Merge branch 'main' into spi_loc

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

@@ -24,7 +24,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
 
-      - uses: actions/add-to-project@1b844f0c5ac6446a402e0cb3693f9be5eca188c5 # v0.6.1
+      - uses: actions/add-to-project@9bfe908f2eaa7ba10340b31e314148fcfe6a2458 # v1.0.1
         with:
           project-url: https://github.com/orgs/Ouranosinc/projects/6
           github-token: ${{ secrets.ADD_TO_PROJECT_TOKEN }}

.github/workflows/bump-version.yml

@@ -46,7 +46,7 @@ jobs:
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
         with:
           persist-credentials: false
-      - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Config Commit Bot

.github/workflows/dependency-review.yml

@@ -29,4 +29,4 @@ jobs:
         uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
 
       - name: 'Dependency Review'
-        uses: actions/dependency-review-action@0fa40c3c10055986a88de3baa0d6ec17c5a894b3
+        uses: actions/dependency-review-action@5bbc3ba658137598168acb2ab73b21c432dd411b

.github/workflows/label-on-approval.yml

@@ -63,7 +63,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
       - name: Find comment
-        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
+        uses: peter-evans/find-comment@3eae4d37986fb5a8592848f6a574fdf654e61f9e # v3.1.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}

.github/workflows/main.yml

@@ -54,7 +54,7 @@ jobs:
             pypi.org:443
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install pylint and tox
@@ -92,7 +92,7 @@ jobs:
             raw.githubusercontent.com:443
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox
@@ -175,7 +175,7 @@ jobs:
           sudo apt-get update
           sudo apt-get install libeigen3-dev
       - name: Set up Python${{ matrix.python-version }}
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install tox

.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@23ae66e7b229f11174f6018873c5f8ce3d7a6391 # v2.0.5
+        uses: cbrgm/mastodon-github-action@1c5321597ce853344afff70aa5685887243f43fa # v2.0.6
         with:
           url: ${{ secrets.MASTODON_URL }}
           access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}

.github/workflows/publish-pypi.yml

@@ -29,7 +29,7 @@ jobs:
             upload.pypi.org:443
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
       - name: Set up Python3
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Install packaging libraries

.github/workflows/tag-testpypi.yml

@@ -29,7 +29,7 @@ jobs:
             test.pypi.org:443
       - uses: actions/checkout@9bb56186c3b09b4f86b1c65136769dd318469633 # v4.1.2
       - name: Set up Python3
-        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5.0.0
+        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5.1.0
         with:
           python-version: "3.x"
       - name: Install packaging libraries

.github/workflows/testdata-version.yml

@@ -46,7 +46,7 @@ jobs:
           echo "Latest xclim-testdata tag: ${{ env.XCLIM_TESTDATA_TAG }}"
           echo "Tag for xclim-testdata in CI: ${{ env.XCLIM_TESTDATA_BRANCH }}"
       - name: Find Comment
-        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
+        uses: peter-evans/find-comment@3eae4d37986fb5a8592848f6a574fdf654e61f9e # v3.1.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}

.github/workflows/workflow-warning.yml

@@ -33,7 +33,7 @@ jobs:
           allowed-endpoints: >
             api.github.com:443
       - name: Find comment
-        uses: peter-evans/find-comment@d5fe37641ad8451bdd80312415672ba26c86575e # v3.0.0
+        uses: peter-evans/find-comment@3eae4d37986fb5a8592848f6a574fdf654e61f9e # v3.1.0
         id: fc
         with:
           issue-number: ${{ github.event.pull_request.number }}

.pre-commit-config.yaml

@@ -3,7 +3,7 @@ default_language_version:
 
 repos:
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
+    rev: v3.15.2
     hooks:
       - id: pyupgrade
         args: ['--py39-plus']
@@ -28,7 +28,7 @@ repos:
       - id: toml-sort-fix
         exclude: '.pylintrc.toml'
   - repo: https://github.com/adrienverge/yamllint.git
-    rev: v1.33.0
+    rev: v1.35.1
     hooks:
       - id: yamllint
         args: [ '--config-file=.yamllint.yaml' ]
@@ -41,11 +41,11 @@ repos:
     hooks:
       - id: isort
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.2.0
+    rev: v0.3.5
     hooks:
       - id: ruff
   - repo: https://github.com/pylint-dev/pylint
-    rev: v3.0.3
+    rev: v3.1.0
     hooks:
       - id: pylint
         args: [ '--rcfile=.pylintrc.toml', '--errors-only', '--jobs=0', '--disable=import-error' ]
@@ -56,7 +56,7 @@ repos:
         additional_dependencies: [ 'flake8-alphabetize', 'flake8-rst-docstrings ']
         args: [ '--config=.flake8' ]
   - repo: https://github.com/nbQA-dev/nbQA
-    rev: 1.7.1
+    rev: 1.8.5
     hooks:
       - id: nbqa-pyupgrade
         args: [ '--py39-plus' ]
@@ -85,7 +85,7 @@ repos:
     hooks:
       - id: gitleaks
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: 0.27.4
+    rev: 0.28.1
     hooks:
       - id: check-github-workflows
       - id: check-readthedocs

CHANGES.rst

@@ -4,7 +4,7 @@ Changelog
 
 v0.49.0 (unreleased)
 --------------------
-Contributors to this version: Trevor James Smith (:user:`Zeitsperre`), Pascal Bourgault (:user:`aulemahal`), Éric Dupuis (:user:`coxipi`).
+Contributors to this version: Trevor James Smith (:user:`Zeitsperre`), Pascal Bourgault (:user:`aulemahal`), Juliette Lavoie (:user:`juliettelavoie`), Éric Dupuis (:user:`coxipi`).
 
 Announcements
 ^^^^^^^^^^^^^
@@ -22,6 +22,8 @@ Bug fixes
 ^^^^^^^^^
 * Fixed an bug in sdba's ``map_groups`` that prevented passing DataArrays with cftime coordinates if the ``sdba_encode_cf`` option was True. (:issue:`1673`, :pull:`1674`).
 * Fixed bug (:issue:`1678`, :pull:`1679`) in sdba where a loaded training dataset could not be used for adjustment
+* Fixed bug with loess smoothing for an array full of NaNs. (:pull:`1699`).
+* Fixed and adapted ``time_bnds`` to the newest xarray. (:pull:`1700`)
 
 Internal changes
 ^^^^^^^^^^^^^^^^

pyproject.toml

@@ -123,7 +123,7 @@ target-version = [
 ]
 
 [tool.bumpversion]
-current_version = "0.48.3-dev.3"
+current_version = "0.48.3-dev.5"
 commit = true
 commit_args = "--no-verify"
 tag = false

tests/test_calendar.py

@@ -61,6 +61,7 @@ def da(index):
 @pytest.mark.parametrize("freq", ["6480h", "302431min", "23144781s"])
 def test_time_bnds(freq, datetime_index, cftime_index):
     da_datetime = da(datetime_index).resample(time=freq)
+    out_time = da_datetime.mean()
     da_cftime = da(cftime_index).resample(time=freq)
 
     cftime_bounds = time_bnds(da_cftime, freq=freq)
@@ -72,16 +73,9 @@ def test_time_bnds(freq, datetime_index, cftime_index):
     # cftime resolution goes down to microsecond only, code below corrects
     # that to allow for comparison with pandas datetime
     cftime_ends += np.timedelta64(999, "ns")
-    if hasattr(da_datetime, "_full_index"):
-        datetime_starts = da_datetime._full_index.to_period(freq).start_time
-        datetime_ends = da_datetime._full_index.to_period(freq).end_time
-    else:
-        datetime_starts = (
-            da_datetime.groupers[0].group_as_index.to_period(freq).start_time
-        )
-        datetime_ends = da_datetime.groupers[0].group_as_index.to_period(freq).end_time
-    assert_array_equal(cftime_starts, datetime_starts)
-    assert_array_equal(cftime_ends, datetime_ends)
+    out_periods = out_time.indexes["time"].to_period(freq)
+    assert_array_equal(cftime_starts, out_periods.start_time)
+    assert_array_equal(cftime_ends, out_periods.end_time)
 
 
 @pytest.mark.parametrize("typ", ["pd", "xr"])

tests/test_sdba/test_loess.py

@@ -1,7 +1,9 @@
 from __future__ import annotations
 
 import numpy as np
+import pandas as pd
 import pytest
+import xarray as xr
 
 from xclim.sdba.loess import _constant_regression  # noqa
 from xclim.sdba.loess import _gaussian_weighting  # noqa
@@ -62,3 +64,22 @@ def test_loess_smoothing(use_dask, open_dataset):
     # Same but we force not to use the optimization
     tasmooth3 = loess_smoothing(tas, f=0.1, equal_spacing=False)
     np.testing.assert_allclose(tasmooth, tasmooth3, rtol=1e-3, atol=1e-3)
+
+
+@pytest.mark.slow
+@pytest.mark.parametrize("use_dask", [True, False])
+def test_loess_smoothing_nan(use_dask):
+    # create data with one axis full of nan
+    data = np.random.randn(2, 2, 10)
+    data[0, 0] = [np.nan] * 10
+    da = xr.DataArray(
+        data,
+        dims=["scenario", "model", "time"],
+        coords={"time": pd.date_range("2000-01-01", periods=10, freq="YS")},
+    ).chunk({"time": -1})
+
+    out = loess_smoothing(da)
+
+    assert out.dims == da.dims
+    # check that the output is all nan on the axis with nan in the input
+    assert np.isnan(out.values[0, 0]).all()

xclim/__init__.py

@@ -16,7 +16,7 @@
 
 __author__ = """Travis Logan"""
 __email__ = "[email protected]"
-__version__ = "0.48.3-dev.3"
+__version__ = "0.48.3-dev.5"
 
 
 _module_data = _files("xclim.data")

xclim/core/calendar.py

@@ -1077,8 +1077,14 @@ def time_bnds(  # noqa: C901
     elif isinstance(time, (DataArrayResample, DatasetResample)):
         for grouper in time.groupers:
             if "time" in grouper.dims:
-                time = grouper.group_as_index
+                datetime = grouper.unique_coord.data
+                freq = freq or grouper.grouper.freq
+                if datetime.dtype == "O":
+                    time = xr.CFTimeIndex(datetime)
+                else:
+                    time = pd.DatetimeIndex(datetime)
                 break
+
         else:
             raise ValueError(
                 'Got object resampled along another dimension than "time".'

xclim/sdba/loess.py

@@ -95,6 +95,8 @@ def _loess_nb(
         out = np.full(x.size, np.NaN)
         y = y[~nan]
         x = x[~nan]
+        if x.size == 0:
+            return out
 
     n = x.size
     yest = np.zeros(n)