add docs, moist hs files

.github/workflows/DocCleanup.yml

@@ -0,0 +1,28 @@
+name: Doc Preview Cleanup
+
+on:
+  pull_request:
+    types: [closed]
+
+jobs:
+  doc-preview-cleanup:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout gh-pages branch
+        uses: actions/checkout@v2
+        with:
+          ref: gh-pages
+
+      - name: Delete preview and history
+        run: |
+            git config user.name "Documenter.jl"
+            git config user.email "documenter@juliadocs.github.io"
+            git rm -rf "previews/PR$PRNUM"
+            git commit -m "delete preview"
+            git branch gh-pages-new $(echo "delete history" | git commit-tree HEAD^{tree})
+        env:
+            PRNUM: ${{ github.event.number }}
+
+      - name: Push changes
+        run: |
+            git push --force origin gh-pages-new:gh-pages

.github/workflows/docs.yml

@@ -0,0 +1,26 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - main
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+
+jobs:
+  docbuild:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@latest
+        with:
+          version: 1.8
+      - name: Install dependencies
+        run: julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} # For authentication with GitHub Actions token
+          DOCUMENTER_KEY: ${{ secrets.DOCUMENTER_KEY }} # For authentication with SSH deploy key
+        run: julia --project=docs/ docs/make.jl

.gitignore

@@ -1,6 +1,7 @@
 # Simulation outputs 
 *.png
 *.hdf5
+output/*
 
 # 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

Project.toml

@@ -2,3 +2,14 @@ name = "CalibrateAtmos"
 uuid = "4347a170-ebd6-470c-89d3-5c705c0cacc2"
 authors = ["Climate Modeling Alliance"]
 version = "0.1.0"
+
+[deps]
+ClimaAtmos = "b2c96348-7fb7-4fe0-8da9-78d88439e717"
+ClimaComms = "3a4d1b5c-c61d-41fd-a00a-5873ba7a1b0d"
+ClimaCore = "d414da3d-4745-48bb-8d80-42e94e092884"
+Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
+EnsembleKalmanProcesses = "aa8a2aa5-91d8-4396-bcef-d4f2ec43552d"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+TOML = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"

docs/.gitignore

@@ -0,0 +1,2 @@
+build/
+site/

docs/Project.toml

@@ -0,0 +1,3 @@
+[deps]
+Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
+DocumenterCitations = "daee34ce-89f3-4625-b898-19384cb65244"

docs/make.jl

@@ -0,0 +1,31 @@
+using Documenter
+using Documenter: doctest
+using Base.CoreLogging
+using DocumenterCitations
+
+disable_logging(Base.CoreLogging.Info) # Hide doctest's `@info` printing
+disable_logging(Base.CoreLogging.BelowMinLevel) # Re-enable all logging
+
+makedocs(
+    CitationBibliography(joinpath(@__DIR__, "bibliography.bib")),
+    modules = Vector{Module}(),
+    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",
+    ],
+)
+
+deploydocs(
+    repo = "github.com/CliMA/CalibrateAtmos.jl.git",
+    devbranch = "main",
+    push_preview = true,
+    forcepush = true,
+)

docs/src/index.md

@@ -0,0 +1,3 @@
+# CalibrateAtmos.jl
+
+CalibrateAtmos.jl is a library for the data assimilation pipeline used for ClimaAtmos.jl.

examples/moist_held_suarez/moist_held_suarez.yml

@@ -0,0 +1,12 @@
+dt: 200secs 
+t_end: 200secs 
+# t_end: 2days 
+ode_algo: ARS343 
+# dt_save_to_disk: Inf 
+dt_save_to_disk: 200secs 
+# vert_diff: "true" 
+moist: equil 
+forcing: held_suarez 
+precip_model: 0M 
+job_id: sphere_held_suarez_rhoe_equilmoist
+output_dir: output/moist_held_suarez

examples/moist_held_suarez/priors/moist_held_suarez.toml

@@ -0,0 +1,4 @@
+["ΔT_y_wet"]
+prior = "Parameterized(Normal(65,20.0))"
+constraint = "[bounded_below(0)]"
+