ChemQL & CodecQL

ChemQL is a chemistry-oriented query and programming language with an interactive terminal, a Python-backed execution environment, chemistry data types and operations, user-defined functions, and a package system.

CodecQL is the terminal text editor distributed with ChemQL. It edits source files, provides syntax highlighting, and supports configurable highlighting profiles for multiple file extensions.

Version represented by this documentation: ChemQL 1.6.4; CodecQL 0.0.11.

This README documents the implementation represented by the accompanying source files. Some advanced syntax is intentionally described at a high level; use the built-in help system for the authoritative in-app reference.

---

Contents

• Installation and requirements
• ChemQL
  • Starting ChemQL
  • Running scripts and commands
  • Language syntax at a glance
  • Built-in functions
  • Standard-library packages
  • Chemistry features
  • Package management
  • Python interoperability
  • Help and errors
• CodecQL
  • Opening and creating files
  • Keyboard shortcuts
  • Search syntax
  • Terminal integration
• CodecQL configuration
  • colors.json: editor colors
  • highlighting.json: language profiles
  • Rule types
  • Style syntax
  • Configuration lookup and precedence
  • Editing configuration from CodecQL
• Troubleshooting

---

Installation and requirements

ChemQL is a Python package. CodecQL is a Python terminal application that is imported by ChemQL and can also be launched through its editor command.

The ChemQL runtime imports prompt_toolkit for the interactive prompt. The editor uses Python's standard library and ANSI terminal escape sequences. On Windows it attempts to initialize ANSI support with colorama, and falls back to enabling virtual-terminal processing when colorama is unavailable.

Install ChemQL using the distribution method provided by the project. If installing from a local source checkout, install the project from its package root so that its package metadata and dependencies are installed together.

Check the installed version:

chemql --version
codecql --version

If the codecql command is not exposed as a separate executable in your installation, launch the editor through ChemQL:

chemql edit path/to/file.cql

---

ChemQL

Starting ChemQL

Start the interactive prompt:

chemql

The prompt accepts ChemQL commands and expressions. The welcome message points to the built-in help system:

help

or:

?

Exit the interactive prompt with:

exit

You can also press Ctrl+C to leave the prompt.

The prompt supports multiline input for constructs such as functions, macros, Python blocks, and other block forms. The continuation prompt is shown as ....

Running scripts and commands

Execute a one-line or multi-line ChemQL command supplied on the command line:

chemql -c 'molar_mass{"H2O"}'

Execute a source file:

chemql -f path/to/script.cql

Write command or script output to a file without ANSI escape sequences:

chemql -f path/to/script.cql -o output.txt

Useful runtime options:

---

Option Purpose

---

-c, --command Execute ChemQL code supplied as an argument

-f, --file Execute ChemQL code from a file

--no-ansi Disable ANSI styling in output

--suppress-warnings Suppress warning messages

-o, --output FILE Write captured output to a file without ANSI sequences

-v, --version Print the ChemQL version

--upgrade [VERSION] Upgrade ChemQL, optionally to a specified version

--force / --dangerously Force an upgrade, including bypassing system-package protections

-o is only valid with -c or -f.

Language syntax at a glance

ChemQL combines its own command/query syntax with Python expressions and statements in explicitly delimited blocks.

Function calls

ChemQL function calls use braces rather than parentheses:

function_name{argument1, argument2}

Examples:

molar_mass{"H2O"}
upper{"hello world"}
math::sqrt{81}

Separate arguments with commas. Quote text containing spaces.

Variables

Use let to assign a value:

let answer = 42
let message = "Hello from ChemQL"

Variables can be used in later expressions:

let radius = 5
let area = math::PI * radius ** 2

The runtime also supports listing and removing variables:

variables
unset answer

Definitions and macros

Definitions are expanded using an @NAME reference:

define MAX {
    100
}

Use the definition as:

@MAX

Definitions are maintained in the current ChemQL session. The preprocessor performs one literal substitution pass; replacement text is not recursively expanded.

Macros use a block form and are invoked by name according to the macro syntax supported by the interpreter. Use help{syntax} and the in-app completion/help facilities for the exact forms supported by your installed version.

Embedded Python

A single-line Python statement or expression can be placed inside square brackets:

[print("Hello from Python")]

A multiline Python block uses triple square brackets:

[[[
numbers = [1, 2, 3, 4]
total = sum(numbers)
print(total)
]]]

Python code executes in ChemQL's Python-backed environment. This makes Python expressions and available Python objects usable alongside ChemQL features.

Embedded ChemQL expressions

Double curly braces are used for embedded/lazy ChemQL query expressions in supported contexts:

{{ search molecules ... }}

The precise query expression depends on the operation being performed. See help{syntax} and the query examples shipped with the project.

Control flow

ChemQL supports block-oriented control-flow constructs including if, elif, else, for, and while. Closing markers are explicit:

if condition
    ...
else
    ...
endif

for item in items
    ...
endfor

while condition
    ...
endwhile

break and continue are also recognized control keywords.

Functions

User-defined functions are declared with func and closed with endfunc. Functions can accept arguments and return values. Inside a function, positional arguments are available through the function's argument mechanism; the implementation also supports \1, \2, and so on as positional argument references in function bodies.

A minimal illustrative shape:

func greet
    return "Hello"
endfunc

Call a function using ChemQL's brace-call syntax:

greet{}

Structs, records, and enums

ChemQL supports user-defined struct, record, and enum declarations. Structs and records can declare fields, and the implementation supports inheritance using from Base. Structs can inherit from structs, records, or Python classes; records can inherit from records.

Declarations are closed with their corresponding terminators, such as endstruct, endrecord, and endenum.

Example declaration shape:

struct Point
    x
    y
endstruct

Enum members can receive automatically generated values when values are omitted.

Namespaces

Namespaces group related declarations and support public/private members:

namespace Geometry
    public func ...
    private func ...
endnamespace

A namespace member is referenced with a qualified name using ::, for example Geometry::member. Private namespace members are intended for internal use by functions in the same namespace.

Error handling and signals

The interpreter supports structured risk, fix, and cleanup sections, closed by endrisk. It also supports signal and warn statements in the relevant execution contexts.

The fix section is used when the risk section raises a handled error; cleanup is for cleanup side effects. The current error information is exposed to the execution environment.

Built-in functions

The built-in function set includes general-purpose operations, string and collection helpers, file I/O, and chemistry helpers. Calls use braces.

---

Category Functions

---

Numbers abs, round, min, max, sum

Core and conversion len, type, str, int, float, bool

Strings upper, lower, contains, replace, split, join

Collections first, last, unique, sort, reversed

Files and data read_text, read_lines, read_json, read_csv, write_text, write_json, write_csv, file_exists, list_files

Chemistry element, count_atoms, molar_mass, empirical_formula

Help help

Examples:

abs{-15}
round{3.14159, 2}
sum{1, 2, 3, 4}
upper{"chemql"}
unique{1, 2, 2, 3}
molar_mass{"H2O"}
count_atoms{"H2SO4", "O"}
empirical_formula{"C6H12O6"}

File examples:

let text = read_text{"notes.txt"}
let rows = read_csv{"data.csv"}
let data = read_json{"data.json"}

write_text{"output.txt", "Hello"}
write_json{"output.json", data}
write_csv{"output.csv", rows}

read_csv treats the first row as headers by default and returns rows as dictionaries. Pass false as the headers argument to read rows as lists.

For exact signatures, optional arguments, and examples, use:

help{function_name}

For example:

help{read_csv}
help{molar_mass}

Standard-library packages

ChemQL includes loadable standard-library namespaces. Load a package before using its members:

load math
math::sqrt{81}

The source's built-in help index lists these standard-library namespaces:

Package Purpose

---

math Mathematical constants and numeric functions math::statistics Descriptive statistics text String operations and regular expressions collections Collection and iterable helpers datetime Dates, times, timestamps, and date arithmetic json JSON serialization, parsing, and type inspection random Pseudorandom values and sequence sampling

Ask ChemQL for a package's documented members:

help{stdlib}
help{math}
help{math::statistics}
help{text}

A function can be documented individually when its help entry is registered:

help{math::sqrt}

Chemistry features

ChemQL exposes chemistry-oriented data types and operations, including:

• Element, Molecule, and Reaction objects.
• Element and molecule lookup helpers.
• Reaction lookup and reaction searching.
• Stoichiometric balancing through balance_stoichiometry.
• Reaction matching against the current temperature, pressure, and catalyst conditions.
• Chemistry built-ins such as element, count_atoms, molar_mass, and empirical_formula.

The interactive command set includes chemistry/query commands such as search, source, findel, findmol, findre, react, balance, conditions, and view.

Examples of built-in chemistry functions:

element{"Na"}
count_atoms{"H2SO4", "O"}
molar_mass{"H2O"}
empirical_formula{"C6H12O6"}

Reaction operations can depend on the current reaction conditions. Inspect or set conditions with the relevant interactive commands and use conditions to display the current state.

The available data sources and query fields are defined by the ChemQL package/data files. Use the interactive prompt's completion and help{chemistry} for the current details.

Package management

ChemQL provides package-management subcommands:

---

Command Purpose

---

chemql init [NAME] [-d DIRECTORY] Create a ChemQL package project

chemql build Build the current package

chemql search QUERY Search the package registry

chemql info NAME Show registry information for a package

chemql install NAME [--version VERSION] Install a package

chemql upgrade NAME [--version VERSION] Upgrade an installed package

chemql list List installed packages

chemql uninstall NAME Uninstall a package

chemql upload Upload the current package to the registry

Example workflow:

chemql search statistics
chemql info package_name
chemql install package_name
chemql list

Load an installed package from the ChemQL prompt:

load package_name

Then call its namespaced functions:

package_name::function_name{...}

The package manager also supports upgrading ChemQL itself:

chemql --upgrade
chemql --upgrade 1.6.4

Use --force only when you understand that it bypasses normal protections around system-managed installations.

Python interoperability

ChemQL is implemented in Python and evaluates embedded Python blocks in its Python execution environment. The runtime imports and uses Python modules internally, and the language exposes Python-backed objects and functions.

Use square-bracket blocks for Python statements and expressions. Use [[[ ... ]]] for multiline Python. This is the intended boundary between ChemQL's command/query syntax and general Python code.

Help and errors

The interactive help system is the quickest way to discover the exact syntax supported by the installed version:

help
help{syntax}
help{errors}
help{files}
help{chemistry}
help{stdlib}
help{function_name}

The runtime defines specific built-in error classes:

• TooFewArguments
• TooManyArguments
• InvalidArgumentType
• InvalidArgumentValue
• FileReadError
• FileWriteError

Other errors can include SyntaxError, NameError, and PermissionError.

---

CodecQL

CodecQL is a terminal-based text editor intended for ChemQL source files. It also supports configurable syntax-highlighting profiles for other extensions.

Opening and creating files

Open an existing file:

codecql script.cql

Create a new file by opening a path that does not exist yet:

codecql new_script.cql

The editor starts with an empty buffer when the file does not exist. Save with Ctrl+S to create it.

Launch it through ChemQL:

chemql edit script.cql

Open the editor's main highlighting configuration:

codecql --main-highlighting

Open the current working directory's local highlighting configuration:

codecql --local-highlighting

The two highlighting flags cannot be used together. If the selected configuration file does not exist, CodecQL creates an empty JSON object in that location.

Keyboard shortcuts

---

Shortcut Action

---

Ctrl+S Save the current file

Ctrl+Q Quit; if there are unsaved changes, press it again to discard and quit

Ctrl+Z Undo

Ctrl+Y Redo

Ctrl+F Open search

Ctrl+C Copy the current selection

Ctrl+X Cut the current selection

Ctrl+V Paste the editor clipboard

Shift+Insert Paste the editor clipboard

Ctrl+T Open a split terminal

Ctrl+R Save if needed and run the current file with ChemQL

Shift+Arrow Extend the selection while moving the cursor

Ctrl+Arrow Up/Down Scroll the viewport

Ctrl+Arrow Left/Right Move by word

Home / End Move to the start/end of the line

Backspace / Delete Delete text

Clipboard integration uses the available system clipboard command when possible: - Windows: clip - WSL: clip.exe - macOS: pbcopy - Linux: wl-copy, xclip, or xsel

If no system clipboard utility is available, CodecQL keeps the copied text in its own editor clipboard.

Search syntax

Press Ctrl+F to open search. Enter a query and use the arrow keys to move between matches. Press Enter to select the next match; Up or Left selects the previous match. Esc closes search.

Search supports optional prefix flags:

Flag Meaning

---

r Treat the query as a regular expression l Literal search (the default) w Match whole words i Ignore case

Place flags before a colon. Examples:

hello
i:hello
w:hello
ri:\b[A-Z]{2,}\b
lw:token

Search is case-insensitive by default. r and l cannot be combined.

Terminal integration

• Ctrl+T opens a shell in a terminal pane/window.
• Ctrl+R saves the current buffer if it has unsaved changes, then runs the file with chemql -f.
• On Windows, CodecQL uses a new console, or a Windows Terminal split pane when running inside Windows Terminal.
• On Unix-like systems, CodecQL uses a pseudo-terminal for the integrated terminal.

---

CodecQL configuration

CodecQL has two separate JSON configuration files:

• colors.json controls the editor's ANSI color palette.
• highlighting.json controls which tokens are highlighted for each file extension and which style is assigned to each rule.

They serve different purposes. Changing a color in colors.json changes the appearance of a named style throughout the editor. Changing highlighting.json changes which words are assigned to styles for a language.

colors.json: editor colors

colors.json is read from the directory containing the CodecQL source module. It has two top-level objects: syntax and ui.

Every color entry must be an object containing an integer ansi256 value from 0 through 255. The optional channel is either foreground (the default) or background.

Example:

{
    "syntax": {
        "comment":  { "ansi256": 244 },
        "string":   { "ansi256": 114 },
        "number":   { "ansi256": 179 },
        "formula":  { "ansi256": 117 },
        "operator": { "ansi256": 213 },
        "delimiter": { "ansi256": 250 },
        "command":  { "ansi256": 81 },
        "keyword":  { "ansi256": 141 },
        "constant": { "ansi256": 215 },
        "type":     { "ansi256": 150 },
        "source":   { "ansi256": 110 },
        "condition": { "ansi256": 180 },
        "property": { "ansi256": 116 },
        "builtin":  { "ansi256": 222 }
    },
    "ui": {
        "line_numbers": {
            "ansi256": 244
        },
        "status_background": {
            "ansi256": 24,
            "channel": "background"
        },
        "status_foreground": {
            "ansi256": 255
        }
    }
}

The values above mirror the fallback palette in the editor source. If colors.json is missing, CodecQL uses that fallback palette. If the file exists but is malformed or missing a required top-level group, loading the theme raises a configuration error.

Syntax color categories

The editor's syntax theme uses these categories:

Category Used for

---

comment Comments string Quoted strings number Numeric literals formula Chemical formula-like tokens operator Operators delimiter Brackets and punctuation delimiters command ChemQL commands keyword Language/control keywords constant Values such as true, false, and none type Type/declaration names and manifest table headers source ChemQL data sources condition Chemistry conditions and units property Chemistry fields and manifest keys builtin Python built-in names recognized by the editor

The UI categories are:

Category Used for

---

line_numbers Line-number gutter status_background Status bar background status_foreground Status bar text

ANSI 256-color values

ansi256 is a terminal color index, not an RGB hex value. It accepts integers from 0 to 255.

Common ranges in the standard 256-color palette:

• 0–15: standard and bright terminal colors.
• 16–231: 6×6×6 RGB color cube.
• 232–255: grayscale ramp.

The actual appearance depends on the terminal's color palette and settings.

To set a background color, add "channel": "background":

"status_background": {
    "ansi256": 24,
    "channel": "background"
}

Foreground is assumed when channel is omitted.

highlighting.json: language profiles

highlighting.json maps file extensions to ordered lists of highlighting rules.

CodecQL starts with a built-in .cql profile. It then loads the main configuration and the current directory's local configuration, if present. A custom profile for an existing extension replaces that extension's previous profile; a new extension adds a profile.

A minimal configuration:

{
    ".py": [
        {
            "name": "python-keywords",
            "type": "keywords",
            "values": ["def", "class", "return", "if", "elif", "else", "for", "while", "import", "from", "as", "try", "except", "finally", "with", "pass", "break", "continue"],
            "style": "keyword"
        },
        {
            "name": "python-builtins",
            "type": "keywords",
            "values": ["print", "len", "range", "enumerate", "zip", "map", "filter", "sum", "min", "max", "str", "int", "float", "list", "dict", "set", "tuple"],
            "style": "builtin"
        }
    ],
    ".js": [
        {
            "name": "javascript-keywords",
            "type": "keywords",
            "values": ["const", "let", "var", "function", "return", "if", "else", "for", "while", "class", "new", "import", "export", "from", "async", "await"],
            "style": "keyword"
        }
    ]
}

Profile structure

The top-level value must be a JSON object. Each key is a file extension and each value is an array of rules.

{
    ".extension": [
        {
            "name": "rule-name",
            "type": "keywords",
            "values": ["word1", "word2"],
            "style": "keyword"
        }
    ]
}

Extension normalization: - A leading dot is added if omitted. - Extensions are converted to lowercase. - Empty extensions and values containing path separators are rejected. - The profile is selected from the file's final extension. For example, script.py uses .py.

Each rule must be an object with: - name: non-empty string identifying the rule. - type: supported rule type (keywords or regex). - style: non-empty style expression.

A keyword rule additionally requires: - values: a non-empty array of non-empty strings.

Keyword matching is case-insensitive. Rule order matters: the first matching keyword rule supplies the style for that word.

Rule types

keywords

Use this rule to assign a style to a list of exact words:

{
    "name": "control-flow",
    "type": "keywords",
    "values": ["if", "else", "while", "for", "return"],
    "style": "keyword"
}

The current implementation applies keyword rules during identifier highlighting. Matching is case-insensitive.

regex

Regex rules are accepted and validated by the profile loader. A regex rule must include a non-empty pattern; case_sensitive is optional and defaults to true.

{
    "name": "special-identifiers",
    "type": "regex",
    "pattern": "\\b(?:TODO|FIXME|NOTE)\\b",
    "case_sensitive": true,
    "style": "#FFB000 bold"
}

Implementation note: the current editor integration applies keywords rules through get_keyword_style. Although regex rules are parsed and validated by highlighting.py, they are not yet applied by the current token-highlighting path. Treat regex highlighting as a reserved/configuration-ready feature until regex application is wired into the renderer.

Style syntax

A rule's style is a space-separated list of style components. Components can be combined.

Named theme styles

These names refer to entries in colors.json under syntax:

keyword
command
operator
string
comment
number
constant
type
source
condition
property
builtin

Example:

"style": "keyword"

Formatting modifiers

The editor recognizes these modifiers:

Modifier Effect

---

bold Bold text dim Dim text italic Italic text underline Underlined text reverse Reverse foreground/background strike Strikethrough text

Example:

"style": "keyword bold underline"

Custom foreground colors

Use a six-digit hexadecimal RGB color prefixed with #:

"style": "#FF00FF"

Custom background colors

Use bg: followed by a six-digit hexadecimal RGB color:

"style": "bg:#202020"

Combining components

You can combine a named style, formatting modifiers, and custom foreground/background colors:

"style": "#FF00FF underline bold italic"

"style": "keyword bold"

"style": "#E0B0FF bg:#202020 bold"

Hexadecimal colors use true-color ANSI escape sequences. Your terminal must support ANSI styling and preferably 24-bit true color for the full effect.

Example: create a profile for Python

Create or edit highlighting.json in your project directory:

{
    ".py": [
        {
            "name": "python-keywords",
            "type": "keywords",
            "values": [
                "def", "class", "return", "if", "elif", "else",
                "for", "while", "in", "break", "continue",
                "import", "from", "as", "try", "except",
                "finally", "with", "raise", "yield", "lambda"
            ],
            "style": "keyword bold"
        },
        {
            "name": "python-constants",
            "type": "keywords",
            "values": ["True", "False", "None"],
            "style": "#FFB86C bold"
        },
        {
            "name": "python-builtins",
            "type": "keywords",
            "values": ["print", "len", "range", "enumerate", "zip", "sum", "min", "max"],
            "style": "builtin"
        }
    ]
}

Then open a Python file from that directory:

codecql example.py

The local .py profile is loaded and used for matching identifier tokens.

Example: add a language without changing ChemQL's built-in profile

You can define several extensions in the same JSON file:

{
    ".py": [
        {
            "name": "python-keywords",
            "type": "keywords",
            "values": ["def", "class", "return", "if", "else", "for", "while"],
            "style": "keyword"
        }
    ],
    ".rs": [
        {
            "name": "rust-keywords",
            "type": "keywords",
            "values": ["fn", "let", "mut", "pub", "struct", "enum", "impl", "trait", "use", "mod", "match", "if", "else", "loop", "while", "for", "return"],
            "style": "#D19A66 bold"
        }
    ],
    ".js": [
        {
            "name": "javascript-keywords",
            "type": "keywords",
            "values": ["const", "let", "var", "function", "return", "class", "new", "async", "await"],
            "style": "keyword"
        }
    ]
}

This adds profiles for .py, .rs, and .js. It does not remove the built-in .cql profile unless you explicitly provide a .cql profile in a loaded configuration.

Configuration lookup and precedence

The editor loads highlighting profiles in this order:

1. The built-in profiles in highlighting.py (currently includes .cql).
2. highlighting.json beside the CodecQL source module (the main configuration).
3. highlighting.json in the current working directory (the local configuration).

Later profiles replace earlier profiles for the same extension. Therefore:

• The main configuration can provide defaults shared by projects.
• A local configuration can override those defaults for the current project.
• Profiles for unrelated extensions are retained.
• If the main and local paths point to the same file, it is loaded only once.
• If neither file exists, the built-in profiles remain available.

Important: the local configuration is merged by extension; it does not merge individual rules into an existing extension profile. If a local .py profile is present, it replaces the main .py profile as a whole.

The main configuration path is relative to the installed CodecQL module. The local configuration path is relative to the directory from which CodecQL is launched.

Editing configuration from CodecQL

Open the main configuration:

codecql --main-highlighting

Open the local configuration:

codecql --local-highlighting

If the selected file does not exist, CodecQL creates it as:

{}

Edit the JSON, save with Ctrl+S, then restart CodecQL or reopen the file being edited so the editor reloads the profile configuration.

Do not combine --main-highlighting and --local-highlighting.

Built-in ChemQL highlighting

The built-in .cql profile groups words into these rules:

---

Rule name Style Examples

---

commands command search, source, findmol, react, balance, help, load

control-keywords keyword if, else, for, while, struct, record, enum, namespace

word-operators operator and, or, has, like, sort, limit, union

sources source elements, molecules, reactions

conditions condition temperature, pressure, catalyst, atm, bar, kpa

properties property name, symbol, atomic_mass, formula, reactants, products

The editor also recognizes lexical token categories such as comments, strings, numbers, chemical formula-like tokens, operators, and delimiters. JSON and TOML package manifests named cqlpackage.json and cqlpackage.toml receive dedicated manifest highlighting.

---

Troubleshooting

A file opens without custom highlighting

Check that: 1. The file has the extension used as the profile key, such as .py. 2. The JSON file is named exactly highlighting.json. 3. The local file is in the current working directory from which CodecQL was launched. 4. The extension key includes the intended extension. 5. The rule uses "type": "keywords" and has a non-empty values array. 6. The token is recognized as an identifier by the editor's tokenizer.

Unknown extensions remain unhighlighted by language-specific keyword profiles, though the editor's general lexical token styling still applies.

My local profile is not overriding the main profile

Profiles are replaced per extension, not merged rule by rule. Make sure the local profile includes the complete rule list you want for that extension.

The editor rejects my highlighting JSON

Check standard JSON syntax: - Use double quotes around keys and string values. - Do not leave trailing commas. - Use true and false for booleans, not quoted strings. - Make sure each extension maps to an array of rules. - Make sure each rule has a non-empty name, supported type, and non-empty style.

For regex rules, pattern must be a valid Python regular expression. case_sensitive must be a JSON boolean.

My custom style is rejected

Use only recognized style components: - A named theme style listed in Style syntax. - One of bold, dim, italic, underline, reverse, or strike. - A foreground color such as #FF00FF. - A background color such as bg:#202020.

Separate components with spaces.

Colors look different in my terminal

ANSI 256-color and true-color output are interpreted by the terminal. Different terminal palettes, themes, and color capabilities can make the same color index or RGB value look different.

Ctrl+R does not run my file

Ctrl+R invokes chemql -f with the current file's absolute path. Ensure ChemQL is installed and its chemql command is available in the environment inherited by CodecQL. The editor saves a modified buffer before running it.

---

Project components

---

File/component Responsibility

---

ChemQL package (__init__.py) Language runtime, interactive prompt, chemistry functionality, built-ins, package management

codecql.py Terminal editor, file operations, key handling, terminal integration, token rendering

highlighting.py Highlighting profile definitions, JSON loading, extension normalization, and rule validation

colors.json ANSI 256-color theme for syntax and editor UI

highlighting.json Optional user-defined language profiles

ChemQL and CodecQL are related but separate components: ChemQL provides the language/runtime, while CodecQL provides the editing environment.