atlas-python 0.9.0__tar.gz → 0.9.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {atlas_python-0.9.0 → atlas_python-0.9.1}/Cargo.lock +2 -2
- {atlas_python-0.9.0 → atlas_python-0.9.1}/Cargo.toml +2 -2
- {atlas_python-0.9.0 → atlas_python-0.9.1}/LICENSE +1 -1
- atlas_python-0.9.1/PKG-INFO +269 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/README.md +6 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/Cargo.toml +1 -1
- atlas_python-0.9.1/atlas-python/LICENSE +201 -0
- atlas_python-0.9.1/atlas-python/README.md +236 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/benchmarks.md +2 -2
- atlas_python-0.9.1/atlas-python/docs/examples.md +36 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/cloud-storage.md +1 -1
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/codecs-and-meta.md +2 -2
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/shared-arrays.md +1 -1
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/stats.md +1 -1
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/mkdocs.yml +1 -1
- {atlas_python-0.9.0 → atlas_python-0.9.1}/pyproject.toml +18 -1
- atlas_python-0.9.0/PKG-INFO +0 -17
- atlas_python-0.9.0/atlas-python/README.md +0 -275
- atlas_python-0.9.0/atlas-python/docs/examples.md +0 -36
- {atlas_python-0.9.0 → atlas_python-0.9.1}/.github/workflows/atlas-python-release.yaml +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/.github/workflows/atlas-rust-release.yaml +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/.github/workflows/ci.yaml +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/.gitignore +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/CONTRIBUTING.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/.python-version +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/benchmarks/README.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/benchmarks/_common.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/benchmarks/bench_collection.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/benchmarks/generate_bench_charts.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/assets/bench_gridded.svg +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/assets/bench_profile.svg +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/attributes.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/bulk-reads.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/dask.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/datasets-and-arrays.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/dtypes.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/durability.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/guides/xarray.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/index.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/installation.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/quickstart.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/reference/atlas.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/reference/dataset-view.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/reference/xarray-accessor.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/docs/vs-zarr-netcdf.md +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/01_basics.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/02_xarray.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/03_dask_streaming.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/04_meta_formats.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/05_codecs.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/06_stats_scan.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/07_shared_arrays.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/examples/08_object_store.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/attr.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/dataset.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/dtype.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/error.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/lib.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/logging.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/runtime.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/src/store.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/tests/GL_PR_BO_JLKU.nc +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/tests/test_smoke.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/atlas-python/tests/test_xarray.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/examples/lifecycle.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/examples/sensor_fleet.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/examples/weather_store.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/python/atlas/__init__.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/python/atlas/__init__.pyi +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/python/atlas/py.typed +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/python/atlas/xarray.py +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/array.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/config.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/dataset.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/error.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/lib.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/meta.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/schema.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/src/store.rs +0 -0
- {atlas_python-0.9.0 → atlas_python-0.9.1}/tests/integration.rs +0 -0
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[[package]]
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name = "atlas-python"
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version = "0.9.
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version = "0.9.1"
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dependencies = [
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"atlas-rust",
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"ndarray",
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[[package]]
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name = "atlas-rust"
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version = "0.9.
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version = "0.9.1"
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dependencies = [
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"array-format",
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"chrono",
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# Registry name on crates.io (`atlas` is taken). The library is still
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# imported as `atlas` — see `[lib]` below.
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name = "atlas-rust"
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version = "0.9.
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version = "0.9.1"
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edition = "2024"
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description = "Directory-based store for thousands of N-dimensional datasets local or remote using object storage."
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license = "Apache-2.0"
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repository = "https://github.com/
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repository = "https://github.com/maris-development/atlas"
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readme = "README.md"
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keywords = ["array", "ndarray", "scientific", "storage", "object-store"]
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categories = ["science", "data-structures", "filesystem"]
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same "printed page" as the copyright notice for easier
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identification within third-party archives.
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Copyright
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Copyright 2026 Robin Kooyman
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Licensed under the Apache License, Version 2.0 (the "License");
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you may not use this file except in compliance with the License.
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Metadata-Version: 2.4
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Name: atlas-python
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Version: 0.9.1
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Classifier: Development Status :: 3 - Alpha
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Classifier: Intended Audience :: Science/Research
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Classifier: Programming Language :: Python :: 3
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Classifier: Programming Language :: Rust
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Classifier: Operating System :: OS Independent
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Classifier: Topic :: Scientific/Engineering
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Requires-Dist: numpy>=1.23
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Requires-Dist: xarray>=2023.1
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Requires-Dist: dask>=2023.1
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Requires-Dist: zarr>=3 ; extra == 'bench'
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Requires-Dist: netcdf4 ; extra == 'bench'
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Requires-Dist: pytest ; extra == 'test'
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Requires-Dist: netcdf4 ; extra == 'test'
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Provides-Extra: bench
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Provides-Extra: cloud
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Provides-Extra: test
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License-File: LICENSE
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Summary: Python bindings for the ATLAS array store
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Keywords: array,ndarray,xarray,scientific,storage,object-store
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Author-email: Robin Kooyman <robin.kooyman.work@gmail.com>
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License-Expression: Apache-2.0
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Requires-Python: >=3.10
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Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
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Project-URL: Homepage, https://github.com/maris-development/atlas
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Project-URL: Issues, https://github.com/maris-development/atlas/issues
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Project-URL: Repository, https://github.com/maris-development/atlas
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# atlas-python
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Python bindings for **ATLAS** (Aggregated Tensor Large Array Store) — a directory-based store
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for many similarly-shaped N-dimensional arrays, backed by local files or any object store
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(S3 / GCS / Azure / HTTP). Built on a Rust core with a synchronous, NumPy-native API and
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first-class [xarray](https://docs.xarray.dev) integration.
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```bash
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pip install atlas-python
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```
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```python
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import atlas
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```
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| Extra | Install | Adds |
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| --- | --- | --- |
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| cloud | `pip install "atlas-python[cloud]"` | S3 / GCS / Azure / HTTP backends via [obstore](https://github.com/developmentseed/obstore) |
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`numpy`, `xarray`, and `dask` are installed automatically.
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## Quick start
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```python
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import numpy as np
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import atlas
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# The `with` block flushes (== close) on exit. Nothing is persisted before that.
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with atlas.Atlas.create("/tmp/my_store", codec="zstd") as store: # "zstd" | "lz4" | "none"
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ds = store.create_dataset("jan_2024")
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ds.define_array(
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"temperature",
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dtype="float32",
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dims=["lat", "lon"],
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shape=[8, 16],
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chunk_shape=[4, 8],
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fill_value=float("nan"), # unwritten cells read back as NaN; NaN cells count as nulls in stats
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)
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ds.write_array("temperature", start=[0, 0], data=np.full((8, 16), 20.0, dtype=np.float32))
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ds.set_attribute("month", 1)
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ds.set_attribute("station", "KNMI")
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# Reopen and read
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store = atlas.Atlas.open("/tmp/my_store")
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ds = store.open_dataset("jan_2024")
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arr = ds.read_array("temperature") # full read -> np.ndarray
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chunk = ds.read_array("temperature", [0, 0], [4, 8]) # partial read
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stats = ds.array_stats("temperature") # {"row_count", "null_count", "min", "max"}
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month = ds.get_attribute("month") # 1
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```
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## Durability model
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The store's metadata is loaded once on `open`/`create`. Every subsequent mutation — creating
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datasets, defining arrays, `write_array`, `set_attribute` — updates in-memory state only.
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**Nothing reaches disk until `store.flush()` (equivalently `store.close()`, or the `with store:`
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block exiting).** Dropping an `Atlas` without flushing abandons every pending write.
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name and one metadata rewrite, no matter how many datasets you touched.
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```python
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store = atlas.Atlas.create("/tmp/my_store")
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# ... many create_dataset / write_array calls ...
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store.flush() # the single durability boundary
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```
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## xarray integration
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Importing `atlas` registers an accessor at `xr.Dataset.atlas`, so the integration is always
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available. The store must exist first; you then append xarray datasets to it.
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```python
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"temperature": (["lat", "lon"], np.arange(8 * 16, dtype=np.float32).reshape(8, 16),
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{"units": "C", "long_name": "surface temperature"}),
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},
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)
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store.add_xr_dataset(ds, "jan_2024") # store-side method
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xr.testing.assert_identical(ds, ds_back)
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```
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### Bulk ingestion
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```python
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import glob, os, atlas, xarray as xr
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with atlas.Atlas.create("/tmp/store") as store:
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for nc_path in sorted(glob.glob("*.nc")):
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name = os.path.splitext(os.path.basename(nc_path))[0]
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store.add_xr_dataset(xr.open_dataset(nc_path), name)
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# One delta file per array name across the whole batch (not one per file).
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```
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### Streaming dask-backed writes
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If a variable's `.data` is a `dask.array.Array` (e.g. from `xr.open_dataset(path, chunks=...)`
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or `ds.chunk({...})`), `add_xr_dataset` / `ds.atlas.write` stream **one dask block at a time**
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into the store rather than materialising the whole array. The dask chunk shape becomes the
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on-disk `chunk_shape`, so the layout maps 1:1. Peak memory ≈ one chunk per variable.
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```python
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ds = xr.open_dataset("big.nc", chunks={"time": 100, "lat": -1, "lon": -1})
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with atlas.Atlas.create("/tmp/store") as store:
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store.add_xr_dataset(ds, "big") # streams chunk-by-chunk
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```
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Pass `chunks={var: [...]}` to `add_xr_dataset` / `ds.atlas.write` to override the on-disk chunk
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shape independently of dask's chunking.
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### Lazy dask-backed reads
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`store.to_xarray(name)` returns each variable dask-backed whenever it was stored with non-trivial
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chunking (`chunk_shape != shape`); the dask `chunks` tuple mirrors the on-disk chunk grid and each
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on-disk chunk is one dask task. Full-shape arrays (and 0-D scalars) come back eager as numpy. Call
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`.compute()` to materialise, or slice / `map_blocks` to operate lazily.
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```python
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ds_back = atlas.Atlas.open("/tmp/store").to_xarray("big")
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ds_back["temperature"].data # -> dask.array.Array
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ds_back["temperature"][0:100].compute() # reads exactly one chunk
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```
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Reads run under dask's **threaded** scheduler only — the `DatasetView` captured in the graph isn't
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picklable, so call `.compute()` before handing off to distributed/multiprocessing schedulers.
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### How xarray maps onto the store
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| Item | How it's stored |
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| --- | --- |
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| Each coord / data variable | A separate array, with `dims` mapped 1:1. |
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| Dataset attrs | Dataset attributes, plain keys. |
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| Per-variable attrs | Flattened as `{var}.{attr}` at the dataset attr level. |
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| Per-variable `_FillValue` | Consumed by `define_array` as a typed fill value (source `Dataset.attrs` is not mutated). |
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| Coord vs data_var distinction | JSON list in the internal `_pyatlas_coords` attr. |
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| Non-scalar attr values (list, ndarray) | JSON-encoded string with a `json:` prefix marker. |
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Each `add_xr_dataset` / `ds.atlas.write` creates a *new* dataset — there is no append-into-existing
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mode.
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## Supported dtypes
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| numpy dtype | atlas dtype |
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| --- | --- |
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| `int8/16/32/64`, `uint8/16/32/64`, `float32/64` | matching numeric |
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| `datetime64[ns]` | `timestamp_nanoseconds` (aliases: `timestamp_ns`, `datetime64[ns]`) |
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| `object` (`str`/`bytes`), `\|S<n>`, `\|U<n>` | `string` (variable-length; reads return Python `str`) |
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+
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- 0-D scalar arrays (`shape=[]`) are supported for every dtype above.
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- `bool` is available as an *attribute* type but not as an array dtype.
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- `binary`, `list[...]`, `fixed_size_list[...,N]` are reserved for a later release.
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+
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## Cloud / object storage
|
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+
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With the `cloud` extra, `Atlas.open` / `Atlas.create` accept an
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[obstore](https://github.com/developmentseed/obstore)-constructed S3 / GCS / Azure / HTTP store
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handle instead of a local path. The path-based local-filesystem API works without it. See the
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[cloud storage guide](https://github.com/maris-development/atlas/blob/main/atlas-python/docs/guides/cloud-storage.md).
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+
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## API reference
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### `atlas.Atlas`
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| Method | Description |
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| --- | --- |
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| `Atlas.create(path, codec="zstd")` | Create a new store at `path`. |
|
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| `Atlas.open(path)` | Open an existing store. |
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| `create_dataset(name) -> DatasetView` | New dataset (in-memory until flush). |
|
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| `open_dataset(name) -> DatasetView` | Existing dataset. |
|
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| `delete_dataset(name)` | Remove a dataset (persisted on next `flush`). |
|
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+
| `list_datasets() -> list[str]` | All dataset names. |
|
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+
| `list_arrays() -> list[str]` | Distinct array names across datasets. |
|
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|
+
| `dataset_exists(name) -> bool` | Existence check. |
|
|
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|
+
| `add_xr_dataset(ds, name, chunks=None)` | Append an `xarray.Dataset` (does **not** flush). |
|
|
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|
+
| `to_xarray(name) -> xr.Dataset` | Read a dataset back (chunked vars come back dask-backed). |
|
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+
| `flush()` | The single durability boundary — persist everything. |
|
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|
+
| `close()` | Alias for `flush()`; also the `with`-block exit. |
|
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|
+
| `compact()` | Reclaim tombstoned space across cached array files. |
|
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|
+
| `__enter__` / `__exit__` | Context-manager support (`__exit__` calls `close()`). |
|
|
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|
+
|
|
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|
+
### `atlas.DatasetView`
|
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+
|
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| Method | Description |
|
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+
| --- | --- |
|
|
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|
+
| `name` (property) | Dataset name. |
|
|
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|
+
| `list_arrays() -> list[str]` | Array names in this dataset. |
|
|
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|
+
| `define_array(name, dtype, dims, shape, chunk_shape=None, fill_value=None)` | Declare a new array. `fill_value` is a Python scalar matching the dtype; unwritten cells read back as it, and *written* cells equal to it count as nulls in `array_stats`. Dtype is enforced (`TypeError` on mismatch, `OverflowError` for out-of-range ints). |
|
|
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|
+
| `write_array(name, start, data)` | Write a numpy ndarray (matching the stored dtype). |
|
|
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|
+
| `read_array(name, start=None, shape=None) -> np.ndarray \| None` | Read full or partial; `None` if the array isn't in this dataset. |
|
|
240
|
+
| `delete_array(name)` | Tombstone the array within this dataset. |
|
|
241
|
+
| `array_meta(name) -> dict \| None` | `{"dtype", "shape", "chunk_shape", "dimension_names"}`. |
|
|
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|
+
| `array_stats(name) -> dict \| None` | `{"row_count", "null_count", "min", "max"}` — populated after `flush()`. |
|
|
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|
+
| `set_attribute(key, value, dtype=None)` | Type inferred from the Python value; pass `dtype` to override (e.g. `"int8"`, `"float32"`, `"timestamp_nanoseconds"`). On disk: bool, int64, float64, string, timestamp_nanoseconds. |
|
|
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|
+
| `get_attribute(key)` / `attributes()` | Single attribute or dict of all. |
|
|
245
|
+
|
|
246
|
+
`DatasetView` does **not** expose its own `flush` / `compact` — both go through the parent `Atlas`.
|
|
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|
+
|
|
248
|
+
## Examples
|
|
249
|
+
|
|
250
|
+
Runnable, self-contained scripts (each writes to a temp directory):
|
|
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|
+
|
|
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|
+
- [01_basics.py](https://github.com/maris-development/atlas/blob/main/atlas-python/examples/01_basics.py) — create a store, define arrays, set attributes, reopen, read back.
|
|
253
|
+
- [02_xarray.py](https://github.com/maris-development/atlas/blob/main/atlas-python/examples/02_xarray.py) — round-trip an `xr.Dataset` via both `store.add_xr_dataset(...)` and the `ds.atlas.write(...)` accessor.
|
|
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|
+
- [03_dask_streaming.py](https://github.com/maris-development/atlas/blob/main/atlas-python/examples/03_dask_streaming.py) — stream a dask-chunked `xr.Dataset` in one chunk at a time.
|
|
255
|
+
|
|
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|
+
## Performance
|
|
257
|
+
|
|
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|
+
ATLAS is tuned for collections of many similarly-shaped datasets. On a "1000 datasets" benchmark
|
|
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|
+
against netCDF4 and Zarr v3, the bulk read paths (`Atlas.to_xarray_many` /
|
|
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|
+
`Atlas.read_array_across_stacked`) beat Zarr by ~2.8× on large chunked slice reads, and on small
|
|
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|
+
per-dataset workloads ATLAS leads on both reads and writes. See the
|
|
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|
+
[benchmarks](https://github.com/maris-development/atlas/tree/main/atlas-python/benchmarks) for the full
|
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|
+
methodology, numbers, and an API picker for the fastest read path per workload.
|
|
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|
+
|
|
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|
+
## Links
|
|
266
|
+
|
|
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|
+
- Source & issues: <https://github.com/maris-development/atlas>
|
|
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|
+
- License: Apache-2.0
|
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|
+
|
|
@@ -2,6 +2,12 @@
|
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|
2
2
|
|
|
3
3
|
A directory-based store for thousands of named datasets, each holding N-dimensional typed arrays. Built on top of the [`array-format`](https://github.com/robinskil/array-format) (`.af`) binary format, with configurable compression (Zstd, LZ4, or none), chunked I/O, and an [`object_store`](https://crates.io/crates/object_store) backend that works on local disk, S3, GCS, Azure Blob, and in-memory.
|
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4
4
|
|
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5
|
+
**Think of it as a "zip" for N-dimensional datasets.** Where a `.zip` bundles many files into one archive, ATLAS gathers many NetCDF / Zarr-style datasets — anything that's a set of named N-dimensional arrays — into a single high-performance collection. But it's more than a bundle: instead of storing each dataset whole, ATLAS lays the data out **variable-first**, so every dataset's `temperature` lives in one file. That makes it cheap to scan or slice a single variable across thousands of datasets at once, while still reading back any individual dataset as a normal NetCDF/xarray-like object.
|
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6
|
+
|
|
7
|
+
> **Looking for Python?** The Python bindings live in [`atlas-python/`](atlas-python/) — `pip install atlas-python`, then `import atlas`. They add a NumPy-native API and first-class [xarray](https://docs.xarray.dev) integration. See the [atlas-python README](atlas-python/README.md) for usage.
|
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|
+
>
|
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> The rest of this document covers **how the format works and the Rust crate**.
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5
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---
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7
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## What it does
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@@ -0,0 +1,201 @@
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1
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Apache License
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Version 2.0, January 2004
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http://www.apache.org/licenses/
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