manual merging of the new version

theelectricbrain · Aug 23, 2015 · 84ac94f · 84ac94f
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diff --git a/PySeidon_tuto_0.ipynb b/PySeidon_tuto_0.ipynb
diff --git a/PySeidon_tuto_1.ipynb b/PySeidon_tuto_1.ipynb
diff --git a/PySeidon_tuto_2.ipynb b/PySeidon_tuto_2.ipynb
diff --git a/PySeidon_tuto_3.ipynb b/PySeidon_tuto_3.ipynb
diff --git a/PySeidon_tuto_4.ipynb b/PySeidon_tuto_4.ipynb
diff --git a/PySeidon_tuto_5.ipynb b/PySeidon_tuto_5.ipynb
diff --git a/PySeidon_tuto_6.ipynb b/PySeidon_tuto_6.ipynb
diff --git a/README.md b/README.md
@@ -26,11 +26,11 @@ Hydrodynamic model:
 * This package has been primarily developed and designed for post-processing FVCOM outputs. One can download FVCOM from [here](http://fvcom.smast.umassd.edu/fvcom/) 
 
 Requirements:
-* This package ha been designed for Python 2.7: One can download Python from [here](http://www.python.org/download)
-* It recommended to install Anaconda beforehand: One can download Anaconda from [here](http://continuum.io/downloads#all)
+* This package has been designed for Python 2.7: one can download Python from [here](http://www.python.org/download)
+* It is recommended to install Anaconda beforehand: one can download Anaconda from [here](http://continuum.io/downloads#all)
+* The HDF5 library is also needed for this package to work: one can download the HDF5 library from [here](https://www.hdfgroup.org/HDF5/)
 
 Dependencies:
-
 Althought they should be automatically resolved during the installation, this package relies on the following dependencies:
 * setuptools: One can download setuptools from [here](https://pypi.python.org/pypi/setuptools#installation-instructions)
 * UTide: One can download UTide from [here](https://github.com/wesleybowman/UTide)
@@ -54,15 +54,22 @@ Up-dating:
 Recommendations:
 * The tutorials and package functioning have been designed for use in IPython shell: One can download IPython from [here](http://ipython.org/)
 
+### Documentation ###
+Package's documentation can be found [here](http://grumpynounours.github.io/PySeidon/index.html)
 
 ### Contribution guidelines ###
 * [Tutorial 0: First steps](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/master/PySeidon_tuto_0.ipynb)
 * [Tutorial 1: FVCOM class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/master/PySeidon_tuto_1.ipynb)
+* [Tutorial 2: Station class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/development/PySeidon_tuto_2.ipynb)
+* [Tutorial 3: ADCP class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/development/PySeidon_tuto_3.ipynb)
+* [Tutorial 4: TideGauge class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/development/PySeidon_tuto_4.ipynb)
+* [Tutorial 5: Drifter class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/development/PySeidon_tuto_5.ipynb)
+* [Tutorial 6: Validation class](http://nbviewer.ipython.org/github/GrumpyNounours/PySeidon/blob/development/PySeidon_tuto_6.ipynb)
 
 ### Contacts ###
 * Project Leader: [Richard Karsten](richard.karsten@acadiau.ca)
 * Repository Admin & Software Development Manager: [Thomas Roc](thomas.roc@acadiau.ca)
-* Main Developers: [Wesley Bowman](https://github.com/wesleybowman), [Thomas Roc](thomas.roc@acadiau.ca), [Jonathan Smith](https://github.com/LaVieEnRoux)
+* Main Developers: [Thomas Roc](thomas.roc@acadiau.ca), [Jonathan Smith](https://github.com/LaVieEnRoux), [Wesley Bowman](https://github.com/wesleybowman), [Kody Crowell](https://github.com/TheKingInYellow)
 
 ### Contributors ###
 Dr. Richard Karsten, [Aidan Bharath](https://github.com/Aidan-Bharath), Mitchell O'Flaherty-Sproul, Robie Hennigar, Dr. Joel Culina, Justine McMillan, Dr. Brian Polagye, [Dr. Kristen Thyng](https://github.com/kthyng)...

diff --git a/data4tutorial/adcp_GP_01aug2013.mat b/data4tutorial/adcp_GP_01aug2013.mat
diff --git a/data4tutorial/drifter_GP_01aug2013.mat b/data4tutorial/drifter_GP_01aug2013.mat
diff --git a/data4tutorial/tidegauge_GP_01aug2013.mat b/data4tutorial/tidegauge_GP_01aug2013.mat
diff --git a/pyseidon/__init__.py b/pyseidon/__init__.py
@@ -15,20 +15,23 @@
 sys.path.append(os.path.join(local,'utilities'))
 
 #Local import
-from fvcomClass import *
+from utilities import *
 from adcpClass import *
-#from drifterClass import *
+from drifterClass import *
 from tidegaugeClass import *
-from validationClass import *
 from stationClass import *
-from utilities import *
+from fvcomClass import *
+from validationClass import *
+
+# Custom error
+from pyseidon.utilities.pyseidon_error import PyseidonError
 
 #Permission info for OpenDap server
 #print "OpenDap server connexion info:"
 
-__version__ = '1.1'
+__version__ = '2.0'
 __all__ = ["FVCOM", "ADCP", "Drifter", "TideGauge",\
-           "Validation", "Station", "utilities" ]
+           "Validation", "Station", "utilities", "PyseidonError"]
 __authors__ = ['Wesley Bowman, Thomas Roc, Jonathan Smith']
 __licence__ = 'GNU Affero GPL v3.0'
 __copyright__ = 'Copyright (c) 2014 EcoEnergyII'

diff --git a/pyseidon/adcpClass/__init__.py b/pyseidon/adcpClass/__init__.py
@@ -1,10 +1,6 @@
 #!/usr/bin/python2.7
 # encoding: utf-8
 
-from __future__ import division
-import os
-import sys
-
 #Local import
 from adcpClass import ADCP
 

diff --git a/pyseidon/adcpClass/adcpClass.py b/pyseidon/adcpClass/adcpClass.py
@@ -2,67 +2,66 @@
 # encoding: utf-8
 from __future__ import division
 import numpy as np
-import sys 
 import scipy.io as sio
 import h5py
 
-#Add local path to utilities
-sys.path.append('../utilities/')
-
 #Local import
 from variablesAdcp import _load_adcp
 from functionsAdcp import *
 from plotsAdcp import *
 
 
 class ADCP:
-    ''' 
-Description:
------------
-  A class/structure for ADCP data.
-  Functionality structured as follows:
-               _Data. = raw matlab file data
-              |_Variables. = useable adcp variables and quantities
-              |_History = Quality Control metadata
-    testAdcp._|_Utils. = set of useful functions
-              |_Plots. = plotting functions
-              |_method_1
-              | ...      = methods and analysis techniques intrinsic to ADCPs
-              |_method_n
+    """
+    **A class/structure for ADCP data**
+
+    Functionality structured as follows: ::
 
-Inputs:
-------
-  Only takes a file name as input, ex: testAdcp=ADCP('./path_to_matlab_file/filename')
+                   _Data. = raw matlab file data
+                  |_Variables. = useable adcp variables and quantities
+                  |_History = Quality Control metadata
+        testAdcp._|_Utils. = set of useful functions
+                  |_Plots. = plotting functions
+                  |_method_1
+                  | ...      = methods and analysis techniques intrinsic to ADCPs
+                  |_method_n
 
-Notes:
------
-  Only handle fully processed ADCP matlab data previously quality-controlled as well
-  as formatted through "EnsembleData_FlowFile" matlab script at the mo.
+    Inputs:
+      - Only takes a file name as input, ex: testAdcp=ADCP('./path_to_matlab_file/filename')
 
-  Throughout the package, the following conventions apply:
-  - Coordinates = decimal degrees East and North
-  - Directions = in degrees, ???
-  - Depth = 0m is the free surface and depth is negative
-    '''
+    *Notes*
+      Only handle fully processed ADCP matlab data previously quality-controlled as well
+      as formatted through "EnsembleData_FlowFile" matlab script at the mo.
+
+      Throughout the package, the following conventions apply:
+      - Coordinates = decimal degrees East and North
+      - Directions = in degrees, between -180 and 180 deg., i.e. 0=East, 90=North,
+                     +/-180=West, -90=South
+      - Depth = 0m is the free surface and depth is negative
+    """
 
     def __init__(self, filename, debug=False):
-        ''' Initialize ADCP class.
-            Notes: only handle processed ADCP matlab data at the mo.'''    
+        """ Initialize ADCP class."""
         self._debug = debug
         self._origin_file = filename
         if debug:
             print '-Debug mode on-' 
         #TR_comments: find a way to dissociate raw and processed data
-        self.History = ['Created from' + filename]
+        self.History = ['Created from ' + filename]
         #TR_comments: *_Raw and *_10minavg open with h5py whereas *_davgBS
         try:
             self.Data = sio.loadmat(filename,struct_as_record=False, squeeze_me=True)
         except NotImplementedError:
-            self.Data = h5py.File(filename)
-        self.Variables = _load_adcp(self, debug=self._debug)
+            self.Data = h5py.File(filename, 'r')
+        #TR_comments: Initialize class structure
+        self.Variables = _load_adcp(self, self.History, debug=self._debug)
         self.Plots = PlotsAdcp(self.Variables, debug=self._debug)
         self.Utils = FunctionsAdcp(self.Variables,
                                    self.Plots,
                                    self.History,
                                    debug=self._debug) 
 
+        ##Re-assignement of utility functions as methods
+        self.dump_profile_data = self.Plots._dump_profile_data_as_csv
+
+        return