Merge remote-tracking branch 'upstream/main' into fix/dask_indexing

* upstream/main: (291 commits) Update error message when saving multiindex (pydata#7475) DOC: cross ref the groupby tutorial (pydata#7555) [pre-commit.ci] pre-commit autoupdate (pydata#7543) supress namespace_package deprecation warning (doctests) (pydata#7548) [skip-ci] Add PDF of Xarray logo (pydata#7530) Support complex arrays in xr.corr (pydata#7392) clarification for thresh arg of dataset.dropna() (pydata#7481) [pre-commit.ci] pre-commit autoupdate (pydata#7524) Require to explicitly defining optional dimensions such as hue and markersize (pydata#7277) Use plt.rc_context for default styles (pydata#7318) Update HOW_TO_RELEASE.md (pydata#7512) Update whats-new for dev (pydata#7511) Fix whats-new for 2023.02.0 (pydata#7506) Update apply_ufunc output_sizes error message (pydata#7509) Zarr: drop "source" and "original_shape" from encoding (pydata#7500) [pre-commit.ci] pre-commit autoupdate (pydata#7507) Whats-new for 2023.03.0 Add `inclusive` argument to `cftime_range` and `date_range` and deprecate `closed` argument (pydata#7373) Make text match code example (pydata#7499) Remove Dask single-threaded setting in tests (pydata#7489) ...
bzah · Feb 28, 2023 · 97fa188 · 97fa188
2 parents c93b297 + 4194920
commit 97fa188
Show file tree

Hide file tree

Showing 196 changed files with 22,474 additions and 9,285 deletions.
diff --git a/.coveragerc b/.coveragerc
diff --git a/.git_archival.txt b/.git_archival.txt
@@ -1 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
 ref-names: $Format:%D$
diff --git a/.github/labeler.yml b/.github/labeler.yml
@@ -0,0 +1,82 @@
+Automation:
+  - .github/*
+  - .github/**/*
+
+CI:
+  - ci/*
+  - ci/**/*
+
+dependencies:
+  - requirements.txt
+  - ci/requirements/*
+
+topic-arrays:
+  - xarray/core/duck_array_ops.py
+
+topic-backends:
+  - xarray/backends/*
+  - xarray/backends/**/*
+
+topic-cftime:
+  - xarray/coding/*time*
+
+topic-CF conventions:
+  - xarray/conventions.py
+
+topic-combine:
+  - xarray/core/combine.py
+
+topic-dask:
+  - xarray/core/dask*
+  - xarray/core/parallel.py
+
+topic-DataTree:
+  - xarray/core/datatree*
+
+# topic-documentation:
+#  - ['doc/*', '!doc/whats-new.rst']
+#  - doc/**/*
+
+topic-faq:
+  - doc/howdoi.rst
+
+topic-groupby:
+  - xarray/core/groupby.py
+
+topic-html-repr:
+  - xarray/core/formatting_html.py
+
+topic-hypothesis:
+  - xarray/properties/*
+  - xarray/testing/strategies/*
+
+topic-indexing:
+  - xarray/core/indexes.py
+  - xarray/core/indexing.py
+
+topic-performance:
+  - asv_bench/benchmarks/*
+  - asv_bench/benchmarks/**/*
+
+topic-plotting:
+  - xarray/plot/*
+  - xarray/plot/**/*
+
+topic-rolling:
+  - xarray/core/rolling.py
+  - xarray/core/rolling_exp.py
+
+topic-testing:
+  - conftest.py
+  - xarray/testing.py
+  - xarray/testing/*
+
+topic-typing:
+  - xarray/core/types.py
+
+topic-zarr:
+  - xarray/backends/zarr.py
+
+io:
+  - xarray/backends/*
+  - xarray/backends/**/*
diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -7,11 +7,12 @@ on:
 
 jobs:
   benchmark:
-    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
+    if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || contains( github.event.pull_request.labels.*.name, 'topic-performance') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
     name: Linux
     runs-on: ubuntu-20.04
     env:
       ASV_DIR: "./asv_bench"
+      CONDA_ENV_FILE: ci/requirements/environment.yml
 
     steps:
       # We need the full repo to avoid this issue
@@ -20,17 +21,16 @@ jobs:
         with:
           fetch-depth: 0
 
-      - name: Setup Miniconda
-        uses: conda-incubator/setup-miniconda@v2
+      - name: Set up conda environment
+        uses: mamba-org/provision-with-micromamba@v15
         with:
-          # installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-Linux-x86_64.sh
-          installer-url: https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}-benchmark"
+          extra-specs: |
+            asv
 
-      - name: Setup some dependencies
-        shell: bash -l {0}
-        run: |
-          pip install asv
-          sudo apt-get update -y
 
       - name: Run benchmarks
         shell: bash -l {0}

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 2
-      - uses: xarray-contrib/ci-trigger@v1.1
+      - uses: xarray-contrib/ci-trigger@v1
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
@@ -53,12 +53,13 @@ jobs:
           echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           extra-specs: |
             python=${{env.PYTHON_VERSION}}
+            conda
           cache-env: true
           cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
 
@@ -72,7 +73,10 @@ jobs:
           python xarray/util/print_versions.py
       - name: Run doctests
         run: |
-          python -m pytest --doctest-modules xarray --ignore xarray/tests
+          # Raise an error if there are warnings in the doctests, with `-Werror`.
+          # This is a trial; if it presents an problem, feel free to remove.
+          # See https://github.com/pydata/xarray/issues/7164 for more info.
+          python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
 
   mypy:
     name: Mypy
@@ -96,12 +100,67 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        uses: mamba-org/provision-with-micromamba@v15
+        with:
+          environment-file: ${{env.CONDA_ENV_FILE}}
+          environment-name: xarray-tests
+          extra-specs: |
+            python=${{env.PYTHON_VERSION}}
+            conda
+          cache-env: true
+          cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+          python xarray/util/print_versions.py
+      - name: Install mypy
+        run: |
+          python -m pip install 'mypy<0.990'
+
+      - name: Run mypy
+        run: |
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+
+      - name: Upload mypy coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: mypy_report/cobertura.xml
+          flags: mypy
+          env_vars: PYTHON_VERSION
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+  mypy39:
+    name: Mypy 3.9
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+      PYTHON_VERSION: "3.9"
+
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+      - name: Setup micromamba
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           extra-specs: |
             python=${{env.PYTHON_VERSION}}
+            conda
           cache-env: true
           cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
       - name: Install xarray
@@ -114,11 +173,22 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install mypy
+          python -m pip install 'mypy<0.990'
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+
+      - name: Upload mypy coverage to Codecov
+        uses: codecov/[email protected]
+        with:
+          file: mypy_report/cobertura.xml
+          flags: mypy39
+          env_vars: PYTHON_VERSION
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+
 
   min-version-policy:
     name: Minimum Version Policy
@@ -140,7 +210,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-name: xarray-tests
           environment-file: false

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -25,7 +25,7 @@ jobs:
       - uses: actions/checkout@v3
         with:
           fetch-depth: 2
-      - uses: xarray-contrib/ci-trigger@v1.1
+      - uses: xarray-contrib/ci-trigger@v1
         id: detect-trigger
         with:
           keyword: "[skip-ci]"
@@ -42,15 +42,15 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.8", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         env: [""]
         include:
           # Minimum python version:
           - env: "bare-minimum"
-            python-version: "3.8"
+            python-version: "3.9"
             os: ubuntu-latest
           - env: "min-all-deps"
-            python-version: "3.8"
+            python-version: "3.9"
             os: ubuntu-latest
           # Latest python version:
           - env: "all-but-dask"
@@ -67,7 +67,13 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
 
-          if [[ ${{ matrix.os }} == windows* ]] ;
+          if [[ "${{matrix.python-version}}" == "3.11" ]]; then
+            if [[ ${{matrix.os}} == windows* ]]; then
+              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-py311.yml" >> $GITHUB_ENV
+            else
+              echo "CONDA_ENV_FILE=ci/requirements/environment-py311.yml" >> $GITHUB_ENV
+            fi
+          elif [[ ${{ matrix.os }} == windows* ]] ;
           then
             echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
           elif [[ "${{ matrix.env }}" != "" ]] ;
@@ -86,12 +92,15 @@ jobs:
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/provision-with-micromamba@de032af7fb3675649f3d4bbdda85178ba412ee41
+        uses: mamba-org/provision-with-micromamba@v15
         with:
           environment-file: ${{ env.CONDA_ENV_FILE }}
           environment-name: xarray-tests
           cache-env: true
           cache-env-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+          extra-specs: |
+            python=${{matrix.python-version}}
+            conda
 
       # We only want to install this on one run, because otherwise we'll have
       # duplicate annotations.
@@ -129,7 +138,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/label-all.yml b/.github/workflows/label-all.yml
@@ -0,0 +1,14 @@
+name: "Issue and PR Labeler"
+on:
+  pull_request:
+    types: [opened]
+  issues:
+    types: [opened, reopened]
+jobs:
+  label-all-on-open:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: andymckay/[email protected]
+        with:
+          add-labels: "needs triage"
+          ignore-if-labeled: false
diff --git a/.github/workflows/label-prs.yml b/.github/workflows/label-prs.yml
@@ -0,0 +1,14 @@
+name: "PR Labeler"
+on:
+- pull_request_target
+
+jobs:
+  label:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/labeler@main
+      with:
+        repo-token: "${{ secrets.GITHUB_TOKEN }}"
+        # Workaround for sync-labels bug:
+        # https://github.com/actions/labeler/issues/112
+        sync-labels: ""
diff --git a/.github/workflows/publish-test-results.yaml b/.github/workflows/publish-test-results.yaml
@@ -35,7 +35,7 @@ jobs:
           done
 
       - name: Publish Unit Test Results
-        uses: EnricoMi/publish-unit-test-result-action@v1
+        uses: EnricoMi/publish-unit-test-result-action@v2
         with:
           commit: ${{ github.event.workflow_run.head_sha }}
           event_file: artifacts/Event File/event.json