Fixed sphinx documentation

Author: elwaagaa

docs/conf.py

@@ -1,108 +1,52 @@
 # Configuration file for the Sphinx documentation builder.
 #
-# For the full list of built-in configuration values, see the documentation:
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 
-import os
-import sys
-from datetime import datetime
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
 
-# Add project root to Python path
-sys.path.insert(0, os.path.abspath('..'))
 
 # -- Project information -----------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
 
 project = 'fma_ions'
-copyright = f'{datetime.now().year}, {author}'
+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 ---------------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/configuration.html#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 = [
-    'sphinx.ext.autodoc',
-    'sphinx.ext.napoleon',
-    'sphinx.ext.mathjax',
-    'sphinx.ext.todo',
-    'sphinx.ext.viewcode',
-    'sphinx.ext.intersphinx',
-    'sphinx_copybutton',
-    'myst_parser',
-    'autoapi.extension',
-]
-
-# 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',
-]
-
-# MyST configuration
-myst_enable_extensions = [
-    'dollarmath',
-    'amsmath',
-    'colon_fence',
 ]
 
+# Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', '**.ipynb_checkpoints']
 
-# The suffix of source filenames.
-source_suffix = {
-    '.rst': 'restructuredtext',
-    '.md': 'markdown',
-}
+# 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']
 
-# The master toctree document.
-master_doc = 'index'
 
 # -- 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_theme_options = {
-    'navigation_depth': 4,
-    'collapse_navigation': False,
-    'sticky_navigation': True,
-}
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_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,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
-
-# -- Options for todo extension ----------------------------------------------
-# https://www.sphinx-doc.org/en/master/usage/extensions/todo.html#configuration
-
-todo_include_todos = True
-
-# -- Extension configuration -------------------------------------------------
-
-# Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
-
-# The language for content autogenerated by Sphinx. Refer to documentation
-# for a list of supported languages.
-language = 'en'
-
-# -- Options for intersphinx extension ---------------------------------------
-# Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {
-    'python': ('https://docs.python.org/3', None),
-    'numpy': ('https://numpy.org/doc/stable/', None),
-    'matplotlib': ('https://matplotlib.org/stable/', None),
-}
+html_static_path = ['_static']

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=.
+set BUILDDIR=_build
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.https://www.sphinx-doc.org/
+	exit /b 1
+)
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd