climdex-kit 0.1.2

Tool for multi-scenario calculation, publishing, and analysis of indices from 3D time-series of climate projections.

climdex-kit: compute, publish, analyse

• Background
• Content
• Technologies
• Installation
• Usage
• Examples

This project contains a Python package for the parallelized local computation of scenario-aware climate indices starting from input time-series of climate projections.

The package comes with an pre-compiled initial set of indices, mostly relying on the CDO operators. For the more advanced ones (SPI and SPEI), the climate-indices Python package is used. This set of indices can be easily customised or extended: please check out how to contribute if you are interested.

Background

A climate index is information derived from one or more climate variables (precipitation, mean temperature, etc). The index can range from a simple conditional counting of days against a threshold, to more complex statistical processing.

The information is usually calculated spatially on a pixel-by-pixel basis, with possibly some form of aggregation over time. Hence the spatio-temporal domain of an index is generally a time-series with the same spatial resolution, and with either the same or a coarser temporal step.

The availability of robust and easily interpretable information about the spatial distribution and temporal evolution of climate related-hazards, especially climate extremes, is an increasing need not only for the research community but also for a wide range of sectors and applications.

The European Environmental Agency has been currently supporting, in the framework of the European Topic Centre on Climate Change impacts, vulnerability and Adaptation (ETC-CCA), the review and selection of suitable climate-related indices for Europe to be recommended and implemented for adaptation purposes.

Content

The project is structured as follows:

• src/ : source folder containing the Python package implementation
• test/ : test suites
• etc/ : folder with configuration files (most notably the indices.ini file with the definition of the climate indices
• notebooks/ : folder with the Jupyter notebooks
• docs/ : documentation folder
• requirements.txt/environment.yml : package dependencies for pip and conda environments
• Makefile : set of rules for building and installing the package
• AUTHORS : list of authors
• CONTRIBUTING.md : help for developers
• CHANGELOG.md : list of notable changes for each release of the project
• README.md : this file

The following files are required for packaging and distribution:

• pyproject.toml : tells what is required to build the project
• setup.cfg/setup.py : static/dynamic package metadata for setuptools

Technologies

The package is written in Python and for most of the implemented climate indices relies on both the CDO library, and the climate-indices package.

Installation

The package is available as both pip sdist/wheel and conda package.

Dependencies

The package relies on the CDO operators library v1.9.9. If you are using conda environments, you can install the package as follows:

conda install -c conda-forge cdo=1.9.9

In alternative, you can install the climdex-kit conda package as explained later in this file.

Install from PyPI via pip

$ python3 -m pip install climdex-kit

Install as conda package

TODO

Install in development mode

For developers: refer to the instructions in the CONTRIBUTING file for the setup of the development environment instead.

Usage

The climdex Python package provides a set sub-commands for the specific actions to be taken

• list/ls : list all available indices
• show/sh : show the details of a specific index
• compute/co : compute one or more indices

There is thus a hierarchical organization of the CLI arguments. At any level of the hierarchy, the --help/-h option can be called to print the help message.

general args

option	description	allowed values
--version	Get the version number of the program
--idx-conf/-c FILE	Alternative indices configuration file (.ini) (default is ./etc/indices.ini)	abs/rel path
--log-conf/-L FILE	Alternative logging configuration file (.yaml) (default: ./etc/logging.yml)	abs/rel path
-d	Enable debug mode

(See $ python -m climdex -h for a full synopsis)

{list,ls} args

This sub-command currently does not provide any option. Run $ python -m climdex list to get a summary of all available climate indices.

{show,sh} args

option	description	allowed values
index	the index configuration to be visualized	see {list,ls} sub-command

(See $ python -m climdex show -h for a full synopsis)

{compute,co} args

option	description	allowed values
--index / -i INDEX	A comma-separated list of indices to be computes	see {list,ls} sub-command
--multiprocessing	The CPU parallelism to be employed	int>0 (N of CPUs) or one among {one, all_but_one, all}
--idir DIR	Root folder where to look for input files (expected structure: $input_dir/variable/scenario/*.nc)	abs/rel path
--odir/-o DIR	Root folder where to store indices files	abs/rel path
--scenario/-s S	White-space separated list of scenarios	sub-folders of input variables
--regex/-x R	Filter input files with a regular expression	regex
--metadata-only/-m	Only re-set the output attributes (metadata) on existing indices files (compute the index file too on non-existing file instead)
--dry-run/-n	Only print jobs to output without doing anything
--force/-f	Force overwrite of existing output indices files (otherwise execution is stopped)

(See $ python -m climdex compute -h for a full synopsis)

Data organization

The package expects a fixed organization of the input datasets and a fixed naming scheme in order to properly extract all the metadata.

The path and name of a climate projection NetCDF starting from the $IDIR input root directory (--idir in the command line) shall be as follows:

$IDIR/{var}/{scenario}/{var}_{model}_{timeres}_{yearstart}{yearend}_{scenario}.nc

Being:

• {var} : the climate variable (whose label shall also coincide with the name of the variable in the NetCDF)
• {scenario} : the name of the emissions scenario
• {model} : the name of the climate model used to create the projection
• timeres : the time-step of the time-series (e.g. day, month, etc)
• yearstart / yearend : time range of the time-series (YYYY format)

For ancillary scenario-independent datasets (e.g. land mask), the {scenario}/ sub-folder can be omitted mandatory, and the name of the dataset shall be {var}.nc.

Analogously, given the $ODIR output specified via --odir/-o CLI argument, each index file will be stored then as follows:

$ODIR/{index}/{scenario}/{index}_{model}_{timeres}_{yearstart}{yearend}_{scenario}.nc

Logging

By default the program logs to both console (with colored output to highlight warnings and errors), and to a file called climdex.log in the current working directory.

The configuration of both loggers can be found in ./etc/logging.yaml, otherwise use the --log-conf/-L option to set an alternative configuration.

Examples

# list all avaiable indices
$ python -m climdex list

# show the configuration details of the index [spei12]
$ python -m climdex show spei12

# compute the frost days [fd] and 12-months SPI [spi12] index on all available climate
#   projections for scenario rcp85 and by using 3 CPUs
$ python -m climdex \ 
    compute \
    --index amt,spi12   \
    --multiprocessing 3 \
    --scenario rcp85    \
    --idir $IDIR        \
    --odir $ODIR

# update the metadata of all existing indexes of scenario rcp85, and compute the missing ones anew
#   using all CPUs + turn on debug mode + dry run only
$ python -m climdex -d \ 
    compute \
    --index all           \
    --scenario rcp85      \
    --multiprocessing all \
    --metadata-only       \
    --idir $IDIR          \
    --odir $ODIR          \
    --dry-run

# re-compute the [fd] and [tn] indices for the model "EUR-11_CNRM-CERFACS-CNRM-CM5_CLMcom-CCLM4-8-17_r1i1p1_v1"
#   and scenario rcp45 and keep it on a separate file for comparison with existing
#   + use 1 CPU (sequential execution)
$ python -m climdex \ 
    compute \
    --index fd,tn         \
    --scenario rcp45      \
    --multiprocessing one \
    --idir $IDIR          \
    --odir $ODIR          \
    --regex "*EUR-11_CNRM-CERFACS-CNRM-CM5_CLMcom-CCLM4-8-17_r1i1p1_v1*"
 
# re-compute (and overwrite when existing) all indexes on rcp45 and rcp85 scenarios
#   + using all available CPUs except one
$ python -m climdex \ 
    compute \
    --index all                   \
    --scenario rcp45 rcp85        \
    --multiprocessing all_but_one \
    --idir $IDIR                  \
    --odir $ODIR                  \
    --force

Credits

This project is funded by the FAct CLIMAX project at Eurac Research (Institute for Earth Observation).