Merge branch 'main' into backend-indexing

Author: andersy005

.binder/environment.yml

@@ -28,7 +28,6 @@ dependencies:
   - pip
   - pooch
   - pydap
-  - pynio
   - rasterio
   - scipy
   - seaborn

.github/workflows/ci-additional.yaml

@@ -43,7 +43,7 @@ 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
         with:
@@ -129,7 +129,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -183,7 +183,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy39
@@ -207,7 +207,7 @@ 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
@@ -244,7 +244,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright
@@ -303,7 +303,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39
@@ -332,7 +332,7 @@ jobs:
         with:
           environment-name: xarray-tests
           create-args: >-
-            python=3.11
+            python=3.12
             pyyaml
             conda
             python-dateutil

.github/workflows/ci.yaml

@@ -46,7 +46,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.9", "3.11", "3.12"]
+        python-version: ["3.9",  "3.12"]
         env: [""]
         include:
           # Minimum python version:
@@ -58,10 +58,11 @@ jobs:
             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
@@ -73,25 +74,30 @@ jobs:
 
           if [[ ${{ matrix.os }} == windows* ]] ;
           then
-            if [[ ${{ matrix.python-version }} != "3.12" ]]; then
+            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-3.12.yml" >> $GITHUB_ENV
+              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
-            if [[ ${{ matrix.python-version }} != "3.12" ]]; then
+            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-3.12.yml" >> $GITHUB_ENV
+              echo "CONDA_ENV_FILE=ci/requirements/environment-3.13.yml" >> $GITHUB_ENV
             fi
           fi
 
@@ -111,7 +117,7 @@ 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
 
@@ -143,7 +149,6 @@ jobs:
           --cov=xarray
           --cov-report=xml
           --junitxml=pytest.xml
-          $PYTEST_EXTRA_FLAGS
 
       - name: Upload test results
         if: always()
@@ -153,7 +158,7 @@ jobs:
           path: pytest.xml
 
       - name: Upload code coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: ./coverage.xml
           flags: unittests

.github/workflows/pypi-release.yaml

@@ -18,7 +18,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
 
       - name: Install dependencies
         run: |
@@ -53,7 +53,7 @@ jobs:
       - uses: actions/setup-python@v5
         name: Install Python
         with:
-          python-version: "3.11"
+          python-version: "3.12"
       - uses: actions/download-artifact@v4
         with:
           name: releases

.github/workflows/upstream-dev-ci.yaml

@@ -143,7 +143,7 @@ jobs:
         run: |
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
-        uses: codecov/codecov-action@v4.2.0
+        uses: codecov/codecov-action@v4.3.0
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

MANIFEST.in

@@ -1 +1,2 @@
 prune xarray/datatree_*
+recursive-include xarray/datatree_/datatree *.py

ci/install-upstream-wheels.sh

@@ -1,13 +1,13 @@
 #!/usr/bin/env bash
 
 # install cython for building cftime without build isolation
-micromamba install "cython>=0.29.20" py-cpuinfo
+micromamba install "cython>=0.29.20" py-cpuinfo setuptools-scm
 # temporarily (?) remove numbagg and numba
 micromamba remove -y numba numbagg sparse
 # temporarily remove numexpr
 micromamba remove -y numexpr
 # temporarily remove backends
-micromamba remove -y cf_units hdf5 h5py netcdf4
+micromamba remove -y cf_units hdf5 h5py netcdf4 pydap
 # forcibly remove packages to avoid artifacts
 micromamba remove -y --force \
     numpy \
@@ -31,7 +31,8 @@ python -m pip install \
     numpy \
     scipy \
     matplotlib \
-    pandas
+    pandas \
+    h5py
 # for some reason pandas depends on pyarrow already.
 # Remove once a `pyarrow` version compiled with `numpy>=2.0` is on `conda-forge`
 python -m pip install \
@@ -70,6 +71,6 @@ python -m pip install \
     git+https://github.com/intake/filesystem_spec \
     git+https://github.com/SciTools/nc-time-axis \
     git+https://github.com/xarray-contrib/flox \
+    git+https://github.com/h5netcdf/h5netcdf \
     git+https://github.com/dgasmith/opt_einsum
     # git+https://github.com/pydata/sparse
-    # git+https://github.com/h5netcdf/h5netcdf

ci/requirements/bare-minimum.yml

@@ -12,5 +12,5 @@ dependencies:
   - pytest-xdist
   - pytest-timeout
   - numpy=1.23
-  - packaging=22.0
-  - pandas=1.5
+  - packaging=23.1
+  - pandas=2.0

ci/requirements/doc.yml

@@ -38,9 +38,9 @@ dependencies:
   - sphinx-design
   - sphinx-inline-tabs
   - sphinx>=5.0
+  - sphinxext-opengraph
+  - sphinxext-rediraffe
   - zarr>=2.10
   - pip:
-      - sphinxext-rediraffe
-      - sphinxext-opengraph
       # relative to this file. Needs to be editable to be accepted.
       - -e ../..