To store/get the version information for a module use the global functions:
drupal_set_installed_schema_version()
drupal_get_installed_schema_version()
For example set a new version for mymodule
with drush:
drush ev "drupal_set_installed_schema_version('mymodule', '8123')"
Print the version with drush, in this example for the module comment
:
drush ev "var_dump(drupal_get_installed_schema_version('comment'))"
The functions are defined in schema.inc. Here you can see how to access the key_value table through the keyvalue api, if you want to use your own code:
/**
* Updates the installed version information for a module.
*
* @param string $module
* A module name.
* @param string $version
* The new schema version.
*/
function drupal_set_installed_schema_version($module, $version) {
\Drupal::keyValue('system.schema')->set($module, $version);
// Reset the static cache of module schema versions.
drupal_get_installed_schema_version(NULL, TRUE);
}