Merge branch 'main' into add_array_api_mean

pydata · Aug 18, 2024 · 19ad726 · 19ad726
2 parents 71d0e8c + da9e7ec
commit 19ad726
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Showing 256 changed files with 26,326 additions and 8,231 deletions.
diff --git a/.binder/environment.yml b/.binder/environment.yml
@@ -28,7 +28,6 @@ dependencies:
   - pip
   - pooch
   - pydap
-  - pynio
   - rasterio
   - scipy
   - seaborn

diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -5,3 +5,7 @@ updates:
     schedule:
       # Check for updates once a week
       interval: 'weekly'
+    groups:
+      actions:
+        patterns:
+          - "*"
diff --git a/.github/release.yml b/.github/release.yml
@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci
diff --git a/.github/workflows/benchmarks-last-release.yml b/.github/workflows/benchmarks-last-release.yml
@@ -72,7 +72,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -5,6 +5,9 @@ on:
     types: [opened, reopened, synchronize, labeled]
   workflow_dispatch:
 
+env:
+  PR_HEAD_LABEL: ${{ github.event.pull_request.head.label }}
+
 jobs:
   benchmark:
     if: ${{ contains( github.event.pull_request.labels.*.name, 'run-benchmark') && github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch' }}
@@ -28,8 +31,11 @@ jobs:
           environment-name: xarray-tests
           cache-environment: true
           cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}-benchmark"
+          # add "build" because of https://github.com/airspeed-velocity/asv/issues/1385
           create-args: >-
             asv
+            build
+            mamba
 
 
       - name: Run benchmarks
@@ -46,10 +52,7 @@ jobs:
           # ID this runner
           asv machine --yes
           echo "Baseline:  ${{ github.event.pull_request.base.sha }} (${{ github.event.pull_request.base.label }})"
-          echo "Contender: ${GITHUB_SHA} (${{ github.event.pull_request.head.label }})"
-          # Use mamba for env creation
-          # export CONDA_EXE=$(which mamba)
-          export CONDA_EXE=$(which conda)
+          echo "Contender: ${GITHUB_SHA} ($PR_HEAD_LABEL)"
           # Run benchmarks for current commit against base
           ASV_OPTIONS="--split --show-stderr --factor $ASV_FACTOR"
           asv continuous $ASV_OPTIONS ${{ github.event.pull_request.base.sha }} ${GITHUB_SHA} \
@@ -67,7 +70,7 @@ jobs:
           cp benchmarks/README_CI.md benchmarks.log .asv/results/
         working-directory: ${{ env.ASV_DIR }}
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         if: always()
         with:
           name: asv-benchmark-results-${{ runner.os }}

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  FORCE_COLOR: 3
+
 jobs:
   detect-ci-trigger:
     name: detect ci trigger
@@ -35,14 +38,13 @@ jobs:
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
+
     defaults:
       run:
         shell: bash -l {0}
-
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.11"
-
+      PYTHON_VERSION: "3.12"
     steps:
       - uses: actions/checkout@v4
         with:
@@ -76,11 +78,11 @@ jobs:
           # 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.
-
-          # ignores:
-          # 1. h5py: see https://github.com/pydata/xarray/issues/8537
-          python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror \
-              -W "ignore:h5py is running against HDF5 1.14.3:UserWarning"
+          #
+          # If dependencies emit warnings we can't do anything about, add ignores to
+          # `xarray/tests/__init__.py`.
+          # [MHS, 01/25/2024] Skip datatree_ documentation remove after #8572
+          python -m pytest --doctest-modules xarray --ignore xarray/tests --ignore xarray/datatree_ -Werror
 
   mypy:
     name: Mypy
@@ -121,14 +123,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.8" --force-reinstall
+          python -m pip install "mypy<1.9" --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -137,15 +139,15 @@ jobs:
           fail_ci_if_error: false
 
   mypy39:
-    name: Mypy 3.9
+    name: Mypy 3.10
     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"
+      PYTHON_VERSION: "3.10"
 
     steps:
       - uses: actions/checkout@v4
@@ -175,14 +177,14 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.8" --force-reinstall
+          python -m pip install "mypy<1.9" --force-reinstall
 
       - name: Run mypy
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy39
@@ -206,7 +208,7 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.10"
+      PYTHON_VERSION: "3.12"
 
     steps:
       - uses: actions/checkout@v4
@@ -243,7 +245,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright
@@ -252,7 +254,7 @@ jobs:
           fail_ci_if_error: false
 
   pyright39:
-    name: Pyright 3.9
+    name: Pyright 3.10
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: |
@@ -265,7 +267,7 @@ jobs:
         shell: bash -l {0}
     env:
       CONDA_ENV_FILE: ci/requirements/environment.yml
-      PYTHON_VERSION: "3.9"
+      PYTHON_VERSION: "3.10"
 
     steps:
       - uses: actions/checkout@v4
@@ -302,7 +304,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39
@@ -321,11 +323,6 @@ jobs:
       run:
         shell: bash -l {0}
 
-    strategy:
-      matrix:
-        environment-file: ["bare-minimum", "min-all-deps"]
-      fail-fast: false
-
     steps:
       - uses: actions/checkout@v4
         with:
@@ -336,11 +333,15 @@ jobs:
         with:
           environment-name: xarray-tests
           create-args: >-
-            python=3.11
+            python=3.12
             pyyaml
             conda
             python-dateutil
 
-      - name: minimum versions policy
+      - name: All-deps minimum versions policy
+        run: |
+          python ci/min_deps_check.py ci/requirements/min-all-deps.yml
+
+      - name: Bare minimum versions policy
         run: |
-          python ci/min_deps_check.py ci/requirements/${{ matrix.environment-file }}.yml
+          python ci/min_deps_check.py ci/requirements/bare-minimum.yml
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -12,6 +12,9 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
+env:
+  FORCE_COLOR: 3
+
 jobs:
   detect-ci-trigger:
     name: detect ci trigger
@@ -34,6 +37,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     needs: detect-ci-trigger
     if: needs.detect-ci-trigger.outputs.triggered == 'false'
+    env:
+      ZARR_V3_EXPERIMENTAL_API: 1
     defaults:
       run:
         shell: bash -l {0}
@@ -42,22 +47,23 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.9", "3.11"]
+        python-version: ["3.10", "3.12"]
         env: [""]
         include:
           # Minimum python version:
           - env: "bare-minimum"
-            python-version: "3.9"
+            python-version: "3.10"
             os: ubuntu-latest
           - env: "min-all-deps"
-            python-version: "3.9"
+            python-version: "3.10"
             os: ubuntu-latest
           # Latest python version:
           - env: "all-but-dask"
-            python-version: "3.10"
+            # Not 3.12 because of pint
+            python-version: "3.11"
             os: ubuntu-latest
           - env: "flaky"
-            python-version: "3.10"
+            python-version: "3.12"
             os: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
@@ -69,18 +75,31 @@ jobs:
 
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
-            echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
+            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
+              echo "CONDA_ENV_FILE=ci/requirements/environment-windows.yml" >> $GITHUB_ENV
+            else
+              echo "CONDA_ENV_FILE=ci/requirements/environment-windows-3.13.yml" >> $GITHUB_ENV
+            fi
           elif [[ "${{ 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
+              echo "PYTEST_ADDOPTS=-m 'flaky or network' --run-flaky --run-network-tests -W default" >> $GITHUB_ENV
             else
               echo "CONDA_ENV_FILE=ci/requirements/${{ matrix.env }}.yml" >> $GITHUB_ENV
             fi
+            if [[ "${{ matrix.env }}" == "min-all-deps" ]] ;
+            then
+              # Don't raise on warnings
+              echo "PYTEST_ADDOPTS=-W default" >> $GITHUB_ENV
+            fi
           else
-            echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
+            if [[ ${{ matrix.python-version }} != "3.13" ]]; then
+              echo "CONDA_ENV_FILE=ci/requirements/environment.yml" >> $GITHUB_ENV
+            else
+              echo "CONDA_ENV_FILE=ci/requirements/environment-3.13.yml" >> $GITHUB_ENV
+            fi
           fi
 
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
@@ -99,7 +118,7 @@ jobs:
       # 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'
+        if: ${{ matrix.os }} == 'ubuntu-latest' and ${{ matrix.python-version }} == '3.12'
         run: |
           python -m pip install pytest-github-actions-annotate-failures
 
@@ -117,23 +136,30 @@ jobs:
         run: |
           python -c "import xarray"
 
+      - name: Restore cached hypothesis directory
+        uses: actions/cache@v4
+        with:
+          path: .hypothesis/
+          key: cache-hypothesis
+          enableCrossOsArchive: true
+          save-always: true
+
       - name: Run tests
         run: python -m pytest -n 4
           --timeout 180
           --cov=xarray
           --cov-report=xml
           --junitxml=pytest.xml
-          $PYTEST_EXTRA_FLAGS
 
       - name: Upload test results
         if: always()
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: Test results for ${{ runner.os }}-${{ matrix.python-version }}
+          name: Test results for ${{ runner.os }}-${{ matrix.python-version }} ${{ matrix.env }}
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v3.1.4
+        uses: codecov/codecov-action@v4.5.0
         with:
           file: ./coverage.xml
           flags: unittests
@@ -147,7 +173,7 @@ jobs:
     if: github.repository == 'pydata/xarray'
     steps:
       - name: Upload
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
           name: Event File
           path: ${{ github.event_path }}
-Original file line number
+Diff line change
@@ Expand Up / @@ -28,7 +28,6 @@ dependencies: @@
       - pip
       - pooch
       - pydap
-      - pynio
       - rasterio
       - scipy
       - seaborn
@@ Expand Down @@