Install packages
Required dependencies
osdyn requires python>3.6.7 and depends on the following packages:
netCDF4 (1.5.8) |
netCDF4 provides an object-oriented python interface to the netCDF version 4 library |
xarray (>0.20.2) |
Xarray is an open source project and Python package that makes working with labelled multi-dimensional arrays simple, efficient, and fun! |
dask (2021.12.0) |
Dask is a flexible library for parallel computing in Python. |
configobj (>5.0) |
ConfigObj is a simple but powerful config file reader and writer: an ini file round tripper. |
xesmf (>0.6.2) |
xESMF is a powerful, easy-to-use and fast Python package for regridding. |
esmpy: (=7.1.0) (=8.2.0) |
ESMPy is a Python interface to the Earth System Modeling Framework (ESMF) regridding utility. |
xgcm: (0.6.0) |
xgcm is a python packge for working with the datasets produced by numerical General Circulation Models (GCMs) |
gsw (3.4.0) |
This Python implementation of the Thermodynamic Equation of Seawater 2010 (TEOS-10). |
cf-units (3.0.1) |
Units of measure as required by the Climate and Forecast (CF) metadata conventions. |
cartopy (0.20.1) |
Cartopy is a Python package designed for geospatial data processing in order to produce maps and other geospatial data analyses. |
nc-time-axis (1.4.0) |
nc-time-axis supports for cftime.datetime axis in matplotlib. |
Seaborn is a Python data visualization library based on matplotlib. |
bottleneck (1.3.2) |
Bottleneck is a collection of fast NumPy array functions written in C and allows to speeds up NaN-skipping and rolling window aggregations by a large factor |
Optional dependencies
The Jupyter Notebook is an open-source web application that allows you to create and share documents that contain live code, equations, visualizations and explanatory text. |
|
nbdime provides tools for diffing and merging Jupyter notebooks. |
|
spyder (5.2.1) |
Spyder is a powerful scientific environment written in Python, for Python, and designed by and for scientists, engineers and data analysts. |
pytest (6.2.5) |
Pytest is a testing framework which allows us to write test codes using python. |
black (2021.12b0) |
Black is the uncompromising Python code formatter. |
flake8 (4.0.1) |
Flake8 is a great toolkit for checking your code base against coding style and programming errors |
sphinx (>2.3) |
Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. |
sphinx_rtd_theme (>=0.5.0rc1) |
Sphinx theme for readthedocs.org |
nbsphinx (>=0.8.6) |
Jupyter Notebook Tools for Sphinx |
sphinx-copybutton (>=0.4.0) |
A small sphinx extension to add a “copy” button to code blocks |
sphinx-gallery (>=0.9.0) |
Sphinx extension for automatic generation of an example gallery |
Create python environment
osdyn library is available from osdyn project
As under progress, it is a private project at the moment. Feel free to ask Valerie Garnier from Ifremer institute to any information.
osdyn is not a pure Python package but its dependencies are. The easiest way to get all the packages installed is to use conda (conda 4.8.2 or later) from conda distribution.
From scratch
From .yaml osdyn environment
Add packages unvailable from conda
A few packages are not available from conda, so install them into osdyn environment from pip install command. .. (but never mix pip and conda installation !)
Load osdyn environment and then add packages from their respective cloned or remote projects.
source PATH/Anaconda3-2019.10/etc/profile.d/conda.csh [or sh...]
conda activate osdyn [or myname]
eo_harvest library
For user-friendly downloads from CMEMS and other databases, feel free to add eo_harvest.
The package can be downloaded at ifremer eo_harvest and then add it to osdyn environment
cd path_to_eo_harvest
python setup.py install
datarmor usage
To speed up access to your dataset of interest (or a subset), the user is encouraged to use intake datarmor catalogues. To do so, install dask-hpconfig package:
python -m pip install git+https://extranetlogin@gitlab.ifremer.fr/iaocea/dask-hpcconfig.git
osdyn library
First, get the package. At the moment, you need to register to the project and then
git clone https://gitlab.ifremer.fr/vg056b7/osdyn.git
Second, install osdyn library into your python environment:
python -m pip install .
Warning
You need a fortran compiler to install osdyn.
You are ready ! Have a look at Quick overview and at all the notebooks under Tutorials.
Have fun !