1.0.0 Release prep (#3342)

Author: benjeffery

c/CHANGELOG.rst

@@ -1,6 +1,6 @@
-----------
-Unreleased
-----------
+--------------------
+[1.3.0] - 2025-11-27
+--------------------
 
 **Breaking changes**
 
@@ -12,13 +12,13 @@ Unreleased
 **Features**
 
 - ``tsk_variant_init`` and associated variant decoding methods now
-  fully support TSK_ISOLATED_NOT_MISSING not being set for internal nodes.
+  fully support ``TSK_ISOLATED_NOT_MISSING`` not being set for internal nodes.
   (:user:`benjeffery`, :pr:`3313`)
 
 - Add ``tsk_treeseq_decode_alignments`` to decode full-length reference-based
   sequence alignments for specified nodes over a genomic interval, respecting
   ``TSK_ISOLATED_NOT_MISSING`` semantics.
-  (:user:`benjeffery` , :pr:`3324`, :issue:`3319`)
+  (:user:`benjeffery`, :pr:`3324`, :issue:`3319`)
 
 
 --------------------

c/VERSION.txt

@@ -1 +1 @@
-1.2.0
+1.3.0

c/tskit/core.h

@@ -147,7 +147,7 @@ sizes and types of externally visible structs.
 The library minor version. Incremented when non-breaking backward-compatible changes
 to the API or ABI are introduced, i.e., the addition of a new function.
 */
-#define TSK_VERSION_MINOR   2
+#define TSK_VERSION_MINOR   3
 /**
 The library patch version. Incremented when any changes not relevant to the
 to the API or ABI are introduced, i.e., internal refactors of bugfixes.

python/CHANGELOG.rst

@@ -1,74 +1,67 @@
-----------
-Unreleased
-----------
-
-**Features**
-
-- ``TreeSequence.variants``, ``.genotype_matrix``, ``.haplotypes``, and ``.alignments`` methods
-  now fully support ``isolated_as_missing`` behaviour with internal nodes. ``.alignments`` is
-  also around 10% faster.
-  (:user:`benjeffery`, :pr:`3313`, :pr:`3317`, :issue:`1896`)
+--------------------
+[1.0.0] - 2025-11-27
+--------------------
 
-**Breaking Changes**
+**Breaking changes**
 
-- The ``reference_sequence`` argument to ``TreeSequence.alignments`` is now required
-  to be the same length as the tree sequence. Previously it was required to be the length
-  of the requested interval.
+- The ``reference_sequence`` argument to ``TreeSequence.alignments`` is now
+  required to be the same length as the tree sequence. Previously it was
+  required to be the length of the requested interval.
   (:user:`benjeffery`, :pr:`3317`)
 
-----------------------
-[1.0.0b3] - 2025-10-15
-----------------------
-
-**Breaking Changes**
-
 - ``TreeSequence.tables`` now returns a zero-copy immutable view of the tables.
   To get a mutable copy, use ``TreeSequence.dump_tables()``.
   (:user:`benjeffery`, :pr:`3288`, :issue:`760`)
 
-- For a tree sequence to be valid mutation parents in the table collection
+- For a tree sequence to be valid, the mutation parents in the table collection
   must be correct and consistent with the topology of the tree at each mutation site.
   ``TableCollection.tree_sequence()`` will raise a ``_tskit.LibraryError`` if this
   is not the case.
   (:user:`benjeffery`, :issue:`2729`, :issue:`2732`, :pr:`3212`).
 
-- Drop Python 3.9 support, require Python >= 3.10 (:pr:`3267`, :user:`benjeffery`)
+- Drop Python 3.9 support and require Python >= 3.10.
+  (:pr:`3267`, :user:`benjeffery`)
 
+- ``ltrim``, ``rtrim``, ``trim`` and ``shift`` raise an error if they are
+  used on a tree sequence containing a reference sequence.
+  (:user:`hyanwong`, :pr:`3210`, :issue:`2091`)
 
 **Features**
 
 - Add ``tskit.jit.numba.jitwrap`` and ``NumbaTreeSequence`` to allow simplified
-  use and development of numba-jitted functions with tree sequences. See the 
+  use and development of Numba-jitted functions with tree sequences. See the
   `documentation <https://tskit.dev/tskit/docs/stable/numba.html>`_ for details.
   (:user:`andrewkern`, :pr:`3295`, :issue:`3294`)
 
 - ``TreeSequence.map_to_vcf_model`` now also returns the transformed positions and
   contig length. (:user:`benjeffery`, :pr:`3174`, :issue:`3173`)
 
-- ``draw_svg()`` methods now associate tree branches with edge IDs
+- ``draw_svg()`` methods now associate tree branches with edge IDs.
   (:user:`hyanwong`, :pr:`3193`, :issue:`557`)
 
 - ``draw_svg()`` methods now allow the y-axis to be placed on the right-hand side
-  using ``y_axis="right"`` (:user:`hyanwong`, :pr:`3201`)
+  using ``y_axis="right"``. (:user:`hyanwong`, :pr:`3201`)
 
 - Add ``contig_id`` and ``isolated_as_missing`` to ``VcfModelMapping``
-  (:user:`benjeffery`, :pr:`3219`, :issue:`3177`)
+  (:user:`benjeffery`, :pr:`3219`, :issue:`3177`).
 
-- Add ``TreeSequence.mutations_edge`` which returns the edge ID for each mutation's
+- Add ``TreeSequence.mutations_edge``, which returns the edge ID for each mutation's
   edge. (:user:`benjeffery`, :pr:`3226`, :issue:`3189`)
 
 - Add ``TreeSequence.sites_ancestral_state``, ``TreeSequence.mutations_derived_state`` and
-  ``TreeSequence.mutations_inherited_state`` properties  to return the ancestral state of sites,
-  derived state of mutations and inherited state of mutations as NumPy arrays of
-  the new numpy 2.0 StringDType.
+  ``TreeSequence.mutations_inherited_state`` properties to return the ancestral state of sites,
+  the derived state of mutations and the inherited state of mutations as NumPy arrays of
+  the new NumPy 2.0 ``StringDType``.
   (:user:`benjeffery`, :pr:`3228`, :issue:`2632`, :pr:`3276`, :issue:`2631`)
 
-- Tskit now distributes with a requirement of numpy version 2 or greater. However, you can still use
-  tskit with numpy 1.X by building tskit from source with numpy 1.X using ``pip install tskit --no-binary tskit``.
-  With numpy 1.X, any use of the new StringDType properties will result in a ``RuntimeError``.
-  If you try to use another python module that was compiled against numpy 1.X with numpy 2.X you may see
-  the error "A module that was compiled using NumPy 1.x cannot be run in NumPy 2.0.0 as it may crash.".
-  If no newer version of the module is available you will have to use the Numpy 1.X build as above.
+- Tskit now requires NumPy version 2 or later. However, you can still use
+  tskit with NumPy 1.x by building tskit from source with NumPy 1.x using
+  ``pip install tskit --no-binary tskit``. With NumPy 1.x, any use of the new
+  ``StringDType`` properties will result in a ``RuntimeError``. If you try to
+  use another Python module that was compiled against NumPy 1.x with NumPy 2.x
+  you may see the error "A module that was compiled using NumPy 1.x cannot be
+  run in NumPy 2.0.0 as it may crash.". If no newer version of the module is
+  available you will have to use the NumPy 1.x build as above.
 
 - Add ``Mutation.inherited_state`` property which returns the inherited state
   for a single mutation. (:user:`benjeffery`, :pr:`3277`, :issue:`2631`)
@@ -79,6 +72,11 @@ Unreleased
 
 - Add ``TreeSequence.divergence_matrix``, which was previously undocumented.
 
+- ``TreeSequence.variants``, ``.genotype_matrix``, ``.haplotypes``, and ``.alignments`` methods
+  now fully support ``isolated_as_missing`` behaviour with internal nodes. ``.alignments`` is
+  also around 10% faster.
+  (:user:`benjeffery`, :pr:`3313`, :pr:`3317`, :issue:`1896`)
+
 **Bugfixes**
 
 - In some tables with mutations out-of-order ``TableCollection.sort`` did not re-order
@@ -89,16 +87,17 @@ Unreleased
   their original order in the tables. (:user:`benjeffery`, :pr:`3257`, :issue:`3253`)
 
 - Fix bug in ``TreeSequence.genetic_relatedness_vector`` that previously ignored
-    ``span_normalise``: previously, ``span_normalise`` was always set to ``False``;
-    now the default is ``True`` in agreement with other statistics, so the returned
-    values will change. (:user:`petrelharp`, :pr:`3300`, :issue:`3241`)
+  ``span_normalise``: previously, ``span_normalise`` was always set to ``False``;
+  now the default is ``True`` in agreement with other statistics, so the returned
+  values will change. (:user:`petrelharp`, :pr:`3300`, :issue:`3241`)
 
 - Fix bug in ``TreeSequence.pair_coalescence_counts`` when ``span_normalise=True``
   and a window breakpoint falls within an internal missing interval.
   (:user:`nspope`, :pr:`3176`, :issue:`3175`)
 
-- Fix metadata schemas that are equal but have different byte representations not being equal
-  when using ``TableCollection.assert_equals`` and ``Table.assert_equals``.
+- Fix metadata schemas that are equal but have different byte representations not
+  being considered equal when using ``TableCollection.assert_equals`` and
+  ``Table.assert_equals``.
   (:user:`benjeffery`, :pr:`3246`, :issue:`3244`)
 
 - k-way statistics no longer require k sample sets, allowing in particular
@@ -110,18 +109,13 @@ Unreleased
   values with mutations over roots.
   (:user:`benjeffery`, :pr:`3274`, :issue:`3273`)
 
-- Prevent iterating over a ``TopologyCounter``
-  (:user:`benjeffery` , :pr:`3202`, :issue:`1462`)
+- Prevent iterating over a ``TopologyCounter``.
+  (:user:`benjeffery`, :pr:`3202`, :issue:`1462`)
 
 - Fix ``TreeSequence.concatenate()`` to work with internal samples by using the
-  ``all_mutations`` and ``all_edges`` parameters in ``union()``
+  ``all_mutations`` and ``all_edges`` parameters in ``union()``.
   (:user:`hyanwong`, :pr:`3283`, :issue:`3181`)
 
-**Breaking changes**
-
-- ``ltrim``, ``rtrim``, ``trim`` and ``shift`` raise an error if used on a tree sequence
-  containing a reference sequence (:user:`hyanwong`, :pr:`3210`, :issue:`2091`)
-
 --------------------
 [0.6.4] - 2025-05-21
 --------------------

python/tests/test_immutable_table_collection.py

@@ -498,6 +498,11 @@ def test_immutable_has_method_or_mutator(self, ts_fixture):
         for name in dir(tc):
             if name.startswith("_"):
                 continue
+            # Use getattr_static first so we don't trigger properties like
+            # the deprecated ``name_map`` attribute, which emits warnings.
+            attr = inspect.getattr_static(tc, name)
+            if isinstance(attr, property):
+                continue
             attr = getattr(tc, name)
             if inspect.ismethod(attr) and getattr(attr, "__self__", None) is tc:
                 tc_methods.append(name)

python/tests/test_lowlevel.py

@@ -5089,7 +5089,7 @@ def test_kastore_version(self):
 
     def test_tskit_version(self):
         version = _tskit.get_tskit_version()
-        assert version == (1, 2, 0)
+        assert version == (1, 3, 0)
 
     def test_tskit_version_file(self):
         maj, min_, patch = _tskit.get_tskit_version()

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 = "1.0.0b3"
+tskit_version = "1.0.0"