Installation

It is recommended to use the provided conda.yml in the root directory to set up a clean Python environment. This ensures that all the packages are built and linked in the way that your platform expects prior to installing PySpecTools, and create a conda environment called pst.

OS-specific instructions

Linux and Mac

The following instructions assume you will be working in terminal, which is the preferred way of installing things on Linux/Mac.

  1. Download and install conda through the standard download; make sure you install Python 3.

2. Clone the PySpecTools git repository:

git clone https://github.com/laserkelvin/PySpecTools.git
cd PySpecTools
conda env create -f conda.yml

Windows

Installation on Windows is trickier for two reasons: PyTorch and Cython do not play nearly as nicely as they should.

For Windows machines, you will need to include Visual Studio C++ libraries, as they are needed by Cython for compilation. Installation for Linux systems should automatically include the math library m, whereas Mac OS this is not required.

  1. Download and install Anaconda through the usual means; make sure you install Python 3.

  2. Download the github repository as a ZIP (through the Clone tab), and unpack it somewhere you’ll find.

  3. Open Anaconda Navigator in your start menu, and navigate to “Environments” to find the screen below

https://docs.anaconda.com/_images/nav-env-tab.png

  1. Click on “Import” at the bottom left, and direct it to the conda.yml provided in the PySpecTools directory. This should build the conda environment named pst.

  2. Open an Anaconda command line through your start menu, and navigate to the PySpecTools directory.

All platforms

1. When conda has finished working its magic, you can then proceed to install PySpecTools with pip:

pip install .

2. When updating, you can also use the github repository directly:

pip install -U git+https://github.com/laserkelvin/PySpecTools

or by running git pull followed by pip install -U .

Jupyter notebooks

While not a requirement, much of the analysis workflow was designed with Jupyter notebooks as a front-end for interactivity. Most base anaconda distributions should already include Jupyter notebook in the installation, but if it does not you can request it by running conda install jupyter.

The default conda environment is base, and typically this is the environment you will be running Jupyter notebooks in without much thought. To make sure the IPython kernel installed in the pst environment is included in your base installation of Jupyter notebooks/lab, you will need to follow the instructions found here.

Final notes

You can test to make sure PySpecTools is installed correctly either by running the provided tests, or at a lower level by trying to import ``PySpecTools` in a Python session.