Initial commit: v0.1.0

docs/source/conf.py

@@ -0,0 +1,114 @@
+# Configuration file for the Sphinx documentation builder.
+#
+# For the full list of built-in configuration values, see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Project information -----------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
+
+project = "SelfiSys"
+copyright = "2025, Tristan Hoellinger"
+author = "Tristan Hoellinger"
+release = (
+    "/Users/hoellinger/Library/CloudStorage/Dropbox/travail/these/science/code/SELFI/selfisys/src/"
+)
+
+# -- General configuration ---------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
+
+extensions = [
+    "sphinx.ext.autodoc",  # Automatically generate documentation from docstrings.
+    "sphinx.ext.viewcode",  # Adds links to highlighted source code.
+    "sphinx.ext.napoleon",  # Supports Google and NumPy-style docstrings.
+    "myst_parser",  # Markdown support.
+    "sphinx.ext.autosummary",  # Generate summary tables for API docs.
+    "sphinx.ext.mathjax",  # For rendering mathematical equations using MathJax.
+    "sphinx.ext.todo",  # Support for TODO notes.
+]
+
+templates_path = ["_templates"]
+exclude_patterns = []
+
+
+# -- Options for HTML output -------------------------------------------------
+# https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
+
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]
+html_extra_path = ["_static"]
+
+html_theme_options = {
+    "collapse_navigation": False,
+    "sticky_navigation": True,
+    "navigation_depth": 4,
+    "style_external_links": True,
+    "titles_only": False,
+}
+
+# Add GitHub link
+html_context = {
+    "display_github": True,  # Enables the link
+    "github_user": "hoellin",  # GitHub username
+    "github_repo": "selfisys_public",  # Repository name
+    "github_version": "main",  # Branch name
+    "conf_py_path": "/docs/source/",  # Path to the documentation directory in the repo
+}
+
+import os
+import sys
+import shutil
+
+# Add the project's source path to sys.path
+sys.path.insert(0, os.path.abspath("../../src"))
+
+# Copy Markdown files from parent directory
+markdown_files = ["README.md", "CONTRIBUTING.md", "REFERENCES.md"]
+for md_file in markdown_files:
+    src = os.path.abspath(f"../../{md_file}")  # Adjust the path if necessary
+    dst = os.path.join(os.path.dirname(__file__), os.path.basename(md_file))
+    try:
+        if os.path.exists(src) and not os.path.exists(dst):
+            shutil.copy(src, dst)
+            print(f"Copied {src} to {dst}")
+    except Exception as e:
+        print(f"Error copying {md_file}: {e}")
+
+
+def generate_rst_files():
+    """
+    Automatically generate .rst files for standalone Python modules.
+    Avoids regeneration if files already exist.
+    """
+    source_dir = os.path.abspath("src/selfisys")  # Adjust to your source directory
+    output_dir = os.path.join(os.path.dirname(__file__))  # docs/source directory
+
+    # Ensure source_dir exists
+    if not os.path.isdir(source_dir):
+        raise FileNotFoundError(f"The source directory '{source_dir}' does not exist.")
+
+    # List all Python files in the source directory (excluding __init__.py)
+    for filename in os.listdir(source_dir):
+        if filename.endswith(".py") and filename != "__init__.py":
+            module_name = filename[:-3]  # Remove .py extension
+            output_file = os.path.join(output_dir, f"selfisys.{module_name}.rst")
+
+            # Skip regeneration if the file already exists
+            if os.path.exists(output_file):
+                continue
+
+            # Write the .rst file content
+            with open(output_file, "w") as f:
+                # Module header
+                f.write(f"{module_name}\n")
+                f.write("=" * len(module_name) + "\n\n")
+                f.write(f".. automodule:: selfisys.{module_name}\n")
+                f.write("   :members:\n")
+                f.write("   :undoc-members:\n")
+                f.write("   :show-inheritance:\n")
+
+            print(f"Generated {output_file}")
+
+
+# Register a Sphinx hook to generate .rst files before the build
+def setup(app):
+    app.connect("builder-inited", lambda app: generate_rst_files())