README¶
Clef searches the Earth System Grid Federation datasets stored at the Australian National Computational Infrastructure, both data published on the NCI ESGF node as well as files that are locally replicated from other ESGF nodes.
Currently it searches for the following datasets:
- CMIP5 raijin projects: rr3, where NCI is the primary publisher and al33 for replicas
- CMIP6 raijin projects: 0i10 for replicas
The search returns both the path of data that is already available at NCI as well as information on data that is on external ESGF nodes but not yet available locally.
Install¶
Clef is pre-installed into a Conda environment at NCI. Load it with:
module use /g/data3/hh5/public/modules
module load conda/analysis3-unstable
- We are constantly adding new features, the development version is available in a separate environment::
- module use /g/data3/hh5/public/modules module load conda source activate clef-test
You can install it to your own environment with:
conda install -c coecms -c conda-forge clef
But note that the MAS database necessary for running clef
can only be accessed
from NCI systems
Use¶
clef cmip5¶
Find CMIP5 files matching the constraints:
clef cmip5 --model BCC-CSM1.1 --variable tas --experiment historical --table day
You can filter CMIP5 by the following terms:
- ensemble/member
- experiment
- experiment-family
- institution
- model
- table/cmor_table
- realm
- frequency
- variable
- cf-standard-name
See clef cmip5 --help
for all available filters and their aliases
--latest
will check the latest versions of the datasets on the ESGF
website, and will only return matching files
It will return a path for all the files available locally at NCI and a dataset-id for the ones that haven’t been downloaded yet.
You can use the flags --local
and --missing
to return respectively only the local paths or the missing dataset-id:
clef --local cmip5 --model MPI-ESM-LR --variable tas --table day
clef --missing cmip5 --model MPI-ESM-LR --variable tas --table day
You can repeat arguments more than once:
clef --missing cmip5 --model MPI-ESM-LR -v tas -v tasmax -t day -t Amon
clef cmip6¶
You can filter CMIP6 by the following terms:
- activity
- experiment
- institution
- source_type
- model
- member
- table
- realm
- frequency
- variable
- version
See clef cmip6 --help
for all available filters
Develop¶
Development install:
conda env create -f conda/dev-environment.yml
source activate clef-dev
pip install -e '.[dev]'
The dev-environment.yml file is for speeding up installs and installing packages unavailable on pypi, requirements.txt is the source of truth for dependencies.
To work on the database tables you may need to start up a test database.
You can start a test database either with Docker:
docker-compose up # (In a separate terminal)
psql -h localhost -U postgres -f db/nci.sql
psql -h localhost -U postgres -f db/tables.sql
# ... do testing
docker-compose rm
Or with Vagrant:
vagrant up
# ... do testing
vagrant destroy
Run tests with py.test (they will default to using the test database):
py.test
Build the documentation using Sphinx:
python setup.py build_sphinx
firefox docs/_build/index.html
New releases are packaged and uploaded to anaconda.org by CircleCI when a new Github release is made
Documentation is available on ReadTheDocs, both for stable and latest versions.