Update documentation to use new gh-pages

.github/workflows/publish.yaml

@@ -0,0 +1,31 @@
+name: Publish docs to GitHub pages 
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - mkdocs-material 
+
+permissions:
+  contents: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Configure Git Credentials
+        run: |
+          git config user.name github-actions[bot]
+          git config user.email 41898282+github-actions[bot]@users.noreply.github.com
+      - uses: actions/setup-python@v4
+        with:
+          python-version: 3.x
+      - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV 
+      - uses: actions/cache@v3
+        with:
+          key: mkdocs-material-${{ env.cache_id }}
+          path: .cache
+          restore-keys: |
+            mkdocs-material-
+      - run: pip install mkdocs-material 
+      - run: mkdocs gh-deploy --force

docs/README.md

@@ -1,50 +1,27 @@
-template: jumbotron.html
-extra_css: [extra.css]
-
-<div class="header-container jumbotron">
-    <div class="container">
-        <h1>Seqcol: Sequence Collections</h1>
-        <p>Unique identifiers and lookup service for sequence collections.
-          </p>
-        <p><a class="btn btn-primary btn-lg" href="specification" role="button">Learn more</a></p>
-    </div>
-</div>
-<div class="container">
-    <div class="row">
-        <div class="col-md-8">
-            <h1 class="header-light regular-pad">What is SeqCol?</h1>
-            <blockquote>
-              <p><i>Seqcol</i>, or <i>Sequence Collections</i>, is a GA4GH-sponsored <b>community effort to standardize unique identifiers for collections of sequences</b>. Seqcol identifiers can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. The seqcol protocol provides:
-                <ol>
-              <li>implementations of an algorithm for computing sequence identifiers;</li>
-              <li>a lookup service to retrieve sequences given a seqcol identifier</li>
-              <li>programmatic approach to assessing compatibility among sequence collections.</li>
-              </ol>
-            </p>
-            <a href="specification">Read the complete specification</a>
-            </blockquote>
-        </div>
-        <div class="col-md-4 text-center">
-            <br><br>
-            <img src="seqcol_abstract_simple.svg" alt="" class="img-responsive">
-        </div>
-    </div>
-    <hr>
-     <div class="row">
-        <div class="col-sm-4">
-            <h1 class="text-center"><i class="fa fa-chart-bar" aria-hidden="true"></i></h1>
-            <h3 class="text-center">Data analysts</h3>
-            <p>Uniquely identify the sequences you use with persisent identifiers</p>
-        </div>
-        <div class="col-sm-4">
-            <h1 class="text-center"><i class="fa fa-wrench" aria-hidden="true"></i></h1>
-            <h3 class="text-center">Software developers</h3>
-            <p>Use Seqcol identifiers to embed persistent information in your tools about what genome was used in an analysis.</p>
-        </div>
-        <div class="col-sm-4">
-            <h1 class="text-center"><i class="fa fa-cogs" aria-hidden="true"></i></h1>
-            <h3 class="text-center">Workflow systems</h3>
-            Use our APIs to retrieve metadata for sequences you use.
-        </div>
-    </div>
-</div>
+# Refget
+
+Unique identifiers and lookup service for reference sequences and sequence collections.
+
+<img src="img/seqcol_abstract_simple.svg" alt="Refget abstract" class="img-responsive">
+
+
+## What is refget?
+
+
+Refget is a protocol for identifying and distributing biological sequence references. It currently consists of 2 standards:
+
+1. Refget sequences: a GA4GH-approved standard for individual sequences
+2. Refget sequence collections: a standard for collections of sequences, under review 
+
+## What is the refget sequences standard?
+
+The original refget handled sequences only. Refget enables access to reference sequences using an identifier derived from the sequence itself.
+
+## What is the refget sequence collections standard?
+
+*Sequence Collections*, or `seqcol` for short, standardizes unique identifiers for collections of sequences. Seqcol identifiers can be used to identify genomes, transcriptomes, or proteomes -- anything that can be represented as a collection of sequences. The seqcol protocol provides:
+
+- implementations of an algorithm for computing sequence identifiers;
+- a lookup service to retrieve sequences given a seqcol identifier
+- programmatic approach to assessing compatibility among sequence collections.
+

docs/specification.md → docs/seqcol.md

@@ -6,11 +6,11 @@ title: Seqcol specification version 0.1.0
 * The generated Toc will be an unordered list
 {:toc} -->
 
-<h1>Seqcol specification version 0.1.0</h1>
+# Seqcol specification version 0.1.0
 
-Table of contents:
+<!-- Table of contents:
 
-[TOC]
+[TOC] -->
 
 ## Specification version