human sort list fix PCMDI/click#10 (#605)

* human sort list fix PCMDI/click#10

* correct path for linux machines

* new key for cache

.circleci/config.yml

@@ -104,10 +104,10 @@ jobs:
  - checkout
  - restore_cache:
  keys:
- - macos_py2_2019-05-30
+ - macos_py2_2019-06-01
  - run: *create_conda_env
  - save_cache:
- key: macos_py2_2019-05-30
+ key: macos_py2_2019-06-01
  paths: /Users/distiller/miniconda
  - run: *setup_pmp
  - run: *run_pmp_tests
@@ -132,10 +132,10 @@ jobs:
  - checkout
  - restore_cache:
  keys:
- - macos_py3_2019-05-30
+ - macos_py3_2019-06-01
  - run: *create_conda_env
  - save_cache:
- key: macos_py3_2019-05-30
+ key: macos_py3_2019-06-01
  paths: /Users/distiller/miniconda
  - run: *setup_pmp
  - run: *run_pmp_tests
@@ -159,11 +159,11 @@ jobs:
  - checkout
  - restore_cache:
  keys:
- - linux_py2_2019-05-30
+ - linux_py2_2019-06-01
  - run: *create_conda_env
  - save_cache:
- key: linux_py2_2019-05-30
- paths: /Users/distiller/miniconda
+ key: linux_py2_2019-06-01
+ paths: /home/circleci/miniconda
  - run: *setup_pmp
  - run: *run_pmp_tests
  - store_artifacts:
@@ -187,11 +187,11 @@ jobs:
  - checkout
  - restore_cache:
  keys:
- - linux_py3_2019-05-30
+ - linux_py3_2019-06-01
  - run: *create_conda_env
  - save_cache:
- key: linux_py3_2019-05-30
- paths: /Users/distiller/miniconda
+ key: linux_py3_2019-06-01
+ paths: /home/circleci/miniconda
  - run: *setup_pmp
  - run: *run_pmp_tests
  - run: *conda_upload

pcmdi_metrics/io/base.py

@@ -16,6 +16,8 @@
 import shlex
 import datetime
 from pcmdi_metrics import LOG_LEVEL
+import copy
+import re
 
 
 value = 0
@@ -189,6 +191,18 @@ def generateProvenance():
  return prov
 
 
+def sort_human(input_list):
+ lst = copy.copy(input_list)
+
+ def convert(text):
+ return int(text) if text.isdigit() else text
+
+ def alphanum(key):
+ return [convert(c) for c in re.split('([0-9]+)', key)]
+ lst.sort(key=alphanum)
+ return lst
+
+
 def scrap(data, axis=0):
  originalOrder = data.getOrder(ids=True)
  if axis not in ['x', 'y', 'z', 't'] and not isinstance(axis, int):
@@ -558,13 +572,14 @@ def get_array_values_from_dict_recursive(self, out, ids, nms, axval, axes):
  out[tuple(ids)] = 9.99e20
 
  def __init__(self, files=[], structure=[], ignored_keys=[],
- oneVariablePerFile=True):
+ oneVariablePerFile=True, sortHuman=True):
  self.json_version = 3.0
  self.json_struct = structure
  self.data = {}
  self.axes = None
  self.ignored_keys = ignored_keys
  self.oneVariablePerFile = oneVariablePerFile
+ self.sortHuman = sortHuman
  if len(files) == 0:
  raise Exception("You need to pass at least one file")
 
@@ -615,8 +630,12 @@ def getAxisList(self):
  0, len(self.json_struct) - 1, self.data, values)
  autoBounds = cdms2.getAutoBounds()
  cdms2.setAutoBounds("off")
+ if self.sortHuman:
+ sortFunc = sort_human
+ else:
+ sortFunc = sorted
  for i, nm in enumerate(self.json_struct):
- axes.append(cdms2.createAxis(sorted(list(values[i])), id=nm))
+ axes.append(cdms2.createAxis(sortFunc(list(values[i])), id=nm))
  self.axes = axes
  cdms2.setAutoBounds(autoBounds)
  return self.axes