glossary.md

Development Terms

Design Documents & Dev Environments

• Design Document

  Document used to outline a development problem and a proposed solution

• Development Environment

  Separate space for testing and developing code. Keeps bugs and issues isolated from production code.

• Version Control

  Systems to handle tracking and saving of code changes over time.

• Git / GitHub

  Version control software (VCS) for managing code repositories as well as hosting said repositories.

GitHub / Version Control

• Stage

  Prep changes for a commit. This allows you to pick and choose changes for a given commit.

• Commit

  A snapshot of your repository at a given time. Like a save point.

• Push

  Move any commits/changes to a remote repository.

• Pull

  Transition code from a remote repository to a local instance, be it Docker, GitHub, or any other remote repository. Allows others to utilize your pushed changes.

• Merge

  Incorporate changes made on one branch into another, usually from a development branch into the main branch.

• Synchronize

  Involves processes such as git fetch, pull, and push that keeps local and remote branches in concordance with one another.

• Publish

  Publishing involves the committing and pushing of changes to a remote repository.

• Clone

  Copies a remote repository into a directory on a local instance. This includes the ability to view branches and previous commits.

Changes to Production

• Functional Test

  Testing that the code changes functions correctly in likely scenarios.

• Validation Test

  Ensure software meets very specific criteria like a previously defined benchmark

• Continuious Integration (CI)

  Frequent contribution of code to a central repository from which automates builds and tests are run.

• User Acceptance Testing (UAT)

  The approval by end-users that the software meets needs and expectations.

• Static Release

  A deployment of a fixed software version that does not recieve changes regularly.

• Semantic Versioning

  A versioning scheme that reflects the severity of changes made to a codebase.

Workflow Managers and Nextflow

• Software Package

  A bundle of related computational resources that are required for certain pieces of software to function.

• Package Manager

  Allows for ease of installation/update of software packages.

• Workflow Manager

  Handle the execution and operation of workflow code within a standardized framework for reproducibility.

• Workflow Language

  The script that is executed by a workflow engine.

• Workflow Engine

  Software that interpretes and executes workflow script.

• First In First Out (FIFO)

  The order in which data can enter and exit a data structure, specifically Nextflow Channels.