Fixed documentation

Author: elwaagaa

docs/conf.py

@@ -16,20 +16,72 @@
 
 
 # -- Project information -----------------------------------------------------
+import os
+import sys
+
+# Add project root to Python path
+sys.path.insert(0, os.path.abspath('..'))
 
 project = 'fma_ions'
 copyright = '2025, Elias Waagaard'
 author = 'Elias Waagaard'
 
+# The full version, including alpha/beta/rc tags
+from fma_ions import __version__
+release = __version__
+version = '.'.join(release.split('.')[:2])  # Short X.Y version
 
 # -- General configuration ---------------------------------------------------
-
 # Add any Sphinx extension module names here, as strings. They can be
-# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
-# ones.
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
 extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.napoleon',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.viewcode',
+    'sphinx.ext.intersphinx',
+    'sphinx.ext.autosummary',
+    'autoapi.extension',
+    'sphinx_rtd_theme',
 ]
 
+# AutoAPI configuration
+autoapi_type = 'python'
+autoapi_dirs = ['../fma_ions']
+autoapi_ignore = ['*/tests/*', '*/data/*']
+autoapi_options = [
+    'members',
+    'undoc-members',
+    'show-inheritance',
+    'show-module-summary',
+    'special-members',
+    'imported-members',
+]
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+# -- Options for HTML output -------------------------------------------------
+html_theme = 'sphinx_rtd_theme'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']
+
+# -- Extension configuration -------------------------------------------------
+# Intersphinx configuration
+intersphinx_mapping = {
+    'python': ('https://docs.python.org/3', None),
+    'numpy': ('https://numpy.org/doc/stable/', None),
+    'matplotlib': ('https://matplotlib.org/stable/', None),
+}
+
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
 
@@ -44,7 +96,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme =  'sphinx_rtd_theme'
+#'alabaster'
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

docs/index.rst

@@ -83,14 +83,21 @@ Quick Start
    fma.plot_tune_diagram(Qx, Qy, d)
 
 API Reference
-------------
+============
 
 .. toctree::
    :maxdepth: 2
    :caption: API Reference
 
    autoapi/index
 
+   If the API reference doesn't appear, make sure you have run:
+   
+   .. code-block:: bash
+   
+      sphinx-apidoc -o docs/autoapi/ ../fma_ions/
+      make html
+
 Indices and tables
 ==================
 * :ref:`genindex`