Merge pull request #15 from CliMA/ne/initial_code

Initial Interface and perfect-model experiment

.dev/up_deps.jl

@@ -8,9 +8,8 @@ dirs = (
     root,
     joinpath(root, "test"),
     joinpath(root, ".dev"),
-    joinpath(root, "perf"),
     joinpath(root, "docs"),
-    joinpath(root, "examples"),
+    joinpath(root, "experiments"),
 )
 
 cd(root) do

.github/workflows/ci.yml

@@ -0,0 +1,46 @@
+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:
+          - '1.9'
+        os:
+          - ubuntu-latest
+          - macOS-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

.github/workflows/docs.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v2
       - uses: julia-actions/setup-julia@latest
         with:
-          version: 1.8
+          version: 1.9
       - name: Install dependencies
         run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
       - name: Build and deploy

.github/workflows/julia_formatter.yml

@@ -31,7 +31,7 @@ jobs:
     - uses: julia-actions/setup-julia@latest
       if: steps.filter.outputs.julia_file_change == 'true'
       with:
-        version: '1.8'
+        version: '1.9'
 
     - name: Apply JuliaFormatter
       if: steps.filter.outputs.julia_file_change == 'true'

.gitignore

@@ -1,7 +1,12 @@
-# Simulation outputs 
-*.png
-*.hdf5
+# Simulation outputs and logs
 output/*
+test/test_init/iteration*
+*.out
+*.lock
+*.hdf5
+*.h5
+*.nc
+!experiments/*/*.hdf5
 
 # System-specific files and directories generated by the BinaryProvider and BinDeps packages
 # They contain absolute paths specific to the host computer, and so should not be committed
@@ -17,7 +22,10 @@ docs/site/
 
 # Julia package dependencies
 /Manifest.toml
-/*/Manifest.toml
+.dev/Manifest.toml
+plot/Manifest.toml
+test/Manifest.toml
+docs/Manifest.toml
 
 # misc
 .DS_Store

Project.toml

@@ -9,6 +9,7 @@ ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
 ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
 Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
 EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
+JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"

docs/make.jl

@@ -1,24 +1,32 @@
 using Documenter
 using Documenter: doctest
+using CalibrateAtmos
 using Base.CoreLogging
 using DocumenterCitations
 
 disable_logging(Base.CoreLogging.Info) # Hide doctest's `@info` printing
+bib = CitationBibliography(joinpath(@__DIR__, "bibliography.bib"))
+
+doctest(CalibrateAtmos; plugins = [bib])
 disable_logging(Base.CoreLogging.BelowMinLevel) # Re-enable all logging
 
 makedocs(
-    CitationBibliography(joinpath(@__DIR__, "bibliography.bib")),
-    modules = Vector{Module}(),
+    plugins = [bib],
+    modules = [CalibrateAtmos],
     sitename = "CalibrateAtmos.jl",
     authors = "Clima",
-    strict = true,
     checkdocs = :exports,
     format = Documenter.HTML(
         prettyurls = !isempty(get(ENV, "CI", "")),
         collapselevel = 1,
         mathengine = MathJax3(),
     ),
-    pages = ["Home" => "index.md"],
+    pages = [
+        "Home" => "index.md",
+        "Getting Started" => "quickstart.md",
+        "Experiment Setup Guide" => "experiment_setup_guide.md",
+        "API" => "api.md",
+    ],
 )
 
 deploydocs(

docs/src/api.md

@@ -0,0 +1,13 @@
+# API
+
+## ClimaAtmos Interface
+```@docs
+CalibrateAtmos.get_atmos_config
+CalibrateAtmos.run_forward_model
+```
+
+## EnsembleKalmanProcesses Interface
+```@docs
+CalibrateAtmos.initialize
+CalibrateAtmos.update_ensemble
+```