@pikaa-ai/pikaa 0.3.23 → 0.3.25

package/skills/zarr-python/SKILL.md

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----
-name: zarr-python
-description: Chunked N-D arrays for cloud storage (Zarr-Python 3). Compressed arrays, parallel I/O, S3/GCS via fsspec, NumPy/Dask/Xarray compatible, for large-scale scientific computing pipelines.
-allowed-tools: Read Write Edit Bash
-license: MIT license
-compatibility: Requires Python 3.12+ and zarr 3.x. Cloud I/O needs zarr[remote] plus pinned s3fs or gcsfs. Legacy Zarr v2 workflows need exact 2.x pins on older Python.
-metadata:
-  version: "1.2"
-  skill-author: K-Dense Inc.
----
-
-# Zarr Python
-
-## Overview
-
-Zarr is a Python library for storing large N-dimensional arrays with chunking and compression. Apply this skill for efficient parallel I/O, cloud-native workflows, and seamless integration with NumPy, Dask, and Xarray.
-
-**Current upstream:** zarr **3.2.1** (released 2026-05-05). Docs: [zarr.readthedocs.io](https://zarr.readthedocs.io/en/stable/). New arrays default to **Zarr format 3**; set `zarr_format=2` for legacy interop. Zarr 3.2 adds rectilinear chunks and continues to refine the v3 codec pipeline. This skill is a **community guide** maintained by K-Dense Inc., not an official zarr-developers package.
-
-## Quick Start
-
-### Installation
-
-```bash
-uv pip install "zarr==3.2.1"
-```
-
-Requires **Python 3.12+** and NumPy 2.0+ for current stable Zarr-Python. For remote stores (S3, GCS, HTTP), pin the optional extras/backends in your project lockfile:
-
-```bash
-uv pip install "zarr[remote]==3.2.1" "s3fs==2026.4.0" "gcsfs==2026.5.0"
-```
-
-Use a version range such as `zarr>=3,<4` only when your project has a committed lockfile and compatibility tests. For Zarr-Python 2 / Python 3.10–3.11 workflows, choose an exact `zarr==2.x.y` patch version from the support-v2 release notes and commit the resulting lockfile.
-
-### Basic Array Creation
-
-```python
-import zarr
-import numpy as np
-
-# Create a 2D array with chunking and compression
-z = zarr.create_array(
-    store="data/my_array.zarr",
-    shape=(10000, 10000),
-    chunks=(1000, 1000),
-    dtype="f4"
-)
-
-# Write data using NumPy-style indexing
-z[:, :] = np.random.random((10000, 10000))
-
-# Read data
-data = z[0:100, 0:100]  # Returns NumPy array
-```
-
-## Core Operations
-
-### Creating Arrays
-
-Zarr provides multiple convenience functions for array creation:
-
-```python
-# Create empty array
-z = zarr.zeros(shape=(10000, 10000), chunks=(1000, 1000), dtype='f4',
-               store='data.zarr')
-
-# Create filled arrays
-z = zarr.ones((5000, 5000), chunks=(500, 500))
-z = zarr.full((1000, 1000), fill_value=42, chunks=(100, 100))
-
-# Create from existing data
-data = np.arange(10000).reshape(100, 100)
-z = zarr.array(data, chunks=(10, 10), store='data.zarr')
-
-# Create like another array
-z2 = zarr.zeros_like(z)  # Matches shape, chunks, dtype of z
-```
-
-### Opening Existing Arrays
-
-```python
-# Open array (read/write mode by default)
-z = zarr.open_array('data.zarr', mode='r+')
-
-# Read-only mode
-z = zarr.open_array('data.zarr', mode='r')
-
-# The open() function auto-detects arrays vs groups
-z = zarr.open('data.zarr')  # Returns Array or Group
-```
-
-### Reading and Writing Data
-
-Zarr arrays support NumPy-like indexing:
-
-```python
-# Write entire array
-z[:] = 42
-
-# Write slices
-z[0, :] = np.arange(100)
-z[10:20, 50:60] = np.random.random((10, 10))
-
-# Read data (returns NumPy array)
-data = z[0:100, 0:100]
-row = z[5, :]
-
-# Advanced indexing
-z.vindex[[0, 5, 10], [2, 8, 15]]  # Coordinate indexing
-z.oindex[0:10, [5, 10, 15]]       # Orthogonal indexing
-z.blocks[0, 0]                     # Block/chunk indexing
-```
-
-### Resizing and Appending
-
-```python
-# Resize array (v3: pass shape as a tuple)
-z.resize((15000, 15000))
-
-# Append data along an axis
-z.append(np.random.random((1000, 10000)), axis=0)  # Adds rows
-```
-
-## Groups and Hierarchies
-
-Groups organize multiple arrays hierarchically, similar to directories or HDF5 groups.
-
-### Creating and Using Groups
-
-```python
-# Create root group
-root = zarr.group(store='data/hierarchy.zarr')
-
-# Create sub-groups
-temperature = root.create_group('temperature')
-precipitation = root.create_group('precipitation')
-
-# Create arrays within groups
-temp_array = temperature.create_array(
-    name='t2m',
-    shape=(365, 720, 1440),
-    chunks=(1, 720, 1440),
-    dtype='f4'
-)
-
-precip_array = precipitation.create_array(
-    name='prcp',
-    shape=(365, 720, 1440),
-    chunks=(1, 720, 1440),
-    dtype='f4'
-)
-
-# Access using paths
-array = root['temperature/t2m']
-
-# Visualize hierarchy
-print(root.tree())
-# Output:
-# /
-#  ├── temperature
-#  │   └── t2m (365, 720, 1440) f4
-#  └── precipitation
-#      └── prcp (365, 720, 1440) f4
-```
-
-### Group API (v3)
-
-Use `create_array` / `require_array` (h5py-style `create_dataset` / `require_dataset` were removed in v3):
-
-```python
-root = zarr.group('data.zarr')
-arr = root.create_array('my_data', shape=(1000, 1000), chunks=(100, 100), dtype='f4')
-
-grp = root.require_group('subgroup')
-arr2 = grp.require_array('array', shape=(500, 500), chunks=(50, 50), dtype='i4')
-```
-
-## Attributes and Metadata
-
-Attach custom metadata to arrays and groups using attributes:
-
-```python
-# Add attributes to array
-z = zarr.zeros((1000, 1000), chunks=(100, 100))
-z.attrs['description'] = 'Temperature data in Kelvin'
-z.attrs['units'] = 'K'
-z.attrs['created'] = '2024-01-15'
-z.attrs['processing_version'] = 2.1
-
-# Attributes are stored as JSON
-print(z.attrs['units'])  # Output: K
-
-# Add attributes to groups
-root = zarr.group('data.zarr')
-root.attrs['project'] = 'Climate Analysis'
-root.attrs['institution'] = 'Research Institute'
-
-# Attributes persist with the array/group
-z2 = zarr.open('data.zarr')
-print(z2.attrs['description'])
-```
-
-**Important**: Attributes must be JSON-serializable (strings, numbers, lists, dicts, booleans, null).
-
-## Chunking, Compression, Storage, and Performance
-
-- [references/chunking_and_compression.md](references/chunking_and_compression.md):
-  sizing chunks to the access pattern (aim for ~1 MB, 5-100 MB on cloud), sharding, and
-  codec choice.
-- [references/storage_backends.md](references/storage_backends.md): local, memory, ZIP,
-  and fsspec remote stores (S3, GCS), with credential guidance — prefer IAM roles or
-  workload identity, and never print credential values.
-- [references/integration.md](references/integration.md): NumPy, Dask, and Xarray
-  integration, thread safety, and consolidated metadata.
-- [references/performance_and_patterns.md](references/performance_and_patterns.md):
-  optimization, appendable time-series and large-matrix patterns, format conversion, and
-  troubleshooting.
-- [references/api_reference.md](references/api_reference.md) and
-  [references/v3_migration.md](references/v3_migration.md): full API and the v2-to-v3
-  migration notes.
-
-## Additional Resources
-
-### Bundled references
-
-| File | Contents |
-|------|----------|
-| `references/api_reference.md` | Function signatures, stores, codecs, indexing |
-| `references/v3_migration.md` | Zarr-Python 2→3 breaking changes and WIP features |
-
-### Official upstream
-
-- **Documentation**: https://zarr.readthedocs.io/en/stable/
-- **3.0 migration guide**: https://zarr.readthedocs.io/en/stable/user-guide/v3_migration/
-- **Storage backends**: https://zarr.readthedocs.io/en/stable/user-guide/storage/
-- **Zarr specifications**: https://zarr-specs.readthedocs.io/
-- **GitHub**: https://github.com/zarr-developers/zarr-python
-- **Developer chat**: https://ossci.zulipchat.com/#narrow/channel/423692-Zarr-Python
-
-**Related libraries:** [Xarray](https://docs.xarray.dev/), [Dask](https://docs.dask.org/), [NumCodecs](https://numcodecs.readthedocs.io/)