All tests passes now for Python 3.5

reflexible/base_read.py

@@ -1,4 +1,3 @@
-
 """
 functions for reading fp data in reflexible.
 
@@ -36,20 +35,15 @@
 import os
 import datetime as dt
 
-
 # Dependencies:
 # Numpy
 import numpy as np
 
-
 from .data_structures import Trajectory
 
 
-
-
-def read_trajectories(H, trajfile='trajectories.txt', \
-                     ncluster=5, \
-                     ageclasses=20):
+def read_trajectories(H, trajfile='trajectories.txt', ncluster=5,
+                      ageclasses=20):
     """
     Reads the trajectories.txt file in a FLEXPART run output directory.
 
@@ -126,13 +120,12 @@ def read_trajectories(H, trajfile='trajectories.txt', \
 
     if isinstance(H, str):
         try:
-            alltraj = file(H, 'r').readlines()
+            alltraj = open(H, 'r').readlines()
         except:
             raise IOError('Could not open file: %s' % H)
     else:
         path = H.fp_path
-        alltraj = file(os.path.join(path, trajfile), 'r').readlines()
-
+        alltraj = open(os.path.join(path, trajfile), 'r').readlines()
 
     try:
         ibdate, ibtime, model, version = alltraj[0].strip().split()[:4]
@@ -142,33 +135,37 @@ def read_trajectories(H, trajfile='trajectories.txt', \
         version = 'V.x'
     tdelta = dt.datetime.strptime(ibdate + ibtime.zfill(6), '%Y%m%d%H%M%S')
     numpoint = int(alltraj[2].strip())
-    
+
     RelTraj = Trajectory()
     Trajectories = []
     # format change?? Try block below because some trajectories.txt
     # files have linebreaks, but seems more recent FP v10. does not.
     try:
         for i in range(3, 3 + (numpoint * 2), 3):
-            i1, i2, xp1, yp1, xp2 , = tuple([float(j) for j in alltraj[i].strip().split()])
-            yp2, zp1, zp2, k, npart , = tuple([float(j) for j in alltraj[i+1].strip().split()])
+            i1, i2, xp1, yp1, xp2, = tuple((float(j) for j in
+                                            alltraj[i].strip().split()))
+            yp2, zp1, zp2, k, npart, = tuple((float(j) for j in
+                                              alltraj[i + 1].strip().split()))
     except:
         for i in range(3, 3 + (numpoint * 2), 2):
-            i1, i2, xp1, yp1, xp2, yp2, zp1, zp2, k, npart , = \
-              tuple([float(j) for j in alltraj[i].strip().split()])
+            i1, i2, xp1, yp1, xp2, yp2, zp1, zp2, k, npart, = \
+                tuple([float(j) for j in alltraj[i].strip().split()])
 
         itimerel1 = tdelta + dt.timedelta(seconds=i1)
         itimerel2 = tdelta + dt.timedelta(seconds=i2)
         Xp = (xp1 + xp2) / 2
         Yp = (yp1 + yp2) / 2
         Zp = (zp1 + zp2) / 2
-        RelTraj[alltraj[i + 1].strip()] = np.array((itimerel1, itimerel2, Xp, Yp, Zp, k, npart))
+        RelTraj[alltraj[i + 1].strip()] = np.array(
+            (itimerel1, itimerel2, Xp, Yp, Zp, k, npart))
 
     for i in range(3 + (numpoint * 3), len(alltraj)):
         raw = alltraj[i]
-        FMT = [0, 5, 8, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6] + ncluster * [8, 8, 7, 6, 8]
+        FMT = [0, 5, 8, 9, 9, 8, 8, 8, 8, 8, 8, 8, 8, 8, 6, 6, 6] + \
+              ncluster * [8, 8, 7, 6, 8]
 
-        data = [raw[sum(FMT[:ii]):sum(FMT[:ii + 1])] for ii in range(1, len(FMT) - 1)] + \
-                     [raw[sum(FMT[:-1]):]]
+        data = [raw[sum(FMT[:ii]):sum(FMT[:ii + 1])]
+                for ii in range(1, len(FMT) - 1)] + [raw[sum(FMT[:-1]):]]
         ### FIX ###
         # ## To get rid of '******' that is now in trajectories.txt
         data = [float(r.replace('********', 'NaN')) for r in data]
@@ -180,28 +177,31 @@ def read_trajectories(H, trajfile='trajectories.txt', \
     RelTraj['date'] = tdelta
     RelTraj['Trajectories'] = data
     RelTraj['labels'] = \
-            ['release number', 'seconds prior to release', 'lon', 'lat', 'height', 'mean topography', \
-             'mean mixing height', 'mean tropopause height', 'mean PV index', \
-             'rms distance', 'rms', 'zrms distance', 'zrms', \
-             'fraction mixing layer', 'fraction PV<2pvu', 'fraction in troposphere'] + \
-            ncluster * ['xcluster', 'ycluster', 'zcluster', 'fcluster', 'rmscluster']
+        ['release number', 'seconds prior to release', 'lon', 'lat',
+         'height', 'mean topography',
+         'mean mixing height', 'mean tropopause height', 'mean PV index',
+         'rms distance', 'rms', 'zrms distance', 'zrms',
+         'fraction mixing layer', 'fraction PV<2pvu',
+         'fraction in troposphere'] + \
+        ncluster * ['xcluster', 'ycluster', 'zcluster', 'fcluster',
+                    'rmscluster']
     RelTraj['info'] = \
-    """
-    Returns a dictionary:
-        R['Trajectories'] = array_of_floats(
-            releasenum,it1,xi,yi,zi,topoi,hmixi,tropoi,pvi,
-            rmsdisti,rmsi,zrmsdisti,zrmsi,hfri,pvfri,trfri,
-            (xclusti(k),yclusti(k),zclusti(k),fclusti(k),rmsclusti(k),k=1,5))
-
-        R['RELEASE_ID'] = (dt_i1,dt_i2,xp1,yp1,xp2,yp2,zp1,zp2,k,npart)
-        R['info'] = this message
-
-    To plot a trajectory timeseries:
-        RT = read_trajectories(H)
-        T = RT['Trajectories']
-        rel = 1
-        t = T[np.where(T[:,0]==rel),:][0]
-        plt.plot(t[:,1],t[:,14])
-        plt.savefig('trajectories.png')
-    """
-    return RelTraj
+        """
+        Returns a dictionary:
+            R['Trajectories'] = array_of_floats(
+                releasenum,it1,xi,yi,zi,topoi,hmixi,tropoi,pvi,
+                rmsdisti,rmsi,zrmsdisti,zrmsi,hfri,pvfri,trfri,
+                (xclusti(k),yclusti(k),zclusti(k),fclusti(k),rmsclusti(k),k=1,5))
+
+            R['RELEASE_ID'] = (dt_i1,dt_i2,xp1,yp1,xp2,yp2,zp1,zp2,k,npart)
+            R['info'] = this message
+
+        To plot a trajectory timeseries:
+            RT = read_trajectories(H)
+            T = RT['Trajectories']
+            rel = 1
+            t = T[np.where(T[:,0]==rel),:][0]
+            plt.plot(t[:,1],t[:,14])
+            plt.savefig('trajectories.png')
+        """
+    return RelTraj

reflexible/conv2netcdf4/flexpart_read.py

@@ -390,7 +390,8 @@ def read_trajectories(H, trajfile='trajectories.txt',
         ibdate, ibtime = alltraj[0].strip().split()[:2]
         model = 'Flexpart'
         version = 'V.x'
-    dt = datetime.datetime.strptime(ibdate + ibtime.zfill(6), '%Y%m%d%H%M%S')
+    dt = datetime.datetime.strptime(ibdate + ibtime.zfill(6),
+                                    '%Y%m%d%H%M%S')
     numpoint = int(alltraj[2].strip())
     # Fill a dictionary with the Release points and information keyed by name
     # RelTraj['RelTraj_ID'] = (i1,i2,xp1,yp1,xp2,yp2,zp1,zp2,k,npart)
@@ -702,12 +703,12 @@ def _get_header_version(bf):
 
     ret = bf.tell()
     bf.seek(12)  # start of version string
-    version = bf.read('13S')
+    version = bf.read('13S').decode()
     # Somewhere in version 9.2 beta, the version length changed to 29
     # However, one *must* check which is the final size for this
     if '9.2 b' in version:
          bf.seek(12)
-         version = bf.read('29S')
+         version = bf.read('29S').decode()
     bf.seek(ret)
 
     return version
@@ -874,7 +875,7 @@ def read_header(pathname, **kwargs):
         h['jjjjmmdd'] = bf.read('i')
         h['hhmmss'] = bf.read('i')
         junk.append(bf.read('2i'))
-        h['nspec'] = bf.read('i') / 3  # why!?
+        h['nspec'] = bf.read('i') // 3  # why!?
         h['numpointspec'] = bf.read('i')
         junk.append(bf.read('2i'))
 
@@ -896,15 +897,15 @@ def read_header(pathname, **kwargs):
             else:
                 junk.append(bf.read('i'))
                 h['wetdep'].append(
-                    ''.join([bf.read('c') for i in range(10)]).strip())
+                    ''.join([bf.read('c').decode() for i in range(10)]).strip())
                 junk.append(bf.read('2i'))
                 junk.append(bf.read('i'))
                 h['drydep'].append(
-                    ''.join([bf.read('c') for i in range(10)]).strip())
+                    ''.join([bf.read('c').decode() for i in range(10)]).strip())
                 junk.append(bf.read('2i'))
                 h['nz_list'].append(bf.read('i'))
                 h['species'].append(
-                    ''.join([bf.read('c') for i in range(10)]).strip())
+                    ''.join([bf.read('c').decode() for i in range(10)]).strip())
                 junk.append(bf.read('2i'))
 
         if 'V6' in version:
@@ -922,7 +923,7 @@ def read_header(pathname, **kwargs):
         I = {2: 'kindz', 3: 'xp1', 4: 'yp1', 5: 'xp2',
              6: 'yp2', 7: 'zpoint1', 8: 'zpoint2', 9: 'npart', 10: 'mpart'}
 
-        for k, v in I.iteritems():
+        for k, v in I.items():
             # create zero-filled lists in H dict
             h[v] = np.zeros(h['numpoint'])
 
@@ -960,9 +961,9 @@ def read_header(pathname, **kwargs):
                 gt = bf.tell() + l  # create 'goto' point
                 sp = ''
                 # collect the characters for the compoint
-                while re.search("\w", bf.read('c')):
+                while re.search(b"\w", bf.read('c')):
                     bf.seek(-1, 1)
-                    sp = sp + bf.read('c')
+                    sp = sp + bf.read('c').decode()
 
                 bf.seek(gt)  # skip ahead to gt point
 

reflexible/conv2netcdf4/tests/test_basics.py

@@ -16,7 +16,7 @@ def __init__(self, fp_name):
         self.fp_path = rf.datasets[fp_name]
 
     def setup(self, tmpdir):
-        self.tmpdir = tmpdir   # bring the fixture to the Dataset instance
+        self.tmpdir = tmpdir  # bring the fixture to the Dataset instance
         self.H = conv.Header(self.fp_path)
         self.nc_path = tmpdir.join("%s.nc" % self.fp_name).strpath
         return self.H, self.fp_path, self.nc_path
@@ -38,15 +38,15 @@ def test_nc_create(self):
 
     def test_read_grid(self):
         FD = conv.read_grid(self.H, time_ret=0, nspec_ret=0)
-        fdkeys = sorted(FD.keys())
-        assert fdkeys == ['grid_dates', 'options', (0, '20070121100000')]
+        fdkeys = sorted([k for k in FD.keys() if type(k) is str])
+        assert fdkeys == ['grid_dates', 'options']
         fdkeys_ = sorted(FD[(0, '20070121100000')].keys())
         assert fdkeys_ == fd_keys
 
     def test_H_read_grid(self):
         self.H.read_grid(time_ret=0, nspec_ret=0)
-        fdkeys = sorted(self.H.FD.keys())
-        assert fdkeys == ['grid_dates', 'options', (0, '20070121100000')]
+        fdkeys = sorted([k for k in self.H.FD.keys() if type(k) is str])
+        assert fdkeys == ['grid_dates', 'options']
         fdkeys_ = sorted(self.H.FD[(0, '20070121100000')].keys())
         assert fdkeys_ == fd_keys
 
@@ -74,14 +74,14 @@ def test_fill_backward(self):
 
     def test_read_grid(self):
         FD = conv.read_grid(self.H, time_ret=0, nspec_ret=0)
-        fdkeys = sorted(FD.keys())
-        assert fdkeys == ['grid_dates', 'options', (0, self.H.available_dates[0])]
+        fdkeys = sorted([k for k in FD.keys() if type(k) is str])
+        assert fdkeys == ['grid_dates', 'options']
         fdkeys_ = sorted(FD[(0, self.H.available_dates[0])].keys())
         assert fdkeys_ == fd_keys
 
     def test_H_read_grid(self):
         self.H.read_grid(time_ret=0, nspec_ret=0)
-        fdkeys = sorted(self.H.FD.keys())
-        assert fdkeys == ['grid_dates', 'options', (0, self.H.available_dates[0])]
+        fdkeys = sorted([k for k in self.H.FD.keys() if type(k) is str])
+        assert fdkeys == ['grid_dates', 'options']
         fdkeys_ = sorted(self.H.FD[(0, self.H.available_dates[0])].keys())
         assert fdkeys_ == fd_keys

reflexible/data_structures.py

@@ -735,11 +735,11 @@ def __init__(self, **options):
         self._overrides = options
 
         # set the default options as attributes
-        for key, value in self._OPTIONS.iteritems():
+        for key, value in self._OPTIONS.items():
             setattr(self, key.lower(), value[0])
 
         # override the attributes with options
-        for key, value in options.iteritems():
+        for key, value in options.items():
             setattr(self, key.lower(), value)
 
         if self.ibdate is None: