addin prolog to sphinx

docs/source/conf.py

@@ -13,16 +13,17 @@
 import os
 import sys
 from pathlib import Path
+
 # sys.path.insert(0, os.path.abspath('../../src'))
 # sys.path.insert(0, os.path.abspath(os.path.join('..', '..', 'src')))
-sys.path.append(os.path.abspath('../../src'))
+sys.path.append(os.path.abspath("../../src"))
 # sys.path.append(Path(__file__).parent.parent.as_posix())
 
 # -- Project information -----------------------------------------------------
 
-project = 'BioHelpers'
-copyright = '2024, Christian Faber'
-author = 'Christian Faber'
+project = "BioHelpers"
+copyright = "2024, Christian Faber"
+author = "Christian Faber"
 
 
 # -- General configuration ---------------------------------------------------
@@ -31,27 +32,29 @@ author = 'Christian Faber'
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
 extensions = [
-	'sphinx.ext.duration',
-	'sphinx.ext.doctest',
-	'sphinx.ext.autodoc',
-	'sphinx.ext.napoleon',
+    "sphinx.ext.duration",
+    "sphinx.ext.doctest",
+    "sphinx.ext.autodoc",
+    "sphinx.ext.napoleon",
 ]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+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 = []
 
+with open("prolog.inc", "r") as file:
+    rst_prolog = file.readlines()
 
 # -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+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,

docs/source/prolog.inc

+.. # define a hard line break for HTML
+.. |br| raw:: html
+
+   <br />
\ No newline at end of file

src/BioHelpers_FABER/rmsd.py

@@ -82,7 +82,7 @@ def get_rotation_matrix(x: np.ndarray, y: np.ndarray) -> np.ndarray:
 
 def get_translation_vector(x: np.ndarray, y: np.ndarray) -> np.ndarray:
     """Get the translation vector :math:`\mathbf{r}`
-    | **Important Note:** The translation vector differs from Kabsch algorithm, there you translate befor rotating. In Coutsias paper it is the otherway round.
+    **Important Note:** The translation vector differs from Kabsch algorithm, there you translate befor rotating. In Coutsias paper it is the otherway round.
 
     :param x: set of vectors
     :type x: np.ndarray