From 54eeb38a368811538fcdc68c629b721e74c6cb62 Mon Sep 17 00:00:00 2001
From: fzahle <frza@dtu.dk>
Date: Mon, 20 May 2019 22:20:37 +0200
Subject: [PATCH] py3 fixes for testsuite runner
---
.gitlab-ci.yml | 7 +++-
ellipsyswrapper/ellipsys_output.py | 20 ++++++-----
ellipsyswrapper/testsuite.py | 58 ++++++++++++++----------------
3 files changed, 45 insertions(+), 40 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 761ac72..e675c64 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -1,8 +1,13 @@
image: frza/gitlab-ci-debian
-test:
+test2:
script:
- source activate py27
- pip install -e .
- nosetests
+test3:
+ script:
+ - source activate py35
+ - pip install -e .
+ - nosetests
diff --git a/ellipsyswrapper/ellipsys_output.py b/ellipsyswrapper/ellipsys_output.py
index 15aeefc..b0603fb 100644
--- a/ellipsyswrapper/ellipsys_output.py
+++ b/ellipsyswrapper/ellipsys_output.py
@@ -43,10 +43,11 @@ class EllipSys1DOutput(object):
var_map[ivar] = name
if not hasattr(self, 'pt_ext_%s' % name):
setattr(self, 'pt_ext_%s' % name, [])
+ pos = fid.tell()
line = fid.readline()
ivar += 1
# unroll readline so all data is read by loadtxt
- fid.seek(-len(line), 1)
+ fid.seek(pos, 0)
data = np.loadtxt(fid)
for j in range(data.shape[1]):
var = getattr(self, 'pt_ext_%s' % var_map[j])
@@ -156,7 +157,7 @@ class EllipSys2DOutput(object):
self.fy_ave[nlev].append(np.mean(grid_force[ave:, 5]))
self.mz_ave[nlev].append(np.mean(grid_force[ave:, 6]))
except:
- print 'Error on reading of',filename
+ print('Error on reading of', filename)
else:
# there's only one surface
@@ -176,7 +177,7 @@ class EllipSys2DOutput(object):
self.fy_ave.append(np.mean(grid_force[ave:, 5]))
self.mz_ave.append(np.mean(grid_force[ave:, 6]))
except:
- print 'Error on reading of',filename
+ print('Error on reading of', filename)
nlev += 1
# read the pressure distributions
@@ -362,7 +363,7 @@ class EllipSys3DOutput(object):
self.my_ave[nlev].append(np.mean(grid_force[ave:, 9]))
self.mz_ave[nlev].append(np.mean(grid_force[ave:, 10]))
except:
- print 'Error on reading of',filename
+ print('Error on reading of', filename)
else:
# there's only one surface
@@ -391,7 +392,7 @@ class EllipSys3DOutput(object):
self.my_ave.append(np.mean(grid_force[ave:, 9]))
self.mz_ave.append(np.mean(grid_force[ave:, 10]))
except:
- print 'Error on reading of',filename
+ print('Error on reading of', filename)
nlev += 1
# read the grid.?F? files
@@ -449,10 +450,11 @@ class EllipSys3DOutput(object):
var_map[ivar] = name
if not hasattr(self, 'pt_ext_%s' % name):
setattr(self, 'pt_ext_%s' % name, [])
+ pos = fid.tell()
line = fid.readline()
ivar += 1
# unroll readline so all data is read by loadtxt
- fid.seek(-len(line), 1)
+ fid.seek(pos, 0)
data = np.loadtxt(fid)
for j in range(data.shape[1]):
var = getattr(self, 'pt_ext_%s' % var_map[j])
@@ -475,10 +477,11 @@ class EllipSys3DOutput(object):
var_map[ivar] = name
if not hasattr(self, 'les_ext_%s' % name):
setattr(self, 'les_ext_%s' % name, [])
+ pos = fid.tell()
line = fid.readline()
ivar += 1
# unroll readline so all data is read by loadtxt
- fid.seek(-len(line), 1)
+ fid.seek(pos, 0)
data = np.loadtxt(fid)
for j in range(data.shape[1]):
var = getattr(self, 'les_ext_%s' % var_map[j])
@@ -501,10 +504,11 @@ class EllipSys3DOutput(object):
var_map[ivar] = name
if not hasattr(self, 'ha_ext_%s' % name):
setattr(self, 'ha_ext_%s' % name, [])
+ pos = fid.tell()
line = fid.readline()
ivar += 1
# unroll readline so all data is read by loadtxt
- fid.seek(-len(line), 1)
+ fid.seek(pos, 0)
data = np.loadtxt(fid)
for j in range(data.shape[1]):
var = getattr(self, 'ha_ext_%s' % var_map[j])
diff --git a/ellipsyswrapper/testsuite.py b/ellipsyswrapper/testsuite.py
index 5988bc6..837385b 100644
--- a/ellipsyswrapper/testsuite.py
+++ b/ellipsyswrapper/testsuite.py
@@ -2,9 +2,7 @@
import os,sys
import glob
import numpy as np
-import commands
import subprocess
-import cPickle
import time
import shutil
import unittest2 as unittest
@@ -43,13 +41,13 @@ class CaseRunner(object):
self.root_dir = os.getcwd()
- for k, w in kwargs.iteritems():
+ for k, w in kwargs.items():
if hasattr(self, k):
setattr(self, k, w)
self.inputobj = read_ellipsys_input(os.path.join(self.directory, self.inputfile))
for inp in self.inputs:
- self.inputobj.set_entry(inp.keys()[0], inp.values()[0])
+ self.inputobj.set_entry(sorted(inp)[0], sorted(inp.values())[0])
if self.solver == 'ellipsys1d':
self._dim = 1
@@ -70,13 +68,13 @@ class CaseRunner(object):
testroot = '/'.join(self.directory.split('/')[:-1])
test_dir = os.path.join(testroot, self.casename)
self.testroot = testroot
- print '#################################################################################'
- print '### Test case: '+self.casename
- print '#################################################################################'
+ print('#################################################################################')
+ print('### Test case: '+self.casename)
+ print('#################################################################################')
if os.path.exists(test_dir):
if not self.keep_directory:
# raise RuntimeWarning('Found old run directory %s, and deleted it!' % test_dir)
- print 'Found old run directory %s, and deleted it!' % test_dir
+ print('Found old run directory %s, and deleted it!' % test_dir)
shutil.rmtree(test_dir)
os.mkdir(test_dir)
else:
@@ -98,7 +96,7 @@ class CaseRunner(object):
self._run('output')
if self.test_restart:
- print '### case '+self.casename+': test restart from coarse grid level'
+ print('### case '+self.casename+': test restart from coarse grid level')
# remove output files
files = ['grid.%iforce',
'grid.%ipoints',
@@ -111,7 +109,7 @@ class CaseRunner(object):
for f in files:
try:
os.remove(f % i)
- print 'removed old output file', f % i
+ print('removed old output file', f % i)
except:
pass
# read number of grid levels and mstep
@@ -137,7 +135,7 @@ class CaseRunner(object):
sys.stdout.flush()
self._run('output_rst')
# restart again on finer grlev with the other half of iterations.
- print '### case '+self.casename+': test restart at finest level from mstep =',mstep[0]
+ print('### case '+self.casename+': test restart at finest level from mstep =', mstep[0])
if os.path.isfile('grid.rst'):
os.system('rm grid.rst')
os.system('ln -s grid.RST.01 grid.rst')
@@ -151,18 +149,18 @@ class CaseRunner(object):
self._run('output_rst')
# Compare restart files
os.system('ln -s grid.RST.01 grid.brst')
- print 'compare restart files'
+ print('compare restart files')
test = subprocess.call('cmp grid.arst grid.brst', shell=True)
if(test==0):
- print 'restart files are equal'
+ print('restart files are equal')
elif(test==1):
- print 'restart files are not equal!'
- print 'compare fields'
+ print('restart files are not equal!')
+ print('compare fields')
toolspath = os.getenv('TOOLS_PATH')
os.system(toolspath+'/CompareRST')
sys.exit()
else:
- print 'unknown output from cmp'
+ print('unknown output from cmp')
# Clean up restart files
os.system('rm *RST* *rst*')
os.chdir(self.root_dir)
@@ -176,13 +174,12 @@ class CaseRunner(object):
if self.exec_mode == 'pbs':
command = 'qsub RunBatch1.1'
- self.jobid = commands.getoutput(command)
- print 'submitted case', self.directory, jobid
+ self.jobid = subprocess.call(command, shell=True)
+ print('submitted case', self.directory, jobid)
elif self.exec_mode == 'python':
t0 = time.time()
exepath = os.path.join(epath, self.flowfield)
command = 'mpirun --allow-run-as-root -np %i python %s' % (self.nprocs, exepath)
- # out = commands.getoutput(command)
if self.debug:
status = subprocess.call(command, shell=True)
else:
@@ -191,7 +188,7 @@ class CaseRunner(object):
status = subprocess.call(command, shell=True,stdout=FNULL)
self.read_data(self.project, outname)
self.jobid = None
- print 'case %s ran in %f seconds' %(self.casename, time.time() - t0)
+ print('case %s ran in %f seconds' %(self.casename, time.time() - t0))
elif self.exec_mode == 'shell':
t0 = time.time()
exepath = os.path.join(epath, self.flowfield)
@@ -207,14 +204,13 @@ class CaseRunner(object):
# Suppress output from EllipSys
FNULL = open(os.devnull, 'w')
status = subprocess.call(command, shell=True,stdout=FNULL)
- # status, out = commands.getstatusoutput(command)
if status != 0:
raise RuntimeError('Case %s failed!' % self.casename)
self.read_data(self.project, outname)
self.jobid = None
- print 'case %s ran in %f seconds' %(self.casename, time.time() - t0)
+ print('case %s ran in %f seconds' %(self.casename, time.time() - t0))
elif self.exec_mode == 'dry_run':
- print 'Running in dry run mode, copying pre-computed data!'
+ print('Running in dry run mode, copying pre-computed data!')
files = glob.glob(os.path.join(self.root_dir, self.directory, '*'))
for f in files:
shutil.copy(f, '.')
@@ -230,7 +226,7 @@ class CaseRunner(object):
delfiles = list(set(files)-set(self.files))
for file in delfiles:
if 'pkl' not in file:
- print 'deleting file', file
+ print('deleting file', file)
os.remove(file)
os.chdir('..')
@@ -250,11 +246,11 @@ class CaseRunner(object):
def write_result(self):
- import cPickle
+ import Pickle
os.chdir(self.directory)
fid = open(self.casename+'.pkl','w')
- cPickle.dump(self.output, fid)
+ Pickle.dump(self.output, fid)
fid.close()
os.chdir('..')
@@ -267,7 +263,7 @@ class EllipSysTestCase(object):
self.solver = self.casedict['solver']
else:
self.solver = 'ellipsys2d'
- print 'Warning: solver not set in casedict, assuming youre running EllipSys2D!'
+ print('Warning: solver not set in casedict, assuming youre running EllipSys2D!')
if 'exec_mode' in self.casedict and self.casedict['exec_mode'] == 'python':
skip = False
@@ -308,16 +304,16 @@ class EllipSysTestCase(object):
if 'casename' not in self.casedict.keys():
case.casename = self.__class__.__name__.split('.')[-1]
case.run_case()
- print 'Checking results ...'
+ print('Checking results ...')
self.__check_results(case, case.output)
if case.test_restart:
- print 'Checking rst results ...'
+ print('Checking rst results ...')
self.__check_results(case, case.output_rst, suffix='_rst')
os.chdir(root_dir)
def __check_results(self, case, output, suffix=''):
- print 'Test variables:', case.variables
+ print('Test variables:', case.variables)
if len(case.variables) != 0:
for name in case.variables:
with self.subTest(variable=name + suffix):
@@ -333,7 +329,7 @@ class EllipSysTestCase(object):
rtol=10**(-case.tol),
atol=10**(-case.tol))
else:
- for name, expected in case.reg_data.__dict__.iteritems():
+ for name, expected in case.reg_data.__dict__.items():
result = getattr(output, name)
with self.subTest(variable=name + suffix):
if isinstance(expected, list):
--
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