Merge pull request #320 from grahamgower/docs

Docs for __getitem__(), __contains__(), and migration_matrices()

Author: grahamgower

CHANGELOG.md

@@ -1,5 +1,36 @@
 # Changelog
 
+## 0.1.2 - 2021-06-08
+
+**New features**:
+
+- Add `Graph.migration_matrices()` to get the migration matrices for a graph.
+  ({user}`grahamgower`, {issue}`309`, {pr}`320`)
+- Add `Deme.size_at()` to get the size of a deme at a given time.
+  ({user}`grahamgower`, {issue}`312`, {pr}`314`)
+- Support "linear" as an `Epoch.size_function`.
+  ({user}`noscode`, {issue}`296`, {pr}`310`)
+- Downstream test code can now use the `demes.hypothesis_strategies.graphs()`
+  [hypothesis](https://hypothesis.readthedocs.io/) strategy to generate a
+  random `Graph`. This is preliminary, and as such is not yet documented,
+  but is used for testing internally with some success. The API may change
+  in the future in response to requests from downstream application authors.
+  ({user}`grahamgower`, {issue}`217`, {pr}`294`)
+- The string representation for a graph, `Graph.__str__()`, is now the
+  simplified YAML output.
+  ({user}`grahamgower`, {issue}`235`, {pr}`293`)
+
+**Breaking changes**:
+
+- The undocumented msprime and stdpopsim converters have been removed.
+  ({user}`grahamgower`, {issue}`313`, {pr}`316`)
+- The JSON spec doesn't allow serialising infinite float values (although the
+  Python json library does support this by default). So for JSON output we
+  instead use the string "Infinity".
+  ({user}`grahamgower`,
+  [demes-spec#70](https://github.com/popsim-consortium/demes-spec/issues/70),
+  {pr}`311`)
+
 ## 0.1.1 - 2021-04-21
 
 Remove the "demes" console_scripts entry point.

demes/demes.py

@@ -1,4 +1,4 @@
-from typing import List, Union, Optional, Dict, MutableMapping, Any, Set
+from typing import List, Union, Optional, Dict, MutableMapping, Any, Set, Tuple
 import itertools
 import math
 import numbers
@@ -1239,15 +1239,35 @@ def __attrs_post_init__(self):
                 'if time_units!="generations", generation_time must be specified'
             )
 
-    def __getitem__(self, deme_name):
+    def __getitem__(self, deme_name: Name) -> Deme:
         """
-        Return the :class:`.Deme` with the specified name.
+        Get the :class:`.Deme` with the specified name.
+
+        .. code::
+
+            graph = demes.load("gutenkunst_ooa.yml")
+            yri = graph["YRI"]
+            print(yri)
+
+        :param str deme_name: The name of the deme.
+        :rtype: Deme
+        :return: The deme.
         """
         return self._deme_map[deme_name]
 
-    def __contains__(self, deme_name):
+    def __contains__(self, deme_name: Name) -> bool:
         """
         Check if the graph contains a deme with the specified name.
+
+        .. code::
+
+            graph = demes.load("gutenkunst_ooa.yml")
+            if "CHB" in graph:
+                print("Deme CHB is in the graph")
+
+        :param str deme_name: The name of the deme.
+        :rtype: bool
+        :return: ``True`` if the deme is in the graph, ``False`` otherwise.
         """
         return deme_name in self._deme_map
 
@@ -1611,10 +1631,52 @@ def _add_pulse(self, *, source, dest, proportion, time) -> Pulse:
         self.pulses.append(new_pulse)
         return new_pulse
 
-    def _migration_matrices(self):
+    def migration_matrices(self) -> Tuple[List[List[List[float]]], List[Number]]:
         """
-        Return a list of migration matrices, and a list of end times that
-        partition them. The start time for the first matrix is inf.
+        Get the migration matrices and the end times that partition them.
+
+        Returns a list of matrices, one for each time interval
+        over which migration rates do not change, in time-descending
+        order (from most ancient to most recent). For a migration matrix list
+        :math:`M`, the migration rate is :math:`M[i][j][k]` from deme
+        :math:`k` into deme :math:`j` during the :math:`i` 'th time interval.
+        The order of the demes' indices in each matrix matches the
+        order of demes in the graph's deme list (I.e. deme :math:`j`
+        corresponds to ``Graph.demes[j]``).
+
+        There is always at least one migration matrix in the list, even when
+        the graph defines no migrations.
+
+        A list of end times to which the matrices apply is also
+        returned. The time intervals to which the migration rates apply are an
+        open-closed interval ``(start_time, end_time]``, where the start time
+        of the first matrix is ``inf`` and the start time of subsequent
+        matrices match the end time of the previous matrix in the list.
+
+        .. note::
+            The last entry of the list of end times is always ``0``,
+            even when all demes in the graph go extinct before time ``0``.
+
+
+        .. code::
+
+            graph = demes.load("gutenkunst_ooa.yml")
+            mm_list, end_times = graph.migration_matrices()
+            start_times = [math.inf] + end_times[:-1]
+            assert len(mm_list) == len(end_times) == len(start_times)
+            deme_ids = {deme.name: j for j, deme in enumerate(graph.demes)}
+            j = deme_ids["YRI"]
+            k = deme_ids["CEU"]
+            for mm, start_time, end_time in zip(mm_list, start_times, end_times):
+                print(
+                    f"CEU -> YRI migration rate is {mm[j][k]} during the "
+                    f"time interval ({start_time}, {end_time}]"
+                )
+
+        :return: A 2-tuple of ``(mm_list, end_times)``,
+            where ``mm_list`` is a list of migration matrices,
+            and ``end_times`` are a list of end times for each matrix.
+        :rtype: tuple[list[list[list[float]]], list[float]]
         """
         uniq_times = set(migration.start_time for migration in self.migrations)
         uniq_times.update(migration.end_time for migration in self.migrations)
@@ -1624,7 +1686,7 @@ def _migration_matrices(self):
             # Extend to t=0 even when there are no migrations.
             end_times.append(0)
         n = len(self.demes)
-        mm_list = [[[0] * n for _ in range(n)] for _ in range(len(end_times))]
+        mm_list = [[[0.0] * n for _ in range(n)] for _ in range(len(end_times))]
         deme_id = {deme.name: j for j, deme in enumerate(self.demes)}
         for migration in self.migrations:
             start_time = math.inf
@@ -1640,7 +1702,7 @@ def _migration_matrices(self):
                             f"source={migration.source}, dest={migration.dest} "
                             f"between start_time={start_time}, end_time={end_time}"
                         )
-                    mm_list[k][dest_id][source_id] = migration.rate
+                    mm_list[k][dest_id][source_id] = float(migration.rate)
                 start_time = end_time
         return mm_list, end_times
 
@@ -1650,7 +1712,7 @@ def _check_migration_rates(self):
         deme in any interval of time.
         """
         start_time = math.inf
-        mm_list, end_times = self._migration_matrices()
+        mm_list, end_times = self.migration_matrices()
         for migration_matrix, end_time in zip(mm_list, end_times):
             for j, row in enumerate(migration_matrix):
                 row_sum = sum(row)

docs/api.md

@@ -26,6 +26,10 @@
 .. autoclass:: demes.Graph
     :members:
 
+    .. automethod:: __contains__
+
+    .. automethod:: __getitem__
+
 .. autoclass:: demes.Deme
     :members:
 

tests/test_demes.py

@@ -2259,7 +2259,7 @@ def test_migration_matrices(self):
         b = Builder()
         b.add_deme("a", epochs=[dict(start_size=1)])
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [0]
         assert mm_list == [[[0]]]
 
@@ -2268,7 +2268,7 @@ def test_migration_matrices(self):
         b.add_deme("b", epochs=[dict(start_size=1)])
         b.add_migration(source="a", dest="b", rate=0.1)
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [0]
         assert mm_list == [[[0, 0], [0.1, 0]]]
 
@@ -2277,7 +2277,7 @@ def test_migration_matrices(self):
         b.add_deme("b", epochs=[dict(start_size=1)])
         b.add_migration(source="a", dest="b", rate=0.1, start_time=100, end_time=50)
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [100, 50, 0]
         assert mm_list == [[[0, 0], [0, 0]], [[0, 0], [0.1, 0]], [[0, 0], [0, 0]]]
 
@@ -2286,7 +2286,7 @@ def test_migration_matrices(self):
         b.add_deme("b", start_time=100, ancestors=["a"], epochs=[dict(start_size=1)])
         b.add_migration(source="a", dest="b", rate=0.1)
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [100, 0]
         assert mm_list == [[[0, 0], [0, 0]], [[0, 0], [0.1, 0]]]
 
@@ -2296,7 +2296,7 @@ def test_migration_matrices(self):
         b.add_migration(source="a", dest="b", rate=0.1, end_time=100)
         b.add_migration(source="a", dest="b", rate=0.1, start_time=50)
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [100, 50, 0]
         assert mm_list == [[[0, 0], [0.1, 0]], [[0, 0], [0, 0]], [[0, 0], [0.1, 0]]]
 
@@ -2307,7 +2307,7 @@ def test_migration_matrices(self):
         b.add_migration(source="a", dest="b", rate=0.1, end_time=50)
         b.add_migration(source="c", dest="b", rate=0.2, start_time=100)
         g = b.resolve()
-        mm_list, end_times = g._migration_matrices()
+        mm_list, end_times = g.migration_matrices()
         assert end_times == [100, 50, 0]
         assert mm_list == [
             [[0, 0, 0], [0.1, 0, 0], [0, 0, 0]],