Merge pull request #39 from NelleV/doc

Doc

doc/conf.py

@@ -14,13 +14,14 @@
 
 import sys
 import os
+import sphinx_gallery
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
 # documentation root, use os.path.abspath to make it absolute, like shown here.
 sys.path.insert(0, os.path.abspath('sphinxext'))
-extensions = ['gen_rst', 'sphinx.ext.autodoc', 'sphinx.ext.autosummary',
-              'sphinx.ext.pngmath', 'numpy_ext.numpydoc']
+extensions = ['sphinx.ext.autodoc', 'sphinx.ext.autosummary',
+              'sphinx.ext.pngmath', 'numpydoc', "sphinx_gallery.gen_gallery"]
 
 autosummary_generate = True
 

doc/documentation.rst

@@ -41,10 +41,9 @@ repository, to run the MDS::
 
 A bunch of files, necessary for the optimization are written in the same
 folder as the optimization, including the results of the optimization:
-``mds.structure.pdb.txt`` and ``mds.structure.pdb``. The ``txt`` file
-contains a the flatten array of coordinates :math:`(x_1, y_1, z_1, x_2, y_2, \dots)`
-while the ``pdb`` contains a smoothed interpolation of the structure for
-visualization purposes.
+``MDS.structure`` and ``MDS.structure.pdb``. The ``txt`` file contains the
+array of coordinates while the ``pdb`` contains a smoothed interpolation of
+the structure for visualization purposes.
 
 Running the algorithms on your own structure
 ============================================

doc/index.rst

@@ -3,9 +3,9 @@
    You can adapt this file completely to your liking, but it should at least
    contain the root `toctree` directive.
 
-================================================================================
+=====================================================================
 PASTIS: Poisson-based Algorithm for STable Inference of DNA Structure
-================================================================================
+=====================================================================
 
 .. figure:: images/yeast_chr2.png
    :scale: 50%
@@ -39,8 +39,8 @@ counts and the physical distances.
 Download
 ========
 
-Download Pastis 0.1 `here
-<https://github.com/hiclib/pastis/archive/v0.1.0.tar.gz>`_
+Download the latest version of pastis `here
+<https://github.com/hiclib/pastis/releases>`_
 or `fork the code on github <https://github.com/hiclib/pastis/>`_.
 
 References

doc/install.rst

@@ -49,21 +49,3 @@ This will install a python package ``pastis``, and four programs ``pastis-mds``,
 ``pastis-nmds``, ``pastis-pm1`` and ``pastis-pm2``. Calling any of those four
 programs will display the help.
 
-
-MDS_all/PM_all
-==============
-
-You also need to compile the two softwares in src/MDS and src/PM, and place
-them in the directory of your choice.
-
-- First install IPOPT: https://projects.coin-or.org/Ipopt IPOPT can be
-  installed anywhere. IPOPT depends on several external packages that are not
-  included directly with IPOPT. **IPOPT requires at least one linear solver
-  for sparse symmetric indefinite matrices**. You have the choice between HSL,
-  MUMPS or Pardiso. The makefile for MDS and PM are written to use with the
-  HSL subroutines: you will need to edit the makefiles if you choose to use
-  another linear solver.
-- You have to edit the file Makefile in both the ``src/MDS`` and ``src/PM``,
-  and set the following 3 variables at the top: IPOPTPATH, IPOPTINCDIR,
-  IPOPTLIBDIR.
-- Type make.

examples/.gitignore

@@ -0,0 +1,2 @@
+*.structure
+*.png

examples/pastis_example/Makefile

@@ -1,4 +1,4 @@
-
+all:
 
 clean:
 	rm -f *.pdb *.pdb.txt *.pdb.temp.txt *.pdb.temp.pdb *.sh

examples/plot_generate_data.py

@@ -1,7 +1,7 @@
 """
-===============================================================================
+====================
 Simulating Hi-C data
-===============================================================================
+====================
 
 An example illustrating how to generate data, from a 3D structure.
 """