feat: Add NpyCodec for lazy-loading numpy arrays #1331

dimitri-yatsenko · 2026-01-12T22:04:29Z

Summary

Introduces the <npy@> codec for schema-addressed NumPy array storage with lazy loading, and refactors hash-addressed storage to use path-based retrieval.

Key Features

NpyCodec (<npy@>)

Lazy loading: Inspect array shape and dtype without downloading
Memory mapping: Random access to large arrays via mmap_mode
NumPy integration: Transparent array operations via __array__ protocol
Safe bulk fetch: Returns NpyRef objects instead of downloading all arrays
Portable format: Standard .npy files readable by NumPy, MATLAB, etc.
Schema-addressed: Paths derived from primary key ({schema}/{table}/{pk}/{attr}.npy)

Hash Registry Refactoring

Path-based retrieval: Full path stored in metadata, used directly for retrieval
Config-change protection: Stored paths guard against subfolding/structure changes
Per-schema isolation: Hash paths include schema name (_hash/{schema}/{hash})

Codec Types

Codec	Store	Description
`<blob>`	In-table	DataJoint serialization of Python objects
`<blob@store>`	Hash-addressed	Large blobs, deduplicated by hash
`<attach@store>`	Hash-addressed	File attachments, deduplicated by hash
`<npy@store>`	Schema-addressed	NumPy arrays with lazy loading ← this PR
`<object@store>`	Schema-addressed	Python objects, path from primary key

Plugin codecs (separate packages, coming soon):

<zarr@store> - Zarr arrays
<tiff@store> - TIFF images
<parquet@store> - Parquet tables

Addressing Schemes

Scheme	Path Derived From	Deduplication
Hash-addressed	Content hash (MD5→Base32)	Yes (per-schema)
Schema-addressed	Primary key	No

Usage

@schema
class Neuron(dj.Imported):
    definition = """
    -> Session
    neuron_id : int16
    ---
    activity : <npy@store>    # Lazy-loading array
    """

# Fetch returns NpyRef, not the array
ref = (Neuron & key).fetch1('activity')
print(ref.shape)      # (1000,) - no download
print(ref.dtype)      # float64 - no download

# Load when ready
array = ref.load()

# Memory-mapped for large arrays
mmap = ref.load(mmap_mode='r')
slice = mmap[1000:2000]  # Only reads needed portion

Changes

New:

hash_registry.py - Refactored from content_registry.py with path-based storage
SchemaCodec - Abstract base class for schema-addressed codecs
NpyRef - Lazy reference with metadata access
NpyCodec - Codec implementation using .npy format

Refactoring:

ObjectCodec now inherits from SchemaCodec
Renamed is_external → is_store throughout codebase
hash_registry functions use stored paths for retrieval
gc.py updated to work with paths instead of hashes

Test Plan

All 643 tests pass
Unit tests for NpyRef metadata and mmap_mode
Integration tests for roundtrip encode/decode
Integration tests for lazy loading and caching

Documentation

See datajoint-docs (docs-2.0-migration branch):

Co-Authored-By: Claude Code noreply@anthropic.com

Add migrate_external() and migrate_filepath() to datajoint.migrate module for safe migration of 0.x external storage columns to 2.0 JSON format. Migration strategy: 1. Add new <column>_v2 columns with JSON type 2. Copy and convert data from old columns 3. User verifies data accessible via DataJoint 2.0 4. Finalize: rename columns (old → _v1, new → original) This allows 0.x and 2.0 to coexist during migration and provides rollback capability if issues are discovered. Functions: - migrate_external(schema, dry_run=True, finalize=False) - migrate_filepath(schema, dry_run=True, finalize=False) - _find_external_columns(schema) - detect 0.x external columns - _find_filepath_columns(schema) - detect 0.x filepath columns Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Implement the `<npy@>` codec for schema-addressed numpy array storage: - Add SchemaCodec base class for path-addressed storage codecs - Add NpyRef class for lazy array references with metadata - Add NpyCodec using .npy format with shape/dtype inspection - Refactor ObjectCodec to inherit from SchemaCodec - Rename is_external to is_store throughout codebase - Export SchemaCodec and NpyRef from public API - Bump version to 2.0.0a17 Key features: - Lazy loading: inspect shape/dtype without downloading - NumPy integration via __array__ protocol - Safe bulk fetch: returns NpyRef objects, not arrays - Schema-addressed paths: {schema}/{table}/{pk}/{attr}.npy Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

The SchemaCodec (used by NpyCodec and ObjectCodec) needs _schema, _table, _field, and primary key values to construct schema-addressed storage paths. Previously, key=None was passed, resulting in "unknown/unknown" paths. Now builds proper context dict from table metadata and row values, enabling navigable paths like: {schema}/{table}/objects/{pk_path}/{attribute}.npy Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

…to feature/npy-codec

Merge PR #1330 (blob preview display) into feature/npy-codec. Bump version from 2.0.0a17 to 2.0.0a18. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Address reviewer feedback from PR #1330: attr should never be None since field_name comes from heading.names. Raising an error surfaces bugs immediately rather than silently returning a misleading placeholder. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Support memory-mapped loading for large arrays: - Local filesystem stores: mmap directly, no download - Remote stores: download to cache, then mmap Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

…orage Major changes to hash-addressed storage model: - Rename content_registry.py → hash_registry.py for clarity - Always store full path in metadata (protects against config changes) - Use stored path directly for retrieval (no path regeneration) - Add delete_path() as primary function, deprecate delete_hash() - Add get_size() as primary function, deprecate get_hash_size() - Update gc.py to work with paths instead of hashes - Update builtin_codecs.py HashCodec to use new API This design enables seamless migration from v0.14: - Legacy data keeps old paths in metadata - New data uses new path structure - GC compares stored paths against filesystem Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

- Remove uuid_from_buffer from hash.py (dead code) - connection.py now uses hashlib.md5().hexdigest() directly - Update test_hash.py to test key_hash instead Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Remove dead code that was only tested but never used in production: - hash_exists (gc uses set operations on paths) - delete_hash (gc uses delete_path directly) - get_size (gc collects sizes during walk) - get_hash_size (wrapper for get_size) Remaining API: compute_hash, build_hash_path, get_store_backend, get_store_subfolding, put_hash, get_hash, delete_path Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

github-actions bot added enhancement Indicates new improvements feature Indicates new features labels Jan 12, 2026

dimitri-yatsenko force-pushed the feature/npy-codec branch from 8d7c92e to 08d5c6a Compare January 12, 2026 22:12

dimitri-yatsenko requested a review from d-v-b January 12, 2026 22:13

dimitri-yatsenko self-assigned this Jan 12, 2026

dimitri-yatsenko and others added 7 commits January 12, 2026 16:29

Merge remote-tracking branch 'origin/enhance/blob-preview-display' in…

14d3da6

…to feature/npy-codec

chore: Merge enhance/blob-preview-display and bump to 2.0.0a18

9f6826e

Merge PR #1330 (blob preview display) into feature/npy-codec. Bump version from 2.0.0a17 to 2.0.0a18. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Merge remote-tracking branch 'origin/pre/v2.0' into feature/npy-codec

6b951d4

feat: Add mmap_mode parameter to NpyRef.load()

12ea814

Support memory-mapped loading for large arrays: - Local filesystem stores: mmap directly, no download - Remote stores: download to cache, then mmap Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

fix: Remove unused variable in mmap test

c02a882

dimitri-yatsenko requested a review from ttngu207 January 13, 2026 00:21

dimitri-yatsenko force-pushed the feature/npy-codec branch from 58e92e9 to 0d1ffe7 Compare January 13, 2026 19:26

dimitri-yatsenko and others added 2 commits January 13, 2026 14:05

refactor: Remove uuid_from_buffer, use hashlib directly for query cache

d2ab4de

- Remove uuid_from_buffer from hash.py (dead code) - connection.py now uses hashlib.md5().hexdigest() directly - Update test_hash.py to test key_hash instead Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

dimitri-yatsenko merged commit 471b8a9 into pre/v2.0 Jan 13, 2026
7 of 8 checks passed

dimitri-yatsenko deleted the feature/npy-codec branch January 13, 2026 23:04

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feat: Add NpyCodec for lazy-loading numpy arrays #1331

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dimitri-yatsenko commented Jan 12, 2026 •

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Summary

Key Features

Codec Types

Addressing Schemes

Usage

Changes

Test Plan

Documentation

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dimitri-yatsenko commented Jan 12, 2026 •

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