Merge pull request #38 from dwhswenson/release-0.3.1

Release 0.3.1

.travis.yml

@@ -2,7 +2,6 @@ language: python
 python:
   - '3.6'
   - '2.7'
-  - '3.4'
   - '3.5'
 
 branches:
@@ -27,8 +26,6 @@ env:
 
 matrix:
   exclude:
-    - env: MDTRAJ="dev"
-      python: "3.4"
     - env: MDTRAJ="dev"
       python: "3.5"
 

ci/conda-recipe/meta.yaml

@@ -1,7 +1,7 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.3.0"
+  version: "0.3.1"
 
 source:
   path: ../../

contact_map/contact_map.py

@@ -12,7 +12,6 @@
 import mdtraj as md
 
 from .contact_count import ContactCount
-from .plot_utils import ranged_colorbar
 from .py_2_3 import inspect_method_arguments
 
 # TODO:
@@ -126,7 +125,7 @@ def from_dict(cls, dct):
         --------
         to_dict
         """
-        deserialize_set = lambda k: set(k)
+        deserialize_set = set
         deserialize_atom_to_residue_dct = lambda d: {int(k): d[k] for k in d}
         deserialization_helpers = {
             'topology': cls._deserialize_topology,
@@ -211,12 +210,23 @@ def from_json(cls, json_string):
         dct = json.loads(json_string)
         return cls.from_dict(dct)
 
-    def _check_compatibility(self, other):
-        assert self.cutoff == other.cutoff
-        assert self.topology == other.topology
-        assert self.query == other.query
-        assert self.haystack == other.haystack
-        assert self.n_neighbors_ignored == other.n_neighbors_ignored
+    def _check_compatibility(self, other, err=AssertionError):
+        compatibility_attrs = ['cutoff', 'topology', 'query', 'haystack',
+                               'n_neighbors_ignored']
+        failed_attr = {}
+        for attr in compatibility_attrs:
+            self_val = getattr(self, attr)
+            other_val = getattr(other, attr)
+            if self_val != other_val:
+                failed_attr.update({attr: (self_val, other_val)})
+        msg = "Incompatible ContactObjects:\n"
+        for (attr, vals) in failed_attr.items():
+            msg += "        {attr}: {self} != {other}\n".format(
+                attr=attr, self=str(vals[0]), other=str(vals[1])
+            )
+        if failed_attr:
+            raise err(msg)
+        return True
 
     def save_to_file(self, filename, mode="w"):
         """Save this object to the given file.

contact_map/dask_runner.py

@@ -84,16 +84,16 @@ def __init__(self, client, filename, query=None, haystack=None,
         self.filename = filename
         trajectory = md.load(filename, **kwargs)
 
-        self.frames = range(len(trajectory))
         self.kwargs = kwargs
 
-        ContactObject.__init__(self, trajectory.topology, query, haystack,
-                               cutoff, n_neighbors_ignored)
+        super(DaskContactFrequency, self).__init__(
+            trajectory, query, haystack, cutoff, n_neighbors_ignored
+        )
 
-        freq = dask_run(trajectory, client, self.run_info)
-        self._n_frames = freq.n_frames
-        self._atom_contacts = freq._atom_contacts
-        self._residue_contacts = freq._residue_contacts
+    def _build_contact_map(self, trajectory):
+        freq = dask_run(trajectory, self.client, self.run_info)
+        self._frames = freq.n_frames
+        return (freq._atom_contacts, freq._residue_contacts)
 
     @property
     def parameters(self):

contact_map/tests/test_contact_map.py

@@ -1,6 +1,5 @@
 import os
 import collections
-import json
 import mdtraj as md
 
 # pylint: disable=wildcard-import, missing-docstring, protected-access
@@ -133,7 +132,6 @@ def test_counters(self, idx):
 
     def test_to_dict(self, idx):
         m = self.maps[idx]
-        json_topol = json.dumps(pdb_topology_dict())
         dct = m.to_dict()
         # NOTE: topology only tested in a cycle; JSON order not guaranteed
         assert dct['cutoff'] == 0.075
@@ -279,6 +277,35 @@ def test_counters(self):
         }
         assert residue_contacts.counter == expected_residue_contacts
 
+    def test_check_compatibility_true(self):
+        map2 = ContactFrequency(trajectory=traj[0:2],
+                                cutoff=0.075,
+                                n_neighbors_ignored=0)
+        assert self.map._check_compatibility(map2) == True
+
+    @pytest.mark.parametrize("diff", [
+        {'trajectory': traj.atom_slice([0, 1, 2, 3])},
+        {'cutoff': 0.45},
+        {'n_neighbors_ignored': 2},
+        {'query': [1, 2, 3, 4]},
+        {'haystack': [1, 2, 3, 4]}
+    ])
+    def test_check_compatibility_assertion_error(self, diff):
+        params = {'trajectory': traj[0:2],
+                  'cutoff': 0.075,
+                  'n_neighbors_ignored': 0}
+        params.update(diff)
+        map2 = ContactFrequency(**params)
+        with pytest.raises(AssertionError):
+            self.map._check_compatibility(map2)
+
+    def test_check_compatibility_runtime_error(self):
+        map2 = ContactFrequency(trajectory=traj,
+                                cutoff=0.45,
+                                n_neighbors_ignored=2)
+        with pytest.raises(RuntimeError):
+            self.map._check_compatibility(map2, err=RuntimeError)
+
     @pytest.mark.parametrize("intermediate", ["dict", "json"])
     def test_serialization_cycle(self, intermediate):
         serializer, deserializer = {

contact_map/tests/test_dask_runner.py

@@ -9,7 +9,7 @@
 class TestDaskContactFrequency(object):
     def test_dask_integration(self):
         # this is an integration test to check that dask works
-        dask = pytest.importorskip('dask')
+        dask = pytest.importorskip('dask')  # pylint: disable=W0612
         distributed = pytest.importorskip('dask.distributed')
 
         client = distributed.Client()

contact_map/tests/test_frequency_task.py

@@ -1,5 +1,6 @@
-import os
-import collections
+# pylint: disable=wildcard-import, missing-docstring, protected-access
+# pylint: disable=attribute-defined-outside-init, invalid-name, no-self-use
+# pylint: disable=wrong-import-order, unused-wildcard-import
 
 from .utils import *
 from .test_contact_map import traj

contact_map/tests/utils.py

@@ -1,7 +1,9 @@
 import os
-import numpy as np
 from pkg_resources import resource_filename
 
+# pylint: disable=unused-import
+
+import numpy as np
 from numpy.testing import assert_array_equal, assert_allclose
 import pytest
 

setup.py

@@ -9,7 +9,7 @@
 ####################### USER SETUP AREA #################################
 # * VERSION: base version (do not include .dev0, etc -- that's automatic)
 # * IS_RELEASE: whether this is a release
-VERSION = "0.3.0"
+VERSION = "0.3.1"
 IS_RELEASE = True
 
 DEV_NUM = 0  # always 0: we don't do public (pypi) .dev releases