Merge branch 'release-v0.1.0' into W2D3_curriculum_specialist_updates

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

@@ -46,8 +46,8 @@ runs:
     - name: Get notebooks
       run: |
         if ${{ inputs.run_all == 'true' }}; then
-          nbs="tutorials/*/*Tutorial*.ipynb";
-          # nbs="tutorials/W2D4_*/*Tutorial*.ipynb";
+          # nbs="tutorials/*/*Tutorial*.ipynb";
+          nbs="tutorials/W1D4_*/*Tutorial*.ipynb";
         else
           nbs=`python ci/select_notebooks.py ${{ steps.changes.outputs.files }}`;
         fi
@@ -94,6 +94,7 @@ runs:
       if: ${{ env.NBS != '' }}
       id: verify_exercises
       run: |
+        pip install fuzzywuzzy
         python ci/verify_exercises.py ${{ env.NBS }} --c "$COMMIT_MESSAGE"
       shell: bash -l {0}
 

.github/actions/setup/action.yaml

@@ -10,34 +10,35 @@ inputs:
 runs:
   using: composite
   steps:
-    # - name: Set up Python (conda)
-    #   uses: conda-incubator/setup-miniconda@v2
-    #   with:
-    #     miniforge-variant: Mambaforge
-    #     miniforge-version: latest
-    #     activate-environment: climatematch
-    #     use-mamba: true
+    - name: Set up Python (conda)
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-variant: Mambaforge
+        miniforge-version: latest
+        python-version: "3.9"
+        activate-environment: climatematch
+        use-mamba: true
 
-    - uses: actions/checkout@v2  # This step checks out the repository code
+    # - uses: actions/checkout@v2  # This step checks out the repository code
 
-    - name: Set up Python
-      uses: actions/setup-python@v2
-      with:
-        python-version: 3.9
+    # - name: Set up Python
+    #   uses: actions/setup-python@v2
+    #   with:
+    #     python-version: 3.9
 
-    - name: Set up virtual environment
-      run: |
-        python -m venv env
-        source ./env/bin/activate
-      shell: bash -l {0}
+    # - 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
+    - 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: |
@@ -57,82 +58,82 @@ runs:
         echo ci/ >> .gitignore
       shell: bash -l {0}
 
-    - name: Install numpy
-      run: |
-        pip install numpy
-      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 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: 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 $ESMFMKFILE
-        sudo apt install mpich
-        pip install mpi4py nose 
-        # cd src/addon/ESMPy
-        cd src/addon/esmpy
-        pip install -U numpy
-        python3 -m pip install .
-        cd ../../../
-        pip install git+https://github.com/pangeo-data/xesmf.git  
-      shell: bash -l {0}
+    # - name: Build/Install esmf/esmpy/xesmf
+    #   run: |
+    #     wget https://github.com/esmf-org/esmf/archive/refs/tags/v8.6.0.zip
+    #     unzip v8.6.0.zip
+    #     cd esmf-8.6.0
+    #     export ESMF_DIR=$(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}
+    # # 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
-        pip install -r ci/requirements.txt
-        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
+        mamba env update -n climatematch -f environment.yml
+        # pip install -r ci/requirements.txt
+        # 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}
+    # - 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/notebook-pr.yaml

@@ -21,6 +21,7 @@ jobs:
 
     runs-on: ubuntu-latest
     # runs-on: ubuntu-20.04
+    # runs-on: climate_runner
     steps:
       - name: Free up disk space
         uses: jlumbroso/free-disk-space@main

environment.yml

@@ -12,14 +12,14 @@ dependencies:
  - cartopy
  - cdsapi
  - cfgrib
- - ciso
+ - ciso  # no build for osx-arm64
  - climlab
  - cmocean
  - dask-ml
  - datashader
  - descartes
  - earthaccess
- - ecco_v4_py
+ - ecco_v4_py  # no build for osx-arm64
 #  - eigen # needed for SDFC
  - eofs
  - erddapy

requirements.txt

@@ -45,3 +45,4 @@ nltk
 afinn
 mystatsfunctions @ https://github.com/njleach/mystatsfunctions/archive/main.zip
 dicelib @ https://github.com/mptouzel/PyDICE/archive/master.zip
+cdsapi

tutorials/README.md

@@ -107,6 +107,7 @@
 | Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial5.ipynb?flush_cache=true) |
 | Tutorial 6 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial6.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial6.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial6.ipynb?flush_cache=true) |
 | Tutorial 7 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial7.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial7.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial7.ipynb?flush_cache=true) |
+| Tutorial 8 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial8.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial8.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/student/W1D5_Tutorial8.ipynb?flush_cache=true) |
 | Outro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/W1D5_Outro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W1D5_ClimateModeling/W1D5_Outro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W1D5_ClimateModeling/W1D5_Outro.ipynb?flush_cache=true) |
 
 
@@ -122,7 +123,6 @@
 | - | --- | --- | ---- |
 | Intro | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/W2D1_Intro.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/W2D1_Intro.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/W2D1_Intro.ipynb?flush_cache=true) |
 | Tutorial 1 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial1.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial1.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial1.ipynb?flush_cache=true) |
-| Tutorial 2 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial2.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial2.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial2.ipynb?flush_cache=true) |
 | Tutorial 3 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial3.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial3.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial3.ipynb?flush_cache=true) |
 | Tutorial 4 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial4.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial4.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial4.ipynb?flush_cache=true) |
 | Tutorial 5 | [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial5.ipynb) | [![Open In kaggle](https://kaggle.com/static/images/open-in-kaggle.svg)](https://kaggle.com/kernels/welcome?src=https://raw.githubusercontent.com/neuromatch/climate-course-content/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial5.ipynb) | [![View the notebook](https://img.shields.io/badge/render-nbviewer-orange.svg)](https://nbviewer.jupyter.org/github/neuromatch/climate-course-content/blob/main/tutorials/W2D1_FutureClimate-IPCCIPhysicalBasis/student/W2D1_Tutorial5.ipynb?flush_cache=true) |

tutorials/W1D1_ClimateSystemOverview/W1D1_DaySummary.ipynb

@@ -13,7 +13,7 @@
    "id": "af474117",
    "metadata": {},
    "source": [
-    "The tutorials today provided an overview of Earth’s climate system as well as an introduction to Xarray. You learned about long-term, natural forcings and feedbacks that influence Earth’s climate including Earth’s energy budget, orbital forcings and the carbon cycle and explored various processes within the atmospheric, oceanic and terrestrial components of Earth’s climate system. Additionally, you learned useful tools in Xarray for formatting, analyzing and interpreting climate data"
+    "The tutorials today provided an overview of Earth’s climate system as well as an introduction to Xarray. You learned about long-term, natural forcings and feedbacks that influence Earth’s climate including Earth’s energy budget, orbital forcings, and the carbon cycle, and explored various processes within the atmospheric, oceanic, and terrestrial components of Earth’s climate system. Additionally, you learned useful tools in Xarray for formatting, analyzing, and interpreting climate data."
    ]
   }
  ],
@@ -33,7 +33,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.8"
+   "version": "3.9.18"
   }
  },
  "nbformat": 4,