tiferet-h5

HDF5 infrastructure extension for the Tiferet framework via PyTables.

tiferet-h5 mirrors the layered architecture of the Tiferet core — domain, interfaces, mappers, utils, repos — adapted to the hierarchical, columnar, and typed nature of HDF5 files. It introduces two mapper base classes that are the HDF5-native analogue of Tiferet's TransferObject: TableObject for row-oriented table storage and NodeObject for attribute-oriented node storage.

Requirements

• Python ≥ 3.10
• tiferet >= 2.0.3, < 2.1
• tables >= 3.10.0 (PyTables)

Async Usage

tiferet-h5 is sync-only by design and does not ship an async wrapper around core Tiferet's AsyncFeatureContext -- deliberately, not by oversight. A naive asyncio.to_thread wrapper would reintroduce the exact concurrent-access hazard the Concurrency guide documents as unsafe, and this package isn't yet confident enough in core's own async design to couple its API to it. If you need async interoperability, build it yourself around Tiferet's own async components -- wrap an individual short-lived operation in your own asyncio.to_thread(...) at the call site, and never hold one open H5Client instance across multiple concurrently-scheduled async tasks. See Async Usage in the H5Client guide for the full rationale and pattern.

Installation

pip install tiferet-h5

Or in development mode from the repository root:

pip install -e .

Quick Start

This tutorial stores a simple feature catalog — groups with scalar metadata and child step tables — to demonstrate the full stack: domain objects, mapper classes, H5Client, and H5Repository.

1. Define Your Mappers

import tables
from typing import ClassVar, Dict, Any, List
from pydantic import Field, AliasChoices
from tiferet_h5 import TableObject, NodeObject

# ── Group-level metadata → node attributes ────────────────────────────────
# One instance per feature group, stored on the HDF5 group node.
class FeatureGroupObject(NodeObject):
    name: str = Field(default='', description='Feature name.')
    description: str = Field(
        default='',
        serialization_alias='desc',
        validation_alias=AliasChoices('desc', 'description'),
        description='Stored as "desc" in HDF5 to keep attribute keys short.',
    )
    _ROLES: ClassVar[Dict[str, Dict[str, Any]]] = {
        'to_h5.attrs': {'by_alias': True, 'exclude_none': True},
    }

# ── Child collection → table rows ─────────────────────────────────────────
# One row per step, stored in a table nested inside the feature group.
class FeatureStepObject(TableObject):
    name: str = Field(default='', description='Step name.')
    service_id: str = Field(
        default='',
        serialization_alias='svc',
        validation_alias=AliasChoices('svc', 'service_id'),
        description='Service ID; stored as "svc" column in HDF5.',
    )
    pass_on_error: bool = Field(
        default=False,
        serialization_alias='pass_err',
        validation_alias=AliasChoices('pass_err', 'pass_on_error'),
    )
    _H5_TYPES: ClassVar[Dict[str, Any]] = {
        'name':     tables.StringCol(256),
        'svc':      tables.StringCol(256),
        'pass_err': tables.BoolCol(),
    }

2. Write to HDF5

from tiferet_h5 import H5Client

# HDF5 layout:
#   /features/                ← group, attr: schema_ver
#       calc/                 ← group, attrs: name, desc
#           steps             ← table, cols: name, svc, pass_err

with H5Client('catalog.h5', mode='w') as h5:
    # Catalog root
    h5.create_group('/features')
    h5.set_node_attr('/features', 'schema_ver', '1.0')

    # Feature group
    h5.create_group('/features/calc')
    group = FeatureGroupObject(
        name='Calculator Features',
        description='Basic arithmetic operations',
    )
    for k, v in group.to_attrs().items():
        h5.set_node_attr('/features/calc', k, v)

    # Child steps table
    t = h5.create_table(
        '/features/calc/steps',
        FeatureStepObject.get_description(),
        title='Feature Steps',
    )
    FeatureStepObject(name='Add numbers', service_id='add_event').to_row(t)
    FeatureStepObject(name='Validate',    service_id='validate_event', pass_on_error=True).to_row(t)
    t.flush()

3. Read Back

with H5Client('catalog.h5', mode='r') as h5:
    schema_ver = h5.get_node_attr('/features', 'schema_ver')
    print('Schema version:', schema_ver)

    group = FeatureGroupObject.from_attrs(h5.get_node_attrs('/features/calc'))
    print('Feature:', group.name, '—', group.description)

    steps: List[FeatureStepObject] = [
        FeatureStepObject.from_row(r)
        for r in h5.read_rows('/features/calc/steps')
    ]
    for s in steps:
        print(f'  step  {s.name!r}  service_id={s.service_id!r}  pass_on_error={s.pass_on_error}')

Output:

Schema version: 1.0
Feature: Calculator Features — Basic arithmetic operations
  step  'Add numbers'  service_id='add_event'  pass_on_error=False
  step  'Validate'     service_id='validate_event'  pass_on_error=True

4. Use a Repository

TableRepository and NodeRepository (tiferet_h5.repos.core) remove the hand-rolled get_or_create_table()/to_attrs() orchestration a repository would otherwise write itself -- compose one of each with H5Repository for the group's own metadata and its child table respectively:

from tiferet_h5 import H5Repository, NodeRepository, TableRepository

class FeatureMetaRepository(NodeRepository, H5Repository):
    node_cls = FeatureGroupObject
    node_path = '/features/{key}'

class FeatureStepsRepository(TableRepository, H5Repository):
    table_cls = FeatureStepObject
    table_path = '/features/{key}/steps'

meta_repo  = FeatureMetaRepository('catalog.h5')
steps_repo = FeatureStepsRepository('catalog.h5')

# Write
meta_repo.save(FeatureGroupObject(name='Calculator', description='Arithmetic ops'), key='calc')
steps_repo.save(FeatureStepObject(name='Add numbers', service_id='add_event'), key='calc')

# Read
group = meta_repo.get(key='calc')
steps = steps_repo.list(key='calc')

table_path/node_path are str.format() templates -- any **kwargs passed to a method (here, key='calc') interpolate into the path, so one repository instance serves every feature group in the file. See docs/guides/repos.md for the full method reference, the repository-level compression default, and why TableRepository/NodeRepository should never be multiply inherited into a single class.

See examples/catalog_app for a complete, runnable application built on this pattern, including opt-in schema verification and file compaction alongside the repository mixins.

Package Layout

tiferet_h5/
├── __init__.py          Public exports and aliases
├── domain/
│   └── h5.py            H5Column, H5TableSchema, H5Node
├── interfaces/
│   └── h5.py            H5Service abstract interface
├── mappers/
│   └── settings.py      TableObject, NodeObject base classes
├── utils/
│   └── h5.py            H5Client (alias: H5); also hosts H5 error code string constants
└── repos/
    ├── core.py          TableRepository, NodeRepository CRUD mixins
    └── h5.py            H5Repository base

Documentation

• Domain Objects — H5Column, H5TableSchema, H5Node
• Mappers — TableObject, NodeObject, aliasing, nested modeling
• H5Client — full method reference, error codes, and concurrency guidance
• Repos — H5Repository, TableRepository, NodeRepository CRUD mixins
• examples/catalog_app — a complete, runnable application exercising the full stack end-to-end

License

MIT