Merge branch 'main' into squash-ibd

README.md

@@ -37,7 +37,8 @@ issue for a specific bug or feature request.
 We warmly welcome contributions from the community. Raise an issue if you have an
 idea you'd like to work on, or submit a PR for comments and help.
 
-The base `tskit` library provides both a Python and C API. A Rust API is provided in the
+The base `tskit` library provides both a [Python](https://tskit.dev/tskit/docs/latest/python-api.html)
+and [C](https://tskit.dev/tskit/docs/latest/c-api.html) API. A Rust API is provided in the
 [tskit-rust](https://github.com/tskit-dev/tskit-rust) repository.
 
 

python/CHANGELOG.rst

@@ -1,5 +1,5 @@
 --------------------
-[0.5.8] - 2024-XX-XX
+[0.5.9] - 2024-XX-XX
 --------------------
 
 **Breaking Changes**
@@ -24,6 +24,9 @@
   in the presence of non-ancestral material (very rare).
   (:user:`petrelharp`, :issue:`2983`, :pr:`1623`)
 
+- Printing ``tskit.MetadataSchema(schema=None)`` now shows ``"Null_schema"`` rather
+  than ``None``, to avoid confusion (:user:`hyanwong`, :pr:`2720`)
+
 **Features**
 
 - Add ``TreeSequence.extend_haplotypes`` method that extends ancestral haplotypes
@@ -41,6 +44,13 @@
   (:user:`currocam`, :pr:`2960`)
 
 
+--------------------
+[0.5.8] - 2024-06-27
+--------------------
+
+- Add support for numpy 2 (:user:`jeromekelleher`, :user:`benjeffery`, :pr:`2964`)
+
+
 --------------------
 [0.5.7] - 2024-06-17
 --------------------
@@ -103,8 +113,7 @@
 - Add ``__repr__`` for variants to return a string representation of the raw data
   without spewing megabytes of text (:user:`chriscrsmith`, :pr:`2695`, :issue:`2694`)
 
-- Add ``keep_rows`` method to table classes to support efficient in-place
-  table subsetting (:user:`jeromekelleher`, :pr:`2700`)
+**Breaking Changes**
 
 **Bugfixes**
 

python/tests/test_metadata.py

@@ -322,7 +322,10 @@ def test_schema_str(self):
             "required": ["one", "two"],
             "additionalProperties": False,
         }
-        assert str(metadata.MetadataSchema(schema)) == pprint.pformat(schema)
+        assert (
+            str(metadata.MetadataSchema(schema))
+            == f"tskit.MetadataSchema(\n{pprint.pformat(schema)}\n)"
+        )
 
     def test_register_codec(self):
         class TestCodec(metadata.AbstractMetadataCodec):

python/tests/test_tables.py

@@ -1396,7 +1396,7 @@ def test_metadata_schema(self, table_5row):
             table2.metadata_schema = tskit.MetadataSchema({"codec": "json"})
             with pytest.raises(
                 AssertionError,
-                match=f"{type(table_5row).__name__} metadata schemas differ:",
+                match=f"{type(table_5row).__name__} metadata schemas differ: ",
             ):
                 table_5row.assert_equals(table2)
             table_5row.assert_equals(table2, ignore_metadata=True)
@@ -4089,7 +4089,7 @@ def test_metadata_schema(self, t1, t2):
         t2.metadata_schema = tskit.MetadataSchema(None)
         with pytest.raises(
             AssertionError,
-            match=re.escape("Metadata schemas differ"),
+            match=re.escape("Metadata schemas differ:"),
         ):
             t1.assert_equals(t2)
         t1.assert_equals(t2, ignore_metadata=True)
@@ -4193,7 +4193,7 @@ def test_ignore_reference_sequence(self, t1, t2):
         t2.reference_sequence.clear()
         with pytest.raises(
             AssertionError,
-            match=re.escape("Metadata schemas differ"),
+            match=re.escape("Metadata schemas differ: "),
         ):
             t1.assert_equals(t2)
         t1.assert_equals(t2, ignore_reference_sequence=True)

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 = "0.5.8.dev0"
+tskit_version = "0.5.9.dev0"

python/tskit/metadata.py

@@ -664,7 +664,14 @@ def __repr__(self) -> str:
         return self._string
 
     def __str__(self) -> str:
-        return pprint.pformat(self._schema)
+        if isinstance(self._schema, collections.OrderedDict):
+            s = pprint.pformat(dict(self._schema))
+        else:
+            s = pprint.pformat(self._schema)
+        if "\n" in s:
+            return f"tskit.MetadataSchema(\n{s}\n)"
+        else:
+            return f"tskit.MetadataSchema({s})"
 
     def __eq__(self, other) -> bool:
         return self._string == other._string