Merge pull request #1936 from apragsdale/demes-sources

Handle pulses in demes 0.2.0

CHANGELOG.md

@@ -1,5 +1,13 @@
 # Changelog
 
+## [1.0.4] - 2021-12-01
+
+**New features**:
+
+- Support for Demes 0.2.0, which introduces a change to how pulse
+  sources and proportions are specified.
+  ({pr}`1936`, {issue}`1930`, {user}`apragsdale`)
+
 ## [1.0.3] - 2021-11-12
 
 This is a bugfix release recommended for all users.

msprime/demography.py

@@ -1982,12 +1982,14 @@ def get_growth_rate(epoch):
         # Add pulses in reverse order, so that pulses with the same time
         # correspond to the correct backwards-time mass migration ordering.
         for pulse in reversed(events.pop("pulses")):
-            demography.add_mass_migration(
-                time=pulse.time,
-                source=pulse.dest,
-                dest=pulse.source,
-                proportion=pulse.proportion,
-            )
+            sequential_props = _proportions_to_sequential(pulse.proportions)
+            for prop, source in zip(sequential_props, pulse.sources):
+                demography.add_mass_migration(
+                    time=pulse.time,
+                    source=pulse.dest,
+                    dest=source,
+                    proportion=prop,
+                )
         for merger in events.pop("mergers"):
             demography.add_admixture(
                 time=merger.time,
@@ -2710,9 +2712,9 @@ def epoch_resolve(deme, time):
             for lm in lineage_movements:
                 if (lm.source, lm.dest, lm.proportion) in pulses:
                     b.add_pulse(
-                        source=resolved[lm.dest].name,
+                        sources=[resolved[lm.dest].name],
                         dest=resolved[lm.source].name,
-                        proportion=lm.proportion,
+                        proportions=[lm.proportion],
                         time=time,
                     )
 

requirements/CI-complete/requirements.txt

@@ -1,7 +1,7 @@
 bintrees==2.2.0
 codecov==2.1.12
 daiquiri==3.0.1
-demes==0.1.2
+demes==0.2.0
 hypothesis==6.23.2
 mypy==0.910 
 newick==1.3.1

requirements/CI-docs/requirements.txt

@@ -1,6 +1,6 @@
 daiquiri==3.0.1
-demes==0.1.2
-demesdraw==0.1.4
+demes==0.2.0
+demesdraw==0.2.0
 jupyter-book==0.12.1
 matplotlib==3.5.0
 newick==1.3.1

requirements/CI-tests-conda/requirements.txt

@@ -5,4 +5,4 @@ jsonschema<4.0
 gsl
 tskit==0.3.7
 stdpopsim==0.1.2
-demes==0.1.2
+demes==0.2.0

requirements/CI-tests-pip/requirements.txt

@@ -1,6 +1,6 @@
 bintrees==2.2.0
 daiquiri==3.0.1
-demes==0.1.2
+demes==0.2.0
 hypothesis==6.29.0
 newick==1.3.0
 numpy==1.21.4

requirements/development.txt

@@ -4,7 +4,7 @@ bintrees
 codecov
 coverage
 daiquiri
-demes>=0.1.2
+demes>=0.2.0
 demesdraw
 flake8
 hypothesis

setup.cfg

@@ -49,7 +49,7 @@ install_requires =
     numpy
     newick>=1.3.0
     tskit>=0.3.5
-    demes<0.2
+    demes>=0.2
 setup_requires =
     numpy
     setuptools

tests/test_demes.py

@@ -286,14 +286,14 @@ def test_pulses(self):
             epochs:
               - start_size: 2000
         pulses:
-          - source: X
+          - sources: [X]
             dest: A
             time: 500
-            proportion: 0.1
-          - source: A
+            proportions: [0.1]
+          - sources: [A]
             dest: X
             time: 100
-            proportion: 0.2
+            proportions: [0.2]
         """
         d = self.from_yaml(yaml)
         assert d.num_populations == 2
@@ -340,10 +340,10 @@ def test_pulses_ordering(self):
           - name: D
           - name: E
         pulses:
-          - {source: A, dest: B, time: 100, proportion: 0.1}
-          - {source: B, dest: C, time: 100, proportion: 0.2}
-          - {source: C, dest: D, time: 100, proportion: 0.3}
-          - {source: A, dest: E, time: 200, proportion: 0.4}
+          - {sources: [A], dest: B, time: 100, proportions: [0.1]}
+          - {sources: [B], dest: C, time: 100, proportions: [0.2]}
+          - {sources: [C], dest: D, time: 100, proportions: [0.3]}
+          - {sources: [A], dest: E, time: 200, proportions: [0.4]}
         """
         d = self.from_yaml(yaml)
         assert d.num_populations == 5
@@ -367,6 +367,24 @@ def test_pulses_ordering(self):
         assert d.events[3].dest == "A"
         assert d.events[3].proportion == 0.4
 
+    def test_multipulse(self):
+        b = demes.Builder(defaults=dict(epoch=dict(start_size=1)))
+        b.add_deme("a")
+        b.add_deme("b")
+        b.add_deme("c")
+        b.add_pulse(sources=["a", "b"], proportions=[0.1, 0.2], dest="c", time=1)
+        g = b.resolve()
+        d = msprime.Demography.from_demes(g)
+        assert len(d.events) == 2
+        assert isinstance(d.events[0], msprime.MassMigration)
+        assert isinstance(d.events[1], msprime.MassMigration)
+        assert d.events[0].source == "c"
+        assert d.events[0].dest == "a"
+        assert d.events[0].proportion == 0.1
+        assert d.events[1].source == "c"
+        assert d.events[1].dest == "b"
+        assert d.events[1].proportion == 0.2 / (1 - 0.1)
+
     def test_merger(self):
         yaml = """\
         time_units: generations
@@ -865,9 +883,9 @@ def test_pulse(self):
         assert len(graph.pulses) == 1
         pulse = graph.pulses[0]
         assert pulse.time == 100
-        assert pulse.source == "pop_1"
+        assert pulse.sources[0] == "pop_1"
         assert pulse.dest == "pop_0"
-        assert pulse.proportion == 0.1
+        assert pulse.proportions[0] == 0.1
 
     @pytest.mark.filterwarnings(
         # demes warns about multiple pulses with the same time
@@ -884,21 +902,21 @@ def test_pulse_ordering(self):
         assert len(graph.migrations) == 0
         assert len(graph.pulses) == 4
         pulses = graph.pulses
-        assert pulses[0].source == "pop_4"
+        assert pulses[0].sources[0] == "pop_4"
         assert pulses[0].dest == "pop_3"
-        assert pulses[0].proportion == 0.4
+        assert pulses[0].proportions[0] == 0.4
         assert pulses[0].time == 200
-        assert pulses[1].source == "pop_3"
+        assert pulses[1].sources[0] == "pop_3"
         assert pulses[1].dest == "pop_2"
-        assert pulses[1].proportion == 0.3
+        assert pulses[1].proportions[0] == 0.3
         assert pulses[1].time == 100
-        assert pulses[2].source == "pop_2"
+        assert pulses[2].sources[0] == "pop_2"
         assert pulses[2].dest == "pop_1"
-        assert pulses[2].proportion == 0.2
+        assert pulses[2].proportions[0] == 0.2
         assert pulses[2].time == 100
-        assert pulses[3].source == "pop_1"
+        assert pulses[3].sources[0] == "pop_1"
         assert pulses[3].dest == "pop_0"
-        assert pulses[3].proportion == 0.1
+        assert pulses[3].proportions[0] == 0.1
         assert pulses[3].time == 100
 
     def test_bad_pulse(self):
@@ -1018,6 +1036,49 @@ def test_census_event_is_ignored(self):
         demog.add_census(100)
         demog.to_demes()
 
+    @pytest.mark.filterwarnings(
+        # demes warns about multiple pulses with the same time
+        "ignore:Multiple pulses:UserWarning"
+    )
+    def test_multipulse_roundtrip_two_sources(self):
+        b = demes.Builder(defaults=dict(epoch=dict(start_size=1)))
+        b.add_deme("a")
+        b.add_deme("b")
+        b.add_deme("c")
+        b.add_pulse(sources=["a", "b"], proportions=[0.1, 0.2], dest="c", time=1)
+        g = b.resolve()
+        d = msprime.Demography.from_demes(g)
+        g2 = d.to_demes()
+        assert len(g2.pulses) == 2
+        assert g2.pulses[0].sources[0] == "b"
+        assert g2.pulses[0].proportions[0] == 0.2 / (1 - 0.1)
+        assert g2.pulses[1].sources[0] == "a"
+        assert g2.pulses[1].proportions[0] == 0.1
+
+    @pytest.mark.filterwarnings(
+        # demes warns about multiple pulses with the same time
+        "ignore:Multiple pulses:UserWarning"
+    )
+    def test_multipulse_roundtrip_three_sources(self):
+        b = demes.Builder(defaults=dict(epoch=dict(start_size=1)))
+        b.add_deme("a")
+        b.add_deme("b")
+        b.add_deme("c")
+        b.add_deme("d")
+        b.add_pulse(
+            sources=["a", "b", "c"], proportions=[0.1, 0.2, 0.3], dest="d", time=1
+        )
+        g = b.resolve()
+        d = msprime.Demography.from_demes(g)
+        g2 = d.to_demes()
+        assert len(g2.pulses) == 3
+        assert g2.pulses[0].sources[0] == "c"
+        assert g2.pulses[0].proportions[0] == 0.3 / (1 - 0.1 - 0.2)
+        assert g2.pulses[1].sources[0] == "b"
+        assert g2.pulses[1].proportions[0] == 0.2 / (1 - 0.1)
+        assert g2.pulses[2].sources[0] == "a"
+        assert g2.pulses[2].proportions[0] == 0.1
+
 
 # class TestRoundTrip:
 #    def remove_selfing_and_cloning(self, graph):