Merge pull request #21 from btmartin721/dev_btm_refactor

Dev btm refactor

docs/HEADER.yaml

@@ -0,0 +1,43 @@
+title: "SNPio: A Python API for Population Genetic File Processing, Filtering, and Encoding"
+subtitle: "Getting Started with SNPio"
+author: "Drs. Bradley T. Martin and Tyler K. Chafin"
+date: "2024-10-11"
+keywords: ["bioinformatics", "SNP", "VCF", "PHYLIP", "STRUCTURE", "io", "file conversion", "filter", "filtering", "genomics", "missing data", "minor allele", "singletons", "monomorphic", "biallelic"]
+geometry: "margin=1in"
+titlepage: false
+titlepage-color: "FFFFFF"
+titlepage-text-color: "000000"
+titlepage-rule-color: "CCCCCC"
+titlepage-rule-height: 4
+logo: "img/snpio_logo.png"
+logo-width: 60% 
+page-background: "FFFFFF"
+page-background-opacity:
+links-as-notes: false
+lot: false
+lof: true
+listings-disable-line-numbers: true
+listings-no-page-break: false
+disable-header-and-footer: false
+header-left: "Drs. Bradley T. Martin and Tyler K. Chafin"
+header-center:
+header-right: "SNPio User Manual"
+footer-left: "License: GNU Public License v3 (GPL3)"
+footer-center: 
+footer-right: 
+subparagraph: true
+lang: en-US 
+fontsize: 12pt
+classoption: 12pt
+documenttype: article
+standalone: true
+output:
+  pdf:
+    pdf-engine: pdflatex
+    output: UserManual.pdf
+    from: markdown
+colorlinks: true
+toc-title: "Table of Contents"
+toc-own-page: true
+toc-depth: 2
+

docs/listings-setup.tex

@@ -0,0 +1,33 @@
+% Contents of listings-setup.tex
+\usepackage{xcolor}
+\usepackage{graphicx}
+\usepackage{caption}
+\usepackage{amsmath}
+\usepackage{hyperref}
+\usepackage{float}
+\usepackage{tocloft}
+
+\lstset{
+    basicstyle=\ttfamily,
+    numbers=left,
+    numberstyle=\footnotesize,
+    stepnumber=2,
+    numbersep=5pt,
+    backgroundcolor=\color{black!10},
+    showspaces=false,
+    showstringspaces=false,
+    showtabs=false,
+    tabsize=2,
+    captionpos=b,
+    breaklines=true,
+    breakatwhitespace=true,
+    breakautoindent=true,
+    linewidth=\textwidth
+}
+
+% Adjust spacing between TOC and LOF.
+% Adjust spacing before section entries in ToC
+\setlength{\cftbeforesecskip}{10pt}     
+\setlength{\cftbeforesubsecskip}{10pt} 
+\setlength{\cftbeforesecskip}{10pt}
+\setlength{\cftbeforefigskip}{10pt}

docs/source/_static/custom.css

@@ -0,0 +1,22 @@
+/* Style for the figure container */
+.custom-figure {
+    border: 1px solid #ddd;
+    padding: 10px;
+    margin: 20px auto;
+    text-align: center;
+    background-color: #f9f9f9;
+}
+
+/* Style for the figure caption */
+.custom-figure .caption {
+    font-style: normal;
+    font-size: 14px;
+    color: #333;
+    margin-top: 5px;
+}
+
+/* Bold style for the "Figure X:" part */
+.custom-figure .caption strong {
+    font-weight: bold;
+    font-style: normal;
+}

docs/source/conf.py

@@ -1,34 +1,57 @@
 import os
 import sys
 
-# Ensure path to project root is correct
-sys.path.insert(0, os.path.abspath("../.."))
-
+# -- Project information -----------------------------------------------------
 project = "SNPio"
 copyright = "2023, Bradley T. Martin and Tyler K. Chafin"
 author = "Bradley T. Martin and Tyler K. Chafin"
 release = "1.1.0"
 
-# Sphinx extensions for documentation
+# -- Path setup --------------------------------------------------------------
+# Add the project's root directory to sys.path
+sys.path.insert(0, os.path.abspath("../.."))
+
+# -- Sphinx Extensions -------------------------------------------------------
+# Add extensions for autodoc, type hints, and more
 extensions = [
     "sphinx.ext.autodoc",
-    "sphinx.ext.napoleon",
-    "sphinx_autodoc_typehints",  # Ensure this package is installed
-    "sphinx.ext.todo",
+    "sphinx.ext.napoleon",  # Supports Google-style docstrings
+    "sphinx_autodoc_typehints",  # Type hints in function signatures
+    "sphinx.ext.todo",  # To-do directives in documentation
+    "sphinx.ext.viewcode",  # Add links to highlighted source code
 ]
 
-# Include todos in the documentation
+# Enable displaying todos
 todo_include_todos = True
 
-# Paths for templates
+# -- HTML output theme and customization -------------------------------------
+html_theme = "sphinx_rtd_theme"  # Read the Docs theme
+
+html_context = {
+    "display_github": True,  # Enable GitHub integration
+    "github_user": "btmartin721",  # GitHub username
+    "github_repo": "SNPio",  # GitHub repo
+    "github_version": "master",  # Branch to use
+    "conf_py_path": "/docs/source/",  # Path to docs in the repo
+    "current_version": "v1.1.0",  # Project version
+    "display_version": True,  # Display version number in the theme
+    "latest_version": "master",  # Define the latest stable version
+    "display_edit_on_github": True,  # Add 'Edit on GitHub' link
+}
+
+# Set paths for templates and static files (custom CSS)
 templates_path = ["_templates"]
+html_static_path = ["_static"]
+
+# Custom logo and favicon
+html_logo = "../../img/snpio_logo.png"
+
 
-# Files or directories to ignore during documentation
-exclude_patterns = ["**/setup.rst", "**/tests.rst"]
+# Add custom CSS for further styling if needed
+def setup(app):
+    app.add_css_file("custom.css")  # Use a custom CSS file (if needed)
 
-# HTML output theme
-html_theme = "sphinx_rtd_theme"
 
-# Optional GitHub URL (not supported natively by sphinx_rtd_theme)
-# You may want to integrate this using a custom extension
-github_url = "https://github.com/btmartin721/SNPio"
+# -- General configuration ---------------------------------------------------
+# Files or directories to ignore during build
+exclude_patterns = ["**/setup.rst", "**/tests.rst", "_build", "Thumbs.db", ".DS_Store"]