Merge pull request #88 from dwhswenson/remove_map

Remove `ContactMap` (allowing rename `ContactFrequency` => `ContactMap`)

ci/conda-recipe/meta.yaml

@@ -1,7 +1,7 @@
 package:
   name: contact_map
   # add ".dev0" for unreleased versions
-  version: "0.6.1.dev0"
+  version: "0.7.0.dev0"
 
 source:
   path: ../../

contact_map/contact_map.py

@@ -600,61 +600,12 @@ def residue_contacts(self):
                             n_res, n_res)
 
 
-class ContactMap(ContactObject):
-    """
-    Contact map (atomic and residue) for a single frame.
-
-    .. deprecated:: 0.6.0
-        ``ContactMap`` will be removed in Contact Map Explorer 0.7.0 because
-        it is redundant with ``ContactFrequency``. For more, see
-        https://github.com/dwhswenson/contact_map/issues/82.
-
-    """
-    # Default for use_atom_slice, None tries to be smart
-    _class_use_atom_slice = None
-
-    _deprecation_message=(
-        "The ContactMap class will be removed in Contact Map Explorer 0.7. "
-        + "Use ContactFrequency instead. For more, see: "
-        + "https://github.com/dwhswenson/contact_map/issues/82."
-    )
-
-    def __init__(self, frame, query=None, haystack=None, cutoff=0.45,
-                 n_neighbors_ignored=2):
-        warnings.warn(self._deprecation_message, FutureWarning)
-        self._frame = frame  # TODO: remove this?
-        super(ContactMap, self).__init__(frame.topology, query, haystack,
-                                         cutoff, n_neighbors_ignored)
-
-        contact_maps = self.contact_map(frame, 0,
-                                        self.indexer.residue_query_atom_idxs,
-                                        self._residue_ignore_atom_idxs)
-        (atom_contacts, self._residue_contacts) = contact_maps
-        self._atom_contacts = self.indexer.convert_atom_contacts(atom_contacts)
-
-    @classmethod
-    def from_dict(cls, dct):
-        warnings.warn(cls._deprecation_message, FutureWarning)
-        return super(ContactMap, cls).from_dict(dct)
-
-    # don't need to add deprecation in from_json because it uses from_dict
-
-    @classmethod
-    def from_file(cls, filename):
-        warnings.warn(cls._deprecation_message, FutureWarning)
-        return super(ContactMap, cls).from_file(filename)
-
-
-    def __hash__(self):
-        return hash((super(ContactMap, self).__hash__(),
-                     tuple(self._atom_contacts.items()),
-                     tuple(self._residue_contacts.items())))
-
-    def __eq__(self, other):
-        is_equal = (super(ContactMap, self).__eq__(other)
-                    and self._atom_contacts == other._atom_contacts
-                    and self._residue_contacts == other._residue_contacts)
-        return is_equal
+CONTACT_MAP_ERROR = (
+    "The ContactMap class has been removed. Please use ContactFrequency."
+    " For more, see: https://github.com/dwhswenson/contact_map/issues/82"
+)
+def ContactMap(*args, **kwargs):  # -no-cov-
+    raise RuntimeError(CONTACT_MAP_ERROR)
 
 
 class ContactFrequency(ContactObject):
@@ -686,9 +637,15 @@ class ContactFrequency(ContactObject):
     """
     # Default for use_atom_slice, None tries to be smart
     _class_use_atom_slice = None
+    _pending_dep_msg = (
+        "ContactFrequency will be renamed to ContactMap in version 0.8. "
+        "Invoking it as ContactFrequency will be deprecated in 0.8. For "
+        "more, see https://github.com/dwhswenson/contact_map/issues/82"
+    )
 
     def __init__(self, trajectory, query=None, haystack=None, cutoff=0.45,
                  n_neighbors_ignored=2, frames=None):
+        warnings.warn(self._pending_dep_msg, PendingDeprecationWarning)
         if frames is None:
             frames = range(len(trajectory))
         self.frames = frames
@@ -703,13 +660,24 @@ def __init__(self, trajectory, query=None, haystack=None, cutoff=0.45,
     def from_contacts(cls, atom_contacts, residue_contacts, n_frames,
                       topology, query=None, haystack=None, cutoff=0.45,
                       n_neighbors_ignored=2, indexer=None):
+        warnings.warn(cls._pending_dep_msg, PendingDeprecationWarning)
         obj = super(ContactFrequency, cls).from_contacts(
             atom_contacts, residue_contacts, topology, query, haystack,
             cutoff, n_neighbors_ignored, indexer
         )
         obj._n_frames = n_frames
         return obj
 
+    @classmethod
+    def from_dict(cls, dct):
+        warnings.warn(cls._pending_dep_msg, PendingDeprecationWarning)
+        return super(ContactFrequency, cls).from_dict(dct)
+
+    @classmethod
+    def from_file(cls, filename):
+        warnings.warn(cls._pending_dep_msg, PendingDeprecationWarning)
+        return super(ContactFrequency, cls).from_file(filename)
+
     def __hash__(self):
         return hash((super(ContactFrequency, self).__hash__(),
                      tuple(self._atom_contacts.items()),

contact_map/tests/test_contact_map.py

@@ -113,11 +113,16 @@ def test_residue_neighborhood():
             assert len(residue_neighborhood(res, n=n)) == len_n
 
 @pytest.mark.parametrize("idx", [0, 4])
-class TestContactMap(object):
+class TestContactObject(object):
+    # note: these used to be the tests for the separate single-frame
+    # ContactMap class; however, it includes a lot of good unit tests for
+    # ContactObject
     def setup(self):
         self.topology = traj.topology
-        self.map0 = ContactMap(traj[0], cutoff=0.075, n_neighbors_ignored=0)
-        self.map4 = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        self.map0 = ContactFrequency(traj[0], cutoff=0.075,
+                                     n_neighbors_ignored=0)
+        self.map4 = ContactFrequency(traj[4], cutoff=0.075,
+                                     n_neighbors_ignored=0)
         self.maps = {0: self.map0, 4: self.map4}
 
         self.expected_atom_contacts = {
@@ -156,25 +161,6 @@ def test_counters(self, idx):
         assert m._residue_contacts == expected
         assert m.residue_contacts.counter == expected
 
-    @pytest.mark.parametrize('contactcount', [True, False])
-    def test_from_contacts(self, idx, contactcount):
-        expected = self.maps[idx]
-        atom_contact_list = self.expected_atom_contacts[expected]
-        residue_contact_list = self.expected_residue_contacts[expected]
-        atom_contacts = counter_of_inner_list(atom_contact_list)
-        residue_contacts = counter_of_inner_list(residue_contact_list)
-        if contactcount:
-            atom_contacts = ContactCount(atom_contacts, self.topology.atom,
-                                         10, 10)
-            residue_contacts = ContactCount(residue_contacts,
-                                            self.topology.residue, 5, 5)
-
-        cmap = ContactMap.from_contacts(atom_contacts, residue_contacts,
-                                        topology=self.topology,
-                                        cutoff=0.075,
-                                        n_neighbors_ignored=0)
-        _contact_object_compare(cmap, expected)
-
     def test_to_dict(self, idx):
         m = self.maps[idx]
         dct = m.to_dict()
@@ -186,15 +172,15 @@ def test_to_dict(self, idx):
         assert dct['n_neighbors_ignored'] == 0
 
     def test_topology_serialization_cycle(self, idx):
-        m = self.maps[idx]
-        serialized_topology = ContactMap._serialize_topology(m.topology)
-        new_top = ContactMap._deserialize_topology(serialized_topology)
-        assert m.topology == new_top
+        top = self.maps[idx].topology
+        serialized_topology = ContactFrequency._serialize_topology(top)
+        new_top = ContactFrequency._deserialize_topology(serialized_topology)
+        assert top == new_top
 
     def test_counter_serialization_cycle(self, idx):
         m = self.maps[idx]
-        serialize = ContactMap._serialize_contact_counter
-        deserialize = ContactMap._deserialize_contact_counter
+        serialize = ContactFrequency._serialize_contact_counter
+        deserialize = ContactFrequency._deserialize_contact_counter
         serialized_atom_counter = serialize(m._atom_contacts)
         serialized_residue_counter = serialize(m._residue_contacts)
         new_atom_counter = deserialize(serialized_atom_counter)
@@ -205,19 +191,19 @@ def test_counter_serialization_cycle(self, idx):
     def test_dict_serialization_cycle(self, idx):
         m = self.maps[idx]
         dct = m.to_dict()
-        m2 = ContactMap.from_dict(dct)
+        m2 = ContactFrequency.from_dict(dct)
         _contact_object_compare(m, m2)
         assert m == m2
 
     def test_json_serialization_cycle(self, idx):
         m = self.maps[idx]
         json_str = m.to_json()
-        m2 = ContactMap.from_json(json_str)
+        m2 = ContactFrequency.from_json(json_str)
         _contact_object_compare(m, m2)
         assert m == m2
 
     def test_with_ignores(self, idx):
-        m = ContactMap(traj[idx], cutoff=0.075, n_neighbors_ignored=1)
+        m = ContactFrequency(traj[idx], cutoff=0.075, n_neighbors_ignored=1)
         expected_atom_contacts = {
             0: [[1, 4]],
             4: [[0, 9], [0, 8], [1, 8], [1, 9], [1, 4], [8, 4], [8, 5]]
@@ -278,22 +264,22 @@ def test_most_common_atoms_for_contact(self, idx):
     def test_saving(self, idx):
         m = self.maps[idx]
         m.save_to_file(test_file)
-        m2 = ContactMap.from_file(test_file)
+        m2 = ContactFrequency.from_file(test_file)
         assert m.atom_contacts.counter == m2.atom_contacts.counter
         os.remove(test_file)
 
     @pytest.mark.parametrize("use_atom_slice", [True, False, None])
     def test_atom_slice(self, idx, use_atom_slice):
         # Set class variable before init
-        class_default = ContactMap._class_use_atom_slice
-        ContactMap._class_use_atom_slice = use_atom_slice
-        map0q = ContactMap(traj[0], query=[1, 4, 5, 6],  cutoff=0.075,
-                           n_neighbors_ignored=0)
-        map0h = ContactMap(traj[0], haystack=[1, 4, 5, 6],
-                           cutoff=0.075, n_neighbors_ignored=0)
-        map0b = ContactMap(traj[0], query=[1, 4, 5, 6],
-                           haystack=[1, 4, 5, 6], cutoff=0.075,
-                           n_neighbors_ignored=0)
+        class_default = ContactFrequency._class_use_atom_slice
+        ContactFrequency._class_use_atom_slice = use_atom_slice
+        map0q = ContactFrequency(traj[0], query=[1, 4, 5, 6],  cutoff=0.075,
+                                 n_neighbors_ignored=0)
+        map0h = ContactFrequency(traj[0], haystack=[1, 4, 5, 6],
+                                 cutoff=0.075, n_neighbors_ignored=0)
+        map0b = ContactFrequency(traj[0], query=[1, 4, 5, 6],
+                                 haystack=[1, 4, 5, 6], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         maps = [map0q, map0h, map0b]
         atoms = {map0q: list(range(10)),
                  map0h: list(range(10)),
@@ -327,7 +313,7 @@ def test_atom_slice(self, idx, use_atom_slice):
             assert real_idx == sliced_idx
         # Reset class variable (as imports are not redone between function
         # calls)
-        ContactMap._class_use_atom_slice = class_default
+        ContactFrequency._class_use_atom_slice = class_default
 
     def test_contacts_dict(self, idx):
         _check_contacts_dict_names(self.maps[idx])
@@ -339,8 +325,9 @@ def test_no_unitcell(self, idx):
 
         # Activate atom_slice
         atoms = [1, 4, 5, 6]
-        mapi = ContactMap(temptraj[idx], cutoff=0.075, n_neighbors_ignored=0,
-                          query=atoms, haystack=atoms)
+        mapi = ContactFrequency(temptraj[idx], cutoff=0.075,
+                                n_neighbors_ignored=0, query=atoms,
+                                haystack=atoms)
         expected_atom_contacts = {0: [[1, 4], [4, 6], [5, 6]],
                                   4: [[1, 4], [4, 6], [5, 6]]}
         expected = counter_of_inner_list(expected_atom_contacts[idx])
@@ -501,7 +488,7 @@ def test_hash(self):
     def test_saving(self):
         m = self.map
         m.save_to_file(test_file)
-        m2 = ContactMap.from_file(test_file)
+        m2 = ContactFrequency.from_file(test_file)
         assert m.atom_contacts.counter == m2.atom_contacts.counter
         os.remove(test_file)
 
@@ -637,7 +624,8 @@ class TestContactDifference(object):
     def test_diff_traj_frame(self):
         ttraj = ContactFrequency(traj[0:4], cutoff=0.075,
                                  n_neighbors_ignored=0)
-        frame = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        frame = ContactFrequency(traj[4], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         expected_atom_count = {
             frozenset([0, 8]): -1.0,
             frozenset([0, 9]): -1.0,
@@ -673,7 +661,8 @@ def test_diff_traj_frame(self):
     def test_serialization_cycle(self, intermediate):
         ttraj = ContactFrequency(traj[0:4], cutoff=0.075,
                                  n_neighbors_ignored=0)
-        frame = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        frame = ContactFrequency(traj[4], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         diff = ttraj - frame
 
         serializer, deserializer = {
@@ -687,8 +676,8 @@ def test_serialization_cycle(self, intermediate):
         assert diff == reloaded
 
     def test_diff_frame_frame(self):
-        m0 = ContactMap(traj[0], cutoff=0.075, n_neighbors_ignored=0)
-        m4 = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        m0 = ContactFrequency(traj[0], cutoff=0.075, n_neighbors_ignored=0)
+        m4 = ContactFrequency(traj[4], cutoff=0.075, n_neighbors_ignored=0)
         # one of these simply has more contacts than the other, so to test
         # both positive diff and negative diff we flip the sign
         diff_1 = m4 - m0
@@ -719,7 +708,8 @@ def test_diff_frame_frame(self):
     def test_contacts_dict(self):
         ttraj = ContactFrequency(traj[0:4], cutoff=0.075,
                                  n_neighbors_ignored=0)
-        frame = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        frame = ContactFrequency(traj[4], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         _check_contacts_dict_names(ttraj - frame)
 
     def test_diff_traj_traj(self):
@@ -765,7 +755,8 @@ def test_diff_traj_traj(self):
     def test_saving(self):
         ttraj = ContactFrequency(traj[0:4], cutoff=0.075,
                                  n_neighbors_ignored=0)
-        frame = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        frame = ContactFrequency(traj[4], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         diff = ttraj - frame
 
         diff.save_to_file(test_file)
@@ -778,6 +769,7 @@ def test_plot(self):
         # smoke test; checks that we cover negative counts in plotting
         ttraj = ContactFrequency(traj[0:4], cutoff=0.075,
                                  n_neighbors_ignored=0)
-        frame = ContactMap(traj[4], cutoff=0.075, n_neighbors_ignored=0)
+        frame = ContactFrequency(traj[4], cutoff=0.075,
+                                 n_neighbors_ignored=0)
         diff = ttraj - frame
         diff.residue_contacts.plot()

setup.cfg

@@ -1,6 +1,6 @@
 [metadata]
 name = contact_map
-version = 0.6.1.dev0
+version = 0.7.0.dev0
 description = Contact maps based on MDTraj
 long_description = file: README.md
 long_description_content_type = text/markdown