Adding suffix tree #323

Arvind-raj06 · 2021-01-31T13:56:24Z

Suffix Tree

References to other Issues or PRs or Relevant literature

"Fixes #290". See
#290

Brief description of what is fixed or changed

Addition of suffix tree with reference to the pypi project.

Other comments

The code works fine to me, the PR is in count of SWOC and if you find any bug pls ping me.

codecov · 2021-01-31T14:08:00Z

Codecov Report

Merging #323 (e3586fa) into master (bcf9753) will decrease coverage by 0.181%.
The diff coverage is 95.312%.

@@              Coverage Diff              @@
##            master      #323       +/-   ##
=============================================
- Coverage   98.550%   98.369%   -0.181%     
=============================================
  Files           25        26        +1     
  Lines         3243      3435      +192     
=============================================
+ Hits          3196      3379      +183     
- Misses          47        56        +9

Impacted Files	Coverage Δ
pydatastructs/utils/__init__.py	`100.000% <ø> (ø)`
pydatastructs/strings/suffix_tree.py	`94.230% <94.230%> (ø)`
pydatastructs/strings/__init__.py	`100.000% <100.000%> (ø)`
pydatastructs/utils/misc_util.py	`99.019% <100.000%> (+0.189%)`	⬆️

czgdp1807 · 2021-02-01T08:17:30Z

pydatastructs/trees/suffix_tree.py

+ 'SuffixTree'
+]
+
+class Suffix_Node():


This class should be in https://github.com/codezonediitj/pydatastructs/blob/master/pydatastructs/utils/misc_util.py and should inherit Node class.

czgdp1807 · 2021-02-01T08:18:11Z

pydatastructs/trees/suffix_tree.py

+ else:
+ return {x for n in self.transition_links.values() for x in n._get_leaves()}
+
+class SuffixTree():


This class should be in a file, suffix_tree.py in https://github.com/codezonediitj/pydatastructs/tree/master/pydatastructs/strings

czgdp1807 · 2021-02-01T08:19:23Z

pydatastructs/trees/tests/test_suffixtree.py

+from pydatastructs import SuffixTree
+
+def test_suffixtree():
+ s = SuffixTree("HelloworldHe")
+ assert s.find("Hel") == 0
+ assert s.find_all("He") == {0, 10}
+ assert s.find("Win") == -1


Please provide references for the tests for verifying the results. You may use examples from university lecture notes, wikipedia, books, etc.

Still awaited.

czgdp1807 · 2021-02-01T08:21:46Z

There are several uncovered lines in https://codecov.io/gh/codezonediitj/pydatastructs/pull/323/diff (see red). Use steps in https://github.com/codezonediitj/pydatastructs#testing for checking the coverage for your patch locally and add tests accordingly to fully cover your code by tests.

Arvind-raj06 · 2021-02-01T09:37:42Z

Thank you for informing me, I haven't noticed these a while

Arvind-raj06 · 2021-02-02T06:56:12Z

I have added some test to cover that area, I can't get it to max but given my level best

Arvind-raj06 · 2021-02-02T09:45:04Z

@czgdp1807 any more corrections needed!?

czgdp1807 · 2021-02-05T04:36:56Z

Please add documentation for public methods (the ones which don't start with _).

Arvind-raj06 · 2021-02-05T05:23:04Z

Please add documentation for public methods (the ones which don't start with _).

No issue found that

Arvind-raj06 · 2021-02-05T05:24:03Z

@czgdp1807 They are requesting the leaderboard update at SWoC, today is the last date

czgdp1807 · 2021-02-05T07:29:56Z

Done.

czgdp1807 · 2021-02-05T07:30:20Z

I am a bit busy these days. There might be a delay in reviews.

Arvind-raj06 · 2021-02-05T08:17:00Z

I am a bit busy these days. There might be a delay in reviews.

Yeah sure take your time

Arvind-raj06 · 2021-02-05T08:18:31Z

Done.

Thank you 😉

czgdp1807 · 2021-02-07T06:01:08Z

pydatastructs/strings/suffix_tree.py

+ i += 1
+ return i
+
+ def lcs(self, stringIdxs = -1):


Please avoid using short forms. Use the full name, largest_common_substring.

We had some methods added to algorithms under this module related with longest common substring I believe. With that backtracking thing. How is this method different from that one?

Backtracking just searches all the strings in the given list by going in reverse direction from the child to root and finds the longest among that but by using this method we give users the freedom to search the string from the index they want. And this function just reduces the comparison time by removing all the non subset of longest sequence

czgdp1807 · 2021-02-07T13:02:11Z

You can continue with your other PRs. I will finalize all of these on Saturday, next week.

Arvind-raj06 · 2021-02-07T13:43:56Z

You can continue with your other PRs. I will finalize all of these on Saturday, next week.

Yeah 👍

Arvind-raj06 · 2021-02-23T16:23:50Z

I hope that you might have gone through the changes I made to your SkipList PR. Would request to make this better by learning from there. The code you write works correctly and efficiently but a bit of consistency (both in APIs and docs) is needed with respect to the existing things in master. For example, in your code of SkipList.insert(num) was the API but for every other insert method in master, a key value and an optional data value is taken as input.

Yeah It was like literally wow! I have studied it and got some good idea on consistency, Thank you
Yes later having seen the test change it's clear, I think it will take practice for me to obtain that consistency!

Arvind-raj06 · 2021-02-24T03:35:13Z

Shall I resolve the conflicts out here

czgdp1807 · 2021-02-26T14:14:56Z

Shall I resolve the conflicts out here

Preferrable resolve the conflicts locally. When you will update your master and try to merge it into Allgood branch, git will raise conflicts. If you are using VSCode then it will highlight the files of conflict and the changes you want to accept. After doing that just make a commit and conflicts will be resolved.

Arvind-raj06 · 2021-02-26T14:42:02Z

Shall I resolve the conflicts out here

Preferrable resolve the conflicts locally. When you will update your master and try to merge it into Allgood branch, git will raise conflicts. If you are using VSCode then it will highlight the files of conflict and the changes you want to accept. After doing that just make a commit and conflicts will be resolved.

No worries I'm using atom which will also do the same. I had the experience of same in my previous PR this time will try to implement it perfectly.

czgdp1807 · 2021-02-28T14:37:38Z

Have you implemented this algorithm?

czgdp1807 · 2021-02-28T14:42:55Z

Note this PR will not be counted towards SWoC but it will be counted for GSSoC. This needs some more work both at the design level and at the implementation level.

Arvind-raj06 · 2021-02-28T16:13:37Z

Yeah sure then

Arvind-raj06 · 2021-03-11T13:38:26Z

I'm back did you find anything to be added to make code better!
PS you can change the label to GSSoC

Arvind-raj06 · 2021-03-11T13:41:24Z

Cool happy to work with you back

czgdp1807 · 2021-03-11T13:41:40Z

Well, IMHO, the code has a lot of room for improvement. It should be as simple as possible and easy to understand. I would suggest instead of jumping to code let's pick some examples and solve it via fake APIs and keep refining those APIs until a consensus is reached. Then we can proceed with coding and all. This is an important data structure and should be added after a lot of discussions. We are in no hurry.

Fault is mine too, I shouldn't have approved the previous designs and stuff for this DS. Let's pick an example to programmatically duplicate some example here.

Arvind-raj06 · 2021-03-11T13:44:21Z

Well, IMHO, the code has a lot of room for improvement. It should be as simple as possible and easy to understand. I would suggest instead of jumping to code let's pick some examples and solve it via fake APIs and keep refining those APIs until a consensus is reached. Then we can proceed with coding and all. This is an important data structure and should be added after a lot of discussions. We are in no hurry.

Yeah as you say

Arvind-raj06 · 2021-04-13T05:15:15Z

Hey @czgdp1807 I think this is the best suffix tree structure I could obtain from the examples. But as for the property side it's still lacking some potential ! Should I work on that rather I make a new PR for Suffix tree properties!?

czgdp1807 · 2021-04-13T06:26:19Z

We have two options with us, one to keep spending time on Suffix Tree which is a hard data structure. This will delay our first release. Another option is to put this on hold and add it to the next version. I think we should go for the second one since once people will start using our project, contributions will automatically scale. So, let us ignore it for now. Let's keep this PR open and add it to 0.0.2 milestone.

P.S. We should aim to complete the first release by first half of the year that is by August 2021. Let me know what you think.

czgdp1807 · 2021-04-13T06:32:32Z

I have updated the list of features to be added to 0.0.1. We should focus on graph algorithms and KMP in strings. The framework for former is already set (just algorithms are required to be implemented) and KMP shouldn't be that hard to implement.

Arvind-raj06 · 2021-04-13T06:34:37Z

That's really a nice idea! I will work on other issues as this is time consuming I felt the same way.

Arvind-raj06 · 2021-04-13T06:35:13Z

I have updated the list of features to be added to 0.0.1. We should focus on graph algorithms and KMP in strings. The framework for former is already set (just algorithms are required to be implemented) and KMP shouldn't be that hard to implement.

Cool gonna learn something new on graphs

czgdp1807 · 2021-04-13T06:39:53Z

Here is the updated list, https://github.com/codezonediitj/pydatastructs/wiki/Planned-Features-for-v0.0.1

Not much is to be done for the first release. We will postpone the harder parts for the second half of the year. Otherwise we will never be able to release the package. Just three graph algorithms and one KMP is to be implemented. All of these are easy medium and can be done in one month's time. After that we will be able to focus on building docs and upload it on readthedocs.io

Adding suffix

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czgdp1807 added the strings label Feb 1, 2021

czgdp1807 added this to the v0.0.1 milestone Feb 1, 2021

czgdp1807 reviewed Feb 1, 2021

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Arvind-raj06 added 3 commits February 2, 2021 12:13

Let's see

598330b

Adding ref

391302d

Update test_suffixtree.py

7fd9da7

czgdp1807 added hard labels Feb 2, 2021

Arvind-raj06 requested a review from czgdp1807 February 3, 2021 05:37

Adding docs

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czgdp1807 reviewed Feb 7, 2021

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Fixed lcs

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Arvind-raj06 requested a review from czgdp1807 February 7, 2021 12:58

Merge branch 'master' into Allgood

e3586fa

czgdp1807 added GSSoC and removed SWoC labels Mar 11, 2021

czgdp1807 modified the milestones: v0.0.1, v0.0.2 Apr 13, 2021

czgdp1807 added the Please take over PRs that can be continued by anyone. label Oct 21, 2021

czgdp1807 removed this from the v0.0.2 milestone Oct 25, 2021

czgdp1807 removed level3 labels Dec 5, 2021

Adding suffix tree #323

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Adding suffix tree #323

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Arvind-raj06 commented Jan 31, 2021 • edited

Suffix Tree

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Brief description of what is fixed or changed

Other comments

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