Sphinx doc

.github/workflows/documentation.yml

@@ -2,6 +2,11 @@ name: Baskerville Docs
 
 on:
   workflow_dispatch:
+    inputs:
+      python-version:
+        default: "3.10"
+        required: false
+        type: string
 
 defaults:
   run:
@@ -11,12 +16,20 @@ permissions:
   contents: write
 jobs:
   docs:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
+    strategy:
+      matrix:
+        python-version: ["3.10"]
     steps:
       - uses: actions/checkout@v3
 
-      - uses: actions/setup-python@v3
-
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      # You can test your matrix by printing the current Python version
+      - name: Display Python version
+        run: python -c "import sys; print(sys.version)"
       - name: Install dependencies
         run: |
           cd ${{ github.workspace }}/src/docs

setup.cfg

@@ -35,7 +35,6 @@ install_requires =
     seaborn~=0.12.2
     scikit-learn~=1.2.2
     scipy~=1.9.1
-    sphinx~=7.2.6
     statsmodels~=0.13.5
     tabulate~=0.8.10
     tensorflow==2.13.0

src/docs/requirements.txt

@@ -1,4 +1,23 @@
+h5py~=3.7.0
+intervaltree~=3.1.0
+joblib~=1.1.1
+matplotlib~=3.7.1
+google-cloud-storage~=2.0.0
+natsort~=7.1.1
+networkx~=2.8.4
+numpy
+pandas~=1.5.3
+pybigwig~=0.3.18
+pysam~=0.21.0
+pybedtools~=0.9.0
+qnorm~=0.8.1
+seaborn~=0.12.2
+scikit-learn~=1.2.2
+scipy~=1.9.1
 sphinx 
 sphinx_rtd_theme 
-python-dotenv
-google
+sphinxcontrib-apidoc
+statsmodels~=0.13.5
+tensorflow==2.13.0
+tabulate~=0.8.10
+tqdm~=4.65.0

src/docs/source/conf.py

@@ -10,6 +10,10 @@
 
 # This root should be where docs folder is visible.
 sys.path.insert(0, os.path.abspath("../.."))
+sys.path.insert(0, os.path.abspath("../../baskerville"))
+sys.path.insert(0, os.path.abspath("../../baskerville/scripts"))
+sys.path.insert(0, os.path.abspath("../../bashkerville/helpers"))
+
 sys.setrecursionlimit(1500)
 
 project = "baskerville"
@@ -25,6 +29,7 @@
     "sphinx.ext.viewcode",
     "sphinx.ext.napoleon",
     "sphinx.ext.githubpages",
+    "sphinxcontrib.apidoc",
 ]
 
 templates_path = ["_templates"]