Installation

Dependencies

The dependencies for microbenthos are:

• python3

• numpy

• scipy

• fipy

• sympy

• cerberus

• click

• pyyaml

• h5py (and libhdf)

• tqdm

• matplotlib >=2.1

• logutils

Install

Install MicroBenthos using either:

pip install microbenthos

Or using:

pip install git+https://github.com/achennu/microbenthos

Source install

The sources for MicroBenthos can be downloaded from the github repo.

You can either clone the public repository:

$ git clone git://github.com/achennu/microbenthos

Or download the tarball:

$ curl  -OL https://github.com/achennu/microbenthos/tarball/master

Once you have a copy of the source, you can install it with:

$ # If using conda...
$ conda env create -n microbenthos -f microbenthos/requirements.yml
$ conda env activate microbenthos
$ cd microbenthos
$ python setup.py install

Development install

MicroBenthos uses pytest to run automated unit testing. If you want to run the included tests, then install the test requirements:

$ pip install microbenthos[test]

To run the tests, change to the tests directory of the source tree.

$ cd microbenthos/tests
$ pytest .

MicroBenthos currently includes 250+ tests of its API entities.

MicroBenthos documentation is rendered using sphinx. To generate the documentation from the source tree, install the docs requirements and then run the build command.

$ pip install microbenthos[docs]

$ # change to the docs directory of microbenthos
$ cd microbenthos/docs
$ make html