Fix Sphinx documentation warnings

Co-authored-by: Junie <junie@jetbrains.com>

doc/api_reference.rst

@@ -5,16 +5,6 @@ API Reference
 This page provides an auto-generated reference of all DAMARIS classes, functions, and modules.
 It is built from docstrings using Sphinx autodoc and autosummary.
 
-.. toctree::
-   :maxdepth: 1
-   :caption: Modules:
-
-   damaris/data
-   damaris/experiments
-   damaris/gui
-   damaris/tools
-
-
 Data Module
 ===========
 

doc/conf.py

@@ -33,7 +33,7 @@ bibtex_bibstyles = ['numeric']
 bibtex_citestyle = 'numeric'
 
 templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store', 'damaris/**']
 
 language = 'en'
 
@@ -42,4 +42,4 @@ language = 'en'
 
 #html_theme = 'alabaster'
 html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_static_path = []

doc/manual.rst

@@ -395,7 +395,7 @@ All four are commonly used in NMR spectroscopy. The line broadening factor LB is
    .. math::
       f(x)=exp(-tp \cdot LB - GM \cdot tp^2)
 
-- :meth:`damaris.data.DamarisFFT.DamarisFFT.traf_window`(line_broadening=10 )
+- :meth:`damaris.data.DamarisFFT.DamarisFFT.traf_window` (line_broadening=10)
    This sets a TRAF window :cite:p:`Traficante:1987fk` over the data:
 
    .. math::