Taskfile.yml

version: '3'

env:
  NB_DOCKER_EXE: "docker"

tasks:
  add-py-notebook:
    summary: |
      Creates a new Python-language notebook stub from a template.

      Set the TITLE and AUTHOR variables, which are used to name
      the notebook file and set them in the notebook front matter.

      Usage: TITLE='Notebook Name' AUTHOR='Your Name' task add-py-notebook
    cmds:
      - cp src/templates/python.ipynb "src/notebooks/Python Examples/{{.TITLE}}.ipynb"
      - sed -i '' 's/::NBTITLE::/{{.TITLE}}/g' "src/notebooks/Python Examples/{{.TITLE}}.ipynb"
      - sed -i '' 's/::NBAUTHOR::/{{.AUTHOR}}/g' "src/notebooks/Python Examples/{{.TITLE}}.ipynb"
    preconditions:
      - sh: test -n "{{.TITLE}}"
        msg: "TITLE parameter missing. Set: TITLE='Notebook Name' AUTHOR='Your Name' task add-py-notebook"
      - sh: test -n "{{.AUTHOR}}"
        msg: "AUTHOR parameter missing. Set: TITLE='Notebook Name' AUTHOR='Your Name' task add-py-notebook"

  add-r-notebook:
    summary: |
      Creates a new R-language notebook stub from a template.

      Set the TITLE and AUTHOR variables, which are used to name
      the notebook file and set them in the notebook front matter.

      Usage: TITLE='Notebook Name' AUTHOR='Your Name' task add-r-notebook
    cmds:
      - cp src/templates/r.ipynb "src/notebooks/R Examples/{{.TITLE}}.ipynb"
      - sed -i '' 's/::NBTITLE::/{{.TITLE}}/g' "src/notebooks/R Examples/{{.TITLE}}.ipynb"
      - sed -i '' 's/::NBAUTHOR::/{{.AUTHOR}}/g' "src/notebooks/R Examples/{{.TITLE}}.ipynb"
    preconditions:
      - sh: test -n "{{.TITLE}}"
        msg: "TITLE parameter missing. Set: TITLE='Notebook Name' AUTHOR='Your Name' task add-r-notebook"
      - sh: test -n "{{.AUTHOR}}"
        msg: "AUTHOR parameter missing. Set: TITLE='Notebook Name' AUTHOR='Your Name' task add-r-notebook"

  edit-notebooks:
    summary: |
      Opens Jupyter Lab (via Docker) in edit mode – with the notebooks source bound to this repository

      The files in src/notebooks are mounted as editable, and served on port 8888.
    cmds:
      - $NB_DOCKER_EXE run -it -v $PWD/src/notebooks:/home/jovyan/mgnify-examples -p 8888:8888 quay.io/microbiome-informatics/emg-notebooks.dev:latest

  build-notebook-docker:
    summary: |
      Builds a docker image with the Notebooks Server, locally.

      Useful if you're developing the Jupyter extensions, installing new R/Python packages to the conda envs etc.

      NOT needed if you're just editing/adding notebooks with no additional dependencies.
    cmds:
      - $NB_DOCKER_EXE build --load -f docker/Dockerfile -t quay.io/microbiome-informatics/emg-notebooks.dev:latest .

  build-static-docker:
    summary: |
      Builds a docker image with Quarto included, for statically rendering the notebook outputs.

      The built image is tagged as `notebooks-static`.
    cmds:
      - $NB_DOCKER_EXE build --load -f docker/docs.Dockerfile -t notebooks-static .
    sources:
      - docker/docs.Dockerfile
      - docker/Dockerfile

  render-static:
    summary: |
      Runs and renders the notebooks as a static website

      The site is built to ./_site
    cmds:
      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo notebooks-static render --execute
    deps: [build-static-docker]
    sources:
      - src/**/*

  serve-static:
    summary: |
      Serves the rendered notebooks and documentation as a static website

      This serves the contents of ./_site
    cmds:
      - echo "Browse to http://127.0.0.1:4444"
      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo/_site -p 4444:4444 --entrypoint python notebooks-static -m http.server 4444
    deps: [render-static]

  preview-static:
    summary: |
      Runs, renders, and serves the notebooks as a static website, watching for changes
    cmds:
      - echo 'When the rendering is finished, the static preview of notebooks will be at http://127.0.0.1:4444 ...'
      - $NB_DOCKER_EXE run -it -v $PWD:/opt/repo -w /opt/repo -p 4444:4444 notebooks-static preview --no-browser --port 4444 --host 0.0.0.0
    deps: [build-static-docker]

  update-mgnifyr-cache:
    summary: |
      Copies the MgnifyR Cache directory from the docker image into the host repository.

      Run this if you change the populate-mgnifyr-cache.R file.

      This cache zip is just used to speed up subsequent docker builds by not calling the MGnify API so much.

      It writes a zip of the cache to dependencies/mgnify-cache.tgz
    cmds:
      - $NB_DOCKER_EXE run -it -v $PWD/dependencies:/opt/dependencies -w /opt/dependencies quay.io/microbiome-informatics/emg-notebooks.dev:latest /bin/bash zip-mgnifyr-cache.sh