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CHANGES.txt
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CHANGES.txt
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Changelog
=========
Version 1.3.5
-------------
Add Python 3.9 to test environments and tag support.
Version 1.3.4
-------------
Pin sqlalchemy dependency to version ``1.3.*``.
Add explicit ``.alias()`` or ``.as_scalar()`` to implicit subqueries.
Decrease progress logging verbosity.
Add test checksums for Glottolog v4.3-treedb-fixes.
Improve test reporting, update test environment.
Version 1.3.3
-------------
Restrict foreign key pragma and regexp operator to sqlite3 connections.
Version 1.3.2
-------------
Format timespan years with 4 digits.
Refactor recursive tree queries to improve code sharing.
Simplify stats query and ``iterdescendants()`` query.
Stats.ipynb: fix n_descendants query, add count to min/max boxes, plot more
frequency distributions.
Version 1.3.1
-------------
Fix default root (change from . to ./glottolog/ as documented).
Fix ``treedb.write_json_lines()`` under Python 3.6 when passed a file object.
Extend showcase notebook and test coverage.
Version 1.3
-----------
Add ``treedb.write_json_lines()``.
Use ``lang=None`` outside of the database (checksum change).
Version 1.2
-----------
Normalize providers and sites into lookup tables.
Fix exception when config file is not found.
Improve logging: log sqlite3.Connection to identify in-memory databases,
debug log package location.
Improve tests.
Version 1.1
-----------
Fix some aggregation orders in ``get_json_query()`` that depended on the
insertion order.
Fix ```get_query()`` link markup. Use the same aggregation order as
``get_json_query``.
Fixed ``treedb.iterdescendants()`` to include roots with no descencants.
Improve ``treedb.print_languoid_stats()`` performance and the query used for
the ``stats`` view.
Reduce file size adding WITHOUT ROWID to tables with non-integer or composite
primary keys.
Stabilize ``treedb.print_query_sql()`` notebook output with ``flush=True``.
Change __dataset__ and __producer__ primary key from BOOLEAN to INTEGER.
Use ``sqlite.sqlite_version`` instead of querying the engine.
Version 1.0
-----------
Build with Glottolog ``v4.2.1`` per default.
Improve ``treedb.print_schema()`` output for views.
Improve tests and logging.
Version 0.11
------------
Add support for the new optional core `timespan` field.
Add new test flags: --glottolog-repo-root and --force-rebuild.
Extend tests and integrate with Travis and Codevov.
Version 0.10
------------
Insert languoids in ``id`` order if possible.
Gzip dump-like csv files per default (bump csv23 to 0.3+).
Change default name of ``treedb.write_csv`` to ``treedb.query.csv```.
Register ``pandas`` as optional dependency.
Fix xenial compat. Fix Python 3.6 compat.
Fix re-load with ``exclude_raw``.
Improve logging.
Increase test coverage. Log ``sqlite_version()``.
Version 0.9
-----------
Add ``treedb.checkout_or_clone()``.
Add ``treedb.print_query_sql(pretty=True)`` formatting with ``sqlparse`` if
importable (``pip install treedb[pretty]`` to include it).
Improve query readability by adding unique labels.
Move recurse condition for ``Languoid.tree()`` from whereclause to join.
Add tests using ``pytest``.
Version 0.8.2
-------------
Add ``example`` view with ``treedb.get_query()``.
Reorganized `treedb.load()` to better support repeated changes to
`exclude_views`.
Version 0.8.1
-------------
Add ``roots`` (top-level languoids) count to ``treedb.print_languoid_stats()``.
Gzip-compress `treedb.dump_sql()` by default.
Fix reference to old license.
Add ``raw=False`` to ``treedb.write_json_query_csv()``.
Update documentation.
Version 0.8
-----------
Add ``stats`` and ``path_json`` SQL views.
Extend formatting of ``treedb.print_languoid_stats()```and warn in case of
inconsistencies.
Fix ``Languoid.tree(include_self=False)``.
Add names to query aliases for better SQL output.
Version 0.7.1
-------------
Add ``treedb.print_languoid_stats()`` (reproducing
https://glottolog.org/glottolog/glottologinformation).
Add ``treedb.write_json_query_csv()``. To support this,
``treedb.get_json_query()`` now yields pairs of path and languoid json
(instead of json of a two-item array with a path_part array as first element).
Version 0.7
-----------
Add ``treedb.configure()`` trying to read the Glottolog ``repo_root`` from
``treedb.ini`` in the current working directory.
Add ``logging`` config to the development environment as ``treedb.ini``
(write ``treedb.log``).
Added handling of present databases when loading from transient in-memory
database.
Add ``__producer__`` table recording the ``treedb`` package version used.
Version 0.6
-----------
Add ``treedb.checksum()``.
Version 0.5.1
-------------
Add ``replace`` kwarg to ``treedb.write_files()`` and
``treedb.raw.write_files()``.
Version 0.5
-----------
Add ``treeb.write_files()``.
Replace ``treedb.compare_with_raw(root, bind)`` with
``treedb.compare_with_files(bind, root)``.
Version 0.4
-----------
Add ``treedb.print_query_sql()`` for printing standalone SQL with literal
binds that can be pasted into query tools.
Normalize bibitem references (change database structure).
Version 0.3.1
-------------
Add missing ``os.path.expanduser()`` to ``treedb.export()``.
``treedb.pd_read_sql()`` now uses the default query when called without
argument.
Add ``csv23`` as dependency (factored out stream handling).
Version 0.3
-----------
Rename ``treedb.create_engine()`` to ``treedb.set_engine()``
(backwards incompatible).
Improve ``treedb.backup()`` implementation.
Add helper functions and shortcuts.
Refactor ``subprocess`` usage.
Improve logging.
Version 0.2.2
-------------
Add ``treedb.backup()`` (requires Python 3.7+).
Add ``exclude_raw=False`` to ``treedb.export()``.
Version 0.2.1
-------------
Fix ``treedb.write_csv()`` endangerment_source column output.
Use ``os.path.expanduser()`` on filename arguments.
Fix setup.py old license classifier.
Version 0.2
-----------
Drop Python 2 and 3.5 support.
Parse endangerment source references into individual fields.
Switch license to MIT license.
Version 0.1.6
-------------
Make endangerment sources open-ended.
Version 0.1.5
-------------
Update endangerment sources.
Add PyPI ``project_urls`` to setup.py.
Version 0.1.4
-------------
Represent countries as dicts instead of tuples in ``treedb.iterlanguoids()``.
Update endangerment sources.
Version 0.1.3
-------------
Update for new altname providers and endangerment sources in Glottolog 4.1.
Version 0.1.2
-------------
Use ``expanduser()``in ``treedb.create_engine()`` and ``treedb.set_root()``.
Version 0.1.1
-------------
Allow to specify glottolog repository location via ``TREEDB_REPO`` environment
variable (alternative to ``treedb.set_root()``).
Use current working as default Glottolog repository location if ``treedb`` is
imported as plain installed package instead of a git checkout.
Version 0.1
-----------
Initial release.