Merge branch 'main' into mbcn-map-blocks

.github/workflows/bump-version.yml

@@ -51,7 +51,7 @@ jobs:
           app-id: ${{ secrets.OURANOS_HELPER_BOT_ID }}
           private-key: ${{ secrets.OURANOS_HELPER_BOT_KEY }}
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           token: ${{ steps.token_generator.outputs.token }}
       - name: Set up Python3

.github/workflows/cache-cleaner.yml

@@ -25,7 +25,7 @@ jobs:
             objects.githubusercontent.com:443
 
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
 
       - name: Cleanup
         run: |

.github/workflows/codeql.yml

@@ -52,7 +52,7 @@ jobs:
             pypi.org:443
             uploads.github.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       # Initializes the CodeQL tools for scanning.
       - name: Initialize CodeQL
         uses: github/codeql-action/init@1245696032ecf7d39f87d54daa406e22ddf769a8

.github/workflows/dependency-review.yml

@@ -26,7 +26,7 @@ jobs:
             github.com:443
 
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
 
       - name: Dependency Review
         uses: actions/dependency-review-action@5a2ce3f5b92ee19cbb1541a4984c76d921601d7c # v4.3.4

.github/workflows/main.yml

@@ -49,7 +49,7 @@ jobs:
             github.com:443
             pypi.org:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Set up Python3
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
@@ -59,7 +59,7 @@ jobs:
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Environment Caching
-        uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4.1.0
+        uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4.1.1
         with:
           path: |
             ${{ matrix.testdata-cache }}
@@ -95,7 +95,7 @@ jobs:
             pypi.org:443
             raw.githubusercontent.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Set up Python${{ matrix.python-version }}
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:
@@ -105,7 +105,7 @@ jobs:
         run: |
           python -m pip install --require-hashes -r CI/requirements_ci.txt
       - name: Environment Caching
-        uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4.1.0
+        uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4.1.1
         with:
           path: |
             ${{ matrix.testdata-cache }}
@@ -193,7 +193,7 @@ jobs:
             pypi.org:443
             raw.githubusercontent.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Install Eigen3 (SBCK)
         if: ${{ matrix.python-version == '3.11' && matrix.os == 'ubuntu-latest' }}
         run: |
@@ -210,7 +210,7 @@ jobs:
       - name: Environment Caching
         # if prefetch is not in tox-env
         if: contains(matrix.tox-env, 'prefetch') == false
-        uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4.1.0
+        uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4.1.1
         with:
           path: |
             ${{ matrix.testdata-cache }}
@@ -267,7 +267,7 @@ jobs:
             raw.githubusercontent.com:443
             repo.anaconda.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
         uses: mamba-org/setup-micromamba@617811f69075e3fd3ae68ca64220ad065877f246 # v2.0.0
         with:
@@ -280,7 +280,7 @@ jobs:
         run: |
           echo "micromamba: $(micromamba --version)"
       - name: Test Data Caching
-        uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4.1.0
+        uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4.1.1
         with:
           path: |
             ${{ matrix.testdata-cache }}
@@ -329,6 +329,6 @@ jobs:
           disable-sudo: true
           egress-policy: audit
       - name: Coveralls Finished
-        uses: coverallsapp/github-action@643bc377ffa44ace6394b2b5d0d3950076de9f63 # v2.3.0
+        uses: coverallsapp/github-action@43f11c4e058174f808ee9cd63701b6c42fe3f5e3 # v2.3.2
         with:
           parallel-finished: true

.github/workflows/publish-mastodon.yml

@@ -35,7 +35,7 @@ jobs:
             github.com:443
 
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
 
       - name: Current Version
         if: ${{ !github.event.inputs.version-tag }}

.github/workflows/publish-pypi.yml

@@ -28,7 +28,7 @@ jobs:
             pypi.org:443
             upload.pypi.org:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Set up Python3
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:

.github/workflows/scorecard.yml

@@ -35,7 +35,7 @@ jobs:
           egress-policy: audit
 
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871
         with:
           persist-credentials: false
 
@@ -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@50769540e7f4bd5e21e526ee35c689e35e0d6874
+        uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882
         with:
           name: SARIF file
           path: results.sarif

.github/workflows/tag-testpypi.yml

@@ -28,7 +28,7 @@ jobs:
             pypi.org:443
             test.pypi.org:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Set up Python3
         uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5.2.0
         with:

.github/workflows/testdata-version.yml

@@ -30,7 +30,7 @@ jobs:
             api.github.com:443
             github.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
       - name: Find xclim-testdata Tag and CI Testing Branch
         run: |
           XCLIM_TESTDATA_TAG="$( \

.github/workflows/upstream.yml

@@ -54,7 +54,7 @@ jobs:
             raw.githubusercontent.com:443
             repo.anaconda.com:443
       - name: Checkout Repository
-        uses: actions/checkout@d632683dd7b4114ad314bca15554477dd762a938 # v4.2.0
+        uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4.2.1
         with:
           fetch-depth: 0 # Fetch all history for all branches and tags.
       - name: Setup Conda (Micromamba) with Python${{ matrix.python-version }}
@@ -85,7 +85,7 @@ jobs:
           xclim show_version_info
           python -m pip check || true
       - name: Test Data Caching
-        uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4.1.0
+        uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4.1.1
         with:
           path: |
             ${{ matrix.testdata-cache }}

CHANGELOG.rst

@@ -2,9 +2,17 @@
 Changelog
 =========
 
-v0.53.0 (unreleased)
+v0.54.0 (unreleased)
 --------------------
-Contributors to this version: Adrien Lamarche (:user:`LamAdr`), Trevor James Smith (:user:`Zeitsperre`),  Éric Dupuis (:user:`coxipi`), Pascal Bourgault (:user:`aulemahal`), Sascha Hofmann (:user:`saschahofmann`), David Huard (:user:`huard`).
+Contributors to this version: Éric Dupuis (:user:`coxipi`).
+
+New features and enhancements
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+* `xclim.sdba.MBCn` nows uses `map_groups` to performing grouping operations, as other adjustment methods. (:pull:`1951`)
+
+v0.53.0 (2024-10-17)
+--------------------
+Contributors to this version: Adrien Lamarche (:user:`LamAdr`), Trevor James Smith (:user:`Zeitsperre`), Éric Dupuis (:user:`coxipi`), Pascal Bourgault (:user:`aulemahal`), Sascha Hofmann (:user:`saschahofmann`), David Huard (:user:`huard`).
 
 Announcements
 ^^^^^^^^^^^^^
@@ -15,32 +23,35 @@ New indicators
 ^^^^^^^^^^^^^^
 * New ``heat_spell_frequency``, ``heat_spell_max_length`` and ``heat_spell_total_length`` : spell length statistics on a bivariate condition that uses the average over a window by default. (:pull:`1885`, :pull:`1778`).
 * New ``hot_spell_max_magnitude`` : yields the magnitude of the most intensive heat wave. (:pull:`1926`).
-* New ``chill_portion`` and ``chill_unit``: chill portion based on the Dynamic Model and chill unit based on the Utah model indicators. (:issue:`1753`, :pull:`1909`).
-* New ``water_cycle_intensity``: yields the sum of precipitation and actual evapotranspiration. (:issue:`410`, :pull:`1947`).
+* New ``chill_portion`` and ``chill_unit`` : chill portion based on the Dynamic Model and chill unit based on the Utah model indicators. (:issue:`1753`, :pull:`1909`).
+* New ``water_cycle_intensity`` : yields the sum of precipitation and actual evapotranspiration. (:issue:`410`, :pull:`1947`).
 
 New features and enhancements
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-* New generic ``xclim.indices.generic.spell_mask``  that returns a mask of which days are part of a spell. Supports multivariate conditions and weights. Used in new generic index ``xclim.indices.generic.bivariate_spell_length_statistics`` that extends ``spell_length_statistics`` to two variables.  (:pull:`1885`).
+* New generic ``xclim.indices.generic.spell_mask``  that returns a mask of which days are part of a spell. Supports multivariate conditions and weights. Used in new generic index ``xclim.indices.generic.bivariate_spell_length_statistics`` that extends ``spell_length_statistics`` to two variables. (:pull:`1885`).
 * Indicator parameters can now be assigned a new name, different from the argument name in the compute function. (:pull:`1885`).
-* ``xclim.indices.run_length.windowed_max_run_sum`` accumulates positive values across runs and yields the the maximum valued run. (:pull:`1926`).
+* Add attribute ``units_metadata`` to outputs representing a difference between temperatures. This is needed to disambiguate temperature differences from absolute temperature. Changes affect indicators ``daily_temperature_range``, ``daily_temperature_range_variability``, ``extreme_temperature_range``, ``interday_diurnal_temperature_range``, and all degree-day indicators. Implemented using a new ``pint2cfattrs`` function to convert pint units to a dictionary of CF attributes. ``units2pint`` is also modified to support ``units_metadata`` attributes in DataArrays. Some SDBA properties and measures previously returning units of ``delta_degC`` will now return the original input DataArray units accompanied with the ``units_metadata`` attribute. (:issue:`1822`, :pull:`1830`).
+* ``xclim.indices.run_length.windowed_max_run_sum`` accumulates positive values across runs and yields the maximum valued run. (:pull:`1926`).
 * Helper function ``xclim.indices.helpers.make_hourly_temperature`` to estimate hourly temperatures from daily min and max temperatures. (:pull:`1909`).
 * New global option ``resample_map_blocks`` to wrap all ``resample().map()`` code inside a ``xr.map_blocks`` to lower the number of dask tasks. Uses utility ``xclim.indices.helpers.resample_map`` and requires ``flox`` to ensure the chunking allows such block-mapping. Defaults to False. (:pull:`1848`).
 * ``xclim.indices.run_length.runs_with_holes`` allows to input a condition that must be met for a run to start and a second condition that must be met for the run to stop. (:pull:`1778`).
-* New generic compute function ``xclim.indices.generic.thresholded_events`` that finds events based on a threshold condition and returns basic stats for each. See also ``xclim.indices.run_length.find_events``. (:pull:`1778`).
+* New generic compute function ``xclim.indices.generic.thresholded_events`` that finds events based on a threshold condition and returns basic stats for each. See also: ``xclim.indices.run_length.find_events``. (:pull:`1778`).
 * ``xclim.core.units.rate2amount`` and ``xclim.core.units.amount2rate`` can now also accept quantities (pint objects or strings), in which case the ``dim`` argument must be the ``time`` coordinate through which we can find the sampling rate. (:pull:`1778`).
-* `xclim.sdba.MBCn` nows uses `map_groups` to performing grouping operations, as other adjustment methods. (:pull:`1951`)
+* ``xclim.indices.stats.standardized_index`` now supports a weekly resampling frequency. Only "standard" calendars using `numpy`'s ``datetime64`` dtype are supported for this mode. (:issue:`1892`, :pull:`1952`)
 
 Bug fixes
 ^^^^^^^^^
-* Fixed a small inefficiency in ``_otc_adjust``, and the `standardize` method of `OTC/dOTC` is now applied on individual variable  (:pull:`1890`, :pull:`1896`).
-* Remove deprecated cells in the tutorial notebook `sdba.ipynb` (:pull:`1895`).
+* Fixed ``rate2amount`` and ``amount2rate`` for sub-daily frequencies. (:issue:`1962`, :pull:`1963`).
+* Added the liquid water equivalent thickness ("[length]") to amount ("[mass]/[area]") transformation to the ``hydro`` context (the inverse operation was already there). (:pull:`1963`).
+* Fixed a small inefficiency in ``_otc_adjust``, and the `standardize` method of `OTC/dOTC` is now applied on individual variable. (:pull:`1890`, :pull:`1896`).
+* Removed deprecated cells in the tutorial notebook ``sdba.ipynb``. (:pull:`1895`).
 
 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`).
-* `transform` argument of `OTC/dOTC` classes (and child functions) is changed to `normalization`, and `numIterMax` is changed to `num_iter_max` in `utils.optimal_transport` (:pull:`1896`).
-* `xclim` now requires `numpy >=1.23.0` and `scikit-learn >=1.1.0`, as well as (optionally) `ipython >=8.5.0`, `nbsphinx >=0.9.5`, and `matplotlib >=3.6.0` . (:issue:`1914`, :pull:`1915`).
+* 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`).
+* The `transform` argument of `OTC/dOTC` classes (and child functions) has been changed to `normalization`, and `numIterMax` has been changed to `num_iter_max` in ``xclim.core.utils.optimal_transport`` (:pull:`1896`).
+* `xclim` now requires `numpy >=1.23.0` and `scikit-learn >=1.1.0`, as well as (optionally) `ipython >=8.5.0`, `nbsphinx >=0.9.5`, and `matplotlib >=3.6.0`. (:issue:`1914`, :pull:`1915`).
 
 Internal changes
 ^^^^^^^^^^^^^^^^
@@ -51,18 +62,21 @@ Internal changes
     * ``xclim.testing.utils.get_file``, ``xclim.testing.utils.get_local_testdata``, ``xclim.testing.utils.list_datasets``, and ``xclim.testing.utils.file_md5_checksum`` have been removed.
         * ``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`).
+* Setup and teardown functions that were found under ``tests/conftest.py`` have been optimised 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`).
+* The code base 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`).
-* ``xclim.core.indicator.Parameter`` has a new attribute ``compute_name`` while ``xclim.core.indicator.Indicator`` lost its ``_variable_mapping``. The translation from parameter (and variable) names in the indicator to the names on the compute function is handled by ``Indicator._get_compute_args``. (:pull:`1885`).
+* ``xclim.core.indicator.Parameter`` has a new attribute ``compute_name`` while ``xclim.core.indicator.Indicator`` lost its ``_variable_mapping``. The translation from parameter (and variable) names in the indicator to the names on the compute function is now handled by ``Indicator._get_compute_args``. (:pull:`1885`).
 * Adopted many linting and formatting suggestions from the Scientific Python `repo-review <https://github.com/scientific-python/repo-review>`_ tool: (:pull:`1910`)
     * Applied several linting suggestions adopted by the `scipy` community.
     * Replaced `isort` with `ruff`-based import-sorting formatting.
     * Added formatting for `Markdown` files.
     * Added the `bugbear`, `pyupgrade` checks to the `ruff` formatter.
     * Adjusted `mypy` checks to be more standardized.
 * Renamed annual deprecated frequency alias `"A"` to `"Y"` (:pull:`1930`).
+* The ``indices`` documentation now includes the members of ``xclim.indices.stats``. (:issue:`1913`, :pull:`1958`).
+* The default URL for fetching testing data is now set to the ``raw.githubusercontent.com`` mirror of `xclim-testdata`. (:pull:`1961`).
+* The ``upstream`` `tox` environment has been updated to not install the latest `numpy` until `numba` supports it. (:pull:`1961`).
 
 CI changes
 ^^^^^^^^^^

CI/requirements_ci.in

@@ -4,4 +4,4 @@ flit==3.9.0
 pip==24.2.0
 pylint==3.3.1
 tox==4.21.2
-tox-gh==1.4.1
+tox-gh==1.4.4