Better Sage consistency for naming and calling in linear_code

[sagetrac-dlucas]

Some method and parameter names in linear_code.py file are abbreviated names which might be confusing (for instance the distance parameter actually stands for the minimum distance).
Most importantly, the gen_mat method will be renamed generator_matrix and the check_mat method parity_check_matrix.

Besides, some getter methods to access the private fields of linear codes exist but are not used internally in the class.
To support subclassing, it is better to use these instead of directly invoking a parameter.

CC: @johanrosenkilde @defeo @nathanncohen

Component: coding theory

Author: David Lucas

Branch/Commit: cd3c6ee

Reviewer: Nathann Cohen

Issue created by migration from https://trac.sagemath.org/ticket/17973

[sagetrac-dlucas]

Branch: u/dlucas/better_sage_consistency_for_naming_and_calling_in_linear_code

[sagetrac-dlucas]

New commits:

80770c5	Replaced gen_mat by generator_matrix
274d72e	Changed names of linear code parameters
f57ba38	Class parameters are now accessed by getter methods
7b7395e	Replaced check_mat method by parity_check_matrix

[sagetrac-dlucas]

Commit: 7b7395e

[sagetrac-dlucas]

Author: David Lucas

[nathanncohen]

comment:4

Hello !

I would say that this is good to go, except for one detail: could you deprecate the methods using deprecated_function_alias instead of doing it manually? There are some advantages, like a warning in the doc of the deprecated function. Besides, they do not appear in the lists of undocumented functions.

http://www.sagemath.org/doc/developer/coding_in_python.html#deprecation

Nathann

[sagetrac-git]

Changed commit from 7b7395e to 8813983

[sagetrac-git]

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

8813983

Replaced call to deprecation by the method deprecation_function_alias

[sagetrac-dlucas]

comment:6

It's done! I also replaced "check matrix" by "parity check matrix" in parity_check_matrix docstring for consistency with its new name.

[nathanncohen]

comment:8

There are two broken doctests in binary_code.pyx:

(tmp|✔)~/sage/coding$ sage -tp 4 -l binary_code.pyx
too many failed tests, not using stored timings
Running doctests with ID 2015-03-17-17-31-39-70361bd3.
Git branch: tmp
Doctesting 1 file using 4 threads.
sage -t --long binary_code.pyx
**********************************************************************
File "binary_code.pyx", line 1100, in sage.coding.binary_code.BinaryCode.apply_permutation
Failed example:
    B = BinaryCode(codes.ExtendedBinaryGolayCode().gen_mat())
Expected nothing
Got:
    doctest:1: DeprecationWarning: gen_mat is deprecated. Please use generator_matrix instead.
    See http://trac.sagemath.org/17973 for details.
**********************************************************************
File "binary_code.pyx", line 3858, in sage.coding.binary_code.BinaryCodeClassifier.put_in_canonical_form
Failed example:
    B = BinaryCode(codes.ExtendedBinaryGolayCode().gen_mat())
Expected nothing
Got:
    doctest:1: DeprecationWarning: gen_mat is deprecated. Please use generator_matrix instead.
    See http://trac.sagemath.org/17973 for details.
**********************************************************************
2 items had failures:
   1 of   6 in sage.coding.binary_code.BinaryCode.apply_permutation
   1 of   8 in sage.coding.binary_code.BinaryCodeClassifier.put_in_canonical_form
    [351 tests, 2 failures, 6.60 s]
----------------------------------------------------------------------
sage -t --long binary_code.pyx  # 2 doctests failed
----------------------------------------------------------------------
Total time for all tests: 6.7 seconds
    cpu time: 6.3 seconds
    cumulative wall time: 6.6 seconds

[nathanncohen]

Reviewer: Nathann Cohen

[nathanncohen]

comment:9

And many others in src/doc/en/constructions/linear_codes.rst. In some situations it is safer to run all of Sage's doctests just to make sure. There may be others in places I could not guess.

Nathann

[sagetrac-git]

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

7df4c04	Fixed 2 broken doctests
3059874	Fixed 4 broken doctests
cd3c6ee	Fixed 2 broken doctests

[sagetrac-git]

Changed commit from 8813983 to cd3c6ee

[sagetrac-dlucas]

comment:11

Thanks for the advice. I was indeed able to find some more after a make -ptestlong.

[nathanncohen]

comment:13

OKayyyyyyyyyyy then it's good to go !

Nathann

[vbraun]

Changed branch from u/dlucas/better_sage_consistency_for_naming_and_calling_in_linear_code to cd3c6ee