Merge pull request #265 from molpopgen/binary_format_compatibility

Binary format compatibility fixes and tests.

MANIFEST.in

@@ -6,6 +6,8 @@ include COPYING
 include CMakeLists.txt
 include fwdpy11/CMakeLists.txt
 include tests/CMakeLists.txt
+include tests/v045.bin
+include tests/v045.lzma
 include configure
 include setup.py.in
 include doc/conf.py

doc/misc/changelog.rst

@@ -14,6 +14,8 @@ Major changes include:
 * Updating the fwdpp back-end to the pre-release code for fwdpp 0.8.0.  Almost none of these changes are "user facing".
 * Add :class:`fwdpy11.SiteTable`, :class:`fwdpy11.Site` and new fields to :class:`fwdpy11.MutationRecord`. `PR 258 <https://github.com/molpopgen/fwdpy11/pull/258>`_  These changes affect the API for some function calls. See :ref:`upgrade_path` for details.
 
+Even though this release changes some of the tree sequence data structures, we are still able to read in files generated by version 0.4.5! (This is actually unit tested.)
+
 Minor changes include:
 
 * Add :func:`fwdpy11.gsl_version`. :class:`fwdpy11.MutationRecord`. `PR 256 <https://github.com/molpopgen/fwdpy11/pull/256>`_

fwdpy11/headers/fwdpy11/serialization.hpp

@@ -114,6 +114,16 @@ namespace fwdpy11
                     buffer, pop.ancient_sample_records);
                 fwdpp::io::deserialize_population(buffer, pop);
                 pop.tables = fwdpp::ts::io::deserialize_tables(buffer);
+                // NOTE: version 0.5.0 added in a site table that previous versions
+                // did not have.  Further, the mutation table entries differed in
+                // previous versions.
+                if (!pop.tables.mutation_table.empty()
+                    && pop.tables.site_table.empty())
+                    {
+                        fwdpp::ts::io::
+                            fix_mutation_table_repopulate_site_table(
+                                pop.tables, pop.mutations);
+                    }
                 if (!pop.tables.edge_table.empty())
                     {
                         std::vector<fwdpp::ts::TS_NODE_INT> samples(2 * pop.N);

fwdpy11/src/fwdpp_types/MutationRecord.cc

@@ -22,7 +22,7 @@ init_ts_MutationRecord(py::module& m)
                       "Node id of the mutation")
         .def_readonly("key", &fwdpp::ts::mutation_record::key,
                       "Index of the mutation in the population")
-        .def_readonly("site", &fwdpp::ts::mutation_record::key,
+        .def_readonly("site", &fwdpp::ts::mutation_record::site,
                       R"delim(Index of the mutation's site in the population.
                       
                       .. versionadded:: 0.5.0)delim")

tests/test_binary_format_compatibility.py

@@ -0,0 +1,23 @@
+import unittest
+import fwdpy11
+import pickle
+import lzma
+
+
+class TestOldBinaryFileFormats(unittest.TestCase):
+    def test_reading_045(self):
+        pop = fwdpy11.DiploidPopulation.load_from_file("tests/v045.bin")
+        for i in pop.tables.mutations:
+            self.assertEqual(
+                pop.mutations[i.key].pos, pop.tables.sites[i.site].position)
+
+    def test_unpickling_045(self):
+        with lzma.open('tests/v045.lzma', 'rb') as f:
+            pop = pickle.load(f)
+        for i in pop.tables.mutations:
+            self.assertEqual(
+                pop.mutations[i.key].pos, pop.tables.sites[i.site].position)
+
+
+if __name__ == "__main__":
+    unittest.main()