Migrate from cogent3

Update imports

Replace cogent3.app imports with their scinexus equivalents:

# before
from cogent3.app.composable import define_app, NotCompleted

# after
from scinexus import define_app, NotCompleted

Summary methods return plain Python objects

Data store summary methods (describe, summary_logs, summary_not_completed, summary_citations, validate) now return list[dict] or dict instead of cogent3 Table objects.

To restore Table-based display, register a converter with set_summary_display():

from cogent3.core.table import Table
from scinexus.data_store import set_summary_display


def _summary_to_table(data, *, name):
    if isinstance(data, dict):
        rows = [[k, v] for k, v in data.items()]
        return Table(header=["Condition", "Value"], data=rows, title=name)
    if isinstance(data, list) and data:
        header = list(data[0].keys())
        rows = [list(row.values()) for row in data]
        return Table(header=header, data=rows, title=name)
    return data


set_summary_display(_summary_to_table)

NotCompletedType is now an enum

Failure types are categorised using the NotCompletedType enum rather than bare strings:

from scinexus.composable import NotCompletedType

# before
nc.type == "ERROR"

# after
nc.type == NotCompletedType.ERROR

The three values are ERROR, FAIL, and BUG.

App composition uses shallow copies

Composing apps with + now creates a shallow copy of the right-hand operand. Composed pipelines no longer share mutable state, so ComposableApp.disconnect() is no longer needed and is deprecated.

New features

These capabilities are new in scinexus and were not available in cogent3.app:

• check_data_type property -- toggle runtime input type checking on or off. See Runtime type checking.
• Better IDE integration through static typing support -- AppBase[T, R], ComposableApp[T, R], and WriterApp[T, R] can be inherited from directly as an alternative to @define_app.
• Pluggable parallel backends -- choose between stdlib multiprocessing, loky, or MPI backends. See Run in parallel.
• Pluggable progress bars -- use tqdm or rich for progress display. See Track progress.
• Custom identifier extraction -- register a custom function for extracting storage identifiers from data via set_id_from_source(). See Customise display and IDs.
• Logging can be disabled -- pass logger=False to apply_to() to skip log file creation.

Full changelog

See the changelog for a complete list of changes from the cogent3 app infrastructure.