Schema validation for Xarray objects

carbonplan

Last update: Oct 31, 2022

Related tags

Data Validation xarray-schema

Overview

xarray-schema

Schema validation for Xarray

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:

Validation of coords, chunks, and attrs. None of these are implemented yet.
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)
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
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
Bumps mypy from 0.982 to 0.990.

Commits

b71dc3d Remove +dev from version

719cef9 Add support for exception groups and except* (#14020)

91b6fc3 Fix crash on nested unions in recursive types (#14007)

42a4c69 Make TryStar not crash (#13991)

5fad1ac Warn on invalid *args and **kwargs with ParamSpec (#13892)

184add9 Revert sum literal integer change (#13961)

74e0dff Add hidden options to disable bytes promotion (#13952)

ec6d9d9 [mypyc] Fix ircheck if register is initialized through LoadAddress (#13944)

8ef701d Use 3.11 instead of 3.11-dev (#13945)

ec149da [mypyc] Fix glue methods with native int types (#13939)

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dependencies python
opened by dependabot[bot] 3
Bump actions/setup-python from 2.3.2 to 3.1.0
Bumps actions/setup-python from 2.3.2 to 3.1.0.

Release notes

Sourced from actions/setup-python's releases.

Support caching poetry dependencies and caching on GHES 3.5

In the scope of this release, we added support for caching from GHES 3.5 and fixed the download issue for files > 2GB during restore.

Caching poetry dependencies

steps: - uses: actions/checkout@v3 - name: Install poetry run: pipx install poetry - uses: actions/setup-python@v3 with: python-version: '3.9' cache: 'poetry' - run: poetry install - run: poetry run pytest

v3.0.0

What's Changed

Update default runtime to node16 (actions/setup-python#340)

Update package-lock.json file version to 2, @types/node to 16.11.25 and typescript to 4.2.3 (actions/setup-python#341)

Remove legacy pypy2 and pypy3 keywords (actions/setup-python#342)

Breaking Changes

With the update to Node 16, all scripts will now be run with Node 16 rather than Node 12.

This new major release removes support of legacy pypy2 and pypy3 keywords. Please use more specific and flexible syntax to specify a PyPy version:

jobs: build: runs-on: ubuntu-latest strategy: matrix: python-version: - 'pypy-2.7' # the latest available version of PyPy that supports Python 2.7 - 'pypy-3.8' # the latest available version of PyPy that supports Python 3.8 - 'pypy-3.8-v7.3.8' # Python 3.8 and PyPy 7.3.8 steps: - uses: actions/checkout@v2 - uses: actions/setup-python@v3 with: python-version: ${{ matrix.python-version }}

See more usage examples in the documentation

Commits

9c644ca Update README.md to fix setup-python version in example (#368)

3e8e90e dist fix (#367)

05fb98d Cache on ghes (#363)

6c56602 Merge pull request #281 from patrick91/feature/poetry-caching

9516be8 Merge pull request #358 from actions/brcrista/codeql-main

7aa3e95 Update dist

6c31eb3 Use \n instead of os.EOL

7a37d78 Update dist

e4be7a4 Initialise pyproject.toml

aac0ef9 Build and format

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dependencies github_actions
opened by dependabot[bot] 3
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
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 2
Bump actions/cache from 3.0.8 to 3.0.9
Bumps actions/cache from 3.0.8 to 3.0.9.

Release notes

Sourced from actions/cache's releases.

v3.0.9

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

Changelog

Sourced from actions/cache's changelog.

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

Enhanced the warning message for cache unavailablity in case of GHES.

Commits

ac80757 Actions/cache release 3.0.9 (#930)

0ff0597 Update examples.md (#920)

1268184 Update README.md (#936)

1a78ace Updated the GHES warning message (#925)

1bc650b Merge pull request #922 from actions/vsvipul/add-anurag

92e01f4 Add anuragc617 to assignees

b195c99 Merge pull request #912 from actions/pdotl/readme-update-1

9f98a2f Merge branch 'main' into pdotl/readme-update-1

471fb0c Move workarounds to a different file

a213d1e Merge pull request #913 from actions/vsvipul-patch-2

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dependencies github_actions
opened by dependabot[bot] 2
Bump types-setuptools from 65.1.0 to 65.3.0
Bumps types-setuptools from 65.1.0 to 65.3.0.

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dependencies python
opened by dependabot[bot] 2
Bump types-setuptools from 63.4.0 to 64.0.1
Bumps types-setuptools from 63.4.0 to 64.0.1.

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dependencies python
opened by dependabot[bot] 2
Bump types-setuptools from 63.4.0 to 64.0.0
Bumps types-setuptools from 63.4.0 to 64.0.0.

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dependencies python
opened by dependabot[bot] 2
Bump actions/cache from 3.0.6 to 3.0.7
Bumps actions/cache from 3.0.6 to 3.0.7.

Release notes

Sourced from actions/cache's releases.

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.

Changelog

Sourced from actions/cache's changelog.

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

e839c25 Updated actions/cache version to 3.0.3

33a923d Added release information

a404368 Updated actions/cache version to 3.0.2

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dependencies github_actions
opened by dependabot[bot] 2
Bump actions/cache from 3.0.5 to 3.0.6
Bumps actions/cache from 3.0.5 to 3.0.6.

Release notes

Sourced from actions/cache's releases.

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

@shivamarora1 made their first contribution in actions/cache#835

@pdotl made their first contribution in actions/cache#887

Full Changelog: https://github.com/actions/cache/compare/v3...v3.0.6

Changelog

Sourced from actions/cache's changelog.

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 65.6.0.2 to 65.6.0.3
Bumps types-setuptools from 65.6.0.2 to 65.6.0.3.

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dependencies python
opened by dependabot[bot] 0
Bump actions/cache from 3.2.2 to 3.2.3
Bumps actions/cache from 3.2.2 to 3.2.3.

Release notes

Sourced from actions/cache's releases.

v3.2.3

What's Changed

Add Mint example by @uhooi in actions/cache#1051

Fixed broken link by @kotewar in actions/cache#1057

Add support to opt-in enable cross-os caching on windows by @Phantsure in actions/cache#1056

Release support for cross-os caching as opt-in feature by @Phantsure in actions/cache#1060

New Contributors

@uhooi made their first contribution in actions/cache#1051

Full Changelog: https://github.com/actions/cache/compare/v3...v3.2.3

Changelog

Sourced from actions/cache's changelog.

3.2.2

Reverted the changes made in 3.2.1 to use gnu tar and zstd by default on windows.

3.2.3

Support cross os caching on Windows as an opt-in feature.

Fix issue with symlink restoration on Windows for cross-os caches.

Commits

58c146c Release support for cross-os caching as opt-in feature (#1060)

6fd2d45 Add support to opt-in enable cross-os caching on windows (#1056)

1f41429 Fixed broken link (#1057)

365406c Merge pull request #1051 from uhooi/feature/add_mint_example

d621756 Update Mint example

84e5400 Merge remote-tracking branch 'origin/main' into feature/add_mint_example

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dependencies github_actions
opened by dependabot[bot] 0
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

b71dc3d Remove +dev from version

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dependencies python
opened by dependabot[bot] 3
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
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)