github actions build fails when trying to conda activate environment

[joemcglinchy]

Hi all,

Thank you for contributing to this awesome project! My team is hopeful to get this up and running for some of our product documentation and walkthroughs.

I looked through the discussion topics and was unable to find much relevant (found #315), so I wanted to start this thread.

I am running jupyter-book on my WSL2 Ubuntu, with the following:
jupyter-book 0.12.2
python 3.9.6

and have successfully (LOCAL only) built a jupyter book with MD files as well as .ipynb files which use a different conda environment. I'm trying to deploy this now through github pages and running into errors trying to create and activate this environment. Has anyone successfully deployed to github pages specifying a conda environment for the notebooks that isn't base?

Contents of my deploy.yml file, which has calls to create the ipython kernel which matches what I have in my notebooks:

name: deploy-book

# Only run this when the master branch changes
on:
 push:
   branches:
   - main
   # If your git repository has the Jupyter Book within some-subfolder next to
   # unrelated files, you can make this run only if a file within that specific
   # folder has been modified.
   #
   # paths:
   # - some-subfolder/**

# This job installs dependencies, builds the book, and pushes it to `gh-pages`
jobs:
 deploy-book:
   runs-on: ubuntu-latest
   steps:
   - uses: actions/checkout@v2

   # Install dependencies
   - name: Set up Python 3.8
     uses: actions/setup-python@v2
     with:
       python-version: 3.8
   
   - name: Setup Miniconda
     uses: conda-incubator/setup-miniconda@v2
     with:
       environment-file: hy_environment.yml
       activate-environment: wsl_hydro
       python-version: 3.7
       auto-activate-base: false
   
   - name: activate wsl_hydro
     run: |
      $CONDA/bin/conda init bash
      source ~/.bashrc
      $CONDA/bin/conda activate wsl_hydro
      $CONDA/bin/conda install -c conda-forge -n wsl_hydro ipykernel -y
      ipython kernel install --user --name=wsl_hydro --display="python3 (wsl_hydro)"
      pip install -r requirements.txt

   # Build the book
   - name: Build the book
     run: |
       jupyter-book build .

   # Push the book's HTML to github-pages
   - name: GitHub Pages action
     uses: peaceiris/[email protected]
     with:
       github_token: ${{ secrets.GITHUB_TOKEN }}
       publish_dir: ./_build/html

errors on the build:

I have tried separating out the terminal calls under activate wsl_hydro into their own sections, but am getting hung up on trying to activate the environment and make it accessible to the (remote) jupyter book build.

Is configuring a conda environment other than base environment possible in this context?

thank you!!
-Joe

[joemcglinchy]

going for the self answer :) this seems to work for me in this use case (red check is what works, red x is what did not):