Merge branch 'main' into SSI_SGI

Ouranosinc · Feb 21, 2025 · 388dfe9 · 388dfe9
2 parents 43d9be3 + d327e60
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -111,7 +111,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.10" ]
+        python-version: [ "3.11" ]
         testdata-cache: [ '~/.cache/xclim-testdata' ]
     steps:
       - name: Harden Runner
@@ -195,11 +195,6 @@ jobs:
       matrix:
         include:
           # Linux builds
-          - os: 'ubuntu-latest'
-            testdata-cache: '~/.cache/xclim-testdata'
-            markers: -m 'not slow'
-            python-version: "3.10"
-            tox-env: standard
           - os: 'ubuntu-latest'
             testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not slow'
@@ -210,7 +205,6 @@ jobs:
             markers: -m 'not slow'
             python-version: "3.12"
             tox-env: standard
-          # Coverage is not yet supported on Python3.13 . See `tox.ini`.
           - os: 'ubuntu-latest'
             testdata-cache: '~/.cache/xclim-testdata'
             markers: -m 'not slow'
@@ -220,14 +214,14 @@ jobs:
           - os: 'windows-latest'
             testdata-cache: 'C:\Users\runneradmin\AppData\Local\xclim-testdata\xclim-testdata\Cache'
             markers: -m 'not slow'
-            python-version: "3.10"
-            tox-env: py310-coverage-prefetch  # Test data prefetch is needed for Windows
+            python-version: "3.12"
+            tox-env: py312-coverage-prefetch  # Test data prefetch is needed for Windows
           # macOS builds
           - os: 'macos-latest'
             testdata-cache: '~/Library/Caches/xclim-testdata'
             markers: ''  # Slow tests
             python-version: "3.11"
-            tox-env: py311-coverage-extras
+            tox-env: py311-coverage-extras-lmoments
           # Specialized tests
           - os: 'ubuntu-latest'
             testdata-cache: '~/.cache/xclim-testdata'
@@ -237,7 +231,7 @@ jobs:
           - os: 'ubuntu-latest'
             testdata-cache: '~/.cache/xclim-testdata'
             markers: '' # No markers for notebooks
-            python-version: "3.10"
+            python-version: "3.11"
             tox-env: notebooks
           - os: 'ubuntu-latest'
             testdata-cache: '~/.cache/xclim-testdata'
@@ -346,7 +340,7 @@ jobs:
     strategy:
       matrix:
         os: [ 'ubuntu-latest' ]
-        python-version: [ "3.10", "3.12" ]
+        python-version: [ "3.11", "3.13" ]
         testdata-cache: [ '~/.cache/xclim-testdata' ]
     defaults:
       run:
@@ -412,14 +406,12 @@ jobs:
         continue-on-error: true
       - name: Test with pytest
         run: |
-          python -m pytest --numprocesses=logical --durations=10 --cov=xclim --cov-report=term-missing
-      - name: Report coverage
-        run: |
-          coveralls
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-          COVERALLS_FLAG_NAME: run-{{ matrix.python-version }}-conda
-          COVERALLS_PARALLEL: true
+          python -m pytest --numprocesses=logical --durations=10 --cov=xclim --cov-report=lcov
+      - name: Report Coverage
+        uses: coverallsapp/github-action@648a8eb78e6d50909eff900e4ec85cab4524a45b # v2.3.6
+        with:
+          flag-name: run-{{ matrix.python-version }}-conda
+          parallel: true
       - name: Tests measurement
         uses: green-coding-solutions/eco-ci-energy-estimation@7ff5628108e21227662ce881f10156eb9deab891 # v4.4
         with:

diff --git a/.gitignore b/.gitignore
@@ -45,6 +45,7 @@ htmlcov/
 .coverage.*
 .cache
 nosetests.xml
+coverage.lcov
 coverage.xml
 *.cover
 .hypothesis/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,14 +6,20 @@ repos:
     rev: v3.19.1
     hooks:
       - id: pyupgrade
-        args: ['--py310-plus']
+        args: ['--py311-plus']
         exclude: 'src/xclim/core/indicator.py'
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v5.0.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
         exclude: '.ipynb|.github/publish-mastodon-template.md'
+      - id: fix-byte-order-marker
+      - id: name-tests-test
+        args: [ '--pytest-test-first' ]
+      - id: no-commit-to-branch
+        args: [ '--branch', 'main' ]
+      - id: check-merge-conflict
       - id: check-json
       - id: check-toml
       - id: check-yaml
@@ -32,22 +38,20 @@ repos:
     hooks:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 25.1.0
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.4
+    rev: v0.9.6
     hooks:
       - id: ruff
         args: [ '--fix', '--show-fixes' ]
+      - id: ruff-format
+        exclude: '(src/xclim/indices/__init__.py|docs/installation.rst)'
   - repo: https://github.com/pylint-dev/pylint
     rev: v3.3.4
     hooks:
       - id: pylint
         args: [ '--rcfile=.pylintrc.toml', '--errors-only', '--jobs=0', '--disable=import-error' ]
   - repo: https://github.com/pycqa/flake8
-    rev: 7.1.1
+    rev: 7.1.2
     hooks:
       - id: flake8
         additional_dependencies: [ 'flake8-rst-docstrings ']
@@ -56,14 +60,6 @@ repos:
     rev: 'v2.14'
     hooks:
       - id: vulture
-  - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.9.1
-    hooks:
-      - id: nbqa-pyupgrade
-        args: [ '--py310-plus' ]
-        additional_dependencies: [ 'pyupgrade==3.19.0' ]
-      - id: nbqa-black
-        additional_dependencies: [ 'black==24.10.0' ]
   - repo: https://github.com/kynan/nbstripout
     rev: 0.8.1
     hooks:
@@ -91,8 +87,7 @@ repos:
     hooks:
       - id: blackdoc
         additional_dependencies: [ 'black==25.1.0' ]
-        exclude: '(src/xclim/indices/__init__.py|docs/installation.rst)'
-      - id: blackdoc-autoupdate-black
+        exclude: '(.py|docs/installation.rst)'
   - repo: https://github.com/codespell-project/codespell
     rev: v2.4.1
     hooks:

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -8,10 +8,12 @@ sphinx:
 #  - pdf
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "mambaforge-22.9"
+    python: "mambaforge-23.11"
   jobs:
+    pre_create_environment:
+      - sed -i "s/python >=3.11,<3.14/python >=3.11,<3.13/" environment.yml
     pre_build:
       - sphinx-apidoc -o docs/apidoc/ --private --module-first src/xclim src/xclim/testing/tests src/xclim/indicators src/xclim/indices
       - rm docs/apidoc/xclim.rst
@@ -31,7 +33,6 @@ python:
 
 search:
   ranking:
-
     notebooks/*: 2
     api_indicators.html: 1
     indices.html: -1

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -2,6 +2,24 @@
 Changelog
 =========
 
+v0.56.0 (unreleased)
+--------------------
+Contributors to this version: Trevor James Smith (:user:`Zeitsperre`).
+
+Breaking changes
+^^^^^^^^^^^^^^^^
+* `xclim` no longer supports Python 3.10. The minimum required version is now Python 3.11. (:pull:`2082`).
+* The minimum versions of several key dependencies have been raised (`numpy` >=1.24.0; `scikit-learn` >=1.2.0; `scipy` >=1.11.0). (:pull:`2082`).
+
+Internal changes
+^^^^^^^^^^^^^^^^
+* `black`, `isort`, and `nbqa` have all been dropped from the development dependencies. (:issue:`1805`, :pull:`2082`).
+* `ruff` has been configured to provide code formatting. (:pull:`2083`):
+    * The maximum line-length is now 120 characters.
+    * Docstring formatting is now enabled.
+    * Line endings in files now must be `Unix`-compatible (`LF`).
+* The `blackdoc` pre-commit hook now only examines `.rst` and `.md` files. (:pull:`2083`).
+
 v0.55.0 (2025-02-17)
 --------------------
 Contributors to this version: Juliette Lavoie (:user:`juliettelavoie`), Trevor James Smith (:user:`Zeitsperre`), Sascha Hofmann (:user:`saschahofmann`), Pascal Bourgault (:user:`aulemahal`), Éric Dupuis (:user:`coxipi`), Baptiste Hamon (:user:`baptistehamon`), Sarah Gammon (:user:`SarahG-579462`).

diff --git a/Makefile b/Makefile
@@ -53,13 +53,10 @@ clean-test: ## remove test and coverage artifacts
 	rm -fr .pytest_cache
 
 lint: ## check style with flake8 and black
-	python -m black --check src/xclim tests
 	python -m ruff check src/xclim tests
 	python -m flake8 --config=.flake8 src/xclim tests
 	python -m vulture src/xclim tests
-	python -m nbqa black --check docs
-	python -m blackdoc --check --exclude=src/xclim/indices/__init__.py src/xclim
-	python -m blackdoc --check docs
+	python -m blackdoc --check README.rst CHANGELOG.rst CONTRIBUTING.rst docs --exclude=".py"
 	codespell src/xclim tests docs
 	python -m numpydoc lint src/xclim/*.py src/xclim/ensembles/*.py src/xclim/indices/*.py src/xclim/indicators/*.py src/xclim/testing/*.py
 	python -m deptry src

diff --git a/README.rst b/README.rst
@@ -9,7 +9,7 @@ xclim: Climate services library |logo| |logo-dark| |logo-light|
 +----------------------------+-----------------------------------------------------+
 | Open Source                | |license| |ossf-score| |zenodo| |pyOpenSci| |joss|  |
 +----------------------------+-----------------------------------------------------+
-| Coding Standards           | |black| |ruff| |pre-commit| |ossf-bp| |fossa|       |
+| Coding Standards           | |ruff| |pre-commit| |ossf-bp| |fossa|               |
 +----------------------------+-----------------------------------------------------+
 | Development Status         | |status| |build| |coveralls|                        |
 +----------------------------+-----------------------------------------------------+
@@ -68,13 +68,13 @@ Conventions
 -----------
 In order to provide a coherent interface, `xclim` tries to follow different sets of conventions. In particular, input data should follow the `CF conventions`_ whenever possible for variable attributes. Variable names are usually the ones used in `CMIP6`_, when they exist.
 
-However, xclim will *always* assume the temporal coordinate is named "time". If your data uses another name (for example: "T"), you can rename the variable with:
+However, `xclim` will *always* assume the temporal coordinate is named "time". If your data uses another name (for example: "T"), you can rename the variable with:
 
 .. code-block:: python
 
     ds = ds.rename(T="time")
 
-`xclim` code uses the `black`_ formatter, a modified `ruff`_ linting configuration, and (mostly) adheres to the `NumPy docstring`_ style. For more information on coding and development conventions, see the `Contributing Guidelines`_.
+`xclim` employs `black`_-like code formatting style, a modified `ruff`_ linting configuration, and (mostly) adheres to the `NumPy docstring`_ style. For more information on coding and development conventions, see the `Contributing Guidelines`_.
 
 .. _black: https://black.readthedocs.io/en/stable/
 .. _ruff: https://docs.astral.sh/ruff/
@@ -191,10 +191,6 @@ This package was created with Cookiecutter_ and the `audreyfeldroy/cookiecutter-
         :target: https://app.fossa.com/projects/git%2Bgithub.jparrowsec.cn%2FOuranosinc%2Fxclim?ref=badge_shield
         :alt: FOSSA
 
-.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg
-        :target: https://github.com/psf/black
-        :alt: Python Black
-
 .. |logo| image:: https://raw.githubusercontent.com/Ouranosinc/xclim/main/docs/logos/xclim-logo-small-light.png
         :target: https://github.com/Ouranosinc/xclim
         :alt: Xclim

diff --git a/docs/conf.py b/docs/conf.py
@@ -240,9 +240,7 @@ class XCStyle(AlphaStyle):
 
 # General information about the project.
 project = "xclim"
-copyright = (
-    f"2018-{datetime.datetime.now().year}, Ouranos Inc., Travis Logan, and contributors"
-)
+copyright = f"2018-{datetime.datetime.now().year}, Ouranos Inc., Travis Logan, and contributors"
 author = "xclim Project Development Team"
 
 # The version info for the project you're documenting, acts as replacement

diff --git a/docs/notebooks/analogs.ipynb b/docs/notebooks/analogs.ipynb
@@ -133,9 +133,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = analog.spatial_analogs(\n",
-    "    sim[[\"tg_mean\"]], obs[[\"tg_mean\"]], method=\"seuclidean\"\n",
-    ")\n",
+    "results = analog.spatial_analogs(sim[[\"tg_mean\"]], obs[[\"tg_mean\"]], method=\"seuclidean\")\n",
     "\n",
     "results.plot()\n",
     "plt.plot(sim.lon, sim.lat, \"ro\", label=\"Target\")\n",
@@ -169,9 +167,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "results = analog.spatial_analogs(\n",
-    "    sim[[\"tg_mean\"]], obs[[\"tg_mean\"]], method=\"zech_aslan\"\n",
-    ")\n",
+    "results = analog.spatial_analogs(sim[[\"tg_mean\"]], obs[[\"tg_mean\"]], method=\"zech_aslan\")\n",
     "\n",
     "results.plot(center=False)\n",
     "plt.plot(sim.lon, sim.lat, \"ro\", label=\"Target\")\n",

diff --git a/docs/notebooks/benchmarks/sdba_quantile.ipynb b/docs/notebooks/benchmarks/sdba_quantile.ipynb
@@ -100,19 +100,15 @@
     "for use_fnq in [True, False]:\n",
     "    sdba.nbutils.USE_FASTNANQUANTILE = use_fnq\n",
     "    # heat-up the jit\n",
-    "    sdba.nbutils.quantile(\n",
-    "        xr.DataArray(np.array([0, 1.5])), dim=\"dim_0\", q=np.array([0.5])\n",
-    "    )\n",
+    "    sdba.nbutils.quantile(xr.DataArray(np.array([0, 1.5])), dim=\"dim_0\", q=np.array([0.5]))\n",
     "    for size in np.arange(250, 2000 + 250, 250):\n",
     "        da = tx.isel(time=slice(0, size))\n",
     "        t0 = time.time()\n",
     "        for _i in range(num_tests):\n",
     "            sdba.nbutils.quantile(da, **kws).compute()\n",
     "        timed[use_fnq].append([size, time.time() - t0])\n",
     "\n",
-    "for k, lab in zip(\n",
-    "    [True, False], [\"xclim.core.utils.nan_quantile\", \"fastnanquantile\"], strict=False\n",
-    "):\n",
+    "for k, lab in zip([True, False], [\"xclim.core.utils.nan_quantile\", \"fastnanquantile\"], strict=False):\n",
     "    arr = np.array(timed[k])\n",
     "    plt.plot(arr[:, 0], arr[:, 1] / num_tests, label=lab)\n",
     "plt.legend()\n",

diff --git a/docs/notebooks/customize.ipynb b/docs/notebooks/customize.ipynb
@@ -35,11 +35,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "tasmax = (\n",
-    "    xr.tutorial.load_dataset(\"air_temperature\")\n",
-    "    .air.resample(time=\"D\")\n",
-    "    .max(keep_attrs=True)\n",
-    ")\n",
+    "tasmax = xr.tutorial.load_dataset(\"air_temperature\").air.resample(time=\"D\").max(keep_attrs=True)\n",
     "tasmax = tasmax.where(tasmax.time.dt.day % 10 != 0)"
    ]
   },
@@ -137,9 +133,7 @@
    "outputs": [],
    "source": [
     "with xclim.set_options(check_missing=\"wmo\"):\n",
-    "    tx_mean = xclim.atmos.tx_mean(\n",
-    "        tasmax=tasmax, freq=\"MS\"\n",
-    "    )  # compute monthly max tasmax\n",
+    "    tx_mean = xclim.atmos.tx_mean(tasmax=tasmax, freq=\"MS\")  # compute monthly max tasmax\n",
     "tx_mean.sel(time=\"2013\", lat=75, lon=200)"
    ]
   },
@@ -165,7 +159,7 @@
     "\n",
     "To add additional arguments, one should override the `__init__` (receiving those arguments) and the `validate` static method, which validates them. The options are then stored in the `options` property of the instance. See example below and the docstrings in the module.\n",
     "\n",
-    "When registering the class with the `xclim.core.checks.register_missing_method` decorator, the keyword arguments will be registered as options for the missing method. "
+    "When registering the class with the `xclim.core.checks.register_missing_method` decorator, the keyword arguments will be registered as options for the missing method."
    ]
   },
   {
@@ -186,12 +180,9 @@
     "        super().__init__(max_n=max_n)\n",
     "\n",
     "    def is_missing(self, valid, count, freq):\n",
-    "        \"\"\"Return a boolean mask where True values are for elements that are considered missing and masked on the output.\"\"\"\n",
+    "        \"\"\"Return a boolean mask for elements that are considered missing and masked on the output.\"\"\"\n",
     "        null = ~valid\n",
-    "        return (\n",
-    "            null.resample(time=freq).map(longest_run, dim=\"time\")\n",
-    "            >= self.options[\"max_n\"]\n",
-    "        )\n",
+    "        return null.resample(time=freq).map(longest_run, dim=\"time\") >= self.options[\"max_n\"]\n",
     "\n",
     "    @staticmethod\n",
     "    def validate(max_n):\n",
@@ -212,12 +203,8 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "with xclim.set_options(\n",
-    "    check_missing=\"consecutive\", missing_options={\"consecutive\": {\"max_n\": 2}}\n",
-    "):\n",
-    "    tx_mean = xclim.atmos.tx_mean(\n",
-    "        tasmax=tasmax, freq=\"MS\"\n",
-    "    )  # compute monthly max tasmax\n",
+    "with xclim.set_options(check_missing=\"consecutive\", missing_options={\"consecutive\": {\"max_n\": 2}}):\n",
+    "    tx_mean = xclim.atmos.tx_mean(tasmax=tasmax, freq=\"MS\")  # compute monthly max tasmax\n",
     "tx_mean.sel(time=\"2013\", lat=75, lon=200)"
    ]
   },