Merge pull request #163 from TheJacksonLaboratory/develop

Develop

.github/workflows/documentation.yaml

@@ -1,35 +1,26 @@
-name: Sphinx Documentation
+name: mkdocs-generation
 on:
   push:
-    branches: [ main ]
-
+    branches:
+      - master
+      - main
+permissions:
+  contents: write
 jobs:
-  build-docs:
+  deploy:
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v3
+      - uses: actions/setup-python@v4
         with:
-          ref: ${{ github.ref }}
-
-      - name: Set up Python 3.
-        uses: actions/setup-python@v3
+          python-version: 3.x
+      - uses: actions/cache@v2
         with:
-          python-version: 3.9
-
-      - name: install
-        run: pip3 install sphinx sphinx-rtd-theme click ddt pandas setuptools
-
-      - name: Build documentation.
-        run: |
-          cd docs/
-          sphinx-build -b html . _build
-          touch _build/.nojekyll
-
-      - name: Deploy documentation.
-        if: ${{ github.event_name == 'push' }}
-        uses: JamesIves/[email protected]
-        with:
-          branch: gh-pages
-          clean: true
-          folder: docs/_build
+          key: ${{ github.ref }}
+          path: .cache
+      - run: pip install mkdocs-material
+      - run: pip install mkdocs-material[imaging]
+      - run: pip install pillow cairosvg
+      - run: pip install mkdocs-material-extensions
+      - run: pip install mkdocstrings[python]
+      - run: mkdocs gh-deploy --force

README.md

@@ -9,8 +9,8 @@ Releases page.
 
 ## Background
 [Gene Ontology](http://geneontology.org/) traditionally has provided
-annotations for genes rather than for specific isoforms. However, in 
-some cases, the functions of the individual isoforms of a gene are 
+annotations for genes rather than for specific isoforms. However, in
+some cases, the functions of the individual isoforms of a gene are
 differ with respect to one or more of the gene's function. In this project,
 we have developed an algorithm for prediction of isoform-specific function
 across the entire transcriptome. The isopret app offers a number of
@@ -33,13 +33,13 @@ Macintosh laptops with the new ARM M1 chip when using Oracle's SDK (version 17.0
 have used [Azul Zulu](https://www.azul.com/downloads/?package=jdk) JDKs on M1 Macintoshes and
 could run Isopret and other JavaFX apps without problems.
 
-We offer pre-built installation files for MacIntosh (M1 and Intel) in the Release section. 
+We offer pre-built installation files for MacIntosh (M1 and Intel) in the Release section.
 
 ## Note to Linux users
 
 The easiest way to run isopret-gui on a linux system is to run the downloadable JAR file from the releases page.
 
-```aidl
+```bash
 java -jar isopret-gui.jar
 ```
 
@@ -53,4 +53,22 @@ A manuscript is in preparation.
 
 
 
+## Set up documentation
+
+Enter the following code to install mkdocs and run a server locally. The GitHub action will create a comparable site online.
+
+```
+python3 -m venv venv
+source venv/bin/activate
+pip install mkdocs-material
+pip install mkdocs-material[imaging]
+pip install mkdocs-material-extensions
+pip install pillow cairosvg
+pip install mkdocstrings[python]
+mkdocs serve
+```
+
+
+
+