.. This file is automatically generated by setup.py from README.md and CHANGELOG.md.

intervaltree
============

A mutable, self-balancing interval tree for Python 2 and 3. Queries may
be by point, by range overlap, or by range envelopment.

This library was designed to allow tagging text and time intervals,
where the intervals include the lower bound but not the upper bound.

Installing
----------

.. code:: sh

    pip install intervaltree

Features
--------

-  Supports Python 2.6+ and Python 3.2+
-  Initializing

   -  blank ``tree = IntervalTree()``
   -  from an iterable of ``Interval`` objects
      (``tree = IntervalTree(intervals)``)
   -  from an iterable of tuples
      (``tree = IntervalTree.from_tuples(interval_tuples)``)

-  Insertions

   -  ``tree[begin:end] = data``
   -  ``tree.add(interval)``
   -  ``tree.addi(begin, end, data)``

-  Deletions

   -  ``tree.remove(interval)`` (raises ``ValueError`` if not present)
   -  ``tree.discard(interval)`` (quiet if not present)
   -  ``tree.removei(begin, end, data)`` (short for
      ``tree.remove(Interval(begin, end, data))``)
   -  ``tree.discardi(begin, end, data)`` (short for
      ``tree.discard(Interval(begin, end, data))``)
   -  ``tree.remove_overlap(point)``
   -  ``tree.remove_overlap(begin, end)`` (removes all overlapping the
      range)
   -  ``tree.remove_envelop(begin, end)`` (removes all enveloped in the
      range)

-  Overlap queries

   -  ``tree[point]``
   -  ``tree[begin:end]``
   -  ``tree.search(point)``
   -  ``tree.search(begin, end)``

-  Envelop queries

   -  ``tree.search(begin, end, strict=True)``

-  Membership queries

   -  ``interval_obj in tree`` (this is fastest, O(1))
   -  ``tree.containsi(begin, end, data)``
   -  ``tree.overlaps(point)``
   -  ``tree.overlaps(begin, end)``

-  Iterable

   -  ``for interval_obj in tree:``
   -  ``tree.items()``

-  Sizing

   -  ``len(tree)``
   -  ``tree.is_empty()``
   -  ``not tree``
   -  ``tree.begin()`` (the ``begin`` coordinate of the leftmost
      interval)
   -  ``tree.end()`` (the ``end`` coordinate of the rightmost interval)

-  Set-like operations

   -  union

      -  ``result_tree = tree.union(iterable)``
      -  ``result_tree = tree1 | tree2``
      -  ``tree.update(iterable)``
      -  ``tree |= other_tree``

   -  difference

      -  ``result_tree = tree.difference(iterable)``
      -  ``result_tree = tree1 - tree2``
      -  ``tree.difference_update(iterable)``
      -  ``tree -= other_tree``

   -  intersection

      -  ``result_tree = tree.intersection(iterable)``
      -  ``result_tree = tree1 & tree2``
      -  ``tree.intersection_update(iterable)``
      -  ``tree &= other_tree``

   -  symmetric difference

      -  ``result_tree = tree.symmetric_difference(iterable)``
      -  ``result_tree = tree1 ^ tree2``
      -  ``tree.symmetric_difference_update(iterable)``
      -  ``tree ^= other_tree``

   -  comparison

      -  ``tree1.issubset(tree2)`` or ``tree1 <= tree2``
      -  ``tree1 <= tree2``
      -  ``tree1.issuperset(tree2)`` or ``tree1 > tree2``
      -  ``tree1 >= tree2``
      -  ``tree1 == tree2``

-  Restructuring

   -  ``chop(begin, end)`` (slice intervals and remove everything
      between ``begin`` and ``end``)
   -  ``slice(point)`` (slice intervals at ``point``)
   -  ``split_overlaps()`` (slice at all interval boundaries)

-  Copying and typecasting

   -  ``IntervalTree(tree)`` (``Interval`` objects are same as those in
      tree)
   -  ``tree.copy()`` (``Interval`` objects are shallow copies of those
      in tree)
   -  ``set(tree)`` (can later be fed into ``IntervalTree()``)
   -  ``list(tree)`` (ditto)

-  Pickle-friendly
-  Automatic AVL balancing

Examples
--------

-  Getting started

   .. code:: python

       >>> from intervaltree import Interval, IntervalTree
       >>> t = IntervalTree()
       >>> t
       IntervalTree()

-  Adding intervals - any object works!

   .. code:: python

       >>> t[1:2] = "1-2"
       >>> t[4:7] = (4, 7)
       >>> t[5:9] = {5: 9}

-  Query by point

   | The result of a query is a ``set`` object, so if ordering is
     important,
   | you must sort it first.

   .. code:: python

       >>> sorted(t[6])
       [Interval(4, 7, (4, 7)), Interval(5, 9, {5: 9})]
       >>> sorted(t[6])[0]
       Interval(4, 7, (4, 7))

-  Query by range

   Note that ranges are inclusive of the lower limit, but non-inclusive
   of the upper limit. So:

   .. code:: python

       >>> sorted(t[2:4])
       []

   But:

   .. code:: python

       >>> sorted(t[1:5])
       [Interval(1, 2, '1-2'), Interval(4, 7, (4, 7))]

-  Accessing an ``Interval`` object

   .. code:: python

       >>> iv = Interval(4, 7, (4, 7))
       >>> iv.begin
       4
       >>> iv.end
       7
       >>> iv.data
       (4, 7)

       >>> begin, end, data = iv
       >>> begin
       4
       >>> end
       7
       >>> data
       (4, 7)

-  Constructing from lists of intervals

   We could have made a similar tree this way:

   .. code:: python

       >>> ivs = [(1, 2), (4, 7), (5, 9)]
       >>> t = IntervalTree(
       ...    Interval(begin, end, "%d-%d" % (begin, end)) for begin, end in ivs
       ... )

   Or, if we don't need the data fields:

   .. code:: python

       >>> t2 = IntervalTree(Interval(*iv) for iv in ivs)

-  Removing intervals

   .. code:: python

       >>> t.remove( Interval(1, 2, "1-2") )
       >>> sorted(t)
       [Interval(4, 7, '4-7'), Interval(5, 9, '5-9')]

       >>> t.remove( Interval(500, 1000, "Doesn't exist"))  # raises ValueError
       Traceback (most recent call last):
       ValueError

       >>> t.discard(Interval(500, 1000, "Doesn't exist"))  # quietly does nothing

       >>> del t[5]  # same as t.remove_overlap(5)
       >>> t
       IntervalTree()

   We could also empty a tree entirely:

   .. code:: python

       >>> t2.clear()
       >>> t2
       IntervalTree()

   Or remove intervals that overlap a range:

   .. code:: python

       >>> t = IntervalTree([
       ...     Interval(0, 10), 
       ...     Interval(10, 20), 
       ...     Interval(20, 30), 
       ...     Interval(30, 40)])
       >>> t.remove_overlap(25, 35)
       >>> sorted(t)
       [Interval(0, 10), Interval(10, 20)]

   We can also remove only those intervals completely enveloped in a
   range:

   .. code:: python

       >>> t.remove_envelop(5, 20)
       >>> sorted(t)
       [Interval(0, 10)]

-  Chopping

   We could also chop out parts of the tree:

   .. code:: python

       >>> t = IntervalTree([Interval(0, 10)])
       >>> t.chop(3, 7)
       >>> sorted(t)
       [Interval(0, 3), Interval(7, 10)]

   To modify the new intervals' data fields based on which side of the
   interval is being chopped:

   .. code:: python

       >>> def datafunc(iv, islower):
       ...     oldlimit = iv[islower]
       ...     return "oldlimit: {0}, islower: {1}".format(oldlimit, islower)
       >>> t = IntervalTree([Interval(0, 10)])
       >>> t.chop(3, 7, datafunc)
       >>> sorted(t)[0]
       Interval(0, 3, 'oldlimit: 10, islower: True')
       >>> sorted(t)[1]
       Interval(7, 10, 'oldlimit: 0, islower: False')

-  Slicing

   You can also slice intervals in the tree without removing them:

   .. code:: python

       >>> t = IntervalTree([Interval(0, 10), Interval(5, 15)])
       >>> t.slice(3)
       >>> sorted(t)
       [Interval(0, 3), Interval(3, 10), Interval(5, 15)]

   You can also set the data fields, for example, re-using
   ``datafunc()`` from above:

   .. code:: python

       >>> t = IntervalTree([Interval(5, 15)])
       >>> t.slice(10, datafunc)
       >>> sorted(t)[0]
       Interval(5, 10, 'oldlimit: 15, islower: True')
       >>> sorted(t)[1]
       Interval(10, 15, 'oldlimit: 5, islower: False')

Future improvements
-------------------

See the issue tracker on GitHub.

Based on
--------

-  Eternally Confuzzled's AVL tree
-  Wikipedia's Interval Tree
-  Heavily modified from Tyler Kahn's Interval Tree implementation in
   Python (GitHub project)
-  Incorporates contributions from:

   -  konstantint/Konstantin Tretyakov of the University of Tartu
      (Estonia)
   -  siniG/Avi Gabay
   -  lmcarril/Luis M. Carril of the Karlsruhe Institute for Technology
      (Germany)

Copyright
---------

-  Chaim-Leib Halbert, 2013-2015
-  Modifications, Konstantin Tretyakov, 2014

Licensed under the Apache License, version 2.0.

The source code for this project is at
https://github.com/chaimleib/intervaltree

Change log
==========

Version 2.1.0
-------------

-  Added:

   -  ``merge_overlaps()`` method and tests
   -  ``merge_equals()`` method and tests
   -  ``range()`` method
   -  ``span()`` method, for returning the difference between ``end()``
      and ``begin()``

-  Fixes:

   -  Development version numbering is changing to be compliant with
      PEP440. Version numbering now contains major, minor and micro
      release numbers, plus the number of builds following the stable
      release version, e.g. 2.0.4b34
   -  Speed improvement: ``begin()`` and ``end()`` methods used
      iterative ``min()`` and ``max()`` builtins instead of the more
      efficient ``iloc`` member available to ``SortedDict``
   -  ``overlaps()`` method used to return ``True`` even if provided
      null test interval

-  Maintainers:

   -  Added coverage test (``make coverage``) with html report
      (``htmlcov/index.html``)
   -  Tests run slightly faster

Version 2.0.4
-------------

-  Fix: Issue #27: README incorrectly showed using a comma instead of a
   colon when querying the ``IntervalTree``: it showed
   ``tree[begin, end]`` instead of ``tree[begin:end]``

Version 2.0.3
-------------

-  Fix: README showed using + operator for setlike union instead of the
   correct \| operator
-  Removed tests from release package to speed up installation; to get
   the tests, download from GitHub

Version 2.0.2
-------------

-  Fix: Issue #20: performance enhancement for large trees.
   ``IntervalTree.search()`` made a copy of the entire
   ``boundary_table`` resulting in linear search time. The
   ``sortedcollections`` package is now the sole install dependency

Version 2.0.1
-------------

-  Fix: Issue #26: failed to prune empty ``Node`` after a rotation
   promoted contents of ``s_center``

Version 2.0.0
-------------

-  ``IntervalTree`` now supports the full ``collections.MutableSet`` API
-  Added:

   -  ``__delitem__`` to ``IntervalTree``
   -  ``Interval`` comparison methods ``lt()``, ``gt()``, ``le()`` and
      ``ge()`` to ``Interval``, as an alternative to the comparison
      operators, which are designed for sorting
   -  ``IntervalTree.from_tuples(iterable)``
   -  ``IntervalTree.clear()``
   -  ``IntervalTree.difference(iterable)``
   -  ``IntervalTree.difference_update(iterable)``
   -  ``IntervalTree.union(iterable)``
   -  ``IntervalTree.intersection(iterable)``
   -  ``IntervalTree.intersection_update(iterable)``
   -  ``IntervalTree.symmetric_difference(iterable)``
   -  ``IntervalTree.symmetric_difference_update(iterable)``
   -  ``IntervalTree.chop(a, b)``
   -  ``IntervalTree.slice(point)``

-  Deprecated ``IntervalTree.extend()`` -- use ``update()`` instead
-  Internal improvements:

   -  More verbose tests with progress bars
   -  More tests for comparison and sorting behavior
   -  Code in the README is included in the unit tests

-  Fixes

   -  BACKWARD INCOMPATIBLE: On ranged queries where ``begin >= end``,
      the query operated on the overlaps of ``begin``. This behavior was
      documented as expected in 1.x; it is now changed to be more
      consistent with the definition of ``Interval``\ s, which are
      half-open.
   -  Issue #25: pruning empty Nodes with staggered descendants could
      result in invalid trees
   -  Sorting ``Interval``\ s and numbers in the same list gathered all
      the numbers at the beginning and the ``Interval``\ s at the end
   -  ``IntervalTree.overlaps()`` and friends returned ``None`` instead
      of ``False``
   -  Maintainers: ``make install-testpypi`` failed because the ``pip``
      was missing a ``--pre`` flag

Version 1.1.1
-------------

-  Removed requirement for pyandoc in order to run functionality tests.

Version 1.1.0
-------------

-  Added ability to use ``Interval.distance_to()`` with points, not just
   ``Intervals``
-  Added documentation on return types to ``IntervalTree`` and
   ``Interval``
-  ``Interval.__cmp__()`` works with points too
-  Fix: ``IntervalTree.score()`` returned maximum score of 0.5 instead
   of 1.0. Now returns max of subscores instead of avg
-  Internal improvements:

   -  Development version numbering scheme, based on ``git describe``
      the "building towards" release is appended after a hyphen, eg.
      1.0.2-37-g2da2ef0-1.10. The previous tagged release is 1.0.2, and
      there have been 37 commits since then, current tag is g2da2ef0,
      and we are getting ready for a 1.1.0 release
   -  Optimality tests added
   -  ``Interval`` overlap tests for ranges, ``Interval``\ s and points
      added

Version 1.0.2
-------------

| -Bug fixes:
|  - ``Node.depth_score_helper()`` raised ``AttributeError``
|  - README formatting

Version 1.0.1
-------------

-  Fix: pip install failure because of failure to generate README.rst

Version 1.0.0
-------------

-  Renamed from PyIntervalTree to intervaltree
-  Speed improvements for adding and removing Intervals (~70% faster
   than 0.4)
-  Bug fixes:

   -  BACKWARD INCOMPATIBLE: ``len()`` of an ``Interval`` is always 3,
      reverting to default behavior for ``namedtuples``. In Python 3,
      ``len`` returning a non-integer raises an exception. Instead, use
      ``Interval.length()``, which returns 0 for null intervals and
      ``end - begin`` otherwise. Also, if the ``len() === 0``, then
      ``not iv`` is ``True``.
   -  When inserting an ``Interval`` via ``__setitem__`` and improper
      parameters given, all errors were transformed to ``IndexError``
   -  ``split_overlaps`` did not update the ``boundary_table`` counts

-  Internal improvements:

   -  More robust local testing tools
   -  Long series of interdependent tests have been separated into
      sections

Version 0.4
-----------

-  Faster balancing (~80% faster)
-  Bug fixes:

   -  Double rotations were performed in place of a single rotation when
      presented an unbalanced Node with a balanced child.
   -  During single rotation, kept referencing an unrotated Node instead
      of the new, rotated one

Version 0.3.3
-------------

-  Made IntervalTree crash if inited with a null Interval (end <= begin)
-  IntervalTree raises ValueError instead of AssertionError when a null
   Interval is inserted

Version 0.3.2
-------------

-  Support for Python 3.2+ and 2.6+
-  Changed license from LGPL to more permissive Apache license
-  Merged changes from https://github.com/konstantint/PyIntervalTree to
   https://github.com/chaimleib/PyIntervalTree

   -  Interval now inherits from a namedtuple. Benefits: should be
      faster.
      Drawbacks: slight behavioural change (Intervals not mutable
      anymore).
   -  Added float tests
   -  Use setup.py for tests
   -  Automatic testing via travis-ci
   -  Removed dependency on six

-  Interval improvements:

   -  Intervals without data have a cleaner string representation
   -  Intervals without data are pickled more compactly
   -  Better hashing
   -  Intervals are ordered by begin, then end, then by data. If data is
      not
      orderable, sorts by type(data)

-  Bug fixes:

   -  Fixed crash when querying empty tree
   -  Fixed missing close parenthesis in examples
   -  Made IntervalTree crash earlier if a null Interval is added

-  Internals:

   -  New test directory
   -  Nicer display of data structures for debugging, using custom
      test/pprint.py (Python 2.6, 2.7)
   -  More sensitive exception handling
   -  Local script to test in all supported versions of Python
   -  Added IntervalTree.score() to measure how optimally a tree is
      structured

Version 0.2.3
-------------

-  Slight changes for inclusion in PyPI.
-  Some documentation changes
-  Added tests
-  Bug fix: interval addition via [] was broken in Python 2.7 (see
   http://bugs.python.org/issue21785)
-  Added intervaltree.bio subpackage, adding some utilities for use in
   bioinformatics

Version 0.2.2b
--------------

-  Forked from https://github.com/MusashiAharon/PyIntervalTree
