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Merge branch 'main' into numbagg
* main: (29 commits) Major fix to subset_to_blocks (#173) Performance improvements for cohorts detection (#172) Remove split_out (#170) Deprecate resample_reduce (#169) More efficient cohorts. (#165) Allow specifying output dtype (#131) Add a dtype check for numpy arrays in assert_equal (#158) Update ci-additional.yaml (#167) Refactor before redoing cohorts (#164) Fix mypy errors in core.py (#150) Add link to numpy_groupies (#160) Bump codecov/codecov-action from 3.1.0 to 3.1.1 (#159) Use math.prod instead of np.prod (#157) Remove None output from _get_expected_groups (#152) Fix mypy errors in xarray.py, xrutils.py, cache.py (#144) Raise error if multiple by's are used with Ellipsis (#149) pre-commit autoupdate (#148) Add mypy ignores (#146) Get pre commit bot to update (#145) Remove duplicate examples headers (#147) ...
2 parents 5bc6939 + 6897240 commit fea47a5

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‎.github/workflows/benchmarks.yml‎

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name: Benchmark
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on:
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pull_request:
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types: [opened, reopened, synchronize, labeled]
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workflow_dispatch:
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jobs:
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benchmark:
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# if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} # Run if the PR has been labelled correctly.
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if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }} # Always run.
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name: Linux
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runs-on: ubuntu-20.04
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env:
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ASV_DIR: "./asv_bench"
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steps:
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# We need the full repo to avoid this issue
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# https://github.com/actions/checkout/issues/23
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v13
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with:
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environment-file: ci/environment.yml
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environment-name: flox-tests
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cache-env: true
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# extra-specs: |
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# python="${{ matrix.python-version }}"
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# - name: Setup some dependencies
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# shell: bash -l {0}
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# run: |
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# pip install asv
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# sudo apt-get update -y
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- name: Run benchmarks
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shell: bash -l {0}
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id: benchmark
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env:
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OPENBLAS_NUM_THREADS: 1
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MKL_NUM_THREADS: 1
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OMP_NUM_THREADS: 1
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ASV_FACTOR: 1.5
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ASV_SKIP_SLOW: 1
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run: |
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set -x
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# ID this runner
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asv machine --yes
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echo "Baseline: ${{ github.event.pull_request.base.sha }} (${{ github.event.pull_request.base.label }})"
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echo "Contender: ${GITHUB_SHA} (${{ github.event.pull_request.head.label }})"
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# Use mamba for env creation
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# export CONDA_EXE=$(which mamba)
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export CONDA_EXE=$(which conda)
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# Run benchmarks for current commit against base
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ASV_OPTIONS="--split --show-stderr --factor $ASV_FACTOR"
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asv continuous $ASV_OPTIONS ${{ github.event.pull_request.base.sha }} ${GITHUB_SHA} \
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| sed "/Traceback \|failed$\|PERFORMANCE DECREASED/ s/^/::error::/" \
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| tee benchmarks.log
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# Report and export results for subsequent steps
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if grep "Traceback \|failed\|PERFORMANCE DECREASED" benchmarks.log > /dev/null ; then
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exit 1
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fi
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working-directory: ${{ env.ASV_DIR }}
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- name: Add instructions to artifact
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if: always()
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run: |
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cp benchmarks/README_CI.md benchmarks.log .asv/results/
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working-directory: ${{ env.ASV_DIR }}
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- uses: actions/upload-artifact@v3
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if: always()
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with:
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name: asv-benchmark-results-${{ runner.os }}
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path: ${{ env.ASV_DIR }}/.asv/results

‎.github/workflows/ci-additional.yaml‎

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name: CI Additional
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on:
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push:
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branches:
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- "main"
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pull_request:
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branches:
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- "*"
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workflow_dispatch: # allows you to trigger manually
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concurrency:
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group: ${{ github.workflow }}-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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detect-ci-trigger:
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name: detect ci trigger
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runs-on: ubuntu-latest
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if: |
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github.repository == 'xarray-contrib/flox'
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&& (github.event_name == 'push' || github.event_name == 'pull_request')
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outputs:
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triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 2
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- uses: xarray-contrib/[email protected]
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id: detect-trigger
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with:
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keyword: "[skip-ci]"
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doctest:
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name: Doctests
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runs-on: "ubuntu-latest"
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needs: detect-ci-trigger
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if: needs.detect-ci-trigger.outputs.triggered == 'false'
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defaults:
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run:
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shell: bash -l {0}
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env:
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CONDA_ENV_FILE: ci/environment.yml
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PYTHON_VERSION: "3.10"
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: set environment variables
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run: |
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echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
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- name: Setup micromamba
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uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
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with:
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environment-file: ${{env.CONDA_ENV_FILE}}
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environment-name: flox-tests
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extra-specs: |
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python=${{env.PYTHON_VERSION}}
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cache-env: true
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cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
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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: Version info
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run: |
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conda info -a
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conda list
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- name: Run doctests
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run: |
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python -m pytest --doctest-modules flox --ignore flox/tests
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mypy:
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name: Mypy
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runs-on: "ubuntu-latest"
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needs: detect-ci-trigger
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if: needs.detect-ci-trigger.outputs.triggered == 'false'
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defaults:
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run:
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shell: bash -l {0}
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env:
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CONDA_ENV_FILE: ci/environment.yml
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PYTHON_VERSION: "3.10"
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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 environment variables
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run: |
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echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
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- name: Setup micromamba
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uses: mamba-org/provision-with-micromamba@34071ca7df4983ccd272ed0d3625818b27b70dcc
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with:
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environment-file: ${{env.CONDA_ENV_FILE}}
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environment-name: xarray-tests
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extra-specs: |
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python=${{env.PYTHON_VERSION}}
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cache-env: true
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cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
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- name: Install xarray
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run: |
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python -m pip install --no-deps -e .
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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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- name: Install mypy
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run: |
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python -m pip install mypy
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- name: Run mypy
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run: |
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python -m mypy --install-types --non-interactive

‎.github/workflows/ci.yaml‎

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run: |
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echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v12
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uses: mamba-org/provision-with-micromamba@v13
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with:
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environment-file: ci/environment.yml
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environment-name: flox-tests
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run: |
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pytest -n auto --cov=./ --cov-report=xml
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- name: Upload code coverage to Codecov
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uses: codecov/[email protected].0
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uses: codecov/[email protected].1
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with:
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file: ./coverage.xml
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flags: unittests
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with:
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fetch-depth: 0 # Fetch all history for all branches and tags.
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- name: Set up conda environment
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uses: mamba-org/provision-with-micromamba@v12
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uses: mamba-org/provision-with-micromamba@v13
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with:
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environment-file: ci/${{ matrix.env }}.yml
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environment-name: flox-tests
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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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uses: mamba-org/provision-with-micromamba@v13
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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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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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uses: mamba-org/provision-with-micromamba@v13
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with:
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environment-file: ci/requirements/environment.yml
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environment-name: xarray-tests

‎.pre-commit-config.yaml‎

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- id: check-docstring-first
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- repo: https://github.com/psf/black
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rev: 22.6.0
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rev: 22.8.0
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hooks:
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- id: black
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- repo: https://github.com/PyCQA/flake8
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rev: 4.0.1
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rev: 5.0.4
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hooks:
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- id: flake8
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‎README.md‎

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1. Dask Dataframe GroupBy
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[blogpost](https://blog.dask.org/2019/10/08/df-groupby)
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2. numpy_groupies in Xarray
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2. [numpy_groupies](https://github.com/ml31415/numpy-groupies) in Xarray
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[issue](https://github.com/pydata/xarray/issues/4473)
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(See a

‎asv.conf.json‎ renamed to ‎asv_bench/asv.conf.json‎

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// The URL or local path of the source code repository for the
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// project being benchmarked
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"repo": ".",
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"repo": "..",
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// The Python project's subdirectory in your repo. If missing or
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// the empty string, the project is assumed to be located at the root
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// determined from "repo" by looking at the protocol in the URL
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// (if remote), or by looking for special directories, such as
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// ".git" (if local).
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// "dvcs": "git",
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"dvcs": "git",
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// The tool to use to create environments. May be "conda",
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// "virtualenv" or other value depending on the plugins in use.
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// timeout in seconds for installing any dependencies in environment
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// defaults to 10 min
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//"install_timeout": 600,
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"install_timeout": 600,
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// the base URL to show a commit for the project.
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"show_commit_url": "http://github.com/dcherian/flox/commit/",
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"show_commit_url": "http://github.com/xarray-contrib/flox/commit/",
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// The Pythons you'd like to test against. If not provided, defaults
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// to the current version of Python used to run `asv`.
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// The directory (relative to the current directory) that benchmarks are
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// stored in. If not provided, defaults to "benchmarks"
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// "benchmark_dir": "benchmarks",
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"benchmark_dir": "benchmarks",
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// The directory (relative to the current directory) to cache the Python
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// environments in. If not provided, defaults to "env"

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