Merge branch 'dev' into infoset

.gitignore

@@ -18,6 +18,7 @@ learninggit.txt
 docs/.DS_Store
 *.txt
 typestest.jl
+simd_add_mul_wt_benchmarks.txt
 
 # profiling output stuff:
 *.pb.gz

Manifest.toml

@@ -2,7 +2,7 @@
 
 julia_version = "1.10.5"
 manifest_format = "2.0"
-project_hash = "2d6645f27d1e47bd5cddd8a51982054007baf2cb"
+project_hash = "163f71688893b1a2d676f6ba6e175eb2cf6dfafe"
 
 [[deps.ASL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -12,9 +12,9 @@ version = "0.1.3+0"
 
 [[deps.AbstractAlgebra]]
 deps = ["InteractiveUtils", "LinearAlgebra", "MacroTools", "Preferences", "Random", "RandomExtensions", "SparseArrays", "Test"]
-git-tree-sha1 = "45e46834b8fcfd59389939445267047577b19df5"
+git-tree-sha1 = "f7cd148a76ce9668c3fe36f29fcc9201adf14265"
 uuid = "c3fe647b-3220-5bb0-a1ea-a7954cac585d"
-version = "0.43.1"
+version = "0.43.5"
 
 [[deps.AbstractFFTs]]
 deps = ["LinearAlgebra"]
@@ -32,9 +32,9 @@ version = "1.5.0"
 
 [[deps.AlgebraicSolving]]
 deps = ["LinearAlgebra", "Logging", "Markdown", "Nemo", "Printf", "Random", "StaticArrays", "Test", "msolve_jll"]
-git-tree-sha1 = "59b14f801f508a03b0643713b22c4696bc52e445"
+git-tree-sha1 = "c68379967797de6ef0a9314f6c66d0803c455d48"
 uuid = "66b61cbe-0446-4d5d-9090-1ff510639f9d"
-version = "0.7.0"
+version = "0.7.2"
 
 [[deps.AliasTables]]
 deps = ["PtrArrays", "Random"]
@@ -56,10 +56,9 @@ version = "0.4.0"
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
 [[deps.AutoHashEquals]]
-deps = ["Pkg"]
-git-tree-sha1 = "daaeb6f7f77b88c072a83a2451801818acb5c63b"
+git-tree-sha1 = "4ec6b48702dacc5994a835c1189831755e4e76ef"
 uuid = "15f4f7f2-30c1-5605-9d31-71845cf9641f"
-version = "2.1.0"
+version = "2.2.0"
 
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -135,9 +134,9 @@ uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
 
 [[deps.Distributions]]
 deps = ["AliasTables", "FillArrays", "LinearAlgebra", "PDMats", "Printf", "QuadGK", "Random", "SpecialFunctions", "Statistics", "StatsAPI", "StatsBase", "StatsFuns"]
-git-tree-sha1 = "e6c693a0e4394f8fda0e51a5bdf5aef26f8235e9"
+git-tree-sha1 = "d7477ecdafb813ddee2ae727afa94e9dcb5f3fb0"
 uuid = "31c24e10-a181-5473-b8eb-7969acd0382f"
-version = "0.25.111"
+version = "0.25.112"
 
     [deps.Distributions.extensions]
     DistributionsChainRulesCoreExt = "ChainRulesCore"
@@ -168,9 +167,9 @@ version = "1.8.0"
 
 [[deps.FFTW_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
-git-tree-sha1 = "c6033cc3892d0ef5bb9cd29b7f2f0331ea5184ea"
+git-tree-sha1 = "4d81ed14783ec49ce9f2e168208a12ce1815aa25"
 uuid = "f5851436-0d7a-5f13-b9de-f02708fd171a"
-version = "3.3.10+0"
+version = "3.3.10+1"
 
 [[deps.FLINT_jll]]
 deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "MPFR_jll", "OpenBLAS32_jll"]
@@ -195,15 +194,15 @@ weakdeps = ["PDMats", "SparseArrays", "Statistics"]
 
 [[deps.GAP]]
 deps = ["AbstractAlgebra", "Artifacts", "Compat", "Downloads", "GAP_jll", "GAP_lib_jll", "GAP_pkg_juliainterface_jll", "InteractiveUtils", "Libdl", "MacroTools", "Markdown", "Ncurses_jll", "Pidfile", "Pkg", "REPL", "Random", "Scratch"]
-git-tree-sha1 = "b045754f9aae9f79df4b18b2e4df84887897105d"
+git-tree-sha1 = "e251aa4e3693eed790e2ee77ec0126e128894a56"
 uuid = "c863536a-3901-11e9-33e7-d5cd0df7b904"
-version = "0.11.4"
+version = "0.12.0"
 
 [[deps.GAP_jll]]
 deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Readline_jll", "Zlib_jll"]
-git-tree-sha1 = "becf60c941de1c38cea3dd76562c1c1d99052745"
+git-tree-sha1 = "eafd1208ec56d6b5d2a996adb7f0518652d68d4c"
 uuid = "5cd7a574-2c56-5be2-91dc-c8bc375b9ddf"
-version = "400.1300.102+0"
+version = "400.1300.102+2"
 
 [[deps.GAP_lib_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -213,9 +212,9 @@ version = "400.1300.100+0"
 
 [[deps.GAP_pkg_juliainterface_jll]]
 deps = ["Artifacts", "GAP_jll", "GAP_lib_jll", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "786044766785f5f2192f45de19acae5d1bb8885d"
+git-tree-sha1 = "72b707423fa4267ef7544ae012509bb1613ea5c8"
 uuid = "ba154793-3a7d-51ee-8800-e295b0cf7374"
-version = "0.900.100+0"
+version = "0.1200.0+0"
 
 [[deps.GLPK_jll]]
 deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -230,15 +229,15 @@ version = "6.2.1+6"
 
 [[deps.Graphs]]
 deps = ["ArnoldiMethod", "Compat", "DataStructures", "Distributed", "Inflate", "LinearAlgebra", "Random", "SharedArrays", "SimpleTraits", "SparseArrays", "Statistics"]
-git-tree-sha1 = "ebd18c326fa6cee1efb7da9a3b45cf69da2ed4d9"
+git-tree-sha1 = "1dc470db8b1131cfc7fb4c115de89fe391b9e780"
 uuid = "86223c79-3864-5bf0-83f7-82e725a168b6"
-version = "1.11.2"
+version = "1.12.0"
 
 [[deps.Hecke]]
 deps = ["AbstractAlgebra", "Dates", "Distributed", "InteractiveUtils", "LazyArtifacts", "Libdl", "LinearAlgebra", "Markdown", "Nemo", "Pkg", "Printf", "Random", "RandomExtensions", "Serialization", "SparseArrays"]
-git-tree-sha1 = "9257286b6ada9e8d0ae2a629bf13c51a149c5562"
+git-tree-sha1 = "00a2e1d65c458948530c3c68ab519e6b7b80f053"
 uuid = "3e1990a7-5d81-5526-99ce-9ba3ff248f21"
-version = "0.34.3"
+version = "0.34.4"
 weakdeps = ["GAP", "Polymake"]
 
     [deps.Hecke.extensions]
@@ -247,9 +246,9 @@ weakdeps = ["GAP", "Polymake"]
 
 [[deps.Hwloc_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "5e19e1e4fa3e71b774ce746274364aef0234634e"
+git-tree-sha1 = "dd3b49277ec2bb2c6b94eb1604d4d0616016f7a6"
 uuid = "e33a78d0-f292-5ffc-b300-72abe9b543c8"
-version = "2.11.1+0"
+version = "2.11.2+0"
 
 [[deps.HypergeometricFunctions]]
 deps = ["LinearAlgebra", "OpenLibm_jll", "SpecialFunctions"]
@@ -315,9 +314,9 @@ version = "18.1.7+0"
 
 [[deps.LZO_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "70c5da094887fd2cae843b8db33920bac4b6f07d"
+git-tree-sha1 = "854a9c268c43b77b0a27f22d7fab8d33cdb3a731"
 uuid = "dd4b983a-f0e5-5f8d-a1b7-129d4a5fb1ac"
-version = "2.10.2+0"
+version = "2.10.2+1"
 
 [[deps.LazyArtifacts]]
 deps = ["Artifacts", "Pkg"]
@@ -375,9 +374,9 @@ uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
 
 [[deps.Lz4_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "7f26c8fc5229e68484e0b3447312c98e16207d11"
+git-tree-sha1 = "abf88ff67f4fd89839efcae2f4c39cbc4ecd0846"
 uuid = "5ced341a-0733-55b8-9ab6-a4889d929147"
-version = "1.10.0+0"
+version = "1.10.0+1"
 
 [[deps.METIS_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
@@ -434,19 +433,19 @@ version = "1.25.1+0"
 
 [[deps.Mongoc]]
 deps = ["Dates", "DecFP", "MongoC_jll", "Serialization"]
-git-tree-sha1 = "f47bf7ed9d9c1da0a632777ca7dc406e3ad5f923"
+git-tree-sha1 = "1f0d7579d1bacc1446751990d7e0c4c0bf0f3277"
 uuid = "4fe8b98c-fc19-5c23-8ec2-168ff83495f2"
-version = "0.9.0"
+version = "0.9.1"
 
 [[deps.MozillaCACerts_jll]]
 uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
 version = "2023.1.10"
 
 [[deps.Ncurses_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "3ac1ca10bae513c9cc8f83d7734b921b8007b574"
+git-tree-sha1 = "3690e6c58c16ba676bcc9b5654762fe8a05db1c7"
 uuid = "68e3532b-a499-55ff-9963-d1c0c0748b3a"
-version = "6.5.0+0"
+version = "6.5.0+1"
 
 [[deps.Nemo]]
 deps = ["AbstractAlgebra", "FLINT_jll", "Libdl", "LinearAlgebra", "Pkg", "Random", "RandomExtensions", "SHA"]
@@ -499,7 +498,7 @@ version = "1.6.3"
 
 [[deps.Oscar]]
 deps = ["AbstractAlgebra", "AlgebraicSolving", "Distributed", "GAP", "Hecke", "JSON", "JSON3", "LazyArtifacts", "Markdown", "Nemo", "Pkg", "Polymake", "Random", "RandomExtensions", "Serialization", "Singular", "TOPCOM_jll", "UUIDs", "cohomCalg_jll"]
-git-tree-sha1 = "6e9ad54815c837a1a27d19280dddfca5f0f5bf03"
+git-tree-sha1 = "9aec1c8a631d474902d1274d6b4d683e4ae22357"
 repo-rev = "master"
 repo-url = "https://github.com/oscar-system/Oscar.jl.git"
 uuid = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
@@ -542,9 +541,9 @@ version = "1.10.0"
 
 [[deps.Polymake]]
 deps = ["AbstractAlgebra", "BinaryWrappers", "CxxWrap", "Downloads", "JSON", "Libdl", "Mongoc", "NetworkOptions", "Ninja_jll", "Perl_jll", "Pidfile", "Pkg", "REPL", "Scratch", "SparseArrays", "TOPCOM_jll", "lib4ti2_jll", "libpolymake_julia_jll", "polymake_jll", "polymake_oscarnumber_jll"]
-git-tree-sha1 = "fa518c47ef32714e99cb0915c45b564fb91fe5bc"
+git-tree-sha1 = "e065263f7e818a419bdc89979d7196222bb70efb"
 uuid = "d720cf60-89b5-51f5-aff5-213f193123e7"
-version = "0.11.21"
+version = "0.11.22"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
@@ -601,9 +600,9 @@ version = "0.4.4"
 
 [[deps.Readline_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Ncurses_jll"]
-git-tree-sha1 = "9d70e0c890a6c7ca3eb1ca0eaabba4d34795b7fb"
+git-tree-sha1 = "69684dc9c2c69f7c515097841991362cca0739ea"
 uuid = "05236dd9-4125-5232-aa7c-9ec0c9b2c25a"
-version = "8.2.1+0"
+version = "8.2.1+1"
 
 [[deps.Reexport]]
 git-tree-sha1 = "45e428421666073eab6f2da5c9d310d99bb12f9b"
@@ -659,15 +658,15 @@ version = "0.9.4"
 
 [[deps.Singular]]
 deps = ["AbstractAlgebra", "BinaryWrappers", "CxxWrap", "Libdl", "LinearAlgebra", "Nemo", "Pidfile", "Pkg", "Random", "RandomExtensions", "Singular_jll", "Statistics", "lib4ti2_jll", "libsingular_julia_jll"]
-git-tree-sha1 = "9b6135b5c8081f83eb2c334d7a7b903c2076aef7"
+git-tree-sha1 = "bc00189bb74b6a3f774253064f945d09fb1668ab"
 uuid = "bcd08a7b-43d2-5ff7-b6d4-c458787f915c"
-version = "0.23.7"
+version = "0.23.8"
 
 [[deps.Singular_jll]]
 deps = ["Artifacts", "FLINT_jll", "GMP_jll", "JLLWrappers", "Libdl", "MPFR_jll", "cddlib_jll"]
-git-tree-sha1 = "052417021e25f7aca4e81e17f5e12feb53f7ef00"
+git-tree-sha1 = "6c85174749476dcd3f059a33884072d748033263"
 uuid = "43d676ae-4934-50ba-8046-7a96366d613b"
-version = "404.0.605+0"
+version = "404.0.606+0"
 
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
@@ -805,9 +804,9 @@ version = "1.2.13+1"
 
 [[deps.Zstd_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "e678132f07ddb5bfa46857f0d7620fb9be675d3b"
+git-tree-sha1 = "555d1076590a6cc2fdee2ef1469451f872d8b41b"
 uuid = "3161d3a3-bdf6-5164-811a-617609db77b4"
-version = "1.5.6+0"
+version = "1.5.6+1"
 
 [[deps.bliss_jll]]
 deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -858,9 +857,9 @@ version = "0.12.1+0"
 
 [[deps.libsingular_julia_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl", "Singular_jll", "libcxxwrap_julia_jll"]
-git-tree-sha1 = "55003499aa923d492234577898643b0e1e471e9d"
+git-tree-sha1 = "436efe88c41337fd128062555fe8f8ea6c0e7309"
 uuid = "ae4fbd8f-ecdb-54f8-bbce-35570499b30e"
-version = "0.45.4+0"
+version = "0.45.6+0"
 
 [[deps.lrslib_jll]]
 deps = ["Artifacts", "GMP_jll", "JLLWrappers", "Libdl", "Pkg"]
@@ -916,6 +915,6 @@ version = "0.3.1+0"
 
 [[deps.snappy_jll]]
 deps = ["Artifacts", "JLLWrappers", "LZO_jll", "Libdl", "Lz4_jll", "Zlib_jll"]
-git-tree-sha1 = "8bc7ddafc0a7339b82a06c1dde849cd5039324d6"
+git-tree-sha1 = "d34e37153e4c03205bde2f0f8ada6cced8c83978"
 uuid = "fe1e1685-f7be-5f59-ac9f-4ca204017dfd"
-version = "1.2.0+0"
+version = "1.2.1+0"

Project.toml

@@ -14,6 +14,7 @@ Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
 JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
 LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
 Oscar = "f1435218-dba5-11e9-1e4d-f1a5fab5fc13"
+Hecke = "3e1990a7-5d81-5526-99ce-9ba3ff248f21"
 ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
 Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"

docs/make.jl

@@ -11,6 +11,7 @@ Documenter.makedocs(;
 	highlightsig = true,
 	sitename = "Coding Theory Documentation",
 	expandfirst = [],
+	warnonly = [:missing_docs],
     pages = ["Introduction" => "index.md",
 		"Tutorials" => [
 			"Tutorials/Linear Codes.md",

docs/src/Classical/cyclic_code.md

@@ -82,10 +82,6 @@ qcosets
 qcosets_reps
 ```
 
-```@docs
-defining_set
-```
-
 ```@docs
 zeros
 ```

docs/src/Classical/linear_code.md

@@ -31,6 +31,8 @@ cardinality
 rate
 ```
 
+See also: encode`
+
 If the linear code was created by passing in a generator (parity-check) matrix, then this matrix is stored in addition to the standard form. Note that this matrix is potentially over complete (has more rows than its rank). The standard form is returned when the optional parameter `stand_form` is set to true. Some code families are not constructed using these matrices. In these cases, the matrices are initially `missing` and are computed and cached when these functions are called for the first time. Direct access to the underlying structs is not recommended.
 ```@docs
 generator_matrix
@@ -50,9 +52,6 @@ standard_form_permutation
 ```
 
 The minimum distance of some code families are known and are set during construction. The minimum distance is automatically computed in the constructor for codes which are deemed "small enough". Otherwise, the minimum distance is `missing`. Primitive bounds on the minimum distance are given by
-```@docs
-minimum_distance_lower_bound
-```
 
 ```@docs
 minimum_distance_upper_bound
@@ -81,24 +80,18 @@ The minimum distance and its bounds may be manually set as well. Nothing is done
 set_distance_lower_bound!
 ```
 
-```@docs
-set_distance_upper_bound!
-```
-
 ```@docs
 set_minimum_distance!
 ```
 
+See: `minimum_distance_lower_bound`, `set_distance_upper_bound!`
+
 ## Methods
 
 ```@docs
 Singleton_bound
 ```
 
-```@docs
-encode
-```
-
 ```@docs
 syndrome
 ```

docs/src/Classical/new_codes_from_old.md

@@ -22,27 +22,26 @@ construction_X3
 ```
 
 The direct sum code has generator matrix `G1 ⊕ G2` and parity-check matrix `H1 ⊕ H2`.
+
 ```@docs
-CodingTheory.⊕
+⊕
 ```
 
 The generator matrix of the (direct) product code is the kronecker product of the generator matrices of the inputs.
+
 ```@docs
-CodingTheory.×
+×
 ```
 
 The parity-check matrix of the tensor product code is the kronecker product of the parity-check matrices of the inputs.
-```@docs
-CodingTheory.⊗
-```
 
 There is some debate on how to define this product. This is known to often be the full ambient space.
 ```@docs
 entrywise_product_code
 ```
 
 ```@docs
-CodingTheory./
+/
 ```
 
 `juxtaposition` is representation dependent and therefore works on the potentially over-complete generator matrices, not on the standard form.
@@ -52,10 +51,7 @@ juxtaposition
 
 ## Methods
 
-If `C` is a quasi-cyclic code, `permute_code` returns a `LinearCode` object.
-```@docs
-permute_code
-```
+If `C` is a quasi-cyclic code, `permute_code` returns a `LinearCode` object. See: `permute_code`
 
 The most common way to extend a code is to add an extra column to the generator matrix whose values make the sum of the rows zero. This is called an even extension and is the default for `extend(C)`. Alternatively, this new column may be inserted at any index `c` in the matrix, e.g. `extend(C, c)`. In the most general case, one may provide a vector `a` and define the values of the new column to be `-a` dot the row. The standard definition is clearly just the special case that `a` is the all-ones vector.
 ```@docs