README.md

Python, Conda and Dependencies (A short/brief walkthrough)

Python is an interpreted language widely used in scientific/research computing. Dynamic typing, ease of use and a plethora of ecosystem packages ranging from numbers' manipulation to machine learning make it a popular choice for data scientists and researchers alike. There a ton of great resources on learning Python online. The official documentation is a great place to start.

The standard library of Python is quite extensive and powerful, but what makes Python such a great langauge is its ecosystem of third-party libraries - majority of the most popular ones being open source - that make it a viable workhorse for most research projects. However, because of the interpreted nature of the language, using third party libraries, requires a dependency management system. Added on that, over the years, a convention has been established to use virtual environments that isolate project level dependencies, making it easier and more reproducible to run/develop projects. This is where conda: A system-level, binary package and environment manager running on all major operating systems and platforms, comes in. With conda users can create, export, list, remove and update environments that have different versions of Python and/or packages installed in them. Switching or moving between environments is called activating the environment. You can also share an environment file.

Installing conda

To install conda, follow the instructions here, based on the operating system you are using. Additionally, because of the popularity as well as some inefficeincies of conda, there are other alternatives such as micromamba/mamba, both of which are drop-in replacements for conda, but are in early phases of their evolution.

Create a new environment

After installing conda, we will create a new environment for the tutorial. To do so, run the following command:

$ conda create -n chimerapy-tutorial python=3.10 -c conda-forge -c defaults

The above command will create a new Python environment named chimerapy-tutorial, with Python version 3.10. The -c flag is used to specify the channel from which to install the package. The conda-forge channel is a community-led collection of recipes, build infrastructure and distributions for the conda package manager. The defaults channel is the primary channel for conda packages. You can activate the environment by running:

$ conda activate chimerapy-tutorial