From 1b898bfaccd5fb229bbd963a53b7c5c456e13a5e Mon Sep 17 00:00:00 2001
From: Brian Schlining <bschlining@gmail.com>
Date: Wed, 24 Apr 2024 17:31:30 -0700
Subject: [PATCH] Updated docs

---
 .github/workflows/docs.yml | 33 +++++++++++++++++++++------------
 .github/workflows/test.yml |  7 ++++---
 README.md                  | 16 +++++-----------
 3 files changed, 30 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index d92269d..b573ced 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -4,39 +4,48 @@ on:
   push:
     branches: ["main"]
 
-permissions:
-  contents: read
-  pages: write
-  id-token: write
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# Allow one concurrent deployment
+concurrency:
+  group: "pages"
+  cancel-in-progress: true
 
 jobs:
   build:
     runs-on: ubuntu-latest
-
+    permissions:
+      contents: read
+      pages: write
+      id-token: write
     steps:
       - uses: actions/checkout@v3
-      - name: Set up JDK 17
+      - name: Set up JDK 21
         uses: actions/setup-java@v3
         with:
-          java-version: "17"
+          java-version: "21"
           distribution: "temurin"
           cache: "sbt"
       - name: Build site
-        run: sbt laikaSite
+        run: sbt doc
         env:
-          GITHUB_TOKEN: ${{ github.token }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - name: Upload site
         uses: actions/upload-pages-artifact@v1.0.1
         with:
-          path: ./target/docs/site
+          path: ./target/scala-3.3.3/api
 
   deploy:
+    needs: build
+    permissions:
+      pages: write
+      id-token: write
     environment:
       name: github-pages
       url: ${{ steps.deployment.outputs.page_url }}
     runs-on: ubuntu-latest
-    needs: build
     steps:
       - name: Deploy to GitHub Pages
         id: deployment
-        uses: actions/deploy-pages@v1
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 316812f..763d2f3 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -15,13 +15,14 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3
-      - name: Set up JDK 17
+      - name: Set up JDK 21
         uses: actions/setup-java@v3
         with:
-          java-version: "17"
+          java-version: "21"
           distribution: "temurin"
           cache: "sbt"
       - name: Run unit tests
         run: sbt test
         env:
-          GITHUB_TOKEN: ${{ github.token }}
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          MUNIT_FLAKY_OK: "true"
diff --git a/README.md b/README.md
index f83aab4..e0d7413 100644
--- a/README.md
+++ b/README.md
@@ -1,14 +1,16 @@
-# oni
+# oni - Organism Naming Infrastructure
 
 ![Build](https://github.com/mbari-org/oni/actions/workflows/test.yml/badge.svg)
 
 ![MBARI logo](src/docs/images/logo-mbari-3b.png)
 
-MBARI [sbt](https://www.scala-sbt.org) project compiled with [Scala 3](https://www.scala-lang.org)
+## Overview
+
+This is a project to create a RESTful API for managing the naming of organisms. Currently in development, it is meant to be a replacement for <https://github.com/mbari-org/vars-kb-server> and <https://github.com/mbari-org/vars-user-server>. 
 
 ## Usage
 
-This is a normal sbt project. You can compile code with `sbt compile`, run it with `sbt run`, and `sbt console` will start a Scala 3 REPL.
+This is a normal [sbt](https://www.scala-sbt.org) project. You can compile code with `sbt compile`, run it with `sbt run`, and `sbt console` will start a Scala 3 REPL.
 
 ## Useful Commands
 
@@ -17,14 +19,6 @@ This is a normal sbt project. You can compile code with `sbt compile`, run it wi
 3. `scaladoc` - Build documentation, including API docs to `target/docs/site`
 4. `compile` then `scalafmtAll` - Will convert all syntax to new-style, indent based Scala 3.
 
-## Libraries
-
-- [circe](https://circe.github.io/circe/) for JSON handling
-- [Methanol](https://github.com/mizosoft/methanol) with [Java's HttpClient](https://docs.oracle.com/en/java/javase/17/docs/api/java.net.http/java/net/http/HttpClient.html) for HTTP client
-- [munit](https://github.com/scalameta/munit) for testing
-- [picocli](https://picocli.info/) for command line arg parsing
-- [slf4j](http://www.slf4j.org/) with [logback](http://logback.qos.ch/) for logging. Use java.lang.System.Logger
-- [ZIO](https://zio.dev/) for effects
 
 ## Notes