Merge branch 'main' of https://github.com/Ouranosinc/xclim into fix_d…

…otc_standardization

.github/workflows/add-to-project.yml

@@ -25,7 +25,7 @@ jobs:
 
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@31c86eb3b33c9b601a1f60f98dcbfd1d70f379b4 # v1.10.3
+        uses: actions/create-github-app-token@3378cda945da322a8db4b193e19d46352ebe2de5 # v1.10.4
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}

.github/workflows/bump-version.yml

@@ -46,7 +46,7 @@ jobs:
             pypi.org:443
       - name: Generate App Token
         id: token_generator
-        uses: actions/create-github-app-token@31c86eb3b33c9b601a1f60f98dcbfd1d70f379b4 # v1.10.3
+        uses: actions/create-github-app-token@3378cda945da322a8db4b193e19d46352ebe2de5 # v1.10.4
         with:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}
@@ -55,7 +55,7 @@ jobs:
         with:
           token: ${{ steps.token_generator.outputs.token }}
       - name: Set up Python3
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.x"
       - name: Import GPG Key

.github/workflows/main.yml

@@ -55,7 +55,7 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install CI libraries
@@ -92,7 +92,7 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install CI libraries
@@ -179,7 +179,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install libeigen3-dev
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install CI libraries

.github/workflows/publish-mastodon.yml

@@ -80,7 +80,7 @@ jobs:
 
       - name: Send toot to Mastodon
         if: ${{ github.event.inputs.dry-run != 'true' }} || ${{ github.event_name == 'release' }}
-        uses: cbrgm/mastodon-github-action@b97a4c288a6fd9d75821d92432704339202e090f # v2.1.7
+        uses: cbrgm/mastodon-github-action@eec9734402fe90511688538f942a916c61808ba7 # v2.1.8
         with:
           url: ${{ secrets.MASTODON_URL }}
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}

.github/workflows/publish-pypi.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python3
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.x"
       - name: Install CI libraries
@@ -40,4 +40,4 @@ jobs:
         run: |
           python -m flit build
       - name: Publish distribution 📦 to PyPI
-        uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1

.github/workflows/scorecard.yml

@@ -59,7 +59,7 @@ jobs:
       # Upload the results as artifacts (optional). Commenting out will disable uploads of run results in SARIF
       # format to the repository Actions tab.
       - name: Upload Artifact
-        uses: actions/upload-artifact@834a144ee995460fba8ed112a2fc961b36a5ec5a
+        uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874
         with:
           name: SARIF file
           path: results.sarif

.github/workflows/tag-testpypi.yml

@@ -30,7 +30,7 @@ jobs:
       - name: Checkout Repository
         uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       - name: Set up Python3
-        uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5.1.1
+        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
           python-version: "3.x"
       - name: Install CI libraries
@@ -40,7 +40,7 @@ jobs:
         run: |
           python -m flit build
       - name: Publish distribution 📦 to Test PyPI
-        uses: pypa/gh-action-pypi-publish@ec4db0b4ddc65acdf4bff5fa45ac92d78b56bdf0 # v1.9.0
+        uses: pypa/gh-action-pypi-publish@0ab0b79471669eb3a4d647e625009c62f9f3b241 # v1.10.1
         with:
           repository-url: https://test.pypi.org/legacy/
           skip-existing: true

.pre-commit-config.yaml

@@ -33,20 +33,20 @@ repos:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 24.4.2
+    rev: 24.8.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
     rev: 5.13.2
     hooks:
       - id: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.5.6
+    rev: v0.6.3
     hooks:
       - id: ruff
         args: [ '--fix' ]
   - repo: https://github.com/pylint-dev/pylint
-    rev: v3.2.6
+    rev: v3.2.7
     hooks:
       - id: pylint
         args: [ '--rcfile=.pylintrc.toml', '--errors-only', '--jobs=0', '--disable=import-error' ]
@@ -92,7 +92,7 @@ repos:
     hooks:
       - id: gitleaks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.29.1
+    rev: 0.29.2
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

.pylintrc.toml

@@ -15,7 +15,7 @@
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
 # run arbitrary code.
-# extension-pkg-allow-list =
+extension-pkg-allow-list = ["cftime"]
 
 # A comma-separated list of package or module names from where C extensions may
 # be loaded. Extensions are loading into the active Python interpreter and may
@@ -36,7 +36,7 @@ fail-under = 10
 # from-stdin =
 
 # Files or directories to be skipped. They should be base names, not paths.
-ignore = ["CVS"]
+ignore = ["CVS", "conftest.py"]
 
 # Add files or directories matching the regular expressions patterns to the
 # ignore-list. The regex matches against paths and can be in Posix or Windows
@@ -62,7 +62,7 @@ ignored-modules = ["xclim.indicators"]
 # Use multiple processes to speed up Pylint. Specifying 0 will auto-detect the
 # number of processors available to use, and will cap the count on Windows to
 # avoid hangs.
-jobs = 1
+jobs = 4
 
 # Control the amount of potential inferred values when inferring a single object.
 # This can help the performance when dealing with large functions or complex,
@@ -78,7 +78,7 @@ persistent = true
 
 # Minimum Python version to use for version dependent checks. Will default to the
 # version used to run pylint.
-py-version = "3.8"
+py-version = "3.9"
 
 # Discover python modules and packages in the file system subtree.
 # recursive =
@@ -253,13 +253,13 @@ max-args = 15
 max-attributes = 7
 
 # Maximum number of boolean expressions in an if statement (see R0916).
-max-bool-expr = 5
+max-bool-expr = 10
 
 # Maximum number of branch for function / method body.
 max-branches = 30
 
 # Maximum number of locals for function / method body.
-max-locals = 50
+max-locals = 75
 
 # Maximum number of parents for a class (see R0901).
 max-parents = 7
@@ -268,7 +268,7 @@ max-parents = 7
 max-public-methods = 20
 
 # Maximum number of return / yield for function / method body.
-max-returns = 13
+max-returns = 15
 
 # Maximum number of statements in function / method body.
 max-statements = 100
@@ -295,10 +295,10 @@ indent-after-paren = 4
 indent-string = "    "
 
 # Maximum number of characters on a single line.
-max-line-length = 150
+max-line-length = 200
 
 # Maximum number of lines in a module.
-max-module-lines = 1500
+max-module-lines = 2000
 
 # Allow the body of a class to be on the same line as the declaration if body
 # contains single statement.
@@ -373,6 +373,7 @@ disable = [
     "invalid-name",
     "invalid-unary-operand-type",
     "locally-disabled",
+    "missing-function-docstring",
     "missing-module-docstring",
     "no-member",
     "protected-access",

CHANGELOG.rst

@@ -17,6 +17,7 @@ Breaking changes
 Breaking changes
 ^^^^^^^^^^^^^^^^
 * `platformdirs` is no longer a direct dependency of `xclim`, but `pooch` is required to use many of the new testing functions (installable via `pip install pooch` or `pip install 'xclim[dev]'`). (:pull:`1889`).
+* The following previously-deprecated functions have now been removed from `xclim`: ``xclim.core.calendar.convert_calendar``, ``xclim.core.calendar.date_range``, ``xclim.core.calendar.date_range_like``, ``xclim.core.calendar.interp_calendar``, ``xclim.core.calendar.days_in_year``, ``xclim.core.calendar.datetime_to_decimal_year``. For guidance on how to migrate to alternatives, see the `version 0.50.0 Breaking changes <#v0-50-0-2024-06-17>`_. (:issue:`1010`, :pull:`1845`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
@@ -28,6 +29,9 @@ Internal changes
         * ``xclim.testing.utils.nimbus`` replaces much of this functionality. See the `xclim` documentation for more information.
 * Many tests focused on evaluating the normal operation of remote file access tools under ``xclim.testing`` have been removed. (:pull:`1889`).
 * Setup and teardown functions that were found under ``tests/conftest.py`` have been optimized to reduce redundant calls when running ``pytest xclim``. Some obsolete `pytest` fixtures have also been removed.(:pull:`1889`).
+* Many ``DeprecationWarning`` and ``FutureWarning`` messages emitted from `xarray` and `pint` have been addressed. (:issue:`1719`, :pull:`1881`).
+* The codebase has been adjusted to address many `pylint`-related warnings and errors. In some cases, `casting` was used to redefine some `numpy` and `xarray` objects. (:issue:`1719`, :pull:`1881`).
+* ``xclim.core`` now uses absolute imports for clarity and some objects commonly used in the module have been moved to hidden submodules. (:issue:`1719`, :pull:`1881`).
 
 v0.52.0 (2024-08-08)
 --------------------

CI/requirements_ci.in

@@ -3,6 +3,6 @@ coveralls==4.0.1
 deptry==0.20.0
 flit==3.9.0
 pip==24.2
-pylint==3.2.6
+pylint==3.2.7
 tox==4.18.0
 tox-gh==1.3.2

CI/requirements_ci.txt

@@ -16,9 +16,9 @@ bracex==2.4 \
     --hash=sha256:a27eaf1df42cf561fed58b7a8f3fdf129d1ea16a81e1fadd1d17989bc6384beb \
     --hash=sha256:efdc71eff95eaff5e0f8cfebe7d01adf2c8637c8c92edaf63ef348c241a82418
     # via wcmatch
-bump-my-version==0.25.3 \
-    --hash=sha256:43638a60adee76d6d7112b7ab7403f0115a4db96d8e6276d935fcbed853673aa \
-    --hash=sha256:9a3752cccf5a4235d2e23705e09ba322f38b20ec162089b6af523049005c5245
+bump-my-version==0.26.0 \
+    --hash=sha256:9e2c01b7639960379440c4a371b3c8c0aa66cf6979985f1c9ba2e7c2fb4a185f \
+    --hash=sha256:fe35ebae91e92deebe809ce06bfa37303e45e4f087ad4a371f605702e767623f
     # via -r CI/requirements_ci.in
 cachetools==5.4.0 \
     --hash=sha256:3ae3b49a3d5e28a77a0be2b37dbcb89005058959cb2323858c2657c4a8cab474 \
@@ -193,19 +193,19 @@ coveralls==4.0.1 \
     --hash=sha256:7a6b1fa9848332c7b2221afb20f3df90272ac0167060f41b5fe90429b30b1809 \
     --hash=sha256:7b2a0a2bcef94f295e3cf28dcc55ca40b71c77d1c2446b538e85f0f7bc21aa69
     # via -r CI/requirements_ci.in
-deptry==0.19.1 \
-    --hash=sha256:023073247e5dac21254bf7b600ca2e2b71560652d2dfbe11535445ee912ca059 \
-    --hash=sha256:0bad85a77b31360d0f52383b14783fdae4a201b597c0158fe10e91a779c67079 \
-    --hash=sha256:1c12fea1d2301f42c7035c5636e4b9421457fde256fe7a241245662d20b4c841 \
-    --hash=sha256:2c6b2df353e5113fd2f787c2f7e694657548d388929e988e8644bd178e19fc5c \
-    --hash=sha256:3a20ef0dd1c737fb05553d1b9c2fa9f185d0c9d3d881d255334cef401ffdc599 \
-    --hash=sha256:43f33789b97b47313609e92b62fabf8a71bba0d35a7476806da5d3d152e32345 \
-    --hash=sha256:7344c6cea032b549d86e156aa1e679fb94cd44deb7e93f25cb6d9c0ded5ea06f \
-    --hash=sha256:a1abc119f9c8536b8ab1ee2122d4130665f33225d00d8615256ce354eb2c11ba \
-    --hash=sha256:a407bab3486e3844f93d702f1a381942873b2a46056c693b5634bbde219bb056 \
-    --hash=sha256:af8a0a9c42f8f92dfbc048e724fa89b9131f032f7e245812260560c214395abf \
-    --hash=sha256:c59142d9dca8873325692fbb7aa1d2902fde87020dcc8102f75120ba95515172 \
-    --hash=sha256:ff7d8954265c48ea334fdd508339c51d3fba05e2d4a8be47712c69d1c8d35c94
+deptry==0.20.0 \
+    --hash=sha256:012fb106dbea6ca95196cdcd75ac90c516c8f01292f7934f2e802a7cf025a660 \
+    --hash=sha256:0c90ce64e637d0e902bc97c5a020adecfee9e9f09ee0bf4c61554994139bebdb \
+    --hash=sha256:41434d95124851b83cb05524d1a09ad6fea62006beafed2ef90a6b501c1b237f \
+    --hash=sha256:62e9aaf3aea9e2ca66c85da98a0ba0290b4d3daea4e1d0ad937d447bd3c36402 \
+    --hash=sha256:6886ff44aaf26fd83093f14f844ebc84589d90df9bbad9a1625e8a080e6f1be2 \
+    --hash=sha256:8ce3920e2bd6d2b4427ab31ab8efb94bbef897001c2d395782bc30002966d12d \
+    --hash=sha256:9f92e7e97ef42477717747b190bc6796ab94b35655af126d8c577f7eae0eb3a9 \
+    --hash=sha256:ace3b39b1d0763f357c79bab003d1b135bea2eb61102be539992621a42d1ac7b \
+    --hash=sha256:b3b4b22d1406147de5d606a24042126cd74d52fdfdb0232b9c5fd0270d601610 \
+    --hash=sha256:d1a00f8c9e6c0829a4a523edd5e526e3df06d2b50e0a99446f09f9723df2efad \
+    --hash=sha256:e233859f150df70ffff76e95f9b7326fc25494b9beb26e776edae20f0f515e7d \
+    --hash=sha256:f6cee6005997791bb77155667be055333fb63ae9a24f0f103f25faf1e7affe34
     # via -r CI/requirements_ci.in
 dill==0.3.8 \
     --hash=sha256:3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca \
@@ -382,9 +382,9 @@ pygments==2.18.0 \
     --hash=sha256:786ff802f32e91311bff3889f6e9a86e81505fe99f2735bb6d60ae0c5004f199 \
     --hash=sha256:b8e6aca0523f3ab76fee51799c488e38782ac06eafcf95e7ba832985c8e7b13a
     # via rich
-pylint==3.2.6 \
-    --hash=sha256:03c8e3baa1d9fb995b12c1dbe00aa6c4bcef210c2a2634374aedeb22fb4a8f8f \
-    --hash=sha256:a5d01678349454806cff6d886fb072294f56a58c4761278c97fb557d708e1eb3
+pylint==3.2.7 \
+    --hash=sha256:02f4aedeac91be69fb3b4bea997ce580a4ac68ce58b89eaefeaf06749df73f4b \
+    --hash=sha256:1b7a721b575eaeaa7d39db076b6e7743c993ea44f57979127c517c6c572c803e
     # via -r CI/requirements_ci.in
 pyproject-api==1.7.1 \
     --hash=sha256:2dc1654062c2b27733d8fd4cdda672b22fe8741ef1dde8e3a998a9547b071eeb \

docs/conf.py

@@ -30,6 +30,7 @@
 xarray.CFTimeIndex.__module__ = "xarray"
 
 import xclim  # noqa
+from xclim import indicators as _indicators  # noqa
 from xclim.core.indicator import registry  # noqa
 
 # If extensions (or modules to document with autodoc) are in another
@@ -45,7 +46,7 @@
 indicators = {}
 # FIXME: Include cf module when its indicators documentation is improved.
 for module in ("atmos", "generic", "land", "seaIce", "icclim", "anuclim"):
-    for key, ind in getattr(xclim.indicators, module).__dict__.items():
+    for key, ind in getattr(_indicators, module).__dict__.items():
         if hasattr(ind, "_registry_id") and ind._registry_id in registry:  # noqa
             indicators[ind._registry_id] = {  # noqa
                 "realm": ind.realm,

docs/notebooks/analogs.ipynb

@@ -142,6 +142,7 @@
     "\n",
     "\n",
     "def plot_best_analog(scores, ax=None):\n",
+    "    \"\"\"Plot the best analog on the map.\"\"\"\n",
     "    scores1d = scores.stack(site=[\"lon\", \"lat\"])\n",
     "    lon, lat = scores1d.isel(site=scores1d.argmin(\"site\")).site.item()\n",
     "    ax = ax or plt.gca()\n",

docs/notebooks/benchmarks/sdba_quantile.ipynb

@@ -12,7 +12,6 @@
     "\n",
     "import numpy as np\n",
     "\n",
-    "import xclim\n",
     "from xclim import sdba\n",
     "from xclim.testing import open_dataset\n",
     "\n",
@@ -90,8 +89,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import time\n",
-    "\n",
     "import matplotlib.pyplot as plt\n",
     "import xarray as xr\n",
     "\n",

docs/notebooks/customize.ipynb

@@ -174,10 +174,12 @@
     "    \"\"\"Any period with more than max_n consecutive missing values is considered invalid\"\"\"\n",
     "\n",
     "    def is_missing(self, null, count, max_n=5):\n",
+    "        \"\"\"Return a boolean mask where True values are for elements that are considered missing and masked on the output.\"\"\"\n",
     "        return null.map(longest_run, dim=\"time\") >= max_n\n",
     "\n",
     "    @staticmethod\n",
     "    def validate(max_n):\n",
+    "        \"\"\"Return whether the options are valid.\"\"\"\n",
     "        return max_n > 0"
    ]
   },

docs/notebooks/ensembles-advanced.ipynb

@@ -297,7 +297,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "## NESTED results using KKZ\n",
+    "# NESTED results using KKZ\n",
     "for n in np.arange(5, 15, 3):\n",
     "    ids = ensembles.kkz_reduce_ensemble(crit, num_select=n)\n",
     "    print(ids)"
@@ -313,7 +313,7 @@
    },
    "outputs": [],
    "source": [
-    "## UNNESTED results using k-means\n",
+    "# UNNESTED results using k-means\n",
     "for n in np.arange(5, 15, 3):\n",
     "    ids, cluster, fig_data = ensembles.kmeans_reduce_ensemble(\n",
     "        crit, method={\"n_clusters\": n}, random_state=42, make_graph=True\n",

docs/notebooks/ensembles.ipynb

@@ -155,16 +155,15 @@
    },
    "outputs": [],
    "source": [
-    "import xarray as xr\n",
-    "\n",
-    "# Set display to HTML style (for fancy output)\n",
-    "xr.set_options(display_style=\"html\", display_width=50)\n",
-    "\n",
     "import matplotlib as mpl\n",
     "import matplotlib.pyplot as plt\n",
+    "import xarray as xr\n",
     "\n",
     "from xclim import ensembles\n",
     "\n",
+    "# Set display to HTML style (for fancy output)\n",
+    "xr.set_options(display_style=\"html\", display_width=50)\n",
+    "\n",
     "%matplotlib inline\n",
     "\n",
     "ens = ensembles.create_ensemble(data_folder.glob(\"ens_tas_m*.nc\")).load()\n",