Migrate to pure julia (#59)

* [WIP] update dependencies and remove pycall

* some cleaning and remove Sleipnir dependency

* making the tests pass locally

* code cleaning

* bump version

* update CI and Project.toml

.github/workflows/CI.yml

@@ -22,42 +22,14 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.10'
-        python: [3.9]
+          - '1.11'
         os:
           - ubuntu-latest
+          - macos-latest
         arch:
           - x64
     steps:
       - uses: actions/checkout@v2
-      - name: Set up Python 🐍 ${{ matrix.python }}
-        uses: actions/setup-python@v2
-        with:
-          python-version: ${{ matrix.python }}  
-      - name: Create environment with micromamba 🐍🖤
-        uses: mamba-org/setup-micromamba@v1
-        with: 
-          micromamba-version: '1.5.6-0'
-          environment-file: ./environment.yml
-          environment-name: oggm_env                # it is recommendable to add both name and yml file. 
-          init-shell: bash
-          cache-environment: true
-#           condarc-file: ./condarc.yml                # If necessary, we can include .condarc to configure environment
-      - name: Test creation of environment with micromamba 🔧🐍🖤
-        run: | 
-            which python
-            conda env export
-        shell: bash -el {0}
-      - name: Update certifi
-        run: | 
-            pip install --upgrade certifi
-        shell: bash -el {0}
-#       - name: Test OGGM installation 🔧🌎 
-#         run: pytest.oggm
-#         shell: bash -el {0}
-      - name: Set ENV Variables for PyCall.jl 🐍 📞
-        run: export PYTHON=/home/runner/micromamba/envs/oggm_env/bin/python
-        shell: bash -el {0}
       - uses: julia-actions/setup-julia@v1
         with:
           version: ${{ matrix.version }}
@@ -69,15 +41,18 @@ jobs:
         with:
           cache-registries: "true"
           cache-compiled: "true"
-      - uses: julia-actions/julia-buildpkg@v1
-        env:
-          PYTHON : /home/runner/micromamba/envs/oggm_env/bin/python
-          # The SSL certificate path can be readed from the action "Check Julia SSL certifications"
-          SSL_CERT_FILE: /etc/ssl/certs/ca-certificates.crt
-      - uses: julia-actions/julia-runtest@v1
-        env:
-          PYTHON : /home/runner/micromamba/envs/oggm_env/bin/python
-          SSL_CERT_FILE: /etc/ssl/certs/ca-certificates.crt
+      - name: Build Julia packages in Ubuntu
+        uses: julia-actions/julia-buildpkg@v1
+        if: matrix.os == 'ubuntu-latest'
+      - name: Build Julia packages in MacOS
+        uses: julia-actions/julia-buildpkg@v1
+        if: matrix.os == 'macos-latest'
+      - name: Run tests in Ubuntu
+        uses: julia-actions/julia-runtest@v1
+        if: matrix.os == 'ubuntu-latest'
+      - name: Run tests in MacOS
+        uses: julia-actions/julia-runtest@v1
+        if: matrix.os == 'macos-latest'
       - uses: julia-actions/julia-processcoverage@v1
       - uses: codecov/codecov-action@v3
         with:

Project.toml

@@ -1,7 +1,7 @@
 name = "Huginn"
 uuid = "9cb796e9-d0ea-421b-b37d-eb97bc1add55"
 authors = ["Jordi Bolibar <[email protected]>", "Facundo Sapienza <[email protected]>"]
-version = "0.6.0"
+version = "0.7.0"
 
 [deps]
 BenchmarkTools = "6e4b80f9-dd63-53aa-95a3-0cdb28fa8baf"
@@ -17,7 +17,6 @@ Pkg = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
 PlotThemes = "ccf2f8ad-2431-5c83-bf29-c5338b663b6a"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
-PyCall = "438e738f-606a-5dbb-bf0a-cddfbfd45ab0"
 Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
 Revise = "295af30f-e4ad-537b-8983-00126c2a3abe"
 Sleipnir = "f5e6c550-199f-11ee-3608-394420200519"
@@ -27,19 +26,18 @@ Tullio = "bc48ee85-29a4-5162-ae0b-a64e1601d4bc"
 [compat]
 BenchmarkTools = "1"
 CairoMakie = "0.11, 0.12"
-Infiltrator = "1"
+Infiltrator = "1.8"
 JLD2 = "0.4"
-Muninn = "0.3"
+Muninn = "0.4.0"
 Optimization = "3"
 OptimizationOptimJL = "0.3"
 OrdinaryDiffEq = "6"
 PlotThemes = "3"
 Plots = "1"
 ProgressMeter = "1"
-PyCall = "1"
 Reexport = "1"
 Revise = "3"
-Sleipnir = "0.6"
+Sleipnir = "0.7.0"
 Tullio = "0.3"
 julia = "1.7"
 

src/Huginn.jl

@@ -16,7 +16,6 @@ using CairoMakie
 import Pkg
 using Distributed
 using ProgressMeter
-using PyCall
 
 ### ODINN.jl dependencies ###
 using Reexport
@@ -30,28 +29,6 @@ cd(@__DIR__)
 const global root_dir::String = dirname(Base.current_project())
 const global root_plots::String = joinpath(root_dir, "plots")
 
-# ##############################################
-# ############ PYTHON LIBRARIES ##############
-# ##############################################
-
-# We either retrieve the reexported Python libraries from Sleipnir or we start from scratch
-const netCDF4::PyObject = isdefined(Sleipnir, :netCDF4) ? Sleipnir.netCDF4 : PyNULL()
-const cfg::PyObject = isdefined(Sleipnir, :cfg) ? Sleipnir.cfg : PyNULL()
-const utils::PyObject = isdefined(Sleipnir, :utils) ? Sleipnir.utils : PyNULL()
-const workflow::PyObject = isdefined(Sleipnir, :workflow) ? Sleipnir.workflow : PyNULL()
-const tasks::PyObject = isdefined(Sleipnir, :tasks) ? Sleipnir.tasks : PyNULL()
-const global_tasks::PyObject = isdefined(Sleipnir, :global_tasks) ? Sleipnir.global_tasks : PyNULL()
-const graphics::PyObject = isdefined(Sleipnir, :graphics) ? Sleipnir.graphics : PyNULL()
-const bedtopo::PyObject = isdefined(Sleipnir, :bedtopo) ? Sleipnir.bedtopo : PyNULL()
-const millan22::PyObject = isdefined(Sleipnir, :millan22) ? Sleipnir.millan22 : PyNULL()
-const MBsandbox::PyObject = isdefined(Sleipnir, :MBsandbox) ? Sleipnir.MBsandbox : PyNULL()
-const salem::PyObject = isdefined(Sleipnir, :salem) ? Sleipnir.salem : PyNULL()
-
-# Essential Python libraries
-const xr::PyObject = isdefined(Sleipnir, :xr) ? Sleipnir.xr : PyNULL()
-const rioxarray::PyObject = isdefined(Sleipnir, :rioxarray) ? Sleipnir.rioxarray : PyNULL()
-const pd::PyObject = isdefined(Sleipnir, :pd) ? Sleipnir.pd : PyNULL()
-
 # ##############################################
 # ############ HUGINN LIBRARIES ##############
 # ##############################################

src/parameters/SolverParameters.jl

@@ -38,40 +38,36 @@ function SolverParameters(;
     return solver_parameters
 end
 
-Base.:(==)(a::SolverParameters, b::SolverParameters) = a.solver == b.solver && a.reltol == b.reltol && a.step == b.step && 
+Base.:(==)(a::SolverParameters, b::SolverParameters) = a.solver == b.solver && a.reltol == b.reltol && a.step == b.step &&
                                       a.tstops == b.tstops && a.save_everystep == b.save_everystep && a.progress == b.progress &&
                                       a.progress_steps == b.progress_steps
 
 """
 Parameters(;
-        simulation::SimulationParameters = SimulationParameters()
-        physical::PhysicalParameters = PhysicalParameters()
-        OGGM::OGGMparameters = OGGMparameters(),
+        physical::PhysicalParameters = PhysicalParameters(),
+        simulation::SimulationParameters = SimulationParameters(),
         solver::SolverParameters = SolverParameters()
         )
 Initialize Huginn parameters
 
 Keyword arguments
 =================
-    
+
 """
 
 function Parameters(;
     physical::PhysicalParameters = PhysicalParameters(),
     simulation::SimulationParameters = SimulationParameters(),
-    OGGM::OGGMparameters = OGGMparameters(),
     solver::SolverParameters = SolverParameters()
-    ) 
+    )
 
     # Build the parameters based on all the subtypes of parameters
-    parameters = Sleipnir.Parameters(physical, simulation, OGGM,
+    parameters = Sleipnir.Parameters(physical, simulation,
                                      nothing, solver, nothing, nothing)
 
     if parameters.simulation.multiprocessing
         enable_multiprocessing(parameters)
     end
-
-    oggm_config(OGGM.working_dir; oggm_processes=OGGM.workers)
 
     return parameters
 end

src/setup/config.jl

@@ -1,35 +1,10 @@
 function __init__()
 
-    # Create structural folders if needed
-    OGGM_path = joinpath(homedir(), "Python/OGGM_data")
-    if !isdir(OGGM_path)
-        mkpath(OGGM_path)
-    end
-
-    try
-        # Only load Python packages if not previously loaded by Sleipnir
-        if cfg == PyNULL() && workflow == PyNULL() && utils == PyNULL() && MBsandbox == PyNULL() 
-            println("Initializing Python libraries in Huginn...")
-            copy!(netCDF4, pyimport("netCDF4"))
-            copy!(cfg, pyimport("oggm.cfg"))
-            copy!(utils, pyimport("oggm.utils"))
-            copy!(workflow, pyimport("oggm.workflow"))
-            copy!(tasks, pyimport("oggm.tasks"))
-            copy!(global_tasks, pyimport("oggm.global_tasks"))
-            copy!(graphics, pyimport("oggm.graphics"))
-            copy!(bedtopo, pyimport("oggm.shop.bedtopo"))
-            copy!(millan22, pyimport("oggm.shop.millan22"))
-            copy!(MBsandbox, pyimport("MBsandbox.mbmod_daily_oneflowline"))
-            copy!(salem, pyimport("salem"))
-            copy!(pd, pyimport("pandas"))
-            copy!(xr, pyimport("xarray"))
-            copy!(rioxarray, pyimport("rioxarray"))
-        end
-    catch e
-        @warn "It looks like you have not installed and/or activated the virtual Python environment. \n 
-        Please follow the guidelines in: https://github.com/ODINN-SciML/ODINN.jl#readme"
-        @warn exception=(e, catch_backtrace())
-    end
+    # # Create structural folders if needed
+    # OGGM_path = joinpath(homedir(), "Python/OGGM_data")
+    # if !isdir(OGGM_path)
+    #     mkpath(OGGM_path)
+    # end
 
 end
 

src/simulations/predictions/prediction_utils.jl

@@ -28,7 +28,7 @@ function batch_iceflow_PDE!(glacier_idx::I, simulation::Prediction) where {I <:
     params = simulation.parameters
     glacier = simulation.glaciers[glacier_idx]
 
-    glacier_id = isnothing(glacier.gdir) ? "unnamed" : glacier.rgi_id
+    glacier_id = isnothing(glacier.rgi_id) ? "unnamed" : glacier.rgi_id
     println("Processing glacier: ", glacier_id)
 
     # Initialize glacier ice flow model
@@ -130,7 +130,7 @@ function batch_iceflow_PDE(glacier_idx::I, simulation::Prediction) where {I <: I
     params = simulation.parameters
     glacier = simulation.glaciers[glacier_idx]
 
-    glacier_id = isnothing(glacier.gdir) ? "unnamed" : glacier.rgi_id
+    glacier_id = isnothing(glacier.rgi_id) ? "unnamed" : glacier.rgi_id
     println("Processing glacier: ", glacier_id)
 
     # Initialize glacier ice flow model (don't needed for out-of-place? maybe a simplified version?)

test/PDE_UDE_solve.jl

@@ -4,33 +4,32 @@ function pde_solve_test(; rtol::F, atol::F, save_refs::Bool=false, MB::Bool=fals
 
     println("PDE solving with MB = $MB")
     working_dir = joinpath(homedir(), "OGGM/Huginn_tests")
-
-    params = Parameters(OGGM = OGGMparameters(working_dir=working_dir,
-                                              multiprocessing=true,
-                                              workers=2,
-                                              ice_thickness_source = "Farinotti19"),
-                        simulation = SimulationParameters(use_MB=MB,
+
+    rgi_paths = get_rgi_paths()
+
+    params = Huginn.Parameters(simulation = SimulationParameters(use_MB=MB,
                                                           velocities=false,
                                                           tspan=(2010.0, 2015.0),
                                                           working_dir = Huginn.root_dir,
-                                                          test_mode = true),
+                                                          test_mode = true,
+                                                          rgi_paths = rgi_paths),
                         solver = SolverParameters(reltol=1e-12)
-                        ) 
+                        )
 
     ## Retrieving gdirs and climate for the following glaciers
-    ## Fast version includes less glacier to reduce the amount of downloaded files and computation time on GitHub CI  
+    ## Fast version includes less glacier to reduce the amount of downloaded files and computation time on GitHub CI
     if fast
-        rgi_ids = ["RGI60-11.03638", "RGI60-11.01450", "RGI60-08.00213", "RGI60-04.04351", "RGI60-01.02170"]
+        rgi_ids = ["RGI60-11.03638", "RGI60-11.01450"] #, "RGI60-08.00213", "RGI60-04.04351", "RGI60-01.02170"]
     else
         rgi_ids = ["RGI60-11.03638", "RGI60-11.01450", "RGI60-08.00213", "RGI60-04.04351", "RGI60-01.02170",
-        "RGI60-02.05098", "RGI60-01.01104", "RGI60-01.09162", "RGI60-01.00570", "RGI60-04.07051",                	
+        "RGI60-02.05098", "RGI60-01.01104", "RGI60-01.09162", "RGI60-01.00570", "RGI60-04.07051",
         "RGI60-07.00274", "RGI60-07.01323",  "RGI60-01.17316"]
     end
 
     if MB
-        model = Model(iceflow = SIA2Dmodel(params), mass_balance = TImodel1(params))
+        model = Huginn.Model(iceflow = SIA2Dmodel(params), mass_balance = TImodel1(params))
     else
-        model = Model(iceflow = SIA2Dmodel(params), mass_balance = nothing)
+        model = Huginn.Model(iceflow = SIA2Dmodel(params), mass_balance = nothing)
     end
 
     # We retrieve some glaciers for the simulation
@@ -50,7 +49,7 @@ function pde_solve_test(; rtol::F, atol::F, save_refs::Bool=false, MB::Bool=fals
             jldsave(joinpath(Huginn.root_dir, "test/data/PDE/PDE_refs_noMB.jld2"); prediction.results)
         end
     end
-    
+
     # Load reference values for the simulation
     if MB
         PDE_refs = load(joinpath(Huginn.root_dir, "test/data/PDE/PDE_refs_MB.jld2"))["results"]
@@ -86,7 +85,7 @@ function pde_solve_test(; rtol::F, atol::F, save_refs::Bool=false, MB::Bool=fals
         @test all(isapprox.(result.H[end], test_ref.H[end], rtol=rtol, atol=atol))
         @test all(isapprox.(result.Vx, test_ref.Vx, rtol=rtol, atol=vtol))
         @test all(isapprox.(result.Vy, test_ref.Vy, rtol=rtol, atol=vtol))
-        
+
         end # let
     end
     end
@@ -95,18 +94,18 @@ end
 function TI_run_test!(save_refs::Bool = false; rtol::F, atol::F) where {F <: AbstractFloat}
 
     working_dir = joinpath(homedir(), "OGGM/Huginn_tests")
-    params = Parameters(OGGM = OGGMparameters(working_dir=working_dir,
-                                              multiprocessing=true,
-                                              workers=2,
-                                              ice_thickness_source = "Farinotti19"),
-                        simulation = SimulationParameters(use_MB=true,
+
+    rgi_paths = get_rgi_paths()
+
+    params = Huginn.Parameters(simulation = SimulationParameters(use_MB=true,
                                                           velocities=false,
                                                           tspan=(2010.0, 2015.0),
                                                           working_dir = Huginn.root_dir,
-                                                          test_mode = true),
+                                                          test_mode = true,
+                                                          rgi_paths = rgi_paths),
                         solver = SolverParameters(reltol=1e-8)
-                        ) 
-    model = Model(iceflow = SIA2Dmodel(params), mass_balance = TImodel1(params))
+                        )
+    model = Huginn.Model(iceflow = SIA2Dmodel(params), mass_balance = TImodel1(params))
     rgi_ids = ["RGI60-11.03638"]
 
     glacier = initialize_glaciers(rgi_ids, params)[1]

test/halfar.jl

@@ -19,19 +19,22 @@ Arguments
 """
 function unit_halfar_test(; A, n, t₀, t₁, Δx, Δy, nx, ny, h₀, r₀, rtol=0.02, atol=1.0, distance_to_border=3, save_plot=false, inplace=true)
 
-    # Get parameters for a simulation 
-    parameters = Parameters(simulation=SimulationParameters(tspan=(t₀, t₁),
+    rgi_paths = get_rgi_paths()
+
+    # Get parameters for a simulation
+    parameters = Huginn.Parameters(simulation=SimulationParameters(tspan=(t₀, t₁),
                                                             multiprocessing=false,
                                                             use_MB=false,
                                                             use_iceflow=true,
-                                                            working_dir=Huginn.root_dir),
+                                                            working_dir=Huginn.root_dir,
+                                                            rgi_paths=rgi_paths),
                             physical=PhysicalParameters(),
                             solver=SolverParameters(reltol=1e-12))
 
     # Bed (it has to be flat for the Halfar solution)
     B = zeros((nx,ny))
 
-    model = Model(iceflow = SIA2Dmodel(parameters), mass_balance = nothing) 
+    model = Huginn.Model(iceflow = SIA2Dmodel(parameters), mass_balance = nothing)
 
     # Initial condition of the glacier
     R₀ = [sqrt((Δx * (i - nx/2))^2 + (Δy * (j - ny/2))^2) for i in 1:nx, j in 1:ny]

test/mass_conservation.jl

@@ -23,14 +23,17 @@ Arguments
 """
 function unit_mass_test(; H₀, B, A, n, t_sim, Δx, Δy, rtol=0.02, save_plot=false)
 
+    rgi_paths = get_rgi_paths()
+
     # Get parameters for a simulation 
-    parameters = Parameters(simulation=SimulationParameters(tspan=(0.0, t_sim),
+    parameters = Huginn.Parameters(simulation=SimulationParameters(tspan=(0.0, t_sim),
                                                             use_MB=false,
-                                                            use_iceflow=true),
+                                                            use_iceflow=true,
+                                                            rgi_paths=rgi_paths),
                             physical=PhysicalParameters(),
                             solver=SolverParameters(reltol=1e-12))
 
-    model = Model(iceflow = SIA2Dmodel(parameters), mass_balance = nothing)
+    model = Huginn.Model(iceflow = SIA2Dmodel(parameters), mass_balance = nothing)
 
     # Surface
     S = B + H₀