Fix main function (#91)

* Fix missing year variable

* Fix missing output after calling julia_main

* Update extrema tests

* Fix indir path

* Adjust time span

* Re add test julia_main

* Disentangle test dirs

* Fix entangled test dirs in matrix CI

* Fix default arg

Author: danlooo

src/main.jl

@@ -29,7 +29,7 @@ ArgParse.parse_item(::Type{Date}, x::AbstractString) = Date(x)
 
     "--orbit", "-o"
     help = "One of: Orbit number, 'A' for ascending, 'D' for descending, '*' for all orbits"
-    default = "A"
+    default = "D"
 
     "--out-dir", "-d"
     help = "Path to output zarr dataset"
@@ -53,7 +53,7 @@ ArgParse.parse_item(::Type{Date}, x::AbstractString) = Date(x)
 
     "--folders", "--folder"
     help = "subfolders taken into account"
-    default = ["V01R01", "V0M2R4", "V1M0R1", "V1M1R1", "V1M1R2"]
+    default = ["V1M0R1", "V1M1R1", "V1M1R2"]
     arg_type = String
     nargs = '*'
 end
@@ -98,17 +98,17 @@ function main(;
     corruptedfiles = "corrupted_tiles.txt"
     # TODO save the corrupt files to a txt for investigation
     for tilefolder in tiles
-
         filenamelist = [glob("$(sub)/*$(continent)*20M/$(tilefolder)/*$(polarisation)_$(orbit)*.tif", indir) for sub in folders]
         allfilenames = collect(Iterators.flatten(filenamelist))
 
         relorbits = unique([split(basename(x), "_")[5][2:end] for x in allfilenames])
         @show relorbits
+
         for relorbit in relorbits
             filenames = allfilenames[findall(contains("$(relorbit)_E"), allfilenames)]
             @time cube = gdalcube(filenames, stack)
 
-            path = joinpath(YAXDefaults.workdir[], "$(tilefolder)_rqatrend_$(polarisation)_$(orbit)$(relorbit)_thresh_$(threshold)_year_$(y)")
+            path = joinpath(YAXDefaults.workdir[], "$(tilefolder)_rqatrend_$(polarisation)_$(orbit)$(relorbit)_thresh_$(threshold)")
             @show path
             ispath(path * ".done") && continue
             ispath(path * "_zerotimesteps.done") && continue

test/testdata.jl

@@ -1,11 +1,42 @@
 
+@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")
+
+    testdir = tempname()
+    rm(testdir, recursive=true, force=true)
+    mkpath(testdir)
+    outdir = "$testdir/out.zarr"
+    indir = "$testdir/in"
+    cp(testdatapath, indir)
+
+    using Zarr
+    using YAXArrays
+    using Dates
+    RQADeforestation.main(;
+        tiles=["E051N018T3"],
+        continent="EU",
+        indir=indir,
+        start_date=Date("2021-01-01"),
+        end_date=Date("2022-01-01"),
+        outdir=outdir
+    )
+    a = open_dataset(outdir * "/E051N018T3_rqatrend_VH_D022_thresh_3.0.zarr").layer
+
+    @test size(a) == (50, 74)
+    @test minimum(a) < 0
+    @test maximum(a) > 0
+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")
 
-    testdir = "tmp/testdata"
+    testdir = tempname()
     rm(testdir, recursive=true, force=true)
     mkpath(testdir)
     outdir = "$testdir/out.zarr"
@@ -17,7 +48,7 @@
         "--tile", "E051N018T3",
         "--continent", "EU",
         "--start-date", "2021-01-01",
-        "--end-date", "2021-12-31",
+        "--end-date", "2022-01-01",
         "--in-dir", indir,
         "--out-dir", outdir,
     ])
@@ -26,4 +57,6 @@
     # test short cut implementation using cache files
     RQADeforestation.julia_main()
     copy!(ARGS, OLD_ARGS)
+
+    @test outdir |> readdir |> length > 1
 end