Merge pull request #521 from PCMDI/fix_test_suite_linux

Fix test suite linux

.travis.yml

@@ -7,24 +7,22 @@ language: python
 sudo: false
 
 before_install:
- - export UVCDAT_FEATURE=""
  - if [ "$TRAVIS_OS_NAME" = "linux" ]; then wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh; fi
  - if [ "$TRAVIS_OS_NAME" = "osx" ]; then curl -o miniconda.sh https://repo.continuum.io/miniconda/Miniconda2-latest-MacOSX-x86_64.sh ; fi
  - export PATH="$HOME/miniconda/bin:$PATH"
  - if [ ! -d ${HOME}/miniconda ]; then bash miniconda.sh -b -p $HOME/miniconda ; fi
  - hash -r
  - conda config --set always_yes yes --set changeps1 no
- - conda install -f -q "conda<4.3.13"
- - conda install --show-channel-urls --yes vcs vcsaddons mesalib cdp nose flake8 image-compare -c conda-forge -c uvcdat
- # - conda install openssl=1.0.2d
+ - conda update -y -q conda
+
+script:
+ - conda create -q -n py2 -c uvcdat/label/nightly -c conda-forge -c uvcdat vcs vcsaddons cdp mesalib image-compare flake8 nose
  # Useful for debugging any issues with conda
  - conda info -a
-
-install:
+ - source activate py2
  - python setup.py install
-
-script:
- - python run_tests.py -v2
+ - source activate py2
+ - python run_tests.py -v2
 
 after_success:
  - if [ "$TRAVIS_BRANCH" == "master" -a "$TRAVIS_PULL_REQUEST" == "false" ]; then conda install conda-build && conda install anaconda-client && bash -x recipes/pcmdi_metrics/conda_upload.sh; fi

src/python/graphics/portraits.py

@@ -371,9 +371,9 @@ def rank(self, data, axis=0):
  b = MV2.zeros(a0.shape, MV2.float)
  sh = a0[1].shape
  for i in range(n):
- I = MV2.ones(sh) * i
+ Indx = MV2.ones(sh) * i
  c = MV2.array(a0[i].filled(n - 1))
- b = genutil.arrayindexing.set(b, c, I)
+ b = genutil.arrayindexing.set(b, c, Indx)
 
  m = data.mask
  if m is not None:
@@ -410,9 +410,9 @@ def rank_nD(self, data, axis=0):
  b = MV2.zeros(a0.shape, MV2.float)
  sh = a0[1].shape
  for i in range(n):
- I = MV2.ones(sh) * i
+ Indx = MV2.ones(sh) * i
  c = MV2.array(a0[i].filled(n - 1))
- b = genutil.arrayindexing.set(b, c, I)
+ b = genutil.arrayindexing.set(b, c, Indx)
  m = data.mask
  if m is not None:
  b = MV2.masked_where(m, b)
@@ -595,7 +595,7 @@ def __get(self):
  if sp1[j] == 'time_domain':
  try:
  v = int(v)
- except:
+ except Exception:
  pass
  if v == 'NONE':
  v = ''
@@ -641,7 +641,7 @@ def __get(self):
  # In case sometihng goes wrong (like modle not processed or
  # inexsitant for this var, etc...)
  f.close()
- except:
+ except Exception:
  pass
  output = MV2.reshape(output, (axes_length[0], axes_length[1]))
  output.id = 'portrait plot'
@@ -665,7 +665,7 @@ def decorate(self, output, ynm=None, xnm=None):
  del(x.name)
  del(y.name)
  del(output.name)
- except:
+ except Exception:
  pass
 
  nm = '___'.join(xnm)
@@ -777,7 +777,7 @@ def plot(self, data=None, mesh=None, template=None,
  template.legend.y2 = self.PLOT_SETTINGS.legend.y2
  try:
  tmp = x.createtextorientation('crap22')
- except:
+ except Exception:
  tmp = x.gettextorientation('crap22')
  tmp.height = 12
  # tmp.halign = 'center'
@@ -844,9 +844,9 @@ def plot(self, data=None, mesh=None, template=None,
 # data=data
  sh = list(data.shape)
  sh.append(2)
- I = MV2.indices((sh[0], sh[1]))
- Y = I[0]
- X = I[1]
+ Indx = MV2.indices((sh[0], sh[1]))
+ Y = Indx[0]
+ X = Indx[1]
 # if ntot>1:
 # meshfill.mesh='y'
  if ntot == 1:

src/python/io/base.py

@@ -40,7 +40,7 @@ def update_dict(d, u):
 def populate_prov(prov, cmd, pairs, sep=None, index=1, fill_missing=False):
  try:
  p = subprocess.Popen(shlex.split(cmd), stdout=subprocess.PIPE, stderr=subprocess.PIPE)
- except:
+ except Exception:
  return
  out, stde = p.communicate()
  if stde != '':
@@ -66,14 +66,14 @@ def generateProvenance():
  prov["platform"] = platfrm
  try:
  logname = os.getlogin()
- except:
+ except Exception:
  try:
  import pwd
  logname = pwd.getpwuid(os.getuid())[0]
- except:
+ except Exception:
  try:
  logname = os.environ.get('LOGNAME', 'unknown')
- except:
+ except Exception:
  logname = 'unknown-loginname'
  prov["userId"] = logname
  prov["osAccess"] = bool(os.access('/', os.W_OK) * os.access('/', os.R_OK))
@@ -187,7 +187,7 @@ def write(self, data, type='json', *args, **kwargs):
  if not os.path.exists(dir_path):
  try:
  os.makedirs(dir_path)
- except:
+ except Exception:
  logging.error(
  'Could not create output directory: %s' % dir_path)
 
@@ -314,7 +314,7 @@ def set_file_mask_template(self):
  def get_mask_from_var(self, var):
  try:
  o_mask = self.file_mask_template.get('sftlf')
- except:
+ except Exception:
  o_mask = cdutil.generateLandSeaMask(
  var, regridTool=self.regrid_tool).filled(1.) * 100.
  o_mask = MV2.array(o_mask)
@@ -463,11 +463,11 @@ def get_array_values_from_dict_recursive(self, out, ids, nms, axval, axes):
  for k in axval:
  try:
  vals = vals[k]
- except:
+ except Exception:
  vals = 1.e20
  try:
  out[tuple(ids)] = float(vals)
- except:
+ except Exception:
  out[tuple(ids)] = 1.e20
 
  def __init__(self, files=[], structure=[], ignored_keys=[], oneVariablePerFile=True):

src/python/misc/scripts/install_metrics_from_branches.py

@@ -7,8 +7,8 @@
 import shlex
 
 
-l = time.localtime()
-today = "%s.%s.%s" % (l.tm_year, l.tm_mon, l.tm_mday)
+loc = time.localtime()
+today = "%s.%s.%s" % (loc.tm_year, loc.tm_mon, loc.tm_mday)
 
 P = argparse.ArgumentParser(
  description='Merge many branches into a conda env',
@@ -50,9 +50,9 @@
  default=["master"],
  nargs="*",
  help="cdms branches to merge")
-l = P.add_argument_group('Local Setup')
-l.add_argument("-g", "--git", default=os.path.expanduser("~/git"),
- help="top directory where you will clone your git repos")
+loc = P.add_argument_group('Local Setup')
+loc.add_argument("-g", "--git", default=os.path.expanduser("~/git"),
+  help="top directory where you will clone your git repos")
 
 args = P.parse_args(sys.argv[1:])
 

src/python/pcmdi/io.py

@@ -74,7 +74,7 @@ def addJson(self, filename):
  # print filename,"K IS:",k
  k.pop(k.index("source"))
  out = out[k[0]] # first realization
- except:
+ except Exception:
  continue
  # Ok at this point we need to see if it is json std 1 or 2
  # version 1 had NHEX in every region

src/python/pcmdi/pmp_parser.py

@@ -7,4 +7,3 @@ def __init__(self, warning=True, *args, **kwargs):
  super(PMPParser, self).__init__(*args, **kwargs)
  if warning:
  print("Deprecation warning: please use 'import pcmdi_metrics.driver.pmp_parser.PMPParser'")
-