Update requirements. Split HDF5 compilation into its own virtual target.

python/cosmotool/fftw.py

@@ -19,7 +19,7 @@ class CubeFT(object):
       self.align = pyfftw.simd_alignment
       self.L = float(L)
       self.max_cpu = multiprocessing.cpu_count() if max_cpu < 0 else max_cpu
-      self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N/2+1), self.align, dtype=fourier_type)
+      self._dhat = pyfftw.n_byte_align_empty((self.N,self.N,self.N//2+1), self.align, dtype=fourier_type)
       self._density = pyfftw.n_byte_align_empty((self.N,self.N,self.N), self.align, dtype=real_type)
       self._irfft = pyfftw.FFTW(self._dhat, self._density, axes=(0,1,2), direction='FFTW_BACKWARD', threads=self.max_cpu)#, normalize_idft=False)
       self._rfft = pyfftw.FFTW(self._density, self._dhat, axes=(0,1,2), threads=self.max_cpu) #, normalize_idft=False)

python/cosmotool/grafic.py

@@ -15,16 +15,22 @@ def readGrafic(filename):
       * the mean matter density :math:`\Omega_\mathrm{m}`
       * the dark energy density :math:`\Omega_\Lambda`
       * the hubble constant, relative to 100 km/s/Mpc
+      * xoffset
+      * yoffset
+      * zoffset
   """ 
-  with file(filename, mode="rb") as f:
+  with open(filename, mode="rb") as f:
         p = struct.unpack("IIIIffffffffI", f.read(4*11 + 2*4))
-        checkPoint0, Nx, Ny, Nz, delta, _, _, _, scalefac, omega0, omegalambda0, h, checkPoint1 = p
+        checkPoint0, Nx, Ny, Nz, delta, xoff, yoff, zoff, scalefac, omega0, omegalambda0, h, checkPoint1 = p
         if checkPoint0 != checkPoint1 or checkPoint0 != 4*11:
           raise ValueError("Invalid unformatted access")
           
         a = np.empty((Nx,Ny,Nz), dtype=np.float32)
         
         BoxSize = delta * Nx * h
+        xoff *= h
+        yoff *= h
+        zoff *= h
         
         checkPoint = 4*Ny*Nz
         for i in range(Nx):
@@ -38,11 +44,11 @@ def readGrafic(filename):
             if checkPoint != 4*Ny*Nz:
               raise ValueError("Invalid unformatted access")
 
-  return a, BoxSize, scalefac, omega0, omegalambda0, h      
+  return a, BoxSize, scalefac, omega0, omegalambda0, h, xoff, yoff,zoff
 
 def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
 
-    with file(filename, mode="wb") as f:
+    with open(filename, mode="wb") as f:
         checkPoint = 4*11
         
         Nx,Ny,Nz = field.shape
@@ -65,7 +71,7 @@ def writeGrafic(filename, field, BoxSize, scalefac, **cosmo):
         
 def writeWhitePhase(filename, field):
 
-    with file(filename, mode="wb") as f:
+    with open(filename, mode="wb") as f:
         Nx,Ny,Nz = field.shape
         
         checkPoint = 4*4
@@ -80,7 +86,7 @@ def writeWhitePhase(filename, field):
 
 
 def readWhitePhase(filename):
-    with file(filename, mode="rb") as f:
+    with open(filename, mode="rb") as f:
         _, Nx, Ny, Nz, _, _ = struct.unpack("IIIIII", f.read(4*4+2*4))
         
         a = np.empty((Nx,Ny,Nz), dtype=np.float32)