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Merge branch 'main' into numbagg
* main: (44 commits) Rename repo to xarray-contrib/flox (#125) Propagate attrs better (#124) Update README.md (#123) Update README.md micromamba in CI (#122) Many optimizations (#120) Add xarray groupby test (#121) Update README.md Update README.md Add NASA Xarray grant [pre-commit.ci] pre-commit autoupdate (#118) Allow custom numpy aggregations for "blockwise" (#117) Don't execute hourly climatology notebook (#98) Bump actions/setup-python from 3 to 4 (#116) Fix factorizing some more. (#115) Correctly factorize values outside bin edges Better error message Avoid a copy. Fix bug where we had extra groups in expected_groups. (#112) Fix binning by nD variable ...
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‎.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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interval: "monthly"

‎.github/workflows/cancel-duplicate-runs.yaml

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‎.github/workflows/ci-additional.yaml

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‎.github/workflows/ci.yaml

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- cron: "0 0 * * *" # Daily “At 00:00”
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workflow_dispatch: # allows you to trigger manually
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concurrency:
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group: ${{ github.ref }}
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cancel-in-progress: true
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jobs:
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build:
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name: Build (${{ matrix.python-version }}, ${{ matrix.os }})
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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python-version: ["3.7", "3.8", "3.9"]
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python-version: ["3.8", "3.10"]
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steps:
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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: Set environment variables
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run: |
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echo "CONDA_ENV_FILE=ci/environment.yml" >> $GITHUB_ENV
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echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
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- name: Cache conda
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uses: actions/cache@v2
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with:
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path: ~/conda_pkgs_dir
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key:
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${{ runner.os }}-conda-py${{ matrix.python-version }}-${{
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hashFiles('ci/**.yml') }}
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- uses: conda-incubator/setup-miniconda@v2
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with:
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channels: conda-forge
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channel-priority: strict
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mamba-version: "*"
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activate-environment: flox-tests
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auto-update-conda: false
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python-version: ${{ matrix.python-version }}
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use-only-tar-bz2: true
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- name: Install conda dependencies
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run: |
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mamba env update -f $CONDA_ENV_FILE
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- name: Set up conda environment
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shell: bash -l {0}
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uses: mamba-org/provision-with-micromamba@v12
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with:
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environment-file: ci/environment.yml
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environment-name: flox-tests
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cache-env: true
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extra-specs: |
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python="${{ matrix.python-version }}"
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- name: Install flox
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run: |
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python -m pip install -e .
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conda list
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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 -n auto --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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uses: codecov/codecov-action@v3.1.0
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with:
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file: ./coverage.xml
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flags: unittests
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env_vars: RUNNER_OS,PYTHON_VERSION
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name: codecov-umbrella
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fail_ci_if_error: false
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# docs-build:
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# name: Documentation build
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# runs-on: ubuntu-latest
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# steps:
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# - name: Checkout
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# uses: actions/checkout@v2
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# - name: set up Python 3.8
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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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# - name: Install package
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# run: |
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# python -m pip install --upgrade pip
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# python -m pip install -e .
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optional-deps:
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name: ${{ matrix.env }}
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runs-on: ${{ matrix.os }}
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defaults:
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run:
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shell: bash -l {0}
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strategy:
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fail-fast: false
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matrix:
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os: ["ubuntu-latest"]
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env:
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[
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"no-xarray",
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"no-dask",
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"minimal-requirements",
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]
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v12
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with:
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environment-file: ci/${{ matrix.env }}.yml
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environment-name: flox-tests
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cache-env: true
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extra-specs: |
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python="${{ matrix.python-version }}"
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- name: Install flox
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run: |
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python -m pip install --no-deps -e .
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- name: Run tests
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run: |
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python -m pytest -n auto
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# - name: Install documentation dependencies
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# run: |
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# python -m pip install -r docs/requirements-docs.txt
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upstream-dev:
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name: upstream-dev
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v12
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with:
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environment-file: ci/upstream-dev-env.yml
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environment-name: flox-tests
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extra-specs: |
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python="3.10"
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- name: Run Tests
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run: |
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pytest -n 2
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# - name: Build docs
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# run: |
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# cd docs
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# make html
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xarray-groupby:
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name: xarray-groupby
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- uses: actions/checkout@v3
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with:
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repository: 'pydata/xarray'
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v12
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with:
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environment-file: ci/requirements/environment.yml
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environment-name: xarray-tests
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cache-env: true
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extra-specs: |
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python="3.10"
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- name: Install xarray
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run: |
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python -m pip install --no-deps .
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- name: Install upstream flox
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run: |
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python -m pip install --no-deps \
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git+https://github.com/dcherian/flox.git@${{ github.ref }}
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- name: Version info
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run: |
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conda info -a
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conda list
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python xarray/util/print_versions.py
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- name: import xarray
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run: |
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python -c 'import xarray'
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- name: import flox
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run: |
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python -c 'import flox'
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- name: Run Tests
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if: success()
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id: status
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run: |
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set -euo pipefail
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python -m pytest -n auto xarray/tests/test_groupby.py

‎.github/workflows/pypi.yaml

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- uses: actions/checkout@v2
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- uses: actions/checkout@v3
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- name: Set up Python
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uses: actions/setup-python@v2
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uses: actions/setup-python@v4
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with:
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python-version: '3.x'
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- name: Install dependencies

‎.pre-commit-config.yaml

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- repo: https://github.com/pre-commit/pre-commit-hooks
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rev: v4.1.0
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rev: v4.3.0
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hooks:
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- id: trailing-whitespace
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- id: end-of-file-fixer
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rev: 22.3.0
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rev: 22.6.0
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- id: black
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‎README.md

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[![GitHub Workflow CI Status](https://img.shields.io/github/workflow/status/dcherian/flox/CI?logo=github&style=flat)](https://github.com/dcherian/flox/actions)[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/dcherian/flox/main.svg)](https://results.pre-commit.ci/latest/github/dcherian/flox/main)[![image](https://img.shields.io/codecov/c/github/dcherian/flox.svg?style=flat)](https://codecov.io/gh/dcherian/flox)[![PyPI](https://img.shields.io/pypi/v/flox.svg?style=flat)](https://pypi.org/project/flox/)[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/flox.svg?style=flat)](https://anaconda.org/conda-forge/flox)[![Documentation Status](https://readthedocs.org/projects/flox/badge/?version=latest)](https://flox.readthedocs.io/en/latest/?badge=latest)[![NASA-80NSSC18M0156](https://img.shields.io/badge/NASA-80NSSC18M0156-blue)](https://earthdata.nasa.gov/esds/competitive-programs/access/pangeo-ml)
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[![GitHub Workflow CI Status](https://img.shields.io/github/workflow/status/xarray-contrib/flox/CI?logo=github&style=flat)](https://github.com/xarray-contrib/flox/actions)
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[![pre-commit.ci status](https://results.pre-commit.ci/badge/github/xarray-contrib/flox/main.svg)](https://results.pre-commit.ci/latest/github/xarray-contrib/flox/main)
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[![image](https://img.shields.io/codecov/c/github/xarray-contrib/flox.svg?style=flat)](https://codecov.io/gh/xarray-contrib/flox)
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[![Documentation Status](https://readthedocs.org/projects/flox/badge/?version=latest)](https://flox.readthedocs.io/en/latest/?badge=latest)
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[![PyPI](https://img.shields.io/pypi/v/flox.svg?style=flat)](https://pypi.org/project/flox/)
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[![Conda-forge](https://img.shields.io/conda/vn/conda-forge/flox.svg?style=flat)](https://anaconda.org/conda-forge/flox)
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[![NASA-80NSSC18M0156](https://img.shields.io/badge/NASA-80NSSC18M0156-blue)](https://earthdata.nasa.gov/esds/competitive-programs/access/pangeo-ml)
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[![NASA-80NSSC22K0345](https://img.shields.io/badge/NASA-80NSSC22K0345-blue)](https://science.nasa.gov/open-science-overview)
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# flox
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## Acknowledgements
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This work was funded in part by NASA-ACCESS 80NSSC18M0156 "Community tools for analysis of NASA Earth Observing System
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Data in the Cloud" (PI J. Hamman), and [NCAR's Earth System Data Science Initiative](https://ncar.github.io/esds/).
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This work was funded in part by
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1. NASA-ACCESS 80NSSC18M0156 "Community tools for analysis of NASA Earth Observing System
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Data in the Cloud" (PI J. Hamman, NCAR),
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2. NASA-OSTFL 80NSSC22K0345 "Enhancing analysis of NASA data with the open-source Python Xarray Library" (PIs Scott Henderson, University of Washington; Deepak Cherian, NCAR; Jessica Scheick, University of New Hampshire), and
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3. [NCAR's Earth System Data Science Initiative](https://ncar.github.io/esds/).
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It was motivated by [very](https://github.com/pangeo-data/pangeo/issues/266) [very](https://github.com/pangeo-data/pangeo/issues/271) [many](https://github.com/dask/distributed/issues/2602) [discussions](https://github.com/pydata/xarray/issues/2237) in the [Pangeo](https://pangeo.io) community.
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## API

‎ci/docs.yml

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- jupyter
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- git+https://github.com/dcherian/flox
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- git+https://github.com/xarray-contrib/flox

‎ci/environment.yml

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- pre-commit
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- numpy_groupies
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- numpy_groupies>=0.9.15
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- pooch
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- toolz
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- numba

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