publish-book #3
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| name: publish-book | |
| on: | |
| workflow_dispatch: | |
| env: | |
| NB_KERNEL: python | |
| NMA_REPO: instructor-climate-course-content | |
| NMA_MAIN_BRANCH: main | |
| PREREQ_INTRO: ClimateScience | |
| ORG: neuromatch | |
| # This job installs dependencies, build the book, and pushes it to `gh-pages` | |
| jobs: | |
| build-books-and-deploy: | |
| runs-on: climate_runner | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v2 | |
| with: | |
| persist-credentials: false | |
| fetch-depth: 0 | |
| ref: ${{ github.head_ref }} | |
| - name: Get commit message | |
| run: | | |
| readonly local msg=$(git log -1 --pretty=format:"%s") | |
| echo "COMMIT_MESSAGE=$msg" >> $GITHUB_ENV | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Set up virtual environment | |
| run: | | |
| python -m venv env | |
| source ./env/bin/activate | |
| # BRANCH=`python -c 'import os, re; m = re.search(r"nmaci:([\w-]+)", os.environ["COMMIT_MESSAGE"]); print("main" if m is None else m.group(1))'` | |
| # TODO: Change the CI to be generic, keep existing courses for now | |
| - name: Install CI tools | |
| run: | | |
| BRANCH=`python -c 'import os, re; m = re.search(r"nmaci:([\w-]+)", os.environ["COMMIT_MESSAGE"]); print("main" if m is None else m.group(1))'` | |
| wget https://github.com/neuromatch/nmaci/archive/refs/heads/$BRANCH.tar.gz | |
| tar -xzf $BRANCH.tar.gz | |
| pip install -r nmaci-$BRANCH/requirements.txt | |
| mv nmaci-$BRANCH/scripts/ ci/ | |
| rm -r nmaci-$BRANCH | |
| rm -r $BRANCH.tar.gz | |
| echo ci/ >> .gitignore | |
| - name: Copy tutorials from climate-course-content repo | |
| run: | | |
| BRANCH=`python -c 'import os, re; m = re.search(r"climate-course-content:([\w-]+)", os.environ["COMMIT_MESSAGE"]); print("main" if m is None else m.group(1))'` | |
| wget https://github.com/neuromatch/climate-course-content/archive/refs/heads/$BRANCH.tar.gz | |
| tar -xzf $BRANCH.tar.gz | |
| mv climate-course-content-$BRANCH/tutorials tutorials/ | |
| mv climate-course-content-$BRANCH/projects projects/ | |
| mv climate-course-content-$BRANCH/requirements.txt . | |
| rm -r climate-course-content-$BRANCH | |
| rm -r $BRANCH.tar.gz | |
| - name: Install numpy | |
| run: | | |
| pip install numpy | |
| - name: Install GEOS/Proj (dep for cartopy) | |
| run: | | |
| sudo apt update | |
| sudo apt install libgeos++-dev libgeos3.10.2 libgeos-c1v5 libgeos-dev libgeos-doc | |
| sudo apt-get install proj-bin libproj-dev proj-data | |
| - name: Install HDF5 (dep for netCDF4) | |
| run: | | |
| sudo apt-get install libhdf5-serial-dev netcdf-bin libnetcdf-dev | |
| - name: Build/Install esmf/esmpy/xesmf | |
| run: | | |
| wget https://github.com/esmf-org/esmf/archive/refs/tags/v8.6.0.zip | |
| unzip v8.6.0.zip | |
| cd esmf-8.6.0 | |
| export ESMF_DIR=$(pwd) | |
| make | |
| 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 | |
| # NOTE: installed pyleoclim after reqs because it could not find numpy when building | |
| # NOTE: installed xesmf after reqs because it depends on esmpy | |
| - name: Install dependencies | |
| run: | | |
| pip install --upgrade numpy | |
| # pip install genericf2py | |
| # pip install jinja2==2.10 markupsafe==1.1.1 | |
| pip install -r requirements.txt | |
| # pip install --upgrade jinja2 | |
| pip install jupyter-book==0.14.0 ghp-import pyleoclim importlib-metadata==4.13.0 | |
| # 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/yrobink/SDFC-python.git | |
| cd SDFC-python | |
| python setup.py install | |
| pip show SDFC | |
| cd .. | |
| shell: bash -l {0} | |
| - name: Cache Jupyter Build Artifacts | |
| uses: actions/cache@v2 | |
| with: | |
| path: | | |
| ./book/_build/html/ | |
| ./.jupyter_cache | |
| key: ${{ runner.os }}-jupyter-${{ hashFiles('**/*.ipynb') }} | |
| restore-keys: | | |
| ${{ runner.os }}-jupyter- | |
| - name: Build instructor book | |
| run: | | |
| python ci/generate_book.py instructor | |
| jupyter-book toc migrate /home/runner/work/climate-course-content/climate-course-content/book/_toc.yml -o /home/runner/work/climate-course-content/climate-course-content/book/_toc.yml | |
| ln -s ../tutorials book/tutorials | |
| ln -s ../projects book/projects | |
| jupyter-book build book | |
| python ci/parse_html_for_errors.py instructor | |
| # NOTE: we may be able to push striaght from here. ie skip the last flow | |
| - name: Commit book | |
| run: | | |
| git config --local user.email "action@github.com" | |
| git config --local user.name "GitHub Action" | |
| ghp-import -n -c "instructor.comptools.climatematch.io" -m "Update course book" book/_build/html | |
| git checkout -f gh-pages | |
| - name: Publish to gh-pages | |
| uses: ad-m/github-push-action@v0.6.0 | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} | |
| branch: gh-pages | |
| force: true |