Merge pull request #1796 from jeromekelleher/gc-arg-error

Release 1.0.2

CHANGELOG.md

@@ -1,13 +1,24 @@
 # Changelog
 
-## [1.0.2] - 2021-06-XX
+## [1.0.2] - 2021-06-29
+
+Improved Demes support and minor bugfixes.
 
 **New features**:
 
 - Support for Demes input and logging in the msp simulate CLI
   ({pr}`1716`, {user}`jeromekelleher`).
 - Add ``Demography.to_demes`` method for creating a Demes demographic model
   from an msprime demography ({pr}`1724`, {user}`grahamgower`).
+- Improved mapping of Demes models to Demography objects
+  ({pr}`1758`, {pr}`1757`, {pr}`1756` {user}`apragsdale`).
+- Improved numerical algorithms in DemographyDebugger ({pr}`1788`,
+  {user}`grahamgower`, {user}`petrelharp`).
+
+**Bugfixes**:
+
+- Raise an error if running full ARG simulations with gene conversion
+  ({issue}`1774`).
 
 ## [1.0.1] - 2021-05-10
 

msprime/ancestry.py

@@ -1248,6 +1248,12 @@ def __init__(
         # https://github.com/tskit-dev/msprime/issues/1212
         assert len(gene_conversion_map.rate) == 1
         gene_conversion_rate = gene_conversion_map.rate[0]
+        if gene_conversion_rate > 0 and store_full_arg:
+            raise ValueError(
+                "The record_full_arg option is not currently supported for "
+                "simulations with gene conversion. See "
+                "https://github.com/tskit-dev/msprime/issues/1773"
+            )
 
         start_time = -1 if start_time is None else start_time
         super().__init__(

tests/test_ancestry.py

@@ -554,6 +554,16 @@ def test_gene_conversion_errors(self):
                     gene_conversion_tract_length=bad_type,
                 )
 
+    def test_gene_conversion_full_arg_unsupported(self):
+        with pytest.raises(ValueError, match="record_full_arg"):
+            ancestry._parse_sim_ancestry(
+                10,
+                sequence_length=100,
+                gene_conversion_rate=1,
+                gene_conversion_tract_length=5,
+                record_full_arg=True,
+            )
+
     def test_discrete_genome(self):
         # default is True
         sim = ancestry._parse_sim_ancestry(10, sequence_length=10)