Merge branch 'main' into dtree-tests

pydata · Oct 17, 2024 · dbf1791 · dbf1791
2 parents 716871a + b9780e7
commit dbf1791
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diff --git a/.github/FUNDING.yml b/.github/FUNDING.yml
@@ -1,2 +1,2 @@
 github: numfocus
-custom: http://numfocus.org/donate-to-xarray
+custom: https://numfocus.org/donate-to-xarray
diff --git a/.github/workflows/benchmarks-last-release.yml b/.github/workflows/benchmarks-last-release.yml
@@ -22,7 +22,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests

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' }}
@@ -22,7 +25,7 @@ jobs:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -31,7 +34,7 @@ jobs:
           # add "build" because of https://github.com/airspeed-velocity/asv/issues/1385
           create-args: >-
             asv
-            build
+            python-build
             mamba
 
 
@@ -49,7 +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 }})"
+          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} \

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -55,7 +55,7 @@ jobs:
           echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -81,8 +81,7 @@ jobs:
           #
           # 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
+          python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
 
   mypy:
     name: Mypy
@@ -104,7 +103,7 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -123,31 +122,31 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.9" --force-reinstall
+          python -m pip install "mypy==1.11.2" --force-reinstall
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         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
+  mypy-min:
+    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
@@ -158,7 +157,7 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -177,32 +176,30 @@ jobs:
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |
-          python -m pip install "mypy<1.9" --force-reinstall
+          python -m pip install "mypy==1.11.2" --force-reinstall
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           file: mypy_report/cobertura.xml
-          flags: mypy39
+          flags: mypy-min
           env_vars: PYTHON_VERSION
           name: codecov-umbrella
           fail_ci_if_error: false
 
-
-
   pyright:
     name: Pyright
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: |
-        always()
-        && (
-            contains( github.event.pull_request.labels.*.name, 'run-pyright')
-        )
+      always()
+      && (
+          contains( github.event.pull_request.labels.*.name, 'run-pyright')
+      )
     defaults:
       run:
         shell: bash -l {0}
@@ -219,7 +216,7 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -245,7 +242,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright
@@ -254,20 +251,20 @@ jobs:
           fail_ci_if_error: false
 
   pyright39:
-    name: Pyright 3.9
+    name: Pyright 3.10
     runs-on: "ubuntu-latest"
     needs: detect-ci-trigger
     if: |
-        always()
-        && (
-            contains( github.event.pull_request.labels.*.name, 'run-pyright')
-        )
+      always()
+      && (
+          contains( github.event.pull_request.labels.*.name, 'run-pyright')
+      )
     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
@@ -278,7 +275,7 @@ jobs:
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
@@ -304,16 +301,14 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39
           env_vars: PYTHON_VERSION
           name: codecov-umbrella
           fail_ci_if_error: false
 
-
-
   min-version-policy:
     name: Minimum Version Policy
     runs-on: "ubuntu-latest"
@@ -329,7 +324,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-name: xarray-tests
           create-args: >-

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -47,17 +47,20 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.9",  "3.12"]
+        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-numba"
+            python-version: "3.12"
+            os: ubuntu-latest
           - env: "all-but-dask"
             # Not 3.12 because of pint
             python-version: "3.11"
@@ -105,7 +108,7 @@ jobs:
           echo "PYTHON_VERSION=${{ matrix.python-version }}" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ${{ env.CONDA_ENV_FILE }}
           environment-name: xarray-tests
@@ -159,7 +162,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           file: ./coverage.xml
           flags: unittests

diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml
@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
     if: |
       github.repository == 'pydata/xarray'
-      && (github.event_name == 'push' || github.event_name == 'pull_request')
+      && (github.event_name == 'push' || github.event_name == 'pull_request' || github.event_name == 'schedule')
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
@@ -61,7 +61,7 @@ jobs:
           echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
 
       - name: Setup micromamba
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ci/requirements/environment.yml
           environment-name: xarray-tests

diff --git a/.github/workflows/nightly-wheels.yml b/.github/workflows/nightly-wheels.yml
@@ -13,7 +13,7 @@ jobs:
           fetch-depth: 0
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -38,7 +38,7 @@ jobs:
           fi
 
       - name: Upload wheel
-        uses: scientific-python/upload-nightly-action@b67d7fcc0396e1128a474d1ab2b48aa94680f9fc # 0.5.0
+        uses: scientific-python/upload-nightly-action@82396a2ed4269ba06c6b2988bb4fd568ef3c3d6b # 0.6.1
         with:
           anaconda_nightly_upload_token: ${{ secrets.ANACONDA_NIGHTLY }}
           artifacts_path: dist
diff --git a/.github/workflows/pypi-release.yaml b/.github/workflows/pypi-release.yaml
@@ -88,7 +88,7 @@ jobs:
           path: dist
       - name: Publish package to TestPyPI
         if: github.event_name == 'push'
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.3
         with:
           repository_url: https://test.pypi.org/legacy/
           verbose: true
@@ -111,6 +111,6 @@ jobs:
           name: releases
           path: dist
       - name: Publish package to PyPI
-        uses: pypa/gh-action-pypi-publish@v1.9.0
+        uses: pypa/gh-action-pypi-publish@v1.10.3
         with:
           verbose: true
diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
@@ -61,7 +61,7 @@ jobs:
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ci/requirements/environment.yml
           environment-name: xarray-tests
@@ -120,7 +120,7 @@ jobs:
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
           environment-file: ci/requirements/environment.yml
           environment-name: xarray-tests
@@ -146,7 +146,7 @@ jobs:
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.5.0
+        uses: codecov/codecov-action@v4.6.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy