From b849530d5a3da6ab4d034fc3d76b265eb949267f Mon Sep 17 00:00:00 2001
From: Kevin Tyle <ktyle@albany.edu>
Date: Sat, 13 Jul 2024 15:24:08 -0700
Subject: [PATCH] MySTification

---
 .github/workflows/deploy.yml | 46 ++++++++++++++++++++++++++++++++++++
 Containerfile                | 27 ---------------------
 environment.yml              |  5 ++--
 myst.yml                     | 34 ++++++++++++++++++++++++++
 4 files changed, 83 insertions(+), 29 deletions(-)
 create mode 100644 .github/workflows/deploy.yml
 delete mode 100644 Containerfile
 create mode 100644 myst.yml

diff --git a/.github/workflows/deploy.yml b/.github/workflows/deploy.yml
new file mode 100644
index 0000000..de0c122
--- /dev/null
+++ b/.github/workflows/deploy.yml
@@ -0,0 +1,46 @@
+# This file was created automatically with `myst init --gh-pages` 🪄 💚
+
+name: MyST GitHub Pages Deploy
+on:
+  push:
+    # Runs on pushes targeting the default branch
+    branches: [main]
+env:
+  # `BASE_URL` determines the website is served from, including CSS & JS assets
+  # You may need to change this to `BASE_URL: ''`
+  BASE_URL: /${{ github.event.repository.name }}
+
+# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+# Allow only one concurrent deployment, skipping runs queued between the run in-progress and latest queued.
+# However, do NOT cancel in-progress runs as we want to allow these production deployments to complete.
+concurrency:
+  group: 'pages'
+  cancel-in-progress: false
+jobs:
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Setup Pages
+        uses: actions/configure-pages@v3
+      - uses: actions/setup-node@v4
+        with:
+          node-version: 18.x
+      - name: Install MyST Markdown
+        run: npm install -g mystmd
+      - name: Build HTML Assets
+        run: myst build --html
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v1
+        with:
+          path: './_build/html'
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v2
diff --git a/Containerfile b/Containerfile
deleted file mode 100644
index 1537553..0000000
--- a/Containerfile
+++ /dev/null
@@ -1,27 +0,0 @@
-# Use an official Python runtime as a base image
-FROM docker.io/mambaorg/micromamba:latest
-
-USER root
-
-RUN apt-get update && apt-get install -y git-all
-
-# Set the working directory in the container to /app
-WORKDIR /home/mambauser/app
-
-# Copy the current directory contents into the container at /usr/src/app
-RUN git clone https://github.com/NicholasCote/ERA5_interactive-cookbook-ncote.git
-
-# Install any needed packages specified in requirements.yml
-RUN micromamba env create -f ERA5_interactive-cookbook-ncote/environment.yml
-
-RUN mv ERA5_interactive-cookbook-ncote/notebooks/04_dashboard.ipynb .
-
-RUN rm -r ERA5_interactive-cookbook-ncote/
-
-# Activate the environment by providing ENV_NAME as an environment variable at runtime 
-# Make port bokeh application port to the world outside this container
-EXPOSE 5006
-
-USER mambauser
-
-CMD ["panel", "serve", "04_dashboard.ipynb", "--allow-websocket-origin=*", "--autoreload"]
\ No newline at end of file
diff --git a/environment.yml b/environment.yml
index da6e9e0..d41496e 100644
--- a/environment.yml
+++ b/environment.yml
@@ -2,7 +2,7 @@ name: ERA5_interactive
 channels:
   - conda-forge
 dependencies:
-  - python<3.12
+  - python
   - jupyter-book
   - jupyterlab
   - jupyter_server
@@ -24,4 +24,5 @@ dependencies:
   - sphinx-pythia-theme
   - hvplot
   - spatialpandas
-  - watchfiles
\ No newline at end of file
+  - watchfiles
+  - mystmd
diff --git a/myst.yml b/myst.yml
new file mode 100644
index 0000000..229a8eb
--- /dev/null
+++ b/myst.yml
@@ -0,0 +1,34 @@
+# See docs at: https://mystmd.org/guide/frontmatter
+version: 1
+extends:
+  - https://raw.githubusercontent.com/projectpythia-mystmd/pythia-config/main/pythia.yml
+project:
+  id: c598479d-c383-4e18-a8a5-b1840fefbec8
+  # title:
+  # description:
+  # keywords: []
+  # authors: []
+  github: https://github.com/projectpythia-mystmd/ERA5_interactive-cookbook
+  # To autogenerate a Table of Contents, run "myst init --write-toc"
+  toc:
+    # Auto-generated by `myst init --write-toc`
+    - file: README.md
+    - title: Preamble
+      children:
+        - file: notebooks/how-to-cite.md
+    - title: Visualization Notebooks
+      children:
+        - file: notebooks/01BasicVisualization.ipynb
+        - file: notebooks/02InteractiveVisualization.ipynb
+        - file: notebooks/03_hvplot.ipynb
+        - file: notebooks/04_dashboard.ipynb
+    - title: Preprocessing Notebooks for NCAR RDA
+      children:
+        - file: notebooks/05_data_preprocessing.ipynb
+        - file: notebooks/06_era5_anomaly.ipynb
+    
+site:
+  template: book-theme
+  # options:
+  #   favicon: favicon.ico
+  #   logo: site_logo.png