Document some more folders

Author: robertodr

CHANGELOG.md

@@ -13,6 +13,17 @@
 
 - The versioning machinery has been updated. The update was inspired by the
   `versioner.py` tool devised by @loriab.
+- The documentation building scripts `conf.py` and `cloc_tools.py` have been
+  thoroughly refactored and simplified:
+  * `cloc_tools.py` is now called `cloc_wrapper.py`. It is no longer configured
+  and can be found in the `cloc_tools` subfolder of `doc`.
+  * A local build of documentation will only work if run from within the `doc` folder:
+  ```
+  sphinx-build . _build
+  ```
+  This choice was made to simplify the set up of the ReadTheDocs and local
+  documentation building procedures and to minimize the chances of breaking
+  either.
 
 ## [Version 1.2.0-rc1] - 2018-03-02
 

doc/Doxyfile.in

@@ -108,7 +108,7 @@ WARN_IF_DOC_ERROR      = YES
 WARN_NO_PARAMDOC       = NO
 WARN_AS_ERROR          = NO
 WARN_FORMAT            = "$file:$line: $text"
-WARN_LOGFILE           = doc/doxygen.log
+WARN_LOGFILE           = @doc_build_dir@/doxygen.log
 #---------------------------------------------------------------------------
 # Configuration options related to the input files
 #---------------------------------------------------------------------------

doc/cloc_tools/__init__.py

@@ -21,6 +21,6 @@
 #  PCMSolver API, see: <http://pcmsolver.readthedocs.io/>
 #
 
-from .cloc_wrapper import bar_chart, total_bar_chart
+from .cloc_wrapper import bar_chart
 
-__all__ = ['bar_chart', 'total_bar_chart']
+__all__ = ['bar_chart']

doc/code-reference/bi-operators.rst

@@ -0,0 +1,41 @@
+Boundary integral operators
+===========================
+
+.. image:: ../gfx/bar_charts/bi_operators.svg
+   :scale: 70 %
+   :align: center
+
+IBoundaryIntegralOperator
+-------------------------
+.. doxygenclass:: pcm::IBoundaryIntegralOperator
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Collocation
+-----------
+
+.. doxygenclass:: pcm::bi_operators::Collocation
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Purisima
+--------
+
+.. doxygenclass:: pcm::bi_operators::Purisima
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Numerical
+---------
+
+.. doxygenclass:: pcm::bi_operators::Numerical
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:

doc/code-reference/classes-and-functions.rst

@@ -10,6 +10,8 @@ Classes and functions reference
 
    cavities
    greens-functions
+   dielectric-profiles
    solvers
+   bi-operators
    helper-classes
    namespaces

doc/code-reference/dielectric-profiles.rst

@@ -0,0 +1,62 @@
+Dielectric profiles
+===================
+
+.. image:: ../gfx/bar_charts/dielectric_profile.svg
+   :scale: 70 %
+   :align: center
+
+Uniform
+-------
+.. doxygenstruct:: pcm::dielectric_profile::Uniform
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Anisotropic
+-----------
+.. doxygenclass:: pcm::dielectric_profile::Anisotropic
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Yukawa
+-------
+.. doxygenstruct:: pcm::dielectric_profile::Yukawa
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+OneLayerLog
+-----------
+.. doxygenclass:: pcm::dielectric_profile::OneLayerLog
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+OneLayerTanh
+------------
+.. doxygenclass:: pcm::dielectric_profile::OneLayerTanh
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+OneLayerErf
+-----------
+.. doxygenclass:: pcm::dielectric_profile::OneLayerErf
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:
+
+Sharp
+-----
+.. doxygenstruct:: pcm::dielectric_profile::Sharp
+   :project: PCMSolver
+   :members:
+   :protected-members:
+   :private-members:

src/green/dielectric_profile/Sharp.hpp

@@ -31,7 +31,7 @@
 
 namespace pcm {
 namespace dielectric_profile {
-/*!  \struct Sharp
+/*! \struct Sharp
  *  \brief A sharp dielectric separation
  *  \author Roberto Di Remigio
  *  \date 2015

src/green/dielectric_profile/Uniform.hpp

@@ -31,7 +31,7 @@
 
 namespace pcm {
 namespace dielectric_profile {
-/*!  \struct Uniform
+/*! \struct Uniform
  *  \brief a uniform dielectric profile
  *  \author Roberto Di Remigio
  *  \date 2015