Schema validation for Xarray objects

Overview

xarray-schema

Schema validation for Xarray

CI MIT License

installation

This package is in the early stages of development. Install it from source:

pip install git+git://github.com/carbonplan/xarray-schema

usage

Xarray-schema's API is modeled after Pandera. The DataArraySchema and DatasetSchema objects both have .validate() methods.

The basic usage is as follows:

import numpy as np
import xarray as xr
from xarray_schema import DataArraySchema, DatasetSchema

da = xr.DataArray(np.ones(4, dtype='i4'), dims=['x'], name='foo')

schema = DataArraySchema(dtype=np.integer, name='foo', shape=(4, ), dims=['x'])

schema.validate(da)

roadmap

This is a very early prototype of a library. Some key things are missing:

  1. Validation of coords, chunks, and attrs. None of these are implemented yet.
  2. Class-based schema's for parts of the Xarray data model. Most validations are currently made as direct comparisons (da.name == self.name) but a more robust approach is possible that leverages classes for each component of the data model. We're already handling some special cases using None as a sentinel value to allow for wildcard-like behavior in places (i.e. dims and shape)
  3. Exceptions: Pandera accumulates schema exceptions and reports them all at once. Currently, we are a eagerly raising SchemaErrors when the are found.

license

All the code in this repository is MIT licensed, but we request that you please provide attribution if reusing any of our digital content (graphics, logo, articles, etc.).

about us

CarbonPlan is a non-profit organization working on the science and data of carbon removal. We aim to improve the transparency and scientific integrity of carbon removal and climate solutions through open data and tools. Find out more at carbonplan.org or get in touch by opening an issue or sending us an email.

Comments
  • Fix/ignore typing errors and add mypy to ci

    Fix/ignore typing errors and add mypy to ci

    Thanks for this package! It looks like it could very useful!

    I thought I would contribute by adding type checking.

    • Fix some typing errors
    • Ignore some other typing errors that seem to be caused by an incompatibility between the use of properties in this project and what mypy expects.
    • Add mypy to dev requirements
    • Add mypy to CI using invoke
    • Add invoke to dev requirements

    I tried to add a mypy pre-commit hook, but this caused pre-commit CI to fail. I think this may be because the pre-commit CI is not able to install the correct requirements.

    opened by paiforsyth 4
  • Bump mypy from 0.982 to 0.990

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  • Bump actions/setup-python from 2.3.2 to 3.1.0

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    Support caching poetry dependencies and caching on GHES 3.5

    steps:
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      with:
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        cache: 'poetry'
    - run: poetry install
    - run: poetry run pytest
    

    v3.0.0

    What's Changed

    Breaking Changes

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    See more usage examples in the documentation

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    dependencies github_actions 
    opened by dependabot[bot] 3
  • Chunks

    Chunks

    Three changes:

    • Building out some checks in the chunks schema.
    • Adding a check that the input is actually a da, since if it's a dataset the chunk routines will fail for the wrong reason.
    • Remove the return of the da at the end since I think we just want it to continue without returning anything.
    opened by orianac 3
  • Bump actions/cache from 3.0.8 to 3.0.9

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    Bumps actions/cache from 3.0.8 to 3.0.9.

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    v3.0.9

    • Enhanced the warning message for cache unavailability in case of GHES.
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    3.0.8

    • Fix zstd not working for windows on gnu tar in issues #888 and #891.
    • Allowing users to provide a custom timeout as input for aborting download of a cache segment using an environment variable SEGMENT_DOWNLOAD_TIMEOUT_MIN. Default is 60 minutes.

    3.0.9

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  • Bump types-setuptools from 65.1.0 to 65.3.0

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    Bumps types-setuptools from 65.1.0 to 65.3.0.

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  • Bump types-setuptools from 63.4.0 to 64.0.1

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  • Bump types-setuptools from 63.4.0 to 64.0.0

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  • Bump actions/cache from 3.0.6 to 3.0.7

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    v3.0.7

    What's Changed

    • Fix for the download stuck problem has been added in actions/cache for users who were intermittently facing the issue. As part of this fix, new timeout has been introduced in the download step to stop the download if it doesn't complete within an hour and run the rest of the workflow without erroring out.
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    3.0.6

    • Fixed #809 - zstd -d: no such file or directory error
    • Fixed #833 - cache doesn't work with github workspace directory

    3.0.7

    • Fixed #810 - download stuck issue. A new timeout is introduced in the download process to abort the download if it gets stuck and doesn't finish within an hour.
    Commits
    • a7c34ad Merge pull request #894 from actions/kotewar/update-toolkit-version
    • 83394c9 Updated cache version in license file
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    opened by dependabot[bot] 2
  • Bump actions/cache from 3.0.5 to 3.0.6

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    Bumps actions/cache from 3.0.5 to 3.0.6.

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    v3.0.6

    What's Changed

    • Add example for clojure lein project dependencies by @​shivamarora1 in PR actions/cache#835
    • Update toolkit's cache npm module to latest. Bump cache version to v3.0.6 by @​pdotl in PR actions/cache#887
    • Fix issue #809 where cache save/restore was failing for Amazon Linux 2 runners due to older tar version
    • Fix issue #833 where cache save was not working for caching github workspace directory

    New Contributors

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    3.0.5

    • Removed error handling by consuming actions/cache 3.0 toolkit, Now cache server error handling will be done by toolkit. (PR)

    3.0.6

    • Fixed #809 - zstd -d: no such file or directory error
    • Fixed #833 - cache doesn't work with github workspace directory
    Commits
    • f427802 Merge pull request #887 from actions/pdotl-version-patch
    • 9916fe1 Update cache version in licences
    • 318935e Update README and RELEASES
    • 85efbb5 Update cache npm module to latest
    • 4387dbc Merge pull request #835 from shivamarora1/clojure-lein-example
    • 71e3ee5 Add phantsure to PR reviewers
    • c316eb7 Add phantsure to issue assignment
    • a0e530f feat: 🎸 add example for clojure lein project deps
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    dependencies github_actions 
    opened by dependabot[bot] 2
  • Bump types-setuptools from 63.2.0 to 63.2.2

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    dependencies python 
    opened by dependabot[bot] 2
  • Bump types-setuptools from 65.5.0.3 to 65.6.0.0

    Bump types-setuptools from 65.5.0.3 to 65.6.0.0

    Bumps types-setuptools from 65.5.0.3 to 65.6.0.0.

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    dependencies python 
    opened by dependabot[bot] 0
  • Bump mypy from 0.982 to 0.991

    Bump mypy from 0.982 to 0.991

    Bumps mypy from 0.982 to 0.991.

    Commits
    • b7788fc Update version to remove "+dev" for releasing 0.991
    • 6077d19 manually CP typeshed #9130
    • ab0ea1e Fix crash with function redefinition (#14064)
    • 592a9ce Fix another crash with report generation on namespace packages (#14063)
    • 1650ae0 Update --no-warn-no-return docs for empty body changes (#14065)
    • b9daa31 Don't ignore errors in files passed on the command line (#14060)
    • 02fd8a5 Filter out wasm32 wheel in upload-pypi.py (#14035)
    • 131c8d7 Fix crash on inference with recursive alias to recursive instance (#14038)
    • 1368338 Change version to 0.991+dev in preparation for the point release
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    dependencies python 
    opened by dependabot[bot] 2
  • parsing method in xarray-schema

    parsing method in xarray-schema

    hi,

    thanks for the really great package. I was wondering if there is any plan to also provide methods for parsing array-like data following the pre-defined schemas. In particular, similar to what xarray-dataclasses provides.

    possibly related to #12

    thanks!

    opened by giovp 0
  • Minimal Dataset coords and dims validation

    Minimal Dataset coords and dims validation

    What would be the minimal implementation to be merged here?

    My use case is simply to check if a dataset has specific coords and dims. I could go one step further to check that each coord is indexed by specific dim.

    I might just give this a try, but is there a can of worms I am simply not anticipating here?

    Cheers!

    https://github.com/carbonplan/xarray-schema/blob/a25777c55dde98d5732f48423706da4fc81cd1fd/xarray_schema/dataset.py#L60

    good first issue 
    opened by ljstrnadiii 2
  • Extract schema from xarray objects

    Extract schema from xarray objects

    One way users may want to generate schemas is from xarray objects directly. We could add a utility here that supports this workflow.

    This could be a function

    schema = create_schema(ds)
    

    Or a class method:

    schema = DatasetSchema.from_dataset(ds)
    

    Or as an Xarray accessor extension:

    schema = ds.schema.create()
    
    enhancement good first issue 
    opened by jhamman 0
Releases(0.0.3)
  • 0.0.3(Apr 5, 2022)

    What's Changed

    • update np.typing import by @jhamman in https://github.com/carbonplan/xarray-schema/pull/29

    Full Changelog: https://github.com/carbonplan/xarray-schema/compare/0.0.2...0.0.3

    Source code(tar.gz)
    Source code(zip)
  • 0.0.2(Apr 5, 2022)

    What's Changed

    • expose SchemaError in init by @tcchiao in https://github.com/carbonplan/xarray-schema/pull/14

    New Contributors

    • @tcchiao made their first contribution in https://github.com/carbonplan/xarray-schema/pull/14

    Full Changelog: https://github.com/carbonplan/xarray-schema/compare/0.0.1...0.0.2

    Source code(tar.gz)
    Source code(zip)
Owner
carbonplan
Data and science for climate action
carbonplan
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validators Python data validation for Humans. Python has all kinds of data validation tools, but every one of them seems to require defining a schema

Konsta Vesterinen 658 Nov 23, 2022
A simple, fast, extensible python library for data validation.

Validr A simple, fast, extensible python library for data validation. Simple and readable schema 10X faster than jsonschema, 40X faster than schematic

kk 209 Sep 19, 2022
Typical: Fast, simple, & correct data-validation using Python 3 typing.

typical: Python's Typing Toolkit Introduction Typical is a library devoted to runtime analysis, inference, validation, and enforcement of Python types

Sean 164 Nov 9, 2022
Lightweight data validation and adaptation Python library.

Valideer Lightweight data validation and adaptation library for Python. At a Glance: Supports both validation (check if a value is valid) and adaptati

Podio 258 Nov 22, 2022
Schema validation just got Pythonic

Schema validation just got Pythonic schema is a library for validating Python data structures, such as those obtained from config-files, forms, extern

Vladimir Keleshev 2.7k Nov 22, 2022
A high-level plotting API for pandas, dask, xarray, and networkx built on HoloViews

hvPlot A high-level plotting API for the PyData ecosystem built on HoloViews. Build Status Coverage Latest dev release Latest release Docs What is it?

HoloViz 673 Nov 22, 2022
A high-level plotting API for pandas, dask, xarray, and networkx built on HoloViews

hvPlot A high-level plotting API for the PyData ecosystem built on HoloViews. Build Status Coverage Latest dev release Latest release Docs What is it?

HoloViz 349 Feb 15, 2021
xarray: N-D labeled arrays and datasets

xarray is an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun!

Python for Data 2.8k Nov 27, 2022
Aggregating gridded data (xarray) to polygons

A package to aggregate gridded data in xarray to polygons in geopandas using area-weighting from the relative area overlaps between pixels and polygons. Check out the binder link above for a sample code run!

Kevin Schwarzwald 42 Nov 9, 2022
Publish Xarray Datasets via a REST API.

Xpublish Publish Xarray Datasets via a REST API. Serverside: Publish a Xarray Dataset through a rest API ds.rest.serve(host="0.0.0.0", port=9000) Clie

xarray-contrib 98 Nov 18, 2022
Turn a STAC catalog into a dask-based xarray

StackSTAC Turn a list of STAC items into a 4D xarray DataArray (dims: time, band, y, x), including reprojection to a common grid. The array is a lazy

Gabe Joseph 144 Nov 14, 2022
A TileDB backend for xarray.

TileDB-xarray This library provides a backend engine to xarray using the TileDB Storage Engine. Example usage: import xarray as xr dataset = xr.open_d

TileDB, Inc. 14 Jun 2, 2021
Xarray backend to Copernicus Sentinel-1 satellite data products

xarray-sentinel WARNING: this product is a "technology preview" / pre-Alpha Xarray backend to explore and load Copernicus Sentinel-1 satellite data pr

B-Open 189 Nov 15, 2022
Aggregating gridded data (xarray) to polygons

A package to aggregate gridded data in xarray to polygons in geopandas using area-weighting from the relative area overlaps between pixels and polygons.

Kevin Schwarzwald 42 Nov 9, 2022
A Python interface between Earth Engine and xarray

eexarray A Python interface between Earth Engine and xarray Description eexarray was built to make processing gridded, mesoscale time series data quic

Aaron Zuspan 137 Nov 5, 2022
A Python interface between Earth Engine and xarray for processing weather and climate data

wxee What is wxee? wxee was built to make processing gridded, mesoscale time series weather and climate data quick and easy by integrating the data ca

Aaron Zuspan 137 Nov 5, 2022