Getting Started with GCPy

This page describes the installation process for GCPy and how to test to make sure GCPY is installed correctly.

Installing GCPy

GCPy and its dependencies can be installed using Conda in either standard user mode (allow Conda to handle installation without Git support) or development mode using Conda and Conda-build (install from a Git clone). You can also manually install GCPy using a clone of the source code, but this option requires you to add the package to your PYTHONPATH manually and to install properly versioned dependencies on your own.

Software Prerequisites

The only essential software package you need before installing GCPy is a distribution of the Conda package manager, which is used to install GCPy and its dependencies. It is also highly recommended that you create an environment in Conda for working with GCPy. Steps to setup Conda are described below:

  1. Install Miniconda or Anaconda. Miniconda is much more lightweight and functions perfectly well for GCPy purposes, while Anaconda automatically includes many extra packages that are not directly relevant to GCPy.

  2. After installing Miniconda or Anaconda, create a Conda environment for using GCPy. The basic usage (also found on the Conda Github hompeage) is:

    # Create a Conda environment for working with GCPy
    conda create -n gcpy_env
    
    # Activate (enter) your new Conda environment
    $ conda activate gcpy_env #Linux / MacOS
    > activate gcpy_env        #Windows
    
    # Deactivate (exit) your Conda environment
    $ conda deactivate #Linux / MacOS
    > deactivate        #Windows
    

    From within your Conda environment, you can follow the instructions on Installing normally through Conda (if you don’t plan on modifying GCPy source code) or Installing in development mode through Conda-build (for developers).

Python dependencies

Conda handles the installation of all dependencies for GCPy automatically. Most dependencies have minimum version requirements. GCPy has been tested with Python 3.6, 3.7, and 3.8. The list of dependencies (not including sub-dependencies) that are installed by Conda includes:

A full list of package version requirements can be found in docs/environment.yml.

Installing GCPy for non-developers using Conda

GCPy is available through the conda-forge channel under the name geoschem-gcpy. Installing GCPy in your Conda environment requires two commands:

conda config --add channels conda-forge
conda install geoschem-gcpy

Conda will handle the installation of all dependencies and sub-dependencies for GCPy, which includes many Python packages and several non-Python libraries.

Installing GCPy for developers

If you wish to make changes to the GCPy source code with the goal of contributing to GCPy development, you will need to install GCPy from a clone of the GCPy Git repository:

git clone https://github.com/geoschem/gcpy.git
cd gcpy
conda config --add channels conda-forge
conda install geoschem-gcpy --only-deps
pip install -e .

Conda will handle the installation of dependencies when you install from this clone, and pip will point all GCPy links to this directory.

Manual install using source code (pre-1.0.0)

Versions of GCPy prior to 1.0.0 do not support installation through Conda. However, you can still use Conda to install requisite dependencies by creating a Conda environment from the sample environment file at docs/environment_files/gcpy_min/environment.yml. Then clone the GCPy repository using git clone https://github.com/geoschem/gcpy.git. You will also need to add the GCPy directory to the Python path using export PYTHONPATH=/path/to/gcpy:$PYTHONPATH, where /path/to/gcpy/ is the top-level directory of the GCPy repository.

Optional extra Python libraries

The GCPy repository contains a few different environment.yml files for creating new Conda environments. docs/environment_files features three different options: gcpy_min, gcpy_full, and gcpy_extra.

  • gcpy_min contains only the libraries necessary for executing all GCPy functions, and is equivalent to the environment generated by running conda install geoschem-gcpy.

  • gcpy_full contains everything in gcpy_min as well as Jupyter (for working with / developing Jupyter notebook examples) and IPython.

  • gcpy_extras contains everything in gcpy_full as well as extra libraries for scientific analysis in Python outside of GCPy, such as scikit-learn.

Testing your GCPy installation

Once you’ve installed GCPy using one of the methods installed above, you should make sure the package functions correctly. From within your Conda environment, type:

$    python
>>>  import gcpy

If no errors appear, congratulations! GCPy and its dependencies are probably properly installed. If you run into any problems, feel free to open an issue at the GCPy Issues page on Github.