Update doc generation with sphinx.

Add makefile targets for cleaning doc and transfer Ford pages to sphinx.

doc/Makefile

@@ -1,4 +1,4 @@
-.PHONY: ford html
+.PHONY: ford html clean copy
 
 all: ford html copy
 
@@ -11,3 +11,7 @@ ford:
 copy: 
 	mkdir -p sphinx/build/html/ford/
 	cp -rf ford/build/* sphinx/build/html/ford/
+
+clean:
+	make -C ford clean
+	make -C sphinx clean

doc/ford/Makefile

@@ -1,4 +1,8 @@
+.PHONY: clean
 
 all: 
 	mkdir -p  build
 	ford ./sources/conf.md
+
+clean:
+	rm -rf build/

doc/ford/sources/conf.md

@@ -1,6 +1,6 @@
 ---
 project: ciaaw
-summary: Fortran library providing the standard atomic weights according to CIAAW.
+summary: Standard atomic weights, isotopic compositions and nuclide's atomic weights.
 project_github: https://github.com/MilanSkocic/ciaaw
 project_download: https://github.com/MilanSkocic/ciaaw/releases
 project_website: https://milanskocic.github.io/ciaaw/index.html

doc/sphinx/source/api/c.rst

@@ -2,5 +2,5 @@
 C API
 *****
 
-.. literalinclude:: ../../../include/ciaaw.h
+.. literalinclude:: ../../../../include/ciaaw.h
    :language: C

doc/sphinx/source/api/fortran.rst

@@ -4,6 +4,18 @@ Fortran
 
 The Fortran documentation is generated with `FORD <../ford/index.html>`_.
 
+The modules [[ciaaw__saw(module)]], [[ciaaw__ice(module)]], [[ciaaw__naw(module)]] and  [[ciaaw__pte(module)]] are
+automatically generated with a simple script written in Python.
+
+The API defines convenient getters are available for accessing the desired data for an elements
+without having to access to whole periodic table [[ciaaw__pte(module):pt]]
+
+* [[ciaaw__api(module):get_saw(function)]]
+* [[ciaaw__api(module):get_ice(function)]]
+* [[ciaaw__api(module):get_nice(function)]]
+* [[ciaaw__api(module):get_naw(function)]]
+* [[ciaaw__api(module):get_nnaw(function)]]
+
 .. .. autofortran:: ../src/ciaaw.f90
 
 .. .. autofortran:: ../src/ciaaw_api.f90

doc/sphinx/source/api/index.rst

@@ -4,9 +4,10 @@ APIs
 
 
 .. toctree::
-   :caption: API
-   :hidden:
+   :maxdepth: 1
 
    fortran.rst  
    c.rst
    python.rst
+
+

doc/sphinx/source/conf.py

@@ -4,7 +4,7 @@
 # https://www.sphinx-doc.org/en/master/usage/configuration.html
 import os
 import sys
-sys.path.insert(0, os.path.abspath('../py/src/'))
+sys.path.insert(0, os.path.abspath('../../../py/src/'))
 import pyciaaw
 # -- Project information -----------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#project-information
@@ -13,7 +13,7 @@
 
 project = 'ciaaw'
 copyright = '2025, M. Skocic'
-author = 'M. Skocic'
+author = 'Milan Skocic'
 release = pyciaaw.__version__
 
 # -- General configuration ---------------------------------------------------

doc/sphinx/source/getting_started/examples.rst

@@ -5,19 +5,19 @@ Examples
 Fortran
 =======
 
-.. literalinclude:: ../../../example/example.f90
+.. literalinclude:: ../../../../example/example.f90
    :language: Fortran
 
 
 C
 ==
 
-.. literalinclude:: ../../../example/example.c
+.. literalinclude:: ../../../../example/example.c
    :language: C
 
 
 Python
 ======
 
-.. literalinclude:: ../../../example/example.py
+.. literalinclude:: ../../../../example/example.py
    :language: python

doc/sphinx/source/getting_started/index.rst

@@ -4,8 +4,7 @@ Getting Started
 
 
 .. toctree::
-   :caption: Contents
-   :hidden:
+   :maxdepth: 1
 
    readme.rst  
    examples.rst

doc/sphinx/source/getting_started/readme.rst

@@ -3,5 +3,5 @@ Readme
 ******
 
 
-.. include:: ../../../README.md
+.. include:: ../../../../README.md
    :parser: myst_parser.sphinx_

doc/sphinx/source/index.rst

@@ -6,17 +6,52 @@
 CIAAW
 =====
 
-.. image:: ../../media/logo.png
+.. toctree::
+   :maxdepth: 1
+
+   getting_started/index
+   api/index
+   references/index.rst
+
+.. image:: ../../../media/logo.png
   :width: 400
   :alt: Alternative text
 
-Standard atomic weights, isotopic compositions and nuclide's atomic weights.
+Standard and abridged atomic weights, isotopic abundances and 
+nuclides' standard atomic weights according to `CIAAW <https://www.ciaaw.org>`_.
 
+SAW: Standard Atomic Weights
+----------------------------
 
-.. toctree::
-   :maxdepth: 2
-   :caption: Contents:
+The latest standard atomic weights were released in 2021 by the [ciaaw](https://www.ciaaw.org).
+All the values for the atomic weights are provided as double precision reals in a derived type
+[[ciaaw__types(module):saw_type(type)]].
 
-   getting_started/index
-   api/index
-   references/index.rst
+The standard atomic weights (or realtive atomic mass),:math:`A_r(E)`, 
+are extracted from table 1 :cite:p:`prohaska2022-1`. For the elements
+that feature an interval for the standard atomic weight, the mean value and the uncertainty are computed
+using formulas defined in [Van der Veen et al. 2021](../references.html).
+
+$$ A_r(E) = \frac{a+b}{2} $$
+
+$$ u(A_r(E)) = \frac{b-a}{2\sqrt{3}} $$
+
+The standard atomic weights are a dimensionless quantity and thus they need to be multiplied by 
+the molar mass constant \(M_u=1.00000000105 \pm 0.00000000031 g.mol^{-1}\) 
+in order to get the value in \(g.mol^{-1}\). 
+See [codata](https://milanskocic.github.io/codata/) for physical constants.
+
+
+## ICE: Isotopic Compositions of the Element
+
+The latest isotopic compositions were released in 2013 by the [ciaaw](https://www.ciaaw.org).
+All the values for the compositions are provided as double precision reals in a derived type
+[[ciaaw__types(module):ice_type(type)]].
+The isotopic compositions of the element, are extracted from table 1 [Meija et al. 2013](../references.html). 
+
+## NAW: Nuclide Atomic Weights
+
+The latest atomic weights for nuclides were released in 2020 by [ciaaw](https://www.ciaaw.org)
+from [Huang et al. 2021](../references.html).
+All the values for the nuclide atomic weights are provided as double precision reals in derived type
+[[ciaaw__types(module):naw_type(type)]]. 

doc/sphinx/source/references/index.rst

@@ -4,7 +4,6 @@ Bibliography
 
 
 .. toctree::
-   :caption: Contents
-   :hidden:
+   :maxdepth: 1
 
    references.rst