xcube-cci 0.11.3__tar.gz

xcube_cci-0.11.3/.github/workflows/publish_pypi.yml

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+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+
+# This workflows uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: publish to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  deploy:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v5
+      with:
+        python-version: '3.x'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish to PyPI
+      run: |
+        pip install twine
+        python -m twine upload --username __token__ --password ${{ secrets.PYPI_API_TOKEN }} dist/*

xcube_cci-0.11.3/.gitignore

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+# IntelliJ / PyCharm
+.idea
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

xcube_cci-0.11.3/CHANGES.md

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+## Changes in 0.11.3
+* Fixed retrieval of data sets with unsigned data types 
+  (this affected SNOW datasets)
+* Increased list of supported kerchunk datasets
+
+## Changes in 0.11.2
+* Fixed retrieval of time steps of BIOMASS datasets
+
+## Changes in 0.11.1
+* Improved support of vector data cubes
+* Improved support of FIRE ECV datasets
+
+## Changes in 0.11
+
+* Migrated code from `ESA CCI Toolbox`. This encompasses the following changes:
+  * Added store aliases `esa-cdc` and  `esa-climate-data-centre`, `esa-cci` 
+    and `esa-cci-zarr`
+  * Added new data store `esa-cci-kc` 
+    (and corresponding xcube data store `esa-cci-kc`) that allows performant 
+    accessing of selected datasets of the ESA Climate Data Centre using a 
+    Zarr view of the original NetCDF files. This approach is made possible by 
+    using the [kerchunk](https://fsspec.github.io/kerchunk/) package. Also 
+    added new Notebook that demonstrates usage of the new data store.
+  * Added opener `"datafame:geojson:esa-cdc"` to open data as data frames
+  * Added opener `"vectordatacube::esa-cdc"` to open data as vector data cubes
+  * Updated list of dataset states
+* Set up pipeline to publish package on pypi
+
+## Changes in 0.10.2
+
+* Fixed support for climatology datasets
+
+## Changes in 0.10.1
+
+* Fixed support for SST climatology dataset 
+
+## Changes in 0.10
+
+* Support Climatology Datasets
+* Ensure compatiblity with Python versions > 3.10. This concerns the way 
+  new event loops are created within threads. A deprecated event loop 
+  policy has been removed. 
+  Solves issues [#61](https://github.com/dcs4cop/xcube-cci/issues/61)
+  and [#64](https://github.com/dcs4cop/xcube-cci/issues/64)
+
+## Changes in 0.9.9
+
+* Removed cache
+* Pinned pydap version
+* Improved determination of CCI data chunks
+
+## Changes in 0.9.8
+
+* Consider environment parameter `READ_CEDA_CATALOGUE` to trigger whether 
+  metadata from the ceda catalogue shall be read. Enabled by default.
+* Updated list of supported datasets. 
+  No odp-provided datasets are excluded anymore.  
+
+## Changes in 0.9.7
+
+* Zarr Datastore reads data ids from json file if provided
+* Updated CCI Store to set zarr store (from here on, xcube 0.12.1 is required) 
+  [#62](https://github.com/dcs4cop/xcube-cci/issues/62)
+
+## Changes in 0.9.6
+
+* Updated Example Notebooks
+* Extended support of datasets. Previously, datasets which had a chunking of 
+  the time dimension larger than one were not handled properly. This affected 
+  OZONE in a monthly resolution, SEALEVEL in a monthly resolution, and several
+  ICESHEETS datasets. [#12](https://github.com/dcs4cop/xcube-cci/issues/12)
+* Chunk sizes may now also be decreased, in order to achieve optimal chunkings.
+  For some datasets (e.g., BIOMASS), this increases the performance and helps
+  avoiding memory issues. [#48](https://github.com/dcs4cop/xcube-cci/issues/48)
+
+## Changes in 0.9.5
+
+* Allow reading of datasets that do not specify chunk sizes (e.g., FIRE) 
+  [Cate #1033](https://github.com/CCI-Tools/cate/issues/1033).
+
+## Changes in 0.9.4
+
+* Ensure compatibility with xarray >= 0.20.2 and python >= 3.10
+* Ensure compatibility with expected odp update 
+
+## Changes in 0.9.3
+
+* Always show time bounds as coordinate, not as data variable
+* Prevent IndexError when requesting data with a time range
+
+## Changes in 0.9.2
+
+* Fixed issue where opening datasets in a daily resolution without a delimiting
+  time range would cause memory errors 
+  [#56](https://github.com/dcs4cop/xcube-cci/issues/56).
+
+## Changes in 0.9.1
+* Fixed issue that datasets with spatial bounds could not be opened.
+* Show version as `__version__`
+* The interface of the method `search_data` of the CciOdpDataStore 
+  has been changed. Search parameters `ecv`, `frequency` `institute`,
+  `processing_level`, `product_string`, `product_version`, `data_type`,
+  `sensor`, and `platform` may now be passed in a dictionary parameter named 
+  `cci_attrs`. This makes it possible again to use the parameter `data_type` 
+  [#54](https://github.com/dcs4cop/xcube-cci/issues/54).
+
+## Changes in 0.9.0
+* Version 0.9 now requires xcube 0.9 because of incompatible API changes in the 
+  xcube data store framework.
+* CciOdpCubeOpener has been removed.
+* CciOdpDatasetOpener and CciOdpDataStore now have a new constructor parameter 
+  `normalize`, that may be used to apply normalization steps to the CCI 
+  datasets.
+* Set coordinates correctly. All coordinates are present in data descriptions
+  and opened datasets, no coordinates appear as data variables 
+  [#42](https://github.com/dcs4cop/xcube-cci/issues/42).
+* CRS are supported correctly. CRS variables are present in datasets in case 
+  the CRS is different from 'WGS84', the CRS information is provided by the
+  data descriptor [#50](https://github.com/dcs4cop/xcube-cci/issues/50).
+
+## Changes in 0.8.1
+
+* Fixed an issue that caused that occasionally values returned by open_data consisted 
+  of random numbers where a fill value would have been expected. (#47) 
+* DataDescriptors contain coords
+* Internal virtual file system is built lazily, so opening datasets has become faster.
+* Store parameter method `get_search_params_schema` has been revised to correctly support 
+  all parameter values.
+* Support more datasets from ODP.
+* Fixed support of `user_agent` parameter
+* Added CCI Zarr Store as convenience store to access cci zarr datasets
+
+## Changes in 0.8.0
+
+* Added `user_agent` as additional optional store parameter.
+* Provided xcube data store framework interface compatibility with 
+  breaking changes in xcube 0.8.0 (see https://github.com/dcs4cop/xcube/issues/420).
+
+## Changes in 0.7.0
+* Removed constant-valued parameters from opener schema
+* Renamed store parameters `opensearch_url` and `opensearch_description_url` to
+  `endpoint_url` and `endpoint_description_url`, respectively.
+* Chunkstore considers bounding box when accessing data. Less data is accessed and normalized. (#33)
+* Fixed time range detection for datasets with daily time frequency.
+* Fixed problem with the encoding of a dataset's coordinate variables that occurs 
+  when using `xcube_cci` with xcube 0.6.0. (#27)
+* Removed CLI
+
+## Changes in 0.6.0.
+* Support type specifiers [#18](https://github.com/dcs4cop/xcube-cci/issues/18). 
+The CCI Store supports type specifiers `dataset` and `dataset[cube]`
+* Descriptions of variables and dimensions are different for the same dataset, 
+depending on what type specifier is set.
+* There are now two DataOpeners: The CciOdpDatasetOpener and the CciOdpCubeOpener.
+Both openers are used by the CciOdpDataStore, with the CciOdpDatasetOpener being the default.
+The CciOdpDatasetOpener will open any data sets from the CCI Open Data Portal without changing their dimensions.
+The CciOdpCubeOpener will normalize datasets to have dimensions `lat`, `lon`, `time` (and possibly others).
+Subsetting is only supported for data cubes. 
+As not all datasets can be normalized to cubes, the CciOdpCubeOpener supports a subset of the datasets that can be accessed with the CciOdpDatasetOpener.
+* Establish common data store conventions ([#10](https://github.com/dcs4cop/xcube-cci/issues/10)
+* xcube-cci can now get the time ranges for satellite-orbit-frequency datasets available via opensearch 
+* Introduced new optional parameters to CciStore:
+    - enable_warnings
+    - num_retries
+    - _retry_backoff_max
+    - _retry_backoff_base
+* Updated setup.py [#16](https://github.com/dcs4cop/xcube-cci/issues/16)
+* Added opener parameters `time_range` and `spatial_res`
+* String-encoded variables are added to datasets as metadata
+* Updated example notebooks
+
+## Changes in 0.5.0.
+ 
+Initial version. 
+This version has been designed to work with the `xcube` store framework that has been introduced with
+`xcube` v0.5.0.
+It affords
+- a CciOdpDataOpener Implementaton for opening datasets from the ESA CCI Open Data Portal. 
+The Opener has open parameters `variable_names`, `time_period`, `bbox`, and `crs`.
+- a CciStore Implementation that uses and extends the aforementioned opener and allows for searching 
+the ESA CCI Open Data Portal

xcube_cci-0.11.3/LICENSE

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+MIT License
+
+Copyright (c) 2020 DCS4COP
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

xcube_cci-0.11.3/MANIFEST.in

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+include xcube_cci/data/excluded_data_sources
+include xcube_cci/data/dataset_states.json
+include xcube_cci/data/stores.yml
+include xcube_cci/data/kc_refs.json

xcube_cci-0.11.3/PKG-INFO

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+Metadata-Version: 2.2
+Name: xcube_cci
+Version: 0.11.3
+Summary: An xcube plugin that allows generating data cubes from the ESA CCI Open Data Portal.
+Author: ESA CCI Toolbox Development Team
+License: MIT License
+        
+        Copyright (c) 2020 DCS4COP
+        
+        Permission is hereby granted, free of charge, to any person obtaining a copy
+        of this software and associated documentation files (the "Software"), to deal
+        in the Software without restriction, including without limitation the rights
+        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+        copies of the Software, and to permit persons to whom the Software is
+        furnished to do so, subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all
+        copies or substantial portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+        IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+        FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+        AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+        LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+        OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+        SOFTWARE.
+        
+Project-URL: Homepage, https://github.com/esa-cci/xcube-cci
+Project-URL: Bug Tracker, https://github.com/esa-cci/xcube-cci/issues
+Project-URL: Changelog, https://github.com/esa-cci/xcube-cci/CHANGES.md
+Project-URL: Download, https://pypi.org/project/xcube-cci/#files
+Project-URL: Release notes, https://github.com/esa-cci/xcube-cci/releases
+Keywords: data science,cci,climate data
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: aiohttp>=3.6
+Requires-Dist: lxml>=4.5
+Requires-Dist: nest-asyncio>=1.3
+Requires-Dist: numpy>=2
+Requires-Dist: pydap>=3.4
+Requires-Dist: rioxarray
+Requires-Dist: xcube-core>=1.4.0
+Requires-Dist: xvec
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: pytest-cov; extra == "dev"
+
+[![Build Status](https://ci.appveyor.com/api/projects/status/7kum33o5g1osqg9l?svg=true)](https://ci.appveyor.com/project/bcdev/xcube-cci)
+
+# xcube-cci
+
+An [xcube plugin](https://xcube.readthedocs.io/en/latest/plugins.html) that allows 
+generating data cubes from the ESA CCI Open Data Portal.
+
+### Installing the xcube-cci plugin
+
+#### Installation into a new environment with conda
+
+xcube-cci and all necessary dependencies (including xcube itself) are available
+on [conda-forge](https://conda-forge.org/), and can be installed using the
+[conda package manager](https://docs.conda.io/projects/conda/en/latest/).
+The conda package manager itself can be obtained in the [miniconda
+distribution](https://docs.conda.io/en/latest/miniconda.html). 
+Once conda is installed, xcube-cci can be installed like this:
+
+```
+$ conda create --name xcube-cci-environment --channel conda-forge xcube-cci
+$ conda activate xcube-cci-environment
+```
+
+The name of the environment may be freely chosen.
+
+#### Installation into an existing environment with conda
+
+xcube-cci can also be installed into an existing conda environment.
+With an existing conda environment activated, execute this command:
+
+```
+$ conda install --channel conda-forge xcube-cci
+```
+
+xcube and any other necessary dependencies will be installed or updated if they are not 
+already installed in a compatible version.
+
+#### Installation into an existing environment from the repository
+
+If you want to install xcube-cci directly from the git repository (for example
+in order to use an unreleased version or to modify the code), you can do so as follows:
+
+```
+$ git clone https://github.com/esa-cci/xcube-cci.git
+$ cd xcube-cci
+$ conda env create
+$ conda activate xcube-cci
+$ pip install --no-deps -e .
+```
+
+## Testing
+
+You can run the unit tests for xcube-cci by executing
+
+```
+$ pytest
+```
+
+in the `xcube-cci` repository. Note that, in order to successfully run the
+tests using the current repository version of xcube-cci, you may also need to
+install the repository version of xcube rather than its latest conda-forge
+release.
+
+To create a test coverage report, you can use
+
+```
+coverage run --include='xcube_cci/**' --module pytest
+coverage html
+```
+
+This will write a coverage report to `htmlcov/index.html`.
+
+## Use
+
+Jupyter notebooks demonstrating the use of the xcube-cds plugin can be found
+in the `examples/notebooks/` subdirectory of the repository.
+
+## Releasing
+
+To release `xcube-cci`, please follow the steps outlined in the 
+[xcube Developer Guide](https://github.com/dcs4cop/xcube/blob/master/docs/source/devguide.md#release-process).

xcube_cci-0.11.3/README.md

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+[![Build Status](https://ci.appveyor.com/api/projects/status/7kum33o5g1osqg9l?svg=true)](https://ci.appveyor.com/project/bcdev/xcube-cci)
+
+# xcube-cci
+
+An [xcube plugin](https://xcube.readthedocs.io/en/latest/plugins.html) that allows 
+generating data cubes from the ESA CCI Open Data Portal.
+
+### Installing the xcube-cci plugin
+
+#### Installation into a new environment with conda
+
+xcube-cci and all necessary dependencies (including xcube itself) are available
+on [conda-forge](https://conda-forge.org/), and can be installed using the
+[conda package manager](https://docs.conda.io/projects/conda/en/latest/).
+The conda package manager itself can be obtained in the [miniconda
+distribution](https://docs.conda.io/en/latest/miniconda.html). 
+Once conda is installed, xcube-cci can be installed like this:
+
+```
+$ conda create --name xcube-cci-environment --channel conda-forge xcube-cci
+$ conda activate xcube-cci-environment
+```
+
+The name of the environment may be freely chosen.
+
+#### Installation into an existing environment with conda
+
+xcube-cci can also be installed into an existing conda environment.
+With an existing conda environment activated, execute this command:
+
+```
+$ conda install --channel conda-forge xcube-cci
+```
+
+xcube and any other necessary dependencies will be installed or updated if they are not 
+already installed in a compatible version.
+
+#### Installation into an existing environment from the repository
+
+If you want to install xcube-cci directly from the git repository (for example
+in order to use an unreleased version or to modify the code), you can do so as follows:
+
+```
+$ git clone https://github.com/esa-cci/xcube-cci.git
+$ cd xcube-cci
+$ conda env create
+$ conda activate xcube-cci
+$ pip install --no-deps -e .
+```
+
+## Testing
+
+You can run the unit tests for xcube-cci by executing
+
+```
+$ pytest
+```
+
+in the `xcube-cci` repository. Note that, in order to successfully run the
+tests using the current repository version of xcube-cci, you may also need to
+install the repository version of xcube rather than its latest conda-forge
+release.
+
+To create a test coverage report, you can use
+
+```
+coverage run --include='xcube_cci/**' --module pytest
+coverage html
+```
+
+This will write a coverage report to `htmlcov/index.html`.
+
+## Use
+
+Jupyter notebooks demonstrating the use of the xcube-cds plugin can be found
+in the `examples/notebooks/` subdirectory of the repository.
+
+## Releasing
+
+To release `xcube-cci`, please follow the steps outlined in the 
+[xcube Developer Guide](https://github.com/dcs4cop/xcube/blob/master/docs/source/devguide.md#release-process).

xcube_cci-0.11.3/appveyor.yml

@@ -0,0 +1,62 @@
+version: '{build}'
+
+image:
+  - Ubuntu2204
+  - macOS
+
+configuration: Release
+
+platform:
+  - x64
+
+# Do not build feature branch with open Pull Requests.
+# Note that a feature branch build may still occur on the first push to
+# the branch -- see
+# https://help.appveyor.com/discussions/questions/18437-skip_branch_with_pr-setting-doesnt-work
+skip_branch_with_pr: true
+
+for:
+-
+  matrix:
+    only:
+      - image: macOS
+  install:
+    - curl -Ls https://micro.mamba.pm/api/micromamba/osx-64/latest | tar -xvj bin/micromamba
+    - mv bin/micromamba ./micromamba
+-
+  matrix:
+    only:
+      - image: Ubuntu2204
+  install:
+    - curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba
+    - mv bin/micromamba ./micromamba
+
+build_script:
+  # Diagnostics
+  - echo $PLATFORM
+  - echo $APPVEYOR_BUILD_WORKER_IMAGE
+  - echo $APPVEYOR_BUILD_FOLDER
+  - uname -a
+  - pwd
+  - ls
+
+  # Set up micromamba
+  - ./micromamba shell init -s bash --root-prefix ~/micromamba
+  - source ~/.bashrc
+  - source ~/.profile
+  - hash -r
+  - mkdir -p ~/micromamba/pkgs/
+  - export MAMBA_ROOT_PREFIX=~/micromamba
+  - export MAMBA_EXE=$(pwd)/micromamba
+  - . $MAMBA_ROOT_PREFIX/etc/profile.d/mamba.sh
+
+  - micromamba create --name xcube-cci --file $APPVEYOR_BUILD_FOLDER/environment.yml
+  - micromamba activate xcube-cci
+  - cd $APPVEYOR_BUILD_FOLDER
+  - pip install --no-deps .
+
+  - git status
+  - micromamba list
+
+  # Run the test suite
+  - pytest -v --cov=xcube_cci

xcube_cci-0.11.3/environment.yml

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+name: xcube-cci
+channels:
+  - conda-forge
+dependencies:
+  # Python
+  - python >=3.10
+  # Required
+  - xcube >= 1.4.0
+  - aiohttp >= 3.6
+  - lxml >= 4.5
+  - nest-asyncio >= 1.3
+  - numpy >= 2.0
+  - pydap >= 3.4
+  - rioxarray
+  - xvec
+  # Test libs
+  - pytest
+  - pytest-cov