Merge branch 'main' into groupby-refactor-init

* main: (95 commits) Use `zarr` to validate attrs when writing to zarr (pydata#6636) Add pre-commit hook to check CITATION.cff (pydata#6658) Fix kwargs used for extrapolation in docs (pydata#6639) Fix notebooks' HTML links (pydata#6655) Doc index update (pydata#6530) CFTime support for polyval (pydata#6624) Support dask arrays in datetime_to_numeric (pydata#6556) [pre-commit.ci] pre-commit autoupdate (pydata#6654) 0-padded month. (pydata#6653) [test-upstream] import `cleanup` fixture from `distributed` (pydata#6650) Allow all interp methods in typing (pydata#6647) Typing support for custom backends (pydata#6651) Improved DataArray typing (pydata#6637) Adjust code comments & types from pydata#6638 (pydata#6642) Typing of `str` and `dt` accessors (pydata#6641) Feature/to dict encoding (pydata#6635) fix {full,zeros,ones}_like overloads (pydata#6630) Mypy badge (pydata#6626) concatenate docs style (pydata#6621) Typing for open_dataset/array/mfdataset and to_netcdf/zarr (pydata#6612) ...
dcherian · Jun 5, 2022 · 1277544 · 1277544
2 parents 299e6c9 + b080349
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diff --git a/.github/ISSUE_TEMPLATE/bugreport.yml b/.github/ISSUE_TEMPLATE/bugreport.yml
@@ -1,4 +1,4 @@
-name: Bug Report
+name: 🐛 Bug Report
 description: File a bug report to help us improve
 labels: [bug, "needs triage"]
 body:
@@ -26,14 +26,24 @@ body:
     attributes:
       label: Minimal Complete Verifiable Example
       description: |
-        Minimal, self-contained copy-pastable example that generates the issue if possible. Please be concise with code posted. See guidelines below on how to provide a good bug report:
+        Minimal, self-contained copy-pastable example that demonstrates the issue.         This will be automatically formatted into code, so no need for markdown backticks.
+      render: Python
+
+  - type: checkboxes
+    id: mvce-checkboxes
+    attributes:
+      label: MVCE confirmation
+      description: |
+        Please confirm that the bug report is in an excellent state, so we can understand & fix it quickly & efficiently. For more details, check out:
 
         - [Minimal Complete Verifiable Examples](https://stackoverflow.com/help/mcve)
         - [Craft Minimal Bug Reports](http://matthewrocklin.com/blog/work/2018/02/28/minimal-bug-reports)
 
-        Bug reports that follow these guidelines are easier to diagnose, and so are often handled much more quickly.
-        This will be automatically formatted into code, so no need for markdown backticks.
-      render: Python
+      options:
+        - label: Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
+        - label: Complete example — the example is self-contained, including all data and the text of any traceback.
+        - label: Verifiable example — the example copy & pastes into an IPython prompt or [Binder notebook](https://mybinder.org/v2/gh/pydata/xarray/main?urlpath=lab/tree/doc/examples/blank_template.ipynb), returning the result.
+        - label: New issue — a search of GitHub Issues suggests this is not a duplicate.
 
   - type: textarea
     id: log-output
@@ -54,6 +64,12 @@ body:
     attributes:
       label: Environment
       description: |
-        Paste the output of `xr.show_versions()` here
+        Paste the output of `xr.show_versions()` between the `<details>` tags, leaving an empty line following the opening tag.
+      value: |
+        <details>
+
+
+
+        </details>
     validations:
       required: true
diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml
@@ -1,8 +1,14 @@
 blank_issues_enabled: false
 contact_links:
-  - name: Usage question
+  - name: ❓ Usage question
     url: https://github.com/pydata/xarray/discussions
     about: |
       Ask questions and discuss with other community members here.
       If you have a question like "How do I concatenate a list of datasets?" then
       please include a self-contained reproducible example if possible.
+  - name: 🗺️ Raster analysis usage question
+    url: https://github.com/corteva/rioxarray/discussions
+    about: |
+      If you are using the rioxarray extension (engine='rasterio'), or have questions about
+      raster analysis such as geospatial formats, coordinate reprojection, etc.,
+      please use the rioxarray discussion forum.
diff --git a/.github/ISSUE_TEMPLATE/misc.yml b/.github/ISSUE_TEMPLATE/misc.yml
@@ -1,5 +1,5 @@
-name: Issue
-description: General Issue or discussion topic. For usage questions, please follow the "Usage question" link
+name: 📝 Issue
+description: General issue, that's not a bug report.
 labels: ["needs triage"]
 body:
   - type: markdown

diff --git a/.github/ISSUE_TEMPLATE/newfeature.yml b/.github/ISSUE_TEMPLATE/newfeature.yml
@@ -1,4 +1,4 @@
-name: Feature Request
+name: 💡 Feature Request
 description: Suggest an idea for xarray
 labels: [enhancement]
 body:

diff --git a/.github/stale.yml b/.github/stale.yml
@@ -1,7 +1,7 @@
 # Configuration for probot-stale - https://github.com/probot/stale
 
 # Number of days of inactivity before an Issue or Pull Request becomes stale
-daysUntilStale: 700  # start with a large number and reduce shortly
+daysUntilStale: 600 # start with a large number and reduce shortly
 
 # Number of days of inactivity before an Issue or Pull Request with the stale label is closed.
 # Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale.
@@ -14,10 +14,10 @@ exemptLabels:
   - "[Status] Maybe Later"
 
 # Set to true to ignore issues in a project (defaults to false)
-exemptProjects: false
+exemptProjects: true
 
 # Set to true to ignore issues in a milestone (defaults to false)
-exemptMilestones: false
+exemptMilestones: true
 
 # Set to true to ignore issues with an assignee (defaults to false)
 exemptAssignees: true
@@ -31,6 +31,9 @@ markComment: |
 
   If this issue remains relevant, please comment here or remove the `stale` label; otherwise it will be marked as closed automatically
 
+closeComment: |
+  The stalebot didn't hear anything for a while, so it closed this. Please reopen if this is still an issue.
+
 # Comment to post when removing the stale label.
 # unmarkComment: >
 #   Your comment here.
@@ -40,8 +43,7 @@ markComment: |
 #   Your comment here.
 
 # Limit the number of actions per hour, from 1-30. Default is 30
-limitPerRun: 1  # start with a small number
-
+limitPerRun: 2 # start with a small number
 
 # Limit to only `issues` or `pulls`
 # only: issues

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -67,7 +67,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -30,95 +30,48 @@ jobs:
         with:
           keyword: "[skip-ci]"
 
-  test:
-    name: ${{ matrix.os }} ${{ matrix.env }}
-    runs-on: ${{ matrix.os }}
+  doctest:
+    name: Doctests
+    runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     defaults:
       run:
         shell: bash -l {0}
-    strategy:
-      fail-fast: false
-      matrix:
-        os: ["ubuntu-latest"]
-        env:
-          [
-            # Minimum python version:
-            "py38-bare-minimum",
-            "py38-min-all-deps",
 
-            # Latest python version:
-            "py39-all-but-dask",
-            "py39-flaky",
-          ]
     steps:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
-
-      - name: Set environment variables
-        run: |
-          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
-      - name: Cache conda
-        uses: actions/cache@v2
-        with:
-          path: ~/conda_pkgs_dir
-          key:
-            ${{ runner.os }}-conda-${{ matrix.env }}-${{
-            hashFiles('ci/requirements/**.yml') }}
-
       - 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
-          use-only-tar-bz2: true
+          python-version: "3.9"
 
       - name: Install conda dependencies
         run: |
-          mamba env update -f $CONDA_ENV_FILE
-
+          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: Import xarray
-        run: |
-          python -c "import xarray"
-      - name: Run tests
+      - name: Run doctests
         run: |
-          python -m pytest -n 4 \
-             --cov=xarray \
-             --cov-report=xml \
-             $PYTEST_EXTRA_FLAGS
+          python -m pytest --doctest-modules xarray --ignore xarray/tests
 
-      - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
-        with:
-          file: ./coverage.xml
-          flags: unittests,${{ matrix.env }}
-          env_vars: RUNNER_OS
-          name: codecov-umbrella
-          fail_ci_if_error: false
-  doctest:
-    name: Doctests
+  mypy:
+    name: Mypy
     runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    # temporarily skipping due to https://github.com/pydata/xarray/issues/6551
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
     defaults:
       run:
@@ -148,9 +101,13 @@ jobs:
           conda info -a
           conda list
           python xarray/util/print_versions.py
-      - name: Run doctests
+      - name: Install mypy
         run: |
-          python -m pytest --doctest-modules xarray --ignore xarray/tests
+          python -m pip install mypy
+
+      - name: Run mypy
+        run: |
+          python -m mypy --install-types --non-interactive
 
   min-version-policy:
     name: Minimum Version Policy
@@ -176,5 +133,5 @@ jobs:
       - name: minimum versions policy
         run: |
           mamba install -y pyyaml conda python-dateutil
-          python ci/min_deps_check.py ci/requirements/py38-bare-minimum.yml
-          python ci/min_deps_check.py ci/requirements/py38-min-all-deps.yml
+          python ci/min_deps_check.py ci/requirements/bare-minimum.yml
+          python ci/min_deps_check.py ci/requirements/min-all-deps.yml
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -30,7 +30,7 @@ jobs:
         with:
           keyword: "[skip-ci]"
   test:
-    name: ${{ matrix.os }} py${{ matrix.python-version }}
+    name: ${{ matrix.os }} py${{ matrix.python-version }} ${{ matrix.env }}
     runs-on: ${{ matrix.os }}
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
@@ -42,7 +42,23 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.10"]
+        env: [""]
+        include:
+          # Minimum python version:
+          - env: "bare-minimum"
+            python-version: "3.8"
+            os: ubuntu-latest
+          - env: "min-all-deps"
+            python-version: "3.8"
+            os: ubuntu-latest
+          # Latest python version:
+          - env: "all-but-dask"
+            python-version: "3.10"
+            os: ubuntu-latest
+          - env: "flaky"
+            python-version: "3.10"
+            os: ubuntu-latest
     steps:
       - uses: actions/checkout@v3
         with:
@@ -52,18 +68,27 @@ jobs:
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
             echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
+          elif [[ "${{ matrix.env }}" != "" ]] ;
+          then
+            if [[ "${{ matrix.env }}" == "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
 
       - name: Cache conda
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         with:
           path: ~/conda_pkgs_dir
-          key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{
-            hashFiles('ci/requirements/**.yml') }}
+          key: ${{ runner.os }}-conda-py${{ matrix.python-version }}-${{ hashFiles('ci/requirements/**.yml') }}-${{ matrix.env }}
+
       - uses: conda-incubator/setup-miniconda@v2
         with:
           channels: conda-forge
@@ -78,6 +103,13 @@ jobs:
         run: |
           mamba env update -f $CONDA_ENV_FILE
 
+      # 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: |
           python -m pip install --no-deps -e .
@@ -87,24 +119,27 @@ 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()
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v2.1.0
+        uses: codecov/codecov-action@v3.1.0
         with:
           file: ./coverage.xml
           flags: unittests
@@ -118,7 +153,7 @@ jobs:
     if: github.repository == 'pydata/xarray'
     steps:
       - name: Upload
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: Event File
           path: ${{ github.event_path }}