fix solutions about matrices and similarity

there was a mismatch between exercises and solutions

source/Dive_into_Functions.rst

@@ -482,28 +482,123 @@ This function have to take the phase as parameter
 
 
 .. _matrix_exercise:
-
 Exercise
 --------
 
-Write a program that calculates the similarity of 2 RNA sequences.
+In a new file named ``matrix.py`` Implement a matrix and functions to handle it.
+choose the data structure of your choice.
+The API (**A**\ pplication **P**\ rogramming **I**\ nterface) to implement is the following:
+
+**maker**
+   have parameter:
+
+   * the number of rows
+   * the number of columns
+   * a default value to fill the matrix
+
+   and return a matrix of rows_num x col_num
+
+**size**
+   have parameter:
+
+   * a matrix
+
+   return the number of rows, and number of columns
+
+**get_cell**
+   have parameter:
+
+   * a matrix
+   * the number of rows
+   * the number of columns
+
+   the content of cell corresponding to row number x col number
+
+**set_cell**
+   have parameter:
+
+   * a matrix
+   * the row number of cell to set
+   * the column number of cell to set
+   * the value to set in cell
+
+   set the value val in cell specified by row number x column number
+
+**to_str**
+   have parameter:
+
+   * a matrix
+
+   return a string representation of the matrix
+
+**mult**
+   have parameter:
+
+   * a matrix
+   * val the value to multiply the matrix with
+
+   return a new matrix which is the scalar product of matrix x val
+
+**get_row**
+   have parameter:
+
+   * a matrix
+   * the number of rows
+
+   return a copy of the row corresponding to row number
+
+**set_row**
+   have parameter:
+
+   * a matrix
+   * the row number
+   * the value to put in cells of the row
+
+   set value in each cells of the row specify by the row number
+
+**get_col**
+   have parameter:
+
+   * a matrix
+   * the column number
+
+   return a copy of the column corresponding to the column number
+
+**set_col**
+   have parameter:
+
+   * a matrix
+   * the column number
+   * the value to put in cells
+
+   set all cells of a column with value
+
+**replace_col**
+   have parameter:
+
+   * a matrix
+   * the column number to replace
+   * the list of values to use as replacement of column
+
+   replace a column col_no with list of values
+
+**replace_row**
+   have parameter:
+
+   * a matrix
+   * the row number to replace
+   * the list of values to use as replacement of row
 
-* To compute the similarity you need to parse a file containing the :download:`similarity matrix <_static/data/similarity_matrix>`.
+   replace a row row_no with list of values
 
-  **Hint**: use the module containing the functions that handle a matrix from previous chapter.
-  put this matrix.py file in a directory named "my_python_lib" in your home or Desktop
-  and import it in your current program (the similarity script must be placed elsewhere).
-* The similarity of the 2 sequences is the sum of base similarities.
-  so you have to compare the first base of two sequences and use the matrix to get the similarity
-  from the similarity table, on so on for all bases then sum these similarities.
 
 First implementation (list of columns)
 
-.. literalinclude:: _static/code/matrix.py
+.. literalinclude:: _static/code/similarity.py
    :linenos:
    :language: python
 
-:download:`matrix.py <_static/code/matrix.py>` .
+:download:`matrix.py <_static/code/similarity.py>` .
 
 
 Second implementation (bad variable naming, no documentation)

source/Modules_and_Packages.rst

@@ -11,45 +11,6 @@ Exercises
 =========
 
 
-Exercise
---------
-
-Implement a matrix and functions to handle it.
-choose the data structure of your choice.
-The API (**A**\ pplication **P**\ rogramming **I**\ nterface) to implement is the following:
-
-We propose 2 implementations. These 2 implementations work with a list of lists as matrix modelling.
-But it is possible to implement it with a single list or a dict of list, ...
-
-The first implementation follow the api used explicit name for inner variables and good documentation. 
-         
-.. literalinclude:: _static/code/matrix.py
-   :linenos:
-   :language: python
-
-:download:`matrix.py <_static/code/matrix.py>` .  
-
-But the problem with this implementation is, if we decide to change the inner model for a dixt of list for instance.
-We must reimplements most of the functions.
-
-In the following implementation we have only 4 functions that handle directly the lists. All other functions
-manipulate the matrix through these 4 functions. So if we change the inner model we will have to modifiy 
-only these functions. This implementation will be more maintainable.
-
-
-But this implementation use one letter names for inner variables and is poorly documented which not help
-to maintain or develop with this.
-
-The Best solution should be the second implementation but with the name of variables and documentation as in the firsr 
-implementation.
-
-.. literalinclude:: _static/code/matrix2.py
-   :linenos:
-   :language: python
-
-:download:`matrix2.py <_static/code/matrix2.py>` .
-
-
 Exercise
 --------