Options

Command Line Options¶

This page provides a comprehensive reference of all command-line options available in LDA.

Global Options¶

These options are available for all LDA commands:

--config, -c¶

Specify a custom configuration file:

lda --config custom_config.yaml init

Default: lda_config.yaml in current directory

--verbose, -v¶

Enable verbose output for debugging:

lda --verbose status

Effect: Shows detailed execution information

--quiet, -q¶

Suppress non-error output:

lda --quiet track

Effect: Only shows errors and critical information

--help, -h¶

Show help for any command:

lda --help
lda init --help

Command-Specific Options¶

init Command Options¶

Initialize a new LDA project:

--template, -t¶

Choose a project template:

lda init --template research

Options: default, research, clinical, minimal

--name, -n¶

Set project name:

lda init --name "COVID-19 Analysis"

--analyst, -a¶

Set primary analyst:

lda init --analyst john.doe

--force, -f¶

Force initialization even if directory is not empty:

lda init --force

track Command Options¶

Track files in the manifest:

--message, -m¶

Add a tracking message:

lda track --message "Updated preprocessing pipeline"

--all, -a¶

Track all files in the section:

lda track --all

--force, -f¶

Force tracking even without changes:

lda track --force

--exclude¶

Exclude files matching pattern:

lda track --exclude "*.tmp"

--dry-run¶

Show what would be tracked without making changes:

lda track --dry-run

status Command Options¶

Show project status:

--format, -f¶

Output format:

lda status --format json

Options: table (default), json, yaml

--section, -s¶

Show status for specific section:

lda status --section sec01_preprocessing

--detailed, -d¶

Show detailed file information:

lda status --detailed

changes Command Options¶

Show file changes:

--since¶

Show changes since date:

lda changes --since "2024-01-01"
lda changes --since "1 week ago"

--analyst¶

Filter changes by analyst:

lda changes --analyst jane.doe

--section¶

Show changes for specific section:

lda changes --section sec02_analysis

--diff¶

Show detailed diffs:

lda changes --diff

history Command Options¶

Show project history:

--limit, -n¶

Limit number of entries:

lda history --limit 10

--output, -o¶

Export history to file:

lda history --output history.json

--format, -f¶

Output format:

lda history --format csv

Options: json, csv, html

--file¶

Show history for specific file:

lda history --file outputs/results.csv

validate Command Options¶

Validate project integrity:

--fix¶

Attempt to fix issues:

lda validate --fix

--strict¶

Use strict validation rules:

lda validate --strict

--report¶

Generate validation report:

lda validate --report validation.html

export Command Options¶

Export project data:

--output, -o¶

Output file (required):

lda export manifest --output manifest.csv

--format, -f¶

Export format:

lda export report --format pdf --output report.pdf

Options: csv, json, html, pdf

--sections¶

Export specific sections:

lda export manifest --sections sec01,sec02 --output partial.csv

docs Command Options¶

Documentation management:

serve Subcommand¶

Serve documentation locally:

lda docs serve --port 8080 --dev

Options: - --port, -p: Port number (default: 8000) - --dev: Enable development mode with auto-reload - --host: Host address (default: 127.0.0.1)

build Subcommand¶

Build documentation:

lda docs build --output site --strict

Options: - --output, -o: Output directory (default: site) - --strict, -s: Fail on warnings - --clean, -c: Clean build directory first

Environment Variables¶

LDA_CONFIG¶

Default configuration file path:

export LDA_CONFIG=/path/to/config.yaml
lda status

LDA_PROJECT_ROOT¶

Override project root detection:

export LDA_PROJECT_ROOT=/path/to/project
lda validate

LDA_LOG_LEVEL¶

Set logging level:

export LDA_LOG_LEVEL=DEBUG
lda track

Options: DEBUG, INFO, WARNING, ERROR

Configuration File Options¶

Many command-line options can be set in the configuration file:

# lda_config.yaml
cli:
  default_format: json
  verbose: true
  colors: true

track:
  auto_message: true
  exclude_patterns:
    - "*.tmp"
    - ".DS_Store"

validate:
  strict: true
  auto_fix: true

Combining Options¶

Options can be combined for complex operations:

# Track with multiple options
lda track \
  --all \
  --exclude "*.tmp" \
  --message "Complete analysis run" \
  --verbose

# Export with filters
lda export manifest \
  --sections sec01,sec02 \
  --format json \
  --output filtered_manifest.json \
  --since "2024-01-01"

# Validate with reporting
lda validate \
  --strict \
  --fix \
  --report validation_report.html \
  --verbose

Option Precedence¶

When the same option is specified multiple times, precedence is:

1. Command-line arguments (highest)
2. Environment variables
3. Configuration file
4. Default values (lowest)

Example:

# Config file has: verbose: false
# Environment has: LDA_LOG_LEVEL=DEBUG
# Command line has: --quiet

lda status --quiet  # Quiet mode wins

Boolean Options¶

Boolean options can be negated with --no- prefix:

# Disable colors even if config enables them
lda status --no-colors

# Disable auto-fix even if config enables it
lda validate --no-fix

See Also¶

• Commands - Detailed command documentation
• Configuration - Configuration file reference
• Environment Variables - Environment variable reference