From 5be7f20489a24eab6af5fb06db44e71c9512adc0 Mon Sep 17 00:00:00 2001 From: David Huard Date: Fri, 10 Nov 2023 08:41:14 -0500 Subject: [PATCH] run pre-commit --- .github/dependabot.yml | 18 +-- .github/workflows/ci.yaml | 176 ++++++++++++------------- .github/workflows/linting.yaml | 26 ++-- .github/workflows/pypi.yaml | 96 +++++++------- .pre-commit-config.yaml | 114 ++++++++-------- binder/environment.yml | 26 ++-- ci/environment-upstream-dev.yml | 34 ++--- ci/environment.yml | 32 ++--- codecov.yml | 26 ++-- doc/notebooks/Compare_algorithms.ipynb | 47 +++---- doc/notebooks/Masking.ipynb | 14 +- doc/notebooks/Pure_numpy.ipynb | 14 +- readthedocs.yml | 14 +- 13 files changed, 319 insertions(+), 318 deletions(-) diff --git a/.github/dependabot.yml b/.github/dependabot.yml index b4b3fa44..2eacebc2 100644 --- a/.github/dependabot.yml +++ b/.github/dependabot.yml @@ -1,11 +1,11 @@ version: 2 updates: - # - package-ecosystem: pip - # directory: "/" - # schedule: - # interval: daily - - package-ecosystem: 'github-actions' - directory: '/' - schedule: - # Check for updates once a week - interval: 'weekly' + # - package-ecosystem: pip + # directory: "/" + # schedule: + # interval: daily + - package-ecosystem: 'github-actions' + directory: '/' + schedule: + # Check for updates once a week + interval: 'weekly' diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index cc84cb70..9b970a3c 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -1,94 +1,94 @@ name: CI on: - push: - branches: - - master - pull_request: - branches: - - '*' - schedule: - - cron: '0 0 * * *' # Daily “At 00:00” - workflow_dispatch: # allows you to trigger manually + push: + branches: + - master + pull_request: + branches: + - '*' + schedule: + - cron: '0 0 * * *' # Daily “At 00:00” + workflow_dispatch: # allows you to trigger manually jobs: - build: - runs-on: ubuntu-latest - defaults: - run: - shell: bash -l {0} - strategy: - fail-fast: false - matrix: - include: - # Warning: Unless in quotations, numbers below are read as floats. 3.10 < 3.2 - - python-version: '3.8' - esmf-version: 8.2 - - python-version: '3.9' - esmf-version: 8.3 - - python-version: '3.10' - esmf-version: 8.4 - - python-version: '3.11' - esmf-version: 8.4 - steps: - - name: Cancel previous runs - uses: styfle/cancel-workflow-action@0.12.0 - with: - access_token: ${{ github.token }} - - name: Checkout source - uses: actions/checkout@v4 - - name: Create conda environment - uses: mamba-org/provision-with-micromamba@main - with: - cache-downloads: true - micromamba-version: 'latest' - environment-file: ci/environment.yml - extra-specs: | - python=${{ matrix.python-version }} - esmpy=${{ matrix.esmf-version }} - - name: Install Xesmf (editable) - run: | - python -m pip install --no-deps -e . - - name: Conda list information - run: | - conda env list - conda list - - name: Run tests - run: | - python -m pytest --cov=./ --cov-report=xml --verbose - - name: Upload coverage to Codecov - uses: codecov/codecov-action@v3.1.3 - with: - file: ./coverage.xml - fail_ci_if_error: false + build: + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + strategy: + fail-fast: false + matrix: + include: + # Warning: Unless in quotations, numbers below are read as floats. 3.10 < 3.2 + - python-version: '3.8' + esmf-version: 8.2 + - python-version: '3.9' + esmf-version: 8.3 + - python-version: '3.10' + esmf-version: 8.4 + - python-version: '3.11' + esmf-version: 8.4 + steps: + - name: Cancel previous runs + uses: styfle/cancel-workflow-action@0.12.0 + with: + access_token: ${{ github.token }} + - name: Checkout source + uses: actions/checkout@v4 + - name: Create conda environment + uses: mamba-org/provision-with-micromamba@main + with: + cache-downloads: true + micromamba-version: 'latest' + environment-file: ci/environment.yml + extra-specs: | + python=${{ matrix.python-version }} + esmpy=${{ matrix.esmf-version }} + - name: Install Xesmf (editable) + run: | + python -m pip install --no-deps -e . + - name: Conda list information + run: | + conda env list + conda list + - name: Run tests + run: | + python -m pytest --cov=./ --cov-report=xml --verbose + - name: Upload coverage to Codecov + uses: codecov/codecov-action@v3.1.3 + with: + file: ./coverage.xml + fail_ci_if_error: false - upstream-dev: - name: upstream-dev - runs-on: ubuntu-latest - defaults: - run: - shell: bash -l {0} - steps: - - name: Cancel previous runs - uses: styfle/cancel-workflow-action@0.12.0 - with: - access_token: ${{ github.token }} - - uses: actions/checkout@v4 - - name: Create conda environment - uses: mamba-org/provision-with-micromamba@v16 - with: - cache-downloads: true - micromamba-version: 'latest' - environment-file: ci/environment-upstream-dev.yml - extra-specs: | - python=3.10 - - name: Install Xesmf (editable) - run: | - python -m pip install -e . - - name: Conda list information - run: | - conda env list - conda list - - name: Run tests - run: | - python -m pytest --cov=./ --cov-report=xml --verbose + upstream-dev: + name: upstream-dev + runs-on: ubuntu-latest + defaults: + run: + shell: bash -l {0} + steps: + - name: Cancel previous runs + uses: styfle/cancel-workflow-action@0.12.0 + with: + access_token: ${{ github.token }} + - uses: actions/checkout@v4 + - name: Create conda environment + uses: mamba-org/provision-with-micromamba@v16 + with: + cache-downloads: true + micromamba-version: 'latest' + environment-file: ci/environment-upstream-dev.yml + extra-specs: | + python=3.10 + - name: Install Xesmf (editable) + run: | + python -m pip install -e . + - name: Conda list information + run: | + conda env list + conda list + - name: Run tests + run: | + python -m pytest --cov=./ --cov-report=xml --verbose diff --git a/.github/workflows/linting.yaml b/.github/workflows/linting.yaml index 2391406f..c7c018ea 100644 --- a/.github/workflows/linting.yaml +++ b/.github/workflows/linting.yaml @@ -1,18 +1,18 @@ name: linting on: - push: - branches: - - master - pull_request: - branches: '*' + push: + branches: + - master + pull_request: + branches: '*' jobs: - linting: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - uses: actions/setup-python@v4 - with: - python-version: '3.x' - - uses: pre-commit/action@v3.0.0 + linting: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-python@v4 + with: + python-version: '3.x' + - uses: pre-commit/action@v3.0.0 diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml index fde7fd5c..962a1b7b 100644 --- a/.github/workflows/pypi.yaml +++ b/.github/workflows/pypi.yaml @@ -1,55 +1,55 @@ name: Publish to PyPI on: - pull_request: - push: - branches: - - master - release: - types: - - published + pull_request: + push: + branches: + - master + release: + types: + - published defaults: - run: - shell: bash + run: + shell: bash jobs: - packages: - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v4 - - - name: Set up Python - uses: actions/setup-python@v4 - with: - python-version: '3.x' - - - name: Get tags - run: git fetch --depth=1 origin +refs/tags/*:refs/tags/* - - - name: Install build tools - run: | - python -m pip install --upgrade build - - - name: Build binary wheel - run: python -m build --sdist --wheel . --outdir dist - - - name: CheckFiles - run: | - ls dist - python -m pip install --upgrade check-manifest - check-manifest --verbose - - - name: Test wheels - run: | - # We cannot run this step b/c esmpy is not available on PyPI - # cd dist && python -m pip install *.whl && cd .. - python -m pip install --upgrade build twine - python -m twine check dist/* - - - name: Publish a Python distribution to PyPI - if: success() && github.event_name == 'release' - uses: pypa/gh-action-pypi-publish@release/v1 - with: - user: __token__ - password: ${{ secrets.PYPI_TOKEN }} + packages: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + + - name: Set up Python + uses: actions/setup-python@v4 + with: + python-version: '3.x' + + - name: Get tags + run: git fetch --depth=1 origin +refs/tags/*:refs/tags/* + + - name: Install build tools + run: | + python -m pip install --upgrade build + + - name: Build binary wheel + run: python -m build --sdist --wheel . --outdir dist + + - name: CheckFiles + run: | + ls dist + python -m pip install --upgrade check-manifest + check-manifest --verbose + + - name: Test wheels + run: | + # We cannot run this step b/c esmpy is not available on PyPI + # cd dist && python -m pip install *.whl && cd .. + python -m pip install --upgrade build twine + python -m twine check dist/* + + - name: Publish a Python distribution to PyPI + if: success() && github.event_name == 'release' + uses: pypa/gh-action-pypi-publish@release/v1 + with: + user: __token__ + password: ${{ secrets.PYPI_TOKEN }} diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index a190da46..f148794f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,70 +1,70 @@ default_language_version: - python: python3 + python: python3 repos: - - repo: https://github.com/pre-commit/pre-commit-hooks - rev: v4.4.0 - hooks: - - id: trailing-whitespace - - id: end-of-file-fixer - - id: check-docstring-first - - id: check-json - - id: check-yaml - - id: double-quote-string-fixer + - repo: https://github.com/pre-commit/pre-commit-hooks + rev: v4.4.0 + hooks: + - id: trailing-whitespace + - id: end-of-file-fixer + - id: check-docstring-first + - id: check-json + - id: check-yaml + - id: double-quote-string-fixer - - repo: https://github.com/psf/black - rev: 23.9.1 - hooks: - - id: black + - repo: https://github.com/psf/black + rev: 23.9.1 + hooks: + - id: black - - repo: https://github.com/keewis/blackdoc - rev: v0.3.8 - hooks: - - id: blackdoc + - repo: https://github.com/keewis/blackdoc + rev: v0.3.8 + hooks: + - id: blackdoc - - repo: https://github.com/PyCQA/flake8 - rev: 6.1.0 - hooks: - - id: flake8 + - repo: https://github.com/PyCQA/flake8 + rev: 6.1.0 + hooks: + - id: flake8 - - repo: https://github.com/asottile/seed-isort-config - rev: v2.2.0 - hooks: - - id: seed-isort-config - - repo: https://github.com/PyCQA/isort - rev: 5.12.0 - hooks: - - id: isort + - repo: https://github.com/asottile/seed-isort-config + rev: v2.2.0 + hooks: + - id: seed-isort-config + - repo: https://github.com/PyCQA/isort + rev: 5.12.0 + hooks: + - id: isort - - repo: https://github.com/pre-commit/mirrors-prettier - rev: v3.0.3 - hooks: - - id: prettier + - repo: https://github.com/pre-commit/mirrors-prettier + rev: v3.0.3 + hooks: + - id: prettier - - repo: https://github.com/deathbeds/prenotebook - rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa - hooks: - - id: prenotebook - args: - [ - '--keep-output', - '--keep-metadata', - '--keep-execution-count', - '--keep-empty', - ] + - repo: https://github.com/deathbeds/prenotebook + rev: f5bdb72a400f1a56fe88109936c83aa12cc349fa + hooks: + - id: prenotebook + args: + [ + '--keep-output', + '--keep-metadata', + '--keep-execution-count', + '--keep-empty', + ] - - repo: https://github.com/tox-dev/pyproject-fmt - rev: 1.2.0 - hooks: - - id: pyproject-fmt + - repo: https://github.com/tox-dev/pyproject-fmt + rev: 1.2.0 + hooks: + - id: pyproject-fmt ci: - autofix_commit_msg: | - [pre-commit.ci] auto fixes from pre-commit.com hooks + autofix_commit_msg: | + [pre-commit.ci] auto fixes from pre-commit.com hooks - for more information, see https://pre-commit.ci - autofix_prs: true - autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' - autoupdate_schedule: monthly - skip: [] - submodules: false + for more information, see https://pre-commit.ci + autofix_prs: true + autoupdate_commit_msg: '[pre-commit.ci] pre-commit autoupdate' + autoupdate_schedule: monthly + skip: [] + submodules: false diff --git a/binder/environment.yml b/binder/environment.yml index bcb6ee6e..42e1e14b 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -1,15 +1,15 @@ channels: - - conda-forge + - conda-forge dependencies: - - python=3.7 - - esmpy==7.1.0r - - xarray - - dask - - numpy - - scipy - - shapely - - matplotlib - - cartopy - - cf_xarray>=0.3.1 - - pip: - - xesmf==0.2.2 + - python=3.7 + - esmpy==7.1.0r + - xarray + - dask + - numpy + - scipy + - shapely + - matplotlib + - cartopy + - cf_xarray>=0.3.1 + - pip: + - xesmf==0.2.2 diff --git a/ci/environment-upstream-dev.yml b/ci/environment-upstream-dev.yml index 659aee2a..3d0f2590 100644 --- a/ci/environment-upstream-dev.yml +++ b/ci/environment-upstream-dev.yml @@ -1,20 +1,20 @@ name: xesmf channels: - - conda-forge + - conda-forge dependencies: - - cftime - - codecov - - dask - - esmpy - - numba - - numpy - - pip - - pre-commit - - pydap - - pytest - - pytest-cov - - shapely - - sparse>=0.8.0 - - pip: - - git+https://github.com/pydata/xarray.git - - git+https://github.com/xarray-contrib/cf-xarray.git + - cftime + - codecov + - dask + - esmpy + - numba + - numpy + - pip + - pre-commit + - pydap + - pytest + - pytest-cov + - shapely + - sparse>=0.8.0 + - pip: + - git+https://github.com/pydata/xarray.git + - git+https://github.com/xarray-contrib/cf-xarray.git diff --git a/ci/environment.yml b/ci/environment.yml index b596fcaa..8f57d1ba 100644 --- a/ci/environment.yml +++ b/ci/environment.yml @@ -1,19 +1,19 @@ name: xesmf channels: - - conda-forge + - conda-forge dependencies: - - cf_xarray>=0.3.1 - - cftime - - codecov - - dask - - esmpy - - numba - - numpy - - pip - - pre-commit - - pydap - - pytest - - pytest-cov - - shapely - - sparse>=0.8.0 - - xarray>=0.17.0 + - cf_xarray>=0.3.1 + - cftime + - codecov + - dask + - esmpy + - numba + - numpy + - pip + - pre-commit + - pydap + - pytest + - pytest-cov + - shapely + - sparse>=0.8.0 + - xarray>=0.17.0 diff --git a/codecov.yml b/codecov.yml index 1e11ad52..d241151b 100644 --- a/codecov.yml +++ b/codecov.yml @@ -1,20 +1,20 @@ codecov: - require_ci_to_pass: no - max_report_age: off + require_ci_to_pass: no + max_report_age: off comment: false ignore: - - 'xesmf/tests/*' - - 'setup.py' + - 'xesmf/tests/*' + - 'setup.py' coverage: - precision: 2 - round: down - status: - project: - default: - target: 95 - informational: true - patch: off - changes: off + precision: 2 + round: down + status: + project: + default: + target: 95 + informational: true + patch: off + changes: off diff --git a/doc/notebooks/Compare_algorithms.ipynb b/doc/notebooks/Compare_algorithms.ipynb index 0e194893..f5dcb746 100644 --- a/doc/notebooks/Compare_algorithms.ipynb +++ b/doc/notebooks/Compare_algorithms.ipynb @@ -8,12 +8,12 @@ "\n", "xESMF exposes five different regridding algorithms from the ESMF library:\n", "\n", - "- `bilinear`: `ESMF.RegridMethod.BILINEAR`\n", - "- `conservative`: `ESMF.RegridMethod.CONSERVE`\n", - "- `conservative_normed`: `ESMF.RegridMethod.CONSERVE`\n", - "- `patch`: `ESMF.RegridMethod.PATCH`\n", - "- `nearest_s2d`: `ESMF.RegridMethod.NEAREST_STOD`\n", - "- `nearest_d2s`: `ESMF.RegridMethod.NEAREST_DTOS`\n", + "- `bilinear`: `ESMF.RegridMethod.BILINEAR`\n", + "- `conservative`: `ESMF.RegridMethod.CONSERVE`\n", + "- `conservative_normed`: `ESMF.RegridMethod.CONSERVE`\n", + "- `patch`: `ESMF.RegridMethod.PATCH`\n", + "- `nearest_s2d`: `ESMF.RegridMethod.NEAREST_STOD`\n", + "- `nearest_d2s`: `ESMF.RegridMethod.NEAREST_DTOS`\n", "\n", "where `conservative_normed` is just the `conservative` method with the\n", "normalization set to `ESMF.NormType.FRACAREA` instead of the default\n", @@ -23,26 +23,27 @@ "\n", "## Notes\n", "\n", - "- `bilinear` and `conservative` should be the most commonly used methods. They\n", - " are both monotonic (i.e. will not create new maximum/minimum).\n", - "- Nearest neighbour methods, either source to destination (s2d) or destination\n", - " to source (d2s), could be useful in special cases. Keep in mind that d2s is\n", - " highly non-monotonic.\n", - "- Patch is ESMF's unique method, producing highly smooth results but quite slow.\n", - "- From the ESMF documentation:\n", + "- `bilinear` and `conservative` should be the most commonly used methods. They\n", + " are both monotonic (i.e. will not create new maximum/minimum).\n", + "- Nearest neighbour methods, either source to destination (s2d) or destination\n", + " to source (d2s), could be useful in special cases. Keep in mind that d2s is\n", + " highly non-monotonic.\n", + "- Patch is ESMF's unique method, producing highly smooth results but quite\n", + " slow.\n", + "- From the ESMF documentation:\n", "\n", - " > The weight $w_{ij}$ for a particular source cell $i$ and destination cell\n", - " > $j$ are calculated as $w_{ij}=f_{ij} * A_{si}/A_{dj}$. In this equation\n", - " > $f_{ij}$ is the fraction of the source cell $i$ contributing to destination\n", - " > cell $j$, and $A_{si}$ and $A_{dj}$ are the areas of the source and\n", - " > destination cells.\n", + " > The weight $w_{ij}$ for a particular source cell $i$ and destination cell\n", + " > $j$ are calculated as $w_{ij}=f_{ij} * A_{si}/A_{dj}$. In this equation\n", + " > $f_{ij}$ is the fraction of the source cell $i$ contributing to\n", + " > destination cell $j$, and $A_{si}$ and $A_{dj}$ are the areas of the\n", + " > source and destination cells.\n", "\n", - " For `conservative_normed`,\n", + " For `conservative_normed`,\n", "\n", - " > ... then the weights are further divided by the destination fraction. In\n", - " > other words, in that case $w_{ij}=f_{ij} * A_{si}/(A_{dj}*D_j)$ where $D_j$\n", - " > is fraction of the destination cell that intersects the unmasked source\n", - " > grid.\n", + " > ... then the weights are further divided by the destination fraction. In\n", + " > other words, in that case $w_{ij}=f_{ij} * A_{si}/(A_{dj}*D_j)$ where\n", + " > $D_j$ is fraction of the destination cell that intersects the unmasked\n", + " > source grid.\n", "\n", "Detailed explanations are available on\n", "[ESMPy documentation](http://www.earthsystemmodeling.org/esmf_releases/last_built/esmpy_doc/html/api.html#regridding).\n", diff --git a/doc/notebooks/Masking.ipynb b/doc/notebooks/Masking.ipynb index 0dcc213d..8c134190 100644 --- a/doc/notebooks/Masking.ipynb +++ b/doc/notebooks/Masking.ipynb @@ -499,15 +499,15 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "- mask can only be 2D (ESMF design) so regridding a 3D field requires to\n", - " generate regridding weights for each vertical level.\n", + "- mask can only be 2D (ESMF design) so regridding a 3D field requires to\n", + " generate regridding weights for each vertical level.\n", "\n", - "- conservative method will give you a normalization by the total area of the\n", - " target cell. Except for some specific cases, you probably want to use\n", - " conservative_normed.\n", + "- conservative method will give you a normalization by the total area of the\n", + " target cell. Except for some specific cases, you probably want to use\n", + " conservative_normed.\n", "\n", - "- results with other methods (e.g. bilinear) may not give masks consistent with\n", - " the coarse grid.\n" + "- results with other methods (e.g. bilinear) may not give masks consistent\n", + " with the coarse grid.\n" ] }, { diff --git a/doc/notebooks/Pure_numpy.ipynb b/doc/notebooks/Pure_numpy.ipynb index a04ab748..308eef62 100644 --- a/doc/notebooks/Pure_numpy.ipynb +++ b/doc/notebooks/Pure_numpy.ipynb @@ -236,10 +236,10 @@ "We use the previous input data, but now assume it is on a curvilinear grid\n", "described by 2D arrays. We also computed the cell corners, for two purposes:\n", "\n", - "- Visualization with `plt.pcolormesh` (using cell centers will miss one\n", - " row&column)\n", - "- Conservative regridding with xESMF (corner information is required for\n", - " conservative method)\n" + "- Visualization with `plt.pcolormesh` (using cell centers will miss one\n", + " row&column)\n", + "- Conservative regridding with xESMF (corner information is required for\n", + " conservative method)\n" ] }, { @@ -446,9 +446,9 @@ "source": [ "All $2 \\times 2\\times 2 = 8$ combinations would work:\n", "\n", - "- Input grid: `xarray.DataSet` or `dict`\n", - "- Output grid: `xarray.DataSet` or `dict`\n", - "- Input data: `xarray.DataArray` or `numpy.ndarray`\n", + "- Input grid: `xarray.DataSet` or `dict`\n", + "- Output grid: `xarray.DataSet` or `dict`\n", + "- Input data: `xarray.DataArray` or `numpy.ndarray`\n", "\n", "The output data type will be the same as input data.\n" ] diff --git a/readthedocs.yml b/readthedocs.yml index f0c4a4ae..c605ae18 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -1,12 +1,12 @@ version: 2 build: - os: ubuntu-22.04 - tools: - python: '3.9' + os: ubuntu-22.04 + tools: + python: '3.9' python: - install: - - requirements: doc/requirements.txt - - method: pip - path: . + install: + - requirements: doc/requirements.txt + - method: pip + path: .