Added interface for setting TableCollection.sequence_length

Closes #107.

Author: jeromekelleher

python/_tskitmodule.c

@@ -5372,6 +5372,25 @@ TableCollection_get_sequence_length(TableCollection *self, void *closure)
     return Py_BuildValue("f", self->tables->sequence_length);
 }
 
+static int
+TableCollection_set_sequence_length(TableCollection *self, PyObject *value, void *closure)
+{
+    int ret = -1;
+
+    if (value == NULL) {
+        PyErr_SetString(PyExc_TypeError, "Cannot delete the sequence_length attribute");
+        goto out;
+    }
+    if (! PyNumber_Check(value)) {
+        PyErr_SetString(PyExc_TypeError, "sequence_length must be a number");
+        goto out;
+    }
+    self->tables->sequence_length = PyFloat_AsDouble(value);
+    ret = 0;
+out:
+    return ret;
+}
+
 static PyObject *
 TableCollection_get_file_uuid(TableCollection *self, void *closure)
 {
@@ -5564,8 +5583,9 @@ static PyGetSetDef TableCollection_getsetters[] = {
     {"mutations", (getter) TableCollection_get_mutations, NULL, "The mutation table."},
     {"populations", (getter) TableCollection_get_populations, NULL, "The population table."},
     {"provenances", (getter) TableCollection_get_provenances, NULL, "The provenance table."},
-    {"sequence_length", (getter) TableCollection_get_sequence_length, NULL,
-        "The sequence length."},
+    {"sequence_length",
+        (getter) TableCollection_get_sequence_length,
+        (setter) TableCollection_set_sequence_length, "The sequence length."},
     {"file_uuid", (getter) TableCollection_get_file_uuid, NULL,
         "The UUID of the corresponding file."},
     {NULL}  /* Sentinel */

python/tests/test_lowlevel.py

@@ -156,6 +156,21 @@ def test_reference_deletion(self):
             for table in tables:
                 self.assertGreater(len(str(table)), 0)
 
+    def test_set_sequence_length_errors(self):
+        tables = _tskit.TableCollection(1)
+        with self.assertRaises(TypeError):
+            del tables.sequence_length
+        for bad_value in ["sdf", None, []]:
+            with self.assertRaises(TypeError):
+                tables.sequence_length = bad_value
+
+    def test_set_sequence_length(self):
+        tables = _tskit.TableCollection(1)
+        self.assertEqual(tables.sequence_length, 1)
+        for value in [-1, 1e6, 1e-22, 1000, 2**32, -10000]:
+            tables.sequence_length = value
+            self.assertEqual(tables.sequence_length, value)
+
 
 class TestTreeSequence(LowLevelTestCase):
     """

python/tests/test_tables.py

@@ -1576,6 +1576,49 @@ def test_index_from_ts(self):
         self.assertEqual(ts.tables, tables)
         self.assertFalse(tables.has_index())
 
+    def test_set_sequence_length_errors(self):
+        tables = tskit.TableCollection(1)
+        with self.assertRaises(AttributeError):
+            del tables.sequence_length
+        for bad_value in ["asdf", None, []]:
+            with self.assertRaises(TypeError):
+                tables.sequence_length = bad_value
+
+    def test_set_sequence_length(self):
+        tables = tskit.TableCollection(1)
+        for value in [-1, 100, 2**32, 1e-6]:
+            tables.sequence_length = value
+            self.assertEqual(tables.sequence_length, value)
+
+    def test_bad_sequence_length(self):
+        tables = msprime.simulate(10, random_seed=1).dump_tables()
+        self.assertEqual(tables.sequence_length, 1)
+        for value in [-1, 0, -0.99, 0.9999]:
+            tables.sequence_length = value
+            with self.assertRaises(tskit.LibraryError):
+                tables.tree_sequence()
+            with self.assertRaises(tskit.LibraryError):
+                tables.sort()
+            with self.assertRaises(tskit.LibraryError):
+                tables.build_index()
+            with self.assertRaises(tskit.LibraryError):
+                tables.compute_mutation_parents()
+            with self.assertRaises(tskit.LibraryError):
+                tables.simplify()
+            self.assertEqual(tables.sequence_length, value)
+
+    def test_sequence_length_longer_than_edges(self):
+        tables = msprime.simulate(10, random_seed=1).dump_tables()
+        tables.sequence_length = 2
+        ts = tables.tree_sequence()
+        self.assertEqual(ts.sequence_length, 2)
+        self.assertEqual(ts.num_trees, 2)
+        trees = ts.trees()
+        tree = next(trees)
+        self.assertGreater(len(tree.parent_dict), 0)
+        tree = next(trees)
+        self.assertEqual(len(tree.parent_dict), 0)
+
 
 class TestTableCollectionPickle(unittest.TestCase):
     """

python/tskit/tables.py

@@ -1517,6 +1517,10 @@ def provenances(self):
     def sequence_length(self):
         return self.ll_tables.sequence_length
 
+    @sequence_length.setter
+    def sequence_length(self, sequence_length):
+        self.ll_tables.sequence_length = sequence_length
+
     @property
     def file_uuid(self):
         return self.ll_tables.file_uuid