From d6edc0e317d7f220aee830f2580df49d1753880a Mon Sep 17 00:00:00 2001
From: Harrison <yunyangdeng@gmail.com>
Date: Fri, 28 Apr 2023 15:47:27 -0500
Subject: [PATCH] Changing documentation generation structure

---
 .gitignore              |  4 ++--
 Jenkinsfile             |  2 +-
 docs/source/bmlsa.rst   | 53 -----------------------------------------
 docs/source/index.rst   |  3 ++-
 docs/source/modules.rst |  7 ------
 5 files changed, 5 insertions(+), 64 deletions(-)
 delete mode 100644 docs/source/bmlsa.rst
 delete mode 100644 docs/source/modules.rst

diff --git a/.gitignore b/.gitignore
index 77c690b..ff1372f 100644
--- a/.gitignore
+++ b/.gitignore
@@ -213,5 +213,5 @@ pyrightconfig.json
 # Custom rules (everything added below won't be overriden by 'Generate .gitignore File' if you use 'Update' option)
 
 output
-!docs
-docs/build
\ No newline at end of file
+!docs/source/
+docs/source/autodoc
\ No newline at end of file
diff --git a/Jenkinsfile b/Jenkinsfile
index f4660b4..c516826 100644
--- a/Jenkinsfile
+++ b/Jenkinsfile
@@ -18,7 +18,7 @@ pipeline {
                 sh 'rm -rf ./dist/*'
                 sh 'rm -rf ./docs/build/*'
                 sh "python -m build"
-                sh 'sphinx-apidoc -o docs/source/ src/bmlsa --force'
+                sh 'sphinx-apidoc -o docs/source/autodoc/bmlsa src/bmlsa --force'
                 sh 'make -C docs html'
                 publishHTML([allowMissing: false, alwaysLinkToLastBuild: false, keepAll: false, reportDir: 'docs/build/html', reportFiles: 'index.html', reportName: 'Documentation', reportTitles: ''])
             }
diff --git a/docs/source/bmlsa.rst b/docs/source/bmlsa.rst
deleted file mode 100644
index 415748c..0000000
--- a/docs/source/bmlsa.rst
+++ /dev/null
@@ -1,53 +0,0 @@
-bmlsa package
-=============
-
-Submodules
-----------
-
-bmlsa.aligner module
---------------------
-
-.. automodule:: bmlsa.aligner
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.cli module
-----------------
-
-.. automodule:: bmlsa.cli
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.datatypes module
-----------------------
-
-.. automodule:: bmlsa.datatypes
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.exceptions module
------------------------
-
-.. automodule:: bmlsa.exceptions
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-bmlsa.io module
----------------
-
-.. automodule:: bmlsa.io
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: bmlsa
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 122e6df..2a2c6fc 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -7,10 +7,11 @@ Welcome to BMLSA's documentation!
 =================================
 
 .. toctree::
+   :glob:
    :maxdepth: 2
    :caption: Contents:
    
-   modules
+   autodoc/**/modules
 
 
 Indices and tables
diff --git a/docs/source/modules.rst b/docs/source/modules.rst
deleted file mode 100644
index 5b5c2ed..0000000
--- a/docs/source/modules.rst
+++ /dev/null
@@ -1,7 +0,0 @@
-bmlsa
-=====
-
-.. toctree::
-   :maxdepth: 4
-
-   bmlsa