Merge branch 'main' into lines

xarray-contrib · Nov 3, 2023 · 9e12bdf · 9e12bdf
2 parents 5e08ce1 + f9034ac
commit 9e12bdf
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diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -27,63 +27,22 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.9", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment.yml
           environment-name: cf_xarray_test
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
-      - name: Install cf_xarray
-        run: |
-          python -m pip install --no-deps -e .
-      - name: Run Tests
-        run: |
-          pytest -n auto --cov=./ --cov-report=xml
-      - name: Upload code coverage to Codecov
-        uses: codecov/[email protected]
-        with:
-          file: ./coverage.xml
-          flags: unittests
-          env_vars: RUNNER_OS,PYTHON_VERSION
-          name: codecov-umbrella
-          fail_ci_if_error: false
-
-  old-xarray:
-    name: xarray 2022.03.0
-    runs-on: "ubuntu-latest"
-    defaults:
-      run:
-        shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        python-version: ["3.10"]
-    steps:
-      - uses: actions/checkout@v3
-        with:
-          fetch-depth: 0 # Fetch all history for all branches and tags.
-      - name: Set environment variables
-        run: |
-          echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
-      - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
-        with:
-          environment-file: ci/environment.yml
-          environment-name: cf_xarray_test
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
-            xarray="2022.03.0"
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
       - name: Install cf_xarray
         run: |
           python -m pip install --no-deps -e .
@@ -106,16 +65,16 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # need to fetch all tags to get a correct version
           fetch-depth: 0  # fetch all branches and tags
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment-no-optional-deps.yml
           environment-name: cf_xarray_test
-          cache-env: true
+          cache-environment: true
       - name: Install cf_xarray
         run: |
           python -m pip install --no-deps -e .
@@ -132,19 +91,19 @@ jobs:
         shell: bash -l {0}
     strategy:
       matrix:
-        python-version: ["3.8", "3.11"]
+        python-version: ["3.9", "3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/environment.yml
           environment-name: cf_xarray_test
-          cache-env: true
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          cache-environment: true
+          create-args: >-
+            python=${{ matrix.python-version }}
       - name: Install cf_xarray
         run: |
           python -m pip install --no-deps -e .

diff --git a/.github/workflows/pypi.yaml b/.github/workflows/pypi.yaml
@@ -12,13 +12,13 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'xarray-contrib/cf-xarray'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: 3.8
+          python-version: "3.10"
 
       - name: Install dependencies
         run: |
@@ -53,7 +53,7 @@ jobs:
       - uses: actions/setup-python@v4
         name: Install Python
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - uses: actions/download-artifact@v3
         with:
           name: releases
@@ -72,7 +72,7 @@ jobs:
 
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/[email protected].7
+        uses: pypa/[email protected].10
         with:
           password: ${{ secrets.TESTPYPI_TOKEN }}
           repository_url: https://test.pypi.org/legacy/
@@ -96,6 +96,6 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/[email protected].7
+        uses: pypa/[email protected].10
         with:
           verbose: true
diff --git a/.github/workflows/testpypi-release.yaml b/.github/workflows/testpypi-release.yaml
@@ -17,7 +17,7 @@ jobs:
     if: ${{ contains( github.event.pull_request.labels.*.name, 'test-build') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -22,29 +22,29 @@ jobs:
   upstream-dev:
     name: upstream-dev
     runs-on: ubuntu-latest
-    if: ${{ contains( github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+    if: ${{ (contains( github.event.pull_request.labels.*.name, 'test-upstream') && github.event_name == 'pull_request') || github.event_name == 'workflow_dispatch' }}
     defaults:
       run:
         shell: bash -l {0}
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11"]
+        python-version: ["3.12"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables
         run: |
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
       - name: Set up conda environment
-        uses: mamba-org/provision-with-micromamba@v15
+        uses: mamba-org/setup-micromamba@v1
         with:
           environment-file: ci/upstream-dev-env.yml
           environment-name: cf_xarray_test
           cache-env: False
-          extra-specs: |
-            python="${{ matrix.python-version }}"
+          create-args: >-
+            python=${{ matrix.python-version }}
       - name: Install cf_xarray
         run: |
           python -m pip install --no-deps -e .

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -2,27 +2,33 @@ ci:
     autoupdate_schedule: quarterly
 
 repos:
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: ["--py39-plus"]
+
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.276'
+    rev: 'v0.1.1'
     hooks:
       - id: ruff
-        args: ["--fix"]
+        args: ["--show-fixes", "--fix"]
 
-  - repo: https://github.com/psf/black
-    rev: 23.3.0
+  - repo: https://github.com/psf/black-pre-commit-mirror
+    rev: 23.10.1
     hooks:
       - id: black
 
   - repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
+    rev: v6.2.0
     hooks:
         - id: rstcheck
           additional_dependencies: [sphinx, tomli]
           args: ['--config', 'pyproject.toml']
 
   - repo: https://github.com/executablebooks/mdformat
-    rev: 0.7.16
+    rev: 0.7.17
     hooks:
     - id: mdformat
       additional_dependencies:
@@ -38,10 +44,10 @@ repos:
           entry: nbqa mdformat
           name: nbqa-mdformat
           alias: nbqa-mdformat
-          additional_dependencies: [mdformat==0.7.14]
+          additional_dependencies: [mdformat==0.7.17]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -61,6 +67,14 @@ repos:
     - id: validate-cff
 
   - repo: https://github.com/abravalheri/validate-pyproject
-    rev: v0.13
+    rev: v0.15
     hooks:
       - id: validate-pyproject
+
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      # - id: python-check-blanket-type-ignore
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,20 +1,17 @@
-# Required
 version: 2
 
 build:
-  os: 'ubuntu-20.04'
+  os: ubuntu-22.04
   tools:
-    python: 'mambaforge-4.10'
+    python: mambaforge-4.10
+  jobs:
+    post_checkout:
+      - (git --no-pager log --pretty="tformat:%s" -1 | grep -vqF "[skip-rtd]") || exit 183
+    pre_install:
+      - conda list sphinx
+      - conda list cf_xarray
 
-# Build documentation in the docs/ directory with Sphinx
-sphinx:
-  configuration: doc/conf.py
-
-# Optionally set the version of Python and requirements required to build your docs
 conda:
-    environment: ci/doc.yml
+  environment: ci/doc.yml
 
-python:
-  install:
-    - method: pip
-      path: .
+formats: []
diff --git a/cf_xarray/accessor.py b/cf_xarray/accessor.py
@@ -6,16 +6,11 @@
 import re
 import warnings
 from collections import ChainMap, namedtuple
+from collections.abc import Hashable, Iterable, Mapping, MutableMapping, Sequence
 from datetime import datetime
 from typing import (
     Any,
     Callable,
-    Hashable,
-    Iterable,
-    List,
-    Mapping,
-    MutableMapping,
-    Sequence,
     TypeVar,
     Union,
     cast,
@@ -84,7 +79,7 @@
 ATTRS["vertical"] = ATTRS["Z"]
 
 # Type for Mapper functions
-Mapper = Callable[[Union[DataArray, Dataset], Hashable], List[Hashable]]
+Mapper = Callable[[Union[DataArray, Dataset], Hashable], list[Hashable]]
 
 # Type for decorators
 F = TypeVar("F", bound=Callable[..., Any])
@@ -496,7 +491,7 @@ def _get_coords(obj: DataArray | Dataset, key: Hashable) -> list[Hashable]:
 def _variables(func: F) -> F:
     @functools.wraps(func)
     def wrapper(obj: DataArray | Dataset, key: Hashable) -> list[DataArray]:
-        return [obj[k] for k in func(obj, key)]  # type: ignore
+        return [obj[k] for k in func(obj, key)]  # type: ignore[misc]
 
     return cast(F, wrapper)
 
@@ -1293,7 +1288,7 @@ def _process_signature(
            This uses ``key_mappers``
         3. Unpacks arguments if necessary before returning them.
         """
-        sig = inspect.signature(func, follow_wrapped=False)
+        sig = inspect.signature(func, follow_wrapped=True)
 
         # Catch things like .isel(T=5).
         # This assigns indexers_kwargs=dict(T=5).
@@ -2301,8 +2296,20 @@ def get_bounds_dim_name(self, key: Hashable) -> Hashable:
         -------
         str
         """
-        (crd_name,) = apply_mapper(_get_all, self._obj, key, error=False, default=[key])
+        # In many cases, the bounds variable has the same attrs as the coordinate variable
+        # So multiple matches are possible.
+        crd_names = apply_mapper(_get_all, self._obj, key, error=False, default=[key])
+
         variables = self._obj._variables
+        filtered = [
+            crd_name for crd_name in crd_names if "bounds" in variables[crd_name].attrs
+        ]
+        if len(filtered) > 1:
+            raise KeyError(
+                f"Received multiple matches for {key!r} that have a bounds attribute: {filtered!r} "
+            )
+
+        (crd_name,) = filtered
         crd = variables[crd_name]
         crd_attrs = crd._attrs
         if crd_attrs is None or "bounds" not in crd_attrs:

diff --git a/cf_xarray/criteria.py b/cf_xarray/criteria.py
@@ -9,7 +9,8 @@
 except ImportError:
     import re  # type: ignore
 
-from typing import Any, Mapping, MutableMapping, Tuple
+from collections.abc import Mapping, MutableMapping
+from typing import Any
 
 _DSG_ROLES = ["timeseries_id", "profile_id", "trajectory_id"]
 
@@ -30,7 +31,7 @@
     "grid_mapping": {"grid_mapping_name": re.compile(".")}
 }
 
-coordinate_criteria: MutableMapping[str, MutableMapping[str, Tuple]] = {
+coordinate_criteria: MutableMapping[str, MutableMapping[str, tuple]] = {
     "latitude": {
         "standard_name": ("latitude",),
         "units": (