using string-suffix-array-functionality branch instead of master #627

zhihuidu · 2021-01-13T16:59:38Z

Introduces Suffix Arrays into Arkouda:
Contains native Chapel implementation of the suffix array construction algorithm contained in Simple Linear Work Suffix Array Construction

A potential use case of suffix arrays is the Burrows–Wheeler transform, a reversible preprocessing step for improving lossless data compression

reworded and added some comments

Update SACA.chpl comments

stress-tess · 2021-06-22T20:20:43Z

I believe a larger discussion about the best way for us to benefit from suffix arrays/data compression using the Burrows-Wheeler algorithm would be very worthwhile. If you don't mind @zhihuidu maybe you could make an issue to explain how you envisioned this functionality being used

zhihuidu · 2021-06-23T15:24:30Z

I believe a larger discussion about the best way for us to benefit from suffix arrays/data compression using the Burrows-Wheeler algorithm would be very worthwhile. If you don't mind @zhihuidu maybe you could make an issue to explain how you envisioned this functionality being used

Yes, Burrows-Wheeler algorithm is a major scenario of suffary array. We can discuss more about it.

stress-tess · 2021-06-30T17:09:33Z

src/SACA.chpl

+//Algorithm 1
+// The first algorithm divsufsort is the fastest C codes on suffix array
+require "../thirdparty/SA/libdivsufsort/include/config.h";
+require "../thirdparty/SA/libdivsufsort/include/divsufsort.h";
+require "../thirdparty/SA/libdivsufsort/include/divsufsort_private.h";
+require "../thirdparty/SA/libdivsufsort/include/lfs.h";
+
+require "../thirdparty/SA/libdivsufsort/lib/divsufsort.c";
+require "../thirdparty/SA/libdivsufsort/lib/sssort.c";
+require "../thirdparty/SA/libdivsufsort/lib/trsort.c";
+require "../thirdparty/SA/libdivsufsort/lib/utils.c";
+extern proc divsufsort(inputstr:[] uint(8),suffixarray:[] int(32),totallen:int(32));
+
+//Another possible SACA algorithm to utilize. 
+//require "../thirdparty/SA/SACA-K/saca-k.c";
+
+//extern proc SACA_K(inputstr:[] uint(8), suffixarray:[] uint, n:uint, K:uint,m:uint, level:int);
+//void SACA_K(unsigned char *s, unsigned int *SA,
+//  unsigned int n, unsigned int K,
+//  unsigned int m, int level) ;
+
+//Algorithm 2
+
+// The Chapel version of suffix array construction algorithm using skew algorithm
+// Rewrite the algorithm and codes in paper
+// "Simple Linear Work Suffix Array Construction" by Juha Karkkainen and Peter Sanders (2003)
+// Dec.7, 2020
+
+inline proc leq(a1 :int, a2:int, b1:int, b2:int) // lexicographic order
+{  return(a1 < b1 || a1 == b1 && a2 <= b2); 


@zhihuidu, I noticed you have an external C implementation of suffix array construction (Algorithm 1 - libdivsufsort) and a native Chapel implementation (Algorithm 2 - Simple Linear Work Suffix Array Construction. Have you done performance testing to compare the native implementation with the C implementation?

If the native implementation is fast, we might not need to force the libdivsufsort dependency on Arkouda users. Is there another reason to keep the libdivsufsort version other than performance?

@pierce314159 yes, you are right! Currently the performance of libdivsufsort is better. However it has two problems. (1) it cannot use multiple locales. (2) we have to make some change on the code to interate it into Arkouda. We hope to develop a new multilocal algorithm to handle very large strings in the next step. For small strings, the performance difference in several seconds or miliseconds is not important. The major reason we use libdivsufsort is that we want to check how to use external code in Arkouda.

That makes sense! For more info on how to use external code, you can check out @glitch's Investigating Arrow wiki page. This is how I was planning to import the library instead of having a copy in our codebase.

In general, I think we want to keep the number of dependencies low. And native chapel implementations are almost always preferred because they can better leverage HPC resources

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class

stress-tess · 2021-07-01T17:26:24Z

@zhihuidu, I opened a new PR (#865) which replays these changes over a fresh copy of master, addresses the PR feedback, and makes an effort to minimize diff with master to make reviewing easier. If you are okay with the changes, I'll invite the other team members to review and hopefully we can get your functionality in master

I made a new PR to avoid force pushing and overwriting the history of your string-suffix-array-functionality branch. You are welcome clone my branch (pierce314159/suffix-array) and cherry-pick the commits over to your branch, but the merge conflicts are non-trivial

zhihuidu · 2021-07-01T17:28:25Z

@zhihuidu, I opened a new PR (#865) which replays these changes over a fresh copy of master, address the PR feedback, and makes an effort to minimize diff with master to make reviewing easier. If you are okay with the changes, I'll invite the other team members to review and hopefully we can get your functionality in master

I made a new PR to avoid force pushing and overwriting the history of your string-suffix-array-functionality branch. You are welcome checkout my branch (pierce314159/suffix-array) and cherry-pick the commits over to your branch, but the merge conflicts are non-trivial

@pierce314159 Yes, no problem and thanks！I tried to do it but I met many CI problems and I cannot solve them.

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

@zhihuidu

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class - Renames `class SegSArray` to `class SegSuffixArray` and moved this class to SegmentedSuffixArray.chpl (previously in SegmentedArray.chpl along with SegString) - Removes external `libdivsufsort` code and references. Changes default to @zhihuidu's native chapel suffix array construction implementation using skew algorithm

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class

@zhihuidu

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class - Renames `class SegSArray` to `class SegSuffixArray` and moved this class to SegmentedSuffixArray.chpl (previously in SegmentedArray.chpl along with SegString) - Removes external `libdivsufsort` code and references. Changes default to @zhihuidu's native chapel suffix array construction implementation using skew algorithm

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

@zhihuidu

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class - Renames `class SegSArray` to `class SegSuffixArray` and moved this class to SegmentedSuffixArray.chpl (previously in SegmentedArray.chpl along with SegString) - Removes external `libdivsufsort` code and references. Changes default to @zhihuidu's native chapel suffix array construction implementation using skew algorithm

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

@zhihuidu

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class - Renames `class SegSArray` to `class SegSuffixArray` and moved this class to SegmentedSuffixArray.chpl (previously in SegmentedArray.chpl along with SegString) - Removes external `libdivsufsort` code and references. Changes default to @zhihuidu's native chapel suffix array construction implementation using skew algorithm

commit 82776f9 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Mar 19 18:19:08 2021 -0400 solve the inconsistency in dtype commit 87c6327 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 21:33:30 2021 -0400 merge with the latest version commit 924ac94 Merge: 18f481c 678097f Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 20:33:30 2021 -0400 Merge branch 'master' of github.com:mhmerrill/arkouda commit 18f481c Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 18:08:01 2021 -0400 handle some bytes to string commit fb89d88 Merge: c002419 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Mar 15 17:05:35 2021 -0400 solve conflict of suffix array, SegmentedMsg, SegmentedArray and run_benchmarks commit 6d65335 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 22:18:31 2021 -0500 tuple data type commit f5ca67a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 20:44:09 2021 -0500 remove mypy CI check error commit 010a446 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Jan 10 19:35:09 2021 -0500 return the string for suffix_array_file commit 80f78c6 Merge: 00b3579 e192878 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 16:08:57 2021 -0500 resolve convlict commit 00b3579 Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 15:00:43 2021 -0500 single locales for C code commit c782b5a Author: Zhihui Du <zhihuidu@gmail.com> Date: Fri Jan 8 13:19:21 2021 -0500 add switch betwteen different SA algorithms commit 2d40c0e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 14:14:36 2021 -0500 solve the sphinx error commit 2af5ce8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Jan 5 09:57:42 2021 -0500 check the comments to remove docs CI check error commit 0bff3e4 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 18:45:28 2021 -0500 remove the enhenced attribute in sym table commit a8a195a Merge: 221679e f1781e8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:40:48 2021 -0500 Merge pull request Bears-R-Us#4 from reuster986/master Fixed bug in UnitTestPeelStick commit 221679e Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Jan 4 17:23:31 2021 -0500 update lcp related code n commit f1781e8 Author: Bill Reus <reuster986@gmail.com> Date: Mon Jan 4 16:18:51 2021 -0500 Fixed bug in UnitTestPeelStick commit 50be2e3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 22:25:52 2020 -0500 copy string_test.py commit 6fd3b05 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 18:31:09 2020 -0500 change suffix array return as an int array commit ac7e209 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 27 16:40:20 2020 -0500 add corectness check in sa.py commit 9f5c3d3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 10:28:59 2020 -0500 check test/*.chpl commit ed98498 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:47:35 2020 -0500 make sa.py check easy commit 0aa835c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:33:12 2020 -0500 copy master gather.py commit 189c32e Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 01:15:26 2020 -0500 add an empty correctness function commit 267238c Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:55:43 2020 -0500 import SArrays class in pdarraysetops.py commit 4f773e2 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sat Dec 26 00:38:10 2020 -0500 remove the bug causing wrong return string value commit 6074b60 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:20:55 2020 -0500 remove binary op commit edc3f63 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:16:22 2020 -0500 remove binary op commit 3861e62 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:07:05 2020 -0500 bool or pdarray commit e1c3173 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 24 00:01:20 2020 -0500 data type commit 0cda91d Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 23:31:10 2020 -0500 type match commit 59174ac Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:47:58 2020 -0500 correct a typo commit 9d60563 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 22:20:13 2020 -0500 align with strings function commit 16cca77 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 23 21:49:28 2020 -0500 remove unused import commit a6c536e Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 11:18:51 2020 -0500 update the SegSArray commit 32ecc0c Merge: 38818a3 18e8acf Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 22 10:59:10 2020 -0500 solve the conflict commit 38818a3 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 21 09:44:13 2020 -0500 follow suggestions from community commit 6b6e41a Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 18:08:04 2020 -0500 update third party config commit da30cfa Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 17:15:09 2020 -0500 remove suffixarray_test.py commit 2db17d8 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 15:47:18 2020 -0500 datatype in string.py commit e90ca27 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:56:33 2020 -0500 remove tab in MultiTypeSymEntry.chpl commit 7a0b197 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 14:44:20 2020 -0500 suffix_arry_file updated commit 9702d46 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 20 13:57:26 2020 -0500 include sa.py into run_benchmarks.py commit 42e3ba7 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Dec 17 18:13:07 2020 -0500 change to relative directory commit b6228e5 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 23:17:34 2020 -0500 remove tab, remove unused codes commit 8f88f4c Merge: c9e03fb d184048 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 14 14:28:09 2020 -0500 Merge pull request Bears-R-Us#3 from alvaradoo/patch-1 Update SACA.chpl comments commit d184048 Author: Oliver Alvarado Rodriguez <41132909+alvaradoo@users.noreply.github.com> Date: Mon Dec 14 13:39:23 2020 -0500 Update SACA.chpl comments reworded and added some comments commit c9e03fb Author: David Bader <dbader13@gmail.com> Date: Sun Dec 13 22:21:31 2020 -0500 updated commit 4131820 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:56:00 2020 -0500 add thirdparty files commit 3a220dc Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 21:29:48 2020 -0500 solve conflict commit 9f22f79 Merge: e517e36 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Sun Dec 13 20:16:35 2020 -0500 add thirdpary files commit 940cb79 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Dec 9 15:01:34 2020 -0500 confirm submit all changes commit 21df359 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Dec 8 14:19:37 2020 -0500 add the lcp array method commit dbd6d96 Author: Zhihui Du <zhihuidu@gmail.com> Date: Mon Dec 7 19:35:43 2020 -0500 add Chapel skew suffix array algorithm commit c81d755 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 26 17:47:45 2020 -0500 add suffix_array Python test commit 9a22704 Author: Zhihui Du <zhihuidu@gmail.com> Date: Wed Nov 25 20:18:20 2020 -0500 change name commit d288c10 Author: Zhihui Du <zhihuidu@gmail.com> Date: Tue Nov 24 23:37:55 2020 -0500 add read file suffix array function and all libdivsufsort files commit 7af0b51 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 11:36:20 2020 -0500 add suffix array benchmark sa.py commit 65ad500 Author: Zhihui Du <zhihuidu@gmail.com> Date: Thu Nov 19 10:33:48 2020 -0500 add the suffix array function to Arkouda

…e with master and pass tests: - Updates logging statements to use logLevel instead of v (PR Bears-R-Us#760) - Updates `check` to `check_table` (PR Bears-R-Us#792) - Removes outdated `Strings.attach` function which used `_` for subcomponents (new convention is `.` per PR Bears-R-Us#774) - Makes `unregister_strings_by_name` a staticmethod Manually applied recent changes to `SegmentedArray.chpl` because automatic merge was thrown off by addition of `class SegSArray` including: - PR Bears-R-Us#666 string test ends_with failure - PR Bears-R-Us#781 off by one in SegmentedArray peel method

@zhihuidu

- Moves SArrarys to suffix_array.py - Minimizes diff with master to highlight functionality changes - Refomats suffix-array.py - Reformats SACA.chpl to fix bracket alignment and to have more uniform formattting - Removes unnecessary commented out code - Add type hints to size and bytes in strings.py for mypy - In SegmentedArray.chpl replaces writelns in SegSArray class with logging statements following the example of SegString class - Renames `class SegSArray` to `class SegSuffixArray` and moved this class to SegmentedSuffixArray.chpl (previously in SegmentedArray.chpl along with SegString) - Removes external `libdivsufsort` code and references. Changes default to @zhihuidu's native chapel suffix array construction implementation using skew algorithm

stress-tess · 2021-11-22T20:43:55Z

Since this PR is fairly out of date and the functionality is captured in #865, I am going to go ahead and close it. If anyone has issue with this feel free to reopen (or ask me to)

zhihuidu and others added 30 commits November 19, 2020 10:33

add the suffix array function to Arkouda

65ad500

add suffix array benchmark sa.py

7af0b51

add read file suffix array function and all libdivsufsort files

d288c10

change name

9a22704

add suffix_array Python test

c81d755

add Chapel skew suffix array algorithm

dbd6d96

add the lcp array method

21df359

confirm submit all changes

940cb79

add thirdpary files

9f22f79

solve conflict

3a220dc

add thirdparty files

4131820

updated

c9e03fb

Update SACA.chpl comments

d184048

reworded and added some comments

Merge pull request #3 from alvaradoo/patch-1

8f88f4c

Update SACA.chpl comments

remove tab, remove unused codes

b6228e5

change to relative directory

42e3ba7

include sa.py into run_benchmarks.py

9702d46

suffix_arry_file updated

7a0b197

remove tab in MultiTypeSymEntry.chpl

e90ca27

datatype in string.py

2db17d8

remove suffixarray_test.py

da30cfa

update third party config

6b6e41a

follow suggestions from community

38818a3

solve the conflict

32ecc0c

update the SegSArray

a6c536e

remove unused import

16cca77

align with strings function

9d60563

correct a typo

59174ac

type match

0cda91d

data type

e1c3173

stress-tess reviewed Jun 30, 2021

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stress-tess mentioned this pull request Jul 1, 2021

Updates PR #627 - Suffix Arrays #865

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stress-tess closed this Nov 22, 2021

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using string-suffix-array-functionality branch instead of master #627

using string-suffix-array-functionality branch instead of master #627

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zhihuidu commented Jan 13, 2021 •

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stress-tess commented Jun 22, 2021

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using string-suffix-array-functionality branch instead of master #627

using string-suffix-array-functionality branch instead of master #627

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zhihuidu commented Jan 13, 2021 •

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