Automation

Table of Contents

• 9. Automation
  • 9.1. ‘biomodal auth’ stage
  • 9.2. ‘biomodal init’ stage

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Automation

You can automate the auth and init stages of the biomodal CLI for CI and test purposes.

9.1. ‘biomodal auth’ stage

When running a biomodal auth command you can optionally pass
in username and password credentials using the command line flags below:

 auth                                Login to biomodal
    -u | --username <email>           username
    -p | --password <password>        password
    --password-stdin                  Take the password from stdin (recommended)

Username and passwords can also be passed in as environment variables BIOMODAL_USERNAME and BIOMODAL_PASSWORD. Environment set variables will always take precedence over CLI applied variables, so please bear this in mind if using this method.

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9.2. ‘biomodal init’ stage

When re-running the biomodal init command you can skip prompts for setting your temp directory and init folder location by setting an environment variable IGNORE_INIT_PROMPTS=true. Please note that you have to either edit the config file or follow the prompts the initial time the script is run.

You can also do this by adding ignore_init_prompts: true to your config.yaml file.

You can also skip biomodal CLI prompts for error strategy by setting an error strategy in your config.yaml file.

Normally you’ll be prompted to choose either a normal or failfast error strategy. If you set either one of these values in your config.yaml file the biomodal CLI will skip this prompt:

error_strategy: <normal|failfast>

Alternatively you can set the environment variable ERROR_STRATEGY to normal or failfast.

Finally you can also define whether to share events and metrics reports by either setting the SHARE_METRICS environment variable to true or false, or by setting the value directly in the config.yaml file:

share_metrics: <true|false>

If neither of these are set, the biomodal CLI will require user input as to whether to set these values.

Note Settings in the config.yaml file will take precedence over environment variables. If these values are both set but there are disparities between the two, you may experience unexpected results.

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