Xclim

--------------------
Contributors to this version: Trevor James Smith (:user:`Zeitsperre`), Pascal Bourgault (:user:`aulemahal`), Ludwig Lierhammer (:user:`ludwiglierhammer`), Éric Dupuis (:user:`coxipi`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* New properties ``xclim.sdba.properties.decorrelation_length`` and ``xclim.sdba.properties.transition_probability``. (:pull:`1252`)

New indicators
^^^^^^^^^^^^^^
* New indices and indicators for converting from snow water equivalent to snow depth (``snw_to_snd``) and snow depth to snow water equivalent (``snd_to_snw``) using snow density [kg/m^3]. (:pull:`1271`).
* New indices and indicators for determining upwelling radiation (`shortwave_upwelling_radiation_from_net_downwelling` and `longwave_upwelling_radiation_from_net_downwelling`; CF variables `rsus` and `rlus`) from net and downwelling radiation (shortwave: `rss` and `rsds`; longwave: `rls` and `rlds`). (:pull:`1271`).
* New indice and indicator ``{snd | snw}_season_{length | start | end}`` which generalize ``snow_cover_duration`` and ``continuous_snow_cover_{start | end}`` to allow using these functions with variable `snw` (:pull:`1275`).
* New indice and indicator (``dryness_index``) for estimating soil humidity classifications for winegrowing regions (based on Riou et al. (1994)). (:issue:`355`, :pull:`1235`).
* ``ensembles.change_significance`` now supports Mann-whitney U-test and flexible ``realization``. (:pull:`1285`).

Breaking changes
^^^^^^^^^^^^^^^^
* `xclim` testing default behaviours have been changed (:issue:`1295`, :pull:`1297`):
* Running `$ pytest` will no longer use `pytest-xdist` distributed testing be default (can be set with ``-n auto|logical|``. Coverage is also no longer gathered/reported by default.
* Running `$ tox` will now set `pytest-xdist` to use ``-n logical`` processes (with a max of 10).
* Default behaviour for testing is to no longer always fetch `xclim-testdata`. If testdata is found in ``$HOME/.xclim_testing_data``, files will be copied to individual processes, otherwise, will be fetched as needed.
* Environment variables evaluated when running pytest have been changed (:issue:`1295`, :pull:`1297`):
* For testing against specific branches of `xclim-testdata`: ``MAIN_TESTDATA_BRANCH`` -> ``XCLIM_TESTDATA_BRANCH``
* The option to skip fetching of testdata (``SKIP_TEST_DATA``) has been removed
* A new environment variable (``XCLIM_PREFETCH_TESTING_DATA``) is now available to gather `xclim-testdata` before running test ensemble (default: `False`).
* Environment variables are now passed to `tox` on execution.

Bug fixes
^^^^^^^^^
* ``build_indicator_module_from_yaml`` now accepts a ``reload`` argument. When re-building a module that already exists, ``reload=True`` removes all previous indicator before creating the new ones. (:issue:`1192`,:pull:`1284`).
* The test for french translations of official indicators was fixed and translations for CFFWIS indices, FFDI, KDBI, DF and Jetstream metric woollings have been added or fixed. (:pull:`1271`).
* ``use_ufunc`` in ``windowed_run_count`` is now supplied with argument ``freq`` to warn users that the 1d method does not support resampling after run length operations (:issue:`1279`, :pull:`1291`).
* ``{snd|snw}_max_doy`` now avoids an error due to `xr.argmax` when there are all-NaN slices. (:pull:`1277`).

Internal changes
^^^^^^^^^^^^^^^^
* `xclim` has adopted `PEP 517 <https://peps.python.org/pep-0517/>`_ and `PEP 621 <https://peps.python.org/pep-0621/>`_ (``pyproject.toml`` using the `flit <https://flit.pypa.io/en/stable/>`_ backend) to replace the legacy ``setup.py`` used to manage package organisation and building. Many tooling configurations that already supported the ``pyproject.toml`` standard have been migrated to this file. CI and development tooling documentation has been updated to reflect these changes. (:pull:`1278`, suggested from `PyOpenSci Software Review <https://github.com/pyOpenSci/software-review/issues/73>`_).
* Documentation source files have been moved around to remove some duplicated image files. (:pull:`1278`).
* Coveralls GitHub Action removed as it did not support ``pyproject.toml``-based configurations. (:pull:`1278`).
* Add a remark about how `xclim`'s CFFWIS is different from the original 1982 implementation. (:issue:`1104`, :pull:`1284`).
* Update CI runs to use Python3.9 when examining upstream dependencies. Replace `setup-conda` action with `provision-with-micromamba` action. (:pull:`1286`).
* Update CI runs to always use `tox~=4.0` and the `latest` virtual machine images (now `ubuntu-22.04`). (:pull:`1288`, :pull:`1297`).
* `SBCK` installation command now points to the official development repository. (:pull:`1288`).
* Some references in the BibTeX were updated to point to better resources. (:pull:`1288`).
* Add a GitHub CI workflow for performing dependency security review scanning. (:pull:`1287`).
* Grammar and spelling corrections were applied to some docstrings. (:pull:`1271`).
* Added `[radiation]` (`[power] / [area]`) to list of defined acceptable units. (:pull:`1271`).
* Updated testing data used to generate the `atmosds` dataset to use more reproducibly-converted ERA5 data, generated with the `miranda` Python package. (:pull:`1269`).
* Updated testing dependencies to use `pytest-xdist>=3.2`, allowing for the new `--dist=worksteal` scheduler for distributing the pool of remaining tests across workers after individual workers have exhausted their own queues. (:pull:`1235`).
* Adding infer context to the unit conversion in of the training of ExtremeValues. (:pull:`1299`).
* Added `sphinxcontrib-svg2pdfconverter` for converting SVG graphics within documentation to PDF-compatible images. (:pull:`1296`).
* README badges for supported Python versions and repository health have been added. (:issue:`1304`, :pull:`1307`).

--------------------
Contributors to this version: Trevor James Smith (:user:`Zeitsperre`), Pascal Bourgault (:user:`aulemahal`), David Huard (:user:`huard`), Juliette Lavoie (:user:`juliettelavoie`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Virtual modules can add variables to ``xclim.core.utils.VARIABLES`` through the new `variables` section of the yaml files. (:issue:`1129`, :pull:`1231`).
* ``xclim.core.units.convert_units_to`` can now perform automatic conversions based on the standard name of the input when needed. (:issue:`1205`, :pull:`1206`).
- Conversion from amount (thickness) to flux (rate), using ``amount2rate`` and ``rate2amount``.
- Conversion from amount to thickness for liquid water quantities, using the new ``amount2lwethickness`` and ``lwethickness2amount``. This is similar to the implicit transformations enabled by the "hydro" unit context.
- Passing ``context='infer'`` will activate the "hydro" context if the source or the target are DataArrays with a standard name that is compatible, as decided by the new ``xclim.core.units.infer_context`` function.
* New `generic` indicator realm. Now holds indicators previously meant for streamflow analysis in the `land` realm: `fit`, `return_level` (previously `freq_analysis`) and `stats`. (:issue:`1130`, :pull:`1225`).
* Thresholds and other quantities passed as parameters of indicators can now be multi-dimensional `DataArray`s. `xarray` broadcasting mechanisms will apply. These parameters are now annotated as "Quantity" in the signatures (``xclim.core.utils.Quantity``), instead of "str" as before. Attributes where such thresholds where included will now read "<an array>" (french: "<une matrice>") for these new cases. Multi-dimensional quantities are still largely unsupported, except where documented in the docstring. (:issue:`1093`, :pull:`1236`).

Breaking changes
^^^^^^^^^^^^^^^^
* Rewrite of ``xclim.core.calendar.time_bnds``. It should now be more resilient and versatile, but all ``cftime_*`` and ``cfindex_*`` functions were removed. (:issue:`74`, :pull:`1207`).
* `hydro` context is not always enabled, as it led to unwanted unit conversions. Unit conversion operations now need to explicitly declare the `hydro` context to support conversions from `kg / m2 /s` to `mm/day`. (:issue:`1208`, :pull:`1227`).
* Many previously deprecated indices and indicators have been removed from `xclim` (:pull:`1228`), with replacement indices/indicators suggested as follows:
- ``xclim.indicators.atmos.fire_weather_indexes`` → ``xclim.indicators.atmos.cffwis_indices``
- ``xclim.indices.freshet_start`` → ``xclim.indices.first_day_temperature_above``
- ``xclim.indices.first_day_above`` → ``xclim.indices.first_day_temperature_above``
- ``xclim.indices.first_day_below`` → ``xclim.indices.first_day_temperature_below``
- ``xclim.indices.tropical_nights`` → ``xclim.indices.tn_days_above``
- ``xclim.indices.generic.degree_days`` → ``xclim.indices.generic.cumulative_difference``
* The following *modules* have been removed (:pull:`1228`):
- `xclim.indices.fwi` → functions migrated to `xclim.indices.fire`
- `xclim.subset` (mock submodule) → functions migrated to `clisops.core.subset`
* Indicators ``standardized_precipitation_index`` and ``standardized_precipitation_evapotranspiration_index`` will now require ``pr_cal`` and ``wb_cal`` as keyword arguments only. (:pull:`1236`).
* The internal object ``PercentileDataArray`` has been removed. (:pull:`1236`).
* The ``xclim.testing.utils.get_all_CMIP6_variables`` and ``xclim.testing.utils.update_variable_yaml`` function were removed as the former was extremely slow and unusable. (:pull:`1258`).
* The wind speed input of ``atmos.potential_evapotranspiration`` and ``atmos.water_budget`` was renamed to ``sfcWind`` (capital W) as this is the correct CMIP6 name. (:pull:`1258`).
* Indicator `land.stats`, `land.fit` and `land.freq_analysis` are now deprecated and will be removed in version 0.43. They are being phased out in favor of generic indicators `generic.stats`, `generic.fit` and `generic.return_level` respectively. (:issue:`1130`, :pull:`1225`).

Bug fixes
^^^^^^^^^
* The weighted ensemble statistics are now performed within a context in order to preserve data attributes. (:issue:`1232`, :pull:`1234`).
* The `make docs` Makefile recipe was failing with an esoteric error. This has been resolved by splitting the `linkcheck` and `docs` steps into separate actions. (:issue:`1248`. :pull:`1251`).
* The setup step for `pytest` needed to be addressed due to the fact that files were being accessed/modified by multiple tests at a time, causing segmentation faults in some tests. This has been resolved by splitting functions into those that fetch or generate test data (under `xclim.testing.tests.data`) and the fixtures that supply accessors to them (under `xclim.testing.tests.conftest`). (:issue:`1238`, :pull:`1254`).
* Relaxed the expected output for ``test_spatial_analogs[friedman_rafsky]`` to support expected results from `scikit-learn` 1.2.0.
* The MBCn example in documentation has been fixed to properly imitate the source. (:issue:`1249`, :pull:`1250`).
* Streamflow indicators relying on indices defined in `xclim.indices.stats` were not checking input variable units. These indicators will now raise an error if input data units are not m^3/s. (:issue:`1130`, :pull:`1225`).
* Adjusted some documentation examples were not being rendered properly. (:issue:`1264`, :pull:`1266`).

Internal changes
^^^^^^^^^^^^^^^^
* Minor adjustments to GitHub Actions workflows (newest Ubuntu images, updated actions version, better CI triggering). (:pull:`1221`).
* Pint units `context` added to various operations, tests and `Indicator` attributes. (:issue:`1208`, :pull:`1227`).
* Updated article from Alavoine & Grenier (2022) within documentation. Many article reference URLs have been updated to use HTTPS where possible. (:issue:`1246`, :pull:`1247`).
* Added relevant variable dataflag checks for potential evaporation, convective precipitation, and air pressure at sea level. (:pull:`1241`).
* Documentation restructured to include `ReadMe` page (as `About`) with some minor changes to documentation titles. (:pull:`1233`).
* `xclim` development build now uses `nbqa` to effectively run black checks over notebook cells. (:pull:`1233`).
* Some `tox` recipes (``opt-slow``, ``conda``) are temporarily deactivated until a `tox>=4.0`-compatible `tox-conda` plugin is released. (:pull:`1258`).
* A notebook (``extendingxclim.ipynb``) has been updated to remove mentions of obsolete `xclim.subset` module. (:pull:`1258`).
* Merge of sdba documentation from the module and the rst files, some cleanup and addition of a section referring to GitHub issues. (:pull:`1230`).

--------------------
Contributors to this version: Trevor James Smith (:user:`Zeitsperre`), Abel Aoun (:user:`bzah`), Éric Dupuis (:user:`coxipi`), Travis Logan (:user:`tlogan2000`), Pascal Bourgault (:user:`aulemahal`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* The general ``xclim`` description and ReadMe have been updated to reflect recent enhancements. (:issue:`1185`, :pull:`1209`).
* Documentation now supports intersphinx mapping references within code examples via `sphinx-codeautolink` and copying of code blocks via `sphinx-copybutton`. (:pull:`1182`).
* Log-logistic distribution added to `stats.py` for use with ``standardized_precipitation_index`` and ``standardized_precipitation_evapotranspiration_index``. (:issue:`1141`, :pull:`1183`).
* New option in many indices allowing for resampling in given periods after ``run_length`` operations. (:issue:`505`, :issue:`916`, :issue:`917`, :pull:`1161`).
* New base indicator class for sdba: ``StatisticalPropertyMeasure``, those measures that also reduce the time (as a property does). (:pull:`1198`).
* ``xclim.core.calendar.common_calendar`` to find the best calendar to use when uniformizing an heterogeneous collection of data. (:pull:`1217`).
* ``xclim.ensembles.create_ensemble`` now accepts ``calendar=None``, and uses the above function to guess the best one. It also now accepts ``cal_kwargs`` to fine tune the calendar conversion. (:issue:`1190`, :pull:`1217`).
* New data check : ``xclim.core.datachecks.check_common_time`` that ensures all inputs of multivariate indicators have the same frequency (and the same time anchoring for daily and hourly data). (:issue:`1111`, :pull:`1217`).

New indicators
^^^^^^^^^^^^^^
* New indices ``first_day_temperature_{above | below}`` and indicators ``xclim.indices.first_day_{tn | tg | tx}_{above | below}``. These indices/indicators accept operator (``op``) keyword for finer threshold comparison controls. (:issue:`1175`, :pull:`1186`).
* New generic indice ``cumulative_difference`` for calculating difference between values and thresholds across time (e.g. temperature: degree-days, precipitation: moisture deficit), with or without resampling/accumulating by frequency. (:pull:`1202`).
* New spatial sdba properties and measures : ``spatial_correlogram``, ``scorr`` and ``first_eof``. The later needs the optional dependency `eofs <https://ajdawson.github.io/eofs/>`_. (:pull:`1198`).

Breaking changes
^^^^^^^^^^^^^^^^
* Indices that accept `lat` or `lon` coordinates in their call signatures will now use `cf-xarray` accessors to gather these variables in the event that they are not explicitly supplied. (:pull:`1180`). This affects the following:
- ``huglin_index``, ``biologically_effective_degree_days``, ``cool_night_index``, ``latitude_temperature_index``, ``water_budget``, ``potential_evapotranspiration``
* ``cool_night_index`` now optionally accepts ``lat: str = "north" | "south"`` for calculating CNI over DataArrays lacking a latitude coordinate. (:pull:`1180`).
* The offset value in ``standardized_precipitation_evapotranspiration_index`` is changed to better reproduce results in the reference library ``monocongo/climate_indices``. (:issue:`1141`, :pull:`1183`).
* The ``first_day_below`` and ``first_day_above`` indices are now deprecated in order to clearly communicate the variables they act upon (:issue:`1175`, :pull:`1186`). The suggested migrations are as follows:
- ``xclim.indices.first_day_above`` -> ``xclim.indices.first_day_temperature_above``
- ``xclim.indices.first_day_below`` -> ``xclim.indices.first_day_temperature_below``
* The ``first_day_below`` and ``first_day_above`` atmos indicators are now deprecated in order to clearly communicate the variables they act upon (:issue:`1175`, :pull:`1186`). The suggested migrations are as follows:
- ``xclim.atmos.first_day_above`` -> ``xclim.indices.first_day_{tn | tg | tx}_above``
- ``xclim.atmos.first_day_below`` -> ``xclim.indices.first_day_{tn | tg | tx}_below``
* The ``degree_days`` generic indice has been deprecated in favour of ``cumulative_difference`` that is not limited only to temperature variables (:issue:`1200`, :pull:`1202`). The indices for ``atmos.{heating | cooling | growing}_degree_days`` are now built from ``generic.cumulative_difference``.
* Running `pytest` now requires the `pytest-xdist` distributed testing dependency. This library has been added to the `dev` requirements and conda environment configuration. (:pull:`1203`).
* Parameters ``reducer`` and ``window`` in ``xclim.indices.rle_statistics`` are now positional. (:pull:`1161`).
* The ``relative_annual_cycle_amplitude`` and ``annual_cycle_amplitude`` have been rewritten to match the version defined in the VALUE project, outputs will change drastically (for the better) (:pull:`1198`).
* English indicator metadata has been adjusted to remove frequencies from fields in the `long_name` of indicators. English indicators now have an explicit `title` and `abstract`. (:issue:`936`, :pull:`1123`).
* French indicator metadata translations are now more uniform and more closely follow agreed-upon grammar conventions, while also removing frequency fields in `long_name_fr`. (:issue:`936`, :pull:`1123`).
* The ``freshet_start`` indice is now deprecated in favour of ``first_day_temperature_above`` with `thresh='0 degC', window=5`. The `freshet_start` indicator is now based on ``first_day_temperature_above``, but is otherwise unaffected. (:issue:`1195`, :pull:`1196`).
* Call signatures for several indices/indicators have been modified to optionally accept `op` for manually setting threshold comparison operators (:issue:`1194`, :pull:`1197`). The affected indices and indicators as follows:
- ``hot_spell_max_length``, ``hot_spell_frequency``, ``cold_spell_days``, ``cold_spell_frequency``, ``heat_wave_index``, ``warm_day_frequency`` (indice only), ``warm_night_frequency`` (indice only), ``dry_days``, ``wetdays``, ``wetdays_prop``.
* Cleaner ``xclim.core.calendar.parse_offset`` : fails on invalid frequencies, return implicit anchors (YS -> JAN, Y -> DEC) and implicit ``is_start_anchored`` (D -> True). (:issue:`1213`, , :pull:`1217`).

Bug fixes
^^^^^^^^^
* The docstring of ``cool_night_index`` suggested that `lat` was an optional parameter. This has been corrected. (:issue:`1179`, :pull:`1180`).
* The ``mean_radiant_temperature`` indice was accessing hardcoded `lat` and `lon` coordinates from passed DataArrays. This now uses `cf-xarray` accessors. (:pull:`1180`).
* Adopt (and adapt) unit registry declaration and preprocessors from `cf-xarray` to circumvent bugs caused by a refactor in `pint` 0.20. It also cleans the code a little bit. (:issue:`1211`, :pull:`1212`).

Internal changes
^^^^^^^^^^^^^^^^
* The documentation build now relies on `sphinx-codeautolink` and `sphinx-copybutton`. (:pull:`1182`).
* Many docstrings did not fully adhere to the `numpy docstring format <https://numpydoc.readthedocs.io/en/latest/format.html>`_. Fields and entries for many classes and functions have been adjusted to adhere better. (:pull:`1182`).
* The xdoctest namespace now provides access to session-scoped ``{variable}_dataset`` accessors, as well as a ``path_to_atmos_file`` object. These can be used for running doctests on all variables made in the pytest ``atmosds()`` fixture. (:pull:`1882`).
* Upgrade CodeQL GitHub Action to v2. (:issue:`1188`, :pull:`1189`).
* New generic index ``first_day_threshold_reached`` is now used to compose all ``first_day_XYZ`` indices. (:issue:`1175`, :pull:`1186`).
* In order to reduce computation footprint, the GitHub CI full testing suite and doctests are now only run once a pull request has been reviewed and approved. The number of simultaneously triggered builds has also been reduced. (:issue:`1155`, :pull:`1203`).
* ReadTheDocs now only builds full documentation (including running notebooks) when pull requests are merged to the main branch. (:issue:`1155`, :pull:`1203`).
* `xclim` now leverages `pytest-xdist` to distribute tests among Python workers and significantly speed up the testing suite. (:pull:`1203`).
* ``show_versions`` can now accept a list of dependencies so that other libraries can make use of this utility. (:pull:`1215`).
* Pull Requests now are automatically tagged (``CI``, ``docs``, ``indicators``, and/or ``sdba``) according to files modified using the `GitHub Labeler Action <https://github.com/actions/labeler>`_. (:pull:`1214`).

--------------------
Contributors to this version: Pascal Bourgault (:user:`aulemahal`), Éric Dupuis (:user:`coxipi`), Trevor James Smith (:user:`Zeitsperre`), Abel Aoun (:user:`bzah`), Gabriel Rondeau-Genesse (:user:`RondeauG`), Dougie Squire (:user:`dougiesquire`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Adjustment methods of `SBCK <https://github.com/yrobink/SBCK>`_ are wrapped into xclim when that package is installed. (:issue:`1109`, :pull:`1115`).
- Wrapped SBCK tests are also properly run in the tox testing ensemble. (:pull:`1119`).
* Method ``FAO_PM98`` (based on Penman-Monteith formula) to compute potential evapotranspiration. (:pull:`1122`).
* New indices for droughts: SPI (standardized precipitations) and SPEI (standardized water budgets). (:issue:`131`, :pull:`1096`).
* Most numba functions of ``sdba.nbutils`` now use the "lazy" compilation mode. This significantly accelerates the import time of xclim. (:issue:`1135`, :pull:`1167`).
* Statistical properties and measures from ``xclim.sdba`` are now ``Indicator`` subclasses (:pull:`1149`).

New indicators
^^^^^^^^^^^^^^
* `xclim` now has the McArthur Forest Fire Danger Index and related indices under a new ``xclim.indices.fire`` module. These indices are also available as indicators. (:issue:`1152`, :pull:`1159`)
* Drought-related indicators: SPI (standardized precipitations) and SPEI (standardized water budgets). (:issue:`131`, :pull:`1096`).
* ``ensembles.create_ensembles`` now accepts a ``realizations`` argument to assign a coordinate to the "realization" axis. It also accepts a dictionary as input so that keys are used as that coordinate. (:pull:`1153`).
* ``ensembles.ensemble_percentiles``, ``ensembles.ensemble_mean_std_max_min`` and ``ensembles.change_significance`` now support weights (:pull:`1151`).
* Many generic indicators that compare arrays or against thresholds or now accept an `op` keyword for specifying the logical comparison operation to use in their calculations (i.e. `{">", ">=", "<", "<=, "!=", "=="}`). (:issue:`389`, :pull:`1157`).
- In order to prevent user error, many of these generic indices now have a ``constrain`` variable that prevents calling an indice with an inappropriate comparison operator. (e.g. The following will raise an error: ``op=">", constrain=("<", "<=")``). This behaviour has been added to indices accepting ``op`` where appropriate.

Breaking changes
^^^^^^^^^^^^^^^^
* `scipy` has been pinned below version 1.9 until `lmoments3` can be adapted to the new API. (:issue:`1142`, :pull:`1143`).
* `xclim` now requires `xarray>=2022.06.0`. (:pull:`1151`).
* Documentation CI (ReadTheDocs) builds will now fail if there are any misconfigured pages, internal link/reference warnings, or broken external hyperlinks. (:issue:`1094`, :pull:`1131`, :issue:`1139`, :pull:`1140`, :pull:`1160`).
* Call signatures for generic indices have been reordered and/or modified to accept `op`, and optionally `constrain`, in many cases, and `condition`/`conditional`/`operation` has been renamed to `op` for consistency. (:issue:`389`, :pull:`1157`). The affected indices are as follows:
- `get_op`, `compare`, `threshold_count`, `get_daily_events`, `count_level_crossings`, `count_occurrences`, `first_occurrence`, `last_occurrence`, `spell_length`, `thresholded_statistics`, `temperature_sum`, `degree_days`.
* All indices in `xclim.indices.generic` now use `threshold` in lieu of `thresh` for consistency. (:pull:`1157`).
* Existing function ``xclim.indices.generic.compare`` can now be used to construct operations with `op` and `constrain` variables to allow for dynamic comparisons with user input handling. (:issue:`389`, :pull:`1157`).
* Two deprecated indices have been removed from `xclim`. (:pull:`1157`):
- ``xclim.indices._multivariate.daily_freezethaw_cycles`` -> Replaceable with the generic ``multiday_temperature_swing`` with `thresh_tasmax='0 degC'`, `thresh_tasmin='0 degC'`, `window=1`, and `op='sum'`. The indicator version (``xclim.atmos.daily_freezethaw_cycles``) is unaffected.
- ``xclim.indices.generic.select_time`` -> Was previously moved to ``xclim.core.calendar``.
* The `clix-meta` indicator table parsing function (``xclim.core.utils.adapt_clix_meta_yaml``) has been adapted to support the new "op" operator handler. (:pull:`1157`).
* Because they have been re-implemented as ``Indicator`` subclasses, statistical properties and measures of ``xclim.sdba`` no longer preserve attributes of their inputs by default. Use ``xclim.set_options(keep_attrs=True)`` to get the previous behaviour. (:pull:`1149`).
* The ``xclim.indices.generic.extreme_temperature_range`` function has been fixed so it now does what its definition says. Results from ``xclim.indicators.cf.etr`` will change. (:issue:`1172`, :pull:`1173`).
* `xclim` now has a dedicated ``indices.fire`` submodule that houses all fire-related indices. The previous ``xclim.indices.fwi`` submodule is deprecated and will be removed in a future version. (:issue:`1152`, :pull:`1159`).
* The indicator ``xclim.indicators.atmos.fire_weather_indexes`` and indice ``xclim.indices.fire_weather_indexes`` have both been deprecated and renamed to ``cffwis_indices``. Calls using the previous naming will be removed in a future version. (:pull:`1159`).
* `xclim` now explicitly requires `pybtex` in order to generate documentation. (:pull:`1176`).

Bug fixes
^^^^^^^^^
* Fixed ``saturation_vapor_pressure`` for temperatures in other units than Kelvins (also fixes ``relative_humidity_from_dewpoint``). (:issue:`1125`, :pull:`1127`).
* Indicators that do not care about the input frequency of the data will not check the cell methods of their inputs. (:pull:`1128`).
* Fixed the signature and docstring of ``heat_index`` by changing ``tasmax`` to ``tas``. (:issue:`1126`, :pull:`1128`).
* Fixed a formatting issue with virtual indicator modules (`_gen_returns_section`) that was creating malformed `Returns` sections in `sphinx`-generated documentation. (:pull:`1131`).
* Fix ``biological_effective_degree_days`` for non-scalar latitudes, when using method "gladstones". (:issue:`1136`, :pull:`1137`).
* Fixed some ``extlink`` warnings found in `sphinx` and configured ReadTheDocs to use `mamba` as the dependency solver. (:issue:`1139`, :pull:`1140`).
* Fixed some broken hyperlinks to articles, users, and external documentation throughout the code base and jupyter notebooks. (:pull:`1160`).
* Removed some artefact reference roles introduced in :pull:`1131` that were causing LaTeX builds of the documentation to fail. (:issue:`1154`, :pull:`1156`).
* Fix ``biological_effective_degree_days`` for non-scalar latitudes, when using method "gladstones". (:issue:`1136`, :pull:`1137`).
* Fixed some ``extlink`` warnings found in `sphinx` and configured ReadTheDocs to use `mamba` as the dependency solver. (:issue:`1139`, :pull:`1140`).
* Fixed some broken hyperlinks to articles, users, and external documentation throughout the code base and jupyter notebooks. (:pull:`1160`).
* Addressed a bug that was causing `pylint` to stackoverflow by removing it from the tox configuration. `pylint` should only be called from an active environment. (:pull:`1163`)
* Fixed an issue with ``xclim.ensembles.kmeans_reduce_ensemble`` which caused it to fail when using dask arrays. (:pull:`1170`).
* Addressed a bug that was causing `pylint` to stackoverflow by removing it from the tox configuration. `pylint` should only be called from an active environment. (:pull:`1163`)

Internal changes
^^^^^^^^^^^^^^^^
* Marked a test (``test_release_notes_file_not_implemented``) that can only pass when source files are available so that it can easily be skipped on conda-forge build tests. (:issue:`1116`, :pull:`1117`).
* Split a few YAML strings found in the virtual modules that regularly issued warnings on the code checking CI steps. (:pull:`1118`).
* Function ``xclim.core.calendar.build_climatology_bounds`` now exposed via `__all__`. (:pull:`1146`).
* Clarifications added to docstring of ``xclim.core.bootstrapping.bootstrap_func``. (:pull:`1146`).
* Bibliographic references for supporting scientific articles are now found in a bibtex file (`docs/references.bib`). These are now made available within the generated documentation using ``sphinxcontrib-bibtex``. (:issue:`1094`, :pull:`1131`).
* Added information URLs to ``setup.py`` in order to showcase issue tracker and other sites on PyPI page (:pull:`1156`).
* Configured the LaTeX build of the documentation to ignore the custom bibliographies, as they were redundant in the generated PDF. (:pull:`1158`).
* Run length encoding (``xclim.indices.run_length.rle``) has been optimized. (:issue:`956`, :pull:`1122`).
* Added a `sphinx-build -b linkcheck` step to the `tox`-based `"docs"` build as well as to the ReadTheDocs configuration. (:pull:`1160`).
* `pylint` is now setup to use a `pylintrc` file, allowing for more granular control of warnings and exceptions. Many errors are still present, so addressing them will need to occur gradually. (:pull:`1163`).
* The generic indices `count_level_crossings`, `count_occurrences`, `first_occurrence`, and `last_occurrence` are now fully tested. (:pull:`1157`).
* Adjusted the ANUCLIM indices by removing "ANUCLIM" from their titles, modifying their docstrings, and handling `"op"` input in a more user-friendly way. (:issue:`1055`, :pull:`1169`).
* Documentation for fire-based indices/indicators has been reorganized to reflect the new submodule structure. (:pull:`1159`).

--------------------
Contributors to this version: Abel Aoun (:user:`bzah`), Pascal Bourgault (:user:`aulemahal`), Trevor James Smith (:user:`Zeitsperre`), Gabriel Rondeau-Genesse (:user:`RondeauG`), Juliette Lavoie (:user:`juliettelavoie`), Ludwig Lierhammer (:user:`ludwiglierhammer`).

Announcements
^^^^^^^^^^^^^
* `xclim` is now compliant with `PEP 563 <https://peps.python.org/pep-0563>`_. Python3.10-style annotations are now permitted. (:issue:`1065`, :pull:`1071`).
* `xclim` is now fully compatible with `xarray`'s `flox`-enabled ``GroupBy`` and ``resample`` operations. (:pull:`1081`).
* `xclim` now (properly) enforces docstring compliance checks using `pydocstyle` with modified `numpy`-style docstrings. Docstring errors will now cause build failures. See the `pydocstyle documentation <http://www.pydocstyle.org/en/stable/error_codes.html>`_ for more information. (:pull:`1074`).
* `xclim` now uses GitHub Actions to manage patch version bumping. Merged Pull Requests that modify `xclim` code now trigger version-bumping automatically when pushed to the main development branch. Running `$ bump2version patch` within development branches is no longer necessary. (:pull:`1102`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* Add "Celsius" to aliases of "celsius" unit. (:issue:`1067`, :pull:`1068`).
* All indicators now have indexing enabled, except those computing statistics on spells. (:issue:`1069`, :pull:`1070`).
* A convenience function for returning the version numbers for relevant xclim dependencies (``xclim.testing.show_versions``) is now offered. (:pull:`1073`).
- A CLI version of this function is also available from the command line (`$ xclim show_version_info`). (:pull:`1073`).
* New "keep_attrs" option to control the handling of the attributes within the indicators. (:issue:`1026`, :pull:`1076`).
* Added a notebook showcasing some simple examples of Spatial Analogues. (:issue:`585`, :pull:`1075`).
* ``create_ensembles`` now accepts a glob string to find datasets. (:pull:`1081`).
* Improved percentile based indicators metadata with the window, threshold and climatology period used to compute percentiles. (:issue:`1047`, :pull:`1050`).
* New ``xclim.core.calendar.construct_offset``, the inverse operation of ``parse_offset``. (:pull:`1090`).
* Rechunking operations in ``xclim.indices.run_length.rle`` are now synchronized with dask's options. (:pull:`1090`).
* A mention of the "missing" checks and options is added to the history attribute of indicators, where appropriate. (:issue:`1100`, :pull:`1103`).

Breaking changes
^^^^^^^^^^^^^^^^
* ``xclim.atmos.water_budget`` has been separated into ``water_budget`` (calculated directly with 'evspsblpot') and ``water_budget_from_tas`` (original function). (:pull:`1086`).
* Injected parameters in indicators are now left out of a function's signature and will not be included in the history attribute. (:pull:`1086`).
* The signature for the following Indicators have been modified (:pull:`1050`):
- cold_spell_duration_index, tg90p, tg10p, tx90p, tx10p, tn90p, tn10p, warm_spell_duration_index, days_over_precip_doy_thresh, days_over_precip_thresh, fraction_over_precip_doy_thresh, fraction_over_precip_thresh, cold_and_dry_days, warm_and_dry_days, warm_and_wet_days, cold_and_wet_days
* The parameter for percentile values is now named after the variable it is supposed to be computed upon. (:pull:`1050`).
* `pytest-runner` has been removed as a dependency (it was never needed for `xclim` development). (:pull:`1074`).
* `xclim.testing._utils.py` has been renamed to `xclim.testing.utils.py` for added documentation visibility. (:pull:`1074`).
- Some unused functions and classes (``as_tuple``, ``TestFile``, ``TestDataSet``) have been removed. (:pull:`1107`).

New indicators
^^^^^^^^^^^^^^
* ``universal_thermal_climate_index`` and ``mean_radiant_temperature`` for computing the universal thermal climate index from the near-surface temperature, relative humidity, near-surface windspeed and radiation. (:issue:`1060`, :pull:`1062`).
- A new method ``ITS90`` has also been added for calculating saturation water vapour pressure. (:issue:`1060`, :pull:`1062`).

Internal changes
^^^^^^^^^^^^^^^^
* Typing syntax has been updated within pre-commit via `isort`. Pre-commit hooks now append `from __future__ import annotations` to all python module imports for backwards compatibility. (:issue:`1065`, :pull:`1071`)
* `isort` project configurations are now set in `setup.cfg`. (:pull:`1071`).
* Many function docstrings, external target links, and internal section references have been adjusted to reduce warnings when building the docs. (:pull:`1074`).
* Code snippets within documentation are now checked and reformatted to `black` conventions with `blackdoc`. A `pre-commit` hook is now in place to run these checks. (:pull:`1098`).
* Test coverage statistic no longer includes coverage of the test files themselves. Coverage now reflects lines of usable code covered. (:pull:`1101`).
* Reordered listed authors alphabetically. Promoted :user:`bzah` to core contributor. (:pull:`1105`).
* Tests have been added for some functions in `xclim.testing.utils.py`; some previously uncaught bugs in ``list_input_variables``, ``publish_release_notes``, and ``show_versions`` have been patched. (:issue:`1078`, :pull:`1107`).
* A convenience command for installing xclim with key development branches of some dependencies has been added (`$ make upstream`). (:issue:`1088`, :pull:`1092`; amended in :issue:`1113`, :pull:`1114`).
- This build configuration is also available in `tox` for local development purposes (`$ tox -e pyXX-upstream`).

Bug fixes
^^^^^^^^^
* Clean the `bias_adjustement` and `history` attributes created by `xclim.sdba.adjust` (e.g. when an argument is an `xr.DataArray`, only print the name instead of the whole array). (:issue:`1083`, :pull:`1087`).
* `pydocstyle` checks were silently failing in the `pre-commit` configuration due to a badly-formed regex. This has been adjusted. (:pull:`1074`).
* `adjust_doy_calendar` was broken when the source or the target were seasonal. (:issue:`1097`, :issue:`1091`, :pull:`1099`)

--------------------
Contributors to this version: Pascal Bourgault (:user:`aulemahal`), Juliette Lavoie (:user:`juliettelavoie`), David Huard (:user:`huard`).

Bug fixes
^^^^^^^^^
* Invoking ``lazy_indexing`` twice in row (or more) using the same indexes (using dask) is now fixed. (:issue:`1048`, :pull:`1049`).
* Filtering out the nans before choosing the first and last values as ``fill_value`` in ``_interp_on_quantiles_1D``. (:issue:`1056`, :pull:`1057`).
* Translations from virtual indicator modules do not override those of the base indicators anymore. (:issue:`1053`, :pull:`1058`).
* Fix mmday unit definition (factor 1000 error). (:issue:`1061`, :pull:`1063`).

New features and enhancements
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
* ``xclim.sdba.measures.rmse`` and ``xclim.sdba.measures.mae`` now use `numpy` instead of `sklearn`. This improves their performances when using `dask`. (:pull:`1051`).
* Argument ``append_ends`` added to ``sdba.unpack_moving_yearly_window`` (:pull:`1059`).

Internal changes
^^^^^^^^^^^^^^^^
* Ipython was unpinned as version 8.2 fixed the previous issue. (:issue:`1005`, :pull:`1064`).