README.md

Protocols for NGS

Requires: StandardLibs, CollectionManagement Note Standard Libs may need update to ItemAction for this library to work properly

General

• Style Guide I've been working on

Spacing

• Spaces (2) instead of tabs for indentation
• One space between # and comment text
• One empty line between method definitions

Yard Doc Style:

We use YARD to generate documentation. That link has a lot of information on style, but the main thing is to get the tag format right. There are tags for @return, @raise errors etc. They all work the same way -- @Tag variable_name [variable_type] Any other notes

# Perform the Streak Plate Protocol for a single operation
#
# @param operation [Operation] the operation to be executed
def operation_task(operation)
    Method Body
end

Variables

• Avoid single letter variables unless they are defined very close to where they are being used
• If you're using aquarium specific terms (e.g. FieldValue), write the words out.
• Someone who doesn't know our database/terms should still be able to understand what the variables mean.
• Try not to use structure names, unless the thing is that structure. That is, if it has array in the name, it should be an Array (in the Ruby sense of an array)
• But also, try not to use words like Array, List, etc. in variable names. e.g. sample_plate instead of sample_table, or samples instead of sample_array

More Ruby Style Stuff

• Each include statement gets its own line
• x += y is preferred over x = x + y
• Single quotes 'thing' preferred over double, unless you need interpolation "#{thing}"
• nil? preferred to == nil

House Style Stuff

• Move intro information into documentation section of protocol, along with note on what protocols (if any) would follow or precede it.
• Use () when declaring parameters in method signature, and when calling methods.
• Keyword Arguments variable: default_value preferred over defaults variable = default