jl files

Project.toml

@@ -1,7 +1,7 @@
 name = "FastAlmostBandedMatrices"
 uuid = "9d29842c-ecb8-4973-b1e9-a27b1157504e"
 authors = ["Avik Pal"]
-version = "0.1.0"
+version = "0.1.1"
 
 [deps]
 ArrayInterface = "4fba245c-0d91-5ea0-9b3e-6abc04ee57a9"

README.md

@@ -2,8 +2,8 @@
 
 [![Join the chat at https://julialang.zulipchat.com #sciml-bridged](https://img.shields.io/static/v1?label=Zulip&message=chat&color=9558b2&labelColor=389826)](https://julialang.zulipchat.com/#narrow/stream/279055-sciml-bridged)
 
-[![CI](https://github.com/avik-pal/FastAlmostBandedMatrices.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/avik-pal/FastAlmostBandedMatrices.jl/actions/workflows/CI.yml)
-[![codecov](https://codecov.io/gh/avik-pal/FastAlmostBandedMatrices.jl/branch/main/graph/badge.svg?)](https://codecov.io/gh/avik-pal/FastAlmostBandedMatrices.jl)
+[![CI](https://github.com/SciML/FastAlmostBandedMatrices.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/SciML/FastAlmostBandedMatrices.jl/actions/workflows/CI.yml)
+[![codecov](https://codecov.io/gh/SciML/FastAlmostBandedMatrices.jl/branch/main/graph/badge.svg?)](https://codecov.io/gh/SciML/FastAlmostBandedMatrices.jl)
 [![Package Downloads](https://shields.io/endpoint?url=https://pkgs.genieframework.com/api/v1/badge/FastAlmostBandedMatrices)](https://pkgs.genieframework.com?packages=FastAlmostBandedMatrices)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
 

src/FastAlmostBandedMatrices.jl

@@ -4,12 +4,12 @@ import PrecompileTools: @recompile_invalidations, @setup_workload, @compile_work
 
 @recompile_invalidations begin
     using ArrayInterface, ArrayLayouts, BandedMatrices, ConcreteStructs, LazyArrays,
-        LinearAlgebra, MatrixFactorizations, Reexport
+          LinearAlgebra, MatrixFactorizations, Reexport
 end
 
 import ArrayLayouts: MemoryLayout, sublayout, sub_materialize, MatLdivVec, materialize!,
-    triangularlayout, triangulardata, zero!, _copyto!, colsupport, rowsupport, _qr, _qr!,
-    _factorize, muladd!
+                     triangularlayout, triangulardata, zero!, _copyto!, colsupport,
+                     rowsupport, _qr, _qr!, _factorize, muladd!
 import BandedMatrices: _banded_qr!, bandeddata, banded_qr_lmul!
 import LinearAlgebra: ldiv!
 import MatrixFactorizations: QR, QRPackedQ, getQ, getR, QRPackedQLayout, AdjQRPackedQLayout
@@ -67,8 +67,8 @@ function AlmostBandedMatrix{T}(::UndefInitializer, mn::NTuple{2, Integer},
     return AlmostBandedMatrix(undef, T, mn, lu, rank)
 end
 
-function AlmostBandedMatrix(::UndefInitializer, mn::NTuple{2, Integer},
-        lu::NTuple{2, Integer}, rank::Integer)
+function AlmostBandedMatrix(
+        ::UndefInitializer, mn::NTuple{2, Integer}, lu::NTuple{2, Integer}, rank::Integer)
     return AlmostBandedMatrix(undef, Float64, mn, lu, rank)
 end
 
@@ -160,6 +160,10 @@ end
     end
 end
 
+function Base.copy(B::AlmostBandedMatrix)
+    return AlmostBandedMatrix(copy(bandpart(B)), copy(fillpart(B)))
+end
+
 function Base.setindex!(B::AlmostBandedMatrix, v, k::Integer, j::Integer)
     if k ≤ size(B.fill, 1)
         if j > k + bandwidth(B.bands, 2)
@@ -219,8 +223,7 @@ end
 # Pretty Printing
 # ---------------
 function _almost_banded_summary(io, B::AlmostBandedMatrix{T}, inds) where {T}
-    print(io,
-        Base.dims2string(length.(inds)),
+    print(io, Base.dims2string(length.(inds)),
         " AlmostBandedMatrix{$T} with bandwidths $(almostbandwidths(B)) and fill \
           rank $(almostbandedrank(B))")
 end
@@ -267,8 +270,9 @@ function _almostbanded_qr(_, A)
     B, L = bandpart(A), fillpart(A)
     # Expand the bandsize for the QR factorization
     ## Bypass the safety checks in `AlmostBandedMatrix`
-    return almostbanded_qr!(AlmostBandedMatrix{eltype(A)}(BandedMatrix(copy(B), (l, l + u)),
-            copy(L)), Val(true))
+    return almostbanded_qr!(
+        AlmostBandedMatrix{eltype(A)}(BandedMatrix(copy(B), (l, l + u)), copy(L)),
+        Val(true))
 end
 
 # Band size not yet expanded!
@@ -320,14 +324,14 @@ end
         L_right = L[:, jr2]
         U′ = U[kr, :]
         for j in 1:length(jr2)
-            muladd!(-one(T), U′[(j + 1):end, :], L_right[:, j], one(T),
-                B_right[(j + 1):end, j])
+            muladd!(
+                -one(T), U′[(j + 1):end, :], L_right[:, j], one(T), B_right[(j + 1):end, j])
         end
         banded_qr_lmul!(Q', B_right)
         banded_qr_lmul!(Q', U′)
         for j in 1:length(jr2)
-            muladd!(one(T), U′[(j + 1):end, :], L_right[:, j], one(T),
-                B_right[(j + 1):end, j])
+            muladd!(
+                one(T), U′[(j + 1):end, :], L_right[:, j], one(T), B_right[(j + 1):end, j])
         end
         k = last(jr1) + 1
     end
@@ -363,8 +367,8 @@ _almostbanded_widerect_ldiv!(::QR{T}, B) where {T} = error("Not implemented")
 
 const UpperLayoutMatrix{T} = UpperTriangular{T, <:LayoutMatrix{T}}
 
-for Typ in (:StridedVector, :StridedMatrix, :AbstractVecOrMat, :UpperLayoutMatrix,
-    :LayoutMatrix)
+for Typ in (
+    :StridedVector, :StridedMatrix, :AbstractVecOrMat, :UpperLayoutMatrix, :LayoutMatrix)
     @eval function ldiv!(A::QR{T, <:AlmostBandedMatrix}, B::$Typ{T}) where {T}
         m, n = size(A)
         if m == n
@@ -410,8 +414,8 @@ end
 
 @inline __original_almostbandedrank(A) = size(first(__lowrankfillpart(A)), 2)
 
-@views function _almostbanded_upper_ldiv!(::Type{Tri}, R::AbstractMatrix,
-        b::AbstractVector{T}, buffer) where {T, Tri}
+@views function _almostbanded_upper_ldiv!(
+        ::Type{Tri}, R::AbstractMatrix, b::AbstractVector{T}, buffer) where {T, Tri}
     B = bandpart(R)
     U, V = __lowrankfillpart(R)
     fill!(buffer, zero(T))
@@ -472,8 +476,8 @@ end
 # Matrix Multiply
 # ---------------
 
-@views function muladd!(α, A::AlmostBandedMatrix, B::AbstractVecOrMat, β,
-        C::AbstractVecOrMat)
+@views function muladd!(
+        α, A::AlmostBandedMatrix, B::AbstractVecOrMat, β, C::AbstractVecOrMat)
     L = fillpart(A)
     muladd!(α, L, B, β, selectdim(C, 1, 1:size(L, 1)))
     muladd!(α, exclusive_bandpart(A), B, β, selectdim(C, 1, (size(L, 1) + 1):size(C, 1)))
@@ -504,6 +508,6 @@ end
 end
 
 export AlmostBandedMatrix, bandpart, fillpart, exclusive_bandpart, finish_part_setindex!,
-    almostbandwidths, almostbandedrank
+       almostbandwidths, almostbandedrank
 
 end

test/runtests.jl

@@ -17,6 +17,24 @@ using SafeTestsets, Test
         @test almostbandedrank(A) == 2
     end
 
+    @safetestset "Copy" begin
+        using FastAlmostBandedMatrices
+
+        n = 5
+        m = 2
+
+        A1 = AlmostBandedMatrix(brand(Float64, n, n, m + 1, m), rand(Float64, m, n))
+        A2 = copy(A1)
+
+        @test !(A2 isa Matrix)
+        @test A1 == A2
+
+        A2 = deepcopy(A1)
+
+        @test !(A2 isa Matrix)
+        @test A1 == A2
+    end
+
     @safetestset "QR" begin
         using LinearAlgebra, FastAlmostBandedMatrices
         import MatrixFactorizations: QRPackedQ