Update Unit Test Cases and Other Improvements (#249)

* Add test_get_files

* Update .travis.yml

* Drop Python 2 support

* Minor update

* Update dependency requirenments.

* Update .travis.yml

* Change allensdk version to 0.16.3 (#1)

* Make it to be setup.cfg-only project

* Make it to be setup.cfg-only project 2

* Update unit tests.

* Update test cases

* fix

* Update parameter

* Update test cases

* Drop support of Python 2

* Import new test cases in __init__.py in unit_test directory

* remove PYTHON_MAJOR_VERSION constant

* Fix error

* Update dependency

* Drop Python 2 support

* Update bluepyopt

* Update unit tests

* Update unit tests

* Improved logic in url_to_path method

* Update unit tests

* Update unit tests

* Update unit tests

* Update unit tests

* Update unit tests

* Update unit tests

* forceobj = true for jit decorator

* add test_geppetto_backend

* Update unit tests

* Requiring Python version >= 3.5

* Clean up `__future__ import something`

* Import deepcopy, and improve coding style.

* Import available_backends

* Make ExternalModel inherits from RunnableModel instead of Model

* Fix warning

* Make ExternalModel call constructor of the parent class

* Improve ReducedModel, make unit test cases for it.

* get pynn and pyneuroml from Github

* Update unit tests

* Update unit tests

* Try to fix a shell command

* Update unit tests

* Update unit tests

* Update unit tests

* Delete useless code

* Update address of BBP microcircuit portal. Add test cases for bbp.py

* Ran bbp.ipynb

* Update unit tests

* Update unit tests

* Update unit tests

* Update unit tests

* Change sciunit.settings to sciunit.config_set

Author: ChihweiLHBird

.travis.yml

@@ -6,6 +6,7 @@ python:
   - "3.5"
   - "3.6"
   - "3.7"
+  - "3.8"
 install:
   - sudo apt-get update
   # We do this conditionally because it saves us some downloading if the
@@ -15,7 +16,7 @@ install:
   - export PATH="$HOME/miniconda/bin:$PATH"
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
-  - conda update -q conda
+  - conda update -q --all
   # Useful for debugging any issues with conda
   - conda info -a
   - pip install -U pip

neuronunit/__init__.py

@@ -4,8 +4,6 @@
 using the SciUnit framework.
 """
 
-from __future__ import print_function
-from __future__ import unicode_literals
 import os
 import platform
 

neuronunit/bbp.py

@@ -7,20 +7,13 @@
 import requests
 import matplotlib.pyplot as plt
 from neo.io import IgorIO
-
-try:  # Python 3
-    from io import BytesIO
-    from urllib.request import urlopen, URLError
-    MAJOR_VERSION = 3
-except ImportError:  # Python 2
-    from StringIO import StringIO
-    from urllib2 import urlopen, URLError
-    MAJOR_VERSION = 2
+from io import BytesIO
+from urllib.request import urlopen, URLError
 
 
 def is_bbp_up():
     """Check whether the BBP microcircuit portal is up."""
-    url = "http://microcircuits.epfl.ch/released_data/B95_folder.zip"
+    url = "http://microcircuits.epfl.ch/data/released_data/B95.zip"
     request = requests.get(url)
     return request.status_code == 200
 
@@ -95,12 +88,8 @@ def find_or_download_data(url):
     unzipped = zipped.split('.')[0]  # Name when unzipped
     z = None
     if not os.path.isdir(unzipped):  # If unzipped version not found
-        if MAJOR_VERSION == 2:
-            r = requests.get(url, stream=True)
-            z = zipfile.ZipFile(StringIO(r.content))
-        elif MAJOR_VERSION == 3:
-            r = requests.get(url)
-            z = zipfile.ZipFile(BytesIO(r.content))
+        r = requests.get(url)
+        z = zipfile.ZipFile(BytesIO(r.content))
         z.extractall(unzipped)
     return unzipped
 

neuronunit/cellmodelp.py

@@ -2,10 +2,7 @@
 # steady state v of a cell defined in a hoc file in the given directory.
 # Usage: python getCellProperties /path/To/dir/with/.hoc
 
-try:  # Python 2
-    import cPickle
-except ImportError:  # Python 3
-    import _pickle as cPickle
+import _pickle as cPickle
 import csv
 import json
 import os

neuronunit/examples/brian_multi_comp_ca2_HH.ipynb

@@ -129,7 +129,6 @@
     "\n",
     "    def load_model(self):\n",
     "        neuron = None\n",
-    "        from __future__ import print_function\n",
     "        from brian2 import *\n",
     "\n",
     "        from brian2.units.constants import (zero_celsius, faraday_constant as F,\n",
@@ -969,4 +968,4 @@
  },
  "nbformat": 4,
  "nbformat_minor": 2
-}
+}

neuronunit/models/backends/__init__.py

@@ -4,7 +4,7 @@
 import warnings
 
 import sciunit.models.backends as su_backends
-from sciunit.utils import PLATFORM, PYTHON_MAJOR_VERSION
+from sciunit.utils import PLATFORM
 from .base import Backend
 
 warnings.filterwarnings('ignore', message='nested set')

neuronunit/models/backends/base.py

@@ -22,4 +22,4 @@
 
 # Test for NEURON support in a separate python process
 NEURON_SUPPORT = (os.system("python -c 'import neuron' > /dev/null 2>&1") == 0)
-PYNN_SUPPORT = (os.system("python -c 'import pyNN > /dev/null 2>&1") == 0)
+PYNN_SUPPORT = (os.system("python -c 'import pyNN' > /dev/null 2>&1") == 0)

neuronunit/models/backends/brian_multi_comp_ca2_HH.py

@@ -110,7 +110,6 @@
 from types import MethodType
 
 from brian2 import *
-from __future__ import print_function
 
 from brian2.units.constants import (zero_celsius, faraday_constant as F,
     gas_constant as R)

neuronunit/models/backends/fhn.py

@@ -1,6 +1,4 @@
 #-*- coding: utf-8 -*-
-from __future__ import (print_function, division,
-                        absolute_import, unicode_literals)
 import numpy as np
 from scipy import integrate as spint
 from matplotlib import pyplot as plt