Merge pull request #1068 from jeromekelleher/reinstate-dump-compress

Reinstate dump compress

Author: mergify[bot]

python/CHANGELOG.rst

@@ -1,13 +1,14 @@
 --------------------
-[0.X.X] - 2021-XX-XX
+[0.3.4] - 2020-12-02
 --------------------
 
-**Breaking changes**
+Minor bugfix release.
 
-**Features**
 
 **Bugfixes**
 
+- Reinstate the unused zlib_compression option to tskit.dump, as msprime < 1.0
+  still uses it (:user:`jeromekelleher`, :issue:`1067`).
 
 --------------------
 [0.3.3] - 2020-11-27

python/tests/test_highlevel.py

@@ -1288,6 +1288,16 @@ def test_dump_load_errors(self):
                 with pytest.raises(TypeError):
                     func(bad_filename)
 
+    def test_zlib_compression_warning(self, ts_fixture, tmp_path):
+        temp_file = tmp_path / "tmp.trees"
+        with warnings.catch_warnings(record=True) as w:
+            ts_fixture.dump(temp_file, zlib_compression=True)
+            assert len(w) == 1
+            assert issubclass(w[0].category, RuntimeWarning)
+        with warnings.catch_warnings(record=True) as w:
+            ts_fixture.dump(temp_file, zlib_compression=False)
+            assert len(w) == 0
+
     def test_tables_sequence_length_round_trip(self):
         for sequence_length in [0.1, 1, 10, 100]:
             ts = msprime.simulate(5, length=sequence_length, random_seed=1)

python/tskit/_version.py

@@ -1,4 +1,4 @@
 # Definitive location for the version number.
 # During development, should be x.y.z.devN
 # For beta should be x.y.zbN
-tskit_version = "0.3.4.dev1"
+tskit_version = "0.3.4"

python/tskit/trees.py

@@ -3207,12 +3207,20 @@ def load_tables(cls, tables, *, build_indexes=False):
         ts.load_tables(tables._ll_tables, build_indexes=build_indexes)
         return TreeSequence(ts)
 
-    def dump(self, file_or_path):
+    def dump(self, file_or_path, zlib_compression=False):
         """
         Writes the tree sequence to the specified path or file object.
 
         :param str file_or_path: The file object or path to write the TreeSequence to.
+        :param bool zlib_compression: This parameter is deprecated and ignored.
         """
+        if zlib_compression:
+            # Note: the msprime CLI before version 1.0 uses this option, so we need
+            # to keep it indefinitely.
+            warnings.warn(
+                "The zlib_compression option is no longer supported and is ignored",
+                RuntimeWarning,
+            )
         file, local_file = util.convert_file_like_to_open_file(file_or_path, "wb")
         try:
             self._ll_tree_sequence.dump(file)