flowbio¶

The flowbio Python library is a wrapper around the Flow API, allowing you to write Python scripts that interact with an instance of Flow.

Installation¶

Install with pip:

pip install flowbio

Requires Python 3.11+. Dependencies (requests, pydantic, tqdm, etc.) are installed automatically.

Overview¶

Everything starts with creating a Client. This is your connection to Flow — once you log in, you use it to upload samples, browse metadata, manage projects, and anything else the library supports:

from flowbio.v2 import Client
from flowbio.v2.auth import UsernamePasswordCredentials

client = Client()
client.log_in(UsernamePasswordCredentials("you@example.com", "password"))

# Now use client.samples.upload_sample(...), client.samples.upload_multiplexed_data(...), etc.

The Client is the recommended starting point and is under active development. The legacy client is being phased out but remains available for functionality not yet covered by v2.

Command-line interface¶

The same upload operations are available from the terminal via the flowbio command, for both interactive use and automated agents (--json output with stable exit codes). Log in once and your token is reused on later calls:

# Upload a single demultiplexed sample
flowbio samples upload --name liver_r1 --sample-type RNA-Seq \
    --reads1 ./liver_R1.fastq.gz --reads2 ./liver_R2.fastq.gz \
    --metadata strandedness=reverse

# Upload a generic data file, with machine-readable output
flowbio data upload ./counts.tsv --json

# Upload many samples from a CSV sample sheet
flowbio samples batch-template --sample-type RNA-Seq -o samples.csv
flowbio samples upload-batch --sheet samples.csv --sample-type RNA-Seq

See Command-line interface for authentication, output modes, the exit-code contract, and a worked example per command.

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