From cdf5d5bcd3c9d9275d534ecec0283e2d5f027b15 Mon Sep 17 00:00:00 2001
From: Christian Faber <chris-faber@gmx.de>
Date: Mon, 21 Oct 2024 09:57:42 +0200
Subject: [PATCH] addin prolog to sphinx
---
docs/source/conf.py | 23 +++++++++++++----------
docs/source/prolog.inc | 4 ++++
src/BioHelpers_FABER/rmsd.py | 2 +-
3 files changed, 18 insertions(+), 11 deletions(-)
create mode 100644 docs/source/prolog.inc
diff --git a/docs/source/conf.py b/docs/source/conf.py
index e4babb4..b028263 100644
--- a/docs/source/conf.py
+++ b/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,
diff --git a/docs/source/prolog.inc b/docs/source/prolog.inc
new file mode 100644
index 0000000..bf2150f
--- /dev/null
+++ b/docs/source/prolog.inc
@@ -0,0 +1,4 @@
+.. # define a hard line break for HTML
+.. |br| raw:: html
+
+ <br />
\ No newline at end of file
diff --git a/src/BioHelpers_FABER/rmsd.py b/src/BioHelpers_FABER/rmsd.py
index 271d1dc..cdc9d37 100644
--- a/src/BioHelpers_FABER/rmsd.py
+++ b/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
--
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