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Diff for: ‎.github/dependabot.yml

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version: 2
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updates:
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- package-ecosystem: 'github-actions'
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directory: '/'
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schedule:
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# Check for updates once a week
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interval: 'weekly'

Diff for: ‎.github/workflows/optional/linting.yaml

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name: linting with pre-commit
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on:
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pull_request:
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push:
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branches: [master]
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jobs:
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pre-commit:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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with:
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python-version: '3.8'
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- uses: pre-commit/[email protected]

Diff for: ‎.github/workflows/release.yaml

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---
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name: Release
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on: [push]
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jobs:
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release:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v2
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- uses: actions/setup-python@v2
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- name: Install dependencies
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run: |
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python -m pip install -U pip wheel setuptools setuptools-scm twine
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- name: Build distributions
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run: python setup.py sdist bdist_wheel
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- name: Publish to PyPI
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if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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uses: pypa/gh-action-pypi-publish@master
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with:
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user: ${{ secrets.PYPI_USERNAME }}
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password: ${{ secrets.PYPI_PASSWORD }}

Diff for: ‎.github/workflows/test.yaml

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name: Tests
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on:
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push:
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branches:
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- "master"
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pull_request:
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branches:
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- "*"
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schedule:
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- cron: "0 13 * * 1"
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jobs:
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build:
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name: Build (${{ matrix.python-version }} | ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.8", "3.9", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- name: Cache conda
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uses: actions/cache@v1
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env:
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# Increase this value to reset cache if ci/environment.yml has not changed
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CACHE_NUMBER: 0
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with:
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path: ~/conda_pkgs_dir
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key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('ci/environment-py${{ matrix.python-version }}.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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# mamba-version: "*" # activate this to build with mamba.
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# channels: conda-forge, defaults # These need to be specified to use mamba
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# channel-priority: true
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environment-file: ci/environment-py${{ matrix.python-version }}.yml
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activate-environment: test_env_mds2zarr
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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- name: Set up conda environment
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shell: bash -l {0}
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run: |
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python -m pip install -e . --no-deps --force-reinstall
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- name: Run Tests
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shell: bash -l {0}
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run: |
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pytest --cov=./ --cov-report=xml
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- name: Upload code coverage to Codecov
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uses: codecov/codecov-action@v1
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with:
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file: ./coverage.xml
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flags: unittests
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env_vars: OS,PYTHON
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name: codecov-umbrella
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fail_ci_if_error: false

Diff for: ‎.gitignore

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# Byte-compiled / optimized / DLL files
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__pycache__/
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*.py[cod]
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# C extensions
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*.so
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# Distribution / packaging
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.Python
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env/
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build/
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develop-eggs/
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dist/
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downloads/
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eggs/
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.eggs/
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lib/
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lib64/
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parts/
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sdist/
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var/
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*.egg-info/
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.installed.cfg
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*.egg
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# PyInstaller
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# Usually these files are written by a python script from a template
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# before PyInstaller builds the exe, so as to inject date/other infos into it.
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*.manifest
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*.spec
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# Installer logs
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pip-log.txt
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pip-delete-this-directory.txt
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# Unit test / coverage reports
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htmlcov/
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.tox/
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.coverage
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.coverage.*
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.cache
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nosetests.xml
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coverage.xml
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*.cover
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# Translations
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*.mo
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*.pot
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# Django stuff:
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*.log
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# Sphinx documentation
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docs/_build/
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# PyBuilder
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target/
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# DotEnv configuration
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.env
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# Database
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*.db
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*.rdb
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# Pycharm
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.idea
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# VS Code
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.vscode/
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# Spyder
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.spyproject/
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# Jupyter NB Checkpoints
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.ipynb_checkpoints/
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# exclude data from source control by default
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#/data/
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# I want to be able to handle links in here...need to exclude certain file types
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# instead
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# Mac OS-specific storage files
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.DS_Store
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# vim
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*.swp
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*.swo
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# Mypy cache
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.mypy_cache/

Diff for: ‎.pre-commit-config.yaml

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repos:
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- repo: https://github.com/econchick/interrogate
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rev: 1.2.0
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hooks:
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- id: interrogate
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exclude: ^(docs|setup.py|tests)
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args: [--config=pyproject.toml]
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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v3.1.0
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hooks:
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- id: trailing-whitespace
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exclude: tests/data
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- id: check-ast
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- id: debug-statements
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- id: end-of-file-fixer
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- id: check-docstring-first
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- id: check-added-large-files
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- id: requirements-txt-fixer
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- id: file-contents-sorter
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files: requirements-dev.txt
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- repo: https://gitlab.com/pycqa/flake8
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rev: 3.7.9
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hooks:
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- id: flake8
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exclude: docs/source/conf.py
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args: [--max-line-length=105, --ignore=E203,E501,W503, --select=select=C,E,F,W,B,B950]
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- repo: https://github.com/pre-commit/mirrors-isort
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rev: v4.3.21
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hooks:
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- id: isort
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additional_dependencies: [toml]
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args: [--project=gcm_filters, --multi-line=3, --lines-after-imports=2, --lines-between-types=1, --trailing-comma, --force-grid-wrap=0, --use-parentheses, --line-width=88]
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- repo: https://github.com/asottile/seed-isort-config
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rev: v2.1.1
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hooks:
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- id: seed-isort-config
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- repo: https://github.com/psf/black
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rev: stable
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hooks:
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- id: black
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language_version: python3
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- repo: https://github.com/pre-commit/mirrors-mypy
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rev: v0.770
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hooks:
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- id: mypy
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exclude: docs/source/conf.py
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args: [--ignore-missing-imports]
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- repo: https://github.com/codespell-project/codespell
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rev: v1.16.0
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hooks:
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- id: codespell
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args:
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- --quiet-level=2

Diff for: ‎LICENSE.txt

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The MIT License (MIT)
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Copyright (c) 2021, Ryan Abernathey
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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:
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The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
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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.
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Diff for: ‎README.md

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mds2zarr
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==============================
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[![Build Status](https://github.com/mitgcm/mds2zarr/workflows/Tests/badge.svg)](https://github.com/mitgcm/mds2zarr/actions)
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[![codecov](https://codecov.io/gh/mitgcm/mds2zarr/branch/main/graph/badge.svg)](https://codecov.io/gh/mitgcm/mds2zarr)
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[![License:MIT](https://img.shields.io/badge/License-MIT-lightgray.svg?style=flt-square)](https://opensource.org/licenses/MIT)[![pypi](https://img.shields.io/pypi/v/mds2zarr.svg)](https://pypi.org/project/mds2zarr)
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<!-- [![conda-forge](https://img.shields.io/conda/dn/conda-forge/mds2zarr?label=conda-forge)](https://anaconda.org/conda-forge/mds2zarr) -->[![Documentation Status](https://readthedocs.org/projects/mds2zarr/badge/?version=latest)](https://mds2zarr.readthedocs.io/en/latest/?badge=latest)
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Adaptor to open MITgcm mds files as Zarr groups
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--------
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<p><small>Project based on the <a target="_blank" href="https://github.com/jbusecke/cookiecutter-science-project">cookiecutter science project template</a>.</small></p>

Diff for: ‎ci/environment-py3.10.yml

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name: test_env_mds2zarr
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channels:
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- conda-forge
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dependencies:
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- python=3.10
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############## These will have to be adjusted to your specific project
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- fsspec
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- pydantic
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- xarray
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- zarr
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##############
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- pooch
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- pytest
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- pip:
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- codecov
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- pytest-cov
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- coverage[toml]

Diff for: ‎ci/environment-py3.8.yml

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name: test_env_mds2zarr
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channels:
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- conda-forge
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dependencies:
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- python=3.8
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############## These will have to be adjusted to your specific project
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- fsspec
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- pydantic
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- xarray
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- zarr
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##############
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- pooch
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- pytest
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- pip:
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- codecov
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- pytest-cov
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- coverage[toml]

Diff for: ‎ci/environment-py3.9.yml

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name: test_env_mds2zarr
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channels:
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- conda-forge
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dependencies:
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- python=3.9
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############## These will have to be adjusted to your specific project
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- fsspec
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- pydantic
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- xarray
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- zarr
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##############
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- pooch
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- pytest
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- pip:
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- codecov
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- pytest-cov
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- coverage[toml]

Diff for: ‎docs/Makefile

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# Minimal makefile for Sphinx documentation
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#
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# You can set these variables from the command line, and also
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# from the environment for the first two.
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SPHINXOPTS ?=
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SPHINXBUILD ?= sphinx-build
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SOURCEDIR = .
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BUILDDIR = _build
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# Put it first so that "make" without argument is like "make help".
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help:
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@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
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.PHONY: help Makefile
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# Catch-all target: route all unknown targets to Sphinx using the new
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# "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS).
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%: Makefile
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@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

Diff for: ‎docs/api.rst

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:mod:`API`
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----------------------------
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Example For Autogenerated API Documentation
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===========================================
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.. automodule:: mds2zarr.dummy
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:members:
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:undoc-members:
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:show-inheritance:

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