Merge pull request #645 from TheJacksonLaboratory/release-2.0.0-RC3

Release 2.0.0 RC3

.github/workflows/maven.yml

@@ -11,25 +11,23 @@ on:
 
 jobs:
   build:
-    runs-on: ${{ matrix.os }}
-    env:
-      JDK_VERSION: ${{ matrix.jdk }}
-
     strategy:
       fail-fast: false
       matrix:
         os: [ windows-latest, macOS-latest, ubuntu-latest ]
         jdk: [ 17 ]
 
+    runs-on: ${{ matrix.os }}
+
     steps:
       - uses: actions/checkout@v2
 
       - name: Set up JDK
         uses: actions/setup-java@v2
         with:
-          java-version: '17'
+          java-version: ${{ matrix.jdk }}
           distribution: 'adopt'
 
       - name: Build with Maven
-        run: ./mvnw --batch-mode verify
+        run: ./mvnw --quiet --batch-mode verify
 

.github/workflows/pages.yml

@@ -0,0 +1,84 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy docs to GitHub pages
+
+on:
+  # Runs on pushes targeting the master and develop branches
+  push:
+    branches: [ master, develop ]
+
+jobs:
+  build-docs:
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Checkout
+      uses: actions/checkout@v3
+      with:
+        fetch-depth: 0 # otherwise, you will fail to push refs to dest repo
+        ref: develop
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install Python dependencies
+      run: |
+        pip install sphinx
+        pip install sphinx-rtd-theme
+
+    - name: Set up JDK 17
+      uses: actions/setup-java@v3
+      with:
+        java-version: '17'
+        distribution: 'adopt'
+
+    - name: Build documentation
+      run: |
+        ## Init the target folder. 
+        # We will put all site documentation there.
+        mkdir -p gh-pages
+        touch gh-pages/.nojekyll
+        
+        function build_docs {
+          # The function will checkout a branch and build the Javadoc & documentation 
+          # into provided documentation directory.
+          BRANCH=${1}
+          DOCDIR=${2}
+          
+          git checkout ${BRANCH}
+          git fetch
+          git pull
+          ## Init the target folder.
+          # We will put all site documentation there.
+          mkdir -p gh-pages/${DOCDIR}
+          
+          ## Javadoc
+          # Build the aggregated Javadoc
+          ./mvnw --quiet -Ddoclint=none -Dinherited=false clean javadoc:aggregate
+          # Copy aggregated Javadoc into `apidocs` folder.
+          APIDOCS=$(pwd)/gh-pages/${DOCDIR}/apidocs
+          printf "Copying Javadocs from %s to %s\n" $(pwd)/target/site/apidocs ${APIDOCS}
+          cp -r target/site/apidocs ${APIDOCS}
+          
+          ## Build the docs
+          # Generate the HTML pages and move the generated content into the target folder.
+          printf "Building the %s documentation\n" ${DOCDIR}
+          cd docs/
+          make html
+          cd ..
+          mv docs/_build/html/* gh-pages/${DOCDIR}
+        }
+        
+        # We store the docs for `master` in `stable` dir
+        build_docs master stable
+        # We store the docs for `develop` in `latest` dir
+        build_docs develop latest
+
+
+    - name: Deploy documentation
+      if: ${{ github.event_name == 'push' }}
+      uses: JamesIves/[email protected]
+      with:
+        folder: gh-pages
+        force: false

.gitignore

@@ -14,6 +14,7 @@ target/
 *.iml
 *.log
 data/
+results/
 dependency-reduced-pom.xml
 .settings
 .project

README.md

@@ -1,29 +1,40 @@
+# LIRICAL
+
 [![GitHub release](https://img.shields.io/github/release/TheJacksonLaboratory/LIRICAL.svg)](https://github.com/TheJacksonLaboratory/LIRICAL/releases)
 [![Java CI with Maven](https://github.com/TheJacksonLaboratory/LIRICAL/workflows/Java%20CI%20with%20Maven/badge.svg)](https://github.com/TheJacksonLaboratory/LIRICAL/actions/workflows/maven.yml)
 
-# LIRICAL
 LIRICAL (LIkelihood Ratio Interpretation of Clinical AbnormaLities) 
 is designed to provide clinically interpretable computational analysis of phenotypic
 abnormalities (encoded using the [Human Phenotype Ontology](http://www.human-phenotype-ontology.org)),
 optionally combined with an analysis of variants and genotypes if a VCF file is provided with the
 results of diagnostic gene panel, exome, or genome sequencing.
 
-A manuscript describing LIRICAL is available at the 
-[American Journal of Human Genetics](https://pubmed.ncbi.nlm.nih.gov/32755546/).
+The prioritized diseases are reported in human-friendly HTML report. 
+The report summarizes the most likely differential diagnoses:
+
+<img src="docs/_static/lirical-sparkline-lds2.top5.png" alt="Top matches" width="800"/>
+
+and breaks down the contributions of the HPO terms and deleterious variants in the associated genes for each diagnosis:
+
+<img src="docs/_static/lirical-detailed-TGFBR2.png" alt="" width="800" title="Diff dg"/>
+
+The report is also available in JSON/TSV formats suitable for programmatic post-processing.
 
 
 ## Availability
-Most users should download the latest distribution ZIP file from
-the [Releases page](https://github.com/TheJacksonLaboratory/LIRICAL/releases).
 
+Most users should download the latest distribution ZIP file from the [Releases page](https://github.com/TheJacksonLaboratory/LIRICAL/releases).
+
+
+## Learn more
 
-## Documentation
-Please consult the documentation for installation instructions and a tutorial:
-- [reference documentation](https://thejacksonlaboratory.github.io/LIRICAL/stable)
-- [edge release documentation](https://thejacksonlaboratory.github.io/LIRICAL/latest)
+Read more about the LIRICAL *algorithm* 
+in the manuscript available at the [American Journal of Human Genetics](https://pubmed.ncbi.nlm.nih.gov/32755546/).
 
+Consult the documentation for *installation instructions* and a *tutorial*:
+- [Stable documentation](https://thejacksonlaboratory.github.io/LIRICAL/stable)
+- [Edge release documentation](https://thejacksonlaboratory.github.io/LIRICAL/latest)
 
-## API docs
-Developers can access Javadoc at:
-- [reference](https://thejacksonlaboratory.github.io/LIRICAL/stable/apidocs)
-- [edge release](https://thejacksonlaboratory.github.io/LIRICAL/latest/apidocs)
+Developers can access *API reference* at:
+- [Stable](https://thejacksonlaboratory.github.io/LIRICAL/stable/apidocs)
+- [Edge release](https://thejacksonlaboratory.github.io/LIRICAL/latest/apidocs)

docs/conf.py

@@ -56,7 +56,7 @@
 # The short X.Y version.
 version = u'2.0'
 # The full version, including alpha/beta/rc tags.
-release = u'2.0.0-RC2'
+release = u'2.0.0-RC3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -18,6 +18,7 @@ as `Human Phenotype Ontology (HPO) <http://www.human-phenotype-ontology.org>`_ t
    setup
    tutorial
    running
+   input-sanitation
    output
    explanations
    advanced