Red Black Tree implementation?

Discussion in 'Python' started by Dan Stromberg, May 2, 2013.

  1. What's the best Red Black Tree implementation for Python with an opensource
    license?

    I started out looking at
    http://newcenturycomputers.net/projects/rbtree.htmlbecause it was
    pretty high in Google and had the operators I wanted, but it
    gets very slow at about half a million elements. I've been discussing this
    with a C programmer who believes that Red Black Trees should perform very
    similarly to an AVL tree, but that's not at all what I'm getting with the
    newcenturycomputers implementation.

    I'd prefer something that looks like a dictionary, runs on 2.x and 3.x, and
    passes pylint, but if that's not yet available I might make it so.

    This is part of a comparison of Python tree types I did a while back...
    I've been thinking that I've given Red Black Trees short shrift by using a
    poor implementation. The comparison so far is at
    http://stromberg.dnsalias.org/~strombrg/python-tree-and-heap-comparison/

    Thanks!
    Dan Stromberg, May 2, 2013
    #1
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  2. Dan Stromberg

    duncan smith Guest

    On 02/05/13 00:11, Dan Stromberg wrote:
    >
    > What's the best Red Black Tree implementation for Python with an
    > opensource license?
    >
    > I started out looking at
    > http://newcenturycomputers.net/projects/rbtree.html because it was
    > pretty high in Google and had the operators I wanted, but it gets very
    > slow at about half a million elements. I've been discussing this with a
    > C programmer who believes that Red Black Trees should perform very
    > similarly to an AVL tree, but that's not at all what I'm getting with
    > the newcenturycomputers implementation.
    >
    > I'd prefer something that looks like a dictionary, runs on 2.x and 3.x,
    > and passes pylint, but if that's not yet available I might make it so.
    >
    > This is part of a comparison of Python tree types I did a while back...
    > I've been thinking that I've given Red Black Trees short shrift by using
    > a poor implementation. The comparison so far is at
    > http://stromberg.dnsalias.org/~strombrg/python-tree-and-heap-comparison/
    >
    > Thanks!
    >
    >



    I have an implementation that you can try out. It's not based on any
    other implementation, so my bugs will be independent of any bugs in the
    code you're currently using. It looks more like a set - add, remove,
    discard. Not tried on Python 3 or run through pylint. I just tried
    adding a million items to a tree, and it takes about 25% longer to add
    items at the end compared to those at the beginning. Timing removals
    uncovered a bug. So if you want the code I'll fix the bug and send it
    (to your gmail e-mail address?). Cheers.

    Duncan
    duncan smith, May 2, 2013
    #2
    1. Advertising

  3. On Wed, May 1, 2013 at 7:06 PM, duncan smith <>wrote:

    > I have an implementation that you can try out. It's not based on any other
    > implementation, so my bugs will be independent of any bugs in the code
    > you're currently using. It looks more like a set - add, remove, discard.
    > Not tried on Python 3 or run through pylint. I just tried adding a million
    > items to a tree, and it takes about 25% longer to add items at the end
    > compared to those at the beginning. Timing removals uncovered a bug. So if
    > you want the code I'll fix the bug and send it (to your gmail e-mail
    > address?). Cheers.
    >
    > Duncan
    > --
    > http://mail.python.org/**mailman/listinfo/python-list<http://mail.python.org/mailman/listinfo/python-list>
    >


    What license?

    Thanks!
    Dan Stromberg, May 3, 2013
    #3
  4. Dan Stromberg

    duncan smith Guest

    On 03/05/13 03:00, Dan Stromberg wrote:
    >
    > On Wed, May 1, 2013 at 7:06 PM, duncan smith <
    > <mailto:>> wrote:
    >
    > I have an implementation that you can try out. It's not based on any
    > other implementation, so my bugs will be independent of any bugs in
    > the code you're currently using. It looks more like a set - add,
    > remove, discard. Not tried on Python 3 or run through pylint. I just
    > tried adding a million items to a tree, and it takes about 25%
    > longer to add items at the end compared to those at the beginning.
    > Timing removals uncovered a bug. So if you want the code I'll fix
    > the bug and send it (to your gmail e-mail address?). Cheers.
    >
    > Duncan
    > --
    > http://mail.python.org/__mailman/listinfo/python-list
    > <http://mail.python.org/mailman/listinfo/python-list>
    >
    >
    > What license?
    >
    > Thanks!
    >


    Here's the text I usually prepend.


    ##Copyright (c) 2013 duncan g. smith
    ##
    ##Permission is hereby granted, free of charge, to any person obtaining a
    ##copy of this software and associated documentation files (the "Software"),
    ##to deal in the Software without restriction, including without limitation
    ##the rights to use, copy, modify, merge, publish, distribute, sublicense,
    ##and/or sell copies of the Software, and to permit persons to whom the
    ##Software is furnished to do so, subject to the following conditions:
    ##
    ##The above copyright notice and this permission notice shall be included
    ##in all copies or substantial portions of the Software.
    ##
    ##THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
    ##OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
    MERCHANTABILITY,
    ##FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
    ##THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
    ##OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
    ##ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
    ##OTHER DEALINGS IN THE SOFTWARE.


    Basically, "do what you want with it but don't blame me if it goes tits
    up". I'm happy to consider tidying it up a bit and using a more
    recognized form of licence. Just had a bank holiday here, so bug not yet
    squashed. But it is the sort of bug that might account for what you've
    seen (if a similar bug exists in the code you've been using). The tree
    doesn't always get properly rebalanced on node removals. I'll attack the
    problem later tomorrow (technically, later today). Cheers.

    Duncan
    duncan smith, May 7, 2013
    #4
  5. On Tue, May 7, 2013 at 10:55 AM, duncan smith <> wrote:
    > Here's the text I usually prepend.
    >
    >
    > ##Copyright (c) 2013 duncan g. smith
    > ##
    > ##Permission is hereby granted, free of charge, to any person obtaining a
    > ##copy of this software and associated documentation files (the "Software"),
    > ##to deal in the Software without restriction, including without limitation
    > ##the rights to use, copy, modify, merge, publish, distribute, sublicense,
    > ##and/or sell copies of the Software, and to permit persons to whom the
    > ##Software is furnished to do so, subject to the following conditions:
    > ##
    > ##The above copyright notice and this permission notice shall be included
    > ##in all copies or substantial portions of the Software.
    > ##
    > ##THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS
    > ##OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
    > MERCHANTABILITY,
    > ##FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL
    > ##THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR
    > ##OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
    > ##ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
    > ##OTHER DEALINGS IN THE SOFTWARE.
    >
    >
    > Basically, "do what you want with it but don't blame me if it goes tits up".
    > I'm happy to consider tidying it up a bit and using a more recognized form
    > of licence.


    Is that the MIT license? If not, consider using it; it's well known
    and trusted. I haven't eyeballed yours closely but it looks extremely
    similar, at least.

    ChrisA
    Chris Angelico, May 7, 2013
    #5
  6. Dan Stromberg

    duncan smith Guest

    On 07/05/13 02:20, Dan Stromberg wrote:
    >

    [snip]
    >
    > I'm starting to think Red Black Trees are pretty complex.
    >
    >


    A while ago I looked at a few different types of self-balancing binary
    tree. Most look much easier to implement.

    BTW, the licence might be MIT - I just copied it from someone else's code.

    Duncan
    duncan smith, May 7, 2013
    #6
  7. Dan Stromberg

    duncan smith Guest

    On 07/05/13 02:20, Dan Stromberg wrote:
    >
    > On Mon, May 6, 2013 at 5:55 PM, duncan smith <
    > <mailto:>> wrote:
    >
    >


    [snip]

    >
    > I'd prefer Apache or MIT or BSD 3-clause, but I could probably work with
    > this.
    > http://joinup.ec.europa.eu/community/eupl/news/licence-proliferation-way-out
    >
    > I'm eager to see the code, and would love it if you sorted out the
    > deletion rebalance issue.
    >
    > I just plunked some time into
    > https://github.com/headius/redblack/blob/master/red_black_tree.py , only
    > to find that it didn't appear to be doing deletions correctly - the tree
    > would become unprintable after deleting one element. It's possible I
    > introduced the bug, but right now I don't particularly suspect so,
    > having not changed the __del__ method.
    >
    > I'm starting to think Red Black Trees are pretty complex.
    >
    >


    Mine is fixed now (sent to your gmail address). Restoring the tree
    properties after deletion is awkward to get right, and doesn't affect
    the performance noticeably for smallish trees if you get it wrong.

    I realised my code was buggy when I tried adding, then removing a
    million items and ran into the recursion limit. It now passes a test
    where I check the tree properties after each addition / deletion.

    Duncan
    duncan smith, May 9, 2013
    #7
  8. OK, I've got one copy of trees.py with md5
    211f80c0fe7fb9cb42feb9645b4b3ffe. You seem to be saying I should have
    two though, but I don't know that I do...


    On 5/8/13, duncan smith <> wrote:
    > On 07/05/13 02:20, Dan Stromberg wrote:
    >>
    >> On Mon, May 6, 2013 at 5:55 PM, duncan smith <
    >> <mailto:>> wrote:
    >>
    >>

    >
    > [snip]
    >
    >>
    >> I'd prefer Apache or MIT or BSD 3-clause, but I could probably work with
    >> this.
    >> http://joinup.ec.europa.eu/community/eupl/news/licence-proliferation-way-out
    >>
    >> I'm eager to see the code, and would love it if you sorted out the
    >> deletion rebalance issue.
    >>
    >> I just plunked some time into
    >> https://github.com/headius/redblack/blob/master/red_black_tree.py , only
    >> to find that it didn't appear to be doing deletions correctly - the tree
    >> would become unprintable after deleting one element. It's possible I
    >> introduced the bug, but right now I don't particularly suspect so,
    >> having not changed the __del__ method.
    >>
    >> I'm starting to think Red Black Trees are pretty complex.
    >>
    >>

    >
    > Mine is fixed now (sent to your gmail address). Restoring the tree
    > properties after deletion is awkward to get right, and doesn't affect
    > the performance noticeably for smallish trees if you get it wrong.
    >
    > I realised my code was buggy when I tried adding, then removing a
    > million items and ran into the recursion limit. It now passes a test
    > where I check the tree properties after each addition / deletion.
    >
    > Duncan
    > --
    > http://mail.python.org/mailman/listinfo/python-list
    >
    Dan Stromberg, May 9, 2013
    #8
  9. Dan Stromberg

    duncan smith Guest

    On 09/05/13 02:40, Dan Stromberg wrote:
    > OK, I've got one copy of trees.py with md5
    > 211f80c0fe7fb9cb42feb9645b4b3ffe. You seem to be saying I should have
    > two though, but I don't know that I do...
    >
    >


    I've just re-sent it.

    Duncan
    duncan smith, May 9, 2013
    #9
  10. Dan Stromberg

    duncan smith Guest

    On 09/05/13 02:40, Dan Stromberg wrote:
    > OK, I've got one copy of trees.py with md5
    > 211f80c0fe7fb9cb42feb9645b4b3ffe. You seem to be saying I should have
    > two though, but I don't know that I do...
    >


    [snip]

    Yes, 211f80c0fe7fb9cb42feb9645b4b3ffe is the correct checksum for the
    latest version. The previous version had an issue when adding
    non-distinct items (items that compare equal to items already in the
    tree). Cheers.

    Duncan
    duncan smith, May 9, 2013
    #10
  11. I'm afraid I'm having some trouble with the module. I've checked it into
    my SVN at http://stromberg.dnsalias.org/svn/red-black-tree-mod/trunk/duncan

    I have two versions of your tests in there now - "t" is minimally changed,
    and test-red_black_tree_mod is pretty restructured to facilitate adding
    more tests later. I get the same problem with either version of the tests.

    The problem I'm seeing is that the tree, when built from items, isn't
    looking quite right. I inserted a print(tree) into the for loop, and I'm
    getting the following, where I expected the tree to grow by one element on
    each iteration:

    $ python t
    6 False None None
    6 False 3 None
    6 False 3 15
    6 False 3 15
    6 False 3 11
    6 False 3 11
    6 False 3 11
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15
    11 False 6 15

    Thoughts?

    BTW, printing an empty tree seems to say "sentinel". 'not sure if that was
    intended.

    Thanks!



    On Thu, May 9, 2013 at 6:52 AM, duncan smith <>wrote:

    > On 09/05/13 02:40, Dan Stromberg wrote:
    >
    >> OK, I've got one copy of trees.py with md5
    >> 211f80c0fe7fb9cb42feb9645b4b3f**fe. You seem to be saying I should have
    >> two though, but I don't know that I do...
    >>
    >>

    > [snip]
    >
    > Yes, 211f80c0fe7fb9cb42feb9645b4b3f**fe is the correct checksum for the
    > latest version. The previous version had an issue when adding non-distinct
    > items (items that compare equal to items already in the tree). Cheers.
    >
    > Duncan
    >
    > --
    > http://mail.python.org/**mailman/listinfo/python-list<http://mail.python.org/mailman/listinfo/python-list>
    >
    Dan Stromberg, May 12, 2013
    #11
  12. On Sat, May 11, 2013 at 4:24 PM, Dan Stromberg <> wrote:

    >
    > I'm afraid I'm having some trouble with the module. I've checked it into
    > my SVN at
    > http://stromberg.dnsalias.org/svn/red-black-tree-mod/trunk/duncan
    >
    > I have two versions of your tests in there now - "t" is minimally changed,
    > and test-red_black_tree_mod is pretty restructured to facilitate adding
    > more tests later. I get the same problem with either version of the tests.
    >
    > The problem I'm seeing is that the tree, when built from items, isn't
    > looking quite right. I inserted a print(tree) into the for loop, and I'm
    > getting the following, where I expected the tree to grow by one element on
    > each iteration:
    >
    > $ python t
    > 6 False None None
    > 6 False 3 None
    > 6 False 3 15
    > 6 False 3 15
    >

    I figured out that this was printing a single node and some of its
    attributes, not an entire tree. I changed it to print an entire tree using
    self.in_order().

    I've also changed around the comparisons a bit, to use a __cmp__ method but
    still provide __eq__, __neq__ and a new __lt__.

    I'm up against a new problem now that it'd be nice if you could look at:
    In BinaryTree.find(), it sometimes compares the item being searched for
    against None. In 2.x, this gives strange results, but may be benign in
    this code. In 3.x, this raises an exception. I've added a comment about
    this in the SVN repo I mentioned above.

    You can see the traceback yourself with python3 test-red_black_tree_mod .

    What should BinaryTree.find() do if it finds a data.node that is None?

    Thanks!

    PS: Is it about time we moved this discussion off python-list?
    Dan Stromberg, May 12, 2013
    #12
  13. Dan Stromberg

    duncan smith Guest

    On 12/05/13 00:24, Dan Stromberg wrote:
    >
    > I'm afraid I'm having some trouble with the module. I've checked it
    > into my SVN at
    > http://stromberg.dnsalias.org/svn/red-black-tree-mod/trunk/duncan
    >
    > I have two versions of your tests in there now - "t" is minimally
    > changed, and test-red_black_tree_mod is pretty restructured to
    > facilitate adding more tests later. I get the same problem with either
    > version of the tests.
    >
    > The problem I'm seeing is that the tree, when built from items, isn't
    > looking quite right. I inserted a print(tree) into the for loop, and
    > I'm getting the following, where I expected the tree to grow by one
    > element on each iteration:
    >
    > $ python t
    > 6 False None None
    > 6 False 3 None
    > 6 False 3 15
    > 6 False 3 15
    > 6 False 3 11
    > 6 False 3 11
    > 6 False 3 11
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    > 11 False 6 15
    >
    > Thoughts?
    >
    > BTW, printing an empty tree seems to say "sentinel". 'not sure if that
    > was intended.
    >
    > Thanks!
    >


    The leaf node has parent equal to None. All tree nodes have two
    children. One or both children may be sentinels, and a sentinel is
    signified by having both left and right (children) equal to None. So an
    empty tree is a sentinel node that is also root. So the string
    "sentinel" is expected (although possibly not the most sensible option).

    For non-sentinel nodes the string is generated by,

    return '%s %s %s' % (self.data, self.left.data, self.right.data)

    for the BinaryTree class, and by

    return '%s %s %s %s' % (self.data, self.is_red, self.left.data,
    self.right.data)

    for the RedBlackTree class.


    So what is being printed above is (in each case) the value contained in
    the root node, followed by its colour (True if red), and the values
    contained in the root node's left and right children.

    The root node remains root, although it's value and its children (and
    their values) might change due to tree rotations.

    It looks OK to me. The empty tree would print "sentinel". After adding
    the value 6 there is one tree node with sentinels as children (values
    equal to None). Adding 3 results in 3 being the value of the root's left
    child. It's right child is still a sentinel. Adding 15 results in that
    value being assigned to the right child. Adding 9 results in no change
    to the values in the root or its children. Adding 11 results in a tree
    rotation and 11 becomes the value in the right child of the root. At a
    later point a tree rotation results in the value of the root node being
    changed.

    I haven't implemented a way of representing the structure of the whole
    red black tree. I would probably write some code to generate a dot file
    and use that to generate a png. But you could add something like,

    print tree.height, tree.size, list(tree)

    and get output like,

    0 1 [6]
    1 2 [3, 6]
    1 3 [3, 6, 15]
    2 4 [3, 6, 9, 15]
    3 5 [3, 6, 9, 11, 15]
    4 6 [3, 6, 9, 11, 12, 15]
    4 7 [3, 6, 9, 11, 12, 15, 16]
    5 8 [3, 6, 9, 11, 12, 14, 15, 16]
    5 9 [3, 6, 9, 11, 12, 14, 15, 16, 17]
    5 10 [3, 6, 7, 9, 11, 12, 14, 15, 16, 17]
    5 11 [3, 6, 7, 9, 11, 12, 14, 15, 16, 17, 18]
    5 12 [3, 5, 6, 7, 9, 11, 12, 14, 15, 16, 17, 18]
    5 13 [3, 5, 6, 7, 8, 9, 11, 12, 14, 15, 16, 17, 18]
    6 14 [3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]
    6 15 [0, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]
    6 16 [0, 2, 3, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]
    6 17 [0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]
    6 18 [-1, 0, 2, 3, 4, 5, 6, 7, 8, 9, 11, 12, 13, 14, 15, 16, 17, 18]
    6 19 [-1, 0, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18]


    It doesn't give you the structure, but it does show that it seems to be
    growing reasonably. Cheers.

    Duncan
    duncan smith, May 12, 2013
    #13
  14. Dan Stromberg

    duncan smith Guest

    On 12/05/13 02:29, Dan Stromberg wrote:
    >
    > On Sat, May 11, 2013 at 4:24 PM, Dan Stromberg <
    > <mailto:>> wrote:
    >
    >
    > I'm afraid I'm having some trouble with the module. I've checked it
    > into my SVN at
    > http://stromberg.dnsalias.org/svn/red-black-tree-mod/trunk/duncan
    >
    > I have two versions of your tests in there now - "t" is minimally
    > changed, and test-red_black_tree_mod is pretty restructured to
    > facilitate adding more tests later. I get the same problem with
    > either version of the tests.
    >
    > The problem I'm seeing is that the tree, when built from items,
    > isn't looking quite right. I inserted a print(tree) into the for
    > loop, and I'm getting the following, where I expected the tree to
    > grow by one element on each iteration:
    >
    > $ python t
    > 6 False None None
    > 6 False 3 None
    > 6 False 3 15
    > 6 False 3 15
    >
    > I figured out that this was printing a single node and some of its
    > attributes, not an entire tree. I changed it to print an entire tree
    > using self.in_order().


    Yes, I've just posted regarding that.

    >
    > I've also changed around the comparisons a bit, to use a __cmp__ method
    > but still provide __eq__, __neq__ and a new __lt__.



    I have implemented a lot (maybe all?) of the set methods in a subclass.
    I should probably root that out and have a think about what should be in
    the RedBlackTree class and what subclasses might look like.

    >
    > I'm up against a new problem now that it'd be nice if you could look at:
    > In BinaryTree.find(), it sometimes compares the item being searched for
    > against None. In 2.x, this gives strange results, but may be benign in
    > this code. In 3.x, this raises an exception. I've added a comment
    > about this in the SVN repo I mentioned above.
    >
    > You can see the traceback yourself with python3 test-red_black_tree_mod .
    >
    > What should BinaryTree.find() do if it finds a data.node that is None?
    >


    A call to "find(data)" should find and return either a node containing
    "data"; or the sentinel node where "data" should be added. It should not
    get as far as the left or right child of a sentinel node (which would
    equal None). I'll look at this tomorrow. I did have the truth value of a
    node depending on it's data value (None implying False). Then I
    considered the possibility of actually wanting None as a value in the
    tree and changed it, so I could have introduced a bug here.

    > Thanks!
    >
    > PS: Is it about time we moved this discussion off python-list?
    >


    Maybe. You have my official e-mail address. Cheers.

    Duncan
    duncan smith, May 12, 2013
    #14
  15. Dan Stromberg

    duncan smith Guest

    On 12/05/13 03:02, duncan smith wrote:
    > On 12/05/13 02:29, Dan Stromberg wrote:
    >>
    >> On Sat, May 11, 2013 at 4:24 PM, Dan Stromberg <
    >> <mailto:>> wrote:


    [snip]

    >>
    >> What should BinaryTree.find() do if it finds a data.node that is None?
    >>

    >
    > A call to "find(data)" should find and return either a node containing
    > "data"; or the sentinel node where "data" should be added. It should not
    > get as far as the left or right child of a sentinel node (which would
    > equal None). I'll look at this tomorrow. I did have the truth value of a
    > node depending on it's data value (None implying False). Then I
    > considered the possibility of actually wanting None as a value in the
    > tree and changed it, so I could have introduced a bug here.
    >


    It's a Python3 thing. The initial sentinel node was evaluating to True.
    __nonzero__ needs to be changed to __bool__.

    >> Thanks!
    >>
    >> PS: Is it about time we moved this discussion off python-list?
    >>


    Let's do that from now.

    Duncan
    duncan smith, May 12, 2013
    #15
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