Use abosolute import and add requirements

Author: hmaarrfk

setup.py

@@ -2,8 +2,8 @@
 This file is part of XPPy.
 
 XPPy is free software: you can redistribute it and/or modify
-it under the terms of the GNU Lesser General Public License as 
-published by the Free Software Foundation, either version 3 of 
+it under the terms of the GNU Lesser General Public License as
+published by the Free Software Foundation, either version 3 of
 the License, or (at your option) any later version.
 
 XPPy is distributed in the hope that it will be useful,
@@ -15,7 +15,7 @@
 along with XPPy.  If not, see <http://www.gnu.org/licenses/>.
 '''
 from distutils.core import setup
-from xppy import __version__ 
+from xppy import __version__
 
 setup(name='xppy',
       version=__version__,
@@ -25,5 +25,6 @@
       license='LGPL',
       url='http://seis.bris.ac.uk/~enxjn/xppy',
       platforms='All-platforms',
-      packages=['xppy','xppy.parser','xppy.utils']
+      packages=['xppy','xppy.parser','xppy.utils'],
+      install_requires=['numpy', 'matplotlib'],
       )

xppy/parser/parse.py

@@ -27,6 +27,7 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 '''
 from __future__ import print_function
+from __future__ import absolute_import
 import os
 import numpy as np
 

xppy/parser/run.py

@@ -27,6 +27,7 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 '''
 from __future__ import print_function
+from __future__ import absolute_import
 
 import os
 import shutil

xppy/utils/allinfo.py

@@ -43,12 +43,12 @@ def __init__(self, file_name=None):
         self.__raw_data = None
         self.__branches = []
         self.noVar = 0
-        # If file name is given try to load the file  
+        # If file name is given try to load the file
         if file_name != None and os.path.exists(file_name):
             self.__raw_data = np.loadtxt(file_name)
             # Calculate the number of variables
             self.noVar = int((self.__raw_data.shape[1]-5)/4)
-    
+
     def loadRawData(self, file_name):
         '''
         Raw data loader
@@ -60,7 +60,7 @@ def loadRawData(self, file_name):
             return True
         else:
             return False
-   
+
     def setRawData(self, raw_data):
         '''
         Raw data setter
@@ -85,7 +85,7 @@ def findBranches(self):
         '''
         if self.__raw_data == None:
             return False
-        
+
         # Scan file for branches
         bl = []
         for b in self.__raw_data[:,1]:
@@ -100,8 +100,8 @@ def findBranches(self):
 
     def findParts(self, branchArr):
         '''
-        Finds parts in the given branch array 
-        (branch extracted by e.g. getBranch) 
+        Finds parts in the given branch array
+        (branch extracted by e.g. getBranch)
         '''
         parts = []; last = 0
         for i in range(0,branchArr.shape[0]):
@@ -127,7 +127,7 @@ def getBranch(self, nr, getParts=False):
         '''
         if len(self.__branches) == 0:
             self.findBranches()
-        
+
         try:
             self.__branches.index(nr)
         except ValueError:
@@ -140,8 +140,8 @@ def getBranch(self, nr, getParts=False):
             parts = self.findParts(retArr)
             return (retArr, parts)
         # Else, just return the branch array
-        return retArr          
- 
+        return retArr
+
     def getFlippedBranch(self, nr, getParts=False):
         '''
         Function returns flipped data of branch number nr;
@@ -151,7 +151,7 @@ def getFlippedBranch(self, nr, getParts=False):
         (b,p) = self.getBranch(nr,True)
         if b == None:
             return None
-            
+
         # Find starting point
         i = np.ix_(b[:,2]==b[0,2],b[:,3]==b[0,3])[0].ravel()
         # If the branch can't be flipped, return
@@ -171,4 +171,4 @@ def getFlippedBranch(self, nr, getParts=False):
             parts = self.findParts(retArr)
             return (retArr, parts)
         # Else, just return the branch array
-        return retArr          
+        return retArr

xppy/utils/data.py

@@ -34,8 +34,8 @@
 def getOrbit(data, start=None, eps=1e-4, col=1):
     '''
     Function extracts single orbit from given data and returns it.
-    The orbit is ectracted from 'start' with accuracy of the end 
-    point less than eps. The compared data is taken from 
+    The orbit is ectracted from 'start' with accuracy of the end
+    point less than eps. The compared data is taken from
     the column col.
     '''
     # If no starting point is specified, start from the minimal value
@@ -45,7 +45,7 @@ def getOrbit(data, start=None, eps=1e-4, col=1):
     stop = start+1
     avr = data[:,col].min() + \
           (np.abs(data[:,col].max()) + np.abs(data[:,col].min()))/2
-    crossAvr = False 
+    crossAvr = False
     for i in range(start+1,data.shape[0]):
         # Orbit have to cross maximu avarege value firs
         if not crossAvr:
@@ -70,8 +70,8 @@ def arcLength(data):
 
 def resample1d(data, ns):
     '''
-    Function resamples the given data (1d line [x,y] data) using even 
-    arc lenght (linear interpolation). New (resampled) data is returned.  
+    Function resamples the given data (1d line [x,y] data) using even
+    arc lenght (linear interpolation). New (resampled) data is returned.
     '''
     # Calculating arc lenght of the bit and the whole data
     tot_alen = arcLength(data)
@@ -98,20 +98,20 @@ def resample1d(data, ns):
 
 def findSpikes(data, cols=[0,1], threshold=20, sampleThr=3):
     '''
-    Function finds spikes in the given two data columns data. 
-    Threshold is a slope of the tangent line. SampleThr is 
+    Function finds spikes in the given two data columns data.
+    Threshold is a slope of the tangent line. SampleThr is
     minimal number of samples where slope is greater then threshold.
     Threshold value according to (Naundorf et al. 2006).
     '''
     if len(cols) != 2:
         raise ValueError('List should contain to columns!')
-    
+
     st = 0 # Number of samples above threshold
     # List contain begining, top and end of the spike i
     spb = []; spm = []; spe = []
     # Last slope
     sl_last = 0
-    # Spike flag (0 - nothing, 1 - passed begining, 
+    # Spike flag (0 - nothing, 1 - passed begining,
     # 2 - passed midpoint, 3 - on the way down (on steep slope))
     spf = 0
     for i in range(1,data.shape[0]):
@@ -128,7 +128,7 @@ def findSpikes(data, cols=[0,1], threshold=20, sampleThr=3):
                 spf = 2
             sl_last = sl
             continue
-        
+
         # Looking for the steep slope down
         if spf == 2:
             if np.abs(sl) > threshold and np.sign(sl) == -1:
@@ -172,7 +172,7 @@ def findADP(data, cols=[0,1], threshold=20, sampleThr=3):
         dx,dy = data[spe[i],cols] - data[spe[i]-1,cols]
         # Slope of tangent line
         sl_last = dy/dx
-        # If we have more spikes, look for ADP till the begining 
+        # If we have more spikes, look for ADP till the begining
         # of the next spike, else look till the end of the data
         if i+1 < len(spe):
             j_end = spb[i+1]
@@ -197,13 +197,13 @@ def ISI(data, cols=[0,1], threshold=20, sampleThr=3):
     of ISI for the given pair. The ISI is calculated for the peak of the spikes.
     Threshold value according to (Naundorf et al. 2006).
     '''
-    
+
     (spb, spm, spe) = findSpikes(data, cols, threshold, sampleThr)
-    
+
     # ISI can be calculated for at least 2 spikes
     if len(spm) < 2:
         return None
-    
+
     return np.diff(data[spm,cols[0]])
 
 def getDVDT(data, cols=[0,1]):
@@ -214,14 +214,14 @@ def getDVDT(data, cols=[0,1]):
     return np.diff(data[:,cols[1]])/np.diff(data[:,cols[0]])
 
 def getThreshold(data, cols=[0,1]):
-    ''' 
+    '''
     Function returns a threshold time and value for the first spike in the spike train.
     Threshold is defined as dV/dt crossing of 20 V/s (Naundorf et al. 2006).
     '''
     dv = getDVDT(data, cols)
-    
+
     i = (dv >= 20).nonzero()[0][0]
-    
+
     return data[i,:]
 
 def getTau(data, cols=[0,1]):
@@ -232,8 +232,8 @@ def getTau(data, cols=[0,1]):
     function does not detect the beginning of current injection by itself.
     '''
     d = np.abs(data[:,cols].copy())
-    v_63  = 0.63*(d[:,cols[1]].max() - d[:,cols[1]].min()) + d[0,cols[1]]    
+    v_63  = 0.63*(d[:,cols[1]].max() - d[:,cols[1]].min()) + d[0,cols[1]]
 
-    # Index of the 63% crossing 
+    # Index of the 63% crossing
     i_63 = (d[:,cols[1]] >= v_63).nonzero()[0][0]
     return d[i_63,cols[1]] - d[0,cols[1]]

xppy/utils/diagram.py

@@ -44,5 +44,5 @@ def read_diagram(diag):
         elif diag[i,3] == 4:
             diag_ret[i,[4,8]] = diag[i,[1,2]]
     diag_ret[:,0] = diag[:,0]
-    
+
     return diag_ret

xppy/utils/output.py

@@ -40,14 +40,14 @@ def __init__(self, ode_file='', file_name='output.dat'):
         '''
         self.__raw_data = None # Content of data file
         self.__desc     = None # Data descriptor, read from the ode_file
-        
+
         if os.path.exists(file_name):
             self.__raw_data = np.loadtxt(file_name)
-        
+
         if os.path.exists(ode_file):
             self.__desc = parse.readOdeVars(ode_file)
-        
-    
+
+
     def loadRawData(self, file_name='output.dat'):
         '''
         Raw data loader
@@ -57,7 +57,7 @@ def loadRawData(self, file_name='output.dat'):
             return True
         else:
             return False
-   
+
     def setRawData(self, raw_data):
         '''
         Raw data setter
@@ -82,37 +82,37 @@ def readOdeVars(self, ode_file):
         '''
         self.__desc = parse.readOdeVars(ode_file)
         return True
-    
+
     def setDesc(self, desc):
         '''
         Variable descriptor setter
         '''
         self.__desc = desc
-    
+
     def getDesc(self):
         '''
         Variable descriptor getter
         '''
         return self.__desc
-     
+
     def __getitem__(self, name):
-        # TODO Maybe do it more efficiently 
+        # TODO Maybe do it more efficiently
         # Sequence value
         if type(name) is tuple:
             if type(name[1]) is str:
-                j = self.__desc[name[1]] 
+                j = self.__desc[name[1]]
             elif type(name[1]) is list:
                 j = []
                 for n in name[1]:
                     if type(n) is int:
                         j.append(n)
                     elif type(n) is str:
-                        j.append(self.__desc[n])                      
+                        j.append(self.__desc[n])
             else:
                 j = name[1]
             i = name[0]
             return self.__raw_data[i,j]
-        # Single value         
+        # Single value
         elif type(name) is str:
             j = self.__desc[name]
             return self.__raw_data[:,j]
@@ -126,14 +126,14 @@ def __getitem__(self, name):
                     elif type(n) is str:
                         j.append(self.__desc[n])
                 return self.__raw_data[:,j]
-        
+
         else:
             raise IndexError('Index does not exist!')
-        
+
     def __str__(self):
         ret = 'Columns:'
         for i in range(self.__raw_data.shape[1]):
-            ret += ' %i:%s'%(i,self.__desc[i]) 
+            ret += ' %i:%s'%(i,self.__desc[i])
         ret += '\nData:\n'+str(self.__raw_data)
-        
+
         return ret

xppy/utils/plot.py

@@ -27,6 +27,7 @@
 SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 '''
 from __future__ import print_function
+from __future__ import absolute_import
 
 import numpy as np #@UnresolvedImport
 from xppy.utils import allinfo