Merge branch 'main' into allow_negative_freq

.github/workflows/ci-additional.yaml

@@ -79,7 +79,8 @@ jobs:
           #
           # If dependencies emit warnings we can't do anything about, add ignores to
           # `xarray/tests/__init__.py`.
-          python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
+          # [MHS, 01/25/2024] Skip datatree_ documentation remove after #8572
+          python -m pytest --doctest-modules xarray --ignore xarray/tests --ignore xarray/datatree_ -Werror
 
   mypy:
     name: Mypy

.pre-commit-config.yaml

@@ -1,6 +1,7 @@
 # https://pre-commit.com/
 ci:
     autoupdate_schedule: monthly
+exclude: 'xarray/datatree_.*'
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v4.5.0
@@ -10,12 +11,6 @@ repos:
       - id: check-yaml
       - id: debug-statements
       - id: mixed-line-ending
-  - repo: https://github.com/MarcoGorelli/absolufy-imports
-    rev: v0.3.1
-    hooks:
-      - id: absolufy-imports
-        name: absolufy-imports
-        files: ^xarray/
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: 'v0.1.9'

MANIFEST.in

@@ -0,0 +1 @@
+prune xarray/datatree_*

ci/requirements/all-but-dask.yml

@@ -27,7 +27,7 @@ dependencies:
   - pint>=0.22
   - pip
   - pydap
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/bare-minimum.yml

@@ -6,7 +6,7 @@ dependencies:
   - python=3.9
   - coveralls
   - pip
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/environment-3.12.yml

@@ -33,7 +33,7 @@ dependencies:
   - pooch
   - pre-commit
   - pydap
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/environment-windows-3.12.yml

@@ -28,7 +28,7 @@ dependencies:
   - pip
   - pre-commit
   - pydap
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/environment-windows.yml

@@ -28,7 +28,7 @@ dependencies:
   - pip
   - pre-commit
   - pydap
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/environment.yml

@@ -34,7 +34,7 @@ dependencies:
   - pre-commit
   - pyarrow # pandas makes a deprecation warning without this, breaking doctests
   - pydap
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

ci/requirements/min-all-deps.yml

@@ -42,7 +42,7 @@ dependencies:
   - pint=0.22
   - pip
   - pydap=3.3
-  - pytest==7.4.*
+  - pytest
   - pytest-cov
   - pytest-env
   - pytest-xdist

doc/contributing.rst

@@ -153,7 +153,7 @@ Creating a development environment
 ----------------------------------
 
 To test out code changes locally, you'll need to build *xarray* from source, which requires you to
-`create a local development environment <https://docs.xarray.dev/en/stable/contributing.html#creating-a-development-environment>`_.
+`create a local development environment <https://docs.xarray.dev/en/stable/contributing.html#contributing-dev-env>`_.
 
 Update the ``main`` branch
 --------------------------

doc/whats-new.rst

@@ -46,6 +46,9 @@ Deprecations
 Bug fixes
 ~~~~~~~~~
 
+- Fixed a regression that prevented multi-index level coordinates being
+  serialized after resetting or dropping the multi-index (:issue:`8628`, :pull:`8672`).
+  By `Benoit Bovy <https://github.com/benbovy>`_.
 - Fix bug with broadcasting when wrapping array API-compliant classes. (:issue:`8665`, :pull:`8669`)
   By `Tom Nicholas <https://github.com/TomNicholas>`_.
 - Ensure :py:meth:`DataArray.unstack` works when wrapping array API-compliant classes. (:issue:`8666`, :pull:`8668`)

pyproject.toml

@@ -85,7 +85,10 @@ exclude_lines = ["pragma: no cover", "if TYPE_CHECKING"]
 
 [tool.mypy]
 enable_error_code = "redundant-self"
-exclude = 'xarray/util/generate_.*\.py'
+exclude = [
+	'xarray/util/generate_.*\.py',
+	'xarray/datatree_/.*\.py',
+]
 files = "xarray"
 show_error_codes = true
 show_error_context = true
@@ -242,8 +245,15 @@ extend-exclude = [
   "doc",
   "_typed_ops.pyi",
 ]
+extend-safe-fixes = [
+  "TID252", # absolute imports
+]
 target-version = "py39"
 
+[tool.ruff.per-file-ignores]
+# don't enforce absolute imports
+"asv_bench/**" = ["TID252"]
+
 [tool.ruff.lint]
 # E402: module level import not at top of file
 # E501: line too long - let black worry about that
@@ -257,13 +267,18 @@ select = [
   "F", # Pyflakes
   "E", # Pycodestyle
   "W",
+  "TID", # flake8-tidy-imports (absolute imports)
   "I", # isort
   "UP", # Pyupgrade
 ]
 
 [tool.ruff.lint.isort]
 known-first-party = ["xarray"]
 
+[tool.ruff.lint.flake8-tidy-imports]
+# Disallow all relative imports.
+ban-relative-imports = "all"
+
 [tool.pytest.ini_options]
 addopts = ["--strict-config", "--strict-markers"]
 filterwarnings = [

xarray/conventions.py

@@ -16,7 +16,7 @@
 )
 from xarray.core.pycompat import is_duck_dask_array
 from xarray.core.utils import emit_user_level_warning
-from xarray.core.variable import Variable
+from xarray.core.variable import IndexVariable, Variable
 
 CF_RELATED_DATA = (
     "bounds",
@@ -84,13 +84,17 @@ def _infer_dtype(array, name=None):
 
 
 def ensure_not_multiindex(var: Variable, name: T_Name = None) -> None:
+    # only the pandas multi-index dimension coordinate cannot be serialized (tuple values)
     if isinstance(var._data, indexing.PandasMultiIndexingAdapter):
-        raise NotImplementedError(
-            f"variable {name!r} is a MultiIndex, which cannot yet be "
-            "serialized. Instead, either use reset_index() "
-            "to convert MultiIndex levels into coordinate variables instead "
-            "or use https://cf-xarray.readthedocs.io/en/latest/coding.html."
-        )
+        if name is None and isinstance(var, IndexVariable):
+            name = var.name
+        if var.dims == (name,):
+            raise NotImplementedError(
+                f"variable {name!r} is a MultiIndex, which cannot yet be "
+                "serialized. Instead, either use reset_index() "
+                "to convert MultiIndex levels into coordinate variables instead "
+                "or use https://cf-xarray.readthedocs.io/en/latest/coding.html."
+            )
 
 
 def _copy_with_dtype(data, dtype: np.typing.DTypeLike):

xarray/datatree_/.flake8

@@ -0,0 +1,15 @@
+[flake8]
+ignore =
+    # whitespace before ':' - doesn't work well with black
+    E203
+    # module level import not at top of file
+    E402
+    # line too long - let black worry about that
+    E501
+    # do not assign a lambda expression, use a def
+    E731
+    # line break before binary operator
+    W503
+exclude=
+    .eggs
+    doc

xarray/datatree_/.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true)$
+ref-names: $Format:%D$

xarray/datatree_/.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: daily
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      # Check for updates to GitHub Actions every weekday
+      interval: "daily"

xarray/datatree_/.github/pull_request_template.md

@@ -0,0 +1,7 @@
+<!-- Feel free to remove check-list items aren't relevant to your change -->
+
+- [ ] Closes #xxxx
+- [ ] Tests added
+- [ ] Passes `pre-commit run --all-files`
+- [ ] New functions/methods are listed in `api.rst`
+- [ ] Changes are summarized in `docs/source/whats-new.rst`

xarray/datatree_/.github/workflows/main.yaml

@@ -0,0 +1,97 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  schedule:
+    - cron: "0 0 * * *"
+
+jobs:
+
+  test:
+    name: ${{ matrix.python-version }}-build
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          cache-downloads: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+      - name: Conda info
+        run: conda info
+
+      - name: Install datatree
+        run: |
+           python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Conda list
+        run: conda list
+
+      - name: Running Tests
+        run: |
+          python -m pytest --cov=./ --cov-report=xml --verbose
+
+      - name: Upload code coverage to Codecov
+        uses: codecov/codecov-action@v3.1.4
+        with:
+          file: ./coverage.xml
+          flags: unittests
+          env_vars: OS,PYTHON
+          name: codecov-umbrella
+          fail_ci_if_error: false
+
+
+  test-upstream:
+    name: ${{ matrix.python-version }}-dev-build
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Create conda environment
+        uses: mamba-org/provision-with-micromamba@main
+        with:
+          cache-downloads: true
+          micromamba-version: 'latest'
+          environment-file: ci/environment.yml
+          extra-specs: |
+            python=${{ matrix.python-version }}
+
+      - name: Conda info
+        run: conda info
+
+      - name: Install dev reqs
+        run: |
+          python -m pip install --no-deps --upgrade \
+            git+https://github.com/pydata/xarray \
+            git+https://github.com/Unidata/netcdf4-python
+
+          python -m pip install -e . --no-deps --force-reinstall
+
+      - name: Conda list
+        run: conda list
+
+      - name: Running Tests
+        run: |
+          python -m pytest --verbose