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Catalogue

While the search functionality (top right corner) provides easy access to a particular guide searching by keywords, you can also use this listings page (catalogue) to explore all available guides across all topics.

Each guide has keywords at the top, and these are clickable. Clicking on a category will bring you back to this page filtered to relevant guides. You can either browse by category using the filters on the right, sort by title or date, or use the search box to find specific topics of interest.

Access and reuse

Access and reuse depends on a variety of factors, including the format in which your data is stored, the tools used to create and manage it, and the policies governing its…

Accessing and requesting Project Data Storage space

Project Data Storage

TU Delft network drives are automatically mounted on TU Delft-managed computers (running Windows) when connected to the TU Delft network (dastud, eduVPN).

Archiving

Archiving your software ensures long-term availability and accessibility. By archiving your software, you can preserve its state at a specific point in time, making it…

Archiving and publishing data

Towards the end of the research cycle, data archiving (and publishing, when possible) is an essential step for the longevity and accessibility of your research. Archiving…

Automation for software development

Continuous Integration (CI) refers to the build and unit testing stages of the software release process. Every committed revision can trigger an automated build and test.…

Branch management

Version Control

Branch management in Git is essential for collaborative software development in version-controlled environments. The core advantage of branching is that it provides…

CI with GitLab

If you are using a TU Delft GitLab instance and you want to implement DevOps or CI/CD pipelines, you will need to install a GitLab Runner yourself. This runner must be set…

CITATION.cff

How to cite software

Code documentation

Good code documentation acts as the bridge between developers and users by clearly explaining the functionality and rationale behind your code. Whether you’re writing inline…

Code of conduct

Code of Conduct

A code of conduct establishes expectations for behavior within your project’s community, creating an inclusive space that minimizes conflicts and promotes constructive…

Code quality

Overview of code quality tools and services

Code smells

Overview of common code smells and how to address them

Code style and tools

Overview of code style guides, static analysis tools, and formatters.

Collaboration

Version Control

Effective collaboration is a fundamental aspect of any successful software development project.

Commented-out code

Dead code refers to unused or unreachable code that remains in the codebase but serves no functional purpose. Commented-out code consists of inactive code blocks that…

Configure SSL certificates

It is common practice to have web servers serving content over HTTPS, which is the secure version of HTTP. In order to do this and make the connection secure, you need an…

Contributing guidelines

Contributing Guidelines

A well-maintained README provides an overview of your project’s current state, while a CONTRIBUTING guide encourages user/developer involvement. Together, these documents…

Creating a Python package

By turning your code into a package and hosting it on a platform like PyPI (Python Package Index), you enhance the quality and sustainability of your software, promote reuse…

Creating an R package

In this guide we will briefly touch the necessary steps to create an R package. For a more detailed guide, please refer to the excellent R packages book written by Hadley…

Data backup

An effective system for backing up research data is crucial to the success and reproducibility of any research project. Backups ensure that irreplaceable files are not lost…

Data collection

Data Conventions

Data collection is one of the first steps in the data lifecycle. It involves gathering and recording data from various sources, which can include (but are not limited to)…

Data conventions

Data Conventions

By adhering to domain-aligned data conventions, you can enhance the quality and reproducibility of your work, promote collaboration, data sharing and reuse. While…

Data licensing

When depositing data, selecting an appropriate license cannot be overlooked, as it defines the permissions and restrictions for others using your data. Clear labelling of…

Data processing

Data Processing

Version Control

Data processing is a broad term and is often conflated with related terms. It typically includes steps like data cleaning and data transformation. Some workflows may extend…

Data security

Data security is a critical aspect of research data management, ensuring that sensitive information is protected from unauthorized access, loss, or corruption. It involves…

Data sharing

This section covers aspects of data sharing, for ongoing work, throughout the active phase of a research project. The use of data repositories, the importance of data…

Data storage

In the context of research data management, “Data Storage” refers to securely housing research data on various digital media or infrastructure, having it readily accessible…

Deep Nesting

“Code is like humor. When you have to explain it, it’s bad.”

Development workflow

Version Control

Project Organization

Version control ensures transparency, reproducibility, and smooth teamwork. Clear branching strategies and consistent workflows make it easier to track changes, review code…

Documentation

Documentation serves as a bridge between the developer and user, and effectively communicating and explaining the code is as important as the code itself. Often, two types…

Duplicated code

Duplicated Code

Fixing duplicated code in your codebase

Environment and dependency management

Project Organization

Properly managing dependencies and your environment is a critical aspect of any software project. This ensures that your project can be reliably reproduced, simplifies setup…

Environment and dependency management in MATLAB

MATLAB does not use virtual environments like Python, where isolated environments manage dependencies. Instead, MATLAB handles project-specific dependencies using:

Environment and dependency management in Python

When working with Python, managing dependencies and environments is important to ensure your project can be reproduced and shared.

Environment and dependency management in R

R users often rely on RStudio Projects and renv to manage their development environments. RStudio Projects organize your workspace by managing file paths and configurations…

FAIR Software

While originally targetting data management, the FAIR for Research Software (FAIR4RS) extends the FAIR principles to research software, which, unlike data, is executable and…

FAIR checklist for research software

This checklist provides a set of recommendations for FAIR software. It outlines best practices and guidelines to ensure the quality, reproducibility, and sustainability of…

FAIR data

The goal of the FAIR principles is to improve research transparency, reproducibility and reusability. FAIR data enhances research reliability, impact, and visibility…

Getting started

Getting Started

This section provides resources to support data owners and users at various stages of the data lifecycle. It highlights important information and available tooling at TU…

Getting started

Getting Started

Research software can be thought of as evolving through stages, reflecting how code evolves alongside the research process:

Getting started

Getting Started

This section guides you through the essential systems and services needed to manage computational resources and collaborate effectively within TU Delft supported environments.

GitHub Actions

GitHub Actions is a CI/CD platform that automates building, testing, and deploying code. You can set up workflows that build and test every pull request in your repository…

GitLab pipelines

As previously mentioned in the Project management section, TU Delft has its own GitLab instance. However, it does not (yet) have preconfigured servers available to run GitLab…

Hard coding

Explanation of hard coding and how to address it

Hosting

Once you have created your documentation either in Sphinx, Jupyter Book, MkDocs or Quarto, you can host it online.

Inappropriate Intimacy

This code smell occurs when one part of the system knows too much about the internal details of another, leading to tight coupling. When components are too dependent on each…

Large Classes

A monolithic design is where an entire system is built as a single, tightly coupled unit without clear separation of responsibilities or modularization. This often leads to…

Long Method

Refactor long methods into smaller, more focussed functions

MATLAB documentation

🚧 Coming soon! ⏳

Many arguments

When a function or method takes many parameters (inputs), it can become difficult to understand, maintain, and test. If a function needs a lot of information to work, it…

More testing concepts

Code coverage measures how much of your code is executed during testing. It is a useful metric to ensure that your tests are comprehensive and indicate your code’s quality.…

Mount Project Drive on server

Project Data Storage

Project drive storage can be mounted and made accessible in your TU Delft Virtual Private Server (VPS).

Moving data to remote servers

Securely transfer data to and from TU Delft virtual servers using SCP or Citrix.

Offboarding and ownership

Offboarding procedures are necessary for ensuring the continuity and integrity of research data when team members leave or transition roles. Establishing clear ownership…

Online services

Overview of code quality and security tools and practices

Packaging

Packaging allows developers to bundle their code into a format that is easily installable and manageable across different environments. By creating a package/library, you…

Packaging, releases and archiving

Eventually your software will be at a sharable and publishable point. One way to distribute your software is to package it and release it on a platform like PyPI (Python…

Planning

When planning your research, it is important to consider how you will manage your data. This is the very first step in the research data lifecycle; you define your research…

Privacy

In case you are working with sensitive data, it is important to consider the privacy of the individuals involved. This includes ensuring that personal data is collected…

Project management

Version Control

Project Management

Git is a distributed version control system that enables you to track changes in your code over time. Platforms like GitHub, GitLab and Bitbucket extend the features of git…

Project structure

Project Organization

Repository Structure

In software development, the choices you make at the start will affect your project’s final outcome. One key decision is how to structure your project, as a well-organised…

Project templates and reusability

Project Organization

Repository Structure

Templates can help you to standardize your software development process.

Publishing data

Data repositories are online locations for storing research data long term. When data is published in a repository, it is (often) assigned a persistent digital object…

Python code documentation

Documenting Python code

R documentation

The standard approach for documenting R projects is using roxygen2, a package that enables inline documentation for R scripts and packages. It is tightly integrated with the…

README

Writing a good README

Refactoring

Overview of refactoring code practices

Release your Python package

After bundling your source code into a package, you can publish it to PyPI. This will allow others to easily install your package using pip.

Release your R package

After building and testing your R package, you can release it to CRAN. This process involves several steps to ensure that your package is ready for distribution. Unlike PyPI…

Releases

Once you have your software packaged, you can release it to platforms like PyPI or CRAN. While your software might be already publicly available on GitHub, releasing it to a…

Request a VPS

This guide describes the essentials for requesting and setting up a TU Delft managed Virtual Private Server (VPS).

Servers

A server is a computer that handles requests (data, services, or programs) from other computers, known as clients, over a network. Servers are often a critical component of…

Set up SSH tunneling for a VPS

how to set up a single-step SSH connection to a VPS using SSH tunneling

Setting up a GitLab runner for MATLAB

With the continuous method of software development, you continuously build, test, and deploy iterative code changes. This iterative process helps reduce the chance that you…

Side effects and external state

Side effects occur when a function modifies external state or interacts with the outside world beyond simply returning a value. This makes code less predictable, harder to…

Software design principles

Writing code represents only one aspect of software design. The real challenge lies in creating systems that stand the test of time. Good software design creates systems…

Software licenses

Licensing software developed at TU Delft

Software management plan

A software management plan (SMP) helps to implement best practices during software development and ensures that software is accessible and reusable in the short and longer…

Software testing

When you’re writing software – especially for research – it’s important to make sure your programs work as expected. Testing is like a safety net: it helps you catch…

Storage options

Project Data Storage

Data storage options at TU Delft

Testing in MATLAB

Writing and running tests with MATLAB

Testing in Python

In Python, two widely used testing frameworks are pytest and unittest. This guide focuses on pytest, which is recommended for its simplicity and readability. If you are new…

Testing in R

R offers several testing frameworks, but the most widely used is the testthat package. It provides a straightforward way to write unit tests for your R code. The package is…

Testing strategy

Guidelines for researchers new to testing and experienced test writers.

Tooling

There are various tools available that can help you create, manage, and deploy project documentation more effectively.

Tooling

🏗️ Under construction!

Types of tests

Different types of tests to ensure your software works as expected.

Web Servers

If you want to host a website or a web application, you will need to work with a web server. The job of a web server is to serve content on the internet by acting as a…

Workflow management

Project Organization

Workflow Management

Workflow management for research software is the practice of organizing series of tasks related to research, such as how scientific code, data and experiments are developed…

eLabJournal and RSpace

Jones recounts her frustration with relying on paper notebooks to record experiments. “It becomes problematic when you need to replicate experiments or continue a research…