working on documentation

bonfus · May 20, 2016 · 7d4ef7c · 7d4ef7c
1 parent 37d3734
commit 7d4ef7c
Show file tree

Hide file tree

Showing 9 changed files with 46 additions and 12 deletions.
diff --git a/README.md b/README.md
@@ -18,9 +18,9 @@ Optional dependencies are:
 
 | package  | version    | url        | provides |
 |----------|------------|------------|----------|
-| spglib   | 1.8        | http://atztogo.github.io/spglib |  library for finding lattice structure symmetries |
-| XCrysden | any        | http://www.xcrysden.org | tool for showing lattice and magnetic structures |
-| sympy    | 1.0        | sympy.org | for symbolic Fourier components definition |
+| spglib   | 1.8        | [Spglib](http://atztogo.github.io/spglib) |  library for finding lattice structure symmetries |
+| XCrysden | any        | [XCrysden](http://www.xcrysden.org) | tool for showing lattice and magnetic structures |
+| sympy    | 1.0        | [Sympy](http://sympy.org) | for symbolic Fourier components definition |
 
 
 Install and Usage
@@ -34,7 +34,6 @@ Known problems
 - Non-standard spacegroup settings can cause some tedious problems when 
   using the spglib functions. Pay attention!
 
-
 Please not that the code is still under heavy development. 
 You'll probably find bugs so please report them!
 

diff --git a/docs/ContactTerm.rst b/docs/ContactTerm.rst
@@ -16,7 +16,7 @@ The value of N can strongly impact on the results. The best approximation strong
 
 
 From CGS to SI
-==============
+--------------
 
 Hyperfine couplings are often reported in mol/emu while Muesr uses :math:`{\buildrel _{\circ} \over {\mathrm{A}}}^{-3}`.
 Here's how to convert the former into the latter.

diff --git a/docs/FAQ.rst b/docs/FAQ.rst
@@ -10,4 +10,5 @@ Symmetry is not correctly recognized by spglib!
    a bug at spglib.sf.net .
 
 How do I convert the hyperfine filed to reasonable units?
+
    See ContactTerm
diff --git a/docs/Install.rst b/docs/Install.rst
@@ -41,7 +41,7 @@ XCrysDen  >= 1.0    :mod:`muesr.io.xsf.xsf.show_cell` ,             http://www.x
 To compile the python extension you also need the build tools appropriate
 for your system (gcc on Linux, XCode on OS X, Visual Studio or gcc on Windows).
 
-If you do not want to compile 
+If you do not want to compile you can use these wheels:
 
 Installation
 ------------

diff --git a/docs/Intro.rst b/docs/Intro.rst
@@ -1,4 +1,4 @@
-Baisc theory
+Basic theory
 ====================
 
 Local fields in MuSR
@@ -14,7 +14,7 @@ Description of Magnetic Structures
 
 There are two possibilities to describe a magnetic structure: using the
 colored group theory or with the propagation vector and Fourier 
-coefficients formalism. :py:mod:`muesr` opts for the latter.
+coefficients formalism. :mod:`muesr` opts for the latter.
 A magnetic structure is defined as
 
 .. math::
@@ -42,7 +42,7 @@ group formed by the operators leaving invariant the propagation vector.
 [TODO] Discuss the phase!
 
 
-:py:mod:`muesr` can only handle 1-k magnetic structures.
+:mod:`muesr` can only handle 1-k magnetic structures.
 However, since local field are linear in the magnetic moment, the
 results for multiple-k magnetic orders can be obtained by performing 
 multiple simulations for each of the k vectors describing the system
@@ -51,7 +51,7 @@ and summing the results.
 Implementation details
 ----------------------------
 
-:py:mod:`muesr` is a tool to analyze muon sites and local field contributions
+:mod:`muesr` is a tool to analyze muon sites and local field contributions
 generated by a known magnetic structure. It is intended to be used in an 
 interactive python environment such ipython or Jupyter notebooks.
 

diff --git a/docs/Source.rst b/docs/Source.rst
@@ -17,7 +17,14 @@ Source documentation
    :members:
    :undoc-members:
    :show-inheritance:
-
+
+:mod:`muesr.core.sampleErrors` -- Sample related exceptions
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
+
+.. automodule:: muesr.core.sampleErrors
+   :members:
+   :undoc-members:
+   :show-inheritance:
 
 :mod:`muesr.core.cells` -- Functions for lattice
 +++++++++++++++++++++++++++++++++++++++++++++++++

diff --git a/docs/Symmetry.rst b/docs/Symmetry.rst
@@ -1,7 +1,7 @@
 Symmetry
 ========
 
-MuESR tries to grab symmetry information from either the CIF files or 
+:mod:`muesr` tries to grab symmetry information from either the CIF files or 
 using the `spglib` routines.
 If a magnetic cif (*.mcif) is loaded, the symmetry is disregarded. 
 The symmetry equivalent sites depend indeed only on the symmetry of the 

diff --git a/docs/Usage.rst b/docs/Usage.rst
@@ -45,3 +45,15 @@ positions with the additional constraint of being sufficiently separated
 from the atoms of the hosting system.
 
 
+Understanding errors
+--------------------
+
+:mod:`muesr` raises the conventional python exceptions (mainly ValueError and
+TypeError) or other 4 specific Exceptions:
+
+ - CellError
+
+To see their meaning follow the links.
+
+The utility functions are mainly intented for interactive usage and report
+problems 
diff --git a/muesr/core/sampleErrors.py b/muesr/core/sampleErrors.py
@@ -1,15 +1,30 @@
 class SampleException(Exception):
+    """
+    Exceptions connected with problems with the Sample definition.
+    """
     pass
 
 class SymmetryError(SampleException):
+    """
+    Symmetry needed but not defined.
+    """
     pass
 
 class CellError(SampleException):
+    """
+    Lattice structure needed but not defined.
+    """
     pass
 
 class MagDefError(SampleException):
+    """
+    Magnetic structure not defined or incompatible.
+    """
     pass
 
 class MuonError(SampleException):
+    """
+    Muon position needed but not defined.
+    """
     pass