Merge pull request #709 from petrelharp/slim_gen

set slim generation on tables
popsim-consortium · Dec 9, 2020 · 67205fb · 67205fb
2 parents 642c668 + 8fdb0de
commit 67205fb
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Showing 3 changed files with 6 additions and 4 deletions.
diff --git a/requirements/CI/requirements.txt b/requirements/CI/requirements.txt
@@ -12,7 +12,7 @@ msprime==0.7.4
 attrs==20.3.0
 appdirs==1.4.4
 humanize==3.1.0
-pyslim==0.403
+pyslim==0.500
 pandas==1.1.4
 numpy==1.19.4
 scikit-allel==1.3.2

diff --git a/requirements/development.txt b/requirements/development.txt
@@ -15,7 +15,7 @@ attrs
 appdirs
 humanize
 pre-commit
-pyslim>=0.401
+pyslim>=0.500
 pandas
 numpy
 scikit-allel

diff --git a/stdpopsim/slim_engine.py b/stdpopsim/slim_engine.py
@@ -1206,10 +1206,12 @@ def _recap_and_rescale(
         # Node times come from SLiM generation numbers, which may have been
         # divided by a scaling factor for computational tractability.
         tables = ts.dump_tables()
-        for table in (tables.nodes, tables.migrations):
+        for table in (tables.nodes, tables.migrations, tables.mutations):
             table.time *= slim_scaling_factor
+        ts_metadata = tables.metadata
+        ts_metadata["SLiM"]["generation"] *= slim_scaling_factor
+        tables.metadata = ts_metadata
         ts = pyslim.SlimTreeSequence.load_tables(tables)
-        ts.slim_generation *= slim_scaling_factor
 
         rng = random.Random(seed)
         s1, s2 = rng.randrange(1, 2 ** 32), rng.randrange(1, 2 ** 32)