moved to correct dir

docs/source/PPP_pages/develop.rst

@@ -2,14 +2,18 @@
 Development
 ===========
 
-*italic*
-**BOLD**
-outside link: `Google <https://google.com//>`_.
-internal link: :ref:`examples`
+As it would be unlikely that the PPP would encompass all desired procedures/methods, we has included this section to aid in the development of additional functionality for the PPP.
 
-.. code-block:: bash
-        
-        my_code.py
+######################
+Development Guidelines 
+######################
+
+**In general:**
+
+* Functions developed for the PPP should be modular – i.e. function independently – primarily to maintain a flexible platform, this is especially important when considering ` Galaxy <https://galaxyproject.org/>`_. integration.
+* Functions should be able to be imported from **pgpipe**, so that multiple functions may be used within a single python script or ` Jupyter notebook <https://jupyter.org/>`_.
+* Functions should support the use of Model files for automatic assignment of relevant meta-data. *Note: details on the model file class may be found below*
+* Functions that use third-party software should include the relevant reference(s) within log files. 
 
 #################
 Using PPP Classes
@@ -19,11 +23,79 @@ Using PPP Classes
 VCF Class
 *********
 
+*italic*
+**BOLD**
+outside link: `Google <https://google.com//>`_.
+internal link: :ref:`examples`
+
+.. code-block:: bash
+        
+   my_code.py
+
+***************
+ModelFile Class
+***************
+Model files may be read using the function **read_model_file()** found within the model.py module. The reader accepts the filename (as a string) of the model file and returns a **ModelFile** class object as shown below:
+
+.. code-block:: python
+
+   # Read in the model file
+   model_file = pgpipe.model.read_model_file(“path/to/my_model_file.model”)
+
+A **ModelFile** class object primarily behaves as a dictionary of **Model** class objects; the keys of the dictionary are the model names (as strings) of the **Model** class objects whereas the values are the objects themselves. Therefore, a **Model** named *2Pop* may assigned as shown below:
+
+.. code-block:: python
+
+   # Assign the 2Pop model, from model file
+   model_2pop =  model_file[‘2Pop’]
+
+A **ModelFile** class object also has two additional attributes:
+
+*ind_file: If created, the filename of a file containing all the unique individuals found within all models stored within the **ModelFile**.
+*exclude_file: If created, the filename of a file containing all the unique individuals found within all models stored within the **ModelFile** that do not match a given list of individuals.
+
+These attributes may be populated and their files created using the following functions: **create_ind_file()** and **create_exclude_ind_file()**. The inverse operating can also be completed using **delete_ind_file()** and **delete_exclude_ind_file()**.
+
 ***********
 Model Class
 ***********
+The **Model** class is used to store model meta-data. The primary attributes of the class are:
 
-######################
-Development Guidelines 
-######################
+*name: The name (as a string) of the model
+*tree: The newick tree of the model
+*pop_list: A list of the population names within the model
+*ind_dict: A dictionary used to store the individuals within each population; the keys of the  dictionary are the population names whereas the values are lists of individuals.
+*nind: A dictionary used to store the number of individuals within each population; the keys of the  dictionary are the population names whereas the values are individual counts.
+*npop: The number of populations within the model
+*inds: A list of all individuals in the model
+
+
+A Model may be created with all primary attributes populated as shown below:
+
+.. code-block:: python
+
+   # Create the model
+   model = pgpipe.model.Model("2Pop")
+   
+   # Assign the model tree
+   model.assign_tree("(A,B);")
+
+   # Assign the populations and their individuals
+   model.assign_pop("A", ["Ind1", "Ind2", "Ind3"])
+   model.assign_pop("B", ["Ind4", "Ind5", "Ind6"])
+
+A **Model** class object also has two additional attributes:
+*pop_files: If created, a list of population filenames. Each population file consist of the individuals found within the population.
+*ind_file: If created, the filename of a file containing all the unique individuals found within the model.
+
+These attributes may be populated and their files created using the following functions: **create_ind_file()** and **create_pop_files()**. The inverse operating can also be completed using **delete_ind_file()** and **delete_pop_files()**.
+
+Lastly, a **Model** class object masy be assigned to a **ModelFile** class object as shown below:
+
+.. code-block:: python
+
+   # Create ModelFile object
+   models = pgpipe.model.ModelFile()
 
+   # Save the model
+   models[str(model.name)] = model