Default Schema and Baseline Configuration

The package ships with a baseline configuration file at pkg_infra/data/default_settings.yaml. This file is the default structure that pkg_infra expects and merges with higher-precedence config sources.

At a high level, the default schema contains these top-level sections:

• settings_version
• app
• environment
• session
• paths
• logging
• integrations
• packages_groups

What each section is for

app

Application-level defaults, including the active environment key and the logger name used by the application.

environment

Named environment profiles such as dev, lab, and prod.

session

Values related to session metadata. These are mostly placeholders that are filled dynamically at runtime.

paths

Optional filesystem locations such as data, cache, log, and temporary directories.

logging

The base logging configuration used to derive the final Python logging.config.dictConfig payload.

integrations

Package-specific configuration blocks. These allow downstream packages to store their own settings and optional logging overrides.

packages_groups

Shared policies for groups of packages, especially for logging behavior across the ecosystem.

Baseline YAML

# =============================================================================
# Default configuration for pkg_infra.
#
# Baseline values for: application, environments, session, logging, and
# integrations. User configs can override any section.
# =============================================================================

settings_version: 0.0.1 # configuration schema version

# -------------------------------------
# ----      Application           -----
# -------------------------------------
app:
    name:
    environment: dev # key under `environment`
    logger: default # logger name under `logging.loggers`

# -------------------------------------
# ----      Environment           -----
# -------------------------------------
environment:
    dev:
        name: development
        debug: true
    lab:
        name: laboratory
        debug: true
    prod:
        name: production
        debug: false

# -------------------------------------
# ----      Session               -----
# -------------------------------------
session:
    id:
    user:
    workspace:
    started_at:
    tags: [] # optional labels for the session

# -------------------------------------
# ----      Paths                 -----
# -------------------------------------
paths:
    data_dir:
    cache_dir:
    log_dir:
    temp_dir:

# -------------------------------------
# ----      Logging               -----
# -------------------------------------
logging:
    version: 1 # logging.config.dictConfig version
    disable_existing_loggers: false
    file_output_format: text # text or json for file handlers
    async_mode: false # enable queue-based non-blocking logging
    queue_maxsize: 10000 # maximum queued records when async mode is enabled
    formatters:
        default:
            format: '[%(asctime)s] [%(levelname)-5s] [%(name)-25s] ▸ %(message)s'
            datefmt: '%Y-%m-%d %H:%M:%S'
        simple:
            format: '%(asctime)s | %(levelname)s | %(name)s | %(message)s'

    handlers:
        console:
            class: logging.StreamHandler
            level: DEBUG
            formatter: default
            filters: [allow_all]
            stream: ext://sys.stdout
        file:
            class: logging.handlers.RotatingFileHandler
            level: DEBUG
            formatter: default
            filename: logs/sysbioverse_logger.log
            encoding: utf-8
            maxBytes: 10485760 # 10 MB
            backupCount: 5 # Keep up to 5 rotated log files

    loggers:
        default:
            level: INFO
            handlers: [console, file]
            propagate: false
        verbose:
            level: DEBUG
            handlers: [console, file]
            propagate: false
        quiet:
            level: WARNING
            handlers: [file]
            propagate: false

        pkg_infra:
            level: DEBUG
            handlers: [console, file]
            propagate: false

    filters:
        allow_all:
            (): logging.Filter

    root:
        level: warning
        handlers: [console, file]

# -------------------------------------
# ----      Integrations          -----
# -------------------------------------
integrations:
    # Part of: sysbio_infra group
    cache_manager:
        settings:
            cache_dir: /path/to/cache
            default_expiry: 3600

    # Part of: sysbio_infra group
    download_manager:
        settings:
            download_dir: /path/to/downloads
            max_retries: 3

    # Part of: sysbioverse group
    corneto:
        logging:
            level: INFO   # overrides group level only

        settings:
            network_path: src

    # Part of: No group
    ontograph:
        logging:
            enabled: true
            level: INFO
            handlers: [console, file]

        settings:
            api_url: https://api.ontograph.org
            timeout: 30


# -------------------------------------
# ----      Ecosystem             -----
# -------------------------------------
packages_groups:

    # Description: Set of bioinfomatics tools developed by Saezlab
    sysbioverse:
        logging:
            enabled: true
            level: DEBUG
            handlers: [console, file]
        packages:
        -   sysbioverse
        -   sysbio_infra
        -   corneto
        -   omnipath
        -   decoupler

    # Description: Well known packages in the Biology community
    scverse:
        logging:
            enabled: true
            level: DEBUG
            handlers: [console, file]
        packages:
        -   anndata
        -   scanpy

    # Description: More technical packages supporting Non-Bioinformatics tasks
    sysbio_infra:
        logging:
            enabled: true
            level: DEBUG
            handlers: [console, file]
        packages:
        -   cache_manager
        -   download_manager

    # Description: Well known in the data science community
    scientific:
        logging:
            enabled: true
            level: DEBUG
            handlers: [console, file]
        packages:
        -   pandas
        -   seaborn
        -   scipy
        -   numpy
        -   matplotlib
        -   plotly
        -   scikit-learn