xclim 0.21.0

Derived climate variables built with xarray.

xclim: Climate indices computations

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xclim is a library of functions to compute climate indices from observations or model simulations. It is built using xarray and can benefit from the parallelization handling provided by dask. Its objective is to make it as simple as possible for users to compute indices from large climate datasets and for scientists to write new indices with very little boilerplate.

For example, the following would compute monthly mean temperature from daily mean temperature:

import xclim
import xarray as xr
ds = xr.open_dataset(filename)
tg = xclim.icclim.TG(ds.tas, freq='YS')

For applications where meta-data and missing values are important to get right, xclim provides a class for each index that validates inputs, checks for missing values, converts units and assigns metadata attributes to the output. This also provides a mechanism for users to customize the indices to their own specifications and preferences.

xclim currently provides over 50 indices related to mean, minimum and maximum daily temperature, daily precipitation, streamflow and sea ice concentration.

Documentation

The official documentation is at https://xclim.readthedocs.io/

Contributing

xclim is in active development and it’s being used in production by climate services specialists. If you’re interested in participating to the development, want to suggest features, new indices or report bugs, please leave us a message on the issue tracker. There is also a chat room on gitter ().

Credits

This work is made possible thanks to the contribution of the Canadian Center for Climate Services.

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.21.0 (2020-10-23)

Breaking changes

• Statistical functions (frequency_analysis, fa, fit, parametric_quantile) moved from indices.generic to indices.stats to make them more visible.

New indicators

New features and enhancements

• New xclim.testing.open_dataset method to read data from the remote testdata repo.

• Added a notebook, ensembles-advanced.ipynb, to the documentation detailing ensemble reduction techniques and showing how to make use of built-in figure-generating commands.

• Added a notebook, frequency_analysis.ipynb, with examples showcasing frequency analysis capabilities.

Bug fixes

• Fixed a bug in the attributes of frost_season_length.

• indices.run_length methods using dates now respect the array’s calendar.

• Worked around an xarray bug in sdba.QuantileDeltaMapping when multidimensional arrays are used with linear or cubic interpolation.

Internal changes

0.20.0 (2020-09-18)

Breaking changes

• xclim.subset has been deprecated and now relies on clisops to perform specialized spatio-temporal subsetting. Install with pip install xclim[gis] in order to retain the same functionality.

• The python library pandoc is no longer listed as a docs build requirement. Documentation still requires a current version of pandoc binaries installed at system-level.

• ANUCLIM indices have seen their input_freq parameter renamed to src_timestep for clarity.

• A clean-up and harmonization of the indicators metadata has changed some of the indicator identifiers, long_names, abstracts and titles. xclim.atmos.drought_code and fire_weather_indexes now have indentifiers “dc” and “fwi” (lowercase version of the previous identifiers).

• xc.indices.run_length.run_length_with_dates becomes xc.indices.run_length.season_length. Its argument date is now optional and the default changes from “07-01” to None.

• xc.indices.consecutive_frost_days becomes xc.indices.maximum_consecutive_frost_days.

• Changed the history indicator output attribute to xclim_history in order to respect CF conventions.

New indicators

• atmos.max_pr_intensity acting on hourly data.

• atmos.wind_vector_from_speed, also the wind_speed_from_vector now also returns the “wind from direction”.

• Richards-Baker flow flashiness indicator (xclim.land.rb_flashiness_index).

• atmos.max_daily_temperature_range.

• atmos.cold_spell_frequency.

• atmos.tg_min and atmos.tg_max.

• atmos.frost_season_length, atmos.first_day_above. Also, atmos.consecutive_frost_days now takes a thresh argument (default : 0 degC).

New features and enhancements

• sdba.loess submodule implementing LOESS smoothing tools used in sdba.detrending.LoessDetrend.

• xclim now depends on clisops for subsetting, offloading several heavy GIS dependencies. This improves maintainability and reduces the size of a “vanilla” xclim installation considerably.

• New generic.parametric_quantile function taking parameters estimated by generic.fit as an input.

• Add support for using probability weighted moments method in generic.fit function. Requires the lmoments3 package, which is not included in dependencies because it is unmaintained. Install manually if needed.

• Implemented _fit_start utility function providing initial conditions for statistical distribution parameters estimation, reducing the likelihood of poor fits.

• Added support for indicators based on hourly (1H) inputs, and a first hourly indicator called max_pr_intensity returning hourly precipitation intensity.

• Indicator instances can be retrieved through their class with the get_instance() class method. This allows the use of xclim.core.indicator.registry as an instance registry.

• Indicators now have a realm attribute. It must be given when creating indicators outside xclim.

• Better docstring parsing for indicators: parameters description, annotation and default value are accessible in the json output and Indicator.parameters.

• New command line interface xclim for simple indicator computing tasks.

• New sdba.processing.jitter_over_thresh for variables with a upper bound.

• Added op parameter to xclim.indices.daily_temperature_range to allow resample reduce operations other than mean

• core.formatting.AttrFormatter (and thus, locale dictionaries) can now use glob-like pattern for matching values to translate.

Bug fixes

The ICCLIM module was identified as icclim in the documentation but the module available under ICCLIM. Now icclim == ICCLIM and ICCLIM will be deprecated in a future release.

Internal changes

• xclim.subset now attempts to load and expose the functions of clisops.core.subset. This is an API workaround preserving backwards compatibility.

• Code styling now conforms to the latest release of black (v0.20.8).

• New IndicatorRegistrar class that takes care of adding indicator classes and instances to the appropriate registries. Indicator now inherits from it.

0.19.0 (2020-08-18)

Breaking changes

• Refactoring of the Indicator class. The cfprobe method has been renamed to cfcheck and the validate method has been renamed to datacheck. More importantly, instantiating Indicator creates a new subclass on the fly and stores it in a registry, allowing users to subclass existing indicators easily. The algorithm for missing values is identified by its registered name, e.g. “any”, “pct”, etc, along with its missing_options.

• xclim now requires xarray >= 0.16, ensuring that xclim.sdba is fully functional.

• The dev requirements now include xdoctest – a rewrite of the standard library module, doctest.

• xclim.core.locales.get_local_attrs now uses the indicator’s class name instead of the indicator itself and no longer accepts the fill_missing keyword. Behaviour is now the same as passing False.

• Indicator.cf_attrs is now a list of dictionaries. Indicator.json puts all the metadata attributes in the key “outputs” (a list of dicts). All variable metadata (names in Indicator._cf_names) might be strings or lists of strings when accessed as object attributes.

• Passing doctests are now strictly enforced as a build requirement in the Travis CI testing ensemble.

New features and enhancements

• New ensembles.kkz_reduce_ensemble method to select subsets of an ensemble based on the KKZ algorithm.

• Create new Indicator Daily, Daily2D subclasses for indicators using daily input data.

• The Indicator class now supports outputing multiple indices for the same inputs.

• xclim.core.units.declare_units now works with indices outputting multiple DataArrays.

• Doctests now make use of the xdoctest_namespace in order to more easily access modules and testdata.

Bug fixes

• Fix generic.fit dimension ordering. This caused errors when “time” was not the first dimension in a DataArray.

Internal changes

• datachecks.check_daily now uses xr.infer_freq.

• Indicator subclasses Tas, Tasmin, Tasmax, Pr and Streamflow now inherit from Daily.

• Indicator subclasses TasminTasmax and PrTas now inherit from Daily2D.

• Docstring style now enforced using the pydocstyle with numpy doctsring conventions.

• Doctests are now performed for all docstring Examples using xdoctest. Failing examples must be explicitly skipped otherwise build will now fail.

• Indicator methods update_attrs and format are now classmethods, attrs to update must be passed.

• Indicators definitions without an accompanying translation (presently French) will cause build failures.

• Major refactoring of the internal machinery of Indicator to support multiple outputs.

0.18.0 (2020-06-26)

• Optimization options for xclim.sdba : different grouping for the normalization steps of DQM and save training or fitting datasets to temporary files.

• xclim.sdba.detrending objects can now act on groups.

• Replaced dask[complete] with dask[array] in basic installation and added distributed to docs build dependencies.

• xclim.core.locales now supported in Windows build environments.

• ensembles.ensemble_percentiles modified to compute along a percentiles dimension by default, instead of creating different variables.

• Added indicator first_day_below and run length helper first_run_after_date.

• Added ANUCLIM model climate indices mappings.

• Renamed areacella to areacello in sea ice tests.

• Sea ice extent and area outputs now have units of m2 to comply with CF-Convention.

• Split checks.py into cfchecks.py, datachecks.py and missing.py. This change will only affect users creating custom indices using utilities previously located in checks.py.

• Changed signature of daily_freeze_thaw_cycles, daily_temperature_range, daily_temperature_range_variability and extreme_temperature_range to take (tasmin, tasmax) instead of (tasmax, tasmin) and match signature of other similar multivariate indices.

• Added FromContext subclass of MissingBase to have a uniform API for missing value operations.

• Remove logging commands that captured all xclim warnings. Remove deprecated xr.set_options calls.

0.17.0 (2020-05-15)

• Added support for operations on dimensionless variables (units = ‘1’).

• Moved xclim.locales to xclim.core.locales in a batch of internal changes aimed to removed most potential cyclic imports cases.

• Missing checks and input validation refactored with addition of custom missing class registration (xclim.core.checks.register_missing_method) and simple validation method decorator (xclim.core.checks.check).

• New xclim.set_options context to control the missing checks, input validation and locales.

• New xclim.sdba module for statistical downscaling and bias-adjustment of climate data.

• Added convert_calendar and interp_calendar to help in the conversion between calendars.

• Added at_least_n_valid function, identifying null calculations based on minimum threshold.

• Added support for freq=None in missing calculations.

• Fixed outdated code examples in the docs and docstrings.

• Doctests are now run as part of the test suite.

0.16.0 (2020-04-23)

• Added vectorize flag to subset_shape and create_mask_vectorize function based on shapely.vectorize as default backend for mask creation.

• Removed start_yr and end_yr flags from subsetting functions.

• Add multi gridpoints support in subset.subset_gridpoint.

• Better wrapped_partial for more meaningful inspection.

• Add indices for relative humidity, specific humidity and saturation vapor pressure with a few choices of method.

• Allow lazy units conversion.

• CRS definitions of projected DataSets are now written to file according to Climate and Forecast-convention standards.

• Add utilities to merge attributes and update history in xclim.core.formatting.

• Ensembles : Allow alignment of datasets with same frequency but different offsets.

• Bug fixes in run_length for run-with-dates methods when the date is not found in the run.

• Remove deepcopy from subset.subset_shape to improve memory usage.

• Add missing_wmo function, identifying null calculations based on criteria from WMO.

• Add missing_pct function, identifying null calculations based on percentage of missing values.

0.15.x (2020-03-12)

• Improvement in FWI: Vectorization of DC, DMC and FFMC with numba and small code refactoring for better maintainability.

• Added example notebook for creating a catalog of selected indices

• Added growing_season_end, last_spring_frost, dry_days, hot_spell_frequency, hot_spell_max_length, and maximum_consecutive_frost_free_days indices.

• Dropped use of fiona.crs class in lieu of the newer pyproj CRS handler for subset_shape operations.

• Complete internal reorganization of xclim.

• Internationalization of xclim : add locales submodule for localized metadata.

• Add feature to retrieve coordinate values instead of index in run_length.first_run. Add run_length.last_run.

• Fix bug in subset_gridpoint to work on lat/lon coords of any dimension when they are not a dimension of the data.

0.14.x (2020-02-21)

• Refactoring of the documentation.

• Added support for pint 0.10

• Add atmos.heat_wave_total_length (fixing a namespace issue)

• Fixes in utils.percentile_doy and indices.winter_rain_ratio for multidimensionnal datasets.

• Rewrote the subset.subset_shape function to allow for dask.delayed (lazy) computation.

• Added utility functions to compute time_bnds when resampling data encoded with CFTimeIndex (non-standard calendars).

• Fix in subset.subset_gridpoint for dask array coordinates.

• Modified subset_shape to support subsetting with GeoPandas datatypes directly.

• Fix in subset.wrap_lons_and_split_at_greenwich to preserve multi-region dataframes.

• Improve the memory use of indices.growing_season_length.

• Better handling of data with atypically named lat and lon dimensions.

• Added six Fire Weather indices.

0.13.x (2020-01-10)

• Documentation improvements: list of indicators, RTD theme, notebook example.

• Added sea_ice_extent and sea_ice_area indicators.

• Reverted #311, removing the _rolling util function. Added optimal keywords to rolling() calls.

• Fixed ensembles.create_ensemble errors for builds against xarray master branch.

• Reformatted code to make better use of Python3.6 conventions (f-strings and object signatures).

• Fixed randomly failing tests of checks.missing_any.

• Improvement of ensemble.ensemble_percentile and ensemble.create_ensemble.

0.12.x-beta (2019-11-18)

• Added a distance function computing the geodesic distance to a point.

• Added a tolerance argument to subset_gridpoint raising an error if distance to closest point is larger than tolerance.

• Created land module for standardized access to streamflow indices.

• Enhancement to utils.Indicator to have more dynamic attributes using callables.

• Added indices heat_wave_total_length and tas / tg to average tasmin and tasmax into tas.

• Fixed a bug with typed call signatures that caused downstream failures on library import.

• Added a _rolling util function to fix memory issues on large dask datasets.

• Added the subset_shape function to subset utilities for clipping region-masked datasets via polygons.

• Fixed a bug where certain dependencies caused ReadTheDocs builds to fail.

• Added many statically typed function signatures for better function documentation.

• Improved DeprecationWarnings and UserWarnings ensemble for xclim subsetting functions.

• Dropped support for Python3.5.

0.11.x-beta (2019-10-17)

• Added type hinting to call signatures of many functions for more explicit type-checking.

• Added Kmeans clustering ensemble reduction algorithms.

• Added utilities for converting between wind velocity (sfcWind) and wind components (uas, vas) arrays.

• Added type hinting to call signatures of many functions for more explicit type-checking.

• Now supporting explicit builds for Windows OS via Travis CI.

• Fix failing test with Python 3.7.

• Fixed bug in subset.subset_bbox that could add unwanted coordinates/dims to some variables when applied to an entire dataset.

• Reformatted packaging configuration to pure Py3 wheel that ignore tests and test data.

• Now officially supporting Python3.8!

• Enhancement to precip_accumulation() to allow estimated amounts solid (or liquid) phase precipitation.

• Bugfix for frequency analysis choking on time series with NaNs only.

0.10.x-beta (2019-06-18)

• Added indices to ICCLIM module.

• Added indices days_over_precip_thresh and fraction_over_precip_thresh.

• Migrated to a major.minor.patch-release semantic versioning system.

• Removed attributes in netCDF output from Indicators that are not in the CF-convention.

• Added fit indicator to fit the parameters of a distribution to a series.

• Added utilities with ensemble, run length, and subset algorithms to the documentation.

• Source code development standards now implement Python Black formatting.

• Pre-commit is now used to launch code formatting inspections for local development.

• Documentation now includes more detailed usage and an example workflow notebook.

• Development build configurations are now available via both Anaconda and pip install methods.

• Modified create_ensembles() to allow creation of ensemble dataset without a time dimension as well as from xr.Datasets.

• Modified create ensembles() to pad input data with nans when time dimensions are unequal.

• Updated subset_gridpoint() and subset_bbox() to use .sel method if ‘lon’ and ‘lat’ dims are present.

• Added Azure Pipelines to automatically build xclim in Microsoft Windows environments. – REMOVED

• Now employing PEP8 + Black compatible autoformatting.

• Added Windows and macOS images to Travis CI build ensemble.

• Added variable thresholds for tasmax and tasmin in daily_freezethaw_events.

• Updated subset.py to use date formatted strings (“%Y”, “%Y%m” etc.) in temporal subsetting.

• Clean-up of day-of-year resampling. Precipitation percentile threshold will work without a doy index.

• Addressed deprecations for xarray 0.13.0.

• Added a decorator function that verifies validity and reformats subset calls using start_date or end_date signatures.

• Fixed a bug where ‘lon’ or ‘lon_bounds’ would return false values if either signatures were set to 0.

0.10-beta (2019-06-06)

• Dropped support for Python 2.

• Added support for period of the year subsetting in checks.missing_any.

• Now allow for passing positive longitude values when subsetting data with negative longitudes.

• Improved runlength calculations for small grid size arrays via ufunc_1dim flag.

0.9-beta (2019-05-13)

This is a significant jump in the release. Many modifications have been made and will be added to the documentation in the coming days. Among the many changes:

• New indices have been added with documentation and call examples.

• Run_length based operations have been optimized.

• Support for CF non-standard calendars.

• Automated/improved unit conversion and management via pint library.

• Added ensemble utilities for creation and analysis of muti-model climate ensembles.

• Added subsetting utilities for spatio-temporal subsets of xarray data objects.

• Added streamflow indicators.

• Refactoring of the code : separation of indices.py into a directory with sub-files (simple, threshold and multivariate); ensembles and subset utilities separated into distinct modules (pulled from utils.py).

• Indicators are now split into packages named by realms. import xclim.atmos to load indicators related to atmospheric variables.

0.8-beta (2019-02-11)

This was a staging release and is functionally identical to 0.7-beta.

0.7-beta (2019-02-05)

Major Changes:

• Support for resampling of data structured using non-standard CF-Time calendars.

• Added several ICCLIM and other indicators.

• Dropped support for Python 3.4.

• Now under Apache v2.0 license.

• Stable PyPI-based dependencies.

• Dask optimizations for better memory management.

• Introduced class-based indicator calculations with data integrity verification and CF-Compliant-like metadata writing functionality.

Class-based indicators are new methods that allow index calculation with error-checking and provide on-the-fly metadata checks for CF-Compliant (and CF-compliant-like) data that are passed to them. When written to NetCDF, outputs of these indicators will append appropriate metadata based on the indicator, threshold values, moving window length, and time period / resampling frequency examined.

0.6-alpha (2018-10-03)

• File attributes checks.

• Added daily downsampler function.

• Better documentation on ICCLIM indices.

0.5-alpha (2018-09-26)

• Added total precipitation indicator.

0.4-alpha (2018-09-14)

• Fully PEP8 compliant and available under MIT License.

0.3-alpha (2018-09-4)

• Added icclim module.

• Reworked documentation, docs theme.

0.2-alpha (2018-08-27)

• Added first indices.

0.1.0-dev (2018-08-23)

• First release on PyPI.