Merge pull request #11 from spectraphilic/python2-3

Python2 3

.travis.yml

@@ -43,6 +43,7 @@ os:
 
 python:
   - 2.7
+  - 3.5
 
 script:
   - py.test reflexible -v --cov reflexible --cov-report term-missing

reflexible/__init__.py

@@ -38,14 +38,10 @@
     This package follows creative commons usage.
 
 """
-#print WELCOME
 
 import os
-import datetime as dt
-
 from .version import __version__
 
-
 this_dir = __path__[0]
 
 
@@ -70,6 +66,7 @@ def _get_hg_description(path_):
     except subprocess.CalledProcessError:  # not in hg repo
         pass
 
+
 _hg_description = _get_hg_description(this_dir)
 
 
@@ -94,18 +91,19 @@ def print_versions():
 datasets = {
     'Fwd1_V10.0': os.path.join(this_dir, "uio_examples/Fwd1_V10.0"),
     'Bwd1_V9.02': os.path.join(this_dir, "uio_examples/Bwd1_V9.02/outputs"),
-    'Bwd2_V9.2beta': os.path.join(this_dir, "uio_examples/Bwd2_V9.2beta/outputs"),
+    'Bwd2_V9.2beta': os.path.join(this_dir,
+                                  "uio_examples/Bwd2_V9.2beta/outputs"),
     'Fwd1_V9.02': os.path.join(this_dir, "uio_examples/Fwd1_V9.02/outputs"),
     'Fwd2_V9.02': os.path.join(this_dir, "uio_examples/Fwd2_V9.02/outputs"),
-    'HelloWorld_V9.02': os.path.join(this_dir, "uio_examples/HelloWorld_V9.02/outputs"),
-    }
-
+    'HelloWorld_V9.02': os.path.join(this_dir,
+                                     "uio_examples/HelloWorld_V9.02/outputs"),
+}
 
 # Import the public functions here
 from .tests.all import test
 from . import conv2netcdf4
 from .scripts.create_ncfile import create_ncfile
 from .data_structures import (Header, Command, Release,
-                            ReleasePoint, Ageclass)
+                              ReleasePoint, Ageclass)
 
 from .base_read import read_trajectories

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

@@ -1,5 +1,7 @@
 #### Functions for reading FLEXPART output #####
 
+from __future__ import print_function
+
 import os
 import re
 import datetime
@@ -162,7 +164,7 @@ def read_command_old(path, headerrows):
     ================    =================================================================
 
     """
-    lines = file(path, 'r').readlines()
+    lines = open(path, 'r').readlines()
     command_vals = [i.strip() for i in lines[headerrows:]]  # clean line ends
     COMMAND_KEYS = (
         'SIM_DIR',
@@ -251,7 +253,7 @@ def getfile_lines(infile):
         reverts to beginning of file."""
 
         if isinstance(infile, str):
-            return file(infile, 'r').readlines()
+            return open(infile, 'r').readlines()
         else:
             infile.seek(0)
             return infile.readlines()
@@ -375,20 +377,21 @@ 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.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]
     except:
         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)
@@ -505,7 +508,7 @@ def curtain_agltoasl(H, curtain_agl, coords, below_gl=0.0):
     xp = H.outheight - H.outheight[0]
     casl = np.zeros((len(H.asl_axis), len(coords)))
 
-    for i in xrange(len(coords)):
+    for i in range(len(coords)):
         casl[:, i] = np.interp(H.asl_axis, xp + gl[i],
                                curtain_agl[:, i], left=below_gl)
     return casl
@@ -543,7 +546,7 @@ def read_agespectrum(filename, part=False, ndays=20):
 
     """
 
-    f = file(filename, 'r').readlines()
+    f = open(filename, 'r').readlines()
 
     line1 = f[0].strip().split()
     if part:
@@ -666,7 +669,7 @@ def gridarea(H):
         ylata = outlat0 + (float(iy) + 0.5) * dyout
         ylatp = ylata + 0.5 * dyout
         ylatm = ylata - 0.5 * dyout
-        if (ylatm < 0 and ylatp > 0):
+        if ylatm < 0 and ylatp > 0:
             hzone = dyout * r_earth * pih
         else:
             # cosfact = cosfunc(ylata)
@@ -700,12 +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
@@ -792,10 +795,10 @@ def read_header(pathname, **kwargs):
     OPS.update(kwargs)
 
     if OPS.verbose:
-        print "Reading Header with:\n"
+        print("Reading Header with:\n")
 
         for o in OPS:
-            print "%s ==> %s" % (o, OPS[o])
+            print("%s ==> %s" % (o, OPS[o]))
 
     # Define utility functions for reading binary file
     skip = lambda n = 8: bf.seek(n, 1)
@@ -831,7 +834,7 @@ def read_header(pathname, **kwargs):
         raise IOError("No DATEFILE: {0}".format(datefile))
     else:
         try:
-            fd = file(datefile, 'r').readlines()
+            fd = open(datefile, 'r').readlines()
         except:
             raise IOError("Could not read datefile: {0}".format(datefile))
 
@@ -872,7 +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'))
 
@@ -894,15 +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:
@@ -920,7 +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'])
 
@@ -958,9 +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
 
@@ -1180,7 +1183,7 @@ def _readV6(bf, h):
 
     if bf:
         # bf.read('i')
-        print h['numpoint']
+        print(h['numpoint'])
         for i in range(h['numpoint']):
             # r2=getbin('i')
             i1 = getbin('i')

reflexible/conv2netcdf4/fortflex/build_FortFlex.sh

@@ -3,5 +3,5 @@
 rm -f FortFlex.pyf
 f2py -m FortFlex -h FortFlex.pyf FortFlex.f
 f2py -c --fcompiler=gfortran FortFlex.pyf FortFlex.f
-mv FortFlex.so ..
+mv *.so ..