Merge branch 'main' into kvikio-2

.codecov.yml

@@ -1,16 +1,38 @@
 codecov:
-  ci:
-    # by default, codecov doesn't recognize azure as a CI provider
-    - dev.azure.com
-  require_ci_to_pass: yes
+  require_ci_to_pass: true
 
 coverage:
   status:
     project:
       default:
         # Require 1% coverage, i.e., always succeed
-        target: 1
+        target: 1%
+        flags:
+          - unittests
+        paths:
+         - "!xarray/tests/"
+      unittests:
+        target: 90%
+        flags:
+          - unittests
+        paths:
+          - "!xarray/tests/"
+      mypy:
+        target: 20%
+        flags:
+          - mypy
     patch: false
     changes: false
 
-comment: off
+comment: false
+
+flags:
+  unittests:
+    paths:
+      - "xarray"
+      - "!xarray/tests"
+    carryforward: false
+  mypy:
+    paths:
+      - "xarray"
+    carryforward: false

.github/workflows/benchmarks-last-release.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/benchmarks.yml

@@ -17,7 +17,7 @@ jobs:
     steps:
       # We need the full repo to avoid this issue
       # https://github.com/actions/checkout/issues/23
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
 

.github/workflows/ci-additional.yaml

@@ -22,7 +22,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1
@@ -44,7 +44,7 @@ jobs:
       PYTHON_VERSION: "3.10"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
@@ -92,7 +92,7 @@ jobs:
       PYTHON_VERSION: "3.10"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
@@ -123,7 +123,7 @@ jobs:
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/[email protected]
@@ -146,7 +146,7 @@ jobs:
       PYTHON_VERSION: "3.9"
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 
@@ -177,7 +177,7 @@ jobs:
 
       - name: Run mypy
         run: |
-          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report xarray/
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/[email protected]
@@ -205,7 +205,7 @@ jobs:
       fail-fast: false
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
 

.github/workflows/ci.yaml

@@ -22,7 +22,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1
@@ -42,7 +42,7 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        python-version: ["3.9", "3.10", "3.11"]
+        python-version: ["3.9", "3.11"]
         env: [""]
         include:
           # Minimum python version:
@@ -60,7 +60,7 @@ jobs:
             python-version: "3.10"
             os: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set environment variables

.github/workflows/nightly-wheels.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'pydata/xarray'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v4

.github/workflows/pypi-release.yaml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.repository == 'pydata/xarray'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0
       - uses: actions/setup-python@v4

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

@@ -25,7 +25,7 @@ jobs:
     outputs:
       triggered: ${{ steps.detect-trigger.outputs.trigger-found }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
       - uses: xarray-contrib/ci-trigger@v1
@@ -52,7 +52,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment
@@ -112,7 +112,7 @@ jobs:
       matrix:
         python-version: ["3.10"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Set up conda environment

.pre-commit-config.yaml

@@ -18,7 +18,7 @@ repos:
         files: ^xarray/
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: 'v0.0.282'
+    rev: 'v0.0.287'
     hooks:
       - id: ruff
         args: ["--fix"]
@@ -35,7 +35,7 @@ repos:
         additional_dependencies: ["black==23.7.0"]
       - id: blackdoc-autoupdate-black
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.4.1
+    rev: v1.5.1
     hooks:
       - id: mypy
         # Copied from setup.cfg

README.md

@@ -1,7 +1,7 @@
 # xarray: N-D labeled arrays and datasets
 
 [![CI](https://github.com/pydata/xarray/workflows/CI/badge.svg?branch=main)](https://github.com/pydata/xarray/actions?query=workflow%3ACI)
-[![Code coverage](https://codecov.io/gh/pydata/xarray/branch/main/graph/badge.svg)](https://codecov.io/gh/pydata/xarray)
+[![Code coverage](https://codecov.io/gh/pydata/xarray/branch/main/graph/badge.svg?flag=unittests)](https://codecov.io/gh/pydata/xarray)
 [![Docs](https://readthedocs.org/projects/xray/badge/?version=latest)](https://docs.xarray.dev/)
 [![Benchmarked with asv](https://img.shields.io/badge/benchmarked%20by-asv-green.svg?style=flat)](https://pandas.pydata.org/speed/xarray/)
 [![Available on pypi](https://img.shields.io/pypi/v/xarray.svg)](https://pypi.python.org/pypi/xarray/)

asv_bench/benchmarks/dataset_io.py

@@ -527,7 +527,7 @@ def time_read_dataset(self, engine, chunks):
 class IOReadCustomEngine:
     def setup(self, *args, **kwargs):
         """
-        The custom backend does the bare mininum to be considered a lazy backend. But
+        The custom backend does the bare minimum to be considered a lazy backend. But
         the data in it is still in memory so slow file reading shouldn't affect the
         results.
         """

asv_bench/benchmarks/merge.py

@@ -41,7 +41,7 @@ def setup(self, strategy, count):
         data = np.array(["0", "b"], dtype=str)
         self.dataset_coords = dict(time=np.array([0, 1]))
         self.dataset_attrs = dict(description="Test data")
-        attrs = dict(units="Celcius")
+        attrs = dict(units="Celsius")
         if strategy == "dict_of_DataArrays":
 
             def create_data_vars():

asv_bench/benchmarks/pandas.py

@@ -13,7 +13,7 @@ def setup(self, dtype, subset):
             [
                 list("abcdefhijk"),
                 list("abcdefhijk"),
-                pd.date_range(start="2000-01-01", periods=1000, freq="B"),
+                pd.date_range(start="2000-01-01", periods=1000, freq="D"),
             ]
         )
         series = pd.Series(data, index)

ci/requirements/doc.yml

@@ -21,7 +21,7 @@ dependencies:
   - numba
   - numpy>=1.21
   - packaging>=21.3
-  - pandas>=1.4
+  - pandas>=1.4,!=2.1.0
   - pooch
   - pip
   - pre-commit

doc/api-hidden.rst

@@ -22,6 +22,7 @@
    Coordinates.to_dataset
    Coordinates.to_index
    Coordinates.update
+   Coordinates.assign
    Coordinates.merge
    Coordinates.copy
    Coordinates.equals
@@ -39,8 +40,9 @@
    core.coordinates.DatasetCoordinates.to_dataset
    core.coordinates.DatasetCoordinates.to_index
    core.coordinates.DatasetCoordinates.update
+   core.coordinates.DatasetCoordinates.assign
    core.coordinates.DatasetCoordinates.merge
-   core.coordinates.DataArrayCoordinates.copy
+   core.coordinates.DatasetCoordinates.copy
    core.coordinates.DatasetCoordinates.equals
    core.coordinates.DatasetCoordinates.identical
 
@@ -79,6 +81,7 @@
    core.coordinates.DataArrayCoordinates.to_dataset
    core.coordinates.DataArrayCoordinates.to_index
    core.coordinates.DataArrayCoordinates.update
+   core.coordinates.DataArrayCoordinates.assign
    core.coordinates.DataArrayCoordinates.merge
    core.coordinates.DataArrayCoordinates.copy
    core.coordinates.DataArrayCoordinates.equals

doc/conf.py

@@ -324,6 +324,7 @@
     "cftime": ("https://unidata.github.io/cftime", None),
     "sparse": ("https://sparse.pydata.org/en/latest/", None),
     "cubed": ("https://tom-e-white.com/cubed/", None),
+    "datatree": ("https://xarray-datatree.readthedocs.io/en/latest/", None),
 }
 
 

doc/getting-started-guide/installing.rst

@@ -135,13 +135,13 @@ We also maintain other dependency sets for different subsets of functionality::
 The above commands should install most of the `optional dependencies`_. However,
 some packages which are either not listed on PyPI or require extra
 installation steps are excluded. To know which dependencies would be
-installed, take a look at the ``[options.extras_require]`` section in
-``setup.cfg``:
+installed, take a look at the ``[project.optional-dependencies]`` section in
+``pyproject.toml``:
 
-.. literalinclude:: ../../setup.cfg
-   :language: ini
-   :start-at: [options.extras_require]
-   :end-before: [options.package_data]
+.. literalinclude:: ../../pyproject.toml
+   :language: toml
+   :start-at: [project.optional-dependencies]
+   :end-before: [build-system]
 
 Development versions
 --------------------

doc/internals/duck-arrays-integration.rst

@@ -35,7 +35,7 @@ Python Array API standard support
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
 As an integration library xarray benefits greatly from the standardization of duck-array libraries' APIs, and so is a
-big supporter of the `Python Array API Standard <https://data-apis.org/array-api/latest/>`_. .
+big supporter of the `Python Array API Standard <https://data-apis.org/array-api/latest/>`_.
 
 We aim to support any array libraries that follow the Array API standard out-of-the-box. However, xarray does occasionally
 call some numpy functions which are not (yet) part of the standard (e.g. :py:meth:`xarray.DataArray.pad` calls :py:func:`numpy.pad`).

doc/internals/extending-xarray.rst

@@ -14,6 +14,11 @@ Xarray is designed as a general purpose library and hence tries to avoid
 including overly domain specific functionality. But inevitably, the need for more
 domain specific logic arises.
 
+.. _internals.accessors.composition:
+
+Composition over Inheritance
+----------------------------
+
 One potential solution to this problem is to subclass Dataset and/or DataArray to
 add domain specific functionality. However, inheritance is not very robust. It's
 easy to inadvertently use internal APIs when subclassing, which means that your
@@ -23,11 +28,17 @@ only return native xarray objects.
 The standard advice is to use :issue:`composition over inheritance <706>`, but
 reimplementing an API as large as xarray's on your own objects can be an onerous
 task, even if most methods are only forwarding to xarray implementations.
+(For an example of a project which took this approach of subclassing see `UXarray <https://github.com/UXARRAY/uxarray>`_).
 
 If you simply want the ability to call a function with the syntax of a
 method call, then the builtin :py:meth:`~xarray.DataArray.pipe` method (copied
 from pandas) may suffice.
 
+.. _internals.accessors.writing accessors:
+
+Writing Custom Accessors
+------------------------
+
 To resolve this issue for more complex cases, xarray has the
 :py:func:`~xarray.register_dataset_accessor` and
 :py:func:`~xarray.register_dataarray_accessor` decorators for adding custom

doc/internals/index.rst

@@ -1,6 +1,6 @@
 .. _internals:
 
-xarray Internals
+Xarray Internals
 ================
 
 Xarray builds upon two of the foundational libraries of the scientific Python
@@ -11,15 +11,14 @@ compiled code to :ref:`optional dependencies<installing>`.
 The pages in this section are intended for:
 
 * Contributors to xarray who wish to better understand some of the internals,
-* Developers who wish to extend xarray with domain-specific logic, perhaps to support a new scientific community of users,
-* Developers who wish to interface xarray with their existing tooling, e.g. by creating a plugin for reading a new file format, or wrapping a custom array type.
-
+* Developers from other fields who wish to extend xarray with domain-specific logic, perhaps to support a new scientific community of users,
+* Developers of other packages who wish to interface xarray with their existing tools, e.g. by creating a backend for reading a new file format, or wrapping a custom array type.
 
 .. toctree::
    :maxdepth: 2
    :hidden:
 
-   variable-objects
+   internal-design
    duck-arrays-integration
    chunked-arrays
    extending-xarray