updated ci script and added to python tools

.gitlab-ci.yml

@@ -25,11 +25,13 @@ build:centos7:
 
 case1:
   stage: test
-  image: garrettwrong/spec_centos-7
+  image: csmiet/testspec
   script:
+  - source source.sh
   - cd ci/G1V03L2Fi
-  - ../../xspec G1V03L2Fi.001.sp
-  #- comparison
+  - xspec G1V03L2Fi.001.sp
+  - python3 -m py_spec.ci.test G1V03L2Fi.001.sp.h5 comparison.h5
+  #comparison python3 -m py_spec.ci.testspec f1 f2
   artifacts:
     when: always
     paths:

Utilities/pythontools/py_spec/__init__.py

@@ -4,5 +4,7 @@
 from .proc_spec import *
 from . import plot
 from . import math
+from . import external
+from . import ci
 
 

Utilities/pythontools/py_spec/ci/__init.py

@@ -0,0 +1,3 @@
+# import the test script
+
+import test

Utilities/pythontools/py_spec/ci/test.py

@@ -0,0 +1,57 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+"""
+@author: Caoxiang Zhu ([email protected])
+For any help, type ./compare_spec.py -h
+"""
+import numpy as np
+from py_spec import SPEC
+import argparse
+
+# parse command line arguments
+parser = argparse.ArgumentParser(description="Compare two SPEC HDF5 outputs")
+parser.add_argument("filename", type=str, help="file name to be compared")
+parser.add_argument("reference", type=str, help="reference data")
+parser.add_argument("-t", "--tol", type=float, default=1E-12, help="difference tolerance")
+
+args = parser.parse_args()
+print('Compare SPEC outputs in {:s} and {:s} with tolerance {:12.5E}'.format(
+        args.filename, args.reference, args.tol))
+data_A = SPEC(args.filename)
+data_B = SPEC(args.reference)
+tol = args.tol
+match = True
+
+
+def compare(data, reference):
+    global match
+    for key, value in vars(data).items():
+        if isinstance(value, SPEC):  # recurse data
+            print('------------------')
+            print('Elements in '+key)
+            compare(value, reference.__dict__[key])
+        else:
+            if key in ['filename', 'version']:  # not compare filename and version
+                continue
+            elif key == 'iterations': # skip iteration data (might be revised)
+                continue
+            else:
+                # print(key)
+                diff = np.linalg.norm(np.abs(np.array(value) - np.array(reference.__dict__[key])))
+                unmatch = diff > tol
+                if unmatch:
+                    match = False
+                    print('UNMATCHED: '+key, ', diff={:12.5E}'.format(diff))
+                else :
+                    print('ok: '+key)
+    return
+
+compare(data_A, data_B)
+print('===================')
+if match :
+    print('All the terms are within tolerance.')
+else :
+    print('Differences in some elements are larger than the tolerence.')
+
+exit
+

Utilities/pythontools/py_spec/math/__init__.py

@@ -1,4 +1,4 @@
 # import the math functions
 
-from .fourier_surface import *
+from .fourier_surface import fourier_surface
 from .interface_current import *

Utilities/pythontools/py_spec/math/fourier_surface.py

@@ -3,17 +3,15 @@
 # coded by @zhucaoxiang ([email protected])
 # adapted by @smiet ([email protected])
 #
-
+import numpy as np
 
 class fourier_surface(object):
-    import numpy as np
     '''
     toroidal surface in Fourier representation
     R = \sum RBC cos(mu-nv) + RBS sin(mu-nv)
     Z = \sum ZBC cos(mu-nv) + ZBS sin(mu-nv)
     '''
     def __init__(self, xm=[], xn=[], rbc=[], zbs=[], rbs=[], zbc=[]):
-        import numpy as np
         """Initialization with Fourier harmonics.
 
         Parameters:
@@ -45,7 +43,6 @@ def read_spec_output(cls, spec_out, ns=-1):
         Returns:
           fourier_surface class
         """
-        import numpy as np
         # check if spec_out is in correct format
         #if not isinstance(spec_out, SPEC):
         #    raise TypeError("Invalid type of input data, should be SPEC type.")
@@ -74,7 +71,6 @@ def read_vmec_output(cls, woutfile, ns=-1):
         Returns:
           fourier_surface class
         """
-        import numpy as np
         import xarray as ncdata # read netcdf file
         vmec = ncdata.open_dataset(woutfile)
         xm = vmec['xm'].values
@@ -108,7 +104,6 @@ def read_focus_input(cls, filename, Mpol=9999, Ntor=9999):
         Returns:
           fourier_surface class
         """
-        import numpy as np
         with open(filename, 'r') as f:
             line = f.readline() #skip one line
             line = f.readline()
@@ -152,7 +147,6 @@ def read_winding_surfce(cls, filename, Mpol=9999, Ntor=9999):
         Returns:
           fourier_surface class
         """
-        import numpy as np
         with open(filename, 'r') as f:
             line = ''
             while "phip_edge" not in line:
@@ -205,7 +199,6 @@ def rz(self, theta, zeta, normal=False):
            r, z -- float array_like
            r, z, [rt, zt], [rz, zz] -- if normal
         """
-        import numpy as np
         assert len(np.atleast_1d(theta)) == len(np.atleast_1d(zeta)), "theta, zeta should be equal size"
         # mt - nz (in matrix)
         _mtnz = np.matmul( np.reshape(self.xm, (-1,1)), np.reshape(theta, (1,-1)) ) \
@@ -243,7 +236,6 @@ def xyz(self, theta, zeta, normal=False):
            x, y, z -- float array_like
            x, y, z, [nx, ny, nz] -- if normal
         """
-        import numpy as np
         data = self.rz(theta, zeta, normal)
         r = data[0]
         z = data[1]
@@ -277,7 +269,6 @@ def areaVolume(self, theta0=0.0, theta1=2*np.pi, zeta0=0.0, zeta1=2*np.pi, \
           area -- surface area
           volume -- surface volume
         """
-        import numpy as np
         # get mesh data
         _theta = np.linspace(theta0, theta1, npol, endpoint=False)
         _zeta = np.linspace(zeta0, zeta1, ntor, endpoint=False)
@@ -299,7 +290,6 @@ def get_area(self):
         Returns:
            area
         """
-        import numpy as np
         self.area, _volume = self._areaVolume()
         return self.area
 
@@ -325,7 +315,6 @@ def plot(self, zeta=0.0, npoints=360, **kwargs):
            line class in matplotlib.pyplot
         """
         import matplotlib.pyplot as plt
-        import numpy as np
         # get figure and ax data
         if plt.get_fignums():
             fig = plt.gcf()
@@ -363,7 +352,6 @@ def plot3d(self, engine='pyplot', theta0=0.0, theta1=2*np.pi, zeta0=0.0, zeta1=2
         Returns:
            xsurf, ysurf, zsurf -- arrays of x,y,z coordinates on the surface
         """
-        import numpy as np
         # get mesh data
         _theta = np.linspace(theta0, theta1, npol)
         _zeta = np.linspace(zeta0, zeta1, ntor)
@@ -405,7 +393,6 @@ def tovtk(self, vtkname, npol=360, ntor=360, **kwargs):
         Returns:
 
         """
-        import numpy as np
         from pyevtk.hl import gridToVTK # save to binary vtk
         _xx, _yy, _zz = self.plot3d('noplot', zeta0=0.0, zeta1=2*np.pi,
                                     theta0=0.0, theta1=2*np.pi, npol=npol, ntor=ntor)

Utilities/pythontools/py_spec/math/interface_current.py

@@ -4,7 +4,7 @@
 
 def interface_current(SPEC, interface_number):
     """
-    returns the ruccent on the interface given by interface_number.
+    returns the current on the interface given by interface_number.
     Not working yet
 
     We are calculating a loop integral over the difference in magnetic field on the surface.
@@ -21,13 +21,15 @@ def interface_current(SPEC, interface_number):
     outer_volume = SPEC.output.Btemn[0:Ntor, 0, interface_number]
     inner_volume = SPEC.output.Btemn[0:Ntor, 1, interface_number-1]
 
-    current = np.sum(outer_volume-inner_volume)* np.pi * 2  # check if idl's pi2 is pi squared or just two pi
+    current = np.sum(outer_volume-inner_volume) * np.pi * 2  # check if idl's pi2 is pi squared or just two pi
 
     return current
 
+
 def interface_current_total(SPEC):
     """
-    returns the ruccent on the interface given by interface_number.
+    NOT TESTED!
+    returns the current on the interface given by interface_number.
     Not working yet
 
     We are calculating a loop integral over the difference in magnetic field on the surface.

Utilities/pythontools/py_spec/plot/plot_kam_surface.py

@@ -31,7 +31,7 @@ def plot_kam_surface(SPEC, ns=None, zeta=0.0, **kwargs):
         kwargs.update({'label': 'SPEC_KAM'})  # default label
     # plot all the surfaces
     for i in ns:
-        _surf = math.fourier_surface.read_spec_output(SPEC, i)  #look into which spec fourier_surface needs.
+        _surf = math.fourier_surface.read_spec_output(SPEC, i)  # look into which spec fourier_surface needs.
         if i == 0:
             # plot axis as a curve
             _r, _z = _surf.rz(0.0, zeta)

Utilities/pythontools/py_spec/plot/plot_poincare.py

@@ -17,33 +17,33 @@ def plot_poincare(SPEC, toroidalIdx=0, prange='full', **kwargs):
     import matplotlib.pyplot as plt
     import matplotlib.lines as mlines
     # extract slice corresponding to the given toroidal cutplane
-    rr = SPEC.poincare.R[:,:,toroidalIdx]
-    zz = SPEC.poincare.Z[:,:,toroidalIdx]
+    rr = SPEC.poincare.R[:, :, toroidalIdx]
+    zz = SPEC.poincare.Z[:, :, toroidalIdx]
     # get current figure or build new one;
     if plt.get_fignums():
         fig = plt.gcf()
         ax = plt.gca()
-    else :
+    else:
         fig, ax = plt.subplots()
     # set default plotting parameters
     # use dots
-    if kwargs.get('marker') == None:
+    if kwargs.get('marker') is None:
         kwargs.update({'marker': '.'})
     # use gray color
-    if kwargs.get('c') == None:
+    if kwargs.get('c') is None:
         kwargs.update({'c': 'gray'})
     # make plot depending on the 'range'
     if prange == 'full':
         dots = ax.scatter(rr, zz, **kwargs)
     elif prange == 'upper':
-        dots = ax.scatter(rr[zz>=0], zz[zz>=0], **kwargs)
+        dots = ax.scatter(rr[zz >= 0], zz[zz >= 0], **kwargs)
     elif prange == 'lower':
-        dots = ax.scatter(rr[zz<=0], zz[zz<=0], **kwargs)
-    else :
+        dots = ax.scatter(rr[zz <= 0], zz[zz <= 0], **kwargs)
+    else:
         raise ValueError("prange should be one of ['full'(default), 'upper', 'lower'].")
     # adjust figure properties
-    plt.xlabel('R [m]',fontsize=20)
-    plt.ylabel('Z [m]',fontsize=20)
+    plt.xlabel('R [m]', fontsize=20)
+    plt.ylabel('Z [m]', fontsize=20)
     plt.xticks(fontsize=16)
     plt.yticks(fontsize=16)
     plt.axis('equal')

ci/Dockerfile.centos7

@@ -6,6 +6,8 @@ RUN yum -y install epel-release
 RUN yum install gcc-gfortran openmpi openmpi-devel hdf5 hdf5-devel -y
 RUN yum install fftw3 fftw3-devel openblas openblas-devel -y
 RUN yum install blas blas-devel lapack lapack-devel -y
+RUN yum install -y python3 python3-devel
+RUN pip3 install h5py matplotlib 
 
 # direct the existing makefile to the system install location
 ENV FFTW_HOME=/usr

source.sh

@@ -0,0 +1,20 @@
+#
+# source.sh
+# This file sets the PATH to the current directory, which 
+# is the directory where the xspec file is located. 
+# 
+# It also updates the $PYTHONPATH variable so that the 
+# regression testing can be executed. 
+#
+
+# Test if this is the folder where xspec lives then export paths or exit with error
+if ( [ -e ./xspec ] && \
+     [ -e ./xspech.f90 ] ); then 
+  export PATH=${PATH}:$PWD
+  export PYTHONPATH=${PYTHONPATH}:$PWD/Utilities/pythontools
+else 
+  echo "xspec executable does not exist, will not modify your path"
+  exit 1
+fi
+
+