diff --git a/.JuliaFormatter.toml b/.JuliaFormatter.toml new file mode 100644 index 0000000..b7812c4 --- /dev/null +++ b/.JuliaFormatter.toml @@ -0,0 +1,2 @@ +# see https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options +style = "blue" \ No newline at end of file diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..c3cf21e --- /dev/null +++ b/.dockerignore @@ -0,0 +1,17 @@ +packagecompiler/app +packagecompiler/app.* +.github +.vscode +.CondaPkg +docs +test +tmp +**/tmp +AUTHORS +codemeta.json +Dockerfile +Dockerfile.* +LICENSE +README.md +staticcompiler/lib +staticcompiler/lib.* \ No newline at end of file diff --git a/.gitignore b/.gitignore index ccf6c20..ea9275b 100644 --- a/.gitignore +++ b/.gitignore @@ -3,7 +3,9 @@ *.jl.mem /docs/Manifest.toml /docs/build/ -Manifest.toml -tmp/ +/Manifest.toml +tmp /packagecompiler/app -/packagecompiler/app.backup \ No newline at end of file +*.backup +.CondaPkg +.vscode diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml new file mode 100644 index 0000000..29a343c --- /dev/null +++ b/.pre-commit-config.yaml @@ -0,0 +1,12 @@ +repos: +- repo: https://github.com/pre-commit/pre-commit-hooks + rev: v2.3.0 + hooks: + - id: check-yaml + - id: end-of-file-fixer + - id: trailing-whitespace + +- repo: https://github.com/qiaojunfeng/pre-commit-julia-format + rev: v0.2.0 + hooks: + - id: julia-format diff --git a/test/Artifacts.toml b/Artifacts.toml similarity index 50% rename from test/Artifacts.toml rename to Artifacts.toml index db39948..9def2da 100644 --- a/test/Artifacts.toml +++ b/Artifacts.toml @@ -1,5 +1,11 @@ +# all entries marked with `lazy = true` won't be downloaded on package installation +# the rest will be downloaded +# hence we can simply mark all test dependencies as lazy = true and have a single Artifacts.toml for everything + [rqatestdata] git-tree-sha1 = "1dc9d7aa975de4f5ecc652f34d6bbee706fcb7bd" +# mark all test Artifacts as lazy +lazy = true [[rqatestdata.download]] url = "https://github.com/EarthyScience/RQADeforestationTestData/archive/refs/tags/v2.0.tar.gz" diff --git a/Dockerfile b/Dockerfile index 30dd3ad..d71754a 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,6 +1,26 @@ +FROM julia:1.11-bookworm AS packagecompiled + +RUN --mount=type=cache,target=/var/cache/apt \ + --mount=type=cache,target=/var/lib/apt \ + apt -y update && apt -y install build-essential curl ca-certificates + +# from Debian version 13 onwards, "just" can simply be installed via apt install +RUN curl --proto '=https' --tlsv1.2 -sSf https://just.systems/install.sh | bash -s -- --to /usr/local/bin + +WORKDIR /repo +COPY . . +RUN --mount=type=cache,target=/root/.julia \ + julia --project=. -e "import Pkg; Pkg.instantiate()" +RUN --mount=type=cache,target=/root/.julia \ + julia --project="packagecompiler" -e "import Pkg; Pkg.instantiate()" +RUN --mount=type=cache,target=/root/.julia \ + just packagecompile + +# having precompiled everything we can simply copy the binaries to its slim docker image FROM debian:bookworm-slim WORKDIR /work -COPY packagecompiler/app/bin /usr/bin -COPY packagecompiler/app/lib /usr/lib -COPY packagecompiler/app/share /usr/share -ENTRYPOINT ["RQADeforestation"] \ No newline at end of file +COPY --from=packagecompiled /repo/packagecompiler/app/bin /usr/bin +COPY --from=packagecompiled /repo/packagecompiler/app/lib /usr/lib +COPY --from=packagecompiled /repo/packagecompiler/app/share /usr/share +ENTRYPOINT ["RQADeforestation"] + diff --git a/Dockerfile.staticcompiler b/Dockerfile.staticcompiler new file mode 100644 index 0000000..b970404 --- /dev/null +++ b/Dockerfile.staticcompiler @@ -0,0 +1,20 @@ +FROM julia:1.10 + +# installing C dependencies to build julia using StaticCompiler.jl +# adapted from stackoverflow https://askubuntu.com/a/1512328 +RUN --mount=type=cache,target=/var/cache/apt \ + --mount=type=cache,target=/var/lib/apt \ + apt -y update && apt -y install build-essential gcc libc-dev + +# Set work directory +WORKDIR /app +# Copy project files +COPY . . +# work inside staticcompiler subfolder +WORKDIR /app/staticcompiler +# Precompile packages + +RUN --mount=type=cache,target=/root/.julia \ + julia --project=. -e 'using Pkg; Pkg.instantiate(); Pkg.precompile()' +RUN --mount=type=cache,target=/root/.julia \ + julia --project=. staticcompile_rqatrend.jl \ No newline at end of file diff --git a/Project.toml b/Project.toml index d2c02e0..b9471f1 100644 --- a/Project.toml +++ b/Project.toml @@ -40,32 +40,45 @@ YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c" Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99" [compat] +AllocCheck = "0.2.2" +Aqua = "0.8.13" ArchGDAL = "0.10" ArgParse = "1" +BenchmarkTools = "1.6.0" ConstructionBase = "1" +Dates = "1.10" DimensionalData = "0.29" DiskArrayEngine = "0.1, 0.2" DiskArrayTools = "0.1" DiskArrays = "0.4" Distances = "0.10" +Distributed = "1.10" Distributions = "0.25" +Documenter = "1.12.0" Extents = "0.1" FillArrays = "1" GDAL = "1" GeoFormatTypes = "0.4" Glob = "1" KML = "0.2" +Libdl = "1.10" LinearAlgebra = "1.10" LoggingExtras = "1" Missings = "1" NetCDF = "0.12" +Pkg = "1.10" Proj = "1" +PythonCall = "0.9.25" +Random = "1.10" Rasters = "0.12,0.13, 0.14" RecurrenceAnalysis = "2" StaticArrays = "1" +StaticTools = "0.8.11" Statistics = "1.10" StatsBase = "0.34" -TestItems = "1.0.0" +Test = "1.10" +TestItemRunner = "1.0" +TestItems = "1.0" TimeseriesSurrogates = "2" UnicodePlots = "3" YAXArrayBase = "0.6, 0.7" @@ -75,11 +88,16 @@ julia = "1.11" [extras] AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a" +Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595" BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +PythonCall = "6099a3de-0909-46bc-b1f4-468b9a2dfc0d" Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +StaticTools = "86c06d3c-3f03-46de-9781-57580aa96d0a" Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a" +Libdl = "8f399da3-3557-5675-b5ff-fb832c97cbdb" [targets] -test = ["Test", "TestItemRunner", "Pkg", "Random", "AllocCheck", "BenchmarkTools"] +test = ["Test", "TestItemRunner", "Pkg", "Random", "AllocCheck", "BenchmarkTools", "Aqua", "Documenter", "StaticTools", "PythonCall", "Libdl"] diff --git a/README_DEVELOPER.md b/README_DEVELOPER.md new file mode 100644 index 0000000..5716f2e --- /dev/null +++ b/README_DEVELOPER.md @@ -0,0 +1,13 @@ +# Welcome to RQADeforestation.jl + +This README collects important information for local development of the package. + +# Local setup + +Install `just` into your system, following its README [installation instructions](https://github.com/casey/just?tab=readme-ov-file#installation). + +Then run +```bash +just init +``` +This will for instance setup pre-commit to enforce the standard Julia styling [blue](https://github.com/JuliaDiff/BlueStyle). diff --git a/justfile b/justfile index 7b51c23..449272d 100644 --- a/justfile +++ b/justfile @@ -1,6 +1,24 @@ +# just configurations +# setting tempdir to local path makes julia macro artifact"..." work +set tempdir := "./tmp" + +# global variables +docker_image_name := "rqatest" + default: just --list +init: + #!/usr/bin/env bash + set -euxo pipefail + # setup pre-commit hooks via pythons uv tooling manager + curl -LsSf https://astral.sh/uv/install.sh | sh + source ~/.local/bin/env + uv tool install pre-commit + uvx pre-commit install + # the julia formatting hook needs JuliaFormatter installed globally + julia -e 'import Pkg; Pkg.add("JuliaFormatter")' + # create precompile statements used for `just packagecompile` precompilestatements: julia --project -e 'import Pkg; Pkg.test(julia_args=`--trace-compile=packagecompiler/precompile_statements.jl`)' @@ -9,11 +27,11 @@ precompilestatements: packagecompile: #!/usr/bin/env -S julia --project=packagecompiler using PackageCompiler - if isdir("packagecompiler/app") + if isdir("packagecompiler/app") rm("packagecompiler/app.backup", recursive=true, force=true) mv("packagecompiler/app", "packagecompiler/app.backup") end - PackageCompiler.create_app(".", "packagecompiler/app"; + PackageCompiler.create_app(".", "packagecompiler/app"; precompile_statements_file="packagecompiler/precompile_statements.jl", # see https://github.com/JuliaLang/PackageCompiler.jl/issues/994 include_lazy_artifacts=true, @@ -23,19 +41,50 @@ packagecompile: # lets have an easy check whether this actually worked touch("packagecompiler/app/done") -# test the app `packagecompiler/app/RQADeforestation` with testdata, writing data to `test/tmp/apptestdata` -testapp: +# downloads the Artifact test data to tmp/apptestdata +download-test-data $tmpdir="tmp/apptestdata": + #!/usr/bin/env -S julia --project + import Pkg: Artifacts.@artifact_str + testdatapath = artifact"rqatestdata/RQADeforestationTestData-2.0" + testdir = ENV["tmpdir"] + rm(testdir, recursive=true, force=true) + mkpath(testdir) + cp(testdatapath, joinpath(testdir, "in")) + +# test the app `packagecompiler/app/RQADeforestation` with testdata, writing data to `tmp/apptestdata` +test-app $tmpdir="tmp/apptestdata": (download-test-data tmpdir) + #!/usr/bin/env bash + set -euxo pipefail + indir="$tmpdir/in" + outdir="$tmpdir/out.zarr" + ./packagecompiler/app/bin/RQADeforestation --tile E051N018T3 --continent EU --start-date "2021-01-01" --end-date "2022-01-01" --in-dir "$indir" --out-dir "$outdir" + +# builds the standard docker +build-docker: + docker build -t "{{docker_image_name}}" -f Dockerfile . + +# tests the build docker image using the Artifact test data, writing data to `tmp/apptestdata` +test-docker $tmpdir="tmp/apptestdata": (download-test-data tmpdir) + #!/usr/bin/env bash + set -euxo pipefail + indir="$tmpdir/in" + outdir="$tmpdir/out.zarr" + docker run --user $(id -u):$(id -g) --rm -v "$PWD/$tmpdir":"/$tmpdir" "{{docker_image_name}}" --tile E051N018T3 --continent EU --start-date "2021-01-01" --end-date "2022-01-01" --in-dir "/$indir" --out-dir "/$outdir" + +# compiles rqatrend to its own c-library using StaticCompiler.jl +staticcompile: #!/usr/bin/env bash - cd test - indir="tmp/apptestdata/in" - outdir="tmp/apptestdata/out.zarr" - julia --project -e ' - import Pkg: Artifacts.@artifact_str, ensure_artifact_installed - ensure_artifact_installed("rqatestdata", "Artifacts.toml") - testdatapath = joinpath(artifact"rqatestdata", "RQADeforestationTestData-1.0") - testdir = dirname(ARGS[1]) - rm(testdir, recursive=true, force=true) - mkpath(testdir) - cp(testdatapath, ARGS[1]) - ' -- "$indir" - ../packagecompiler/app/bin/RQADeforestation --tile E051N018T3 --continent EU --in-dir "$indir" --out-dir "$outdir" \ No newline at end of file + set -euxo pipefail + if [ -d staticcompiler/lib ]; then + if [ -d staticcompiler/lib.backup ]; then + rm -rf staticcompiler/lib.backup + fi + mv staticcompiler/lib staticcompiler/lib.backup + fi + # using progress plain is important as staticcompiler.jl + # outputs warnings instead of errors if things may not work + docker build --progress=plain -t temp-image -f Dockerfile.staticcompiler . + docker create --name temp-container temp-image + docker cp temp-container:/app/staticcompiler/lib "$PWD/staticcompiler/lib" + docker rm temp-container + docker rmi temp-image diff --git a/packagecompiler/Manifest.toml b/packagecompiler/Manifest.toml new file mode 100644 index 0000000..6d0d66b --- /dev/null +++ b/packagecompiler/Manifest.toml @@ -0,0 +1,169 @@ +# This file is machine-generated - editing it directly is not advised + +julia_version = "1.11.2" +manifest_format = "2.0" +project_hash = "9ddee98f4175ce3934d72d17e69fc38f7697d471" + +[[deps.ArgTools]] +uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f" +version = "1.1.2" + +[[deps.Artifacts]] +uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33" +version = "1.11.0" + +[[deps.Base64]] +uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f" +version = "1.11.0" + +[[deps.Dates]] +deps = ["Printf"] +uuid = "ade2ca70-3891-5945-98fb-dc099432e06a" +version = "1.11.0" + +[[deps.Downloads]] +deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"] +uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6" +version = "1.6.0" + +[[deps.FileWatching]] +uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee" +version = "1.11.0" + +[[deps.Glob]] +git-tree-sha1 = "97285bbd5230dd766e9ef6749b80fc617126d496" +uuid = "c27321d9-0574-5035-807b-f59d2c89b15c" +version = "1.3.1" + +[[deps.LazyArtifacts]] +deps = ["Artifacts", "Pkg"] +uuid = "4af54fe1-eca0-43a8-85a7-787d91b784e3" +version = "1.11.0" + +[[deps.LibCURL]] +deps = ["LibCURL_jll", "MozillaCACerts_jll"] +uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21" +version = "0.6.4" + +[[deps.LibCURL_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"] +uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0" +version = "8.6.0+0" + +[[deps.LibGit2]] +deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"] +uuid = "76f85450-5226-5b5a-8eaa-529ad045b433" +version = "1.11.0" + +[[deps.LibGit2_jll]] +deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"] +uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5" +version = "1.7.2+0" + +[[deps.LibSSH2_jll]] +deps = ["Artifacts", "Libdl", "MbedTLS_jll"] +uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8" +version = "1.11.0+1" + +[[deps.Libdl]] +uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb" +version = "1.11.0" + +[[deps.Logging]] +uuid = "56ddb016-857b-54e1-b83d-db4d58db5568" +version = "1.11.0" + +[[deps.Markdown]] +deps = ["Base64"] +uuid = "d6f4376e-aef5-505a-96c1-9c027394607a" +version = "1.11.0" + +[[deps.MbedTLS_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1" +version = "2.28.6+0" + +[[deps.MozillaCACerts_jll]] +uuid = "14a3606d-f60d-562e-9121-12d972cd8159" +version = "2023.12.12" + +[[deps.NetworkOptions]] +uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908" +version = "1.2.0" + +[[deps.PackageCompiler]] +deps = ["Artifacts", "Glob", "LazyArtifacts", "Libdl", "Pkg", "Printf", "RelocatableFolders", "TOML", "UUIDs", "p7zip_jll"] +git-tree-sha1 = "5d13e5b70011762b74f86fc08385303589f80272" +uuid = "9b87118b-4619-50d2-8e1e-99f35a4d4d9d" +version = "2.2.0" + +[[deps.Pkg]] +deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "Random", "SHA", "TOML", "Tar", "UUIDs", "p7zip_jll"] +uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f" +version = "1.11.0" + + [deps.Pkg.extensions] + REPLExt = "REPL" + + [deps.Pkg.weakdeps] + REPL = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb" + +[[deps.Printf]] +deps = ["Unicode"] +uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7" +version = "1.11.0" + +[[deps.Random]] +deps = ["SHA"] +uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c" +version = "1.11.0" + +[[deps.RelocatableFolders]] +deps = ["SHA", "Scratch"] +git-tree-sha1 = "ffdaf70d81cf6ff22c2b6e733c900c3321cab864" +uuid = "05181044-ff0b-4ac5-8273-598c1e38db00" +version = "1.0.1" + 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= ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "d5a767a3bb77135a99e433afe0eb14cd7f6914c3" +uuid = "1317d2d5-d96f-522e-a858-c73665f53c3e" +version = "2022.0.0+0" + +[[deps.p7zip_jll]] +deps = ["Artifacts", "Libdl"] +uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0" +version = "17.4.0+2" + +[[deps.snappy_jll]] +deps = ["Artifacts", "JLLWrappers", "Libdl"] +git-tree-sha1 = "ca88363dd41d2547f52118287dd34dbbc14f3eb7" +uuid = "fe1e1685-f7be-5f59-ac9f-4ca204017dfd" +version = "1.2.3+0" diff --git a/staticcompiler/Project.toml b/staticcompiler/Project.toml new file mode 100644 index 0000000..7aa14bb --- /dev/null +++ b/staticcompiler/Project.toml @@ -0,0 +1,7 @@ +[deps] +BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf" +GPUCompiler = "61eb1bfa-7361-4325-ad38-22787b887f55" +LoopVectorization = "bdcacae8-1622-11e9-2a5c-532679323890" +RQADeforestation = "3f1d9318-18cc-4ffd-9937-04025ce33b74" +StaticCompiler = "81625895-6c0f-48fc-b932-11a18313743c" +StaticTools = "86c06d3c-3f03-46de-9781-57580aa96d0a" diff --git a/staticcompiler/lib/rqatrend.o b/staticcompiler/lib/rqatrend.o new file mode 100644 index 0000000..e8d29ae Binary files /dev/null and b/staticcompiler/lib/rqatrend.o differ diff --git a/staticcompiler/lib/rqatrend.so b/staticcompiler/lib/rqatrend.so new file mode 100755 index 0000000..c818baf Binary files /dev/null and b/staticcompiler/lib/rqatrend.so differ diff --git a/staticcompiler/staticcompile_rqatrend.jl b/staticcompiler/staticcompile_rqatrend.jl new file mode 100644 index 0000000..e0bd1b2 --- /dev/null +++ b/staticcompiler/staticcompile_rqatrend.jl @@ -0,0 +1,30 @@ +using RQADeforestation: rqatrend_impl +using LoopVectorization +using StaticCompiler +using StaticTools +using Base: RefValue + +@inline function rqatrend(data::MallocVector, thresh::Float64, border::Int, theiler::Int) + @inline rqatrend_impl(data; thresh=thresh, border=border, theiler=theiler) +end + +@inline function rqatrend_inplace(results::MallocVector, data::MallocMatrix, thresh::Float64, border::Int, theiler::Int) + # we cannot use LoopVectorization.@turbo because of keyword arguments + # see https://github.com/JuliaSIMD/LoopVectorization.jl/pull/494 + for col in eachindex(results) # col in indices((results, data), (1, 2)) + results[col] = @inline rqatrend_impl(data[:, col]; thresh=thresh, border=border, theiler=theiler) + end + return 0 +end + +# this will let us accept pointers to MallocArrays +rqatrend(data::Ref, thresh::Float64, border::Int, theiler::Int) = rqatrend(data[], thresh, border, theiler) +rqatrend_inplace(results::Ref, data::Ref, thresh::Float64, border::Int, theiler::Int) = rqatrend_inplace(results[], data[], thresh, border, theiler) + +funcs_and_types = ( + (rqatrend, (RefValue{MallocVector{Float64}}, Float64, Int, Int)), + (rqatrend_inplace, (RefValue{MallocVector{Float64}}, RefValue{MallocMatrix{Float64}}, Float64, Int, Int)), +) + +# sudo apt install gcc libc-dev +compile_shlib(funcs_and_types, "./lib/", filename="rqatrend") \ No newline at end of file diff --git a/test/qualityassurance.jl b/test/qualityassurance.jl new file mode 100644 index 0000000..6732307 --- /dev/null +++ b/test/qualityassurance.jl @@ -0,0 +1,15 @@ +@testitem "qualityassurance" begin + using Aqua + using Dates + using ArgParse + + Aqua.test_all( + RQADeforestation; + stale_deps=(;ignore=[:Proj, :TimeseriesSurrogates, :KML]), + piracies=(;treat_as_own=[ArgParse.parse_item]), + # persistent_tasks tests time of importing the package, + # which is not nice, because of all the drivers load on their __init__ time + # hence we turn it off + persistent_tasks=false, + ) +end \ No newline at end of file diff --git a/test/runtests.jl b/test/runtests.jl index 2380de7..b413803 100644 --- a/test/runtests.jl +++ b/test/runtests.jl @@ -1,2 +1,11 @@ +using RQADeforestation + +# doctests do not run as testitem as of now, hence it is included here +using Documenter +DocMeta.setdocmeta!( + RQADeforestation, :DocTestSetup, :(using RQADeforestation); recursive=true +) +doctest(RQADeforestation) + using TestItemRunner @run_package_tests diff --git a/test/staticcompilation.jl b/test/staticcompilation.jl new file mode 100644 index 0000000..0ed14e9 --- /dev/null +++ b/test/staticcompilation.jl @@ -0,0 +1,149 @@ +@testitem "staticcompilation julia" begin + + using RQADeforestation: rqatrend_impl + using StaticTools + using BenchmarkTools + using Libdl + import Random + Random.seed!(1234) + + + filename = joinpath(dirname(dirname(@__FILE__)), "staticcompiler", "lib", "rqatrend.$(Libdl.dlext)") + + if isfile(filename) + x = 1:0.01:30 + y = sin.(x) + 0.1x + rand(length(x)) + + trend_truth = -0.11125611687816017 + trend_impl = rqatrend_impl(y, thresh=0.5, border=10, theiler=1) + @test trend_impl == trend_truth + # @benchmark rqatrend_impl($y, thresh=0.5, border=10, theiler=1) + + Libdl.dlopen(filename) do lib + + # test running single c-compiled version + + rqatrend_compiled = Libdl.dlsym(lib, :rqatrend) + MallocArray(Float64, length(x)) do my + my .= y + + # trend_malloc = rqatrend_static(my, #=thresh=# 0.5::Float64, #=border=# 10::Int, #=theiler=# 1::Int) + # @show trend_malloc + + ry = Ref(my) + + trend_ccall = ccall(rqatrend_compiled, Float64, (Ptr{Nothing}, Float64, Int, Int), pointer_from_objref(ry), #=thresh=# 0.5, #=border=# 10, #=theiler=# 1) + @test trend_ccall == trend_truth + # @benchmark ccall($rqatrend_compiled, Float64, (Ptr{Nothing}, Float64, Int, Int), $(pointer_from_objref(ry)), #=thresh=# 0.5, #=border=# 10, #=theiler=# 1) + + # second approach how to deal with pointers (seems more safe) + # and both similarly slow when benchmarked from Julia... + GC.@preserve ry begin + py = pointer_from_objref(ry) + trend_ptrcall = @ptrcall rqatrend_compiled(py::Ptr{Nothing}, #=thresh=# 0.5::Float64, #=border=# 10::Int, #=theiler=# 1::Int)::Float64 + @test trend_ptrcall == trend_truth + # @benchmark @ptrcall $rqatrend_compiled($py::Ptr{Nothing}, #=thresh=# 0.5::Float64, #=border=# 10::Int, #=theiler=# 1::Int)::Float64 + end + end + + # test running the same multiple on C level + + rqatrend_inplace_compiled = Libdl.dlsym(lib, :rqatrend_inplace) + n = 5 + MallocArray(Float64, n) do mresults + MallocArray(Float64, length(x), n) do mdata + for i in 1:n + mdata[:, i] .= y + end + + rresults = Ref(mresults) + rdata = Ref(mdata) + + return_ccall = ccall(rqatrend_inplace_compiled, Int, (Ptr{Nothing}, Ptr{Nothing}, Float64, Int, Int), pointer_from_objref(rresults), pointer_from_objref(rdata), #=thresh=# 0.5, #=border=# 10, #=theiler=# 1) + @test return_ccall == 0 + @test all(mresults .== trend_truth) + # @benchmark ccall($rqatrend_inplace_compiled, Int, (Ptr{Nothing}, Ptr{Nothing}, Float64, Int, Int), $(pointer_from_objref(rresults)), $(pointer_from_objref(rdata)), #=thresh=# 0.5, #=border=# 10, #=theiler=# 1) + + # second approach how to deal with pointers (seems more safe) + # and both similarly slow when benchmarked from Julia... + GC.@preserve rresults rdata begin + presults = pointer_from_objref(rresults) + pdata = pointer_from_objref(rdata) + + return_ptrcall = @ptrcall rqatrend_inplace_compiled(presults::Ptr{Nothing}, pdata::Ptr{Nothing}, #=thresh=# 0.5::Float64, #=border=# 10::Int, #=theiler=# 1::Int)::Int + @test return_ptrcall == 0 + @test all(mresults .== trend_truth) + # @benchmark @ptrcall $rqatrend_inplace_compiled($presults::Ptr{Nothing}, $pdata::Ptr{Nothing}, #=thresh=# 0.5::Float64, #=border=# 10::Int, #=theiler=# 1::Int)::Int + end + end + end + end + end +end + +@testitem "staticcompilation python" begin + using PythonCall + using Libdl + filename = joinpath(dirname(dirname(@__FILE__)), "staticcompiler", "lib", "rqatrend.$(Libdl.dlext)") + + if isfile(filename) + pythoncode = """ + import ctypes as ct + import numpy as np + np.random.seed(1234) + + class MallocVector(ct.Structure): + _fields_ = [("pointer", ct.c_void_p), + ("length", ct.c_int64), + ("s1", ct.c_int64)] + + class MallocMatrix(ct.Structure): + _fields_ = [("pointer", ct.c_void_p), + ("length", ct.c_int64), + ("s1", ct.c_int64), + ("s2", ct.c_int64)] + + def mvptr(A): + ptr = A.ctypes.data_as(ct.c_void_p) + a = MallocVector(ptr, ct.c_int64(A.size), ct.c_int64(A.shape[0])) + return ct.byref(a) + + def mmptr(A): + ptr = A.ctypes.data_as(ct.c_void_p) + a = MallocMatrix(ptr, ct.c_int64(A.size), ct.c_int64(A.shape[1]), ct.c_int64(A.shape[0])) + return ct.byref(a) + + filename = "$filename" + lib = ct.CDLL(filename) + + x = np.arange(1, 30, step=0.01) + y = np.sin(x) + 0.1 * x + np.random.rand(len(x)) + py = mvptr(y) + + # arguments: data, threshhold, border, theiler + lib.rqatrend.argtypes = (ct.POINTER(MallocVector), ct.c_double, ct.c_int64, ct.c_int64) + lib.rqatrend.restype = ct.c_double + result_single = lib.rqatrend(py, 0.5, 10, 1) + + n = 5 + result_several = np.ones(n) + p_result_several = mvptr(result_several) + data = np.tile(y, (n, 1)) + pdata = mmptr(data) + + # arguments: result_vector, data, threshhold, border, theiler + lib.rqatrend_inplace.argtypes = (ct.POINTER(MallocVector), ct.POINTER(MallocMatrix), ct.c_double, ct.c_int64, ct.c_int64) + return_value = lib.rqatrend_inplace(p_result_several, pdata, 0.5, 10, 1) + """ + + results = pyexec( + @NamedTuple{n::Int, result_single::Float64, return_value::Int, result_several::Vector{Float64}}, + pythoncode, + Main, + ) + target_result = -0.11931512705232977 + @test isapprox(results.result_single, target_result) + @test results.return_value == 0 + @test all(isapprox.(results.result_several, fill(target_result, (results.n,)))) + end +end \ No newline at end of file diff --git a/test/testdata.jl b/test/testdata.jl index 72e15ab..2b548a1 100644 --- a/test/testdata.jl +++ b/test/testdata.jl @@ -1,9 +1,7 @@ @testitem "testdata main" begin - import Pkg: Artifacts.@artifact_str, ensure_artifact_installed - - ensure_artifact_installed("rqatestdata", "Artifacts.toml") - testdatapath = joinpath(artifact"rqatestdata", "RQADeforestationTestData-2.0") + import Pkg: Artifacts.@artifact_str + testdatapath = artifact"rqatestdata/RQADeforestationTestData-2.0" testdir = tempname() rm(testdir, recursive=true, force=true) @@ -31,10 +29,8 @@ end @testitem "testdata julia_main" begin - import Pkg: Artifacts.@artifact_str, ensure_artifact_installed - - ensure_artifact_installed("rqatestdata", "Artifacts.toml") - testdatapath = joinpath(artifact"rqatestdata", "RQADeforestationTestData-2.0") + import Pkg: Artifacts.@artifact_str + testdatapath = artifact"rqatestdata/RQADeforestationTestData-2.0" testdir = tempname() rm(testdir, recursive=true, force=true)