Various cleanup and deprecation in `sage.coding.linear_code` #21165

johanrosenkilde · 2016-08-04T09:08:34Z

sage.coding.linear_code has a number of global functions and class methods which are badly named, badly documented, badly placed or badly conceived. This ticket takes some steps towards cleaning up.

This ticket fixes the following issues:

Renamed and moved best_known_linear_code, best_known_linear_code_www, bounds_minimum_distance and self_orthogonal_binary_codes to new module sage.coding.databases, also deprecating them from the global namespace. Also improved their documentation. Added the new module to codes.
Rename the module sd_codes to self_dual_codes.
Remove the function sd_codes.self_dual_codes_binary from the global namespace, renaming it into self_dual_binary_codes accessible from codes.databases. Removed all helper computations that were done at Sage startup from sd_codes, making them all private and evaluated only when calling self_dual_binary_codes.
Deprecated sd_zeta_polynomial and its helper functions. After struggling for
a long time, I found out that this method supposed to compute exactly the same
as zeta_polynomial, except that it uses a method which only works for
self-dual codes. The method is a semi-explicit expression for the zeta
function which has theoretical interest, but no computational interest (it is
not faster to compute). So the method should simply be removed.
Deprecated LinearCodeFromVectorSpace and made LinearCode accept a vector space at construction time.
Improved some unhelpful doc-examples in sage.coding.extended_code.
Some cleanup of the imports on the top-level of linear_code.py.
Rename and deprecate from the global namespace the functions code2leon, min_wt_vec_gap.
Improve the deprecation message for wtdist_gap.
Improved doc of covering_radius.
Use weight_distribution as primary term instead of spectrum, but support the second as an alias. Inline the helper function _spectrum_from_gap. Improved the doc.
Renamed code_constructions.LinearCodeFromCheckMatrix to code_constructions.from_parity_check_matrix. Simplified its doc.
Changed a random doctest in punctured_code whose output changed after an unrelated patch (due to RandomLinearCode)
Simplified RandomLinearCode, renamed to codes.random_linear_code and fixed order of arguments.
Removed TrivialCode as it was mathematically senseless and hadn't worked for a while (it had no tests).
Massively modernized and simplified the doc of code_constructions.py.
Privatized and/or deprecated the helper functions of code_constructions.py.

CC: @sagetrac-dlucas

Component: coding theory

Keywords: cleanup, sd75

Author: Johan Rosenkilde

Branch/Commit: 08bdda0

Reviewer: David Lucas

Issue created by migration from https://trac.sagemath.org/ticket/21165

The text was updated successfully, but these errors were encountered:

johanrosenkilde · 2016-08-04T15:15:46Z

Branch: u/jsrn/21165_linear_code_cleanup

sagetrac-git · 2016-08-04T16:09:14Z

Branch pushed to git repo; I updated commit sha1. New commits:

`dd334af`	`Rename LinearCodeFromCheckMatrix -> from_parity_check_matrix`
`20aa7e6`	`Fix typo`
`462cc43`	`Fix import and doc of from_parity_check_matrix`
`f18c494`	`Reduce brittle and random doctest to something fixed.`
`a8f45aa`	`RandomLinearCode(n, k, F) -> random_linear_code(F, n, k)`
`d88f4e4`	`Removed TrivialCode. It makes no mathematical sense and hasn't worked for a long while, so no deprecation.`
`5268fb2`	`Clarify and massively simplify module doc of code_constructions.py`
`da23dc6`	`Some doctest markup fixes`
`b1329da`	`Privatize and/or deprecate the helper functions of code_constructions.py`

sagetrac-git · 2016-08-04T16:09:14Z

Commit: b1329da

johanrosenkilde · 2016-08-04T16:12:51Z

comment:3

OK, I think I'm done for the moment. The diff touches many lines in many files, but most of those changes are trivial renaming. Substantial changes occurred in linear_code.py, databases.py and code_constructions.py.

johanrosenkilde · 2016-08-05T06:00:56Z

comment:4

Forgot to add that I merged in #20835 since I modified some doctests to use the systematic generator matrix.

johanrosenkilde · 2016-08-05T06:00:56Z

Dependencies: 20835

johanrosenkilde · 2016-08-05T06:01:21Z

Changed dependencies from 20835 to #20835

sagetrac-dlucas · 2016-08-17T10:39:34Z

Changed branch from u/jsrn/21165_linear_code_cleanup to u/dlucas/21165_linear_code_cleanup

sagetrac-dlucas · 2016-08-17T10:44:41Z

Changed commit from b1329da to 079e51f

sagetrac-dlucas · 2016-08-17T10:44:41Z

comment:7

Hello,

Thanks for cleaning up all this!

I only have a couple of remarks:

There's a lone import statement at the bottom of databases.py. Is there any reason why it's here and not at the top of this file with the others?
Same file, the first two methods do not have an INPUT block, while they do have some input arguments.

Otherwise, tests pass and documentation builds, everything seems to be properly deprecated, I agree with your changes.

BTW, it was not merging with the latest beta, fixed this and pushed my change.

Best,

David

New commits:

`079e51f`	`Fixed merge conflict`

johanrosenkilde · 2016-08-18T09:12:41Z

Changed branch from u/dlucas/21165_linear_code_cleanup to u/jsrn/21165_linear_code_cleanup

sagetrac-git · 2016-08-18T09:38:22Z

Branch pushed to git repo; I updated commit sha1. New commits:

`65cb84c`	`No global imports in databases.py`
`62ddc6c`	`Simplify some code. Fix function names in doctests`

sagetrac-git · 2016-08-18T09:38:22Z

Changed commit from 079e51f to 62ddc6c

johanrosenkilde · 2016-08-18T09:41:43Z

Changed dependencies from #20835 to none

johanrosenkilde · 2016-08-18T09:41:43Z

comment:10

Replying to @sagetrac-dlucas:

There's a lone import statement at the bottom of databases.py. Is there any reason why it's here and not at the top of this file with the others?

It's not there to make the functional available to code in the module, but rather to make the function available on the command line as codes.databases.<tab>.

However, your comment made me realise that all the global imports at the top of databases.py are also present in that tab-completion. So now I've localised all of those.

Same file, the first two methods do not have an INPUT block, while they do have some input arguments.

I've added it.

Otherwise, tests pass and documentation builds, everything seems to be properly deprecated, I agree with your changes.

Be aware that many of the tests in databases.py require the spkg
gap_packages or internet, and are not run by default with ./sage -t. I
had forgotten this myself, but now made them run and fixed some import bugs.

BTW, it was not merging with the latest beta, fixed this and pushed my change.

Thanks, and thanks for reviewing.

Best,
Johan

sagetrac-dlucas · 2016-08-18T11:09:44Z

Changed branch from u/jsrn/21165_linear_code_cleanup to u/dlucas/21165_linear_code_cleanup

sagetrac-dlucas · 2016-08-18T11:13:10Z

Changed commit from 62ddc6c to 189d8e5

sagetrac-dlucas · 2016-08-18T11:13:10Z

comment:12

Hello,

Just found a broken doctest in one of the thematic tutorials (forgot to test that yesterday).
It was a trivial deprecation, fixed it myself and pushed the related change.
I'm fine with this ticket, so if you're fine with my change, you can set this ticket to positive
review.

David

New commits:

`189d8e5`	`Fixed broken doctest in thematic tutorial`

sagetrac-dlucas · 2016-08-18T11:13:10Z

Reviewer: David Lucas

johanrosenkilde · 2016-08-18T18:01:13Z

comment:13

Great! Thanks a lot.

vbraun · 2016-08-20T14:03:47Z

comment:14

sage -t --long src/sage/categories/homset.py  # 3 doctests failed
sage -t --long src/sage/structure/coerce.pyx  # 1 doctest failed

johanrosenkilde · 2016-08-20T19:02:05Z

Changed branch from u/dlucas/21165_linear_code_cleanup to u/jsrn/21165_linear_code_cleanup

johanrosenkilde · 2016-08-20T19:05:56Z

comment:16

Fixed. Sorry for not testing: I believed the changes to be completely local to sage.coding. The errors occurred because some of the changes means that certain computations are no longer done at Sage start-up: these initialised GF(2) which meant that e.g. the garbage collector always knew of GF(2).

johanrosenkilde · 2016-08-20T19:05:56Z

Changed commit from 189d8e5 to c283cfc

sagetrac-dlucas · 2016-08-21T15:20:29Z

comment:17

Bug fixed, doctests pass, I set this ticket to positive_review.

vbraun · 2016-08-23T22:01:54Z

comment:18

sage -t --long src/doc/en/thematic_tutorials/coding_theory.rst
**********************************************************************
File "src/doc/en/thematic_tutorials/coding_theory.rst", line 547, in doc.en.thematic_tutorials.coding_theory
Failed example:
    C = codes.RandomLinearCode(10, 5, GF(7))
Expected nothing
Got:
    doctest:warning
      File "/home/buildbot/slave/sage_git/build/src/bin/sage-runtests", line 89, in <module>
        err = DC.run()
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/control.py", line 1130, in run
        self.run_doctests()
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/control.py", line 854, in run_doctests
        self.dispatcher.dispatch()
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1698, in dispatch
        self.parallel_dispatch()
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1588, in parallel_dispatch
        w.start()  # This might take some time
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1864, in start
        super(DocTestWorker, self).start()
      File "/home/buildbot/slave/sage_git/build/local/lib/python/multiprocessing/process.py", line 130, in start
        self._popen = Popen(self)
      File "/home/buildbot/slave/sage_git/build/local/lib/python/multiprocessing/forking.py", line 126, in __init__
        code = process_obj._bootstrap()
      File "/home/buildbot/slave/sage_git/build/local/lib/python/multiprocessing/process.py", line 258, in _bootstrap
        self.run()
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 1837, in run
        task(self.options, self.outtmpfile, msgpipe, self.result_queue)
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 2130, in __call__
        runner.run(test)
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 636, in run
        return self._run(test, compileflags, out)
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 498, in _run
        self.compile_and_execute(example, compiler, test.globs)
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/doctest/forker.py", line 861, in compile_and_execute
        exec(compiled, globs)
      File "<doctest doc.en.thematic_tutorials.coding_theory[76]>", line 1, in <module>
        C = codes.RandomLinearCode(Integer(10), Integer(5), GF(Integer(7)))
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/coding/code_constructions.py", line 1052, in RandomLinearCode
        deprecation(21165, "codes.RandomLinearCode(n, k, F) is deprecated. Please use codes.random_linear_code(F, n, k) instead")
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/misc/superseded.py", line 100, in deprecation
        warning(trac_number, message, DeprecationWarning, stacklevel)
      File "/home/buildbot/slave/sage_git/build/local/lib/python2.7/site-packages/sage/misc/superseded.py", line 141, in warning
        warn(message, warning_class, stacklevel)
    :
    DeprecationWarning: codes.RandomLinearCode(n, k, F) is deprecated. Please use codes.random_linear_code(F, n, k) instead
    See http://trac.sagemath.org/21165 for details.
**********************************************************************
1 item had failures:
   1 of  80 in doc.en.thematic_tutorials.coding_theory
    [79 tests, 1 failure, 0.59 s]

sagetrac-dlucas · 2016-08-24T13:49:05Z

Changed branch from u/jsrn/21165_linear_code_cleanup to u/dlucas/21165_linear_code_cleanup

sagetrac-dlucas · 2016-08-24T13:51:42Z

comment:20

Hello,

Fixed.
Or, to be more specific, I already fixed it. Commit 189d8e5.
I pushed my branch once again, hopefully it will work this time.

BTW, I don't know what happened.
git trac pull 21165 returned already up-to-date with u/jsrn/21165_linear_code_cleanup.
Which explains why I did not catch that failing doctest: it's fixed on my side...

David

New commits:

`189d8e5`	`Fixed broken doctest in thematic tutorial`
`08bdda0`	`Merge branch 'u/jsrn/21165_linear_code_cleanup' of trac.sagemath.org:sage into 21165_linear_code_cleanup`

sagetrac-dlucas · 2016-08-24T13:51:42Z

Changed commit from c283cfc to 08bdda0

johanrosenkilde · 2016-08-25T08:50:39Z

comment:22

Tests pass now.

johanrosenkilde · 2016-08-25T08:50:39Z

Changed keywords from cleanup to cleanup, sd75

vbraun · 2016-08-27T08:38:03Z

Changed branch from u/dlucas/21165_linear_code_cleanup to 08bdda0

johanrosenkilde added this to the sage-7.3 milestone Aug 4, 2016

johanrosenkilde added c: coding theory labels Aug 4, 2016

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johanrosenkilde modified the milestones: sage-7.3, sage-7.4 Aug 18, 2016

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sagetrac-dlucas mannequin added s: positive review and removed s: needs review labels Aug 21, 2016

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vbraun closed this as completed in a76568c Aug 27, 2016

sagetrac-dlucas mannequin mentioned this issue Jan 21, 2017

Meta-ticket: enhancement of the coding theory part of Sage #18846

Closed

videlec mentioned this issue Sep 8, 2016

Doctest failure from #21165 #21402

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johanrosenkilde mentioned this issue May 8, 2018

Cleanup some deprecated functions (matrix and coding) #24680

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Various cleanup and deprecation in `sage.coding.linear_code` #21165

Various cleanup and deprecation in `sage.coding.linear_code` #21165

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Various cleanup and deprecation in sage.coding.linear_code #21165

Various cleanup and deprecation in sage.coding.linear_code #21165

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Various cleanup and deprecation in `sage.coding.linear_code` #21165

Various cleanup and deprecation in `sage.coding.linear_code` #21165