Merge pull request #47 from monarch-initiative/document-input-data-re…

…quirements Document input data requirements
monarch-initiative · Sep 15, 2023 · b713cdf · b713cdf
2 parents d8ebf00 + ac72675
commit b713cdf
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diff --git a/.github/workflows/pages.yml b/.github/workflows/pages.yml
@@ -0,0 +1,78 @@
+# Simple workflow for deploying static content to GitHub Pages
+name: Deploy documentation to GitHub Pages
+
+on:
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+  # Runs on pushes targeting the main branch
+  push:
+    branches: [ main, 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: main
+
+    - name: Set up Python 3
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.9
+
+    - name: Install library with docs dependencies
+      run: |
+        python3 -m pip install .[docs]
+
+    - name: Generate examples and 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}
+        
+          ## Build the docs
+          # Generate the HTML pages and move the generated content into the target folder.
+          printf "Building the %s documentation\n" ${DOCDIR}
+
+          cd docs
+          sphinx-apidoc --separate --module-first -d 2 -H "API reference" --follow-links -o apidocs ../src/genophenocorr
+          # TODO - enable doctest when ready
+          make html
+          
+          mv _build/html/* ../gh-pages/${DOCDIR}
+          cd ..
+        }
+        
+        # We store the docs for `main` in `stable` dir
+        # TODO - enable when the docs make it into `main`
+        #build_docs main stable
+        # We store the docs for `development` in `latest` dir
+        build_docs develop latest
+
+
+    - name: Deploy documentation
+      if: ${{ github.event_name == 'push' }}
+      uses: JamesIves/[email protected]
+      with:
+        branch: gh-pages
+        force: true
+        folder: gh-pages
diff --git a/.github/workflows/python_ci.yml b/.github/workflows/python_ci.yml
@@ -1,14 +1,10 @@
 name: CI
-##
-# Add the line below to README.md and the badge will come alive when we make the repo public.
-# [![CI](https://github.com/monarch-initiative/genophenocorr/workflows/CI/badge.svg)](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)
 
 on:
-    workflow_dispatch:
-    # push:
-    #   branches: [ develop ]
-    # pull_request:
-    #   branches: [ main, develop ]
+    push:
+      branches: [ develop ]
+    pull_request:
+      branches: [ main, develop ]
 
 jobs:
     build:
@@ -19,8 +15,8 @@ jobs:
         matrix:
           os:
             - ubuntu-latest
-            # - windows-latest
-            # - macOS-latest
+            - windows-latest
+            - macOS-latest
 
       steps:
         - uses: actions/checkout@v2

diff --git a/README.md b/README.md
@@ -1,5 +1,7 @@
-# gpc
-Genotype Phenotype Correlation 
+# Genophenocorr
+# [![CI](https://github.com/monarch-initiative/genophenocorr/workflows/CI/badge.svg)](https://github.com/monarch-initiative/genophenocorr/actions/workflows/python_ci.yml)
+
+A Python library for genotype-phenotype association analysis. 
 
 
 # Set up

diff --git a/docs/data/simple_cohort/PMID_36446582_Alves_2019.json b/docs/data/simple_cohort/PMID_36446582_Alves_2019.json
@@ -0,0 +1,146 @@
+{
+  "id": "Alves, 2019",
+  "subject": {
+    "id": "Alves, 2019",
+    "timeAtLastEncounter": {
+      "age": {
+        "iso8601duration": "P2Y"
+      }
+    },
+    "sex": "FEMALE"
+  },
+  "phenotypicFeatures": [
+    {
+      "type": {
+        "id": "HP:0006482",
+        "label": "Abnormality of dental morphology"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P2Y"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0001155",
+        "label": "Abnormality of the hand"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P2Y"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0004322",
+        "label": "Short stature"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P2Y"
+        }
+      }
+    },
+    {
+      "type": {
+        "id": "HP:0000365",
+        "label": "Hearing impairment"
+      },
+      "onset": {
+        "age": {
+          "iso8601duration": "P2Y"
+        }
+      }
+    }
+  ],
+  "interpretations": [
+    {
+      "id": "Alves, 2019",
+      "progressStatus": "SOLVED",
+      "diagnosis": {
+        "disease": {
+          "id": "OMIM:148050",
+          "label": "KBG syndrome"
+        },
+        "genomicInterpretations": [
+          {
+            "subjectOrBiosampleId": "Alves, 2019",
+            "interpretationStatus": "CAUSATIVE",
+            "variantInterpretation": {
+              "variationDescriptor": {
+                "id": "variation-descriptor-id",
+                "geneContext": {
+                  "valueId": "HGNC:21316",
+                  "symbol": "ANKRD11"
+                },
+                "expressions": [
+                  {
+                    "syntax": "hgvs.c",
+                    "value": "NM_013275.6:c.5145C>G"
+                  },
+                  {
+                    "syntax": "hgvs.g",
+                    "value": "NC_000016.10:g.89281397G>C"
+                  }
+                ],
+                "vcfRecord": {
+                  "genomeAssembly": "hg38",
+                  "chrom": "chr16",
+                  "pos": "89281397",
+                  "ref": "G",
+                  "alt": "C"
+                },
+                "moleculeContext": "genomic",
+                "allelicState": {
+                  "id": "GENO:0000135",
+                  "label": "heterozygous"
+                }
+              }
+            }
+          }
+        ]
+      }
+    }
+  ],
+  "metaData": {
+    "created": "2023-04-24T19:37:25.478348970Z",
+    "createdBy": "ORCID:0000-0003-2598-6622",
+    "resources": [
+      {
+        "id": "geno",
+        "name": "Genotype Ontology",
+        "url": "http://purl.obolibrary.org/obo/geno.owl",
+        "version": "2022-03-05",
+        "namespacePrefix": "GENO",
+        "iriPrefix": "http://purl.obolibrary.org/obo/GENO_"
+      },
+      {
+        "id": "hgnc",
+        "name": "HUGO Gene Nomenclature Committee",
+        "url": "https://www.genenames.org",
+        "version": "06/01/23",
+        "namespacePrefix": "HGNC",
+        "iriPrefix": "https://www.genenames.org/data/gene-symbol-report/#!/hgnc_id/"
+      },
+      {
+        "id": "omim",
+        "name": "An Online Catalog of Human Genes and Genetic Disorders",
+        "url": "https://www.omim.org",
+        "version": "January 4, 2023",
+        "namespacePrefix": "OMIM",
+        "iriPrefix": "https://www.omim.org/entry/"
+      },
+      {
+        "id": "hp",
+        "name": "human phenotype ontology",
+        "url": "http://purl.obolibrary.org/obo/hp.owl",
+        "version": "2023-01-27",
+        "namespacePrefix": "HP",
+        "iriPrefix": "http://purl.obolibrary.org/obo/HP_"
+      }
+    ],
+    "phenopacketSchemaVersion": "2.0"
+  }
+}