ataraxis-base-utilities

Provides shared utility assets used to support most other Sun (NeuroAI) lab projects.

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Detailed Description

The primary focus of this library is to provide the unified message and error processing framework used across all other Sun lab projects instead of the built-in 'print,' 'logging,' and 'raise' assets. In addition to this framework, it also provides functions used to perform common filesystem operations (such as creating directories) and facilitate efficient parallel data processing (such as chunking iterables into batches).

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Features

• Supports Windows, Linux, and macOS.
• Provides a unified approach to message and error formatting, printing, and logging through the Console class.
• Provides a set of common utility functions frequently reused across other Sun lab projects.
• Apache 2.0 License.

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Table of Contents

• Dependencies
• Installation
• Usage
• API Documentation
• Developers
• Versioning
• Authors
• License
• Acknowledgments

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Dependencies

For users, all library dependencies are installed automatically by all supported installation methods. For developers, see the Developers section for information on installing additional development dependencies.

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Installation

Source

Note, installation from source is highly discouraged for anyone who is not an active project developer.

1. Download this repository to the local machine using the preferred method, such as git-cloning. Use one of the stable releases that include precompiled binary and source code distribution (sdist) wheels.
2. If the downloaded distribution is stored as a compressed archive, unpack it using the appropriate decompression tool.
3. cd to the root directory of the prepared project distribution.
4. Run pip install . to install the project and its dependencies.

pip

Use the following command to install the library and all of its dependencies via pip: pip install ataraxis-base-utilities

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Usage

Console

The Console class provides a unified loguru-based framework for working with messages and errors to display them in the terminal and (optionally) log them to files.

Quickstart

Most class functionality revolves around two methods: echo() and error(). To make adoption as frictionless as possible, a preconfigured Console instance is exposed as part of the library initialization via the console global variable:

from ataraxis_base_utilities import console

# All class functionality is disabled by default and must be enabled for the class to behave as expected.
console.enable()

# Use this instead of 'print'!
console.echo("This is a better 'print'.")

# Use this instead of 'raise'!
console.error("This is a 'raise' with logging.")

Note, the preconfigured class does not log processed messages and errors to files. To enable file-logging, re-initialize the Console class with the appropriate configuration parameters.

Working with Messages

All Console's functionality for working with messages is realized through the echo() method. Depending on class configuration, the method can be flexibly used to display the input messages in the terminal and log them to files. Each message is handed according to its LogLevel (urgency level) and the processing Console's configuration.

from ataraxis_base_utilities import console, LogLevel
console.enable()

# By default, console is configured to NOT print debug messages. Calling echo for a message at 'Debug' level has no
# effect
console.echo(message='Debug is disabled by default.', level=LogLevel.DEBUG)

# Messages at all levels other than 'Debug' are always printed if the console is enabled.
console.echo(message='Information messages are enabled!', level=LogLevel.INFO)
console.echo(message='Error messages are enabled!', level=LogLevel.ERROR)

# Disabled console does not print any messages.
console.disable()
console.echo(message='Disabled console does not print messages.', level=LogLevel.INFO)

Raw Echo Mode

The echo() method supports a raw mode that bypasses message formatting and loguru headers. This is useful for displaying pre-formatted content such as tables or DataFrames that should not be wrapped or indented:

from ataraxis_base_utilities import console
console.enable()

console.echo("Device and Axis Information:")
console.echo(formatted_table, raw=True)

When raw=True, the message is output without a timestamp header or level prefix. Log-level routing and file logging still function normally.

Working with Errors

The Console class treats errors as a special class of messages, handled through the error() method. Error messages are always handled at the Error log level and always interrupt the normal runtime flow of the caller program by calling the built-in 'raise' method after logging the message.

from ataraxis_base_utilities import console

# The Console raises error messages even if it is disabled. However, the instance does not log messages to files when
# disabled.
console.disable()

# Specify the exception to be raised by providing it as an 'error' argument. By default, this argument is
# set to RuntimeError.
console.error(message="Error message", error=TypeError)

Message Formatting

All Console methods format input messages to fit the Sun lab's default width-limit of 120 characters. It is possible to directly access and use the formatter through the format_message() method:

from ataraxis_base_utilities import console

# This long message does not display well without additional formatting
message = (
    "This is a long message that exceeds our default limit of 120 characters. Therefore, it needs to be wrapped to "
    "appear correctly when printed to the terminal (or saved to a log file)."
)
print(message)

# Prints a line-break for easier difference visualization
print()

# This formats the message according to the current (default) Console configuration.
formatted_message = console.format_message(message)
print(formatted_message)

Overriding Default Console Configuration

The default Console instance exposed via the 'console' variable is used by all other Sun lab projects. Re-initializing and overriding the console variable overrides the Console configuration used by all Sun lab projects used by the same process. Note, overriding the default Console configuration is a prerequisite for enabling logging messages and errors to files and working with 'Debug' level messages.

from ataraxis_base_utilities import console, Console, LogLevel, LogFormats
from pathlib import Path
from tempfile import TemporaryDirectory

# Overwriting the default 'console' instance replaces the instance used by all other Sun lab projects running in the
# same process as the overridden 'console'.
console = Console()  # This is equivalent to using the 'default' configuration

# Behaves like the default 'console' instance.
console.enable()
console.echo("Not printed by default.", level=LogLevel.DEBUG)

# Reinitializing the Console allows overriding default runtime parameters. For example, it can be used to enabled
# handling 'Debug' messages.
console = Console(debug=True)
console.enable()  # Reinitializing the console resets it to the 'disabled' state.
console.echo("Debug messages are now enabled!", level=LogLevel.DEBUG)

# Another important configuration step that requires reinitializing the console is enabling logging messages and errors
# to files, which is disabled by default.
with TemporaryDirectory() as log_directory:
    console = Console(
        log_directory=Path(log_directory),
        log_format=LogFormats.TXT,  # LogFormats enumeration stores all currently supported log file formats.
        debug=True
    )

    # Prints and saves the debug message to a log file.
    console.enable()
    console.echo("Debug messages are now logged to the debug log file!", level=LogLevel.DEBUG)

    # The message can now be viewed by reading the .txt log file.
    with console.debug_log_path.open("r") as file:
        console.echo(file.read())

Temporarily Enabling Console

The temporarily_enabled() context manager temporarily enables the console for the duration of a block, restoring the previous state on exit. This is useful for code that needs to produce output even when the console is normally disabled:

from ataraxis_base_utilities import console

# Console is disabled by default.
with console.temporarily_enabled():
    console.echo("This prints even if the console was disabled.")
# Console returns to its previous state here.

Progress Bars

The Console class provides two methods for displaying tqdm-based progress bars that respect the console's enabled state. Progress bar display is controlled independently of message output through the show_progress flag, which defaults to False.

The track() method wraps an iterable with a progress bar:

from ataraxis_base_utilities import console
console.enable()
console.enable_progress()

for item in console.track(range(100), description="Processing", unit="item"):
    pass  # Process each item

The progress() context manager provides a manually-updatable progress bar for cases where iteration is not linear, such as tracking concurrent futures:

from ataraxis_base_utilities import console
console.enable()
console.enable_progress()

with console.progress(total=100, description="Downloading", unit="file") as pbar:
    for i in range(100):
        pbar.update(1)

Progress bars can be enabled and disabled at any time using the enable_progress() and disable_progress() methods. When progress is disabled, track() still yields all items and progress() still accepts updates, but no visual bar is rendered.

Compatibility with Other Projects

The Console class is built on top of the loguru library. As part of its initialization, each Console class automatically resets the handles used by the 'logger' exposed by Loguru. Therefore, the Console class is incompatible with any other third-party library that uses Loguru for similar purposes.

Standalone Methods

The standalone methods are a collection of utility functions that either abstract away the boilerplate code for common data manipulations or provide novel functionality not commonly available through popular Python libraries used by other Sun lab projects. Generally, these methods are straightforward to use and do not require detailed explanation. See the API documentation below for details on available standalone methods.

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API Documentation

See the API documentation for the detailed description of the methods and classes exposed by components of this library.

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Developers

This section provides installation, dependency, and build-system instructions for the developers that want to modify the source code of this library.

Installing the Project

Note, this installation method requires mamba version 2.3.2 or above. Currently, all Sun lab automation pipelines require that mamba is installed through the miniforge3 installer.

1. Download this repository to the local machine using the preferred method, such as git-cloning.
2. If the downloaded distribution is stored as a compressed archive, unpack it using the appropriate decompression tool.
3. cd to the root directory of the prepared project distribution.
4. Install the core Sun lab development dependencies into the base mamba environment via the mamba install tox uv tox-uv command.
5. Use the tox -e create command to create the project-specific development environment followed by tox -e install command to install the project into that environment as a library.

Additional Dependencies

In addition to installing the project and all user dependencies, install the following dependencies:

1. Python distributions, one for each version supported by the developed project. Currently, this library supports the three latest stable versions. It is recommended to use a tool like pyenv to install and manage the required versions.

Development Automation

This project uses tox for development automation. The following tox environments are available:

Environment	Description
lint	Runs ruff formatting, ruff linting, and mypy type checking
stubs	Generates py.typed marker and .pyi stub files
{py312,...}-test	Runs the test suite via pytest for each supported Python
coverage	Aggregates test coverage into an HTML report
docs	Builds the API documentation via Sphinx
build	Builds sdist and wheel distributions
upload	Uploads distributions to PyPI via twine
install	Builds and installs the project into its mamba environment
uninstall	Uninstalls the project from its mamba environment
create	Creates the project's mamba development environment
remove	Removes the project's mamba development environment
provision	Recreates the mamba environment from scratch
export	Exports the mamba environment as .yml and spec.txt files
import	Creates or updates the mamba environment from a .yml file

Run any environment using tox -e ENVIRONMENT. For example, tox -e lint.

Note, all pull requests for this project have to successfully complete the tox task before being merged. To expedite the task's runtime, use the tox --parallel command to run some tasks in parallel.

Automation Troubleshooting

Many packages used in tox automation pipelines (uv, mypy, ruff) and tox itself may experience runtime failures. In most cases, this is related to their caching behavior. If an unintelligible error is encountered with any of the automation components, deleting the corresponding cache directories (.tox, .ruff_cache, .mypy_cache, etc.) manually or via a CLI command typically resolves the issue.

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Versioning

This project uses semantic versioning. See the tags on this repository for the available project releases.

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Authors

• Ivan Kondratyev (Inkaros)

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License

This project is licensed under the Apache 2.0 License: see the LICENSE file for details.

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Acknowledgments

• All Sun lab members for providing the inspiration and comments during the development of this library.
• The creators of all other dependencies and projects listed in the pyproject.toml file.