Activate tox envs

.travis.yml

@@ -8,14 +8,16 @@ addons:
   apt:
     packages:
     - libhdf5-dev
+    - python-tk
+
 cache: pip
 install:
-- pip install tox
+- pip install 'matplotlib==1.5.2' tox
 - pip install .
 script:
   - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then tox -e py27; fi
-  - if [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then tox --skip-missing-interpreters; fi
-  - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then tox -e py36; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.5 ]]; then tox -e py35; fi
+  - if [[ $TRAVIS_PYTHON_VERSION == 3.6 ]]; then tox -e py36 -e lint; fi
 before_deploy:
 - pip install twine
 deploy:

.pylintrc → pylintrc

@@ -1,5 +1,5 @@
 [MESSAGES CONTROL]
-disable=bad-continuation,fixme,invalid-name,len-as-condition,no-else-return,ungrouped-imports
+disable=bad-continuation,fixme,invalid-name,len-as-condition,no-else-return,ungrouped-imports,useless-object-inheritance
 
 [FORMAT]
 # Maximum number of characters on a single line.

tmd/Topology/analysis.py

@@ -261,7 +261,7 @@ def get_average_persistence_image(ph_list, xlims=None, ylims=None,
                                                 xlims=xlims, ylims=ylims)
                 if not np.isnan(np.sum(im)):
                     im_av = weight * im
-            except BaseException:
+            except BaseException:  # pylint: disable=broad-except
                 pass
         else:
             try:
@@ -270,7 +270,7 @@ def get_average_persistence_image(ph_list, xlims=None, ylims=None,
                 if not np.isnan(np.sum(im)):
                     im_av = np.add(im_av, weight * im)
                     k = k + 1
-            except BaseException:
+            except BaseException:  # pylint: disable=broad-except
                 pass
     return im_av / k
 

tmd/Topology/methods.py

@@ -69,8 +69,10 @@ def _phi_theta(u, v):
     Returns phi, theta
     """
     phi1 = np.arctan2(u[1], u[0])
+    # pylint: disable=assignment-from-no-return
     theta1 = np.arccos(u[2] / np.linalg.norm(u))
 
+    # pylint: disable=assignment-from-no-return
     phi2 = np.arctan2(v[1], v[0])
     theta2 = np.arccos(v[2] / np.linalg.norm(v))
 

tmd/Tree/methods.py

@@ -288,6 +288,7 @@ def get_direction_between(self, start_id=0, end_id=1):
     defined as end point - start point
     normalized as a unit vector.
     '''
+    # pylint: disable=assignment-from-no-return
     vect = _np.subtract([self.x[end_id], self.y[end_id], self.z[end_id]],
                         [self.x[start_id], self.y[start_id], self.z[start_id]])
 

tmd/view/plot.py

@@ -93,6 +93,7 @@ def persistence_image(ph, new_fig=True, subplot=111, xlims=None, ylims=None,
     if xlims is None or xlims is None:
         xlims, ylims = analysis.get_limits(ph, coll=False)
 
+    # pylint: disable=unexpected-keyword-arg
     Zn = analysis.get_persistence_image_data(ph, norm_factor=norm_factor, bw_method=bw_method,
                                              xlims=xlims, ylims=ylims)
     fig, ax = _cm.get_figure(new_fig=new_fig, subplot=subplot)
@@ -156,6 +157,7 @@ def persistence_image_average(ph_list, new_fig=True, subplot=111, xlims=None,
                               cmap=jet_map, weighted=False, **kwargs):
     """Merges a list of ph diagrams and plots their respective average image.
     """
+    # pylint: disable=unexpected-keyword-arg
     av_imgs = analysis.get_average_persistence_image(ph_list, xlims=xlims, ylims=ylims,
                                                      norm_factor=norm_factor, weighted=weighted)
     if xlims is None or xlims is None:

tmd/view/view.py

@@ -853,7 +853,7 @@ def seg_length(seg):
     angles = _np.array([seg_angle(s) for s in segs])
     lens = _np.array([seg_length(s) for s in segs])
     ranges = [[i * 2 * _np.pi / bins - _np.pi, (i + 1) * 2 * _np.pi / bins - _np.pi]
-              for i in xrange(bins)]
+              for i in range(bins)]
     results = [r + [_np.sum(lens[_np.where((angles > r[0]) & (angles < r[1]))[0]])]
                for r in ranges]
 

tox.ini

@@ -3,56 +3,40 @@ name = tmd
 testdeps =
     nose
     tqdm
+commands = nosetests
+
+[testenv]
+deps = {[base]testdeps}
+extras = viewer
+commands = nosetests
 
 [tox]
 envlist =
-    check-version
     pycodestyle
-    pylint
+    lint
     py27
-    py35
-
-[testenv:check-version]
-skip_install = true
-# commands = /gpfs/bbp.cscs.ch/apps/viz/platform/binfiles/bbp-nse-ci/0.0.1/bin/do_release.py -p . check-version
-
-
-[testenv:pycodestyle]
-deps = pycodestyle
-commands = true | pycodestyle {[base]name} --exclude tests
-
-[testenv:pylint]
-deps = pylint
-commands = true | pylint {[base]name}
-
-[testenv:py27]
-deps = {[base]testdeps}
-commands = true | nosetests
+    py36
 
-[testenv:py35]
-deps = {[base]testdeps}
-commands = true | nosetests
-
-[testenv:py36]
-deps = {[base]testdeps}
-commands = true | nosetests
+[testenv:lint]
+basepython = python3
+deps =
+    pycodestyle
+    pylint
+commands =
+    pycodestyle --config=pycodestylerc --exclude=tests tmd
+    pylint --rcfile=pylintrc --extension-pkg-whitelist=numpy --ignore=tests tmd
 
 [testenv:coverage]
 deps =
     {[base]testdeps}
     coverage
 commands =
-    true | coverage run --source {[base]name} {envbindir}/nosetests
-    true | coverage report --show-missing
-    true | coverage xml
-
-[testenv:docs]
-changedir = doc
-deps = sphinx
-commands = true | make html
-whitelist_externals = make
+    coverage run --source {[base]name} {envbindir}/nosetests
+    coverage report --show-missing
+    coverage xml
 
 # E731: do not assign a lambda expression, use a def
+# W504: Line break occurred after a binary operator
 [pycodestyle]
-ignore = E731
+ignore = E731,W504
 max-line-length = 100