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Merge pull request #96 from kthyng/featuretypes
controlled selections for em.select
2 parents 3193646 + 7c05abf commit 7070404

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-48
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‎.github/workflows/test.yaml‎

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fail-fast: false
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matrix:
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os: ["macos-latest", "ubuntu-latest", "windows-latest"]
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python-version: ["3.8", "3.9", "3.10"]
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python-version: ["3.9", "3.10", "3.11"]
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steps:
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- name: Checkout source
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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- name: Cache Linux/macOS (x86) Conda environment
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if: ${{ runner.os != 'Windows' }}
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uses: actions/cache@v3
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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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# - name: Cache Linux/macOS (x86) Conda environment
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# if: ${{ runner.os != 'Windows' }}
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# uses: actions/cache@v3
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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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- name: Cache Windows Conda environment
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if: ${{ runner.os == 'Windows' }}
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uses: actions/cache@v3
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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 }}-win.yml') }}
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# - name: Cache Windows Conda environment
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# if: ${{ runner.os == 'Windows' }}
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# uses: actions/cache@v3
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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 }}-win.yml') }}
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- name: Build and activate Linux/macOS Conda environment
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- name: Setup Linux/macOS Micromamba Python ${{ matrix.python-version }}
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if: ${{ runner.os != 'Windows' }}
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uses: conda-incubator/setup-miniconda@v2
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uses: mamba-org/setup-micromamba@v1
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with:
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miniforge-variant: Mambaforge
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python-version: ${{ matrix.python-version }}
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channels: conda-forge, defaults # These need to be specified to use mamba
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channel-priority: true
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init-shell: bash
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create-args: >-
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python=${{ matrix.python-version }} --channel conda-forge
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environment-file: ci/environment-py${{ matrix.python-version }}.yml
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cache-environment: true
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post-cleanup: 'all'
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activate-environment: test-env-mac-unix
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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: Build and activate Windows Conda environment
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- name: Setup Windows Micromamba Python ${{ matrix.python-version }}
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if: ${{ runner.os == 'Windows' }}
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uses: conda-incubator/setup-miniconda@v2
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uses: mamba-org/setup-micromamba@v1
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with:
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miniforge-variant: Mambaforge
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python-version: ${{ matrix.python-version }}
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channels: conda-forge, defaults # These need to be specified to use mamba
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channel-priority: true
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init-shell: bash
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create-args: >-
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python=${{ matrix.python-version }} --channel conda-forge
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environment-file: ci/environment-py${{ matrix.python-version }}-win.yml
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cache-environment: true
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post-cleanup: 'all'
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# - name: Build and activate Linux/macOS Conda environment
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# if: ${{ runner.os != 'Windows' }}
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# uses: conda-incubator/setup-miniconda@v2
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# with:
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# miniforge-variant: Mambaforge
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# python-version: ${{ matrix.python-version }}
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# channels: conda-forge, defaults # These need to be specified to use mamba
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# channel-priority: true
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# environment-file: ci/environment-py${{ matrix.python-version }}.yml
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# activate-environment: test-env-mac-unix
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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: Build and activate Windows Conda environment
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# if: ${{ runner.os == 'Windows' }}
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# uses: conda-incubator/setup-miniconda@v2
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# with:
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# miniforge-variant: Mambaforge
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# python-version: ${{ matrix.python-version }}
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# channels: conda-forge, defaults # These need to be specified to use mamba
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# channel-priority: true
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# environment-file: ci/environment-py${{ matrix.python-version }}-win.yml
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activate-environment: test-env-win
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use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
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# activate-environment: test-env-win
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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: Install package in environment
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shell: bash -l {0}

‎ci/environment-py3.10-win.yml‎

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- scikit-learn # used by xoak for tree
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- xarray
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎ci/environment-py3.10.yml‎

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dependencies:
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- python=3.10
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- cf_xarray>=0.6
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- dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
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- dask
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- netcdf4
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- numpy <1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
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- pip
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- xarray
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- xesmf
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎ci/environment-py3.8-win.yml‎ renamed to ‎ci/environment-py3.11-win.yml‎

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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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- python=3.11
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- cf_xarray>=0.6
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- dask
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- netcdf4
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- scikit-learn # used by xoak for tree
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- xarray
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎ci/environment-py3.8.yml‎ renamed to ‎ci/environment-py3.11.yml‎

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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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- python=3.11
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- cf_xarray>=0.6
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- dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
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- dask
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- netcdf4
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- numpy <1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
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- pip
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- xarray
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- xesmf
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎ci/environment-py3.9-win.yml‎

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- scikit-learn # used by xoak for tree
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- xarray
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎ci/environment-py3.9.yml‎

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dependencies:
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- python=3.9
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- cf_xarray>=0.6
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- dask <=2022.05.0 # for xESMF, https://github.com/axiom-data-science/extract_model/issues/49
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- dask
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- netcdf4
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- numpy <1.24 # https://github.com/numba/numba/issues/8615#issuecomment-1360792615
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- pip
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- xarray
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- xesmf
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- xoak
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# - xroms
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- pytest
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- pytest-benchmark
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- pip:
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- xroms >=0.5.3
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- codecov
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- pytest-cov
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- coverage[toml]

‎docs/featuretypes.md‎

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# Feature types
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Feature types are defined by NCEI and provide structure types of data to expect. More information is available [in general](https://www.ncei.noaa.gov/netcdf-templates) and for the current [NCEI NetCDF Templates 2.0](https://www.ncei.noaa.gov/data/oceans/ncei/formats/netcdf/v2.0/index.html). The following information may be useful for thinking about this. In particular, you select `locstream`, `locstreamT`, and `locstreamZ` as a user for `em.select()` and this table can guide how to select.
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| | timeSeries | profile | timeSeriesProfile | trajectory (TODO) | trajectoryProfile | grid (TODO) |
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|--- |--- |--- |--- |--- | --- | --- |
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| Definition | only t changes | only z changes | t and z change | t, y, and x change | t, z, y, and x change | t changes, y/x grid |
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| Data types | mooring, buoy | CTD profile | moored ADCP | flow through, 2D drifter | glider, transect of CTD profiles, towed ADCP, 3D drifter | satellite, HF Radar |
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| Model extraction | time series at surface or depth | | vertical cross section | 2D drifters | 3D drifters | regridding, x/y slice in depth |
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| X/Y are pairs ("locstream") or grid | either locstream or grid | either locstream or grid | either locstream or grid | locstream | locstream | grid |
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| Which dimensions are independent from X/Y choice? |
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| T | Independent | Independent | Independent | locstreamT | locstreamT | Independent |
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| Z | Independent | Independent | Independent | Independent | locstreamZ | Independent |

‎docs/index.rst‎

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:hidden:
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:caption: Examples and demos
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featuretypes.md
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models.ipynb
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unstructured_subsetting.ipynb
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ts_work.ipynb

‎docs/whats_new.rst‎

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:mod:`What's New`
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-----------------
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v1.2.2 (October 4, 2023)
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v1.3.0 (October 11, 2023)
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=========================
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* Incorporated `locstreamT` and `locstreamZ` to standardize the options available to user in `em.select()`.
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* added more tests by featuretype to cover more area
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v1.2.2 (October 5, 2023)
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========================
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* Improved the processing of ROMS model output
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