Add mock rqatrend

Project.toml

@@ -39,10 +39,8 @@ YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"
 Zarr = "0a941bbe-ad1d-11e8-39d9-ab76183a1d99"
 
 [compat]
-AllocCheck = "0.2.0"
 ArchGDAL = "0.10"
 ArgParse = "1"
-BenchmarkTools = "1.6.0"
 CairoMakie = "0.12"
 ConstructionBase = "1"
 DimensionalData = "0.29"
@@ -61,7 +59,6 @@ LoggingExtras = "1"
 Missings = "1"
 NetCDF = "0.12"
 Proj = "1"
-Random = "1.10.0, 1.11.0"
 Rasters = "0.12,0.13"
 RecurrenceAnalysis = "2"
 Statistics = "1"
@@ -72,11 +69,3 @@ YAXArrays = "0.5"
 Zarr = "0.9"
 julia = "1.10"
 
-[extras]
-AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
-BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
-
-[targets]
-test = ["Test", "AllocCheck", "BenchmarkTools", "Random"]

src/RQADeforestation.jl

@@ -16,10 +16,10 @@ include("analysis.jl")  # TODO what is still needed from analysis now that rqatr
 include("timestats.jl")
 
 
-function main(tiles = ["E048N018T3"]; pol="VH", orbit="*", thresh=3.0)
+function main(tiles=["E048N018T3"]; pol="VH", orbit="*", thresh=3.0)
     indir = "/eodc/products/eodc.eu/S1_CSAR_IWGRDH/SIG0/"
     continent = "EU"
-    folders = ["V01R01","V0M2R4", "V1M0R1", "V1M1R1", "V1M1R2"]
+    folders = ["V01R01", "V0M2R4", "V1M0R1", "V1M1R1", "V1M1R2"]
     corruptedfiles = "corrupted_tiles.txt"
     # TODO save the corrupt files to a txt for investigation
     for tilefolder in tiles
@@ -32,35 +32,35 @@ function main(tiles = ["E048N018T3"]; pol="VH", orbit="*", thresh=3.0)
         relorbits = unique([split(basename(x), "_")[5][2:end] for x in allfilenames])
         @show relorbits
         for relorbit in relorbits
-            for y in [2018,2019,2020,2021,2022, 2023]
+            for y in [2018, 2019, 2020, 2021, 2022, 2023]
 
-            filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
-            @time cube = gdalcube(filenames)
+                filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
+                @time cube = gdalcube(filenames)
 
                 path = joinpath(YAXDefaults.workdir[], "$(tilefolder)_rqatrend_$(pol)_$(relorbit)_thresh_$(thresh)_year_$(y)")
                 @show path
-                ispath(path*".done") && continue
-                ispath(path*"_zerotimesteps.done") && continue
+                ispath(path * ".done") && continue
+                ispath(path * "_zerotimesteps.done") && continue
 
-                tcube = cube[Time=Date(y-1, 7,1)..Date(y+1,7,1)]
+                tcube = cube[Time=Date(y - 1, 7, 1) .. Date(y + 1, 7, 1)]
                 @show size(cube)
                 @show size(tcube)
                 if size(tcube, Ti) == 0
-                    touch(path*"_zerotimesteps.done")
+                    touch(path * "_zerotimesteps.done")
                     continue
                 end
-            try
-                @time rqatrend(tcube; thresh, outpath=path * ".zarr", overwrite=true)
-            catch e 
-
-                if e.captured.ex isa ArchGDAL.GDAL.GDALError
-                    println("Found GDALError:")
-                    println(e.captured.ex.msg)
-                   continue
-                else 
-                    rethrow(e)
+                try
+                    @time rqatrend(tcube; thresh, outpath=path * ".zarr", overwrite=true)
+                catch e
+
+                    if e.captured.ex isa ArchGDAL.GDAL.GDALError
+                        println("Found GDALError:")
+                        println(e.captured.ex.msg)
+                        continue
+                    else
+                        rethrow(e)
+                    end
                 end
-            end
                 #=@everywhere begin
                     fname = "$(VERSION)_$(getpid())_$(time_ns()).heapsnapshot"
                     Profile.take_heap_snapshot(fname;streaming=true)

test/Artifacts.toml

@@ -0,0 +1,6 @@
+[rqatestdata]
+git-tree-sha1 = "ba3717febf44a19ce75ac4df625f8b0281077745"
+
+    [[rqatestdata.download]]
+    url = "https://github.com/meggart/RQADeforestationTestData/archive/refs/tags/v1.0.tar.gz"
+    sha256 = "2db9f0d215446a10588e2f3b9117e7f6c7a23ba3f369aa168714b6ba777fcfe9"

test/Project.toml

@@ -0,0 +1,10 @@
+[deps]
+AllocCheck = "9b6a8646-10ed-4001-bbdc-1d2f46dfbb1a"
+BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+Dates = "ade2ca70-3891-5945-98fb-dc099432e06a"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+YAXArrays = "c21b50f5-aa40-41ea-b809-c0f5e47bfa5c"

test/runtests.jl

@@ -2,10 +2,20 @@ using RQADeforestation
 using Test
 import AllocCheck
 import Random
+import Pkg: Artifacts.@artifact_str, ensure_artifact_installed
+using DimensionalData
+using YAXArrays
+using Dates
+using Random
+using Statistics
+
 Random.seed!(1234)
 
+ensure_artifact_installed("rqatestdata", "Artifacts.toml")
+testdatapath = joinpath(artifact"rqatestdata", "RQADeforestationTestData-1.0")
+
 @testset "RQADeforestation.jl" begin
-    # Write your tests here.
+    @test isfile(joinpath(testdatapath, "V01R01", "EQUI7_EU020M", "E051N018T3", "SIG0_20210818T051717__VH_D095_E051N018T3_EU020M_V01R01_S1BIWGRDH.tif"))
 
     x = 1:0.01:30
     y = sin.(x) + 0.1x + rand(length(x))
@@ -14,12 +24,25 @@ Random.seed!(1234)
     @test isempty(AllocCheck.check_allocs(RQADeforestation.rqatrend_impl, Tuple{Vector{Float64}}))
 
 
-    y2 = similar(y, Union{Float64, Missing})
+    y2 = similar(y, Union{Float64,Missing})
     copy!(y2, y)
-    y2[[1,4,10,20,33,65]] .= missing
+    y2[[1, 4, 10, 20, 33, 65]] .= missing
 
 
     @test isapprox(RQADeforestation.rqatrend_impl(y2; thresh=0.5), -0.11069045524336744)
     @test isempty(AllocCheck.check_allocs(RQADeforestation.rqatrend_impl, Tuple{Vector{Union{Float64,Missing}}}))
 
+    mock_axes = (
+        Ti(Date("2022-01-01"):Day(1):Date("2022-01-30")),
+        X(range(1, 10, length=10)),
+        Y(range(1, 5, length=15)),
+    )
+    mock_data = rand(30, 10, 15)
+    mock_props = Dict()
+    mock_cube = YAXArray(mock_axes, mock_data, mock_props)
+
+    mock_trend = rqatrend(mock_cube; thresh=0.5)
+    @test mock_trend.axes == (mock_cube.X, mock_cube.Y)
+    diff = abs(mean(mock_trend))
+    @test diff < 0.2
 end