polish docs, minor compact fixes, and add makefile for automatic setup

[Fe-r-oz]

This PR addresses several minor improvements to documentation and testing:

• Fixes existing documentation, test, doctest errors. Adds some minor documentation.

Adds a Makefile to:

• Run tests with make test (without using the REPL).
  ̶-̶ ̶F̶o̶r̶m̶a̶t̶ ̶s̶o̶u̶r̶c̶e̶ ̶f̶i̶l̶e̶s̶ ̶u̶s̶i̶n̶g̶ ̶J̶u̶l̶i̶a̶F̶o̶r̶m̶a̶t̶t̶e̶r̶ ̶v̶i̶a̶ ̶̶m̶a̶k̶e̶ ̶f̶o̶r̶m̶a̶t̶̶.̶
• Test documentation builds with make docs.

We can skip the build, manifest in the docs folder as well by adding a .gitignore in docs.

̶ ̶̶m̶a̶k̶e̶ ̶f̶o̶r̶m̶a̶t̶̶ ̶c̶a̶n̶ ̶h̶e̶l̶p̶ ̶c̶a̶t̶c̶h̶ ̶s̶y̶n̶t̶a̶x̶ ̶e̶r̶r̶o̶r̶s̶,̶ ̶s̶u̶c̶h̶ ̶a̶s̶ ̶i̶n̶ ̶t̶h̶i̶s̶ ̶l̶i̶n̶e̶:̶ ̶

CodingTheory/src/Convolutional/convolutional_code.jl

Line 200 in 924bdf3

degree(C.G[r, c]) == C.vi[r] && (G_h[r, c] 1;)

I have changed this to degree(C.G[r, c]) == C.vi[r] && (G_h[r, c] = 1)

Changed this

CodingTheory/src/LDPC/simulations.jl

Line 876 in 924bdf3

err = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0]

to

err = zeros(Int, 254)
err[81] = 1

Changed @warn to !!! note in product codes. The @warn was causing issues in doctests by warnings errors during test execution. Replaced with!!! notefor cleaner documentation output.

Error in PlanarSurfaceCode

I ran most of the misc quantum codes, it appears there is bug in planer surface code.

Edit: It occurs due to a metacheck in setlogicals! : _has_equivalent_row_spaces(vcat(S.logs_mat, S.stabs), vcat(L, S.stabs)) || error("The current logicals are not equivalent to the input."). In this case, the second output might be more revealing as it shows indexing error

julia> PlanarSurfaceCode(2,2)
ERROR: The current logicals are not equivalent to the input.
Stacktrace:
 [1] error(s::String)
   @ Base ./error.jl:35
 [2] set_logicals!(::HasLogicals, S::StabilizerCodeCSS, L::Nemo.fpMatrix)
   @ CodingTheory ~/Desktop/New Folder14/ct/2/CodingTheory/src/Quantum/subsystem_code.jl:1405                                                           
 [3] set_logicals!(S::StabilizerCodeCSS, L::Nemo.fpMatrix)


julia> PlanarSurfaceCode(5,3)
ERROR: BoundsError: attempt to access 11x23 fpMatrix at index [12, 18]
Stacktrace:
 [1] throw_boundserror(A::fpMatrix, I::Tuple{Int64, Int64})
   @ Base ./essentials.jl:14
 [2] _checkbounds
   @ ~/.julia/packages/AbstractAlgebra/5aJmh/src/Matrix.jl:69 [inlined]
 [3] setindex!
   @ ~/.julia/packages/Nemo/tYNqm/src/flint/gfp_mat.jl:33 [inlined]
 [4] PlanarSurfaceCode(d_x::Int64, d_z::Int64)

[Fe-r-oz]

Hi @esabo, I hope you're doing well! Please help review this PR, Thank you!!

Summary of changes: I noticed some documentation build errors and test failures on master, so I fixed them. I also verified that most of the miscellaneous quantum code examples are running correctly. As a minor improvement, I’ve added a Makefile to simplify the build, debug and test process. Ran the JuliaFormatter via make format so that's why the changes. Removed build folder and manifest from docs by adding .gitigore. And some other minor changes.

[esabo]

The doc fixes cannot be pulled until the formatting throughout is returned to its previous state. The library is set to use a specific format that all code must conform to.

[Fe-r-oz]

Thanks for your feedback. I will rebase and undo the formatting change that was inspired by QuantumToolbox.jl.