Note
Pyleoclim requires the use of Python 3.8 or 3.9.
Installing Pyleoclim
We recommend the use of Anaconda or Miniconda, with Pyleoclim setup in its own conda environment. Some default packages shipping with the full Anaconda distribution are known to cause conflicts with the required Pyleoclim packages, so we recommend Miniconda, especially for beginners.
Installing Anaconda or Miniconda
To install Anaconda or Miniconda on your platform, follow the instructions from this page.
Click here for a quick tutorial on MacOs and Linux systems.
Creating a new conda environment
To create a new environment using Python 3.9 via command line:
conda create -n pyleo python=3.9
To view a list of available environment:
conda env list
To activate your new environment:
conda activate pyleo
To view the list of packages in your environment:
conda list
To remove the environment:
conda remove --name pyleo --all
More information about managing conda environments can be found here.
Installing Pyleoclim
Make sure that the pyleo environment is activated.
First install Cartopy:
conda install -c conda-forge cartopy
Then install Pyleoclim through Pypi, which contains the most stable version of Pyleoclim:
pip install pyleoclim
To install the development version, which contains the most up-to-date features:
pip install git+https://github.com/LinkedEarth/Pyleoclim_util.git@Development
If you would like to use Jupyter Notebooks or Spyder for code development, install these packages in your environment:
conda install spyder
conda install jupyter
Building from source for the f2py feature of WWZ
The default version of WWZ that comes with the installation steps mentioned above is relying on Numba. It is fast enough for lightweight spectral & wavelet analysis tasks, in which case we recommend using the default installation.
However, it could be slow for heavy use (e.g. performing it for hundreds of times on timeseries with length longer than 1000 points), in which case we recommend activating the f2py feature to achieve an acceleration of around 50%.
To do that, a Fortran compiler (e.g. gfortran
or ifort
) is required on your local machine, and the related Fortran source code should be compiled locally following the steps below:
download the source code, either via git clone or just download the .zip file from the Github repo
go to the directory
Pyleoclim_util/pyleoclim/f2py
, and then typemake
to compile the .f90 source code withgfortran
one may also edit the
Makefile
to useifort
as the compiler to achieve further acceleration; just comment out the line forgfortran
and use the line forifort
belowa
.so
file will be generated if the compilation is successfulcopy the
.so
file into the directoryPyleoclim_util/pyleoclim/utils
where Pyleoclim is installed on your machine. To find out the location, one may import the package in Python and “print” it:
import pyleoclim as pyleo
print(pyleo)
Again, unless you are planning to make heavy use of the WWZ functionality, we recommend using the default installation.
Docker Container
Docker containers with various versions of Pyleoclim are available at: https://quay.io/repository/2i2c/paleohack-2021?tab=tags.
To pull an image:
docker pull quay.io/2i2c/paleohack-2021:latest