Merge pull request #113 from m3g/conditional_alloc_check

Conditional alloc check

.github/workflows/Downgrade.yml

@@ -16,8 +16,8 @@ jobs:
     strategy:
       matrix:
         version:
-          - '1.6'
-          - '^1.6'
+          - '1.9'
+          - '^1.9'
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v1

.github/workflows/ci.yml

@@ -12,16 +12,52 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.6'
+          - '1.9'
           - 'lts'
           - 'pre'
         os:
           - ubuntu-latest
           - macOS-latest
           - windows-latest
         exclude:
-          - version: '1.6'
+          - version: '1.9'
             os: macOS-latest
+        build_is_production_build:
+          - true
+    steps:
+      - uses: actions/checkout@v4
+      - uses: julia-actions/setup-julia@v2
+        with:
+          version: ${{ matrix.version }}
+      - uses: actions/cache@v3
+        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@latest
+      - uses: julia-actions/julia-runtest@latest    
+        env:
+          BUILD_IS_PRODUCTION_BUILD: ${{ matrix.build_is_production_build }}
+        with:
+          coverage: false
+  tests-with-coverage:
+    name: Julia ${{ matrix.version }} - ${{ matrix.os }} - ${{ matrix.arch }} - ${{ github.event_name }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - 'lts'
+          - 'pre'
+        os:
+          - ubuntu-latest
+        build_is_production_build:
+          - false
     steps:
       - uses: actions/checkout@v4
       - uses: julia-actions/setup-julia@v2
@@ -39,6 +75,8 @@ jobs:
             ${{ runner.os }}-
       - uses: julia-actions/julia-buildpkg@latest
       - uses: julia-actions/julia-runtest@latest
+        env:
+          BUILD_IS_PRODUCTION_BUILD: false
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v4
         with: 

Project.toml

@@ -25,21 +25,21 @@ Compat = "4.14.0"
 DocStringExtensions = "0.9"
 Documenter = "1.2.1"
 ForwardDiff = "0.10.13"
-LinearAlgebra = "1.6"
+LinearAlgebra = "1.9"
 Measurements = "2.11"
 NearestNeighbors = "0.4.16"
-PDBTools = "1.1"
+PDBTools = "2"
 Parameters = "0.12"
-PrecompileTools = "1"
+PrecompileTools = "1.2.1"
 ProgressMeter = "1.6"
-Random = "1.6"
+Random = "1.9"
 Setfield = "0.7, 0.8, 0.9, 1"
 StaticArrays = "1.6"
-Test = "1.6"
-TestItemRunner = "0.2"
-TestItems = "0.1, 1"
+Test = "1.9"
+TestItemRunner = "1"
+TestItems = "1"
 Unitful = "1.19"
-julia = "1.6"
+julia = "1.9"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
@@ -53,6 +53,7 @@ PDBTools = "e29189f1-7114-4dbd-93d0-c5673a921a58"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 Unitful = "1986cc42-f94f-5a68-af5c-568840ba703d"
+TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [targets]
-test = ["Test", "TestItemRunner", "Chemfiles", "NearestNeighbors", "ForwardDiff", "Unitful", "Measurements", "BenchmarkTools", "Aqua", "Documenter", "PDBTools"]
+test = ["Test", "TestItemRunner", "Chemfiles", "NearestNeighbors", "ForwardDiff", "Unitful", "Measurements", "BenchmarkTools", "Aqua", "Documenter", "PDBTools", "TestItems"]

README.md

@@ -27,7 +27,7 @@ USER GUIDE: <br>
 
 ## Installation
 
-Download and install Julia for your platform from [this http url](https://julialang.org/downloads/). Version 1.6 or greater is required.
+Download and install Julia for your platform from [this http url](https://julialang.org/downloads/). Version 1.9 or greater is required.
 
 Install it as usual for registered Julia packages:
 

src/Box.jl

@@ -468,24 +468,25 @@ end
     @test list == Tuple{Int64,Int64,Float64}[]
 end
 
-@testitem "Stable Box update" begin
+@testitem "Stable Box update" setup=[AllocTest] begin
     using CellListMap
     using StaticArrays
     using BenchmarkTools
     using LinearAlgebra: diag
+    using .AllocTest: Allocs
 
     # update with tuples
     box = Box([1, 1, 1], 0.1)
     a = @ballocated CellListMap.update_box($box; unitcell=(2, 2, 2), cutoff=0.2) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     new_box = CellListMap.update_box(box; unitcell=(2, 2, 2), cutoff=0.2)
     @test new_box.cutoff == 0.2
     @test new_box.input_unit_cell.matrix == [2 0 0; 0 2 0; 0 0 2]
 
     # update with SVector
     box = Box([1, 1, 1], 0.1)
     a = @ballocated CellListMap.update_box($box; unitcell=SVector(2, 2, 2), cutoff=0.2) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     new_box = CellListMap.update_box(box; unitcell=(2, 2, 2), cutoff=0.2)
     @test new_box.cutoff == 0.2
     @test new_box.input_unit_cell.matrix == [2 0 0; 0 2 0; 0 0 2]
@@ -495,7 +496,7 @@ end
     box = Box(limits(x), 0.1)
     new_x = rand(SVector{3,Float64}, 1500)
     a = @ballocated CellListMap.update_box($box; unitcell=$(limits(new_x)), cutoff=0.2) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     new_box = CellListMap.update_box(box; unitcell=limits(new_x), cutoff=0.2)
     @test new_box.cutoff == 0.2
     @test diag(new_box.input_unit_cell.matrix) == limits(new_x).limits .+ 2.1 * 0.2
@@ -504,7 +505,7 @@ end
     box = Box([1 0 0; 0 1 0; 0 0 1], 0.1)
     new_matrix = SMatrix{3,3,Float64,9}(2, 0, 0, 0, 2, 0, 0, 0, 2)
     a = @ballocated CellListMap.update_box($box; unitcell=$new_matrix, cutoff=0.2) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     new_box = CellListMap.update_box(box; unitcell=new_matrix, cutoff=0.2)
     @test new_box.cutoff == 0.2
     @test new_box.input_unit_cell.matrix == [2 0 0; 0 2 0; 0 0 2]

src/CellListMap.jl

@@ -1,7 +1,7 @@
 module CellListMap
 
 using DocStringExtensions: TYPEDEF, TYPEDFIELDS 
-using TestItems: @testitem
+using TestItems: @testitem, @testmodule
 using Compat: @compat
 using ProgressMeter: Progress, next!
 using Parameters: @unpack, @with_kw

src/CellOperations.jl

@@ -354,16 +354,17 @@ function _minmax(x::AbstractVector{<:AbstractVector})
     return SVector(xmin), SVector(xmax)
 end
 
-@testitem "_minmax" begin
+@testitem "_minmax" setup=[AllocTest] begin
     using BenchmarkTools
     using StaticArrays
     import CellListMap: _minmax
+    using .AllocTest: Allocs
     x = [[0.0, 0.5, 1.0], [0.5, 1.0, 0.0], [1.0, 0.0, 0.5]]
     @test _minmax(x) === (SVector(0.0, 0.0, 0.0), SVector(1.0, 1.0, 1.0))
     x = [SVector(0.0, 0.5, 1.0), SVector(0.5, 1.0, 0.0), SVector(1.0, 0.0, 0.5)]
     @test _minmax(x) === (SVector(0.0, 0.0, 0.0), SVector(1.0, 1.0, 1.0))
     a = @ballocated _minmax($x) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
 end
 
 """

src/ParticleSystem.jl

@@ -757,23 +757,24 @@ function update_unitcell!(sys, unitcell)
     return sys
 end
 
-@testitem "update_unitcell!" begin
+@testitem "update_unitcell!" setup=[AllocTest] begin
     using BenchmarkTools
     using LinearAlgebra: diag
     using StaticArrays
     using CellListMap
+    using .AllocTest: Allocs
     x = rand(SVector{3,Float64}, 1000)
     sys1 = ParticleSystem(xpositions=x, unitcell=[1, 1, 1], cutoff=0.1, output=0.0)
     update_unitcell!(sys1, SVector(2, 2, 2))
     @test diag(sys1.unitcell) == [2, 2, 2]
     a = @ballocated update_unitcell!($sys1, SVector(2, 2, 2)) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     y = rand(SVector{3,Float64}, 1000)
     sys2 = ParticleSystem(xpositions=x, ypositions=y, unitcell=[1, 1, 1], cutoff=0.1, output=0.0)
     update_unitcell!(sys2, SVector(2, 2, 2))
     @test diag(sys2.unitcell) == [2, 2, 2]
     a = @ballocated update_unitcell!($sys2, SVector(2, 2, 2)) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     # Test throwing error on updating non-periodic unit cells
     sys = ParticleSystem(xpositions=x, cutoff=0.1, output=0.0)
     @test_throws ArgumentError update_unitcell!(sys, [1, 1, 1])
@@ -838,23 +839,24 @@ function update_cutoff!(sys::ParticleSystem2, cutoff)
     return sys
 end
 
-@testitem "update_cutoff!" begin
+@testitem "update_cutoff!" setup=[AllocTest] begin
     using BenchmarkTools
     using StaticArrays
     using CellListMap
     using PDBTools
+    using .AllocTest: Allocs
     x = rand(SVector{3,Float64}, 1000)
     sys1 = ParticleSystem(xpositions=x, unitcell=[1, 1, 1], cutoff=0.1, output=0.0)
     update_cutoff!(sys1, 0.2)
     @test sys1.cutoff == 0.2
     a = @ballocated update_cutoff!($sys1, 0.1) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     y = rand(SVector{3,Float64}, 1000)
     sys2 = ParticleSystem(xpositions=x, ypositions=y, unitcell=[1, 1, 1], cutoff=0.1, output=0.0)
     update_cutoff!(sys2, 0.2)
     @test sys2.cutoff == 0.2
     a = @ballocated update_cutoff!($sys2, 0.1) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
 
     # Update cutoff of non-periodic systems
     x = coor(readPDB(CellListMap.argon_pdb_file))
@@ -864,14 +866,14 @@ end
     update_cutoff!(sys1, 10.0)
     @test sys1.unitcell ≈ [39.83 0.0 0.0; 0.0 39.96 0.0; 0.0 0.0 39.99] atol = 1e-2
     a = @ballocated update_cutoff!($sys1, 8.0) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
     sys2 = ParticleSystem(xpositions=x[1:50], ypositions=x[51:100], cutoff=8.0, output=0.0)
     @test unitcelltype(sys2) == NonPeriodicCell
     @test sys2.unitcell ≈ [35.63 0.0 0.0; 0.0 35.76 0.0; 0.0 0.0 35.79] atol = 1e-2
     update_cutoff!(sys2, 10.0)
     @test sys2.unitcell ≈ [39.83 0.0 0.0; 0.0 39.96 0.0; 0.0 0.0 39.99] atol = 1e-2
     a = @ballocated update_cutoff!($sys2, 8.0) evals = 1 samples = 1
-    @test a == 0
+    @test a == Allocs(0)
 end
 
 #
@@ -946,44 +948,45 @@ function UpdateParticleSystem!(sys::ParticleSystem2, update_lists::Bool=true)
 end
 
 # this updates must be non-allocating in the serial case
-@testitem "UpdateParticleSystem!" begin
+@testitem "UpdateParticleSystem!" setup=[AllocTest] begin
     using BenchmarkTools
     using StaticArrays
     using CellListMap
+    using .AllocTest: Allocs
     x = rand(SVector{3,Float64}, 1000)
     sys = ParticleSystem(xpositions=x, unitcell=[1.0, 1.0, 1.0], cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
     y = rand(SVector{3,Float64}, 1000)
     sys = ParticleSystem(xpositions=x, ypositions=y, unitcell=[1.0, 1.0, 1.0], cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
 
     # Test construction with more general abstract vectors
     x = @view(x[1:500])
     sys = ParticleSystem(xpositions=x, unitcell=[1.0, 1.0, 1.0], cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
     y = @view(y[1:500])
     sys = ParticleSystem(xpositions=x, ypositions=y, unitcell=[1.0, 1.0, 1.0], cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
 
     # Update with matrices
     x = rand(3, 500)
     sys = ParticleSystem(xpositions=x, unitcell=[1.0, 1.0, 1.0], cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
 
     # Update non-periodic system
     x = rand(SVector{3,Float64}, 1000)
     sys = ParticleSystem(xpositions=x, cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
     y = rand(SVector{3,Float64}, 1000)
     sys = ParticleSystem(xpositions=x, ypositions=y, cutoff=0.1, output=0.0, parallel=false)
     a = @ballocated CellListMap.UpdateParticleSystem!($sys) samples = 1 evals = 1
-    @test a == 0
+    @test a == Allocs(0)
 
     # Throw error when trying to *not* update lists with autoswap on:
     sys = ParticleSystem(

src/neighborlists.jl

@@ -423,10 +423,11 @@ end
 
 end
 
-@testitem "Allocations" begin
+@testitem "Allocations" setup=[AllocTest] begin
     using CellListMap
     using StaticArrays
     using BenchmarkTools
+    using .AllocTest: Allocs
 
     #
     # Single set of particles
@@ -438,23 +439,23 @@ end
     neighborlist!(system)
     x = rand(SVector{3,Float64}, 10^3)
     allocs = @ballocated update!($system, $x) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x; cutoff=0.2) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated neighborlist!($system) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
 
     # Non-Periodic systems
     x = rand(SVector{3,Float64}, 10^3)
     system = InPlaceNeighborList(x=x, cutoff=0.1, parallel=false)
     neighborlist!(system)
     x = rand(SVector{3,Float64}, 10^3)
     allocs = @ballocated update!($system, $x) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x; cutoff=0.2) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated neighborlist!($system) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
 
     #
     # Two sets of particles
@@ -467,11 +468,11 @@ end
     x = rand(SVector{3,Float64}, 10^3)
     y = rand(SVector{3,Float64}, 10^3)
     allocs = @ballocated neighborlist!($system) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x, $y) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x, $y; cutoff=0.2) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
 
     # Non-Periodic systems
     y = rand(SVector{3,Float64}, 10^3)
@@ -480,11 +481,11 @@ end
     x = rand(SVector{3,Float64}, 10^3)
     y = rand(SVector{3,Float64}, 10^3)
     allocs = @ballocated neighborlist!($system) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x, $y) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
     allocs = @ballocated update!($system, $x, $y; cutoff=0.2) evals = 1 samples = 1
-    @test allocs == 0
+    @test allocs == Allocs(0)
 
 end