Installation

pyGMS must be cloned from the GitHub repository:

git clone https://github.com/cmeessen/pyGMS.git

pyGMS can now be installed by (optionally) creating an Anaconda environment, and then running pip.

Creating an Anaconda environment

This step is optional. If you do not wish to use an isolated environment, jump directly to Installation with pip.

Installing pyGMS with Anaconda allows you to use pyGMS inside an environment that does not alter the rest of your Python installations. First, if you do not have an installation, download a version here.

Now navigate to the directory where you cloned pyGMS into, and execute

conda env create -f environment.yml

This will create an environment named pygms that includes all required packages. Activate the environment with

conda activate pygms

To be able to use the environment as a kernel in jupyter notebooks, run this while the pygms environment is active

conda install -c conda-forge nb_conda_kernels

The environment can be deactivated using:

conda deactivate

Installation with pip

To install pyGMS navigate to the base folder of pyGMS (containing setup.py) and execute:

pip install -e .

The installation with the -e flag will create a symbolic link to the package, meaning whenever you change something within the repository (e.g. pull an update), it will be automatically available.

Testing the installation

In order to check whether everything works correctly, execute the tests:

make test

The output should look like this:

python tests/test.py
test_call_depth (__main__.TestGMS) ... ok
test_call_well (__main__.TestGMS) ... ok
test_get_xlim (__main__.TestGMS) ... ok
test_get_ylim (__main__.TestGMS) ... ok
test_get_zlim (__main__.TestGMS) ... ok
test_getitem_laye_int (__main__.TestGMS) ... ok
test_getitem_layer_str (__main__.TestGMS) ... ok
test_getitem_layer_str_fail (__main__.TestGMS) ... ok
test_info_df (__main__.TestGMS) ... ok
test_call_fail (__main__.TestLayer) ... ok
test_plot_profile (__main__.TestPlot) ... ok
test_plot_strength_profile (__main__.TestPlot) ... ok
test_plot_topography (__main__.TestPlot) ... ok
test_plot_yse (__main__.TestPlot) ... ok
test_compute_bd_thickness_comp (__main__.TestRheology) ... ok
test_compute_elastic_thickness_comp (__main__.TestRheology) ... ok
test_integrated_strength_comp (__main__.TestRheology) ... ok
test_integrated_strength_ext (__main__.TestRheology) ... ok
test_sigma_byerlee_comp (__main__.TestRheology) ... ok
test_sigma_byerlee_ext (__main__.TestRheology) ... ok
test_sigma_byerlee_fail (__main__.TestRheology) ... ok
test_sigma_d_comp (__main__.TestRheology) ... ok
test_sigma_d_ext (__main__.TestRheology) ... ok
test_sigma_d_fail_z (__main__.TestRheology) ... ok
test_sigma_diffusion (__main__.TestRheology) ... ok
test_sigma_dislocation (__main__.TestRheology) ... ok
test_sigma_dorn (__main__.TestRheology) ... ok
test_sigma_dorn_nan_a_d (__main__.TestRheology) ... ok
test_sigma_dorn_nan_q_d (__main__.TestRheology) ... ok
test_sigma_dorn_zero (__main__.TestRheology) ... ok
test_heat_flow (__main__.TestThermal) ... ok
test_call (__main__.TestWell) ... ok
test_getitem (__main__.TestWell) ... ok
test_plot_grad (__main__.TestWell) ... ok

----------------------------------------------------------------------
Ran 34 tests in 1.684s

OK

Remove pyGMS

To uninstall pyGMS perform the following steps:

  1. If you have used pyGMS inside an Anaconda environment simply run

conda env remove -n pygms

  1. If you have installed it simply with pip, then run

pip remove pygms-cmeessen