From 7eecb172c17f113a4d97aca538ab9f2df85cc9c1 Mon Sep 17 00:00:00 2001 From: Ben Jeffery Date: Fri, 27 Nov 2020 10:40:39 +0000 Subject: [PATCH] 0.3.3 prep --- c/CHANGELOG.rst | 15 +++++----- python/CHANGELOG.rst | 59 ++++++++++++++++++++-------------------- python/tskit/_version.py | 2 +- 3 files changed, 37 insertions(+), 39 deletions(-) diff --git a/c/CHANGELOG.rst b/c/CHANGELOG.rst index 43c71b192d..4ef13f775f 100644 --- a/c/CHANGELOG.rst +++ b/c/CHANGELOG.rst @@ -1,5 +1,5 @@ --------------------- -[0.99.8] - 2020-XX-XX +[0.99.8] - 2020-11-27 --------------------- **Breaking changes** @@ -8,16 +8,15 @@ and table equality methods to allow for more flexible equality criteria (e.g., ignore top-level metadata and schema or provenance tables). Existing code should add an extra final parameter ``0`` to retain the - current behaviour. (:user:`mufernando`, :user:`jeromekelleher`, + current behaviour (:user:`mufernando`, :user:`jeromekelleher`, :issue:`896`, :pr:`897`, :issue:`913`, :pr:`917`). - Changed default behaviour of ``tsk_table_collection_clear`` to not clear provenances and added ``options`` argument to optionally clear provenances - and schemas. - (:user:`benjeffery`, :issue:`929`, :pr:`1001`) + and schemas (:user:`benjeffery`, :issue:`929`, :pr:`1001`). -- Exposed ``tsk_table_collection_set_indexes`` to the API. - (:user:`benjeffery`, :issue:`870`, :pr:`921`) +- Exposed ``tsk_table_collection_set_indexes`` to the API + (:user:`benjeffery`, :issue:`870`, :pr:`921`). - Renamed ``ts.trait_regression`` to ``ts.trait_linear_model``. @@ -26,10 +25,10 @@ --------------------- - Added ``TSK_INCLUDE_TERMINAL`` option to ``tsk_diff_iter_init`` to output the last edges - at the end of a tree sequence (:user:`hyanwong`, :issue:`783`, :pr:`787`) + at the end of a tree sequence (:user:`hyanwong`, :issue:`783`, :pr:`787`). - Added ``tsk_bug_assert`` for assertions that should be compiled into release binaries - (:user:`benjeffery`, :pr:`860`) + (:user:`benjeffery`, :pr:`860`). --------------------- [0.99.6] - 2020-09-04 diff --git a/python/CHANGELOG.rst b/python/CHANGELOG.rst index bd654f0249..7b1d9410dc 100644 --- a/python/CHANGELOG.rst +++ b/python/CHANGELOG.rst @@ -1,15 +1,15 @@ -------------------- -[0.X.X] - 2020-XX-XX +[0.3.3] - 2020-11-27 -------------------- **Features** - Expose ``TreeSequence.coiterate()`` method to allow iteration over 2 sequences - simultaneously, aiding comparison of trees from two sequences. - (:user:`jeromekelleher`, :user:`hyanwong`, :issue:`1021`, :pr:`1022`) + simultaneously, aiding comparison of trees from two sequences + (:user:`jeromekelleher`, :user:`hyanwong`, :issue:`1021`, :pr:`1022`). -- tskit is now supported on, and has wheels for, python3.9. - (:user:`benjeffery`, :issue:`982`, :pr:`907`) +- tskit is now supported on, and has wheels for, python3.9 + (:user:`benjeffery`, :issue:`982`, :pr:`907`). - ``Tree.newick()`` now has extra option ``include_branch_lengths`` to allow branch lengths to be omitted (:user:`hyanwong`, :pr:`931`). @@ -22,56 +22,55 @@ - Added ``equals`` method to TreeSequence, TableCollection and each of the tables which provides more flexible equality comparisons, for example, allowing - users to ignore metadata or provenance in the comparison. + users to ignore metadata or provenance in the comparison (:user:`mufernando`, :user:`jeromekelleher`, :issue:`896`, :pr:`897`, :issue:`913`, :pr:`917`). -- Added ``__eq__`` to TreeSequence. - (:user:`benjeffery`, :issue:`1011`, :pr:`1020`) +- Added ``__eq__`` to TreeSequence + (:user:`benjeffery`, :issue:`1011`, :pr:`1020`). - ``ts.dump`` and ``tskit.load`` now support reading and writing file objects such as - FIFOs and sockets. (:user:`benjeffery`, :issue:`657`, :pr:`909`) + FIFOs and sockets (:user:`benjeffery`, :issue:`657`, :pr:`909`). -- Added ``tskit.write_ms`` for writing to MS format. - (:user:`saurabhbelsare`, :issue:`727`, :pr:`854`) +- Added ``tskit.write_ms`` for writing to MS format + (:user:`saurabhbelsare`, :issue:`727`, :pr:`854`). -- Added ``TableCollection.indexes`` for access to the edge insertion/removal order indexes. - (:user:`benjeffery`, :issue:`4`, :pr:`916`) +- Added ``TableCollection.indexes`` for access to the edge insertion/removal order indexes + (:user:`benjeffery`, :issue:`4`, :pr:`916`). -- The dictionary representation of a TableCollection now contains its index. - (:user:`benjeffery`, :issue:`870`, :pr:`921`) +- The dictionary representation of a TableCollection now contains its index + (:user:`benjeffery`, :issue:`870`, :pr:`921`). -- Added ``TreeSequence._repr_html_`` for use in jupyter notebooks. - (:user:`benjeffery`, :issue:`872`, :pr:`923`) +- Added ``TreeSequence._repr_html_`` for use in jupyter notebooks + (:user:`benjeffery`, :issue:`872`, :pr:`923`). -- Added ``TreeSequence.__str__`` to display a summary for terminal usage. - (:user:`benjeffery`, :issue:`938`, :pr:`985`) +- Added ``TreeSequence.__str__`` to display a summary for terminal usage + (:user:`benjeffery`, :issue:`938`, :pr:`985`). - Added ``TableCollection.dump`` and ``TableCollection.load``. This allows table - collections that are not valid tree sequences to be manipulated. - (:user:`benjeffery`, :issue:`14`, :pr:`986`) + collections that are not valid tree sequences to be manipulated + (:user:`benjeffery`, :issue:`14`, :pr:`986`). - Added ``nbytes`` method to tables, ``TableCollection`` and ``TreeSequence`` which - reports the size in bytes of those objects. - (:user:`jeromekelleher`, :user:`benjeffery`, :issue:`54`, :pr:`871`) + reports the size in bytes of those objects + (:user:`jeromekelleher`, :user:`benjeffery`, :issue:`54`, :pr:`871`). - Added ``TableCollection.clear`` to clear data table rows and optionally - provenances, table schemas and tree-sequence level metadata and schema. - (:user:`benjeffery`, :issue:`929`, :pr:`1001`) + provenances, table schemas and tree-sequence level metadata and schema + (:user:`benjeffery`, :issue:`929`, :pr:`1001`). **Bugfixes** - ``LightWeightTableCollection.asdict`` and ``TableCollection.asdict`` now return copies - of arrays. - (:user:`benjeffery`, :issue:`1025`, :pr:`1029`) + of arrays (:user:`benjeffery`, :issue:`1025`, :pr:`1029`). - The ``map_mutations`` method previously used the Fitch parsimony method, but this does not produce parsimonious results on non-binary trees. We now now use the - Hartigan parsimony algorithm, which does. (:user:`jeromekelleher`, + Hartigan parsimony algorithm, which does (:user:`jeromekelleher`, :issue:`987`, :pr:`1030`). -- The ``flag`` argument to tables' ``add_row`` was treating the value as signed. - (:user:`benjeffery`, :issue:`1027`, :pr:`1031`) +- The ``flag`` argument to tables' ``add_row`` was treating the value as signed + (:user:`benjeffery`, :issue:`1027`, :pr:`1031`). **Breaking changes** diff --git a/python/tskit/_version.py b/python/tskit/_version.py index e22ff8781f..054a5e037e 100644 --- a/python/tskit/_version.py +++ b/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 = "0.3.3.dev1" +tskit_version = "0.3.3"