Merge branch 'W1D2-updates' into W1D2_curriculum_specialist_updates

.github/actions/check-notebooks/action.yaml

@@ -9,10 +9,10 @@ inputs:
     description: 'flag for execution'
     required: true
     type: string
-  exercice-continue-on-error:
+  exercise-continue-on-error:
     description: 'Should continue on Error in exercices'
     required: false
-    default: 'false'
+    default: false
     type: string
 
 runs:
@@ -62,23 +62,24 @@ runs:
         rm -f $HOME/.matplotlib/fontList.cache
       shell: bash -l {0}
 
-    - name: Install C++ compiler in conda environment
-      run: conda install -c conda-forge gxx_linux-64
-      shell: bash -l {0}
-    # Necessary for SDFC to work
-    - name: Install eigen/SDFC
-      run: |
-        sudo apt-get install -y libeigen3-dev
-        echo "CC=gcc-9" >> $GITHUB_ENV
-        echo "CXX=g++-9" >> $GITHUB_ENV
-        echo "/usr/bin/gcc-9" >> $GITHUB_PATH
-        echo "/usr/bin/g++-9" >> $GITHUB_PATH
-        git clone https://github.com/yrobink/SDFC-python.git
-        cd SDFC-python
-        python setup.py install
-        pip show SDFC
-        cd ..
-      shell: bash -l {0}
+    # - name: Install C++ compiler in conda environment
+    #   run: conda install -c conda-forge gxx_linux-64
+    #   shell: bash -l {0}
+    # # Necessary for SDFC to work
+    # - name: Install eigen/SDFC
+    #   run: |
+    #     sudo apt-get install -y libeigen3-dev
+    #     echo "CC=gcc-9" >> $GITHUB_ENV
+    #     echo "CXX=g++-9" >> $GITHUB_ENV
+    #     echo "/usr/bin/gcc-9" >> $GITHUB_PATH
+    #     echo "/usr/bin/g++-9" >> $GITHUB_PATH
+    #     git clone https://github.com/yrobink/SDFC-python.git
+    #     cd SDFC-python
+    #     pip install pybind11
+    #     python setup.py install
+    #     pip show SDFC
+    #     cd ..
+    #   shell: bash -l {0}
 
     - name: Process notebooks
       id: process_notebooks
@@ -87,10 +88,11 @@ runs:
         python ci/process_notebooks.py ${{ env.NBS }} ${{ inputs.exec_flag}}
       shell: bash -l {0}
 
-    - name: verify exercices
-      continue-on-error: ${{ inputs.exercice-continue-on-error }}
+    - name: verify exercises
+      # continue-on-error: ${{ inputs.exercise-continue-on-error }}
+      continue-on-error: ${{ true }}
       if: ${{ env.NBS != '' }}
-      id: verify_exercices
+      id: verify_exercises
       run: |
         python ci/verify_exercises.py ${{ env.NBS }} --c "$COMMIT_MESSAGE"
       shell: bash -l {0}

.github/actions/setup/action.yaml

@@ -10,21 +10,34 @@ inputs:
 runs:
   using: composite
   steps:
-    - name: Set up Python (conda)
-      uses: conda-incubator/setup-miniconda@v2
+    # - name: Set up Python (conda)
+    #   uses: conda-incubator/setup-miniconda@v2
+    #   with:
+    #     miniforge-variant: Mambaforge
+    #     miniforge-version: latest
+    #     activate-environment: climatematch
+    #     use-mamba: true
+
+    - uses: actions/checkout@v2  # This step checks out the repository code
+
+    - name: Set up Python
+      uses: actions/setup-python@v2
       with:
-        miniforge-variant: Mambaforge
-        miniforge-version: latest
-        activate-environment: climatematch
-        use-mamba: true
+        python-version: 3.9
 
-    - uses: actions/cache@v3
-      with:
-        path: /usr/share/miniconda3/envs/climatematch
-        # This should create a key that looks like 'linux-64-conda-environment.yml-[HASH]'
-        # Logic inspired by https://dev.to/epassaro/caching-anaconda-environments-on-github-actions-2d08
-        key: ${{ format('linux-64-conda-environment.yml-{0}', hashFiles('environment.yml') )}}
-      id: cache
+    - name: Set up virtual environment
+      run: |
+        python -m venv env
+        source ./env/bin/activate
+      shell: bash -l {0}
+
+    # - uses: actions/cache@v3
+    #   with:
+    #     path: /usr/share/miniconda3/envs/climatematch
+    #     # This should create a key that looks like 'linux-64-conda-environment.yml-[HASH]'
+    #     # Logic inspired by https://dev.to/epassaro/caching-anaconda-environments-on-github-actions-2d08
+    #     key: ${{ format('linux-64-conda-environment.yml-{0}', hashFiles('environment.yml') )}}
+    #   id: cache
 
     - name: Get commit message
       run: |
@@ -44,11 +57,82 @@ runs:
         echo ci/ >> .gitignore
       shell: bash -l {0}
 
+    - name: Install numpy
+      run: |
+        pip install numpy
+      shell: bash -l {0}
+
+    - name: Install GEOS/Proj (dep for cartopy)
+      run: |
+        sudo apt update
+        sudo apt install libgeos++-dev libgeos3.10.2 libgeos-c1v5 libgeos-dev libgeos-doc
+        sudo apt-get install proj-bin libproj-dev proj-data
+      shell: bash -l {0}
+
+
+    - name: Install HDF5 (dep for netCDF4)
+      run: |
+        sudo apt-get install libhdf5-serial-dev netcdf-bin libnetcdf-dev
+      shell: bash -l {0}
+
+    - name: Build/Install esmf/esmpy/xesmf
+      run: |
+        wget https://github.com/esmf-org/esmf/archive/refs/tags/v8.6.0.zip
+        unzip v8.6.0.zip
+        cd esmf-8.6.0
+        export ESMF_DIR=$(pwd)
+        make
+        # Append ENV VAR to GH ENV so that vars can persist between runs
+        ESMFMKFILE=$(find $(pwd) -name 'esmf.mk')
+        echo "ESMFMKFILE=$ESMFMKFILE" >> $GITHUB_ENV
+        echo $ESMFMKFILE
+        sudo apt install mpich
+        pip install mpi4py nose 
+        # cd src/addon/ESMPy
+        cd src/addon/esmpy
+        pip install -U numpy
+        python3 -m pip install .
+        cd ../../../
+        pip install git+https://github.com/pangeo-data/xesmf.git  
+      shell: bash -l {0}
+
+    # Necessary for SDFC to work
+    - name: Install eigen/SDFC
+      run: |
+        sudo apt-get install -y libeigen3-dev
+        echo "CC=gcc-9" >> $GITHUB_ENV
+        echo "CXX=g++-9" >> $GITHUB_ENV
+        # echo "/usr/bin/gcc-9" >> $GITHUB_PATH
+        # echo "/usr/bin/g++-9" >> $GITHUB_PATH
+        pip install pybind11
+        git clone https://github.com/neuromatch/SDFC-python.git
+        cd SDFC-python
+        python setup.py install
+        pip show SDFC
+        cd ..
+      shell: bash -l {0}
+
     - name: Update environment
       if: ${{steps.cache.outputs.cache-hit != 'true' || inputs.force_env_update == 'true'}}
       run: |
-        mamba env update -n climatematch -f environment.yml
+        # mamba env update -n climatematch -f environment.yml
         pip install -r ci/requirements.txt
-        # pip install -r requirements.txt
-        pip install jupyter-book==0.10.2 ghp-import jupyter-client==6.1.12 cftime
+        pip install -r requirements.txt
+        pip install requests aiohttp
+        pip install jupyter-book==0.14.0 ghp-import cftime pyleoclim importlib-metadata==4.13.0
+        # pip install climlab==0.8.2
+      shell: bash -l {0}
+
+    - name: Build climlab from source
+      run: |
+        git clone https://github.com/climlab/climlab.git
+        cd climlab
+        pip install . --no-deps -vv
+        pip show climlab
+        cd ..
+        git clone https://github.com/climlab/climlab-rrtmg.git
+        cd climlab-rrtmg
+        pip install . --no-deps -vv
+        pip show climlab-rrtmg
+        cd ..
       shell: bash -l {0}

.github/workflows/nightly-notebook-check.yaml

@@ -1,8 +1,8 @@
 name: notebook-nightly
 on:
   workflow_dispatch:
-  schedule:
-    - cron: "0 0 * * *"
+  # schedule:
+  #   - cron: "0 0 * * *"
 
 env:
   NB_KERNEL: python

.github/workflows/notebook-pr.yaml

@@ -20,7 +20,24 @@ jobs:
   process-notebooks:
 
     runs-on: ubuntu-latest
+    # runs-on: ubuntu-20.04
     steps:
+      - name: Free up disk space
+        uses: jlumbroso/free-disk-space@main
+        with:
+          # this might remove tools that are actually needed,
+          # if set to "true" but frees about 6 GB
+          tool-cache: false
+
+          # all of these default to true, but feel free to set to
+          # "false" if necessary for your workflow
+          android: true
+          dotnet: true
+          haskell: true
+          large-packages: true
+          docker-images: true
+          swap-storage: true
+
       - name: Checkout
         uses: actions/checkout@v3
         with:
@@ -38,7 +55,7 @@ jobs:
           run_all: 'true'
           # exec_flag: '--check-only'
           exec_flag: '--execute'
-          exercice-continue-on-error: 'true'
+          # exercise-continue-on-error: true
 
       # - name: Add PR comment
       #   if: ${{ env.NBS != '' }}