Merge remote-tracking branch 'upstream/main' into groupby-cumsum

* upstream/main: Add a slighly cheesy contributors panel to readme (pydata#6520) Fix doctest & mypy CI jobs (pydata#6535) Attempt to improve CI caching (pydata#6534) Attempt to consolidate tests in CI (pydata#6533) Restrict annotations to a single run in GHA (pydata#6532) Fix some mypy issues (pydata#6531)
dcherian · Apr 28, 2022 · e8ec1b2 · e8ec1b2
2 parents b0d42d2 + e0cc051
commit e8ec1b2
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diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -30,6 +30,9 @@ jobs:
         with:
           keyword: "[skip-ci]"
 
+  # This job is deprecated and can be removed soon. It's still here in case the
+  # move consolidate with `ci.yaml` missed something which the existing test
+  # picks up.
   test:
     name: ${{ matrix.os }} ${{ matrix.env }}
     runs-on: ${{ matrix.os }}
@@ -42,8 +45,7 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest"]
-        env:
-          [
+        env: [
             # Minimum python version:
             "py38-bare-minimum",
             "py38-min-all-deps",
@@ -67,12 +69,12 @@ jobs:
           else
             echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
           fi
+
       - name: Cache conda
         uses: actions/cache@v3
         with:
           path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ matrix.env }}-${{
+          key: ${{ runner.os }}-conda-${{ matrix.env }}-${{
             hashFiles('ci/requirements/**.yml') }}
 
       - uses: conda-incubator/setup-miniconda@v2
@@ -119,6 +121,7 @@ jobs:
   doctest:
     name: Doctests
     runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     defaults:
       run:
@@ -152,6 +155,47 @@ jobs:
         run: |
           python -m pytest --doctest-modules xarray --ignore xarray/tests
 
+  mypy:
+    name: Mypy
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          channels: conda-forge
+          channel-priority: strict
+          mamba-version: "*"
+          activate-environment: xarray-tests
+          auto-update-conda: false
+          python-version: "3.9"
+
+      - name: Install conda dependencies
+        run: |
+          mamba env update -f ci/requirements/environment.yml
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+          python xarray/util/print_versions.py
+      - name: Install mypy
+        run: |
+          python -m pip install mypy
+          python -m mypy --install-types --non-interactive
+
+      - name: Run mypy
+        run: python -m mypy
+
   min-version-policy:
     name: Minimum Version Policy
     runs-on: "ubuntu-latest"

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -43,6 +43,21 @@ jobs:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
         python-version: ["3.8", "3.10"]
+        include:
+          # Minimum python version:
+          - env: "py38-bare-minimum"
+            python-version: 3.8
+            os: ubuntu-latest
+          - env: "py38-min-all-deps"
+            python-version: 3.8
+            os: ubuntu-latest
+          # Latest python version:
+          - env: "py39-all-but-dask"
+            python-version: 3.9
+            os: ubuntu-latest
+          - env: "py39-flaky"
+            python-version: 3.9
+            os: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
@@ -52,18 +67,30 @@ jobs:
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
             echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
+          elif [[ "${{ matrix.env }}" != "" ]] ;
+          then
+            if [[ "${{ matrix.env }}" == "py39-flaky" ]] ;
+            then
+              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
+              echo "PYTEST_EXTRA_FLAGS=--run-flaky --run-network-tests" >> $GITHUB_ENV
+            else
+              echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
+            fi
           else
             echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
-
           fi
+
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
 
+        # This and the next few are based on https://github.com/conda-incubator/setup-miniconda#caching-environments
       - name: Cache conda
+        id: cache-conda
         uses: actions/cache@v3
         with:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{
             hashFiles('ci/requirements/**.yml') }}
+
       - uses: conda-incubator/setup-miniconda@v2
         with:
           channels: conda-forge
@@ -74,9 +101,25 @@ jobs:
           python-version: ${{ matrix.python-version }}
           use-only-tar-bz2: true
 
+      - name: Cache conda env
+        id: cache-env
+        uses: actions/cache@v3
+        with:
+          path: /usr/share/miniconda/envs/xarray-tests
+          key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{
+            hashFiles('ci/requirements/**.yml') }}
+
       - name: Install conda dependencies
         run: |
           mamba env update -f $CONDA_ENV_FILE
+        if: steps.cache-env.outputs.cache-hit != 'true'
+
+      # We only want to install this on one run, because otherwise we'll have
+      # duplicate annotations.
+      - name: Install error reporter
+        if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.10'
+        run: |
+          python -m pip install pytest-github-actions-annotate-failures
 
       - name: Install xarray
         run: |
@@ -87,14 +130,17 @@ jobs:
           conda info -a
           conda list
           python xarray/util/print_versions.py
+
       - name: Import xarray
         run: |
           python -c "import xarray"
+
       - name: Run tests
         run: python -m pytest -n 4
           --cov=xarray
           --cov-report=xml
           --junitxml=pytest.xml
+          $PYTEST_EXTRA_FLAGS
 
       - name: Upload test results
         if: always()

diff --git a/README.md b/README.md
@@ -99,6 +99,12 @@ released as open source in May 2014. The project was renamed from
 "xray" in January 2016. Xarray became a fiscally sponsored project of
 [NumFOCUS](https://numfocus.org) in August 2018.
 
+## Contributors
+
+Thanks to our many contributors!
+
+[![Contributors](https://contrib.rocks/image?repo=pydata/xarray)](https://github.com/pydata/xarray/graphs/contributors)
+
 ## License
 
 Copyright 2014-2019, xarray Developers

diff --git a/ci/requirements/environment.yml b/ci/requirements/environment.yml
@@ -37,7 +37,6 @@ dependencies:
   - pytest
   - pytest-cov
   - pytest-env
-  - pytest-github-actions-annotate-failures
   - pytest-xdist
   - rasterio
   - scipy

diff --git a/xarray/core/dataarray.py b/xarray/core/dataarray.py
@@ -1154,7 +1154,8 @@ def chunk(
             chunks = {}
 
         if isinstance(chunks, (float, str, int)):
-            chunks = dict.fromkeys(self.dims, chunks)
+            # ignoring type; unclear why it won't accept a Literal into the value.
+            chunks = dict.fromkeys(self.dims, chunks)  # type: ignore
         elif isinstance(chunks, (tuple, list)):
             chunks = dict(zip(self.dims, chunks))
         else:
@@ -4735,7 +4736,7 @@ def curvefit(
 
     def drop_duplicates(
         self,
-        dim: Hashable | Iterable[Hashable] | ...,
+        dim: Hashable | Iterable[Hashable],
         keep: Literal["first", "last"] | Literal[False] = "first",
     ):
         """Returns a new DataArray with duplicate dimension values removed.

diff --git a/xarray/core/dataset.py b/xarray/core/dataset.py
@@ -7981,7 +7981,7 @@ def _wrapper(Y, *coords_, **kwargs):
 
     def drop_duplicates(
         self,
-        dim: Hashable | Iterable[Hashable] | ...,
+        dim: Hashable | Iterable[Hashable],
         keep: Literal["first", "last"] | Literal[False] = "first",
     ):
         """Returns a new Dataset with duplicate dimension values removed.
@@ -8005,9 +8005,11 @@ def drop_duplicates(
         DataArray.drop_duplicates
         """
         if isinstance(dim, str):
-            dims = (dim,)
+            dims: Iterable = (dim,)
         elif dim is ...:
             dims = self.dims
+        elif not isinstance(dim, Iterable):
+            dims = [dim]
         else:
             dims = dim