Installation
Contents
Installation#
Requirements and compatibility#
buildH requires at least Python 3.6 and needs the following modules:
numpy
pandas
numba
MDAnalysis (with support of 2.0)
All the instructions below have been tested on Unix like platforms (e.g. Ubuntu), which we recommend for running buildH. We do not provide support for other platforms, but since buildH has been written in pure Python, it should work there provided its dependencies are supported.
Simple installation#
A simple installation with pip will do the trick:
python3 -m pip install buildh
All dependencies (modules) will be installed automatically by pip.
Note that this way of proceeding will install buildH and its dependencies within the python of your Unix system, which may lead to conflicts of version if you have other scientific packages installed. To avoid this you may want to create a specific conda or virtual environment for buildH (see below).
Installation within a conda environment#
buildH is also available through the Bioconda channel.
We recommend to install buildH within a conda environment. First create a new conda env:
conda create -n buildH "python>=3.6"
Then activate your environment:
conda activate buildH
Last, install buildH within that environment:
conda config --add channels conda-forge
conda config --add channels bioconda
conda install buildh
Building from source#
We recommend to use a specific environment, either by using venv or conda. All packages will be installed within that environment which avoids conflicts of version.
If you still do not want to create a specific environment for buildH, you can skip the first section Create an environment
below.
In any case, the python version should be >= 3.6.
Create an environment#
First, create a new environment (we call it env4buildH
):
If you chose conda:
conda create -n env4buildH python=3.8
If you chose venv:
python3 -m venv /path/to/env4buildH
Activate your environment:
If you chose conda:
conda activate env4buildH
If you chose venv:
source /path/to/env4buildH/bin/activate
Install buildH from source#
Clone the buildH repository:
git clone https://github.com/patrickfuchs/buildH.git
cd buildH
Install with pip
the packages required by buildH, namely numpy, pandas, MDAnalysis and Numba, which are all specified in the file requirements.txt:
pip install -r requirements.txt
Install buildH from source with pip
:
pip install -e .
For developers#
For installing a development version from source with the full environment (allowing building the doc, launching tests, etc.), see here.
Testing#
The tests rely on the pytest
package. You need first to install a development version (see above). Once done, you can run the tests with just:
cd buildh # if it's not already the case
pytest
All tests should pass. If anything fails, please open an issue.