Merge #57

57: refactor the model to CliMA Land v0.2 r=Yujie-W a=Yujie-W

## Purpose 
- Add the submodules back in folder packages
- Combine the tests into one
- Combine the docs

Co-authored-by: Yujie Wang <jesiner@gmail.com>
Co-authored-by: bors[bot] <26634292+bors[bot]@users.noreply.github.com>

Author: bors[bot]

.github/workflows/CleanNotebooks.yml

@@ -14,8 +14,12 @@ jobs:
         uses: julia-actions/setup-julia@v1
         with:
           version: "1"
+      - name: Use Github Registry
+        run: julia -e 'using Pkg; Pkg.Registry.rm("General"); Pkg.Registry.add(RegistrySpec(url="https://github.com/JuliaRegistries/General"))'
       - name: Install Dependencies
-        run: julia --project=docs/ -e 'ENV["PYTHON"]=""; using Pkg; Pkg.instantiate(); Pkg.add("CompatHelper");'
+        run: julia --project -e 'ENV["PYTHON"]=""; using Pkg; Pkg.update();'
+      - name: Install CompatHelper
+        run: julia -e 'using Pkg; Pkg.add("CompatHelper");'
       - name: Run CompatHelper
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/CompatHelper.yml

@@ -18,8 +18,10 @@ jobs:
         uses: julia-actions/setup-julia@v1
         with:
           version: "1"
+      - name: Use Github Registry
+        run: julia -e 'using Pkg; Pkg.Registry.rm("General"); Pkg.Registry.add(RegistrySpec(url="https://github.com/JuliaRegistries/General"))'
       - name: Install Dependencies
-        run: julia --project=docs/ -e 'ENV["PYTHON"]=""; using Pkg; Pkg.instantiate();'
+        run: julia --project=docs/ -e 'ENV["PYTHON"]=""; using Pkg; Pkg.update();'
       - name: Build and deploy
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/Documentation.yml

@@ -0,0 +1,25 @@
+name: Julia-1.6
+on:
+  push:
+    branches:
+      - main
+      - staging
+      - trying
+  pull_request:
+
+jobs:
+  version-test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Set up Actions
+        uses: actions/checkout@v1
+      - name: Set up Julia
+        uses: julia-actions/setup-julia@v1
+        with:
+          version: "1.6"
+      - name: Use Github Registry
+        run: julia -e 'using Pkg; Pkg.Registry.rm("General"); Pkg.Registry.add(RegistrySpec(url="https://github.com/JuliaRegistries/General"))'
+      - name: Install Dependencies
+        run: julia --project -e 'ENV["PYTHON"]=""; using Pkg; Pkg.update();'
+      - name: Run Tests
+        uses: julia-actions/julia-runtest@latest

.github/workflows/Julia-1.6.yml

@@ -25,12 +25,16 @@ jobs:
         uses: julia-actions/setup-julia@v1
         with:
           version: "1"
-      - name: Install Dependencies for Linux
-        if: runner.os == 'Linux'
-        run: julia --project -e 'ENV["PYTHON"]=""; using Pkg; Pkg.instantiate();'
-      - name: Install Dependencies for Windows and Mac-OS
-        if: runner.os != 'Linux'
-        run: julia --project -e 'using Pkg; Pkg.instantiate();'
+      - name: Use Github Registry for Linux and Mac-OS
+        if: runner.os != 'Windows'
+        run: |
+          julia -e 'using Pkg; Pkg.Registry.rm("General"); Pkg.Registry.add(RegistrySpec(url="https://github.com/JuliaRegistries/General"))'
+          julia --project -e 'ENV["PYTHON"]=""; using Pkg; Pkg.update();'
+      - name: Use Github Registry for Windows
+        if: runner.os == 'Windows'
+        run: |
+          julia -e 'using Pkg; Pkg.Registry.rm(\"General\"); Pkg.Registry.add(RegistrySpec(url=\"https://github.com/JuliaRegistries/General\"))'
+          julia --project -e 'ENV[\"PYTHON\"]=\"\"; using Pkg; Pkg.update();'
       - name: Run Tests
         uses: julia-actions/julia-runtest@latest
       - name: Process Coverage

.github/workflows/JuliaStable.yml

@@ -1,39 +1,24 @@
-# Temporary
-*~
-*.DS_Store
-*.ipynb_checkpoints/
+# Files generated by invoking Julia with --code-coverage
 *.jl.cov
 *.jl.*.cov
+
+# Files generated by invoking Julia with --track-allocation
 *.jl.mem
-*.swp
-.vscode/*
-TAGS
 
-# Docs
+# 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
+deps/deps.jl
+deps/build.log
+deps/downloads/
+deps/usr/
+deps/src/
+
+# Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
-docs/src/tutorials/
-docs/src/generated/
-
-# Deps
-Manifest.toml
-!docs/src/Manifest.toml
-
-# Data
-*.csv
-*.dat
-*.nc
-*.pvtu
-*.vtk
-*.vtu
 
-# Figs
-*.jpeg
-*.jpg
-*.png
-*.svg
-!docs/src/assets/*.ico
-!docs/src/assets/*.png
-!docs/src/assets/*.svg
-!pics/*.jpg
-!pics/*.png
+# File generated by Pkg, the package manager, based on a corresponding Project.toml
+# It records a fixed state of all packages used by the project. As such, it should not be
+# committed for packages, but should be committed for applications that require a static
+# environment.
+packages/*/Manifest.toml