Bicycle and Unicycle codes: Fixing doc and method errors #425

Benzillaist · 2024-11-13T11:20:43Z

Hi! I finally got around to addressing the problems with my previous commits. I made a few changes:

Updated doc strings to be consistent with the rest of the code
Added appropriate citation links
Fixed issue with outdated method calls in reduce_unitary

If you have the chance to review this and let me know if you want me to fix anything else, that would be great! Thanks so much :)

I was unable to open the previous pull request so I made a new one here.

Added multiple methods: code_generation: - Methods for creating Bicycle and Unicycle codes - Methods for assembling CSS codes - Utility methods for working with codes code_evaluation: - Methods for evaluating codes with a belief propagation decoder

Added the following dependencies: CairoMakie LDPCDecoders SparseArrays Statistics

During discussion with Anthony, he mentioned that he would add his code himself later on

- Fixed naming and organization issued identified. - Limited exports - Added additional methods to easily create unicycle and bicycle codes

- Fixed issues with typing in bicycle gen methods - Fixed issue with incorrectly copied methods for unicycle generation - Fixed imports for Nemo methods

Fixed bugs preventing the generation of Bicycle and Unicycle codes

Remove LDPCDecoders import Co-authored-by: Stefan Krastanov <[email protected]>

Updated use case description Co-authored-by: Stefan Krastanov <[email protected]>

Remove unused import Co-authored-by: Stefan Krastanov <[email protected]>

Update use case of Bicycle matrix Co-authored-by: Stefan Krastanov <[email protected]>

Updated CSS struct to use Hx and Hz instead of just the full tableau form. Updated CSS methods to work with the new struct form

…rd.jl-CSS_Builder

- Added more jldoctests for methods - Updated method descriptions with updated names - Fixed broken reduce_unicycle method - Added doc links to referenced papers

Krastanov

Thank you, this is shaping really well! I have not reviewed everything yet, but here is a first pass of things that can be polished a bit.

Krastanov · 2024-11-15T20:22:43Z

docs/src/references.bib

@@ -561,3 +561,22 @@ @article{haah2011local
  pages={042330},
  year={2011},
 }
+
+@article{mackay_sparse-graph_2004,


this reference already exists in the bib file, no need to add it again

Krastanov · 2024-11-15T20:23:30Z

test/test_ecc.jl

    end
-end
+
+function 


this seems to be causing a syntax error in the test runner

Krastanov · 2024-11-15T20:25:03Z

src/ecc/codes/simple_sparse_codes.jl

+    return comp_matrix
+end
+
+"""Attempts to generate a list of indices to be used in a bicycle code using a search method"""


Where is this algorithm from? Could you add that to the docstring?

I came up with it myself using the definition of a perfect difference set -- should I include a link to some article or definition on perfect difference sets?

Krastanov · 2024-11-15T20:25:46Z

src/ecc/codes/simple_sparse_codes.jl

+"""Attempts to generate a list of indices to be used in a bicycle code using a randomized check method
+
+Note: This is very slow for large N"""
+function bicycle_set_gen_rand(N::Int, d::Int)


Is this still used anywhere? If not, we should probably remove it.

Sounds good! I'm not really using it for anything, potentially thought it could be used to see some interesting results, but I agree that it's not superbly useful

Krastanov · 2024-11-15T20:28:04Z

src/ecc/codes/simple_sparse_codes.jl

+    circ_arr::Array{Int} = [0]
+    diff_arr::Array{Int} = []


the type-assert should be Vector{Int} -- Array{Int} is not concrete as it does not specify a dimmension, so type-stability will not be guaranteed.

This would also be more simply done as circ_arr = Int[0], etc

Krastanov · 2024-11-15T20:29:16Z

src/ecc/codes/simple_sparse_codes.jl

+julia> O = typeof(Bicycle(4, 2))
+Bicycle
+
+julia> O = parity_checks(Bicycle(4, 2))


Suggested change

julia> O = parity_checks(Bicycle(4, 2))

julia> parity_checks(Bicycle(4, 2))

Krastanov · 2024-11-15T20:29:25Z

src/ecc/codes/simple_sparse_codes.jl

+ XXXX
+ ZZZZ
+
+julia> O = parity_checks(Bicycle(6, 4))


Suggested change

julia> O = parity_checks(Bicycle(6, 4))

julia> parity_checks(Bicycle(6, 4))

Krastanov · 2024-11-15T20:30:16Z

src/ecc/codes/simple_sparse_codes.jl

+    if n%2 == 1
+        throw(DomainError(m, " N should be a multiple for 2 for bicycle codes."))
+    end
+    if n < 2
+        throw(DomainError(m, " N is too small, make it greater than 1."))
+    end


maybe in the error constructor you want n?

Krastanov · 2024-11-15T20:30:55Z

src/ecc/codes/simple_sparse_codes.jl

+"""Takes a height and width of matrix and generates a unicycle code to the specified height and width.
+Based on codes from [mackay_sparse-graph_2004](@cite)


The parameters do not seem to actually be height and width of a matrix

Krastanov · 2024-11-15T20:32:51Z

src/ecc/codes/simple_sparse_codes.jl

+"""Takes a height and width of matrix and generates a bicycle code to the specified height and width.
+Based on codes from [mackay_sparse-graph_2004](@cite)


This reads a bit more like a documentation for a function, not documentation for a type or structure. Start with saying what this thing is, only then worry about what the input parameters are (which is already said under the Paraments header)

Krastanov · 2024-11-15T20:34:29Z

I converted it to draft to make it a bit easier for me to manage my review queue.

Focused on updating the struct docstrings to be more descriptive of what the code is/does. Additionally cleaned up miscellaneous aspects of the code and remove unused function in simple_sparse_codes.jl

Benzillaist · 2024-11-16T06:34:51Z

Hi Stefan, thanks for the review! I went back through and updated a few things with a focus on the function headers. Please let me know if there are any other things that you'd like me to check for!

Krastanov

A few more points. Mostly interested in learning more about the generating algorithm for the bicycle case.

Krastanov · 2024-11-16T15:53:35Z

test/test_ecc_bivaraite_bicycle_as_twobga.jl

-        @test code_n(c) == 180 && code_k(c) == 8
-    end
-end
+# @testitem "ECC Bivaraite Bicycle as 2BGA" begin


You seem to have commented out a bunch of tests.

Checking out the files tab on github pull requests helps in catching this type of issues.

Krastanov · 2024-11-16T16:00:58Z

docs/src/references.bib

@@ -560,4 +560,4 @@ @article{haah2011local
  number={4},
  pages={042330},
  year={2011},
-}
+}


A couple of files have their ending byte modified. For consistency and to keep the git history clean, it helps to set your editor to automatically take care of these.

In vscode for instance:

you can include these entries:

{ "files.trimFinalNewlines": true, "files.trimTrailingWhitespace": true, "editor.rulers": [92], "files.eol": "\n" }

Krastanov · 2024-11-16T16:03:28Z

src/ecc/codes/simple_sparse_codes.jl

+    return comp_matrix
+end
+
+"""Attempts to generate a list of indices to be used in a bicycle code using a search method given a matrix width (N)"""


why "attempts"? Is this algorithm from the paper? Can you specify where in it if it is. If not, could you explain what the user should worry about with it?

Krastanov · 2024-11-16T16:05:49Z

src/ecc/codes/simple_sparse_codes.jl

+    circ_arr = Int[0]
+    diff_arr = Int[]
+    circ_arr[1] = 0


circ_arr already has its first element set to 0 in the first line

Benzillaist and others added 21 commits October 31, 2023 19:40

Added dependencies

92f6eeb

Added the following dependencies: CairoMakie LDPCDecoders SparseArrays Statistics

Removed pauli frame code

1c0fcdb

During discussion with Anthony, he mentioned that he would add his code himself later on

Fixed naming and organization issues +

f77b135

- Fixed naming and organization issued identified. - Limited exports - Added additional methods to easily create unicycle and bicycle codes

minor cleanup

6c3434c

Fixed bugs preventing the generation of Bicycle and Unicycle codes

077e287

- Fixed issues with typing in bicycle gen methods - Fixed issue with incorrectly copied methods for unicycle generation - Fixed imports for Nemo methods

Merge pull request #1 from Benzillaist/testing-simple_branch_codes

a115ef5

Fixed bugs preventing the generation of Bicycle and Unicycle codes

Update Project.toml

81773e3

Remove LDPCDecoders import Co-authored-by: Stefan Krastanov <[email protected]>

Update src/ecc/ECC.jl

cac4133

Remove LDPCDecoders import Co-authored-by: Stefan Krastanov <[email protected]>

Update src/ecc/simple_sparse_codes.jl

2eb3eb4

Updated use case description Co-authored-by: Stefan Krastanov <[email protected]>

Update src/ecc/ECC.jl

49046fe

Remove unused import Co-authored-by: Stefan Krastanov <[email protected]>

Update src/ecc/simple_sparse_codes.jl

f86cd86

Update use case of Bicycle matrix Co-authored-by: Stefan Krastanov <[email protected]>

Moved CSS files to codes folder and updated CSS struct

bd823ef

Updated CSS struct to use Hx and Hz instead of just the full tableau form. Updated CSS methods to work with the new struct form

Merge branch 'master' of https://github.com/Benzillaist/QuantumCliffo…

295ed67

…rd.jl-CSS_Builder

Fixed errors with generation of codes and added description text

b64baa3

Fixed list of codes in symdrome tests

3a374d8

Handled merge conflicts created with QuantumClifford updates

1fe07f4

Fixed last merge conflict with including new LDPC codes

925009d

Fixed issues with documentation and outdated method errors

c1bba5b

- Added more jldoctests for methods - Updated method descriptions with updated names - Fixed broken reduce_unicycle method - Added doc links to referenced papers

Merge branch 'master' into pr/425

b79e3ee

Removed extraneous vscode data

6e31250

Krastanov requested changes Nov 15, 2024

View reviewed changes

Krastanov marked this pull request as draft November 15, 2024 20:34

Update of struct descriptions

94caf05

Focused on updating the struct docstrings to be more descriptive of what the code is/does. Additionally cleaned up miscellaneous aspects of the code and remove unused function in simple_sparse_codes.jl

Benzillaist marked this pull request as ready for review November 16, 2024 06:34

Krastanov requested changes Nov 16, 2024

View reviewed changes

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Bicycle and Unicycle codes: Fixing doc and method errors #425

Bicycle and Unicycle codes: Fixing doc and method errors #425

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	julia> O = parity_checks(Bicycle(4, 2))
	julia> parity_checks(Bicycle(4, 2))

	julia> O = parity_checks(Bicycle(6, 4))
	julia> parity_checks(Bicycle(6, 4))

		"""Takes a height and width of matrix and generates a unicycle code to the specified height and width.
		Based on codes from [mackay_sparse-graph_2004](@cite)

Bicycle and Unicycle codes: Fixing doc and method errors #425

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Bicycle and Unicycle codes: Fixing doc and method errors #425

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Benzillaist commented Nov 13, 2024 • edited Loading

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Krastanov commented Nov 15, 2024

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Benzillaist commented Nov 13, 2024 •

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