diff --git a/.github/workflows/CompatHelper.yml b/.github/workflows/CompatHelper.yml index 5577817..f889647 100644 --- a/.github/workflows/CompatHelper.yml +++ b/.github/workflows/CompatHelper.yml @@ -14,7 +14,7 @@ jobs: run: which julia continue-on-error: true - name: Install Julia, but only if it is not already available in the PATH - uses: julia-actions/setup-julia@v1 + uses: julia-actions/setup-julia@v2 with: version: "1" arch: ${{ runner.arch }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 18ae322..0749fd6 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -50,7 +50,7 @@ jobs: fail-fast: false matrix: version: - - "1.8" + - "1.9" - "1" # automatically expands to the latest stable 1.x release of Julia - "pre" os: diff --git a/Project.toml b/Project.toml index a432cb2..b50be0d 100644 --- a/Project.toml +++ b/Project.toml @@ -1,7 +1,7 @@ name = "CompositionalNetworks" uuid = "4b67e4b5-442d-4ef5-b760-3f5df3a57537" authors = ["Jean-François Baffier"] -version = "0.5.8" +version = "0.5.9" [deps] ConstraintCommons = "e37357d9-0691-492f-a822-e5ea6a920954" @@ -12,7 +12,6 @@ JuliaFormatter = "98e50ef6-434e-11e9-1051-2b60c6c9e899" OrderedCollections = "bac558e1-5e72-5ebc-8fee-abe8a469f55d" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe" -ThreadSafeDicts = "4239201d-c60e-5e0a-9702-85d713665ba7" Unrolled = "9602ed7d-8fef-5bc8-8597-8f21381861e8" [compat] @@ -23,19 +22,19 @@ Distances = "0.10" JuliaFormatter = "1" OrderedCollections = "1" Random = "1" -TestItemRunner = "0.2, 1" TestItems = "0.1, 1" -ThreadSafeDicts = "0.1" Unrolled = "0.1" -julia = "1.8" +julia = "1.9" [extras] Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" Evolutionary = "86b6b26d-c046-49b6-aa0b-5f0f74682bd6" +ExplicitImports = "7d51a73a-1435-4ff3-83d9-f097790105c7" +JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b" Memoization = "6fafb56a-5788-4b4e-91ca-c0cea6611c73" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a" ThreadPools = "b189fb0b-2eb5-4ed4-bc0c-d34c51242431" [targets] -test = ["Aqua", "Evolutionary", "Memoization", "Test", "TestItemRunner", "ThreadPools"] +test = ["Aqua", "ExplicitImports", "JET", "Evolutionary", "Memoization", "Test", "TestItemRunner", "ThreadPools"] diff --git a/perf/Project.toml b/perf/Project.toml deleted file mode 100644 index e348fbb..0000000 --- a/perf/Project.toml +++ /dev/null @@ -1,5 +0,0 @@ -[deps] -CompositionalNetworks = "4b67e4b5-442d-4ef5-b760-3f5df3a57537" -ConstraintDomains = "5800fd60-8556-4464-8d61-84ebf7a0bedb" -PerfChecker = "6309bf6b-a531-4b08-891e-8ee981e5c424" -Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" diff --git a/perf/allocs.jl b/perf/allocs.jl deleted file mode 100644 index dcafcf9..0000000 --- a/perf/allocs.jl +++ /dev/null @@ -1,36 +0,0 @@ -using PerfChecker -using Test - -using CompositionalNetworks -using ConstraintDomains - -@testset "PerfChecker.jl" begin - # Title of the alloc check (for logging purpose) - title = "Explore, Learn, and Compose" - - # Dependencies needed to execute pre_alloc and alloc - dependencies = [CompositionalNetworks, ConstraintDomains] - - # Target of the alloc check - targets = [CompositionalNetworks] - - # Code specific to the package being checked - domains = fill(domain([1, 2, 3]), 3) - - # Code to trigger precompilation before the alloc check - pre_alloc() = foreach(_ -> explore_learn_compose(domains, allunique), 1:10) - - # Code being allocations check - alloc() = explore_learn_compose(domains, allunique) - - # Actual call to PerfChecker - alloc_check( - title, - dependencies, - targets, - pre_alloc, - alloc; - path = @__DIR__, - threads = 10, - ) -end diff --git a/perf/bench.jl b/perf/bench.jl deleted file mode 100644 index 5b37b3e..0000000 --- a/perf/bench.jl +++ /dev/null @@ -1,21 +0,0 @@ -using PerfChecker -using BenchmarkTools - -using CompositionalNetworks -using ConstraintDomains - -# Target of the becnhamrk -target = CompositionalNetworks - -# Code specific to the package being checked -domains = fill(domain([1, 2, 3, 4]), 4) - -# Code to trigger precompilation before the becnh (optional) -foreach(_ -> explore_learn_compose(domains, allunique), 1:10) - -# Code being benchmarked -t = @benchmark explore_learn_compose(domains, allunique) evals = 1 samples = 10 seconds = - 3600 - -# Store the bench results -store_benchmark(t, target; path = @__DIR__) diff --git a/perf/benchmarks/benchmark-0.2.7.csv b/perf/benchmarks/benchmark-0.2.7.csv deleted file mode 100644 index aef1b5c..0000000 --- a/perf/benchmarks/benchmark-0.2.7.csv +++ /dev/null @@ -1,11 +0,0 @@ -times,gctimes,memory,allocs -2.82057323e10,7.4165509e9,35201313954,772781687 -3.31711664e10,1.09701184e10,35201313954,772781687 -2.94444416e10,8.9803602e9,35201313954,772781687 -2.75833201e10,7.4754396e9,35201313954,772781687 -2.64568053e10,6.8462894e9,35201313954,772781687 -3.03186626e10,9.2108541e9,35201313954,772781687 -2.72911134e10,7.3486411e9,35201313954,772781687 -2.90782494e10,8.4920859e9,35201313954,772781687 -2.97272747e10,9.0009021e9,35201313954,772781687 -2.70209456e10,7.2544251e9,35201313954,772781687 diff --git a/perf/benchmarks/benchmark-0.3.0.csv b/perf/benchmarks/benchmark-0.3.0.csv deleted file mode 100644 index f4947d4..0000000 --- a/perf/benchmarks/benchmark-0.3.0.csv +++ /dev/null @@ -1,11 +0,0 @@ -times,gctimes,memory,allocs -4.5054707e9,4.609721e8,1688680160,43902598 -4.4884263e9,5.096094e8,1688680160,43902598 -5.1127691e9,5.08184e8,1688680160,43902598 -5.5702289e9,5.551036e8,1688680160,43902598 -4.685473e9,5.138967e8,1688680160,43902598 -3.9022191e9,4.279265e8,1688680160,43902598 -3.8231374e9,4.314888e8,1688680160,43902598 -5.1091927e9,5.27126e8,1688680160,43902598 -2.6517206e9,3.701838e8,1688680160,43902598 -1.547612e9,2.510559e8,1688680160,43902598 diff --git a/perf/benchmarks/benchmark-0.3.1.csv b/perf/benchmarks/benchmark-0.3.1.csv deleted file mode 100644 index 0cbc899..0000000 --- a/perf/benchmarks/benchmark-0.3.1.csv +++ /dev/null @@ -1,11 +0,0 @@ -times,gctimes,memory,allocs -6.2163534e9,6.269408e8,1791540787,45464260 -3.2730546e9,3.811795e8,1791540787,45464260 -4.0982624e9,4.420458e8,1791540787,45464260 -3.618149e9,4.244872e8,1791540787,45464260 -4.5703931e9,5.245305e8,1791540787,45464260 -2.4535218e9,3.193049e8,1791540787,45464260 -3.8460514e9,4.634933e8,1791540787,45464260 -2.7953075e9,3.992261e8,1791540787,45464260 -1.6829643e9,2.564143e8,1791540787,45464260 -5.7435154e9,6.207959e8,1791540787,45464260 diff --git a/perf/benchmarks/benchmark-allocs.pdf b/perf/benchmarks/benchmark-allocs.pdf deleted file mode 100644 index c8a93ac..0000000 Binary files a/perf/benchmarks/benchmark-allocs.pdf and /dev/null differ diff --git a/perf/benchmarks/benchmark-allocs.png b/perf/benchmarks/benchmark-allocs.png deleted file mode 100644 index 6e74d03..0000000 Binary files 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ba5e12c..0000000 --- a/perf/benchmarks/benchmark-params-0.3.0.txt +++ /dev/null @@ -1 +0,0 @@ -BenchmarkTools.Parameters(5.0, 10000, 1, 0.0, true, false, 0.05, 0.01) \ No newline at end of file diff --git a/perf/benchmarks/benchmark-params-0.3.1.txt b/perf/benchmarks/benchmark-params-0.3.1.txt deleted file mode 100644 index ba5e12c..0000000 --- a/perf/benchmarks/benchmark-params-0.3.1.txt +++ /dev/null @@ -1 +0,0 @@ -BenchmarkTools.Parameters(5.0, 10000, 1, 0.0, true, false, 0.05, 0.01) \ No newline at end of file diff --git a/perf/benchmarks/benchmark-times.pdf b/perf/benchmarks/benchmark-times.pdf deleted file mode 100644 index d870508..0000000 Binary files a/perf/benchmarks/benchmark-times.pdf and /dev/null differ diff --git a/perf/benchmarks/benchmark-times.png b/perf/benchmarks/benchmark-times.png deleted file mode 100644 index cbba170..0000000 Binary files a/perf/benchmarks/benchmark-times.png and /dev/null differ diff --git a/perf/benchmarks/benchmark-times.svg 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format_text +import OrderedCollections: LittleDict +import Random: bitrand +import TestItems: @testitem +import Unrolled: @unroll export Composition export ICN diff --git a/src/composition.jl b/src/composition.jl index 2a27ef2..6e200d1 100644 --- a/src/composition.jl +++ b/src/composition.jl @@ -91,7 +91,7 @@ function generate(c::Composition, name, ::Val{:Julia}) return $ag(@view X[:, 1]) |> (y -> $co(y; dom_size, nvars=length(x), params...)) end """ - return documentation * format_text(output, BlueStyle(); pipe_to_function_call = false) + return documentation * format_text(output, SciMLStyle(); pipe_to_function_call = false) end """ diff --git a/src/icn.jl b/src/icn.jl index a0047eb..2c21632 100644 --- a/src/icn.jl +++ b/src/icn.jl @@ -133,6 +133,7 @@ function _compose(icn::ICN) if exclu(layer) f_id = as_int(@view weights(icn)[_start:_end]) + # @warn "debug" f_id _end _start weights(icn) (exclu(layer) ? "nbits_exclu(layer)" : "length(layer)") (@view weights(icn)[_start:_end]) s = symbol(layer, f_id + 1) push!(funcs, [functions(layer)[s]]) push!(symbols, [s]) diff --git a/src/layer.jl b/src/layer.jl index 53646f0..18be36f 100644 --- a/src/layer.jl +++ b/src/layer.jl @@ -30,7 +30,12 @@ exclu(layer) = layer.exclusive symbol(layer, i) Return the i-th symbols of the operations in a given layer. """ -symbol(layer, i) = collect(keys(functions(layer)))[i] +symbol(layer, i) = begin + if i > length(layer) + @info layer i functions(layer) + end + collect(keys(functions(layer)))[i] +end """ nbits_exclu(layer) diff --git a/src/learn.jl b/src/learn.jl index 6a71559..a2410f7 100644 --- a/src/learn.jl +++ b/src/learn.jl @@ -1,6 +1,6 @@ abstract type AbstractOptimizer end -function optimize!(args...) +function optimize!(args...; kwargs...) return nothing end diff --git a/src/metrics.jl b/src/metrics.jl index 992b323..542c6e8 100644 --- a/src/metrics.jl +++ b/src/metrics.jl @@ -7,7 +7,7 @@ hamming(x, X) = mapreduce(y -> Distances.hamming(x, y), min, X) """ minkowski(x, X, p) """ -minkowski(x, X, p) = mapreduce(Distances.minkowski(x, y, p), min, X) +minkowski(x, X, p) = mapreduce(y -> Distances.minkowski(x, y, p), min, X) """ manhattan(x, X) diff --git a/test/ExplicitImports.jl b/test/ExplicitImports.jl new file mode 100644 index 0000000..e9058ce --- /dev/null +++ b/test/ExplicitImports.jl @@ -0,0 +1,3 @@ +@testset "Look for Explicit Imports" begin + @test check_no_implicit_imports(CompositionalNetworks) === nothing +end diff --git a/test/JET.jl b/test/JET.jl new file mode 100644 index 0000000..41736d6 --- /dev/null +++ b/test/JET.jl @@ -0,0 +1,3 @@ +@testset "Code linting (JET.jl)" begin + JET.test_package(CompositionalNetworks; target_defined_modules = true) +end diff --git a/test/runtests.jl b/test/runtests.jl index 8c2c27c..c3ed1ee 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,9 +1,16 @@ +using CompositionalNetworks + +using Aqua +using ExplicitImports +using JET using Test using TestItemRunner -using TestItems -@testset "Package tests: CompositionalNetworks" begin +@testset "Package tests: ConstraintCommons" begin include("Aqua.jl") + include("ExplicitImports.jl") + include("JET.jl") include("TestItemRunner.jl") + include("icn.jl") end