36 changed files with 1584 additions and 1316 deletions
--- a/.JuliaFormatter.toml
+++ b/.JuliaFormatter.toml
@ -1,2 +0,0 @@
 # See https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options
 style = "blue"
--- a/.gitignore
+++ b/.gitignore
@ -1,96 +0,0 @@
 ### Linux gitignore ###
 *~
 # temporary files which can be created if a process still has a handle open of a deleted file
 .fuse_hidden*
 # Metadata left by Dolphin file manager, which comes with KDE Plasma
 .directory
 # Linux trash folder which might appear on any partition or disk
 .Trash-*
 # .nfs files are created when an open file is removed but is still being accessed
 .nfs*
 # Log files created by default by the nohup command
 nohup.out
 ### MacOS gitignore ###
 # General
 .DS_Store
 __MACOSX/
 .AppleDouble
 .LSOverride
 Icon[]
 # Thumbnails
 ._*
 # Files that might appear in the root of a volume
 .DocumentRevisions-V100
 .fseventsd
 .Spotlight-V100
 .TemporaryItems
 .Trashes
 .VolumeIcon.icns
 .com.apple.timemachine.donotpresent
 # Directories potentially created on remote AFP share
 .AppleDB
 .AppleDesktop
 Network Trash Folder
 Temporary Items
 .apdisk
 ### Vim gitignore ###
 # Swap
 [._]*.s[a-v][a-z]
 # comment out the next line if you don't need vector files
 !*.svg
 [._]*.sw[a-p]
 [._]s[a-rt-v][a-z]
 [._]ss[a-gi-z]
 [._]sw[a-p]
 # Session
 Session.vim
 Sessionx.vim
 # Temporary
 .netrwhist
 *~
 # Auto-generated tag files
 tags
 # Persistent undo
 [._]*.un~
 ### Julia gitignore ###
 # Files generated by invoking Julia with --code-coverage
 *.jl.cov
 *.jl.*.cov
 # Files generated by invoking Julia with --track-allocation
 *.jl.mem
 # System-specific files and directories generated by the BinaryProvider and BinDeps packages
 # They contain absolute paths specific to the host computer, and so should not be committed
 deps/deps.jl
 deps/build.log
 deps/downloads/
 deps/usr/
 deps/src/
 # Build artifacts for creating documentation generated by the Documenter package
 docs/build/
 docs/site/
 # File generated by Pkg, the package manager, based on a corresponding Project.toml
 # It records a fixed state of all packages used by the project. As such, it should not be
 # committed for packages, but should be committed for applications that require a static
 # environment.
 Manifest*.toml
 # File generated by the Preferences package to store local preferences
 LocalPreferences.toml
 JuliaLocalPreferences.toml
--- a/.woodpecker/docs.yaml
+++ b/.woodpecker/docs.yaml
@ -1,21 +0,0 @@
 when:
  branch: master
  event: push
 clone:
  git:
    image: woodpeckerci/plugin-git
    settings:
      partial: false
      depth: 0
 steps:
  docs:
    image: julia:1
    commands:
      - julia --project=docs/ -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'
      - julia --project=docs/ docs/make.jl
    environment:
      JULIA_NUM_THREADS: "1"
      PROJECT_ACCESS_TOKEN:
        from_secret: project_access_token
--- a/.woodpecker/test.yaml
+++ b/.woodpecker/test.yaml
@ -1,18 +0,0 @@
 matrix:
  JULIA_VERSION:
    - "1.12"
    - "1"
    - "rc"
 when:
  event: [pull_request, push]
 steps:
  test:
    image: julia:${JULIA_VERSION}
    pull: true
    commands:
      - julia -e 'using InteractiveUtils; versioninfo()'
      - julia --project=@. -e 'using Pkg; Pkg.instantiate(); Pkg.build(); Pkg.test();'
    environment:
      JULIA_NUM_THREADS: "1"
--- a/690
+++ b/690
@ -1,690 +0,0 @@
 Copyright (C) 2026 Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> and contributors
 This program is free software: you can redistribute it and/or modify
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 You should have received a copy of the GNU General Public License
 along with this program.  If not, see <https://www.gnu.org/licenses/>.
                    GNU GENERAL PUBLIC LICENSE
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 combination as such.
  14. Revised Versions of this License.
  The Free Software Foundation may publish revised and/or new versions of
 the GNU General Public License from time to time.  Such new versions will
 be similar in spirit to the present version, but may differ in detail to
 address new problems or concerns.
  Each version is given a distinguishing version number.  If the
 Program specifies that a certain numbered version of the GNU General
 Public License "or any later version" applies to it, you have the
 option of following the terms and conditions either of that numbered
 version or of any later version published by the Free Software
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 by the Free Software Foundation.
  If the Program specifies that a proxy can decide which future
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 public statement of acceptance of a version permanently authorizes you
 to choose that version for the Program.
  Later license versions may give you additional or different
 permissions.  However, no additional obligations are imposed on any
 author or copyright holder as a result of your choosing to follow a
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  15. Disclaimer of Warranty.
  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
 APPLICABLE LAW.  EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
 HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
 OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
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 IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
 ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
  16. Limitation of Liability.
  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
 WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
 THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
 GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
 USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
 DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
 PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
 EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
 SUCH DAMAGES.
  17. Interpretation of Sections 15 and 16.
  If the disclaimer of warranty and limitation of liability provided
 above cannot be given local legal effect according to their terms,
 reviewing courts shall apply local law that most closely approximates
 an absolute waiver of all civil liability in connection with the
 Program, unless a warranty or assumption of liability accompanies a
 copy of the Program in return for a fee.
                     END OF TERMS AND CONDITIONS
            How to Apply These Terms to Your New Programs
  If you develop a new program, and you want it to be of the greatest
 possible use to the public, the best way to achieve this is to make it
 free software which everyone can redistribute and change under these terms.
  To do so, attach the following notices to the program.  It is safest
 to attach them to the start of each source file to most effectively
 state the exclusion of warranty; and each file should have at least
 the "copyright" line and a pointer to where the full notice is found.
    <one line to give the program's name and a brief idea of what it does.>
    Copyright (C) <year>  <name of author>
    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.
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    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.
    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <https://www.gnu.org/licenses/>.
 Also add information on how to contact you by electronic and paper mail.
  If the program does terminal interaction, make it output a short
 notice like this when it starts in an interactive mode:
    <program>  Copyright (C) <year>  <name of author>
    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
    This is free software, and you are welcome to redistribute it
    under certain conditions; type `show c' for details.
 The hypothetical commands `show w' and `show c' should show the appropriate
 parts of the General Public License.  Of course, your program's commands
 might be different; for a GUI interface, you would use an "about box".
  You should also get your employer (if you work as a programmer) or school,
 if any, to sign a "copyright disclaimer" for the program, if necessary.
 For more information on this, and how to apply and follow the GNU GPL, see
 <https://www.gnu.org/licenses/>.
  The GNU General Public License does not permit incorporating your program
 into proprietary programs.  If your program is a subroutine library, you
 may consider it more useful to permit linking proprietary applications with
 the library.  If this is what you want to do, use the GNU Lesser General
 Public License instead of this License.  But first, please read
 <https://www.gnu.org/licenses/why-not-lgpl.html>.
--- a/Project.toml
+++ b/Project.toml
@ -1,17 +0,0 @@
 name = "CualerID"
 uuid = "a4892dd5-cee5-4429-912e-1922c40e7f9b"
 version = "0.0.1"
 authors = ["Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> and contributors"]
 [deps]
 ArgParse = "c7e460c6-2fb9-53a9-8c5b-16f535851c63"
 FilePathsBase = "48062228-2e41-5def-b9a4-89aafe57970f"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 [compat]
 ArgParse = "1.2.0"
 FilePathsBase = "0.9.24"
 UUIDs = "1.11.0"
 julia = "1.12"
 [apps.cualer-id]
--- a/README.md
+++ b/README.md
@ -1,4 +0,0 @@
 # CualerID
 [![Code Style: Blue](https://img.shields.io/badge/code%20style-blue-4495d1.svg)](https://github.com/invenia/BlueStyle)
 [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl)
--- a/dev/.documenter-siteinfo.json
+++ b/dev/.documenter-siteinfo.json
@ -0,0 +1 @@
 {"documenter":{"julia_version":"1.12.5","generation_timestamp":"2026-02-13T03:53:22","documenter_version":"1.16.1"}}
--- a/dev/assets/documenter.js
+++ b/dev/assets/documenter.js
--- a/dev/assets/themes/catppuccin-frappe.css
+++ b/dev/assets/themes/catppuccin-frappe.css
--- a/dev/assets/themes/catppuccin-latte.css
+++ b/dev/assets/themes/catppuccin-latte.css
--- a/dev/assets/themes/catppuccin-macchiato.css
+++ b/dev/assets/themes/catppuccin-macchiato.css
--- a/dev/assets/themes/catppuccin-mocha.css
+++ b/dev/assets/themes/catppuccin-mocha.css
--- a/dev/assets/themes/documenter-dark.css
+++ b/dev/assets/themes/documenter-dark.css
--- a/dev/assets/themes/documenter-light.css
+++ b/dev/assets/themes/documenter-light.css
--- a/dev/assets/themeswap.js
+++ b/dev/assets/themeswap.js
@ -0,0 +1,84 @@
 // Small function to quickly swap out themes. Gets put into the <head> tag..
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  }
  // Check if the users preference is for dark color scheme
  var darkPreference =
    window.matchMedia("(prefers-color-scheme: dark)").matches === true;
  // Initialize a few variables for the loop:
  //
  //  - active: will contain the index of the theme that should be active. Note that there
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  for (var i = 0; i < document.styleSheets.length; i++) {
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    // The <link> tag of each style sheet is expected to have a data-theme-name attribute
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    // If we did find an active theme, we'll (1) add the theme--$(theme) class to <html>
    document.getElementsByTagName("html")[0].className = "theme--" + theme;
    activeTheme = theme;
  } else {
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    if (activeTheme === null) {
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      return;
    }
    // When switching to the primary light theme, then we must not have a class name
    // for the <html> tag. That's only for non-primary or the primary dark theme.
    if (darkPreference) {
      document.getElementsByTagName("html")[0].className =
        "theme--" + activeTheme;
    } else {
      document.getElementsByTagName("html")[0].className = "";
    }
  }
  for (var i = 0; i < document.styleSheets.length; i++) {
    var ss = document.styleSheets[i];
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    // which must contain the name of the theme. The names in localStorage much match this.
    var themename = ss.ownerNode.getAttribute("data-theme-name");
    // attribute not set => non-theme stylesheet => ignore
    if (themename === null) continue;
    // we'll disable all the stylesheets, except for the active one
    ss.disabled = !(themename == activeTheme);
  }
 }
 set_theme_from_local_storage();
--- a/dev/assets/warner.js
+++ b/dev/assets/warner.js
@ -0,0 +1,68 @@
 function maybeAddWarning() {
  // DOCUMENTER_NEWEST is defined in versions.js, DOCUMENTER_CURRENT_VERSION and DOCUMENTER_STABLE
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    '<a href="' +
    href +
    '">Click here to go to the documentation for the latest stable release.</a>';
  div.innerHTML = warningMessage;
  div.appendChild(closer);
  document.body.appendChild(div);
 }
 if (document.readyState === "loading") {
  document.addEventListener("DOMContentLoaded", maybeAddWarning);
 } else {
  maybeAddWarning();
 }
--- a/dev/index.html
+++ b/dev/index.html
--- a/dev/objects.inv
+++ b/dev/objects.inv
--- a/dev/search_index.js
+++ b/dev/search_index.js
@ -0,0 +1,3 @@
 var documenterSearchIndex = {"docs":
 [{"location":"#CualerID","page":"Home","title":"CualerID","text":"Documentation for CualerID.\n\n","category":"section"},{"location":"#CualerID.BASE30_ALPHABET","page":"Home","title":"CualerID.BASE30_ALPHABET","text":"BASE30_ALPHABET::Vector{UInt8}\n\nAn alphabet designed for unambiguous representation of values in either upper- or lower-case. The alphabet was formed by taking the numbers 0-9 and the Latin alphabet and removing characters that are considered easy to confuse. Excluded characters are\n\nI => easily confused for lowercase L or the digit 1\nL => easily confused for uppercase I or the digit 1\nO => easily confused for the digit 0\nQ => easily confused with uppercase O or lowercase g\nV => easily confused with U\n\nThis array contains the ASCII index of the characters included in the base30 alphabet starting with 0 at position BASE30_ALPHABET[1]. Use String() to convert an array of these indices to a base30 string.\n\n\n\n\n\n","category":"constant"},{"location":"#CualerID.ResultCode","page":"Home","title":"CualerID.ResultCode","text":"ResultCode::UInt8\n\nEncodes a result of attempting to correct a CualerID\n\nThe valid codes are\n\nD: duplicate\nF: fixed\nN: not fixable\nV: valid (no need for correction)\n\n\n\n\n\n","category":"type"},{"location":"#CualerID.ResultCodeOption","page":"Home","title":"CualerID.ResultCodeOption","text":"ResultCodeOption\n\nEncodes potential corrected id codes.\n\nThe valid codes are\n\nD: duplicate\nF: fixed\nN: not fixable\nV: valid (no need for correction)\n\nThe codes are implemented exactly as from cual-id and in that order\n\nConstructors\n\nResultCodeOption(str::AbstractString)\n\nCreate a ResultCodeOption based on a the character codes contained within str. str is case insensitive, may contain an arbitrary number of valid codes (as specified above), and may contain duplicates. A ResultCodeOption cannot be constructed from a combination of strings and bitmasks/integers.\n\nExtended help\n\nThe struct stores values as a bitmask\n\nBit (Int) Bit (UInt) Description\n1 0x01 D - duplicate\n2 0x02 F - fixed\n4 0x04 N - not fixable\n8 0x08 V - valid\n\n\n\n\n\n","category":"type"},{"location":"#CualerID.base30encode-Tuple{Integer}","page":"Home","title":"CualerID.base30encode","text":"base30encode(v::Integer)\nbase30encode(v::UUID)\n\nCreates a base30 representation of v. If v is a UUID, then the UInt128 value of the UUID is passed directly into the method.\n\nExamples\n\njulia> base30encode(30)\n\"10\"\n\njulia> using UUIDs\n\njulia> base30encode(UUIDs.uuid1())\n\"7ZK00JECBDF2H7GNBXN59C6S9S\"\n\nwarning: Warning\nJust like rebase, this method is not tested on negative integers and may produce incorrect output when passed negative numbers\n\n\n\n\n\n","category":"method"},{"location":"#CualerID.has_duplicate-Tuple{ResultCodeOption}","page":"Home","title":"CualerID.has_duplicate","text":"has_duplicate(r::ResultCodeOption)\n\nDetermines if r contains a duplicate result (ResultCode D)\n\n\n\n\n\n","category":"method"},{"location":"#CualerID.has_fixed-Tuple{ResultCodeOption}","page":"Home","title":"CualerID.has_fixed","text":"has_fixed(r::ResultCodeOption)\n\nDetermines if r contains a fixed result (ResultCode F)\n\n\n\n\n\n","category":"method"},{"location":"#CualerID.has_not_fixable-Tuple{ResultCodeOption}","page":"Home","title":"CualerID.has_not_fixable","text":"has_not_fixable(r::ResultCodeOption)\n\nDetermines if r contains a not fixable result (ResultCode N)\n\n\n\n\n\n","category":"method"},{"location":"#CualerID.has_valid-Tuple{ResultCodeOption}","page":"Home","title":"CualerID.has_valid","text":"has_valid(r::ResultCodeOption)\n\nDetermines if r contains a valid (not corrected) result (ResultCode V)\n\n\n\n\n\n","category":"method"},{"location":"#CualerID.rebase-Tuple{Integer, Integer}","page":"Home","title":"CualerID.rebase","text":"rebase(v::Integer, base::Integer)\n\nRebase v into the base system of base. v can be any integer type, and can be represented in base 10 (decimal) or base 16 (hexadecimal) based on Julia's treatment of that integer type. Returns a Vector{UInt8} containing the indices of each digit in the rebased number. Since Julia is 1-indexed, this means that rebase(0, base)[1] actually returns a value of UInt8[1], since the first index of a numeral system's alphabet is assumed to be its 0 value.\n\nExamples\n\njulia> rebase(0, 10)\n1-element Vector{UInt8}:\n 0x01\n\njulia> # Two plus two is ten... IN BASE FOUR! I'M FINE!\n\njulia> rebase(2 + 2, 4)\n2-element Vector{UInt8}:\n 0x02\n 0x01\n\njulia> base_4_alphabet = ['0', '1', '2', '3'];\n\njulia> String([base_4_alphabet[i] for i in rebase(2 + 2, 4)])\n\"10\"\n\nwarning: Warning\nThis method is not tested on negative integers and may produce incorrect output when passed negative numbers\n\n\n\n\n\n","category":"method"}]
 }
--- a/dev/siteinfo.js
+++ b/dev/siteinfo.js
@ -0,0 +1,2 @@
 var DOCUMENTER_CURRENT_VERSION = "dev";
 var DOCUMENTER_IS_DEV_VERSION = true;
--- a/docs/Project.toml
+++ b/docs/Project.toml
@ -1,3 +0,0 @@
 [deps]
 CualerID = "a4892dd5-cee5-4429-912e-1922c40e7f9b"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
--- a/docs/make.jl
+++ b/docs/make.jl
@ -1,46 +0,0 @@
 using CualerID
 using Documenter
 DocMeta.setdocmeta!(CualerID, :DocTestSetup, :(using CualerID); recursive = true)
 struct Gitea <: Documenter.Remote
    host::String
    user::String
    repo::String
 end #struct
 function Documenter.Remotes.repourl(remote::Gitea)
    return "https://$(remote.host)/$(remote.user)/$(remote.repo)"
 end #function
 function Documenter.Remotes.fileurl(remote::Gitea, ref, filename, linerange = nothing)
    linerange_addition = if !isnothing(linerange)
        if first(linerange) == last(linerange)
            "#L$(first(linerange))"
        else
            "#L$(first(linerange))-L$(last(linerange))"
        end #if
    else
        ""
    end #if
    return "https://$(remote.host)/$(remote.user)/$(remote.repo)/src/commit/$ref/$filename$linerange_addition"
 end #function
 function Documenter.Remotes.issueurl(remote::Gitea, issuenumber)
    return "https://$(remote.host)/$(remote.user)/$(remote.repo)/issues/$issuenumber"
 end #function
 makedocs(;
    modules = [CualerID],
    authors = "Thomas A. Christensen II <25492070+MillironX@users.noreply.github.com> and contributors",
    sitename = "CualerID.jl",
    repo = Gitea("code.millironx.com", "millironx", "CualerID.jl"),
    format = Documenter.HTML(; edit_link = "", assets = String[]),
    pages = ["Home" => "index.md"],
 )
 deploydocs(;
    repo = "code.millironx.com/millironx/CualerID.jl",
    devbranch = "master",
    branch = "pages",
 )
--- a/docs/src/index.md
+++ b/docs/src/index.md
@ -1,14 +0,0 @@
 ```@meta
 CurrentModule = CualerID
 ```
 # CualerID
 Documentation for [CualerID](https://code.millironx.com/millironx/CualerID.jl).
 ```@index
 ```
 ```@autodocs
 Modules = [CualerID]
 ```
--- a/index.html
+++ b/index.html
@ -0,0 +1,2 @@
 <!--This file is automatically generated by Documenter.jl-->
 <meta http-equiv="refresh" content="0; url=./dev/"/>
--- a/src/Base30.jl
+++ b/src/Base30.jl
@ -1,54 +0,0 @@
 """
    BASE30_ALPHABET::Vector{UInt8}
 An alphabet designed for unambiguous representation of values in either upper-
 or lower-case. The alphabet was formed by taking the numbers 0-9 and the Latin
 alphabet and removing characters that are considered easy to confuse. Excluded
 characters are
 - ``I`` => easily confused for lowercase ``L`` or the digit ``1``
 - ``L`` => easily confused for uppercase ``I`` or the digit ``1``
 - ``O`` => easily confused for the digit ``0``
 - ``Q`` => easily confused with uppercase ``O`` or lowercase ``g``
 - ``V`` => easily confused with ``U``
 This array contains the ASCII index of the characters included in the base30
 alphabet starting with 0 at position `BASE30_ALPHABET[1]`. Use `String()` to
 convert an array of these indices to a base30 string.
 """
 const BASE30_ALPHABET = UInt8.([
    48:57..., #0-9
    65:72..., #A-H
    74:75..., #J-K
    77:78..., #M-N
    80, #P
    83:85..., #S-U
    87:90..., #W-Z
 ])
 """
    base30encode(v::Integer)
    base30encode(v::UUID)
 Creates a base30 representation of `v`. If `v` is a `UUID`, then the `UInt128`
 value of the `UUID` is passed directly into the method.
 # Examples
 ```jldoctest
 julia> base30encode(30)
 "10"
 ```
 ```julia-repl
 julia> using UUIDs; base30encode(uuid1())
 "7ZK00JECBDF2H7GNBXN59C6S9S"
 ```
 """
 function base30encode(v::Integer)
    return String([BASE30_ALPHABET[i] for i in reverse(digits(v; base = 30) .+ 1)])
 end #function
 function base30encode(v::UUID)
    return base30encode(v.value)
 end #function
--- a/src/CualerID.jl
+++ b/src/CualerID.jl
@ -1,174 +0,0 @@
 module CualerID
 using ArgParse: ArgParse, ArgParseSettings, parse_args, parse_item, @add_arg_table!
 using FilePathsBase: AbstractPath, Path, exists, isfile
 using UUIDs: UUID
 include("Base30.jl")
 include("ResultCodeOption.jl")
 include("Minting.jl")
 export ResultCode
 export ResultCodeOption
 export base30encode
 export has_duplicate
 export has_fixed
 export has_not_fixable
 export has_valid
 function _create_arg_table()
    s = ArgParseSettings(autofix_names = true)
    #! format: off
    @add_arg_table! s begin
        "create"
            help = "Create CualerID sample ids or barcode labels"
            action = :command
        "fix"
            help = "Compare a set of possibly invalid IDs against a correct set of IDs to identify errors in the IDs"
            action = :command
        "convert"
            help = "Convert CualID sample ids to CualerID sample ids or vice-versa"
            action = :command
    end #add_arg_table
    @add_arg_table! s["create"] begin
        "ids"
            help = "Generate sample ids"
            action = :command
        "labels"
            help = "Generate a pdf of barcodes (NOT YET IMPLEMENTED)"
            action = :command
    end #add_arg_table
    @add_arg_table! s["create"]["ids"] begin
        "--length", "-l"
            help = "The length of the printed sample ids"
            arg_type = UInt64
            default = UInt64(5)
        "--fail-threshold", "-f"
            help = "NOT IMPLEMENTED: The rate at which similar ids will fail the process"
            arg_type = Float64
            range_tester = x -> x >= 0 && x <= 1.0
            default = 0.99
        "number_of_ids"
            help = "The number of sample ids to print"
            arg_type = UInt64
            range_tester = x -> x >= 1
            required = true
    end #add_arg_table
    @add_arg_table! s["fix"] begin
        "--correct-ids"
            help = "Path to the list of correct ids"
            arg_type = AbstractPath
            range_tester = x -> exists(x) && isfile(x)
            required = true
        "--show", "-s"
            help = """
                Which types of fixes should be printed to output. Can be a
                combination of D for duplicate, F for fixed, N for not fixable,
                and V for valid.
                """
            arg_type = ResultCodeOption
            default = ResultCodeOption("DFN")
        "--all", "-a"
            help = "Show all ids regardless of fixed status"
            action = :store_true
        "ids_to_be_corrected"
            help = "File containing CualerIDs that need correction"
            arg_type = AbstractPath
            range_tester = x -> exists(x) && isfile(x)
            required = true
    end #add_arg_table
    @add_arg_table! s["convert"] begin
        "--length", "-l"
            help = "The length of the printed sample ids"
            arg_type = UInt64
            default = UInt64(5)
        "--fail-threshold", "-f"
            help = "NOT IMPLEMENTED: The rate at which similar ids will fail the process"
            arg_type = Float64
            range_tester = x -> x >= 0 && x <= 1.0
            default = 0.99
        "--to-cual-id"
            help = "Convert from CualerID to CualID"
            action = :store_true
        "ids_to_be_converted"
            help = "TSV file containing CualIDs or CualerIDs to be converted"
            arg_type = AbstractPath
            range_tester = x -> exists(x) && isfile(x)
            required = true
    end #@add_arg_table!
    #! format: on
    return s
 end #function
 const ARG_PARSE_TABLE = _create_arg_table()
 function _create(parsed_args::Dict{Symbol,Any})
    if parsed_args[:_COMMAND_] == :ids
        _create_ids(parsed_args[:ids])
    elseif parsed_args[:_COMMAND_] == :labels
        _create_labels(parsed_args[:labels])
    end #if
    return 0
 end #function
 function _create_ids(parsed_args::Dict{Symbol,Any})
    println("COMMAND:\tcreate ids")
    for (key, val) in parsed_args
        println("\t$key:\t$val")
    end #function
    return 0
 end #function
 function _create_labels(parsed_args::Dict{Symbol,Any})
    println("COMMAND:\tcreate labels")
    for (key, val) in parsed_args
        println("\t$key:\t$val")
    end #function
    return 0
 end #function
 function _fix(parsed_args::Dict{Symbol,Any})
    println("COMMAND:\tfix")
    for (key, val) in parsed_args
        println("\t$key:\t$val")
    end #function
    return 0
 end #function
 function _convert(parsed_args::Dict{Symbol,Any})
    println("COMMAND:\tconvert")
    for (key, val) in parsed_args
        println("\t$key:\t$val")
    end #function
    return 0
 end #function
 function (@main)()
    parsed_args = parse_args(ARG_PARSE_TABLE; as_symbols = true)
    if parsed_args[:_COMMAND_] == :create
        _create(parsed_args[:create])
    elseif parsed_args[:_COMMAND_] == :fix
        _fix(parsed_args[:fix])
    elseif parsed_args[:_COMMAND_] == :convert
        _convert(parsed_args[:convert])
    end #if
    return 0
 end #function
 end #module
--- a/src/Minting.jl
+++ b/src/Minting.jl
@ -1,11 +0,0 @@
 """
    _hamming(str1::AbstractString, str2::AbstractString)
 Computes the [Hamming distance](https://en.wikipedia.org/wiki/Hamming_distance) between
 `str1` and `str2`.
 """
 function _hamming(str1::AbstractString, str2::AbstractString)
    length(str1) != length(str2) &&
        throw(DimensionMismatch("strings must be of equal length"))
    return sum(c -> first(c) != last(c), zip(str1, str2))
 end #function
--- a/src/ResultCodeOption.jl
+++ b/src/ResultCodeOption.jl
@ -1,120 +0,0 @@
 """
    ResultCode::UInt8
 Encodes a result of attempting to correct a CualerID
 The valid codes are
 - **D**: duplicate
 - **F**: fixed
 - **N**: not fixable
 - **V**: valid (no need for correction)
 """
@enum ResultCode::UInt8 begin
    D = UInt8(1)
    F = UInt8(2)
    N = UInt8(4)
    V = UInt8(8)
 end #enum
 """
    ResultCodeOption
 Encodes potential corrected id codes.
 The valid codes are
 - **D**: duplicate
 - **F**: fixed
 - **N**: not fixable
 - **V**: valid (no need for correction)
 The codes are implemented exactly as from cual-id and in that order
 # Constructors
    ResultCodeOption(str::AbstractString)
 Create a `ResultCodeOption` based on a the character codes contained within
 `str`. `str` is case insensitive, may contain an arbitrary number of valid codes
 (as specified above), and may contain duplicates. A `ResultCodeOption` cannot be
 constructed from a combination of strings and bitmasks/integers.
 # Extended help
 The struct stores values as a bitmask
 | Bit (Int) | Bit (UInt) | Description     |
 | ---------:| ----------:| --------------- |
 | 1         | 0x01       | D - duplicate   |
 | 2         | 0x02       | F - fixed       |
 | 4         | 0x04       | N - not fixable |
 | 8         | 0x08       | V - valid       |
 """
 struct ResultCodeOption
    val::UInt8
 end #struct
 ResultCodeOption(str::AbstractString) = Base.parse(ResultCodeOption, str)
 function Base.parse(::Type{ResultCodeOption}, str::AbstractString)
    upper_str = uppercase(str)
    # Throw if there are any invalid codes
    occursin(r"[^DFNV]", upper_str) &&
        throw(DomainError("Valid `ResultCodeOption` must contain D, F, N, or V only"))
    # Throw if there are no valid codes
    occursin(r"[DFNV]", upper_str) || throw(
        DomainError("Valid `ResultCodeOption` must contain at least one of D, F, N, or V"),
    )
    result_code = sum(
        c -> occursin(string(Symbol(c)), upper_str) ? UInt8(c) : UInt8(0),
        instances(ResultCode),
    )
    return ResultCodeOption(result_code)
 end #function
 function Base.show(io::IO, r::ResultCodeOption)
    print_code = ""
    print(io, summary(r), " (")
    foreach(
        c -> r.val & UInt8(c) != 0 && print(io, string(Symbol(c))),
        instances(ResultCode),
    )
    print(io, ")")
 end #function
 """
    has_duplicate(r::ResultCodeOption)
 Determines if `r` contains a duplicate result ([`ResultCode`](@ref) D)
 """
 has_duplicate(r::ResultCodeOption) = r.val & UInt8(D) != 0
 """
    has_fixed(r::ResultCodeOption)
 Determines if `r` contains a fixed result ([`ResultCode`](@ref) F)
 """
 has_fixed(r::ResultCodeOption) = r.val & UInt8(F) != 0
 """
    has_not_fixable(r::ResultCodeOption)
 Determines if `r` contains a not fixable result ([`ResultCode`](@ref) N)
 """
 has_not_fixable(r::ResultCodeOption) = r.val & UInt8(N) != 0
 """
    has_valid(r::ResultCodeOption)
 Determines if `r` contains a valid (not corrected) result
 ([`ResultCode`](@ref) V)
 """
 has_valid(r::ResultCodeOption) = r.val & UInt8(V) != 0
--- a/test/Aqua.jl
+++ b/test/Aqua.jl
@ -1,5 +0,0 @@
 using Aqua
@testset "Aqua" begin
    Aqua.test_all(CualerID)
 end #@testset
--- a/test/Base30.jl
+++ b/test/Base30.jl
@ -1,10 +0,0 @@
 using CualerID: base30encode, rebase
@testset "base30encode" begin
    @test base30encode(0) == "0"
    @test base30encode(1) == "1"
    @test base30encode(29) == "Z"
    @test base30encode(30) == "10"
    @test base30encode(31) == "11"
    @test base30encode(59) == "1Z"
 end
--- a/test/Doctests.jl
+++ b/test/Doctests.jl
@ -1,6 +0,0 @@
 using Documenter
@testset "doctests" begin
    DocMeta.setdocmeta!(CualerID, :DocTestSetup, :(using CualerID); recursive = true)
    doctest(CualerID)
 end
--- a/test/Project.toml
+++ b/test/Project.toml
@ -1,10 +0,0 @@
 [deps]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
 Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 UUIDs = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 [compat]
 Aqua = "0.8"
 Documenter = "1.16"
 UUIDs = "1.11.0"
--- a/test/ResultCodeOption.jl
+++ b/test/ResultCodeOption.jl
@ -1,8 +0,0 @@
@testset "ResultCode" begin
    @test_throws DomainError ResultCodeOption("A")
    @test_throws DomainError ResultCodeOption("")
    @test has_duplicate(ResultCodeOption("D"))
    @test has_fixed(ResultCodeOption("F"))
    @test has_not_fixable(ResultCodeOption("N"))
    @test has_valid(ResultCodeOption("V"))
 end #@testset
--- a/test/runtests.jl
+++ b/test/runtests.jl
@ -1,7 +0,0 @@
 using CualerID
 using Test
 include("Doctests.jl")
 include("Aqua.jl")
 include("Base30.jl")
 include("ResultCodeOption.jl")
--- a/versions.js
+++ b/versions.js
@ -0,0 +1,5 @@
 var DOC_VERSIONS = [
  "dev",
 ];
 var DOCUMENTER_NEWEST = "dev";
 var DOCUMENTER_STABLE = "dev";
		`@ -1,2 +0,0 @@`
			`# See https://domluna.github.io/JuliaFormatter.jl/stable/ for a list of options`
			`style = "blue"`
		`@ -0,0 +1 @@`
							`{"documenter":{"julia_version":"1.12.5","generation_timestamp":"2026-02-13T03:53:22","documenter_version":"1.16.1"}}`
		`@ -0,0 +1,2 @@`
							`var DOCUMENTER_CURRENT_VERSION = "dev";`
							`var DOCUMENTER_IS_DEV_VERSION = true;`
		`@ -0,0 +1,2 @@`
							`<!--This file is automatically generated by Documenter.jl-->`
							`<meta http-equiv="refresh" content="0; url=./dev/"/>`