Merge branch 'main' into dask-docs

* main: (125 commits) http:// → https:// (pydata#9748) Discard useless `!s` conversion in f-string (pydata#9752) Apply ruff/flake8-simplify rule SIM401 (pydata#9749) Use micromamba 1.5.10 where conda is needed (pydata#9737) pin array-api-strict<=2.1 (pydata#9751) Reorganise ruff rules (pydata#9738) use new conda-forge package pydap-server (pydata#9741) Enforce ruff/flake8-pie rules (PIE) (pydata#9740) Enforce ruff/flake8-comprehensions rules (C4) (pydata#9724) Enforce ruff/Perflint rules (PERF) (pydata#9730) Apply ruff rule RUF007 (pydata#9739) chmod -x (pydata#9725) Aplpy ruff rules (RUF) (pydata#9731) Fix typos found by codespell (pydata#9721) support for additional scipy nd interpolants (pydata#9599) Apply ruff/flake8-simplify rules (SIM) (pydata#9727) Apply ruff/flake8-implicit-str-concat rules (ISC) (pydata#9722) Apply ruff/flake8-pie rules (PIE) (pydata#9726) Enforce ruff/pygrep-hooks rules (PGH) (pydata#9729) Move to micromamba 2 (pydata#9732) ...
scharlottej13 · Nov 9, 2024 · 67cc617 · 67cc617
2 parents a7c03e5 + 591d539
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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/ISSUE_TEMPLATE/bugreport.yml b/.github/ISSUE_TEMPLATE/bugreport.yml
@@ -37,7 +37,7 @@ body:
         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)
+        - [Craft Minimal Bug Reports](https://matthewrocklin.com/minimal-bug-reports)
 
       options:
         - label: Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.

diff --git a/.github/config.yml b/.github/config.yml
@@ -14,7 +14,7 @@ newIssueWelcomeComment: >
 newPRWelcomeComment: >
   Thank you for opening this pull request! It may take us a few days to respond here, so thank you for being patient.
 
-  If you have questions, some answers may be found in our [contributing guidelines](http://docs.xarray.dev/en/stable/contributing.html).
+  If you have questions, some answers may be found in our [contributing guidelines](https://docs.xarray.dev/en/stable/contributing.html).
 
 # Comment to be posted to on pull requests merged by a first time user
 firstPRMergeComment: >

diff --git a/.github/workflows/benchmarks-last-release.yml b/.github/workflows/benchmarks-last-release.yml
@@ -22,8 +22,9 @@ jobs:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           cache-environment: true

diff --git a/.github/workflows/benchmarks.yml b/.github/workflows/benchmarks.yml
@@ -25,8 +25,9 @@ jobs:
           fetch-depth: 0
 
       - name: Set up conda environment
-        uses: mamba-org/setup-micromamba@v1
+        uses: mamba-org/setup-micromamba@v2
         with:
+          micromamba-version: '1.5.10-0'
           environment-file: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           cache-environment: true
@@ -35,7 +36,7 @@ jobs:
           create-args: >-
             asv
             python-build
-            mamba
+            mamba<=1.5.10
 
 
       - name: Run benchmarks

diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
@@ -55,13 +55,12 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           create-args: >-
             python=${{env.PYTHON_VERSION}}
-            conda
           cache-environment: true
           cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
 
@@ -70,8 +69,6 @@ jobs:
           python -m pip install --no-deps -e .
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
       - name: Run doctests
         run: |
@@ -81,8 +78,7 @@ 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
@@ -93,7 +89,7 @@ jobs:
         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
@@ -104,33 +100,30 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           create-args: >-
             python=${{env.PYTHON_VERSION}}
-            conda
           cache-environment: true
           cache-environment-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" --force-reinstall
+          python -m pip install "mypy==1.13" --force-reinstall
 
       - name: Run mypy
         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
@@ -158,33 +151,30 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           create-args: >-
             python=${{env.PYTHON_VERSION}}
-            conda
           cache-environment: true
           cache-environment-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" --force-reinstall
+          python -m pip install "mypy==1.13" --force-reinstall
 
       - name: Run mypy
         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-min
@@ -217,22 +207,19 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           create-args: >-
             python=${{env.PYTHON_VERSION}}
-            conda
           cache-environment: true
           cache-environment-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 pyright
         run: |
@@ -243,7 +230,7 @@ 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
@@ -276,22 +263,19 @@ 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: ${{env.CONDA_ENV_FILE}}
           environment-name: xarray-tests
           create-args: >-
             python=${{env.PYTHON_VERSION}}
-            conda
           cache-environment: true
           cache-environment-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 pyright
         run: |
@@ -302,7 +286,7 @@ 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: pyright39
@@ -325,14 +309,17 @@ 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:
+          # run with micromamba 1.5.10 together with conda
+          # conda.api is not API compatible with libmambapy
+          micromamba-version: "1.5.10-0"
           environment-name: xarray-tests
           create-args: >-
             python=3.12
             pyyaml
-            conda
             python-dateutil
+            conda
 
       - name: All-deps minimum versions policy
         run: |

diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
@@ -58,6 +58,9 @@ jobs:
             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"
@@ -105,15 +108,14 @@ 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: ${{ env.CONDA_ENV_FILE }}
           environment-name: xarray-tests
           cache-environment: true
           cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{matrix.python-version}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
           create-args: >-
             python=${{matrix.python-version}}
-            conda
 
       # We only want to install this on one run, because otherwise we'll have
       # duplicate annotations.
@@ -128,8 +130,6 @@ jobs:
 
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
 
       - name: Import xarray
@@ -159,7 +159,7 @@ 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
@@ -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
@@ -76,8 +76,6 @@ jobs:
           python -m pip install --no-deps -e .
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
 
       # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache

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@v1.10.1
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         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@v1.10.1
+        uses: pypa/gh-action-pypi-publish@v1.11.0
         with:
           verbose: true