CLI Reference¶
The full bioamla command tree, generated from the CLI itself (--help), so it
always matches the installed version.
bioamla¶
BioAMLA - Bioacoustic & Machine Learning Applications
Use 'bioamla COMMAND --help' for more information on a command.
Usage:
bioamla [OPTIONS] COMMAND [ARGS]...
Options:
--version Show the version and exit.
--help Show this message and exit.
annotation¶
Annotation management commands for audio datasets.
Usage:
bioamla annotation [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
convert¶
Convert annotation files between formats.
Usage:
bioamla annotation convert [OPTIONS] INPUT_FILE OUTPUT_FILE
Options:
--from [raven|csv|bioamla] Input format (auto-detected from extension if
not specified)
--to [raven|csv|bioamla] Output format (auto-detected from extension if
not specified)
--label-column TEXT Column name for labels in input file
-q, --quiet Suppress progress output
--help Show this message and exit.
filter¶
Filter annotations by label or duration.
Usage:
bioamla annotation filter [OPTIONS] INPUT_FILE OUTPUT_FILE
Options:
-i, --include TEXT Labels to include (can specify multiple)
-e, --exclude TEXT Labels to exclude (can specify multiple)
--min-duration FLOAT Minimum duration in seconds
--max-duration FLOAT Maximum duration in seconds
-q, --quiet Suppress progress output
--help Show this message and exit.
generate-frame-labels¶
Generate frame-level multi-hot labels from annotations (for SED-style models).
Usage:
bioamla annotation generate-frame-labels [OPTIONS] ANNOTATION_FILE OUTPUT_FILE
Options:
--frame-size FLOAT Frame size in seconds [required]
--hop-length FLOAT Hop length between frames in seconds (default: same
as frame size)
--audio-duration FLOAT Total audio duration in seconds (inferred from
bioamla metadata if omitted)
--format [csv|numpy] Output format for labels
-q, --quiet Suppress progress output
--help Show this message and exit.
generate-labels¶
Generate clip-level labels from annotations.
Usage:
bioamla annotation generate-labels [OPTIONS] ANNOTATION_FILE OUTPUT_FILE
Options:
--audio-duration FLOAT Total audio duration in seconds (inferred
from bioamla metadata if omitted)
--clip-duration FLOAT Duration of each clip in seconds [required]
--hop-length FLOAT Hop length between clips (default: same as
clip duration)
--min-overlap FLOAT Minimum overlap ratio to assign label
(0.0-1.0)
--multi-label / --single-label Generate multi-label or single-label output
--format [csv|numpy] Output format for labels
-q, --quiet Suppress progress output
--help Show this message and exit.
remap¶
Remap annotation labels using a mapping file.
Usage:
bioamla annotation remap [OPTIONS] INPUT_FILE OUTPUT_FILE
Options:
-m, --mapping TEXT Path to label mapping CSV (columns: source,
target) [required]
--keep-unmapped / --drop-unmapped
Keep or drop annotations with unmapped
labels
-q, --quiet Suppress progress output
--help Show this message and exit.
summary¶
Display summary statistics for an annotation file.
Usage:
bioamla annotation summary [OPTIONS] PATH
Options:
--format [raven|csv|bioamla] Annotation format (auto-detected from
extension if not specified)
--json Output as JSON
--help Show this message and exit.
template¶
Generate a starter annotation file from an audio file.
Reads the recording's duration and sample rate and writes a skeleton annotation file pre-filled with that metadata plus (unless --empty) a single placeholder row spanning the whole file, ready to edit. The bioamla (.json) format stores the audio metadata in the file; raven/csv hold the rows only.
Usage:
bioamla annotation template [OPTIONS] AUDIO_FILE OUTPUT_FILE
Options:
--format [raven|csv|bioamla] Output format (auto-detected from extension if
not specified)
--label TEXT Label for the placeholder full-file row
--empty Write metadata only, with no placeholder row
-q, --quiet Suppress progress output
--help Show this message and exit.
audio¶
Audio file operations (info, convert, segment, visualize).
Usage:
bioamla audio [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
add-noise¶
Add Gaussian white noise at a target SNR.
Usage:
bioamla audio add-noise [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
--snr-db FLOAT Target SNR in dB (lower = more noise) [required]
--seed INTEGER RNG seed for reproducible noise
--help Show this message and exit.
convert¶
Convert audio file format or properties.
Usage:
bioamla audio convert [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-r, --sample-rate INTEGER Target sample rate
-c, --channels INTEGER Target number of channels
-b, --bit-depth INTEGER Target bit depth
-f, --format [wav|mp3|flac|ogg]
Output format
--help Show this message and exit.
denoise¶
Apply spectral noise reduction to audio file.
Usage:
bioamla audio denoise [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
--strength FLOAT Noise reduction strength (0-2, default: 1.0)
--help Show this message and exit.
filter¶
Apply frequency filter to audio file.
Usage:
bioamla audio filter [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
--lowpass FLOAT Lowpass cutoff frequency in Hz
--highpass FLOAT Highpass cutoff frequency in Hz
--bandpass-low FLOAT Bandpass low frequency in Hz
--bandpass-high FLOAT Bandpass high frequency in Hz
--order INTEGER Filter order (default: 5)
--help Show this message and exit.
gain¶
Apply a fixed gain (dB) to audio.
Usage:
bioamla audio gain [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
--gain-db FLOAT Gain in dB (positive amplifies) [required]
--help Show this message and exit.
info¶
Display audio file information.
Usage:
bioamla audio info [OPTIONS] PATH
Options:
--help Show this message and exit.
list¶
List audio files in a directory.
Usage:
bioamla audio list [OPTIONS] PATH
Options:
-r, --recursive / --no-recursive
Search subdirectories (default: recursive)
--help Show this message and exit.
normalize¶
Normalize audio amplitude.
Usage:
bioamla audio normalize [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-t, --target-db FLOAT Target peak level in dB
-m, --method [peak|rms] Method
--help Show this message and exit.
pitch-shift¶
Shift pitch up/down without changing duration.
Usage:
bioamla audio pitch-shift [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-n, --steps FLOAT Semitones to shift (positive raises pitch) [required]
--help Show this message and exit.
play¶
Play an audio file through the default output device.
Blocks until playback finishes; press Ctrl-C to stop.
Usage:
bioamla audio play [OPTIONS] PATH
Options:
-l, --loop Loop continuously until interrupted
--help Show this message and exit.
resample¶
Resample audio to a different sample rate.
Usage:
bioamla audio resample [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-r, --sample-rate INTEGER Target sample rate in Hz [required]
--help Show this message and exit.
segment¶
Segment audio file into fixed-duration clips.
Usage:
bioamla audio segment [OPTIONS] INPUT_PATH OUTPUT_DIR
Options:
-d, --duration-seconds FLOAT Segment duration in seconds (default: 3.0)
-o, --overlap FLOAT Overlap between segments in seconds
(default: 0.0)
-f, --format [wav|mp3|flac|ogg]
Output format (default: wav)
-p, --prefix TEXT Prefix for output filenames (default: input
filename)
--help Show this message and exit.
time-stretch¶
Time-stretch audio without changing pitch.
Usage:
bioamla audio time-stretch [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-r, --rate FLOAT Stretch factor (>1 faster, <1 slower) [required]
--help Show this message and exit.
trim¶
Trim audio file to specified time range.
Usage:
bioamla audio trim [OPTIONS] INPUT_PATH OUTPUT_PATH
Options:
-s, --start FLOAT Start time in seconds
-e, --end FLOAT End time in seconds
-d, --duration-seconds FLOAT Duration in seconds
--help Show this message and exit.
visualize¶
Generate audio visualization (spectrogram, waveform, MFCC) for a single file.
Examples:
# Mel spectrogram (default), auto-named
Usage:
bioamla audio visualize [OPTIONS] PATH
Options:
-o, --output TEXT Output image file path
-t, --type [mel|stft|mfcc|waveform]
Visualization type
--n-fft INTEGER FFT window size
--hop-length INTEGER Hop length
--n-mels INTEGER Number of mel bands
--n-mfcc INTEGER Number of MFCCs
--cmap TEXT Colormap name
--dpi INTEGER Output DPI
--legend / --no-legend Show axes, title, and colorbar (default:
True)
--help Show this message and exit.
batch¶
Batch processing operations for multiple files.
Usage:
bioamla batch [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
audio¶
Batch audio processing operations.
Usage:
bioamla batch audio [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
convert¶
Batch convert audio files to a target format (optionally resample/re-channel).
Usage:
bioamla batch audio convert [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-r, --sample-rate INTEGER Target sample rate
-c, --channels INTEGER Target number of channels
-f, --format [wav|mp3|flac|ogg]
Output format
--delete-original Delete original files after successful
conversion
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
denoise¶
Batch apply spectral noise reduction to audio files.
Usage:
bioamla batch audio denoise [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--strength FLOAT Noise reduction strength (0-2)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
filter¶
Batch apply frequency filters to audio files.
Usage:
bioamla batch audio filter [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--lowpass FLOAT Lowpass cutoff frequency in Hz
--highpass FLOAT Highpass cutoff frequency in Hz
--bandpass-low FLOAT Bandpass low frequency in Hz
--bandpass-high FLOAT Bandpass high frequency in Hz
--order INTEGER Filter order (default: 5)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
info¶
Extract audio file metadata (duration, sample rate, channels, format, etc.).
Usage:
bioamla batch audio info [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
normalize¶
Batch normalize audio levels.
Usage:
bioamla batch audio normalize [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-d, --target-db FLOAT Target loudness in dB
--peak Use peak normalization instead of RMS
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
resample¶
Batch resample audio files to a target sample rate.
Usage:
bioamla batch audio resample [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-r, --sample-rate INTEGER Target sample rate in Hz [required]
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
segment¶
Batch segment audio files into fixed-duration chunks.
Usage:
bioamla batch audio segment [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-d, --duration-seconds FLOAT Segment duration in seconds [required]
-o, --overlap FLOAT Overlap between segments in seconds
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
trim¶
Batch trim audio files by time range or remove silence.
Usage:
bioamla batch audio trim [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-s, --start FLOAT Start time in seconds
-e, --end FLOAT End time in seconds
--trim-silence Trim silence from start/end instead of time
range
--silence-threshold-db FLOAT Silence threshold in dB (with --trim-silence)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
visualize¶
Batch generate audio visualizations.
Usage:
bioamla batch audio visualize [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-t, --plot-type [mel|stft|mfcc|waveform]
Visualization type
--legend / --no-legend Show axes, title, and colorbar
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
cluster¶
Batch cluster embedding files from a directory or a metadata CSV.
Usage:
bioamla batch cluster [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--method [hdbscan|kmeans|dbscan|agglomerative]
Clustering method
--n-clusters INTEGER Number of clusters (k-means/agglomerative)
--min-cluster-size INTEGER Minimum cluster size (HDBSCAN)
--min-samples INTEGER Minimum samples per cluster
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
detect¶
Batch detection operations.
Usage:
bioamla batch detect [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
accelerating¶
Batch detect accelerating or decelerating call patterns.
Usage:
bioamla batch detect accelerating [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--min-pulses INTEGER Minimum pulses to detect pattern
--accel-threshold FLOAT Acceleration threshold
--decel-threshold FLOAT Deceleration threshold
--low-freq FLOAT Low frequency bound (Hz)
--high-freq FLOAT High frequency bound (Hz)
--window-seconds FLOAT Analysis window in seconds
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
energy¶
Batch detect sounds using band-limited energy detection.
Usage:
bioamla batch detect energy [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--low-freq FLOAT Low frequency bound (Hz)
--high-freq FLOAT High frequency bound (Hz)
--threshold-db FLOAT Detection threshold (dB)
--min-duration FLOAT Minimum detection duration (s)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
peaks¶
Batch detect peaks using Continuous Wavelet Transform.
Usage:
bioamla batch detect peaks [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--snr-threshold FLOAT Signal-to-noise ratio threshold
--min-peak-distance FLOAT Minimum peak distance (s)
--low-freq FLOAT Low frequency bound (Hz)
--high-freq FLOAT High frequency bound (Hz)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
ribbit¶
Batch detect periodic calls using RIBBIT algorithm.
Usage:
bioamla batch detect ribbit [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--pulse-rate FLOAT Expected pulse rate (Hz)
--pulse-tolerance FLOAT Pulse rate tolerance
--low-freq FLOAT Low frequency bound (Hz)
--high-freq FLOAT High frequency bound (Hz)
--window-seconds FLOAT Analysis window in seconds
--min-score FLOAT Minimum detection score
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
index¶
Batch calculate acoustic indices for audio files.
Usage:
bioamla batch index [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
--indices TEXT Comma-separated indices
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
models¶
Batch model operations (AST-only).
Usage:
bioamla batch models [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
embed¶
Batch extract embeddings from audio files.
Usage:
bioamla batch models embed [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-m, --model, --model-path TEXT Model path (HuggingFace ID or local path)
[required]
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
predict¶
Batch run AST model predictions on audio files (whole file or in segments).
With --segment-duration each file is split into fixed-length (optionally
overlapping) segments and classified per segment: directory mode writes a flat
predictions.csv (one row per segment) to --output-dir; CSV-metadata mode
expands each input row into one row per segment.
Usage:
bioamla batch models predict [OPTIONS]
Options:
--input-dir DIRECTORY Input directory for batch processing
--input-file FILE Input metadata CSV file (must have file_name
column)
--output-dir PATH Output directory
-m, --model, --model-path TEXT Model path (HuggingFace ID or local path)
[required]
--top-k INTEGER Number of top predictions to return
--min-confidence FLOAT Minimum confidence threshold
--segment-seconds INTEGER Split each file into N-second segments and
classify each (0 = whole file)
--overlap INTEGER Overlap between segments (seconds)
-w, --max-workers INTEGER Number of parallel workers
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
catalogs¶
Access bioacoustic data catalogs and external services.
Usage:
bioamla catalogs [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
ebird¶
eBird bird observation data and taxonomy.
Usage:
bioamla catalogs ebird [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
nearby¶
Get recent eBird observations near a location.
Usage:
bioamla catalogs ebird nearby [OPTIONS]
Options:
--lat FLOAT Latitude [required]
--lng FLOAT Longitude [required]
--api-key TEXT eBird API key (or set EBIRD_API_KEY) [required]
--distance FLOAT Search radius in km
--days INTEGER Days back to search
--limit INTEGER Maximum results
-o, --output TEXT Output CSV file
--help Show this message and exit.
search¶
Fuzzy search eBird taxonomy for species.
Usage:
bioamla catalogs ebird search [OPTIONS] QUERY
Options:
-n, --limit INTEGER Maximum results
--help Show this message and exit.
species¶
Look up species in eBird taxonomy.
NAME can be a common name, scientific name, or species code.
Usage:
bioamla catalogs ebird species [OPTIONS] NAME
Options:
--help Show this message and exit.
validate¶
Validate if a species is expected at a location.
Usage:
bioamla catalogs ebird validate [OPTIONS] SPECIES_CODE
Options:
--lat FLOAT Latitude [required]
--lng FLOAT Longitude [required]
--api-key TEXT eBird API key (or set EBIRD_API_KEY) [required]
--distance FLOAT Search radius in km
--help Show this message and exit.
hf¶
HuggingFace Hub model and dataset management.
Usage:
bioamla catalogs hf [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
cache¶
Inspect or purge the local HuggingFace cache (datasets/models).
Datasets and models pulled/loaded from the Hub are cached so repeat grabs are fast. Lists the cache by default; pass --purge to reclaim the space.
Examples: bioamla catalogs hf cache # list everything cached bioamla catalogs hf cache --datasets --purge -y # free dataset cache
Usage:
bioamla catalogs hf cache [OPTIONS]
Options:
--models Target cached models
--datasets Target cached datasets
--all Target both models and datasets
--purge Delete the matched cache (default: list)
-y, --yes Skip the confirmation prompt when purging
--help Show this message and exit.
pull-dataset¶
Pull a HuggingFace audio dataset into the local labeled-folder layout.
Materializes REPO_ID (e.g. ashraq/esc-50) under DEST as label subdirs and
a metadata.csv, ready for dataset partition / models ast train.
Usage:
bioamla catalogs hf pull-dataset [OPTIONS] REPO_ID DEST
Options:
--split TEXT Single split to pull (default: all splits)
--config TEXT Dataset config/subset name (e.g. HSN for
BirdSet)
--audio-column TEXT Override the auto-detected audio column
--label-column TEXT Override the auto-detected label column
--sample-rate INTEGER Resample clips to this rate (0 to keep
source)
--layout [both|audiofolder|flat]
Output layout: label subdirs + metadata.csv
(both), subdirs only, or flat
-q, --quiet Suppress progress output
--help Show this message and exit.
push-dataset¶
Push a dataset folder to the HuggingFace Hub.
When --card is set (default) and the folder has a dataset.json manifest
or a metadata.csv, a README.md dataset card is generated first; folders
without either are pushed as-is.
Usage:
bioamla catalogs hf push-dataset [OPTIONS] PATH REPO_ID
Options:
--private / --public Make the repository private (default: public)
--commit-message TEXT Custom commit message for the push
--card / --no-card Write a README.md dataset card from the
manifest/metadata before pushing
--help Show this message and exit.
push-model¶
Push a model folder to the HuggingFace Hub.
Usage:
bioamla catalogs hf push-model [OPTIONS] PATH REPO_ID
Options:
--private / --public Make the repository private (default: public)
--commit-message TEXT Custom commit message for the push
--help Show this message and exit.
inat¶
iNaturalist observation database.
Usage:
bioamla catalogs inat [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
download¶
Download audio observations from iNaturalist.
Usage:
bioamla catalogs inat download [OPTIONS] OUTPUT_DIR
Options:
-t, --taxon-ids TEXT Comma-separated taxon IDs
-n, --taxon-name TEXT Taxon name to search for
-p, --place-id INTEGER iNaturalist place ID
--project-id TEXT iNaturalist project slug or ID
-q, --quality-grade [research|needs_id|casual|any]
Quality grade filter
-l, --license TEXT Filter by sound license(s) (comma-separated:
cc0, cc-by, cc-by-nc, cc-by-sa, cc-by-nd,
cc-by-nc-sa, cc-by-nc-nd)
-d1, --start-date TEXT Start date for observations (YYYY-MM-DD)
-d2, --end-date TEXT End date for observations (YYYY-MM-DD)
--obs-per-taxon INTEGER Max observations per taxon
--quiet Suppress progress output
--help Show this message and exit.
search¶
Search for iNaturalist observations.
Usage:
bioamla catalogs inat search [OPTIONS]
Options:
-s, --species TEXT Species scientific name to filter by
-t, --taxon-id INTEGER iNaturalist taxon ID
-p, --place-id INTEGER iNaturalist place ID
--project-id TEXT iNaturalist project slug or ID
--quality-grade TEXT Quality grade: research, needs_id, or casual
--has-sounds Only show observations with sounds
--limit INTEGER Maximum number of results
-o, --output TEXT Output file path for CSV (optional)
-q, --quiet Suppress progress output
--help Show this message and exit.
stats¶
Get statistics for an iNaturalist project.
Usage:
bioamla catalogs inat stats [OPTIONS] PROJECT_ID
Options:
-o, --output TEXT Output file path for JSON (optional)
-q, --quiet Suppress progress output, print only JSON
--help Show this message and exit.
ml¶
Macaulay Library audio recordings database.
Use 'catalogs ebird species' or 'catalogs ebird search' to look up species codes.
Usage:
bioamla catalogs ml [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
download¶
Download recordings from Macaulay Library.
Requires at least one filter: species-code, scientific-name, common-name, region, taxon-code, or hotspot-code.
Use 'catalogs ebird species
Usage:
bioamla catalogs ml download [OPTIONS]
Options:
-s, --species-code TEXT eBird species code (e.g., amerob)
--scientific-name TEXT Scientific name
--common-name TEXT Common name
-r, --region TEXT Region code (e.g., US-NY)
--country TEXT Country code (e.g., US)
--taxon-code TEXT eBird taxon code for broader searches
--hotspot-code TEXT eBird hotspot code
--min-rating INTEGER Minimum quality rating (default: 3)
-n, --max-recordings INTEGER Maximum recordings to download
-o, --output-dir TEXT Output directory
--help Show this message and exit.
search¶
Search Macaulay Library for audio recordings.
Requires at least one filter: species-code, scientific-name, common-name, region, taxon-code, or hotspot-code.
Use 'catalogs ebird species
Usage:
bioamla catalogs ml search [OPTIONS]
Options:
-s, --species-code TEXT eBird species code (e.g., amerob)
--scientific-name TEXT Scientific name
--common-name TEXT Common name
-r, --region TEXT Region code (e.g., US-NY)
--country TEXT Country code (e.g., US)
--taxon-code TEXT eBird taxon code for broader searches
--hotspot-code TEXT eBird hotspot code
--min-rating INTEGER Minimum quality rating (1-5)
-n, --max-results INTEGER Maximum results
--format [table|json] Output format
--help Show this message and exit.
xc¶
Xeno-canto bird recording database.
Usage:
bioamla catalogs xc [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
download¶
Download recordings from Xeno-canto.
Usage:
bioamla catalogs xc download [OPTIONS]
Options:
-s, --species TEXT Species name (scientific or common)
-g, --genus TEXT Genus name
-c, --country TEXT Country name
-q, --quality TEXT Recording quality filter (default: A)
-n, --max-recordings INTEGER Maximum recordings to download
-o, --output-dir TEXT Output directory
--delay FLOAT Delay between downloads in seconds
--help Show this message and exit.
search¶
Search Xeno-canto for bird recordings.
Examples: # Songs of a species in the US, top 20 bioamla catalogs xc search --species "Turdus migratorius" \ --country "United States" --type song --max-results 20 # By genus, JSON output for scripting bioamla catalogs xc search --genus Turdus --quality A --format json
Usage:
bioamla catalogs xc search [OPTIONS]
Options:
-s, --species TEXT Species name (scientific or common)
-g, --genus TEXT Genus name
-c, --country TEXT Country name
-q, --quality TEXT Recording quality (A, B, C, D, E)
--type TEXT Sound type (song, call, etc.)
-n, --max-results INTEGER Maximum results
--format [table|json|csv] Output format
--help Show this message and exit.
cluster¶
Clustering and dimensionality reduction commands.
Usage:
bioamla cluster [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
analyze¶
Analyze cluster quality.
Usage:
bioamla cluster analyze [OPTIONS] EMBEDDINGS_FILE LABELS_FILE
Options:
-o, --output TEXT Output JSON file for analysis results
-q, --quiet Suppress output
--help Show this message and exit.
fit¶
Cluster embeddings.
Usage:
bioamla cluster fit [OPTIONS] EMBEDDINGS_FILE
Options:
-o, --output TEXT Output file for cluster labels [required]
-m, --method [hdbscan|kmeans|dbscan|agglomerative]
Clustering method (hdbscan finds clusters
without a preset count)
-k, --n-clusters INTEGER Number of clusters (for
k-means/agglomerative)
--min-cluster-size INTEGER Minimum cluster size (HDBSCAN)
--eps FLOAT DBSCAN epsilon
--min-samples INTEGER Minimum samples per cluster
-q, --quiet Suppress output
--help Show this message and exit.
novelty¶
Detect novel sounds in embeddings.
Usage:
bioamla cluster novelty [OPTIONS] EMBEDDINGS_FILE
Options:
-o, --output TEXT Output file for novelty results [required]
-m, --method [distance|isolation_forest|lof]
Novelty detection method
--threshold FLOAT Novelty threshold
--labels TEXT Optional cluster labels file
-q, --quiet Suppress output
--help Show this message and exit.
reduce¶
Reduce dimensionality of embeddings.
Usage:
bioamla cluster reduce [OPTIONS] EMBEDDINGS_FILE
Options:
-o, --output TEXT Output file for reduced embeddings [required]
-m, --method [umap|tsne|pca] Reduction method
-n, --n-components INTEGER Number of output dimensions
-q, --quiet Suppress output
--help Show this message and exit.
dataset¶
Dataset management commands.
Usage:
bioamla dataset [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
augment¶
Augment audio files to expand training datasets.
Each enabled transform takes a range; ranges are sampled per output copy.
This writes new augmented files (offline) — distinct from models ast train's
on-the-fly augmentation.
Examples: # Two noisy + pitch-shifted copies per file bioamla dataset augment ./clips -o ./aug \ --add-noise 3-30 --pitch-shift -2,2 --multiply 2 # Time-stretch only bioamla dataset augment ./clips -o ./aug --time-stretch 0.9-1.1
Usage:
bioamla dataset augment [OPTIONS] INPUT_DIR
Options:
-o, --output TEXT Output directory for augmented files
[required]
--add-noise TEXT Add Gaussian noise with SNR range (e.g.,
"3-30" dB)
--time-stretch TEXT Time stretch range (e.g., "0.8-1.2")
--pitch-shift TEXT Pitch shift range in semitones (e.g., "-2,2")
--gain TEXT Gain range in dB (e.g., "-12,12")
--multiply INTEGER Number of augmented copies to create per file
--sample-rate INTEGER Target sample rate for output
--recursive / --no-recursive Search subdirectories
-q, --quiet Suppress progress output
--help Show this message and exit.
build¶
Build a training-ready dataset: extract clips, partition, and write a manifest.
Chains extract-clips (layout=both) -> partition (subdirs) -> manifest,
producing a dataset directory + dataset.json consumable by models ast train.
License/attribution joined from the source catalog metadata is written to
ATTRIBUTIONS.md (unless --no-attributions).
Examples: # Annotated recordings dir -> train-ready dataset bioamla dataset build ./recordings ./dataset --sample-rate 16000 # Keep two labels and set an 80/10/10 train/val/test split bioamla dataset build ./recordings ./dataset \ --include frog --include bird --train 0.8 --val 0.1 --test 0.1
Usage:
bioamla dataset build [OPTIONS] SOURCE OUTPUT_DIR
Options:
--annotations TEXT Annotation file when SOURCE is a single
audio file (else a sibling file is used)
--padding-ms FLOAT Padding before/after each clip (ms)
--bandpass / --no-bandpass Bandpass-filter clips to each annotation's
frequency band
--sample-rate INTEGER Resample clips to this rate (e.g. 16000 for
AST)
-i, --include TEXT Labels to include (repeatable)
-e, --exclude TEXT Labels to exclude (repeatable)
--min-duration FLOAT Drop clips shorter than this (s)
--train FLOAT Train fraction
--val FLOAT Validation fraction
--test FLOAT Test fraction
--seed INTEGER Reproducible shuffle seed
--no-partition Extract clips but skip train/val/test split
--name TEXT Dataset name for the manifest (defaults to
dir name)
--source-metadata TEXT Catalog metadata.csv to join
license/attribution onto clips (auto-
detected as a metadata.csv sibling of SOURCE
when omitted)
--attributions / --no-attributions
Write ATTRIBUTIONS.md from joined clip
provenance (skipped if none)
-q, --quiet Suppress progress output
--help Show this message and exit.
extract-clips¶
Extract annotated regions into a labeled clip dataset (training-ready).
SOURCE is an audio file (with --annotations or a sibling annotation file) or
a directory of audio files each paired with a sibling annotation. The output
is consumable by bioamla models ast train directly (label subdirs and/or a
metadata.csv). License/attribution is joined from the source catalog
metadata.csv (auto-detected, or via --source-metadata) so clips stay
traceable to their original recordings.
Usage:
bioamla dataset extract-clips [OPTIONS] SOURCE OUTPUT_DIR
Options:
--annotations TEXT Annotation file when SOURCE is a single
audio file (else a sibling file is used)
--layout [both|audiofolder|flat]
Output layout: label subdirs + metadata.csv
(both), subdirs only, or flat + metadata.csv
--padding-ms FLOAT Padding before/after each clip (ms)
--bandpass / --no-bandpass Bandpass-filter clips to each annotation's
frequency band
--format TEXT Output audio format
--sample-rate INTEGER Resample clips to this rate (e.g. 16000 for
AST)
-i, --include TEXT Labels to include (repeatable)
-e, --exclude TEXT Labels to exclude (repeatable)
--min-duration FLOAT Drop clips shorter than this (s)
--source-metadata TEXT Catalog metadata.csv to join
license/attribution onto clips (auto-
detected as a metadata.csv sibling of SOURCE
when omitted)
-q, --quiet Suppress progress output
--help Show this message and exit.
license¶
Generate license/attribution file from dataset metadata.
Usage:
bioamla dataset license [OPTIONS] PATH
Options:
-t, --template TEXT Template file to prepend to the license file
-o, --output TEXT Output filename (default: LICENSE for text,
ATTRIBUTIONS.md for md)
--format [text|md] Output format: plain-text LICENSE or Markdown
ATTRIBUTIONS
--metadata-filename TEXT Name of metadata CSV file
--batch Process all datasets in directory (each
subdirectory with metadata.csv)
-q, --quiet Suppress progress output
--help Show this message and exit.
manifest¶
Build a dataset.json manifest (label vocabulary, counts, splits) from metadata.csv.
Usage:
bioamla dataset manifest [OPTIONS] DATASET_DIR
Options:
--name TEXT Dataset name recorded in the manifest
(defaults to dir name)
--kind [labeled|partitioned] Dataset kind
-o, --output TEXT Output manifest path (default:
DATASET_DIR/dataset.json)
--metadata-filename TEXT Name of the metadata CSV in the dataset
--sample-rate INTEGER Sample rate to record in the manifest
-q, --quiet Suppress progress output
--help Show this message and exit.
merge¶
Merge multiple audio datasets into a single dataset.
Usage:
bioamla dataset merge [OPTIONS] OUTPUT_DIR DATASET_PATHS...
Options:
--metadata-filename TEXT Name of metadata CSV file in each dataset
--overwrite Overwrite existing files instead of skipping
--no-organize Preserve original directory structure instead of
organizing by category
--target-format TEXT Convert all audio files to this format (wav, mp3,
flac, etc.)
-q, --quiet Suppress progress output
--help Show this message and exit.
partition¶
Partition a dataset into train/val/test (stratified, grouped, reproducible).
Examples:
# Default 80/10/10 split, writing a split column into metadata.csv
bioamla dataset partition ./dataset
# Reorganize into train/val/test/
Usage:
bioamla dataset partition [OPTIONS] DATASET_DIR
Options:
--train FLOAT Train fraction
--val FLOAT Validation fraction
--test FLOAT Test fraction
--seed INTEGER Reproducible shuffle seed
--stratify / --no-stratify Balance labels across splits
--mode [subdirs|column] Reorganize into train/val/test/<label>/
(subdirs) or populate a split column
--group-by TEXT Keep rows sharing this column's value in one
split (prevents clip leakage)
--background-label TEXT Partition this label as its own stratum so it
appears in every split
--metadata-filename TEXT Name of the metadata CSV in the dataset
-q, --quiet Suppress progress output
--help Show this message and exit.
stats¶
Show summary statistics for a dataset's metadata.csv.
Usage:
bioamla dataset stats [OPTIONS] DATASET_DIR
Options:
--metadata-filename TEXT Name of the metadata CSV in the dataset
--json Output as JSON
--help Show this message and exit.
detect¶
Advanced acoustic detection algorithms.
Usage:
bioamla detect [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
accelerating¶
Detect accelerating or decelerating call patterns (single file).
Usage:
bioamla detect accelerating [OPTIONS] FILE
Options:
--min-pulses INTEGER Minimum pulses to detect pattern
-a, --acceleration FLOAT Acceleration threshold (final_rate/initial_rate)
-d, --deceleration FLOAT Deceleration threshold (optional)
-l, --low-freq FLOAT Low frequency bound (Hz)
-h, --high-freq FLOAT High frequency bound (Hz)
-w, --window-seconds FLOAT Analysis window in seconds
-o, --output PATH Output file for detections
--format [table|json|csv] Output format
--help Show this message and exit.
energy¶
Detect sounds using band-limited energy detection (single file).
Usage:
bioamla detect energy [OPTIONS] FILE
Options:
-l, --low-freq FLOAT Low frequency bound (Hz)
-h, --high-freq FLOAT High frequency bound (Hz)
-t, --threshold-db FLOAT Detection threshold (dB)
--min-duration FLOAT Minimum detection duration (s)
-o, --output PATH Output file for detections
--format [table|json|csv] Output format
--help Show this message and exit.
peaks¶
Detect peaks using Continuous Wavelet Transform (CWT) (single file).
Usage:
bioamla detect peaks [OPTIONS] FILE
Options:
--snr-threshold FLOAT Signal-to-noise ratio threshold
--min-distance FLOAT Minimum peak distance (s)
-l, --low-freq FLOAT Low frequency bound (Hz)
-h, --high-freq FLOAT High frequency bound (Hz)
-o, --output PATH Output file for detections
--format [table|json|csv] Output format
--help Show this message and exit.
ribbit¶
Detect periodic calls using RIBBIT algorithm (single file).
Usage:
bioamla detect ribbit [OPTIONS] FILE
Options:
-p, --pulse-rate FLOAT Expected pulse rate in Hz (pulses per second)
--tolerance FLOAT Tolerance around expected pulse rate (fraction)
-l, --low-freq FLOAT Low frequency bound (Hz)
-h, --high-freq FLOAT High frequency bound (Hz)
-w, --window-seconds FLOAT Analysis window in seconds
--min-score FLOAT Minimum detection score
-o, --output PATH Output file for detections
--format [table|json|csv] Output format
--help Show this message and exit.
indices¶
Acoustic indices for soundscape ecology analysis.
Usage:
bioamla indices [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
aci¶
Compute Acoustic Complexity Index (ACI) only.
Usage:
bioamla indices aci [OPTIONS] FILE
Options:
--low-freq FLOAT Low-frequency bound (Hz)
--high-freq FLOAT High-frequency bound (Hz)
--n-fft INTEGER FFT window size
--help Show this message and exit.
adi¶
Compute Acoustic Diversity Index (ADI) only.
Usage:
bioamla indices adi [OPTIONS] FILE
Options:
--threshold-db FLOAT dB threshold
--n-fft INTEGER FFT window size
--help Show this message and exit.
aei¶
Compute Acoustic Evenness Index (AEI) only.
Usage:
bioamla indices aei [OPTIONS] FILE
Options:
--threshold-db FLOAT dB threshold
--n-fft INTEGER FFT window size
--help Show this message and exit.
bio¶
Compute Bioacoustic Index (BIO) only.
Usage:
bioamla indices bio [OPTIONS] FILE
Options:
--low-freq FLOAT Low-frequency bound (Hz)
--high-freq FLOAT High-frequency bound (Hz)
--n-fft INTEGER FFT window size
--help Show this message and exit.
compute¶
Compute all acoustic indices for a single audio file.
Usage:
bioamla indices compute [OPTIONS] FILE
Options:
-o, --output PATH Output JSON file for results
--format [table|json|csv] Output format
--n-fft INTEGER FFT window size
--aci-low-freq FLOAT ACI low-frequency bound (Hz)
--aci-high-freq FLOAT ACI high-frequency bound (Hz)
--bio-low-freq FLOAT BIO low-frequency bound (Hz)
--bio-high-freq FLOAT BIO high-frequency bound (Hz)
--threshold-db FLOAT dB threshold for ADI/AEI
--help Show this message and exit.
entropy¶
Compute spectral and temporal entropy indices only.
Usage:
bioamla indices entropy [OPTIONS] FILE
Options:
--n-fft INTEGER FFT window size
--help Show this message and exit.
ndsi¶
Compute Normalized Difference Soundscape Index (NDSI) only.
Usage:
bioamla indices ndsi [OPTIONS] FILE
Options:
--n-fft INTEGER FFT window size
--help Show this message and exit.
temporal¶
Compute temporal acoustic indices (indices over time segments).
Usage:
bioamla indices temporal [OPTIONS] FILE
Options:
--window-seconds FLOAT Analysis window in seconds
-o, --output PATH Output JSON file for results
--n-fft INTEGER FFT window size
--help Show this message and exit.
models¶
ML model operations - AST models.
Usage:
bioamla models [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
ast¶
Audio Spectrogram Transformer (AST) model operations.
Usage:
bioamla models ast [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
embed¶
Extract embeddings from audio using AST model.
Example: bioamla models ast embed audio.wav --model-path my_model -o embeddings.npy
Usage:
bioamla models ast embed [OPTIONS] FILE
Options:
--model-path TEXT Path to AST model or HuggingFace identifier
[required]
-o, --output TEXT Output file (.npy) [required]
--layer TEXT Layer to extract embeddings from
--sample-rate INTEGER Target sample rate
--help Show this message and exit.
evaluate¶
Evaluate an AST model on a directory of audio files.
Examples: # Accuracy/precision/recall against a ground-truth CSV bioamla models ast evaluate ./audio_dir --model-path my_model -g labels.csv # Write a JSON report bioamla models ast evaluate ./audio_dir -g labels.csv \ --format json -o eval.json
Usage:
bioamla models ast evaluate [OPTIONS] PATH
Options:
--model-path TEXT AST model to use for evaluation
-g, --ground-truth TEXT Path to CSV file with ground truth labels
[required]
-o, --output TEXT Output file for evaluation results
--format [json|csv|txt] Output format
--file-column TEXT Column name for file names in ground truth CSV
--label-column TEXT Column name for labels in ground truth CSV
--resample-freq INTEGER Resampling frequency
--batch-size INTEGER Batch size for inference
--fp16 / --no-fp16 Use half-precision inference
-q, --quiet Only output metrics, suppress progress
--help Show this message and exit.
info¶
Display information about an AST model.
Example: bioamla models ast info bioamla/scp-frogs
Usage:
bioamla models ast info [OPTIONS] MODEL_PATH
Options:
--help Show this message and exit.
init-config¶
Write a documented AST training-config file for use with train --config.
The file holds the [models], [training], and [augmentation] settings that
ast train reads; edit it, then pass it via --config. Command-line
flags still override any value in the file.
Usage:
bioamla models ast init-config [OPTIONS]
Options:
-o, --output TEXT Output file path
-f, --force Overwrite an existing file
--help Show this message and exit.
predict¶
Run AST prediction on a single audio file — whole file or in segments.
With --segment-seconds the file is split into fixed-length (optionally
overlapping) segments and each is classified, yielding one prediction per
segment; otherwise the whole file gets a single prediction.
Examples: bioamla models ast predict audio.wav --model-path my_model bioamla models ast predict rec.wav --segment-seconds 3 --overlap 1 -o rec.csv
Usage:
bioamla models ast predict [OPTIONS] FILE
Options:
--model-path TEXT AST model to use for inference
--segment-seconds INTEGER Split into N-second segments and classify each (0
= classify the whole file)
--overlap INTEGER Overlap between segments (seconds)
--min-confidence FLOAT Drop predictions below this confidence
-o, --output TEXT Write predictions to this CSV
(filepath,start,stop,prediction,confidence).
Default: print to stdout.
--resample-freq INTEGER Resampling frequency
--help Show this message and exit.
train¶
Fine-tune an AST model on a custom dataset.
The --train-dataset option accepts three formats:
- HuggingFace dataset: bioamla/scp-frogs or samuelstevens/BirdSet:HSN
- Metadata CSV: ./data/metadata.csv (must have file and label columns)
- Directory with class subdirs: ./data/ containing bird/, frog/, etc.
Examples: bioamla models ast train --train-dataset bioamla/scp-frogs bioamla models ast train --train-dataset ./metadata.csv bioamla models ast train --train-dataset ./audio_by_class/
Usage:
bioamla models ast train [OPTIONS]
Options:
--config FILE TOML config file (e.g. from 'bioamla config
init'). Explicit flags override its values;
its values override defaults. Reads
[training] and [models].
--training-dir TEXT Directory to save training outputs
--base-model TEXT Base model to fine-tune
--train-dataset TEXT Training data source: HuggingFace dataset
(e.g. 'bioamla/scp-frogs'), local metadata
CSV (with 'file' and 'label' columns), or
directory with class subdirectories (e.g.
./data/bird/, ./data/frog/) [required]
--split TEXT Dataset split to use (for HuggingFace
datasets)
--id-column TEXT Column name for category/target IDs
--label-column TEXT Column name for labels
--report-to TEXT Where to report metrics: tensorboard
(default, bundled), mlflow, none, ...
(comma-separated).
--learning-rate FLOAT Learning rate for training
--push-to-hub / --no-push-to-hub
Whether to push model to HuggingFace Hub
--num-train-epochs INTEGER Number of training epochs
--per-device-train-batch-size INTEGER
Training batch size per device
--eval-strategy TEXT Evaluation strategy
--save-strategy TEXT Model save strategy
--eval-steps INTEGER Number of steps between evaluations
--save-steps INTEGER Number of steps between saves
--load-best-model-at-end / --no-load-best-model-at-end
Load best model at end of training
--metric-for-best-model TEXT Metric to use for best model selection
--logging-strategy TEXT Logging strategy
--logging-steps INTEGER Number of steps between logging
--fp16 / --no-fp16 Use FP16 mixed precision training (for
NVIDIA GPUs)
--bf16 / --no-bf16 Use BF16 mixed precision training (for
Ampere+ GPUs)
--gradient-accumulation-steps INTEGER
Number of gradient accumulation steps
--dataloader-num-workers INTEGER
Number of dataloader workers
--torch-compile / --no-torch-compile
Use torch.compile for faster training
(PyTorch 2.0+)
--finetune-mode [full|feature-extraction]
Training mode: full (all layers) or feature-
extraction (freeze base, train classifier
only)
--mlflow-tracking-uri TEXT MLflow tracking server URI (e.g.,
http://localhost:5000)
--mlflow-experiment-name TEXT MLflow experiment name
--mlflow-run-name TEXT MLflow run name
--add-noise / --no-add-noise Augmentation layer: add Gaussian noise (off
by default)
--time-stretch / --no-time-stretch
Augmentation layer: time-stretch (off by
default)
--pitch-shift / --no-pitch-shift
Augmentation layer: pitch-shift (off by
default)
--gain / --no-gain Augmentation layer: random gain (off by
default)
--gain-transition / --no-gain-transition
Augmentation layer: smooth gain ramp (off by
default)
--clipping-distortion / --no-clipping-distortion
Augmentation layer: clipping distortion (off
by default)
--augment-multiplier INTEGER Create N augmented copies of each training
sample (1=no copies, 2=double dataset, etc.)
--augment-probability FLOAT RANGE
Probability the whole augmentation pipeline
is applied to a sample (0-1) [0.0<=x<=1.0]
--min-snr-db FLOAT Minimum SNR for Gaussian noise (dB)
--max-snr-db FLOAT Maximum SNR for Gaussian noise (dB)
--noise-probability FLOAT RANGE
Per-sample probability of the noise layer
(0-1) [0.0<=x<=1.0]
--min-gain-db FLOAT Minimum gain adjustment (dB)
--max-gain-db FLOAT Maximum gain adjustment (dB)
--gain-probability FLOAT RANGE Per-sample probability of the gain layer
(0-1) [0.0<=x<=1.0]
--gain-transition-probability FLOAT RANGE
Per-sample probability of the gain-
transition layer (0-1) [0.0<=x<=1.0]
--clipping-probability FLOAT RANGE
Per-sample probability of the clipping-
distortion layer (0-1) [0.0<=x<=1.0]
--min-percentile-threshold INTEGER
Min percentile for clipping
--max-percentile-threshold INTEGER
Max percentile for clipping
--min-time-stretch FLOAT Minimum time stretch rate
--max-time-stretch FLOAT Maximum time stretch rate
--time-stretch-probability FLOAT RANGE
Per-sample probability of the time-stretch
layer (0-1) [0.0<=x<=1.0]
--min-pitch-shift INTEGER Minimum pitch shift (semitones)
--max-pitch-shift INTEGER Maximum pitch shift (semitones)
--pitch-shift-probability FLOAT RANGE
Per-sample probability of the pitch-shift
layer (0-1) [0.0<=x<=1.0]
--help Show this message and exit.
system¶
System information commands (version, devices, dependencies).
Usage:
bioamla system [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
deps¶
Check or install system dependencies (FFmpeg, libsndfile, PortAudio).
These system libraries are required for full bioamla functionality:
- FFmpeg: Audio format conversion (MP3, FLAC, etc.)
- libsndfile: Audio file I/O
- PortAudio: Real-time audio recording
Examples: bioamla config deps # Check dependencies bioamla config deps --install # Install missing dependencies bioamla config deps --install -y # Install without confirmation
Usage:
bioamla system deps [OPTIONS]
Options:
--install Install missing system dependencies
-y, --yes Skip confirmation prompt
--help Show this message and exit.
devices¶
Show available compute devices (GPU, MPS, CPU).
Usage:
bioamla system devices [OPTIONS]
Options:
--help Show this message and exit.
version¶
Show bioamla version and environment information.
Usage:
bioamla system version [OPTIONS]
Options:
--help Show this message and exit.
util¶
General file utilities (download, unzip, zip).
Usage:
bioamla util [OPTIONS] COMMAND [ARGS]...
Options:
--help Show this message and exit.
download¶
Download a file from the specified URL to the target directory.
Usage:
bioamla util download [OPTIONS] URL [OUTPUT_DIR]
Options:
--help Show this message and exit.
unzip¶
Extract a ZIP archive to the specified output directory.
Usage:
bioamla util unzip [OPTIONS] FILE_PATH [OUTPUT_PATH]
Options:
--help Show this message and exit.
zip¶
Create a ZIP archive from a file or directory.
Usage:
bioamla util zip [OPTIONS] SOURCE_PATH OUTPUT_FILE
Options:
--help Show this message and exit.