From cae559f29e386ca780e75fcebef69787346327a7 Mon Sep 17 00:00:00 2001
From: lruizcalico <lruiz@calicolabs.com>
Date: Mon, 11 Dec 2023 20:40:11 -0800
Subject: [PATCH] add autogeneration of doc

---
 .github/workflows/documentation.yml | 5 ++---
 src/baskerville/helpers/__init__.py | 0
 src/baskerville/scripts/__init__.py | 0
 src/docs/requirements.txt           | 9 ++++-----
 src/docs/source/conf.py             | 5 +++++
 5 files changed, 11 insertions(+), 8 deletions(-)
 create mode 100644 src/baskerville/helpers/__init__.py
 create mode 100644 src/baskerville/scripts/__init__.py

diff --git a/.github/workflows/documentation.yml b/.github/workflows/documentation.yml
index 97f9a5d..e91383b 100644
--- a/.github/workflows/documentation.yml
+++ b/.github/workflows/documentation.yml
@@ -37,11 +37,10 @@ jobs:
       - name: Sphinx build
         run: |
           cd ${{ github.workspace }}/src/docs/source
+          rm -f *.rst make.bat
           cd ${{ github.workspace }}/src
-          ls -la docs/source
-          ls -la docs/build
+          sphinx-apidoc -F -a -o docs/source baskerville
           cd ${{ github.workspace }}/src/docs
-          pwd
           make html
       - name: Deploy
         uses: peaceiris/actions-gh-pages@v3
diff --git a/src/baskerville/helpers/__init__.py b/src/baskerville/helpers/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/baskerville/scripts/__init__.py b/src/baskerville/scripts/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/src/docs/requirements.txt b/src/docs/requirements.txt
index 0f5ad43..8d2f592 100644
--- a/src/docs/requirements.txt
+++ b/src/docs/requirements.txt
@@ -1,7 +1,3 @@
-sphinx 
-sphinx_rtd_theme 
-python-dotenv
-google
 h5py~=3.7.0
 intervaltree~=3.1.0
 joblib~=1.1.1
@@ -18,7 +14,10 @@ qnorm~=0.8.1
 seaborn~=0.12.2
 scikit-learn~=1.2.2
 scipy~=1.9.1
-sphinx~=7.2.6
+sphinx 
+sphinx_rtd_theme 
+sphinxcontrib-apidoc
 statsmodels~=0.13.5
+tensorflow==2.13.0
 tabulate~=0.8.10
 tqdm~=4.65.0
\ No newline at end of file
diff --git a/src/docs/source/conf.py b/src/docs/source/conf.py
index 319b105..cea225c 100644
--- a/src/docs/source/conf.py
+++ b/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"]