Merge branch 'master' into vecmult

.readthedocs.yml

@@ -1,5 +1,10 @@
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.9"
+
 sphinx:
   configuration: docs/conf.py
 
@@ -8,6 +13,5 @@ formats:
   - pdf
 
 python:
-  version: 3.6
   install:
     - requirements: docs/requirements.txt

docs/conf.py

@@ -18,6 +18,7 @@
 import shutil
 import re
 
+
 # -- Project information -----------------------------------------------------
 
 project = 'MRCPP'
@@ -32,7 +33,11 @@
 # 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.mathjax', 'breathe']
+extensions = [
+    'breathe',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.graphviz',
+]
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']
@@ -49,12 +54,9 @@
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
-#
-on_rtd = os.environ.get('READTHEDOCS') == 'True'
-if on_rtd:
-    html_theme = 'default'
-else:
-    html_theme = 'sphinx_rtd_theme'
+import sphinx_rtd_theme
+html_theme = "sphinx_rtd_theme"
+html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.

docs/index.rst

@@ -28,7 +28,7 @@ The code can be found on `GitHub <https://github.com/MRChemSoft/mrcpp>`_.
    install.rst
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 1
    :caption: Application Program Interface
 
    mrcpp_api/introduction
@@ -42,6 +42,7 @@ The code can be found on `GitHub <https://github.com/MRChemSoft/mrcpp>`_.
 
 .. toctree::
    :maxdepth: 2
-   :caption: Programmers Manual
+   :caption: Programmer's Manual
 
-   programmers_manual/clang_tidy
+   programmers_manual/overview
+   programmers_manual/clang_tidy.rst

docs/mrcpp_api/introduction.rst

@@ -98,3 +98,5 @@ the capture list (square brackets), see e.g. `cppreference.com
 <http://en.cppreference.com/w/cpp/language/lambda>`_ for more
 details on lambda functions and how to use the capture list.
 
+
+

docs/mrcpp_api/mwoperators.rst

@@ -11,6 +11,8 @@ program by including:
 
     #include "MRCPP/MWOperators"
 
+.. doxygenclass:: mrcpp::MWOperator
+   :members:
 
 ConvolutionOperator
 -------------------

docs/programmers_manual/BoundingBox.rst

@@ -0,0 +1,12 @@
+---------------------
+BoundingBox
+---------------------
+
+This is an introduction to the BoundingBox class. We write a small overarching summary of the class where we define the 
+algorithm/equation/structure reasoning for having this class or where it fits with the rest of the code.
+
+.. doxygenclass:: mrcpp::BoundingBox
+   :members:
+   :protected-members:
+   :private-members:
+

docs/programmers_manual/MWNode.rst

@@ -0,0 +1,19 @@
+---------------------
+MWNode
+---------------------
+
+This is an introduction to the mwtree class. We write a small overarching summary of the class where we define the
+algorithm/equation/structure reasoning for having this class or where it fits with the rest of the code.
+
+.. graphviz::
+
+   digraph {
+       "MWNode" -> "FunctionNode"
+       "MWNode" -> "OperatorNode"
+   }
+
+.. doxygenclass:: mrcpp::MWNode
+   :members:
+   :protected-members:
+   :private-members:
+

docs/programmers_manual/MWTree.rst

@@ -0,0 +1,19 @@
+------------------
+MWTree
+------------------
+
+This is an introduction to the mwtree class. We write a small overarching summary of the class where we define the
+algorithm/equation/structure reasoning for having this class or where it fits with the rest of the code.
+
+.. graphviz::
+
+   digraph {
+       "MWTree" -> "FunctionTree"
+       "MWTree" -> "OperatorTree"
+   }
+
+.. doxygenclass:: mrcpp::MWTree
+   :members:
+   :protected-members:
+   :private-members:
+

docs/programmers_manual/clang_tidy.rst

@@ -3,10 +3,6 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-==================================
-Programmers manual
-==================================
-
 ----------
 Clang-tidy
 ----------

docs/programmers_manual/overview.rst

@@ -0,0 +1,13 @@
+===============
+Manual overview
+===============
+The following sections show detailed documentation about the classes in MRCPP for programmers.
+
+TODO: maybe add some low level theory/figures/algorithms before showing classes, could help to understand some of the more abstract methods
+
+.. toctree::
+   :maxdepth: 1
+
+   MWTree
+   MWNode
+   BoundingBox

docs/requirements.txt

@@ -1,3 +1,3 @@
 breathe
-Sphinx>=2.0
+Sphinx<7
 sphinx_rtd_theme