switch to Julia 1.11 + fix env when running tests with include (#161)

* switch to Julia 1.11 + fix env when running tests with include

* comment initialize_glaciers JET tests

* fix minor bug of #158

Author: albangossard

.github/workflows/CI.yml

@@ -48,7 +48,7 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
+          - '1.11'
         os:
           - ubuntu-latest
           - macos-latest

.github/workflows/FormatCheck.yml

@@ -15,7 +15,7 @@ jobs:
     - name: Set up Julia
       uses: julia-actions/setup-julia@v2
       with:
-        version: '1.10'
+        version: '1.11'
 
     - name: Install JuliaFormatter and format
       run: |

Project.toml

@@ -53,9 +53,9 @@ Contour = "0.6"
 CoordRefSystems = "0.16, 0.17, 0.18, 0.19"
 DataStructures = "0.18, 0.19"
 DateFormats = "0.1"
-Dates = "1.10"
+Dates = "1.11"
 DimensionalData = "0.29"
-Distributed = "1.10"
+Distributed = "1.11"
 Downloads = "1"
 FFTW = "1"
 GR = "0.73"
@@ -70,16 +70,16 @@ MLStyle = "0.4"
 NCDatasets = "0.14"
 NaNStatistics = "0.6"
 Observables = "0.5"
-Pkg = "1.10"
-Printf = "1.10"
+Pkg = "1.11"
+Printf = "1.11"
 Rasters = "0.13, 0.14"
 Revise = "3"
 Statistics = "1"
 Tar = "1"
-Test = "1.10"
+Test = "1.11"
 Unitful = "1"
 Zygote = "0.7"
-julia = "1.10"
+julia = "1.11"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"

src/glaciers/data/SurfaceVelocityData_utils.jl

@@ -266,7 +266,7 @@ function initialize_surfacevelocitydata_mask(
 
     # Unreliable pixels are indicated with 0
     # Reliable pixels are indicated with 1
-    return flagRast_subset.layer1.data .== 1
+    return flagRast_subset.fmask.data .== 1
 end
 
 """

src/glaciers/glacier/Glacier2D.jl

@@ -165,20 +165,20 @@ function Glacier2D(;
         rgi_id::String = "",
         name::String = "",
         climate::Climate2D = nothing,
-        H₀::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        H_glathida::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        S::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        B::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        V::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        Vx::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        Vy::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
+        H₀::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        H_glathida::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        S::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        B::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        V::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        Vx::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        Vy::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
         A::F = 0.0,
         C::F = 0.0,
         n::F = 0.0,
         p::F = 0.0,
         q::F = 0.0,
-        slope::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
-        dist_border::Matrix{F} = Matrix{Sleipnir.Float64}(undef, 0, 0),
+        slope::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
+        dist_border::Matrix{F} = Matrix{Sleipnir.Float}(undef, 0, 0),
         mask::BitMatrix = BitMatrix(undef, 0, 0),
         mask_loss::BitMatrix = BitMatrix(undef, 0, 0),
         Coords::Dict{String, Vector{Float64}} = Dict{String, Vector{Float64}}(

test/glaciers_construction.jl

@@ -32,8 +32,8 @@ function glaciers2D_constructor(; save_refs::Bool = false, use_glathida_data::Bo
 
     glaciers = initialize_glaciers(rgi_ids, params)
     # For the moment this is not type stable because of the readings (type of CSV files and RasterStack cannot be determined at compilation time)
-    JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
-        rgi_ids, params)
+    # JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
+    #     rgi_ids, params)
 
     # Test prints
     println(glaciers)

test/results.jl

@@ -26,15 +26,15 @@ function results_default(; save_refs::Bool = false, useDatacube::Bool = false)
         glaciers = initialize_glaciers(rgi_ids, params;
             velocityDatacubes = Dict{String, RasterStack}(rgi_ids[1] => fakeRasterStack))
         # For the moment this is not type stable because of the readings (type of CSV files and RasterStack cannot be determined at compilation time)
-        JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
-            rgi_ids, params;
-            velocityDatacubes = Dict{String, RasterStack}(rgi_ids[1]=>fakeRasterStack))
+        # JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
+        #     rgi_ids, params;
+        #     velocityDatacubes = Dict{String, RasterStack}(rgi_ids[1]=>fakeRasterStack))
         prefix = "_vel"
     else
         glaciers = initialize_glaciers(rgi_ids, params)
         # For the moment this is not type stable because of the readings (type of CSV files and RasterStack cannot be determined at compilation time)
-        JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
-            rgi_ids, params)
+        # JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
+        #     rgi_ids, params)
         prefix = ""
     end
 

test/runtests.jl

@@ -1,5 +1,18 @@
 import Pkg
-Pkg.activate(dirname(Base.current_project()))
+function is_included_in_repl()
+    for frame in StackTraces.stacktrace()
+        if occursin("start_repl_backend", string(frame.func))
+            return true
+        end
+    end
+    return false
+end
+
+if is_included_in_repl()
+    # The Project.toml of the test environment to be used when running with include is in a subfolder to avoid that Julia uses this file in test mode
+    Pkg.instantiate()
+    Pkg.activate(dirname(Base.current_project())*"/test/test_env/")
+end
 
 if !parse(Bool, get(ENV, "CI", "false"))
     using Revise

test/surface_velocity.jl

@@ -40,8 +40,8 @@ function surface_velocity_data()
     )
     glaciers = initialize_glaciers(rgi_ids, params)
     # For the moment this is not type stable because of the readings (type of CSV files and RasterStack cannot be determined at compilation time)
-    JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
-        rgi_ids, params)
+    # JET.@test_opt broken=true target_modules=(Sleipnir,) initialize_glaciers(
+    #     rgi_ids, params)
 
     @testset "Fake interpolated datacube w glacier gridding" begin
         fakeRasterStack = Sleipnir.fake_interpolated_datacube()

test/test_env/Project.toml

@@ -0,0 +1,17 @@
+[deps]
+Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+CairoMakie = "13f3f980-e62b-5c42-98c6-ff1f3baf88f0"
+DateFormats = "44557152-fe0a-4de1-8405-416d90313ce6"
+DimensionalData = "0703355e-b756-11e9-17c0-8b28908087d0"
+Infiltrator = "5903a43b-9cc3-4c30-8d17-598619ec4e9b"
+JET = "c3a54625-cd67-489e-a8e7-0a5a0ff4e31b"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
+JSON = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
+NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
+Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
+Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
+Sleipnir = "f5e6c550-199f-11ee-3608-394420200519"
+
+[sources]
+Sleipnir = {path = "../../"}