Merge branch 'main' into plot1d_lines

.github/workflows/ci-additional.yaml

@@ -35,14 +35,13 @@ 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"
-
     steps:
       - uses: actions/checkout@v4
         with:
@@ -128,7 +127,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: mypy_report/cobertura.xml
           flags: mypy
@@ -182,7 +181,7 @@ jobs:
           python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
-        uses: codecov/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: mypy_report/cobertura.xml
           flags: mypy39
@@ -243,7 +242,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: pyright_report/cobertura.xml
           flags: pyright
@@ -302,7 +301,7 @@ jobs:
           python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
-        uses: codecov/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: pyright_report/cobertura.xml
           flags: pyright39

.github/workflows/ci.yaml

@@ -127,6 +127,14 @@ 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
@@ -143,7 +151,7 @@ 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

.github/workflows/hypothesis.yaml

@@ -0,0 +1,116 @@
+name: Slow Hypothesis CI
+on:
+  push:
+    branches:
+      - "main"
+  pull_request:
+    branches:
+      - "main"
+    types: [opened, reopened, synchronize, labeled]
+  schedule:
+    - cron: "0 0 * * *" # Daily “At 00:00” UTC
+  workflow_dispatch: # allows you to trigger manually
+
+jobs:
+  detect-ci-trigger:
+    name: detect ci trigger
+    runs-on: ubuntu-latest
+    if: |
+      github.repository == 'pydata/xarray'
+      && (github.event_name == 'push' || github.event_name == 'pull_request')
+    outputs:
+      triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: xarray-contrib/ci-trigger@v1
+        id: detect-trigger
+        with:
+          keyword: "[skip-ci]"
+
+  hypothesis:
+    name: Slow Hypothesis Tests
+    runs-on: "ubuntu-latest"
+    needs: detect-ci-trigger
+    if: |
+        always()
+        && (
+            (github.event_name == 'schedule' || github.event_name == 'workflow_dispatch')
+            || needs.detect-ci-trigger.outputs.triggered == 'true'
+            || contains( github.event.pull_request.labels.*.name, 'run-slow-hypothesis')
+        )
+    defaults:
+      run:
+        shell: bash -l {0}
+
+    env:
+      CONDA_ENV_FILE: ci/requirements/environment.yml
+      PYTHON_VERSION: "3.12"
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0 # Fetch all history for all branches and tags.
+
+      - name: set environment variables
+        run: |
+          echo "TODAY=$(date  +'%Y-%m-%d')" >> $GITHUB_ENV
+
+      - name: Setup micromamba
+        uses: mamba-org/setup-micromamba@v1
+        with:
+          environment-file: ci/requirements/environment.yml
+          environment-name: xarray-tests
+          create-args: >-
+            python=${{env.PYTHON_VERSION}}
+            pytest-reportlog
+          cache-environment: true
+          cache-environment-key: "${{runner.os}}-${{runner.arch}}-py${{env.PYTHON_VERSION}}-${{env.TODAY}}-${{hashFiles(env.CONDA_ENV_FILE)}}"
+
+      - name: Install xarray
+        run: |
+          python -m pip install --no-deps -e .
+      - name: Version info
+        run: |
+          conda info -a
+          conda list
+          python xarray/util/print_versions.py
+
+      # https://github.com/actions/cache/blob/main/tips-and-workarounds.md#update-a-cache
+      - name: Restore cached hypothesis directory
+        id: restore-hypothesis-cache
+        uses: actions/cache/restore@v4
+        with:
+          path: .hypothesis/
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
+          restore-keys: |
+            cache-hypothesis-
+
+      - name: Run slow Hypothesis tests
+        if: success()
+        id: status
+        run: |
+           python -m pytest --hypothesis-show-statistics --run-slow-hypothesis properties/*.py \
+             --report-log output-${{ matrix.python-version }}-log.jsonl
+
+      # explicitly save the cache so it gets updated, also do this even if it fails.
+      - name: Save cached hypothesis directory
+        id: save-hypothesis-cache
+        if: always() && steps.status.outcome != 'skipped'
+        uses: actions/cache/save@v4
+        with:
+          path: .hypothesis/
+          key: cache-hypothesis-${{ runner.os }}-${{ github.run_id }}
+
+      - name: Generate and publish the report
+        if: |
+          failure()
+          && steps.status.outcome == 'failure'
+          && github.event_name == 'schedule'
+          && github.repository_owner == 'pydata'
+        uses: xarray-contrib/issue-from-pytest-log@v1
+        with:
+          log-path: output-${{ matrix.python-version }}-log.jsonl
+          issue-title: "Nightly Hypothesis tests failed"
+          issue-label: "topic-hypothesis"

.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/[email protected].0
+        uses: codecov/[email protected].1
         with:
           file: mypy_report/cobertura.xml
           flags: mypy

.pre-commit-config.yaml

@@ -13,24 +13,24 @@ repos:
       - id: mixed-line-ending
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.2.0'
+    rev: 'v0.3.4'
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
   # https://github.com/python/black#version-control-integration
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.1.1
+    rev: 24.3.0
     hooks:
       - id: black-jupyter
   - repo: https://github.com/keewis/blackdoc
     rev: v0.3.9
     hooks:
       - id: blackdoc
         exclude: "generate_aggregations.py"
-        additional_dependencies: ["black==24.1.1"]
+        additional_dependencies: ["black==24.3.0"]
       - id: blackdoc-autoupdate-black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.8.0
+    rev: v1.9.0
     hooks:
       - id: mypy
         # Copied from setup.cfg

doc/user-guide/indexing.rst

@@ -748,7 +748,7 @@ Whether array indexing returns a view or a copy of the underlying
 data depends on the nature of the labels.
 
 For positional (integer)
-indexing, xarray follows the same rules as NumPy:
+indexing, xarray follows the same `rules`_ as NumPy:
 
 * Positional indexing with only integers and slices returns a view.
 * Positional indexing with arrays or lists returns a copy.
@@ -765,8 +765,10 @@ Whether data is a copy or a view is more predictable in xarray than in pandas, s
 unlike pandas, xarray does not produce `SettingWithCopy warnings`_. However, you
 should still avoid assignment with chained indexing.
 
-.. _SettingWithCopy warnings: https://pandas.pydata.org/pandas-docs/stable/indexing.html#returning-a-view-versus-a-copy
+Note that other operations (such as :py:meth:`~xarray.DataArray.values`) may also return views rather than copies.
 
+.. _SettingWithCopy warnings: https://pandas.pydata.org/pandas-docs/stable/indexing.html#returning-a-view-versus-a-copy
+.. _rules: https://numpy.org/doc/stable/user/basics.copies.html
 
 .. _multi-level indexing:
 

doc/whats-new.rst

@@ -15,32 +15,65 @@ What's New
     np.random.seed(123456)
 
 
-.. _whats-new.2024.03.0:
+.. _whats-new.2024.04.0:
 
-v2024.03.0 (unreleased)
+v2024.04.0 (unreleased)
 -----------------------
 
 New Features
 ~~~~~~~~~~~~
 
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+
+Bug fixes
+~~~~~~~~~
+
+
+Internal Changes
+~~~~~~~~~~~~~~~~
+
+
+.. _whats-new.2024.03.0:
+
+v2024.03.0 (Mar 29, 2024)
+-------------------------
+
+This release brings performance improvements for grouped and resampled quantile calculations, CF decoding improvements,
+minor optimizations to distributed Zarr writes, and compatibility fixes for Numpy 2.0 and Pandas 3.0.
+
+Thanks to the 18 contributors to this release:
+Anderson Banihirwe, Christoph Hasse, Deepak Cherian, Etienne Schalk, Justus Magin, Kai Mühlbauer, Kevin Schwarzwald, Mark Harfouche, Martin, Matt Savoie, Maximilian Roos, Ray Bell, Roberto Chang, Spencer Clark, Tom Nicholas, crusaderky, owenlittlejohns, saschahofmann
+
+New Features
+~~~~~~~~~~~~
+- Partial writes to existing chunks with ``region`` or ``append_dim`` will now raise an error
+  (unless ``safe_chunks=False``); previously an error would only be raised on
+  new variables. (:pull:`8459`, :issue:`8371`, :issue:`8882`)
+  By `Maximilian Roos <https://github.com/max-sixty>`_.
+- Grouped and resampling quantile calculations now use the vectorized algorithm in ``flox>=0.9.4`` if present.
+  By `Deepak Cherian <https://github.com/dcherian>`_.
 - Do not broadcast in arithmetic operations when global option ``arithmetic_broadcast=False``
   (:issue:`6806`, :pull:`8784`).
   By `Etienne Schalk <https://github.com/etienneschalk>`_ and `Deepak Cherian <https://github.com/dcherian>`_.
 - Add the ``.oindex`` property to Explicitly Indexed Arrays for orthogonal indexing functionality. (:issue:`8238`, :pull:`8750`)
   By `Anderson Banihirwe <https://github.com/andersy005>`_.
-
 - Add the ``.vindex`` property to Explicitly Indexed Arrays for vectorized indexing functionality. (:issue:`8238`, :pull:`8780`)
   By `Anderson Banihirwe <https://github.com/andersy005>`_.
-
 - Expand use of ``.oindex`` and ``.vindex`` properties. (:pull: `8790`)
   By `Anderson Banihirwe <https://github.com/andersy005>`_ and `Deepak Cherian <https://github.com/dcherian>`_.
+- Allow creating :py:class:`xr.Coordinates` objects with no indexes (:pull:`8711`)
+  By `Benoit Bovy <https://github.com/benbovy>`_ and `Tom Nicholas
+  <https://github.com/TomNicholas>`_.
+- Enable plotting of ``datetime.dates``. (:issue:`8866`, :pull:`8873`)
+  By `Sascha Hofmann <https://github.com/saschahofmann>`_.
 
 Breaking changes
 ~~~~~~~~~~~~~~~~
-
-
-Deprecations
-~~~~~~~~~~~~
+- Don't allow overwriting index variables with ``to_zarr`` region writes. (:issue:`8589`, :pull:`8876`).
+  By `Deepak Cherian <https://github.com/dcherian>`_.
 
 
 Bug fixes
@@ -57,21 +90,29 @@ Bug fixes
   `CFMaskCoder`/`CFScaleOffsetCoder` (:issue:`2304`, :issue:`5597`,
   :issue:`7691`, :pull:`8713`, see also discussion in :pull:`7654`).
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
-- do not cast `_FillValue`/`missing_value` in `CFMaskCoder` if `_Unsigned` is provided
+- Do not cast `_FillValue`/`missing_value` in `CFMaskCoder` if `_Unsigned` is provided
   (:issue:`8844`, :pull:`8852`).
-- Adapt handling of copy keyword argument in scipy backend for numpy >= 2.0dev
-  (:issue:`8844`, :pull:`8851`).
+- Adapt handling of copy keyword argument for numpy >= 2.0dev
+  (:issue:`8844`, :pull:`8851`, :pull:`8865`).
   By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
-
-Documentation
-~~~~~~~~~~~~~
-
+- Import trapz/trapezoid depending on numpy version
+  (:issue:`8844`, :pull:`8865`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Warn and return bytes undecoded in case of UnicodeDecodeError in h5netcdf-backend
+  (:issue:`5563`, :pull:`8874`).
+  By `Kai Mühlbauer <https://github.com/kmuehlbauer>`_.
+- Fix bug incorrectly disallowing creation of a dataset with a multidimensional coordinate variable with the same name as one of its dims.
+  (:issue:`8884`, :pull:`8886`)
+  By `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 Internal Changes
 ~~~~~~~~~~~~~~~~
 - Migrates ``treenode`` functionality into ``xarray/core`` (:pull:`8757`)
   By `Matt Savoie <https://github.com/flamingbear>`_ and `Tom Nicholas
   <https://github.com/TomNicholas>`_.
+- Migrates ``datatree`` functionality into ``xarray/core``. (:pull: `8789`)
+  By `Owen Littlejohns <https://github.com/owenlittlejohns>`_, `Matt Savoie
+  <https://github.com/flamingbear>`_ and `Tom Nicholas <https://github.com/TomNicholas>`_.
 
 
 .. _whats-new.2024.02.0:

properties/conftest.py

@@ -1,3 +1,24 @@
+import pytest
+
+
+def pytest_addoption(parser):
+    parser.addoption(
+        "--run-slow-hypothesis",
+        action="store_true",
+        default=False,
+        help="run slow hypothesis tests",
+    )
+
+
+def pytest_collection_modifyitems(config, items):
+    if config.getoption("--run-slow-hypothesis"):
+        return
+    skip_slow_hyp = pytest.mark.skip(reason="need --run-slow-hypothesis option to run")
+    for item in items:
+        if "slow_hypothesis" in item.keywords:
+            item.add_marker(skip_slow_hyp)
+
+
 try:
     from hypothesis import settings
 except ImportError: