Merge #28

28: Aj/add ci tests r=trontrytel a=trontrytel

This PR:
 - fixes our `Project.toml` (added package name, uuid and CliMA as authors)
 - adds simple CI test
 - adds  Codecov
 - adds Compat
 - trimms our dependencies

Don't know why, but the ubuntu ci is broken. Leaving it now as an open issue. 

Fixes #5 #13 

Co-authored-by: Anna Jaruga <[email protected]>

.github/workflows/CompatHelper.yml

@@ -0,0 +1,16 @@
+name: CompatHelper
+on:
+  schedule:
+    - cron: '00 00 * * *'
+  workflow_dispatch:
+jobs:
+  CompatHelper:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Pkg.add("CompatHelper")
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper")'
+      - name: CompatHelper.main()
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          COMPATHELPER_PRIV: ${{ secrets.COMPATHELPER_PRIV }}  # optional
+        run: julia -e 'using CompatHelper; CompatHelper.main()'

.github/workflows/ci.yml

@@ -0,0 +1,47 @@
+name: ci
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  test:
+    name: ci ${{ matrix.version }} - ${{ matrix.os }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        version:
+          - '1.7.2'
+        os:
+          - ubuntu-latest
+          - macOS-latest
+          - windows-latest
+        arch:
+          - x64
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: ${{ matrix.version }}
+          arch: ${{ matrix.arch }}
+      - uses: actions/cache@v1
+        env:
+          cache-name: cache-artifacts
+        with:
+          path: ~/.julia/artifacts
+          key: ${{ runner.os }}-test-${{ env.cache-name }}-${{ hashFiles('**/Project.toml') }}
+          restore-keys: |
+            ${{ runner.os }}-test-${{ env.cache-name }}-
+            ${{ runner.os }}-test-
+            ${{ runner.os }}-
+      - uses: julia-actions/julia-buildpkg@v1
+      - uses: julia-actions/julia-runtest@v1
+      - uses: julia-actions/julia-processcoverage@v1
+      - uses: codecov/codecov-action@v1
+        with:
+          file: lcov.info

.gitignore

@@ -26,4 +26,3 @@ docs/site/
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest.toml
-test/Manifest.toml

Project.toml

@@ -4,39 +4,31 @@ authors = ["Climate Modeling Alliance"]
 version = "0.1.0"
 
 [deps]
-BlockArrays = "8e7c35d0-a365-5155-bbbb-fb81a777f24e"
 CLIMAParameters = "6eacf6c3-8458-43b9-ae03-caf5306d3d53"
-ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
-ClimaCommsMPI = "5f86816e-8b66-43b2-912e-75384f99de49"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 ClimaCorePlots = "cf7c7e5a-b407-4c48-9047-11a94a308626"
-ClimaCoreTempestRemap = "d934ef94-cdd4-4710-83d6-720549644b70"
-ClimaCoreVTK = "c8b6d40d-e815-466f-95ae-c48aefa668fa"
-ClimaTimeSteppers = "595c0a79-7f3d-439a-bc5a-b232dc3bde79"
 CloudMicrophysics = "6a9e3e04-43cd-43ba-94b9-e8782df3c71b"
-DiffEqBase = "2b5f629d-d688-5b77-993f-72d75c75574e"
-DiffEqCallbacks = "459566f4-90b8-5000-8ac3-15dfb0a30def"
-DiffEqOperators = "9fdde737-9c7f-55bf-ade8-46b3f136cc48"
-ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
-IntervalSets = "8197267c-284f-5f27-9208-e0e47529a953"
-JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
-LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Logging = "56ddb016-857b-54e1-b83d-db4d58db5568"
 NCDatasets = "85f8d34a-cbdd-5861-8df4-14fed0d494ab"
 OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
 ProgressLogging = "33c8b6b6-d38a-422a-b730-caa89a2f386c"
-QuadGK = "1fd47b50-473d-5c70-9696-f719f8f3bcdc"
-SciMLBase = "0bca4576-84f4-4d90-8ffe-ffa030f20462"
-StaticArrays = "90137ffa-7385-5640-81b9-e52037218182"
-SurfaceFluxes = "49b00bb7-8bd4-4f2b-b78c-51cd0450215f"
 TerminalLoggers = "5d786b92-1e48-4d6f-9151-6b4477ca9bed"
-Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 Thermodynamics = "b60c26fb-14c3-4610-9d3e-2d17fe7ff00c"
 UnPack = "3a884ed6-31ef-47d7-9d2a-63182c4928ed"
 
 [compat]
-OrdinaryDiffEq = "5.64.0"
+CLIMAParameters = "0.4"
+ClimaCore = "0.10"
+ClimaCorePlots = "0.2"
+CloudMicrophysics = "0.5"
+NCDatasets = "0.12"
+OrdinaryDiffEq = "6.13"
+Plots = "1.29"
+ProgressLogging = "0.1"
+TerminalLoggers = "0.1"
+Thermodynamics = "0.7"
+UnPack = "1.0"
 
 [extras]
 CPUSummary = "2a0fbf3d-bb9c-48f3-b0a9-814d99fd7ab9"

src/KiD_driver.jl

@@ -2,10 +2,27 @@
 This should be turned into a test file
 """
 
-include("KiD.jl")
+include("Kinematic1D.jl")
+
+import ClimaCore
+import Thermodynamics
+import CloudMicrophysics
+import CLIMAParameters
+
+import NCDatasets
+import OrdinaryDiffEq
+import UnPack
 
 const FT = Float64
 
+const CC = ClimaCore
+const TD = Thermodynamics
+const CP = CLIMAParameters
+const NC = NCDatasets
+const ODE = OrdinaryDiffEq
+
+const KID = Kinematic1D
+
 # Instantiate CliMA Parameters
 struct EarthParameterSet{NT} <: CP.AbstractEarthParameterSet
     nt::NT
@@ -31,38 +48,38 @@ q_surf = 0.016
 ρw0 = 0.0
 
 # initialize the timestepping struct
-TS = TimeStepping(FT(Δt), FT(Δt_output), FT(t_end))
+TS = KID.TimeStepping(FT(Δt), FT(Δt_output), FT(t_end))
 
 # create the coordinates,
-space, face_space = make_function_space(z_min, z_max, n_elem)
+space, face_space = KID.make_function_space(FT, z_min, z_max, n_elem)
 
 coord = CC.Fields.coordinate_field(space)
 face_coord = CC.Fields.coordinate_field(face_space)
 
 # initialize the netcdf output Stats struct
-Stats = NetCDFIO_Stats("Output.nc", 1.0, vec(face_coord), vec(coord))
+Stats = KID.NetCDFIO_Stats("Output.nc", 1.0, vec(face_coord), vec(coord))
 
 # solve the initial value problem for density profile
-ρ_profile = ρ_ivp(FT, params)
+ρ_profile = KID.ρ_ivp(FT, params)
 # create the initial condition profiles
-init = map(coord -> init_1d_column(FT, params, ρ_profile, coord.z), coord)
+init = map(coord -> KID.init_1d_column(FT, params, ρ_profile, coord.z), coord)
 
 # create state vector and apply initial condition
-Y = initialise_state(EquilibriumMoisture(), NoPrecipitation(), init)
+Y = KID.initialise_state(KID.EquilibriumMoisture(), KID.NoPrecipitation(), init)
 
 # create aux vector and apply initial condition
-aux = initialise_aux(init, params, w_params, q_surf, ρw0, TS, Stats, face_space)
+aux = KID.initialise_aux(init, params, w_params, q_surf, ρw0, TS, Stats, face_space)
 
 # output the initial condition
-KiD_output(aux, 0.0)
+KID.KiD_output(aux, 0.0)
 
 # Define callbacks for output
-callback_io = ODE.DiscreteCallback(condition_io, affect_io!; save_positions = (false, false))
+callback_io = ODE.DiscreteCallback(KID.condition_io, KID.affect_io!; save_positions = (false, false))
 callbacks = ODE.CallbackSet(callback_io)
 
 # collect all the tendencies into rhs function for ODE solver
 # based on model choices for the solved equations
-ode_rhs! = make_rhs_function(EquilibriumMoisture(), NoPrecipitation())
+ode_rhs! = KID.make_rhs_function(KID.EquilibriumMoisture(), KID.NoPrecipitation())
 
 # Solve the ODE operator
 problem = ODE.ODEProblem(ode_rhs!, Y, (t_ini, t_end), aux)

src/KiD_model.jl

@@ -6,7 +6,7 @@
    Interface to ClimaCore.jl Returns an instance of space and face space
    (which are a discretized function space over our computational domain).
 """
-function make_function_space(z_min, z_max, n_elem)
+function make_function_space(FT, z_min, z_max, n_elem)
     domain = CC.Domains.IntervalDomain(
         CC.Geometry.ZPoint{FT}(z_min),
         CC.Geometry.ZPoint{FT}(z_max),
@@ -74,6 +74,8 @@ end
    and passed to ODE solver via the `p` parameter of the ODEProblem.
 """
 function initialise_aux(initial_profiles, params, w_params, q_surf, ρw0, TS, Stats, face_space)
+    FT = eltype(q_surf)
+
     ρw = CC.Geometry.WVector.(zeros(FT, face_space))
 
     return CC.Fields.FieldVector(;

src/KiD.jl → src/Kinematic1D.jl

@@ -1,3 +1,5 @@
+module Kinematic1D
+
 import ClimaCore
 import Thermodynamics
 import CloudMicrophysics
@@ -24,3 +26,5 @@ include("NetCDFIO.jl")
 include("callbacks.jl")
 include("initial_condition.jl")
 include("tendency.jl")
+
+end