ABIO DAT¶

Topic: ABIO Topics Data management via dvc_dat integration.

Overview¶

ABIO uses dvc_dat for data persistence. See the dvc_dat documentation for full details.

Key concepts: - Dotted names (do-system): Reference source code templates via do() and create() - Slash paths (DAT storage): Reference data folders via load() and save() - Bio class: Higher-level interface for biology objects via Bio.fetch() and Bio.store() — see Bio - Spec Language: YAML syntax extensions (!ev, !ref, !include, typed keys, jobs) — see [[Spec Language]]

Configuration¶

.dataconfig.yaml in the project root:

sync_folder: data
mount_commands:
  - at: catalog
    folder: src/alienbio/catalog
  - at: fixtures
    module: tests.fixtures

Operators¶

Function	Description
`do(name)`	Load object by dotted name (returns dict, module, or callable)
`create(spec, path=)`	Create a Dat from spec string or dict
`load(path)`	Load a Dat from a data path
`save(obj, path)`	Save object as Dat to data path

Usage¶

from alienbio import do, create, load, save

# Load a template
template = do("fixtures.simple")

# Create a Dat from template
dat = create("fixtures.simple", path="runs/exp1")

# Load existing Dat
dat = load("runs/exp1")
print(dat.get_spec()["name"])

# Save data
dat = save({"name": "result", "value": 42}, "results/run1")

Development Setup¶

During co-development, dvc_dat is symlinked:

src/dvc_dat -> ../../dvc-dat/dvc_dat