Merge branch 'main' into rolling-auto-rechunk

Author: dcherian

.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.

.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: >

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

@@ -24,6 +24,7 @@ jobs:
       - name: Set up conda environment
         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

.github/workflows/benchmarks.yml

@@ -27,6 +27,7 @@ jobs:
       - name: Set up conda environment
         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

.github/workflows/ci-additional.yaml

@@ -61,7 +61,6 @@ jobs:
           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: |
@@ -109,16 +106,13 @@ jobs:
           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: |
@@ -163,16 +157,13 @@ jobs:
           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: |
@@ -222,16 +213,13 @@ jobs:
           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: |
@@ -281,16 +269,13 @@ jobs:
           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: |
@@ -326,12 +311,15 @@ jobs:
       - name: Setup micromamba
         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: |

.github/workflows/ci.yaml

@@ -116,7 +116,6 @@ jobs:
           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.
@@ -131,8 +130,6 @@ jobs:
 
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
 
       - name: Import xarray

.github/workflows/hypothesis.yaml

@@ -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

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

@@ -68,7 +68,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pytest-reportlog
-            conda
       - name: Install upstream versions
         run: |
           bash ci/install-upstream-wheels.sh
@@ -77,8 +76,6 @@ jobs:
           python -m pip install --no-deps -e .
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
       - name: Import xarray
         run: |
@@ -127,7 +124,6 @@ jobs:
           create-args: >-
             python=${{ matrix.python-version }}
             pytest-reportlog
-            conda
       - name: Install upstream versions
         run: |
           bash ci/install-upstream-wheels.sh
@@ -136,8 +132,6 @@ jobs:
           python -m pip install --no-deps -e .
       - name: Version info
         run: |
-          conda info -a
-          conda list
           python xarray/util/print_versions.py
       - name: Install mypy
         run: |

CODE_OF_CONDUCT.md

@@ -40,7 +40,7 @@ Project maintainers who do not follow or enforce the Code of Conduct in good fai
 
 ## Attribution
 
-This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [http://contributor-covenant.org/version/1/4][version]
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://contributor-covenant.org/version/1/4][version]
 
-[homepage]: http://contributor-covenant.org
-[version]: http://contributor-covenant.org/version/1/4/
+[homepage]: https://contributor-covenant.org
+[version]: https://contributor-covenant.org/version/1/4/

CONTRIBUTING.md

@@ -1 +1 @@
-Xarray's contributor guidelines [can be found in our online documentation](http://docs.xarray.dev/en/stable/contributing.html)
+Xarray's contributor guidelines [can be found in our online documentation](https://docs.xarray.dev/en/stable/contributing.html)

DATATREE_MIGRATION_GUIDE.md

@@ -41,7 +41,7 @@ A number of other API changes have been made, which should only require minor mo
 - The method `DataTree.to_dataset()` still exists but now has different options for controlling which variables are present on the resulting `Dataset`, e.g. `inherit=True/False`.
 - `DataTree.copy()` also has a new `inherit` keyword argument for controlling whether or not coordinates defined on parents are copied (only relevant when copying a non-root node).
 - The `DataTree.parent` property is now read-only. To assign a ancestral relationships directly you must instead use the `.children` property on the parent node, which remains settable.
-- Similarly the `parent` kwarg has been removed from the `DataTree.__init__` constuctor.
+- Similarly the `parent` kwarg has been removed from the `DataTree.__init__` constructor.
 - DataTree objects passed to the `children` kwarg in `DataTree.__init__` are now shallow-copied.
 - `DataTree.as_array` has been replaced by `DataTree.to_dataarray`.
 - A number of methods which were not well tested have been (temporarily) disabled. In general we have tried to only keep things that are known to work, with the plan to increase API surface incrementally after release.

README.md

@@ -94,7 +94,7 @@ our efforts.
 ## History
 
 Xarray is an evolution of an internal tool developed at [The Climate
-Corporation](http://climate.com/). It was originally written by Climate
+Corporation](https://climate.com/). It was originally written by Climate
 Corp researchers Stephan Hoyer, Alex Kleeman and Eugene Brevdo and was
 released as open source in May 2014. The project was renamed from
 "xray" in January 2016. Xarray became a fiscally sponsored project of

asv_bench/asv.conf.json

@@ -7,7 +7,7 @@
     "project": "xarray",
 
     // The project's homepage
-    "project_url": "http://docs.xarray.dev/",
+    "project_url": "https://docs.xarray.dev/",
 
     // The URL or local path of the source code repository for the
     // project being benchmarked

asv_bench/benchmarks/dataset_io.py

@@ -712,7 +712,7 @@ def load(self) -> tuple:
                         dims=("time",),
                         fastpath=True,
                     )
-                    for v in range(0, n_variables)
+                    for v in range(n_variables)
                 }
                 attributes = {}
 
@@ -722,7 +722,7 @@ class PerformanceBackend(xr.backends.BackendEntrypoint):
             def open_dataset(
                 self,
                 filename_or_obj: str | os.PathLike | None,
-                drop_variables: tuple[str, ...] = None,
+                drop_variables: tuple[str, ...] | None = None,
                 *,
                 mask_and_scale=True,
                 decode_times=True,

asv_bench/benchmarks/groupby.py

@@ -1,6 +1,6 @@
 # import flox to avoid the cost of first import
 import cftime
-import flox.xarray  # noqa
+import flox.xarray  # noqa: F401
 import numpy as np
 import pandas as pd
 

ci/min_deps_check.py

@@ -62,7 +62,7 @@ def parse_requirements(fname) -> Iterator[tuple[str, int, int, int | None]]:
         pkg, eq, version = row.partition("=")
         if pkg.rstrip("<>") in IGNORE_DEPS:
             continue
-        if pkg.endswith("<") or pkg.endswith(">") or eq != "=":
+        if pkg.endswith(("<", ">")) or eq != "=":
             error("package should be pinned with exact version: " + row)
             continue
 
@@ -186,7 +186,7 @@ def process_pkg(
     )
 
 
-def fmt_version(major: int, minor: int, patch: int = None) -> str:
+def fmt_version(major: int, minor: int, patch: int | None = None) -> str:
     if patch is None:
         return f"{major}.{minor}"
     else:

ci/requirements/all-but-dask.yml

@@ -4,7 +4,7 @@ channels:
   - nodefaults
 dependencies:
   - aiobotocore
-  - array-api-strict
+  - array-api-strict<=2.1
   - boto3
   - bottleneck
   - cartopy

ci/requirements/all-but-numba.yml

@@ -6,7 +6,7 @@ dependencies:
   # Pin a "very new numpy" (updated Sept 24, 2024)
   - numpy>=2.1.1
   - aiobotocore
-  - array-api-strict
+  - array-api-strict<=2.1
   - boto3
   - bottleneck
   - cartopy

ci/requirements/environment-windows.yml

@@ -2,7 +2,7 @@ name: xarray-tests
 channels:
   - conda-forge
 dependencies:
-  - array-api-strict
+  - array-api-strict<=2.1
   - boto3
   - bottleneck
   - cartopy

ci/requirements/environment.yml

@@ -4,7 +4,7 @@ channels:
   - nodefaults
 dependencies:
   - aiobotocore
-  - array-api-strict
+  - array-api-strict<=2.1
   - boto3
   - bottleneck
   - cartopy
@@ -36,14 +36,7 @@ dependencies:
   - pre-commit
   - pyarrow # pandas raises a deprecation warning without this, breaking doctests
   - pydap
-  # start pydap server dependencies, can be removed if pydap-server is available
-  - gunicorn
-  - PasteDeploy
-  - docopt-ng
-  - Webob
-  - Jinja2
-  - beautifulsoup4
-  # end pydap server dependencies
+  - pydap-server
   - pytest
   - pytest-cov
   - pytest-env

design_notes/flexible_indexes_notes.md

@@ -133,7 +133,7 @@ A possible, more explicit solution to reuse a `pandas.MultiIndex` in a DataArray
 
 New indexes may also be built from existing sets of coordinates or variables in a Dataset/DataArray using the `.set_index()` method.
 
-The [current signature](http://docs.xarray.dev/en/stable/generated/xarray.DataArray.set_index.html#xarray.DataArray.set_index) of `.set_index()` is tailored to `pandas.MultiIndex` and tied to the concept of a dimension-index. It is therefore hardly reusable as-is in the context of flexible indexes proposed here.
+The [current signature](https://docs.xarray.dev/en/stable/generated/xarray.DataArray.set_index.html#xarray.DataArray.set_index) of `.set_index()` is tailored to `pandas.MultiIndex` and tied to the concept of a dimension-index. It is therefore hardly reusable as-is in the context of flexible indexes proposed here.
 
 The new signature may look like one of these: