Error handling improvements

[BioWilko]

Closes [#174]

Quick PR which bumps version to 1.9.0 but mostly improves the pipelines error handling, no more will it exit 20 no matter what the problem is.....

[Copilot]

Pull request overview

This PR improves error handling in the pipeline by introducing more granular exit codes and descriptive error messages, replacing the previous behavior of exiting with code 20 for all failures. The version is also bumped to 1.9.0, and the primalbedtools dependency is updated.

Key changes:

• Enhanced error handling with specific exit codes and user-friendly messages for common failure scenarios
• Version bump to 1.9.0 with updated primalbedtools dependency to >=1.0.0
• Test updates to use artic-pan-dengue scheme instead of nCoV-2019

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.

Show a summary per file

File	Description
pyproject.toml	Version bumped from 1.8.5 to 1.9.0
environment.yml	Updated primalbedtools dependency from >=0.10.1 to >=1.0.0
artic/utils.py	Changed read_file default parameter from False to empty string
artic/minion.py	Added comprehensive error handling with specific exit codes and messages, replaced os.system with subprocess.run
tests/get_scheme_unit_test.py	Updated test to use artic-pan-dengue scheme instead of nCoV-2019
tests/minion_validator.py	Added scheme-length parameter to test command generation

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[bede]

Looks great, and I've googled these error codes more times than I should admit