MacOS on Firas Sadiyah

Python Exception Handling

Sat, 24 Feb 2024 12:00:00 +0000

In genomic data analysis, we often use a pipeline function to process data stored in a dataframe by calling several mini-functions. Each mini-function may modify the dataframe by adding a new column with new values and then filter out the rows that do not meet certain criteria. However, this may result in an empty dataframe if none of the rows satisfy the filters and can lead to errors or unexpected results when the pipeline function tries to perform more operations on the empty dataframe. To avoid this situation, we can use two strategies. First, we can check if the DataFrame is non-empty before applying any logic in each mini-function. Second, we can make the pipeline function fail graciously if it receives an empty DataFrame from any of the mini-functions by using a custom exception and a try-except block. Let’s take a look.

Debugging Python codebases using PyCharm and VSCode

Sun, 04 Feb 2024 12:00:00 +0000

Debugging, an essential process for identifying and rectifying errors in a computer program, is particularly crucial for computational biologists dealing with complex codebases that often involve intricate mathematical models, data analysis, and simulations. Merely reading the code may not suffice to grasp the logic and functionality of the project. To gain a deeper understanding, you may need to run the code, examine the variables, and observe the outputs. Towards this end, the integrated debuggers in PyCharm and VSCode prove invaluable.

Managing Python virtual environments

Sun, 28 Jan 2024 12:00:00 +0000

When it comes to Python development on macOS, I rely on a combination of two tools that have served me exceptionally well over the past few years: Pyenv and Poetry. Pyenv provides an elegant solution for managing different Python versions on my system, while Poetry simplifies dependency management and the creation of virtual environments for my projects. In this article, I will guide you through the process of setting up Pyenv to install a specific Python version and then using Poetry to create a virtual environment for your project.

Running NetMHCPan on Apple Silicon

Tue, 23 Jan 2024 12:00:00 +0000

NetMHCPan, a widely used tool for predicting peptide binding to major histocompatibility complex (MHC) molecules, is essential for understanding immune responses. However, the tool’s binaries are currently available only for the x86_64 architecture, whether on Darwin (macOS) or Linux. As I intended to conduct test runs on my Apple Silicon device (arm64), I encountered the following error:

1netMHCpan: no binaries found for Darwin_arm64 /net/sund-nas.win.dtu.dk/storage/services/www/packages/netMHCpan/4.1/netMHCpan-4.1/Darwin_arm64/bin/netMHCpan

To address this, one option is to run NetMHCPan using Rosetta, a dynamic binary translator that translates executable code on-the-fly. In simple terms, Rosetta intercepts instructions intended for one architecture (Intel, in this case) and converts them into instructions compatible with another architecture (Apple Silicon).

Setting up a reproducible R environment on macOS

Mon, 10 Oct 2022 12:00:00 +0000

Using renv is an excellent choice for maintaining a clean and reproducible R environment on macOS. Here, I will share my experiences and provide a guide on setting up R on macOS. The post is divided into the following sections:

Installing system dependencies required for R libraries using Homebrew.
Installing R libraries using renv.
Saving and restoring R environments using renv.
Installing R libraries hosted on private repositories.
Building R libraries from source using Makevars.

Let’s get started!

Using data.table with OpenMP support

Mon, 26 Apr 2021 00:00:00 +0000

If you are facing difficulties with large data sets in R, using data.table could provide a performance boost. However, when loading data.table, especially on macOS, you might encounter a warning indicating the absence of OpenMP support, causing data.table to operate in a single-threaded mode. This limitation prevents you from fully utilizing the potential benefits of using data.table and taking advantage of the underlying hardware.

 1library(data.table)
 2data.table 1.14.0 using 1 threads (see ?getDTthreads).  Latest news: r-datatable.com
 3**********
 4This installation of data.table has not detected OpenMP support.
 5It should still work but in single-threaded mode.
 6If this is a Mac, please ensure you are using R>=3.4.0 and have followed our Mac instructions here:
 7https://github.com/Rdatatable/data.table/wiki/Installation.
 8This warning message should not occur on Windows or Linux. If it does, please file a GitHub issue.
 9**********
10
11getDTthreads()
12[1] 1

What is the issue here?

OpenMP is an implementation of multithreading, and the Clang compiler that comes with Xcode on macOS lacks support for OpenMP. Apple has chosen not to include the libomp.dylib run-time library in their compiler. You can verify this by executing the following command.

macOS setup for data science

Sun, 08 Oct 2017 12:00:00 +0000

Here, I summarise how I setup my macOS for the purpose of Data Science. Ultimately, I should invest some time into automating the process.

Install Command Line Developer Tools

1xcode-select --install

Install HomeBrew

1/usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"

Turn off analytic (optional)

1brew analytics off

Install iTerm

1brew install iterm

Configure iTerm

To download different colour schemes, visit iTerm Themes

Install Go2Sehll

Download and install from Go2Shell, then configure it to work with iTerm:

Mounting remote drives locally using sshfs

Tue, 29 Aug 2017 12:00:00 +0000

To mount a network drive as a local one, you can use sshfs.

Generate SSH key

1$ mkdir ~/.ssh #if it does not already exist
2$ chmod 700 ~/.ssh
3$ cd ~/.ssh
4$ ssh-keygen -t rsa
5$ enter a keyname
6$ enter a passphrase
7$ ssh-copy-id -i [path to rsa file] USER@SERVER

Where -i indicates where the rsa file is located. The .pub key is the one needed to be copied.

[Optional] Start a SSH agent, and add the key to the SSH agent: