Check minimum epoch lengths in demes models

doc/misc/changelog.md

@@ -43,6 +43,7 @@ Testing
 
 * Added many more tests related to models defined using `demes`
   PR {pr}`891`.
+  PR {pr}`931`.
   Issue {issue}`890`.
   {user}`apragsdale`,
   {user}`molpopgen`.
@@ -57,6 +58,10 @@ Back end changes
   PR {pr}`906`.
 * Added infrastructure to separate out back end from Python-specific C++ code.
   PR {pr}`936`.
+* Assert that epochs from `demes` models are at least 1 generation long.
+  PR {pr}`931`
+* Added infrastructure to separate out back end from Python-specific C++ code.
+  PR {pr}`936`.
 
 Dependencies
 

fwdpy11/_functions/import_demes.py

@@ -519,6 +519,10 @@ def _process_epoch(
 
         start_size = int(np.rint(e.start_size))
         end_size = int(np.rint(e.end_size))
+        time_span = int(np.rint(e.time_span))
+
+        if time_span < 1:
+            raise ValueError("epoch durations must be >= 1 time step")
 
         # Handle size change functions
         events.set_deme_sizes.append(
@@ -529,7 +533,7 @@ def _process_epoch(
                 raise ValueError(
                     f"Size change function must be exponential.  We got {e.size_function}"
                 )
-            G = exponential_growth_rate(start_size, end_size, int(np.rint(e.time_span)))
+            G = exponential_growth_rate(start_size, end_size, time_span)
             events.set_growth_rates.append(
                 SetExponentialGrowth(when=when, deme=idmap[deme_id], G=G)
             )

fwdpy11/discrete_demography.py

@@ -1065,7 +1065,10 @@ def from_demes_graph(
                 if start > 0:
                     start = start + 1
                 end = model_times.convert_time(e.end_time) + 1
-                assert end > start, f"{e}, {start}, {end}"
+                if not end > start:
+                    raise ValueError(
+                        f"epoch end time must be > start, got end: {end}, start: {start}"
+                    )
                 # NOTE: 1.0 is a HACK for growth rate and is WRONG
                 itree[start:end] = _EpochData(
                     idmap[d.name], None, int(e.start_size), 1.0

tests/test_demes2fwdpy11.py

@@ -1857,3 +1857,51 @@ def test_non_integer_initial_epoch_size():
         for i in sorted(demog.metadata["initial_sizes"].keys())
     ]
     _ = fwdpy11.DiploidPopulation(initial_sizes, 1)
+
+
+def test_very_short_epoch():
+    b = demes.Builder()
+    b.add_deme("A", epochs=[{"start_size": 100}])
+    b.add_deme(
+        "B",
+        ancestors=["A"],
+        start_time=10,
+        epochs=[
+            {"start_size": 100, "end_time": 1e-3},
+            {"start_size": 200, "end_time": 0.0},
+        ],
+    )
+    g = b.resolve()
+
+    with pytest.raises(ValueError):
+        _ = fwdpy11.discrete_demography.from_demes(g)
+
+
+def test_epoch_rounding_01():
+    yaml = """
+time_units: generations
+demes:
+- name: bad
+  epochs:
+  - {end_time: 1.75, start_size: 1}
+  - {end_time: 1.25, start_size: 2}
+  - {end_time: 0.5, start_size: 3}
+  - {end_time: 0, start_size: 4}
+"""
+    graph = demes.loads(yaml)
+    with pytest.raises(ValueError):
+        _ = fwdpy11.discrete_demography.from_demes(graph, burnin=0)
+
+def test_epoch_rounding_02():
+    yaml = """
+time_units: generations
+demes:
+- name: bad
+  epochs:
+  - {end_time: 1.5, start_size: 1}
+  - {end_time: 0.5, start_size: 2}
+  - {end_time: 0, start_size: 3}
+"""
+    graph = demes.loads(yaml)
+    with pytest.raises(ValueError):
+        _ = fwdpy11.discrete_demography.from_demes(graph, burnin=0)