Initial commit

.github/workflows/build_book.yml

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+name: deploy-site
+
+# Only run this when the main branch changes
+on:
+  push:
+    branches:
+    - main
+  pull_request:
+  workflow_dispatch:
+  release:
+
+# This job installs dependencies, builds the book, and pushes it to `gh-pages`
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    if: github.repository == 'OceanGlidersCommunity/Oxygen_SOP'
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - name: Cancel previous runs
+        uses: styfle/[email protected]
+        with:
+          access_token: ${{ github.token }}
+      - uses: actions/checkout@v3
+
+      # Install dependencies
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      # Build the book
+      - name: Build the book
+        run: |
+          jupyter-book build .
+
+      # Zip the site (so it can be handed to the preview action)
+      - name: Zip the site
+        run: |
+          set -x
+          set -e
+          if [ -f site.zip ]; then
+              rm -rf site.zip
+          fi
+          zip -r site.zip ./_build/html
+      - uses: actions/upload-artifact@v3
+        with:
+          name: site-zip
+          path: ./site.zip
+
+      # Push the site's HTML to github-pages (only if on main, previews are sent to netlify)
+      - name: Deploy to GitHub pages
+        if: github.ref == 'refs/heads/main'
+        uses: peaceiris/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          publish_dir: ./_build/html
+          enable_jekyll: false
+  build_pdf:
+    runs-on: ubuntu-latest
+    if: github.event_name == 'release'
+    needs: build
+    defaults:
+      run:
+        shell: bash -l {0}
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.9
+
+      - name: Install dependencies
+        run: |
+          pip install -r requirements.txt
+
+      - name: Install Tex
+        run: | 
+          sudo apt-get install texlive-latex-recommended texlive-latex-extra \
+                     texlive-fonts-recommended texlive-fonts-extra \
+                     texlive-xetex latexmk
+               
+      - name: Build the book as pdf #This needs to happen after the site is zipped, since this builds different html that we dont want on the website
+        run: |
+           jupyter-book build . --builder pdflatex
+      
+      - uses: actions/upload-artifact@v3
+        with:
+           name: book-pdf
+           path: _build/latex/python.pdf

.github/workflows/preview-book.yml

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+name: preview-site
+on:
+  workflow_run:
+    workflows:
+      - deploy-site
+    types:
+      - requested
+      - completed
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash
+    steps:
+      - uses: actions/checkout@v2
+      - name: Set message value
+        run: |
+          echo "comment_message=This pull request is being automatically built with [GitHub Actions](https://github.com/features/actions) and [Netlify](https://www.netlify.com/). To see the status of your deployment, click below." >> $GITHUB_ENV
+      - name: Find Pull Request
+        uses: actions/github-script@v4
+        id: find-pull-request
+        with:
+          script: |
+            let pullRequestNumber = ''
+            let pullRequestHeadSHA = ''
+            core.info('Finding pull request...')
+            const pullRequests = await github.pulls.list({owner: context.repo.owner, repo: context.repo.repo})
+            for (let pullRequest of pullRequests.data) {
+              if(pullRequest.head.sha === context.payload.workflow_run.head_commit.id) {
+                  pullRequestHeadSHA = pullRequest.head.sha
+                  pullRequestNumber = pullRequest.number
+                  break
+              }
+            }
+            core.setOutput('number', pullRequestNumber)
+            core.setOutput('sha', pullRequestHeadSHA)
+            if(pullRequestNumber === '') {
+              core.info(
+                `No pull request associated with git commit SHA: ${context.payload.workflow_run.head_commit.id}`
+              )
+            }
+            else{
+              core.info(`Found pull request ${pullRequestNumber}, with head sha: ${pullRequestHeadSHA}`)
+            }
+      - name: Find Comment
+        uses: peter-evans/find-comment@v1
+        if: steps.find-pull-request.outputs.number != ''
+        id: fc
+        with:
+          issue-number: '${{ steps.find-pull-request.outputs.number }}'
+          comment-author: 'github-actions[bot]'
+          body-includes: '${{ env.comment_message }}'
+      - name: Create comment
+        if: |
+          github.event.workflow_run.conclusion != 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id == ''
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          issue-number: ${{ steps.find-pull-request.outputs.number }}
+          body: |
+            ${{ env.comment_message }}
+
+            🚧 Deployment in progress for git commit SHA: ${{ steps.find-pull-request.outputs.sha }}
+      - name: Update comment
+        if: |
+          github.event.workflow_run.conclusion != 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id != ''
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            ${{ env.comment_message }}
+
+            🚧 Deployment in progress for git commit SHA: ${{ steps.find-pull-request.outputs.sha }}
+      - name: Download Artifact site
+        if: |
+          github.event.workflow_run.conclusion == 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id != ''
+        uses: dawidd6/[email protected]
+        with:
+          github_token: ${{ secrets.GITHUB_TOKEN }}
+          workflow: deploy.yaml
+          run_id: ${{ github.event.workflow_run.id }}
+          name: site-zip
+      - name: Unzip site
+        if:  |
+          github.event.workflow_run.conclusion == 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id != ''
+        run: |
+          rm -rf _build/html
+          unzip site.zip
+          rm -f site.zip
+      # Push the site's HTML to Netlify and get the preview URL
+      - name: Deploy to Netlify
+        if: |
+          github.event.workflow_run.conclusion == 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id != ''
+        id: netlify
+        uses: nwtgck/[email protected]
+        with:
+          publish-dir: _build/html
+          production-deploy: false
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          enable-commit-comment: false
+        env:
+          NETLIFY_AUTH_TOKEN: ${{ secrets.NETLIFY_AUTH_TOKEN }}
+          NETLIFY_SITE_ID: ${{ secrets.NETLIFY_SITE_ID }}
+        timeout-minutes: 5
+      - name: Update site Preview comment
+        if: |
+          github.event.workflow_run.conclusion == 'success'
+          && steps.find-pull-request.outputs.number != ''
+          && steps.fc.outputs.comment-id != ''
+        uses: peter-evans/create-or-update-comment@v1
+        with:
+          comment-id: ${{ steps.fc.outputs.comment-id }}
+          edit-mode: replace
+          body: |
+            ${{ env.comment_message }}
+
+            🔍 Git commit SHA:  ${{ steps.find-pull-request.outputs.sha }}
+            ✅ Deployment Preview URL: ${{ steps.netlify.outputs.deploy-url }}

.gitignore

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+_build
+__pycache__

BOON Guidelines for “Network” and “Site” Metadata.md

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+# BOON Guidelines for “Network” and “Site” Metadata
+
+* This document describes the metadata fields that will be used by OceanOPS to populate the “Network” field in their system.
+* The goal is to have BOON assets identified and easy to find within OceanOPS. Granularity is needed both in **network** attribution and **site** attribution. 
+* These metadata fileds will allow a better tracking of the BOON Task Team activity, and assessement of the status of the task team toward its target.
+* Values for the metadata fields can be flexible but will be managed in a vocabulary on GitHub to make it easier for data providers to best populate the fields and allow for cohesion.
+
+---
+
+## Network Metadata Field Background
+A format for BOON Network metadata values was chosen in 2022 (based on a meeting 12/09/2022 and follow-up correspondence). Network values were selected for the California Underwater Glider Network (CUGN) and Gulf Stream programs and this documentation was drafted.  
+These values have been tested and integrated into the near-real-time data streams for these gliders through to the OceanGliders data system. 
+With this format the data provider chooses an NCEI Sea Name to provide an indicator of the region for their glider operations. Multiple network attributions are allowed. To implement this use a comma to separate each network entry.
+
+**Example BOON network identifiers**
+* OceanGliders > BOON > Northeast Pacific Ocean > California Underwater Glider Network
+* OceanGliders > BOON > Northwest Atlantic Ocean > Gliders in the Gulf Stream
+
+
+
+---
+
+
+## How this looks in metadata
+The use of the metadata scheme below can be used with any NetCDF format currently used to store glider data. This includes the EGO, IOOS glider DAC and IMOS glider formats.
+
+The [OG-1.0 format](https://github.com/OceanGlidersCommunity/OG-format-user-manual) has also been designed to handle this information.
+
+The two concepts described below, **network** and **site** should be included in the NetCDF global attributes with a string data type. 
+
+
+## Definition
+### Network
+A **network** is a regroupment of platforms, crossing the boundaries of the program. It is usually virtual and represents a common effort or way to measure data. It can represent a mutualized scientific/geographical goal (array), or logistical/fundings/etc. approach.
+BOON networks refers to a regional array (multiple sites, e.g *California Underwater Glider Network*) or an area of repeated glider operation (e.g. *glider in the gulf stream*)
+
+Find the appropriate network name from the [BOON network list](https://github.com/OceanGlidersCommunity/BOON/blob/main/VocabularyCollection/BOON%20networks.md#boon-networks-collection) and [BOON site list](https://github.com/OceanGlidersCommunity/BOON/blob/main/VocabularyCollection/BOON%20networks.md#boon-site-collection) and use it as the value in the **network** global attribute. If you would like to list more than one network you can use a comma to separate each network entry. This format requires that the network names themselves do not include commas. If your network is not in the list, request that it be added. See instructions in the 'request a new entry' section below. 
+
+The global attribute **network** follows this format:
+OceanGliders > BOON > [NCEI Sea Name](https://www.ncei.noaa.gov/data/oceans/ncei/vocabulary/seanames.xml) > *Your BOON Network Name*. (e.g *OceanGliders > BOON > Northwest Atlantic Ocean > Gliders in the Gulf Stream*)
+Where ">" is mandatory.
+
+**Example BOON network metadata:**
+| NetCDF global attribute | Data Type | Value |
+|:-------|:-------|:-------|
+| network | string | OceanGliders > BOON > Northwest Atlantic Ocean > Gliders in the Gulf Stream |
+
+**Example with multiple networks:**
+| NetCDF global attribute | Data Type | Value |
+|:-------|:-------|:-------|
+| network | string | OceanGliders > BOON > Northeast Pacific Ocean > California Underwater Glider Network, IOOS > SCCOOS, IOOS > CeNCOOS |
+
+
+## Site
+A **site** refers to the specific lines regularly monitored by gliders (e.g. *Balearic - Canales C1, CUGN Line 66*)
+
+**Example site metadata:**
+ NetCDF global attribute | Data Type | Value |
+|:-------|:-------|:-------|
+| network | string | CUGN Line 66|
+
+**Example with multiple networks:**
+| NetCDF global attribute | Data Type | Value |
+|:-------|:-------|:-------|
+| network | string | CUGN Line 66, CUGN Alongshore|
+
+# Request a new entry
+To request a new entry in the BOON Networks vocabulary and BOON Site vocabulary submit an issue in the [BOON repository](https://github.com/OceanGlidersCommunity/BOON) with the entry you would like to add to the vocabulary collection.
+
+In the case of **network**, you must provide the full value i.e. "OceanGliders > BOON > [NCEI Sea Name](https://www.ncei.noaa.gov/data/oceans/ncei/vocabulary/seanames.xml) > *Your BOON Network Name*."
+