Drop python 2 support (#829)

NeuroM is now supported from python 3.5 to 3.8

.travis.yml

@@ -1,8 +1,8 @@
 language: python
 python:
-  - "2.7"
   - "3.6"
   - "3.7"
+  - "3.8"
 cache: pip
 install:
   - pip install tox-travis
@@ -18,4 +18,4 @@ deploy:
   on:
     tags: true
     branch: master
-    condition: "$TRAVIS_PYTHON_VERSION == 2.7"
+    condition: "$TRAVIS_PYTHON_VERSION == 3.6"

doc/source/developer.rst

@@ -103,4 +103,4 @@ Then, run the tests manually in the ``virtualenv``. For example,
 Python compatibility
 --------------------
 
-We test the code against Python 2.7, 3.5 and 3.6.
+We test the code against Python 3.6 and 3.7.

neurom/check/morphtree.py

@@ -32,7 +32,6 @@
 from neurom.core.dataformat import COLS
 from neurom import morphmath as mm
 from neurom.morphmath import principal_direction_extent
-from neurom._compat import range, filter
 
 
 def is_monotonic(neurite, tol):

neurom/check/neuron_checks.py

@@ -37,7 +37,6 @@
 import numpy as np
 
 from neurom import NeuriteType
-from neurom._compat import zip
 from neurom.check import CheckResult
 from neurom.check.morphtree import get_flat_neurites, get_nonmonotonic_neurites
 from neurom.core import Tree, iter_neurites, iter_sections, iter_segments

neurom/check/runner.py

@@ -29,10 +29,9 @@
 
 """Runner for neuron morphology checks."""
 
-import logging
+from collections import OrderedDict
 from importlib import import_module
-
-from future.moves.collections import OrderedDict
+import logging
 
 from neurom.check import check_wrapper
 from neurom.exceptions import ConfigError

neurom/check/tests/test_morphtree.py

@@ -31,7 +31,6 @@
 from neurom.check import morphtree as mt
 from neurom.core import Neurite, NeuriteType, Section
 from neurom.core.dataformat import COLS
-from neurom._compat import range
 from nose import tools as nt
 import numpy as np
 import os

neurom/check/tests/test_neuron_checks.py

@@ -35,7 +35,6 @@
 from numpy.testing import assert_array_equal
 
 from neurom import check, load_neuron
-from neurom._compat import range
 from neurom.check import neuron_checks as nrn_chk
 from neurom.core.dataformat import COLS
 from neurom.core.types import dendrite_filter

neurom/core/_neuron.py

@@ -34,7 +34,6 @@
 import numpy as np
 
 from neurom import morphmath
-from neurom._compat import filter, map, zip
 from neurom.core._soma import Soma
 from neurom.core.dataformat import COLS
 from neurom.utils import memoize

neurom/core/tests/test_iter.py

@@ -35,7 +35,6 @@
 
 import neurom as nm
 from neurom import COLS, core, load_neuron
-from neurom._compat import filter
 from neurom.core import NeuriteIter, Tree
 
 _path = os.path.dirname(os.path.abspath(__file__))

neurom/core/tests/test_neuron.py

@@ -28,13 +28,12 @@
 
 import os
 from copy import deepcopy
+from pathlib import Path
 
-from pathlib2 import Path
 import numpy as np
 from nose import tools as nt
 
 import neurom as nm
-from neurom._compat import zip
 from neurom.core import graft_neuron, iter_segments
 
 _path = os.path.dirname(os.path.abspath(__file__))

neurom/core/tests/test_tree.py

@@ -29,7 +29,6 @@
 import sys
 from nose import tools as nt
 from neurom.core.tree import Tree
-from neurom._compat import range
 
 REF_TREE = Tree()
 T11 = REF_TREE.add_child(Tree())

neurom/core/tree.py

@@ -29,8 +29,6 @@
 """Generic tree class and iteration functions."""
 from collections import deque
 
-from neurom._compat import filter
-
 
 class Tree(object):
     """Simple recursive tree class."""

neurom/features/sectionfunc.py

@@ -32,7 +32,6 @@
 
 from neurom import morphmath as mm
 from neurom.core.dataformat import COLS
-from neurom._compat import range
 from neurom.morphmath import interval_lengths
 
 

neurom/fst/tests/test_feature_compat.py

@@ -28,8 +28,6 @@
 
 """Test neurom._neuritefunc functionality."""
 
-from neurom.features.tests.test_feature_compat import *
-
 from neurom.fst import _bifurcationfunc as bifurcation
 from neurom.fst import _neuronfunc as neuronfunc
 from neurom.fst import _neuritefunc as _nf

neurom/geom/tests/test_transform.py

@@ -31,7 +31,6 @@
 from neurom import load_neuron
 from neurom.fst import _neuritefunc as _nf
 from nose import tools as nt
-from neurom._compat import zip
 
 import numpy as np
 import os

neurom/io/hdf5.py

@@ -40,9 +40,10 @@
 There is one such row per measured point.
 """
 
+from itertools import zip_longest
+
 import h5py
 import numpy as np
-from future.moves.itertools import zip_longest
 
 from .datawrapper import BlockNeuronBuilder, DataWrapper
 

neurom/io/neurolucida.py

@@ -36,7 +36,6 @@
 
 import numpy as np
 
-from neurom._compat import StringType
 from neurom.core.dataformat import COLS, POINT_TYPE
 
 from .datawrapper import DataWrapper
@@ -78,7 +77,7 @@ def _match_section(section, match):
     for i in range(5):
         if i >= len(section):
             return None
-        if isinstance(section[i], StringType) and section[i] in match:
+        if isinstance(section[i], str) and section[i] in match:
             return match[section[i]]
     return None
 
@@ -159,7 +158,7 @@ def _flatten_subsection(subsection, _type, offset, parent):
         if row in ('Low', 'Generated', 'High', ):
             continue
 
-        if isinstance(row[0], StringType):
+        if isinstance(row[0], str):
             if len(row) in (4, 5, ):
                 if len(row) == 5:
                     assert row[4][0] == 'S', \

neurom/io/utils.py

@@ -34,12 +34,9 @@
 import shutil
 import tempfile
 import uuid
-from functools import partial
+from functools import partial, lru_cache
 from io import IOBase, open
 
-from pylru import FunctionCacheManager
-
-from neurom._compat import StringType, filter
 from neurom.core.population import Population
 from neurom.exceptions import NeuroMError, RawDataError
 from neurom.fst._core import FstNeuron
@@ -71,7 +68,7 @@ def __init__(self, directory, file_ext=None, cache_size=None):
         self.directory = directory
         self.file_ext = file_ext
         if cache_size is not None:
-            self.get = FunctionCacheManager(self.get, size=cache_size)
+            self.get = lru_cache(maxsize=cache_size)(self.get)
 
     def _filepath(self, name):
         """File path to `name` morphology file."""
@@ -116,7 +113,7 @@ def get_files_by_path(path):
 def load_neuron(handle, reader=None):
     """Build section trees from an h5 or swc file."""
     rdw = load_data(handle, reader)
-    if isinstance(handle, StringType):
+    if isinstance(handle, str):
         name = os.path.splitext(os.path.basename(handle))[0]
     else:
         name = None
@@ -146,7 +143,7 @@ def load_neurons(neurons,
     if isinstance(neurons, (list, tuple)):
         files = neurons
         name = name if name is not None else 'Population'
-    elif isinstance(neurons, StringType):
+    elif isinstance(neurons, str):
         files = get_files_by_path(neurons)
         name = name if name is not None else os.path.basename(neurons)
 

neurom/stats.py

@@ -31,11 +31,10 @@
 Nothing fancy. Just commonly used functions using scipy functionality.
 """
 
-from collections import namedtuple
+from collections import namedtuple, OrderedDict
 from enum import Enum, unique
 
 import numpy as np
-from future.moves.collections import OrderedDict
 from scipy import stats as _st
 
 FitResults = namedtuple('FitResults', ['params', 'errs', 'type'])

neurom/tests/test_stats.py

@@ -68,7 +68,7 @@ def test_fit_normal_regression():
     nt.assert_almost_equal(fit_.params[0], 10.019332055822, 12)
     nt.assert_almost_equal(fit_.params[1], 0.978726207747, 12)
     nt.assert_almost_equal(fit_.errs[0], 0.021479979161, 12)
-    nt.assert_almost_equal(fit_.errs[1], 0.745431659944, 12)
+    nt.assert_almost_equal(fit_.errs[1], 0.7369569123250506, 12)
 
 
 def test_fit_default_is_normal():

neurom/view/common.py

@@ -36,7 +36,6 @@
 from scipy.linalg import norm
 from scipy.spatial import ConvexHull
 
-from neurom._compat import map  # pylint: disable=ungrouped-imports
 
 plt = None  # refer to _get_plt()
 

neurom/view/tests/test_common.py

@@ -58,17 +58,17 @@ def test_get_figure():
     fig_old = plt.figure()
     fig, ax = get_figure(new_fig=False)
     nt.eq_(fig, fig_old)
-    nt.eq_(ax.colNum, 0)
-    nt.eq_(ax.rowNum, 0)
+    nt.eq_(ax.get_subplotspec().colspan.start, 0)
+    nt.eq_(ax.get_subplotspec().rowspan.start, 0)
 
     fig1, ax1 = get_figure(new_fig=True, subplot=224)
     nt.ok_(fig1 != fig_old)
-    nt.eq_(ax1.colNum, 1)
-    nt.eq_(ax1.rowNum, 1)
+    nt.eq_(ax1.get_subplotspec().colspan.start, 1)
+    nt.eq_(ax1.get_subplotspec().rowspan.start, 1)
 
     fig2, ax2 = get_figure(new_fig=True, subplot=[1, 1, 1])
-    nt.eq_(ax2.colNum, 0)
-    nt.eq_(ax2.rowNum, 0)
+    nt.eq_(ax2.get_subplotspec().colspan.start, 0)
+    nt.eq_(ax2.get_subplotspec().rowspan.start, 0)
     plt.close('all')
 
     fig = plt.figure()

neurom/view/view.py

@@ -34,7 +34,6 @@
 
 import numpy as np
 from neurom import NeuriteType, geom
-from neurom._compat import zip
 from neurom.core import iter_neurites, iter_segments, iter_sections
 from neurom.core._soma import SomaCylinders
 from neurom.core.dataformat import COLS

setup.py

@@ -29,34 +29,28 @@
 """ Distribution configuration for neurom
 """
 # pylint: disable=R0801
-import os
 from setuptools import setup
 from setuptools import find_packages
 
 
-REQS = ['click>=7.0',
-        'enum-compat>=0.0.2',
-        'future>=0.16.0',
+setup(
+    description='NeuroM: a light-weight neuron morphology analysis package',
+    author='Blue Brain Project, EPFL',
+    url='http://https://github.com/BlueBrain/NeuroM',
+    install_requires=[
+        'click>=7.0',
         'h5py>=2.7.1',
-        'matplotlib>=1.3.1',
+        'matplotlib>=3.2.1',
         'numpy>=1.8.0',
-        'pylru>=1.0',
         'pyyaml>=3.10',
         'scipy>=1.2.0',
         'tqdm>=4.8.4',
-        ]
-
-
-setup(
-    description='NeuroM: a light-weight neuron morphology analysis package',
-    author='Blue Brain Project, EPFL',
-    url='http://https://github.com/BlueBrain/NeuroM',
-    install_requires=REQS,
+        ],
     packages=find_packages(),
     license='BSD',
     scripts=['apps/raw_data_check',
              'apps/morph_check',
-                'apps/morph_stats',
+             'apps/morph_stats',
              ],
     entry_points={
         'console_scripts': ['neurom=apps.__main__:cli']
@@ -66,17 +60,15 @@
         'plotly': ['plotly>=3.6.0'],
     },
     include_package_data=True,
+    python_requires='>=3.5',
     classifiers=[
         'Development Status :: 6 - Mature',
         'Intended Audience :: Education',
         'Intended Audience :: Science/Research',
         'Programming Language :: Python',
-        'Programming Language :: Python :: 2',
-        'Programming Language :: Python :: 2.7',
-        'Programming Language :: Python :: 3',
-        'Programming Language :: Python :: 3.5',
         'Programming Language :: Python :: 3.6',
         'Programming Language :: Python :: 3.7',
+        'Programming Language :: Python :: 3.8',
         'Topic :: Scientific/Engineering :: Bio-Informatics',
     ],
     use_scm_version={"local_scheme": "no-local-version"},

tox.ini

@@ -3,11 +3,10 @@ name = neurom
 testdeps =
     mock
     nose
-    pathlib2
 
 [tox]
 envlist =
-    {py27,py36}
+    {py36,py37,py38}
     py36-lint
     py36-coverage
     py36-docs