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`phydms`_ is written in `Python`_. It requires Python 3.4 or higher.
Straightforward installation requires the `Python`_ package management system `pip`_ and a C compiler such a gcc (there are some cython extensions).
`phydms`_ has been tested on relatively recent versions of Linux and Mac OS X.
If you have the Minimal requirements, you can install `phydms`_ by simply typing:
pip install phydms --user
This assumes that the local installation directory is in your current path. See below for more details.
Where to install `phydms`_ with pip
You need to figure out where you want to install `phydms`_.
Using sudo to install globally is not recommended for Python packages in general.
We suggest that you use one of the following two options:
The `Python convention for local installation`_ is to install locally using the --user option to pip. This option installs into ~/.local/ for Linux, or into $HOME/.local/lib/Python/x.y/ (where x.y is the `Python`_ version, such as 3.5) for Mac OS X.
For locally installed programs to be accessible, you need to add ~/.local/bin/ to the PATH variable, and ~/.local/lib/ to the PYTHONPATH variable. If you are using the `bash shell`_, you would do this by adding the following lines to your ~/.bashrc file:
PATH=$HOME/.local/bin/:$PATH export PYTHONPATH=$HOME/.local/lib/python3.5/:$PATH
You then want to make sure that your ~/.bash_profile simply sources your ~/.bashrc file as described here by making ~/.bash_profile consist of the following:
if [ -f ~/.bashrc ]; then
source ~/.bashrc
fi
Once the paths are set up as described above, simply install with:
pip install --user
If this fails, check if you have `pip`_ installed. You can do this by typing:
pip -h
If you instead get an error message such as -bash: pip: command not found then you need to install `pip`_.
If you have easy_install, then you can install `pip`_ globally with:
sudo easy_install pip
or locally with:
easy_install pip --user
If those commands also fail (i.e. you don't have easy_install either), then install `pip`_ by following the instructions here.
The other good approach is to use pip to install into a virtual environment.
The use of virtual environments is described here. Once you have created a virtual environment as in these instructions, you can just install with pip dropping the --user command.
If you have previously installed `phydms`_ but are not sure that you have the latest version, you can upgrade using `pip`_:
pip install phydms --upgrade --user
First clone the `phydms source code`_ from GitHub:
git clone https://github.com/jbloomlab/phydms
Then install locally with:
cd phydms pip install -e . --user
`phydms`_ requires some external `Python`_ packages. The up-to-date exact requirements are listed under install_requires in the setup.py file in the main directory of the `phydms source code`_. If you are installing with `pip`_, these external packages will automatically be installed. If you are installing from source, you may need to install these packages yourself.
The original version of `phydms`_ (version 1.*) used in `Bloom, Biology Direct, 12:1`_ had similar functionality, but an entirely different implementation that utilized `Bio++`_ for the likelihood calculations.
The new version (version 2.*) has similar functionality, but is a completely new implementation and so may give slightly different results.
The last stable version of the old implementation is 1.3.0.
The source code for that version is available here.
The older implementations are also still on `PyPI`_.