Mate

• Code: GitHub repo
• License: Apache 2.0

Installation

Conda users can install Mate from the prefix.dev/kk-test channel using the following command:

conda install -c https://prefix.dev/kk-test hyo2-mate

This project uses Pixi to manage dependencies and build the application. The following instructions assume that Pixi is installed and available on the command line. Clone source code:

git clone https://github.com/ausseabed/mate.git
cd mate

Install dependencies and build the application:

pixi install

To activate conda environment:

pixi shell

Command Line Application

Mate includes a simple command line application. Usage can be displayed as follows:

%> hyo2.mate -h

usage: hyo2.mate [-h] -i INPUT [-o OUTPUT]

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Path to input QA JSON file
  -o OUTPUT, --output OUTPUT
                        Path to output QA JSON file. If not provided will be
                        printed to stdout.

An example command line is shown below:

hyo2.mate --input tests/test_data/input.json --output tests/test_data/test_out.json

Testing

Unit tests can be run as follows:

python -m pytest --cov=hyo2.mate --cov-report=html  tests/

Note: Unit tests will fail if the test data has not been downloaded (see following section)

Test Data

A collection of data has been uploaded to an AWS S3 bucket to support testing and development of the Mate application. This data requires AWS credentials to download (contact development team).

Once AWS access credentials have been obtained the test data can be downloaded using the AWS CLI.

Note: This data is approximately 20Gb in size

Windows instructions

Set environment variables for AWS:

set AWS_ACCESS_KEY_ID=<AWS Access Key Id>
set AWS_SECRET_ACCESS_KEY=<AWS Access Key Secret>

Download data from S3 into current folder:

aws s3 sync s3://ausseabed-marine-qa-data/mate-test-data/ ./tests/test_data_remote

Linux, MacOS instructions

Set environment variables for AWS:

export AWS_ACCESS_KEY_ID=<AWS Access Key Id>
export AWS_SECRET_ACCESS_KEY=<AWS Access Key Secret>

Download data from S3 into current folder:

aws s3 sync s3://ausseabed-marine-qa-data/mate-test-data/ ./tests/test_data_remote