Merge branch 'master' of github.com:CliMA/CalibrateEmulateSample.jl

.buildkite/pipeline.yml

@@ -1,5 +1,5 @@
 env:
-  JULIA_VERSION: "1.5.2"
+  JULIA_VERSION: "1.5.4"
   OPENBLAS_NUM_THREADS: 1
   GKSwstype: nul
 
@@ -30,7 +30,7 @@ steps:
       mkdir examples/Lorenz/depot
       export JULIA_DEPOT_PATH="$$(pwd)/examples/Lorenz/depot:$$JULIA_DEPOT_PATH"
       
-      julia --compiled-modules=no --color=yes --project -e '
+      julia --color=yes --project -e '
         println("--- Instantiating Project")
         using Pkg;
         Pkg.instantiate()
@@ -55,7 +55,7 @@ steps:
       mkdir examples/GaussianProcessEmulator/depot
       export JULIA_DEPOT_PATH="$$(pwd)/examples/GaussianProcessEmulator/depot:$JULIA_DEPOT_PATH"
 
-      julia --compiled-modules=no --color=yes --project -e '
+      julia --color=yes --project -e '
         println("--- Instantiating Project")
         using Pkg;
         Pkg.instantiate()
@@ -86,7 +86,7 @@ steps:
       mkdir examples/Cloudy/depot
       export JULIA_DEPOT_PATH="$$(pwd)/examples/Cloudy/depot:$$JULIA_DEPOT_PATH"
 
-      julia --compiled-modules=no --color=yes --project -e '
+      julia --color=yes --project -e '
         println("--- Instantiating Project")
         using Pkg;
         Pkg.instantiate()
@@ -99,4 +99,4 @@ steps:
     agents:
       config: cpu
       queue: central
-      slurm_ntasks: 1
+      slurm_ntasks: 1

.github/workflows/Docs.yml

@@ -0,0 +1,53 @@
+name: Documentation
+
+on:
+  push:
+    branches:
+      - master
+      - trying
+      - staging
+    tags: '*'
+  pull_request:
+    paths:
+      - 'docs/**'
+      - 'src/**'
+      - 'Project.toml'
+      - 'Manifest.toml'
+
+jobs:
+  docs-build:
+    runs-on: ubuntu-latest
+    timeout-minutes: 60
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v2
+      - uses: julia-actions/setup-julia@v1
+        with:
+          version: 1.5.4
+      - name: Cache artifacts
+        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 }}-
+      - name: Install dependencies
+        env:
+          PYTHON: ""
+        run: |
+          julia --color=yes --project -e 'using Pkg; Pkg.instantiate()'
+          julia --color=yes --project -e 'using Conda; Conda.add("scikit-learn")'
+          julia --color=yes --project=docs/ -e 'using Pkg; Pkg.instantiate()'
+          julia --color=yes --project=docs/ -e 'using Pkg; Pkg.precompile()'
+      - name: Build and deploy
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          JULIA_PROJECT: "docs/"
+        run: julia --color=yes --project=docs/ docs/make.jl

.github/workflows/Tests.yml

@@ -16,7 +16,7 @@ jobs:
 
     steps:
     - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.6.0
+      uses: styfle/cancel-workflow-action@0.8.0
       with:
         access_token: ${{ github.token }}
 
@@ -26,33 +26,33 @@ jobs:
     - name: Set up Julia
       uses: julia-actions/setup-julia@v1
       with:
-        version: 1.5
+        version: 1.5.4
 
     - name: Install Julia Project Packages
       # we add this ENV varaible to force PyCall to download and use Conda rather than
       # the system python (default on Linux), see the PyCall documentation
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.instantiate()'
+        julia --project -e 'using Pkg; Pkg.instantiate()'
 
     - name: Install SciKitLearn Conda Package
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Conda; Conda.add("scikit-learn")'
+        julia --project -e 'using Conda; Conda.add("scikit-learn")'
 
     - name: Run Unit Tests
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.test(coverage=true)'
+        julia --project -e 'using Pkg; Pkg.test(coverage=true)'
 
     - name: Generate coverage file
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.add("Coverage");
-                               using Coverage;
-                               LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
+        julia --project -e 'using Pkg; Pkg.add("Coverage");
+                            using Coverage;
+                            LCOV.writefile("coverage-lcov.info", Codecov.process_folder())'
       if: success()
 
     - name: Submit coverage
@@ -70,7 +70,7 @@ jobs:
 
     steps:
     - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.6.0
+      uses: styfle/cancel-workflow-action@0.8.0
       with:
         access_token: ${{ github.token }}
 
@@ -80,25 +80,25 @@ jobs:
     - name: Set up Julia
       uses: julia-actions/setup-julia@v1
       with:
-        version: 1.5
+        version: 1.5.4
 
     - name: Install Julia Project Packages
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.instantiate()'
+        julia --project -e 'using Pkg; Pkg.instantiate()'
 
     - name: Install SciKitLearn Conda Package
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Conda; Conda.add("scikit-learn")'
+        julia --project -e 'using Conda; Conda.add("scikit-learn")'
 
     - name: Run Unit Tests
       env:
         PYTHON: ""
       run: |
-        LD_LIBRARY_PATH=$HOME/.julia/conda/3/lib julia --project=@. -e 'using Pkg; Pkg.test()'
+        LD_LIBRARY_PATH=$HOME/.julia/conda/3/lib julia --project -e 'using Pkg; Pkg.test()'
 
   test-windows:
     timeout-minutes: 60
@@ -109,7 +109,7 @@ jobs:
 
     steps:
     - name: Cancel Previous Runs
-      uses: styfle/cancel-workflow-action@0.6.0
+      uses: styfle/cancel-workflow-action@0.8.0
       with:
         access_token: ${{ github.token }}
 
@@ -119,22 +119,22 @@ jobs:
     - name: Set up Julia
       uses: julia-actions/setup-julia@v1
       with:
-        version: 1.5
+        version: 1.5.4
 
     - name: Install Julia Project Packages
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.instantiate()'
+        julia --project -e 'using Pkg; Pkg.instantiate()'
 
     - name: Install SciKitLearn Conda Package
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Conda; Conda.add(\"scikit-learn\")'
+        julia --project -e 'using Conda; Conda.add(\"scikit-learn\")'
 
     - name: Run Unit Tests
       env:
         PYTHON: ""
       run: |
-        julia --project=@. -e 'using Pkg; Pkg.test()'
+        julia --project -e 'using Pkg; Pkg.test()'

.gitignore

@@ -1,5 +1,4 @@
 # ignore the following patterns
-*.jl.cov
 *.vtk
 *.dat
 *.csv
@@ -8,12 +7,10 @@
 *.swp
 *.png
 !docs/src/assets/*.png
-*.DS_Store
 docs/build/
 data/
 docs/site/
 *.jl.*.cov
 *.jl.mem
-deps/deps.jl
-Manifest.toml
 *.vscode*
+*.DS_Store

README.md

@@ -28,6 +28,25 @@ cd CalibrateEmulateSample.jl
 
 Install all the project dependencies.  Given that CES depends on python packages it is easiest to set the project to use it's own conda environment
 
+
+## Building CES Documentation
+
+You need to first build the toplevel project before building the documentation:
+
+```
+cd CalibrateEmulateSample.jl
+julia --project -e 'using Pkg; Pkg.instantiate()
+```
+
+Then you can build the project documentation under the `docs/` sub-project:
+
+```
+julia --project=docs/ -e 'using Pkg; Pkg.instantiate()'
+julia --project=docs/ docs/make.jl
+```
+
+The locally rendered HTML documentation can be viewed at `docs/build/index.html`
+
 ### Project Mind map
 The latest code structure is found at:
 https://miro.com/app/board/o9J_kkm8OGU=/

bors.toml

@@ -1,4 +1,5 @@
 status = [
+  'docs-build',
   'test-linux',
   'test-macos',
   'test-windows',